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High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children
Background Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection. Methods We recently defined the population structure of S. Typhi, using new sequencing technologies to identify nearly 2,000 single nucleotide polymorphisms (SNPs) that can be used as unequivocal phylogenetic markers. Here we have used the GoldenGate (Illumina) platform to simultaneously type 1,500 of these SNPs in 62 S. Typhi isolates causing severe typhoid in children admitted to Patan Hospital in Kathmandu. Results Eight distinct S. Typhi haplotypes were identified during the 20-month study period, with 68% of isolates belonging to a subclone of the previously defined H58 S. Typhi. This subclone was closely associated with resistance to nalidixic acid, with all isolates from this group demonstrating a resistant phenotype and harbouring the same resistance-associated SNP in GyrA (Phe83). A secondary clone, comprising 19% of isolates, was observed only during the second half of the study. Conclusions Our data demonstrate the utility of SNP typing for monitoring bacterial populations over a defined period in a single endemic setting. We provide evidence for genotype introduction and define a nalidixic acid resistant subclone of S. Typhi, which appears to be the dominant cause of severe pediatric typhoid in Kathmandu during the study period.
Identifying distinct thermal components of a creek
NASA Astrophysics Data System (ADS)
Statistical and heat budget methods for analyzing temperature dynamics of creeks are limited by the ability to resolve thermal processes and fine-grained thermal structures, respectively. Here we describe a hybrid method that identifies distinct thermal components in a stream's heat budget using only temperature data and an algorithm that employs mutual information to "unmix" signals in the temperature data. Spatial resolution is limited only by the number of temperature-logging sensors, which can be quite high for distributed-temperature sensors. Process resolution is at the level of thermal components, defined as distinct collections of heat flux elements sharing coordinated (nonindependent) dynamics. Inference can be used to relate thermal components to meteorological forcing and structural heterogeneity in the fluvial system and to suggest novel hypotheses for further testing with targeted heat budget studies. Applying the method to a small, arid-land creek produced two novel hypotheses: (1) lateral conduction of heat from adjacent dry land (bed, terraces) appeared to cause a substantial heating of the stream, augmented by off-channel flow paths, and (2) riparian vegetation was associated with a subtraction of heat from the stream at a rate proportionate to solar insolation, exceeding the maximum decoupling effect of shade by at least 2°C at midday, and suggesting upwelling heat flux from water to tree canopy proportional to sunlight. The method appears useful for generating new hypotheses, for selecting informative sites for detailed heat budgets, for determining the dimensionality of heat budgets in natural streams, and more broadly for associating thermal components to fluvial structure and processes.
Boughton, David A.; Hatch, Christine; Mora, Ethan
Identifying distinctive subsequences in multivariate time series by clustering
Most time series comparison algorithms attempt to discover what themembers of a set of time series have in common. We investigate a differentproblem, determining what distinguishes time series in that setfrom other time series obtained from the same source. In both casesthe goal is to identify shared patterns, though in the latter case thosepatterns must be distinctive as well. An
Tim Oates
Intracellular SERS Nanoprobes For Distinction Of Different Neuronal Cell Types
Distinction between closely related and morphologically similar cells is difficult by conventional methods especially without labeling. Using nuclear-targeted gold nanoparticles (AuNPs) as intracellular probes we demonstrate the ability to distinguish between progenitor and differentiated cell types in a human neuroblastoma cell line using surface-enhanced Raman spectroscopy (SERS). SERS spectra from the whole cell area as well as only the nucleus were analyzed using principal component analysis that allowed unambiguous distinction of the different cell types. SERS spectra from the nuclear region showed the developments during cellular differentiation by identifying an increase in DNA/RNA ratio and proteins transcribed. Our approach using nuclear-targeted AuNPs and SERS imaging provides label-free and noninvasive characterization that can play a vital role in identifying cell types in biomedical stem cell research.
Identifying the Distinctive Plasma Properties of Coronal Holes
NASA Astrophysics Data System (ADS)
Interest in defining the distinguishing properties of coronal holes has been ongoing for several decades, due in large part to the prevailing view that they are the main source of the fast solar wind. So far, their main distinct signature on the solar disk is reduced absorption in the chromospheric He I 1083 nm line, and significantly reduced emission in EUV emission lines formed at, or above, a temperature of a million degrees. In this study, MDI line of sight photospheric magnetic field measurements are combined with EIT solar disk intensities of the EUV lines of Fe X 171 and Fe XII 195 A to define the boundaries of coronal holes, following the technique recently described by Scholl and Habbal (2007). By complementing this identification with coordinated SUMER Ne VIII intensity and Doppler measurements, it is shown that coronal holes, for the most part, are not the sole regions of outflow on the solar surface. While these results provide a new step in identifying coronal holes, they show that no single criterion can be used to distinguish a number of their plasma properties from those of the surrounding quiet Sun. Their underlying origin remains for the most part a puzzle.
Habbal, S. R.; Scholl, I.; McIntosh, S.
Constructing Taxonomies to Identify Distinctive Forms of Primary Healthcare Organizations
Background. Primary healthcare (PHC) renewal gives rise to important challenges for policy makers, managers, and researchers in most countries. Evaluating new emerging forms of organizations is therefore of prime importance in assessing the impact of these policies. This paper presents a set of methods related to the configurational approach and an organizational taxonomy derived from our analysis. Methods. In 2005, we carried out a study on PHC in two health and social services regions of Quebec that included urban, suburban, and rural areas. An organizational survey was conducted in 473 PHC practices. We used multidimensional nonparametric statistical methods, namely, multiple correspondence and principal component analyses, and an ascending hierarchical classification method to construct a taxonomy of organizations. Results. PHC organizations were classified into five distinct models: four professional and one community. Study findings indicate that the professional integrated coordination and the community model have great potential for organizational development since they are closest to the ideal type promoted by current reforms. Conclusion. Results showed that the configurational approach is useful to assess complex phenomena such as the organization of PHC. The analysis highlights the most promising organizational models. Our study enhances our understanding of organizational change in health services organizations.
Borges Da Silva, Roxane; Pineault, Raynald; Hamel, Marjolaine; Levesque, Jean-Frederic; Roberge, Daniele; Lamarche, Paul
ADHD Combined Type and ADHD Predominantly Inattentive Type Are Distinct and Unrelated Disorders
We comprehensively reviewed research assessing differences in attention-deficit hyperactivity disorder (ADHD) subtypes to examine the possibility that ADHD\\/ combined type (ADHD\\/Q and ADHD\\/predominantly inattentive type (ADHD\\/I) are distinct and unrelated disorders. Differences among subtypes were examined along dimensions identified as being important in documenting the distinctiveness of two disorders. These include essential and associated features, demographics, measures of cognitive and
Richard Milich; Amy C. Balentine; Donald R. Lynam
Individual Distinctiveness in Call Types of Wild Western Female Gorillas
Individually distinct vocalizations play an important role in animal communication, allowing call recipients to respond differentially based on caller identity. However, which of the many calls in a species' repertoire should have more acoustic variability and be more recognizable is less apparent. One proposed hypothesis is that calls used over long distances should be more distinct because visual cues are not available to identify the caller. An alternative hypothesis proposes that close calls should be more recognizable because of their importance in social interactions. To examine which hypothesis garners more support, the acoustic variation and individual distinctiveness of eight call types of six wild western gorilla (Gorilla gorilla) females were investigated. Acoustic recordings of gorilla calls were collected at the Mondika Research Center (Republic of Congo). Acoustic variability was high in all gorilla calls. Similar high inter-individual variation and potential for identity coding (PIC) was found for all call types. Discriminant function analyses confirmed that all call types were individually distinct (although for call types with lowest sample size - hum, grumble and scream - this result cannot be generalized), suggesting that neither the distance at which communication occurs nor the call social function alone can explain the evolution of identity signaling in western gorilla communication.
Salmi, Roberta; Hammerschmidt, Kurt; Doran-Sheehy, Diane M.
Distinct melanoma types based on reflectance confocal microscopy.
Distinct melanoma types exist in relation to patient characteristics, tumor morphology, histopathologic aspects and genetic background. A new diagnostic imaging tool, reflectance confocal microscopy (RCM), allows in vivo analysis of a given lesion with nearly histologic resolution while offering a dynamic view of the tissue in its 'natural' environment. The aim of this study was to analyse cell morphology of consecutive melanomas as they appear on RCM and to correlate morphology with tumor and patient characteristics. One hundred melanomas were visualized by RCM before excision. Clinical data, confocal features and histologic criteria were analysed. Four types of melanomas were identified as follows: (i) Melanomas with a predominantly dendritic cell population ('dendritic-cell melanomas') typically were thin by Breslow index; (ii) Melanomas typified by roundish melanocytes were smaller in size than dendritic cell MMs, but thicker by Breslow index, and predominantly occurred in patients with a high nevus count; (iii) Melanomas characterized by dermal nesting proliferation usually were thick by Breslow index at the time of diagnosis, although frequently smaller in size compared with the other types; and (iv) combined type melanomas may represent an evolution of dendritic cell and/or round cell types. Integration of confocal microscopy with clinical and histologic aspects may help in identifying and managing distinct tumors. PMID:24750486
Pellacani, Giovanni; De Pace, Barbara; Reggiani, Camilla; Cesinaro, Anna Maria; Argenziano, Giuseppe; Zalaudek, Iris; Soyer, H Peter; Longo, Caterina
Novel Subtype-specific Genes Identify Distinct Subpopulations of Callosal Projection Neurons
Little is known about the molecular development and heterogeneity of callosal projection neurons (CPN), cortical commissural neurons that connect homotopic regions of the two cerebral hemispheres via the corpus callosum, and that are critical for bilateral integration of cortical information. Here we report on the identification of a series of genes that individually and in combination define CPN and novel CPN subpopulations during embryonic and postnatal development. We used in situ hybridization analysis, immunocytochemistry, and retrograde labeling to define the layer- and neuron type-specific distribution of these newly identified CPN genes across different stages of maturation. We demonstrate that a subset of these genes (e.g. Hspb3 and Lpl), appear specific to all CPN (in layers II/III and V–VI), while others (e.g. Nectin-3, Plexin-D1 and Dkk3) discriminate between CPN of the deep layers and those of the upper layers. Further, the data show that several genes finely subdivide CPN within individual layers and appear to label CPN subpopulations that have not been previously described using anatomical or morphological criteria. The genes identified here likely reflect the existence of distinct programs of gene expression governing the development, maturation, and function of the newly identified subpopulations of CPN. Together, these data define the first set of genes that identify and molecularly subcategorize distinct populations of callosal projection neurons, often located in distinct subdivisions of the canonical cortical laminae.
Molyneaux, Bradley J.; Arlotta, Paola; Fame, Ryann M.; MacDonald, Jessica L.; MacQuarrie, Kyle L.; Macklis, Jeffrey D.
Comparison of melanoblast expression patterns identifies distinct classes of genes
Summary A full understanding of transcriptional regulation requires integration of information obtained from multiple experimental datasets. These include datasets annotating gene expression within the context of an entire organism under normal and genetically perturbed conditions. Here we describe an expression dataset annotating pigment cell-expressed genes of the developing melanocyte and RPE lineages. Expression images are annotated and available at http://research.nhgri.nih.gov/manuscripts/Loftus/March2009/. Data is also summarized in a standardized manner using a universal melanoblast scoring scale that accounts for the embryonic location of cells and regional cell density. This approach allowed us to classify 14 pigment genes into 4 groupings classified by cell lineage expression, temporal-spatial context, and differential alteration in response to altered MITF and SOX10 status. Significant differences in regional populations were also observed across inbred strain backgrounds highlighting the value of this approach to identify modifier allele influences on melanoblast number and distributions. This analysis revealed novel features of in vivo expression patterns that are not measurable by in vitro-based assays, providing data that in combination with genomic analyses will allow modeling of pigment cell gene expression in development and disease.
Loftus, Stacie K.; Baxter, Laura L.; Buac, Kristina; Watkins-Chow, Dawn E.; Larson, Denise M.; Pavan, William J.
Biochemical analysis of TssK, a core component of the bacterial Type VI secretion system, reveals distinct oligomeric states of TssK and identifies a TssK-TssFG subcomplex
Gram-negative bacteria use the Type VI secretion system (T6SS) to inject toxic proteins into rival bacteria or eukaryotic cells. However, the mechanism of the T6SS is incompletely understood. In the present study, we investigated a conserved component of the T6SS, TssK, using the antibacterial T6SS of Serratia marcescens as a model system. TssK was confirmed to be essential for effector secretion by the T6SS. The native protein, although not an integral membrane protein, appeared to localize to the inner membrane, consistent with its presence within a membrane-anchored assembly. Recombinant TssK purified from S. marcescens was found to exist in several stable oligomeric forms, namely trimer, hexamer and higher-order species. Native-level purification of TssK identified TssF and TssG as interacting proteins. TssF and TssG, conserved T6SS components of unknown function, were required for T6SS activity, but not for correct localization of TssK. A complex containing TssK, TssF and TssG was subsequently purified in vitro, confirming that these three proteins form a new subcomplex within the T6SS. Our findings provide new insight into the T6SS assembly, allowing us to propose a model whereby TssK recruits TssFG into the membrane-associated T6SS complex and different oligomeric states of TssK may contribute to the dynamic mechanism of the system.
English, Grant; Byron, Olwyn; Cianfanelli, Francesca R.; Prescott, Alan R.; Coulthurst, Sarah J.
Biochemical analysis of TssK, a core component of the bacterial Type VI secretion system, reveals distinct oligomeric states of TssK and identifies a TssK-TssFG subcomplex.
Gram-negative bacteria use the Type VI secretion system (T6SS) to inject toxic proteins into rival bacteria or eukaryotic cells. However, the mechanism of the T6SS is incompletely understood. In the present study, we investigated a conserved component of the T6SS, TssK, using the antibacterial T6SS of Serratia marcescens as a model system. TssK was confirmed to be essential for effector secretion by the T6SS. The native protein, although not an integral membrane protein, appeared to localize to the inner membrane, consistent with its presence within a membrane-anchored assembly. Recombinant TssK purified from S. marcescens was found to exist in several stable oligomeric forms, namely trimer, hexamer and higher-order species. Native-level purification of TssK identified TssF and TssG as interacting proteins. TssF and TssG, conserved T6SS components of unknown function, were required for T6SS activity, but not for correct localization of TssK. A complex containing TssK, TssF and TssG was subsequently purified in vitro, confirming that these three proteins form a new subcomplex within the T6SS. Our findings provide new insight into the T6SS assembly, allowing us to propose a model whereby TssK recruits TssFG into the membrane-associated T6SS complex and different oligomeric states of TssK may contribute to the dynamic mechanism of the system. PMID:24779861
English, Grant; Byron, Olwyn; Cianfanelli, Francesca R; Prescott, Alan R; Coulthurst, Sarah J
R-Phycocyanin, a Distinct Type of Biliprotein.
National Technical Information Service (NTIS)
It was shown by fractionation and analytical methods, spectrophotometric and denaturation studies, and microscopic examination of crystalline samples, that R-phycocyanin is a distinct type of biliprotein, contrary to the suggestion of Hattori and Fujita (...
P. O. Carra C. O. hEocha
Brain Networks for Exploration Decisions Utilizing Distinct Modeled Information Types during Contextual Learning.
Exploration permits acquisition of the most relevant information during learning. However, the specific information needed, the influences of this information on decision making, and the relevant neural mechanisms remain poorly understood. We modeled distinct information types available during contextual association learning and used model-based fMRI in conjunction with manipulation of exploratory decision making to identify neural activity associated with information-based decisions. We identified hippocampal-prefrontal contributions to advantageous decisions based on immediately available novel information, distinct from striatal contributions to advantageous decisions based on the sum total available (accumulated) information. Furthermore, network-level interactions among these regions during exploratory decision making were related to learning success. These findings link strategic exploration decisions during learning to quantifiable information and advance understanding of adaptive behavior by identifying the distinct and interactive nature of brain-network contributions to decisions based on distinct information types. PMID:24908493
Wang, Jane X; Voss, Joel L
Distinct types of glial cells populate the Drosophila antenna
Background The development of nervous systems involves reciprocal interactions between neurons and glia. In the Drosophila olfactory system, peripheral glial cells arise from sensory lineages specified by the basic helix-loop-helix transcription factor, Atonal. These glia wrap around the developing olfactory axons early during development and pattern the three distinct fascicles as they exit the antenna. In the moth Manduca sexta, an additional set of central glia migrate to the base of the antennal nerve where axons sort to their glomerular targets. In this work, we have investigated whether similar types of cells exist in the Drosophila antenna. Results We have used different P(Gal4) lines to drive Green Fluorescent Protein (GFP) in distinct populations of cells within the Drosophila antenna. Mz317::GFP, a marker for cell body and perineural glia, labels the majority of peripheral glia. An additional ~30 glial cells detected by GH146::GFP do not derive from any of the sensory lineages and appear to migrate into the antenna from the brain. Their appearance in the third antennal segment is regulated by normal function of the Epidermal Growth Factor receptor and small GTPases. We denote these distinct populations of cells as Mz317-glia and GH146-glia respectively. In the adult, processes of GH146-glial cells ensheath the olfactory receptor neurons directly, while those of the Mz317-glia form a peripheral layer. Ablation of GH146-glia does not result in any significant effects on the patterning of the olfactory receptor axons. Conclusion We have demonstrated the presence of at least two distinct populations of glial cells within the Drosophila antenna. GH146-glial cells originate in the brain and migrate to the antenna along the newly formed olfactory axons. The number of cells populating the third segment of the antenna is regulated by signaling through the Epidermal Growth Factor receptor. These glia share several features of the sorting zone cells described in Manduca.
Sen, Anindya; Shetty, Chetak; Jhaveri, Dhanisha; Rodrigues, Veronica
Fluids, fault zone permeability and two distinct types of pseudotachylyte
NASA Astrophysics Data System (ADS)
The comparative rarity of pseudotachylyte in ancient fault zones is surprising in light of estimates that ca. 90% of the energy budget of an earthquake is expended in frictional heating. One explanation is that frictional melting (pseudotachylyte generation) is suppressed after the initial rupture on a fault zone because fluids infiltrate the zone and thermal pressurization of these fluids inhibits melting in subsequent seismic events. While this seems plausible for many of the iconic occurrences of pseudotachylyte in otherwise undamaged crystalline rocks, some pseudotachylytes clearly formed in host rocks in which permeability was apparently high and fluids were present at the time of frictional melting. In these fault zones, cataclasites and pseudotachylyte commonly have mutually cross cutting relationships, and both types of fault rock have been complexly intruded into the surrounding damage zone. In contrast, cataclasites associated with pseudotachylyte in pristine crystalline rocks occur in smaller volumes and have simpler geometries, typically limited to the margins of fault veins or in dilational jogs. These observations suggest that there may be two distinct physical circumstances under which frictional melting may occur and thus two distinct genetic types of pseudotachylyte. Classic "dry" pseudotachylytes (e.g., Holsnřy, Bergen Arcs, Norway; Gole Larghe Fault, Italy) probably represent the initial seismic rupture of intact, low-permeability rock at high effective stress in the absence of fluids. When fluids are present, however (e.g., central Otago, New Zealand; Nojima fault, Japan), the potential for frictional melting depends on the relative rates at which heat and fluids can escape from a fault zone. Geophysical models of dynamic weakening mechanisms during earthquakes (Rempel and Rice, JGR, 2006) show that thermal pressurization occurs when the hydraulic diffusivity is effectively less than thermal diffusivity, while melting occurs when thermal diffusivity is less than hydraulic diffusivity. Because the hydraulic diffusivity of a fault zone typically decreases over time owing to progressive comminution of grains, "wet" pseudotachylytes - i.e., those formed in hydrated rocks -- may represent an intermediate stage in the evolution of a fault, the period between the formation of a high-permeability damage zone and the development of a low-permeability fault core. Pseudotachylytes may therefore form in either of two distinct permeability 'windows', depending the nature of the host rock and its antecedent fluid history; for dry, intact rock, the pseudotachylyte window closes once fluids get in, while for hydrous and initially permeable rock, that window closes once fluids can no longer get out.
Bjornerud, M.
Whole-genome screening identifies proteins localized to distinct nuclear bodies
The nucleus is a unique organelle that contains essential genetic materials in chromosome territories. The interchromatin space is composed of nuclear subcompartments, which are defined by several distinctive nuclear bodies believed to be factories of DNA or RNA processing and sites of transcriptional and/or posttranscriptional regulation. In this paper, we performed a genome-wide microscopy-based screening for proteins that form nuclear foci and characterized their localizations using markers of known nuclear bodies. In total, we identified 325 proteins localized to distinct nuclear bodies, including nucleoli (148), promyelocytic leukemia nuclear bodies (38), nuclear speckles (27), paraspeckles (24), Cajal bodies (17), Sam68 nuclear bodies (5), Polycomb bodies (2), and uncharacterized nuclear bodies (64). Functional validation revealed several proteins potentially involved in the assembly of Cajal bodies and paraspeckles. Together, these data establish the first atlas of human proteins in different nuclear bodies and provide key information for research on nuclear bodies.
Fong, Ka-wing; Li, Yujing; Wang, Wenqi; Ma, Wenbin; Li, Kunpeng; Qi, Robert Z.; Liu, Dan; Songyang, Zhou
Local phylogenetic analysis identifies distinct trends in transmitted HIV drug resistance: implications for public health interventions
Background HIV transmitted drug resistance (TDR) surveillance is usually conducted by sampling from a large population. However, overall TDR prevalence results may be inaccurate for many individual clinical setting. We analyzed HIV genotypes at a tertiary care setting in Ottawa, Ontario in order to evaluate local TDR patterns among sub-populations. Method Genotyping reports were digitized from ART naďve patients followed at the Immunodeficiency Clinic at the Ottawa Hospital, between 2008 and 2010. Quality controlled, digitized sequence data were assessed for TDR using the Stanford HIV Database. Patient characteristics were analyzed according to TDR patterns. Finally, a phylogenetic tree was constructed to elucidate the observed pattern of HIV TDR. Results Among the 155 clinic patients there was no statistically significantly difference in demographics as compared to the Ontario provincial HIV population. The clinic prevalence of TDR was 12.3%; however, in contrast to the data from Ontario, TDR patterns were inverted with a 21% prevalence among MSM and 5.5% among IDU. Furthermore, nearly 80% of the observed TDR was a D67N/K219Q pattern with 87% of these infections arising from a distinct phylogenetic cluster. Conclusions Local patterns of TDR were distinct to what had been observed provincially. Phylogenetic analysis uncovered a cluster of related infections among MSM that appeared more likely to be recent infections. Results support a paradigm of routine local TDR surveillance to identify the sub-populations under care. Furthermore, the routine application of phylogenetic analysis in the TDR surveillance context provides insights into how best to target prevention strategies; and how to correctly measure outcomes.
Chromosomal radiosensitivity in G2-phase lymphocytes identifies breast cancer patients with distinctive tumour characteristics
A substantial proportion of women with breast cancer exhibit an abnormally high radiosensitivity as measured by the frequency of chromatid breaks induced in G2-phase, PHA stimulated lymphocytes. Chromatid break frequencies were compared for a cohort of previously untreated sporadic breast cancer patients and hospital outpatient controls. In the breast cancer group 46% showed high radiosensitivity compared to 14% of controls (P< 0.001). Comparison of those breast cancer patients with a high G2radiosensitivity (G2RS) versus those with a low G2RS showed no difference in menopausal status or age but the high G2RS group had on average a lower score on the Nottingham Prognostic Index. Predicted survival in the high G2RS group at 15 years was 55% compared to 36% for the low G2RS group. Furthermore, 81% of tumours from the high G2RS were oestrogen receptor positive compared to 45% from the low G2RS group. Thus high G2RS identifies a sub-population of patients with distinctive tumour characteristics and with a predicted improved prognosis as compared with those in the low G2RS group. Our findings imply that besides influencing risk of breast cancer the genetic factors determining G2radiosensitivity also influence the tumour characteristics and prognosis in these patients. © 2001 Cancer Research Campaign??http://www.bjcancer.com
Riches, A C; Bryant, P E; Steel, C M; Gleig, A; Robertson, A J; Preece, P E; Thompson, A M
Gene-expression profiling of microdissected breast cancer microvasculature identifies distinct tumor vascular subtypes
Introduction Angiogenesis represents a potential therapeutic target in breast cancer. However, responses to targeted antiangiogenic therapies have been reported to vary among patients. This suggests that the tumor vasculature may be heterogeneous and that an appropriate choice of treatment would require an understanding of these differences. Methods To investigate whether and how the breast tumor vasculature varies between individuals, we isolated tumor-associated and matched normal vasculature from 17 breast carcinomas by laser-capture microdissection, and generated gene-expression profiles. Because microvessel density has previously been associated with disease course, tumors with low (n = 9) or high (n = 8) microvessel density were selected for analysis to maximize heterogeneity for this feature. Results We identified differences between tumor and normal vasculature, and we describe two subtypes present within tumor vasculature. These subtypes exhibit distinct gene-expression signatures that reflect features including hallmarks of vessel maturity. Potential therapeutic targets (MET, ITGAV, and PDGFR?) are differentially expressed between subtypes. Taking these subtypes into account has allowed us to derive a vascular signature associated with disease outcome. Conclusions Our results further support a role for tumor microvasculature in determining disease progression. Overall, this study provides a deeper molecular understanding of the heterogeneity existing within the breast tumor vasculature and opens new avenues toward the improved design and targeting of antiangiogenic therapies.
Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension
Idiopathic pulmonary arterial hypertension (PAH) is a life-threatening condition characterized by pulmonary arteriolar remodeling. This investigation aimed to identify genes involved specifically in the pathogenesis of PAH and not other forms of pulmonary hypertension (PH). Using genomewide microarray analysis, we generated the largest data set to date of RNA expression profiles from lung tissue specimens from 1) 18 PAH subjects and 2) 8 subjects with PH secondary to idiopathic pulmonary fibrosis (IPF) and 3) 13 normal subjects. A molecular signature of 4,734 genes discriminated among these three cohorts. We identified significant novel biological changes that were likely to contribute to the pathogenesis of PAH, including regulation of actin-based motility, protein ubiquitination, and cAMP, transforming growth factor-?, MAPK, estrogen receptor, nitric oxide, and PDGF signaling. Bone morphogenic protein receptor type II expression was downregulated, even in subjects without a mutation in this gene. Women with PAH had higher expression levels of estrogen receptor 1 than normal women. Real-time quantitative PCR confirmed differential expression of the following genes in PAH relative to both normal controls and PH secondary to IPF: a disintegrin-like and metalloprotease with thrombospondin type 1 motif 9, cell adhesion molecule with homology to L1CAM, cytochrome b558 and ?-polypeptide, coagulation factor II receptor-like 3, A-myb myeloblastosis viral oncogene homolog 1, nuclear receptor coactivator 2, purinergic receptor P2Y, platelet factor 4, phospholamban, and tropomodulin 3. This study shows that PAH and PH secondary to IPF are characterized by distinct gene expression signatures, implying distinct pathophysiological mechanisms.
Rajkumar, Revathi; Konishi, Kazuhisa; Richards, Thomas J.; Ishizawar, David C.; Wiechert, Andrew C.; Kaminski, Naftali
A Comparative Genome Analysis Identifies Distinct Sorting Pathways in Gram-Positive Bacteria
Surface proteins in gram-positive bacteria are frequently required for virulence, and many are attached to the cell wall by sortase enzymes. Bacteria frequently encode more than one sortase enzyme and an even larger number of potential sortase substrates that possess an LPXTG-type cell wall sorting signal. In order to elucidate the sorting pathways present in gram-positive bacteria, we performed a comparative analysis of 72 sequenced microbial genomes. We show that sortase enzymes can be partitioned into five distinct subfamilies based upon their primary sequences and that most of their substrates can be predicted by making a few conservative assumptions. Most bacteria encode sortases from two or more subfamilies, which are predicted to function nonredundantly in sorting proteins to the cell surface. Only ?20% of sortase-related proteins are most closely related to the well-characterized Staphylococcus aureus SrtA protein, but nonetheless, these proteins are responsible for anchoring the majority of surface proteins in gram-positive bacteria. In contrast, most sortase-like proteins are predicted to play a more specialized role, with each anchoring far fewer proteins that contain unusual sequence motifs. The functional sortase-substrate linkage predictions are available online (http://www.doe-mbi.ucla.edu/Services/Sortase/) in a searchable database.
Comfort, David; Clubb, Robert T.
Distinct cellular properties of identified dopaminergic and GABAergic neurons in the mouse ventral tegmental area
Abstract The midbrain ventral tegmental area (VTA) contains neurons largely with either a dopaminergic (DAergic) or GABAergic phenotype. Physiological and pharmacological properties of DAergic neurons have been determined using tyrosine hydroxylase (TH) immunohistochemistry but many properties overlap with non-DAergic neurons presumed to be GABAergic. This study examined properties of GABAergic neurons, non-GABAergic neurons and TH-immunopositive neurons in VTA of GAD67-GFP knock-in mice. Ninety-eight per cent of VTA neurons were either GAD-GFP or TH positive, with the latter being five times more abundant. During cell-attached patch-clamp recordings, GAD-GFP neurons fired brief action potentials that could be completely distinguished from those of non-GFP neurons. Pharmacologically, the ?-opioid agonist DAMGO inhibited firing of action potentials in 92% of GAD-GFP neurons but had no effect in non-GFP neurons. By contrast, dopamine invariably inhibited action potentials in non-GFP neurons but only did so in 8% of GAD-GFP neurons. During whole-cell recordings, the narrower width of action potential in GAD-GFP neurons was also evident but there was considerable overlap with non-GFP neurons. GAD-GFP neurons invariably failed to exhibit the potassium-mediated slow depolarizing potential during injection of positive current that was present in all non-GFP neurons. Under voltage-clamp the cationic current, Ih, was found in both types of neurons with considerable overlap in both amplitude and kinetics. These distinct cellular properties may thus be used to confidently discriminate GABAergic and DAergic neurons in VTA during in vitro electrophysiological recordings.
Chieng, Billy; Azriel, Yael; Mohammadi, Sarasa; Christie, MacDonald J
Distinct cellular properties of identified dopaminergic and GABAergic neurons in the mouse ventral tegmental area.
The midbrain ventral tegmental area (VTA) contains neurons largely with either a dopaminergic (DAergic) or GABAergic phenotype. Physiological and pharmacological properties of DAergic neurons have been determined using tyrosine hydroxylase (TH) immunohistochemistry but many properties overlap with non-DAergic neurons presumed to be GABAergic. This study examined properties of GABAergic neurons, non-GABAergic neurons and TH-immunopositive neurons in VTA of GAD67-GFP knock-in mice. Ninety-eight per cent of VTA neurons were either GAD-GFP or TH positive,with the latter being five times more abundant. During cell-attached patch-clamp recordings, GAD-GFP neurons fired brief action potentials that could be completely distinguished from those of non-GFP neurons. Pharmacologically, the ?-opioid agonist DAMGO inhibited firing of action potentials in 92% of GAD-GFP neurons but had no effect in non-GFP neurons. By contrast, dopamine invariably inhibited action potentials in non-GFP neurons but only did so in 8% of GAD-GFP neurons. During whole-cell recordings, the narrower width of action potential in GAD-GFP neurons was also evident but there was considerable overlap with non-GFP neurons. GAD-GFP neurons invariably failed to exhibit the potassium-mediated slow depolarizing potential during injection of positive current that was present in all non-GFP neurons. Under voltage-clamp the cationic current, I(h), was found in both types of neurons with considerable overlap in both amplitude and kinetics. These distinct cellular properties may thus be used to confidently discriminate GABAergic and DAergic neurons in VTA during in vitro electrophysiological recordings. PMID:21646409
Chieng, Billy; Azriel, Yael; Mohammadi, Sarasa; Christie, MacDonald J
Functional Cell Types in Taste Buds Have Distinct Longevities
Taste buds are clusters of polarized sensory cells embedded in stratified oral epithelium. In adult mammals, taste buds turn over continuously and are replenished through the birth of new cells in the basal layer of the surrounding non-sensory epithelium. The half-life of cells in mammalian taste buds has been estimated as 8–12 days on average. Yet, earlier studies did not address whether the now well-defined functional taste bud cell types all exhibit the same lifetime. We employed a recently developed thymidine analog, 5-ethynil-2?-deoxyuridine (EdU) to re-evaluate the incorporation of newly born cells into circumvallate taste buds of adult mice. By combining EdU-labeling with immunostaining for selected markers, we tracked the differentiation and lifespan of the constituent cell types of taste buds. EdU was primarily incorporated into basal extragemmal cells, the principal source for replenishing taste bud cells. Undifferentiated EdU-labeled cells began migrating into circumvallate taste buds within 1 day of their birth. Type II (Receptor) taste cells began to differentiate from EdU-labeled precursors beginning 2 days after birth and then were eliminated with a half-life of 8 days. Type III (Presynaptic) taste cells began differentiating after a delay of 3 days after EdU-labeling, and they survived much longer, with a half-life of 22 days. We also scored taste bud cells that belong to neither Type II nor Type III, a heterogeneous group that includes mostly Type I cells, and also undifferentiated or immature cells. A non-linear decay fit described these cells as two sub-populations with half-lives of 8 and 24 days respectively. Our data suggest that many post-mitotic cells may remain quiescent within taste buds before differentiating into mature taste cells. A small number of slow-cycling cells may also exist within the perimeter of the taste bud. Based on their incidence, we hypothesize that these may be progenitors for Type III cells.
Perea-Martinez, Isabel; Nagai, Takatoshi; Chaudhari, Nirupa
TGF-?1 activates two distinct type I receptors in neurons
Transforming growth factor-?s (TGF-?s) are pleiotropic cytokines involved in development and maintenance of the nervous system. In several neural lesion paradigms, TGF-?1 exerts potent neuroprotective effects. Neurons treated with TGF-?1 activated the canonical TGF-? receptor I/activin-like kinase receptor 5 (ALK5) pathway. The transcription factor nuclear factor-?B (NF-?B) plays a fundamental role in neuroprotection. Treatment with TGF-?1 enhanced NF-?B activity in gelshift and reporter gene analyses. However, ectopic expression of a constitutively active ALK5 failed to mimic these effects. ALK1 has been described as an alternative TGF-? receptor in endothelial cells. Interestingly, we detected significant basal expression of ALK1 and its injury-induced up-regulation in neurons. Treatment with TGF-?1 also induced a pronounced increase in downstream Smad1 phosphorylation. Overexpression of a constitutively active ALK1 mimicked the effect of TGF-?1 on NF-?B activation and neuroprotection. Our data suggest that TGF-?1 simultaneously activates two distinct receptor pathways in neurons and that the ALK1 pathway mediates TGF-?1–induced NF-?B survival signaling.
Konig, Hans-Georg; Kogel, Donat; Rami, Abdelhaq; Prehn, Jochen H.M.
Biological Analysis of Human Immunodeficiency Virus Type 1 R5 Envelopes Amplified from Brain and Lymph Node Tissues of AIDS Patients with Neuropathology Reveals Two Distinct Tropism Phenotypes and Identifies Envelopes in the Brain That Confer an Enhanced Tropism and Fusigenicity for Macrophages
Complete envelope genes were amplified from autopsy brain tissue of five individuals who had died of AIDS and had neurological complications. Lymph node samples were included for two of the patients. Nineteen different envelope clones from the five patients had distinct V1V2 sequences. Thirteen of the envelopes were functional and conferred fusigenicity and infectivity for CD4+ CCR5+ cells. Infectivity and cell-cell fusion assays showed that most envelopes used both CCR5 and CCR3. One brain-derived envelope used a broad range of coreceptors, while three other brain envelopes from one individual were restricted to CCR5. However, there was no correlation between tissue of origin and coreceptor use. Envelopes showed two very distinct phenotypes depending on their capacity to infect macrophages and to exploit low levels of CD4 and/or CCR5 for infection. Envelopes that were highly fusigenic and tropic for macrophages were identified in brain tissue from four of the five patients. The enhanced macrophage tropism correlated with reduced sensitivity to inhibition by Q4120, a CD4-specific antibody, but not with sensitivity to the CCR5 inhibitor, TAK779. The highly macrophage-tropic envelopes were able to infect cells expressing low levels of CD4 and/or CCR5. Comparison with several well-characterized macrophage-tropic envelopes showed that the four identified patient envelopes were at the top limit of macrophage tropism. In contrast, all four lymph node-derived envelopes exhibited a non-macrophage-tropic phenotype and required high levels of CD4 for infection. Our data support the presence of envelopes that are highly fusigenic and tropic for macrophages in the brains of patients with neurological complications. These envelopes are able to infect cells that express low levels of CD4 and/or CCR5 and may have adapted for replication in brain macrophages and microglia, which are known to express limited amounts of CD4.
Peters, Paul J.; Bhattacharya, Jayanta; Hibbitts, Samantha; Dittmar, Matthias T.; Simmons, Graham; Bell, Jeanne; Simmonds, Peter; Clapham, Paul R.
Evidence for two distinct populations of type Ia supernovae.
Type Ia supernovae (SNe Ia) have been used as excellent standardizable candles for measuring cosmic expansion, but their progenitors are still elusive. Here, we report that the spectral diversity of SNe Ia is tied to their birthplace environments. We found that those with high-velocity ejecta are substantially more concentrated in the inner and brighter regions of their host galaxies than are normal-velocity SNe Ia. Furthermore, the former tend to inhabit larger and more luminous hosts. These results suggest that high-velocity SNe Ia likely originate from relatively younger and more metal-rich progenitors than do normal-velocity SNe Ia and are restricted to galaxies with substantial chemical evolution. PMID:23470733
Wang, Xiaofeng; Wang, Lifan; Filippenko, Alexei V; Zhang, Tianmeng; Zhao, Xulin
Full Genome Sequencing and Genetic Characterization of Eubenangee Viruses Identify Pata Virus as a Distinct Species within the Genus Orbivirus
Eubenangee virus has previously been identified as the cause of Tammar sudden death syndrome (TSDS). Eubenangee virus (EUBV), Tilligery virus (TILV), Pata virus (PATAV) and Ngoupe virus (NGOV) are currently all classified within the Eubenangee virus species of the genus Orbivirus, family Reoviridae. Full genome sequencing confirmed that EUBV and TILV (both of which are from Australia) show high levels of aa sequence identity (>92%) in the conserved polymerase VP1(Pol), sub-core VP3(T2) and outer core VP7(T13) proteins, and are therefore appropriately classified within the same virus species. However, they show much lower amino acid (aa) identity levels in their larger outer-capsid protein VP2 (<53%), consistent with membership of two different serotypes - EUBV-1 and EUBV-2 (respectively). In contrast PATAV showed significantly lower levels of aa sequence identity with either EUBV or TILV (with <71% in VP1(Pol) and VP3(T2), and <57% aa identity in VP7(T13)) consistent with membership of a distinct virus species. A proposal has therefore been sent to the Reoviridae Study Group of ICTV to recognise 'Pata virus' as a new Orbivirus species, with the PATAV isolate as serotype 1 (PATAV-1). Amongst the other orbiviruses, PATAV shows closest relationships to Epizootic Haemorrhagic Disease virus (EHDV), with 80.7%, 72.4% and 66.9% aa identity in VP3(T2), VP1(Pol), and VP7(T13) respectively. Although Ngoupe virus was not available for these studies, like PATAV it was isolated in Central Africa, and therefore seems likely to also belong to the new species, possibly as a distinct 'type'. The data presented will facilitate diagnostic assay design and the identification of additional isolates of these viruses.
Belaganahalli, Manjunatha N.; Maan, Sushila; Maan, Narender S.; Nomikou, Kyriaki; Pritchard, Ian; Lunt, Ross; Kirkland, Peter D.; Attoui, Houssam; Brownlie, Joe; Mertens, Peter P. C.
Identified motor terminals in Drosophila larvae show distinct differences in morphology and physiology
NASA Technical Reports Server (NTRS)
In Drosophila, the type I motor terminals innervating the larval ventral longitudinal muscle fibers 6 and 7 have been the most popular preparation for combining synaptic studies with genetics. We have further characterized the normal morphological and physiological properties of these motor terminals and the influence of muscle size on terminal morphology. Using dye-injection and physiological techniques, we show that the two axons supplying these terminals have different innervation patterns: axon 1 innervates only muscle fibers 6 and 7, whereas axon 2 innervates all of the ventral longitudinal muscle fibers. This difference in innervation pattern allows the two axons to be reliably identified. The terminals formed by axons 1 and 2 on muscle fibers 6 and 7 have the same number of branches; however, axon 2 terminals are approximately 30% longer than axon 1 terminals, resulting in a corresponding greater number of boutons for axon 2. The axon 1 boutons are approximately 30% wider than the axon 2 boutons. The excitatory postsynaptic potential (EPSP) produced by axon 1 is generally smaller than that produced by axon 2, although the size distributions show considerable overlap. Consistent with vertebrate studies, there is a correlation between muscle fiber size and terminal size. For a single axon, terminal area and length, the number of terminal branches, and the number of boutons are all correlated with muscle fiber size, but bouton size is not. During prolonged repetitive stimulation, axon 2 motor terminals show synaptic depression, whereas axon 1 EPSPs facilitate. The response to repetitive stimulation appears to be similar at all motor terminals of an axon. Copyright 2000 John Wiley & Sons, Inc.
Lnenicka, G. A.; Keshishian, H.
Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers.
The impact of different carcinogenic exposures on the specific patterns of somatic mutation in human tumors remains unclear. To address this issue, we profiled 209 cholangiocarcinomas (CCAs) from Asia and Europe, including 108 cases caused by infection with the liver fluke Opisthorchis viverrini and 101 cases caused by non-O. viverrini-related etiologies. Whole-exome sequencing (n = 15) and prevalence screening (n = 194) identified recurrent somatic mutations in BAP1 and ARID1A, neither of which, to our knowledge, has previously been reported to be mutated in CCA. Comparisons between intrahepatic O. viverrini-related and non-O. viverrini-related CCAs demonstrated statistically significant differences in mutation patterns: BAP1, IDH1 and IDH2 were more frequently mutated in non-O. viverrini CCAs, whereas TP53 mutations showed the reciprocal pattern. Functional studies demonstrated tumor suppressive functions for BAP1 and ARID1A, establishing the role of chromatin modulators in CCA pathogenesis. These findings indicate that different causative etiologies may induce distinct somatic alterations, even within the same tumor type. PMID:24185513
Chan-On, Waraporn; Nairismägi, Maarja-Liisa; Ong, Choon Kiat; Lim, Weng Khong; Dima, Simona; Pairojkul, Chawalit; Lim, Kiat Hon; McPherson, John R; Cutcutache, Ioana; Heng, Hong Lee; Ooi, London; Chung, Alexander; Chow, Pierce; Cheow, Peng Chung; Lee, Ser Yee; Choo, Su Pin; Tan, Iain Bee Huat; Duda, Dan; Nastase, Anca; Myint, Swe Swe; Wong, Bernice Huimin; Gan, Anna; Rajasegaran, Vikneswari; Ng, Cedric Chuan Young; Nagarajan, Sanjanaa; Jusakul, Apinya; Zhang, Shenli; Vohra, Priya; Yu, Willie; Huang, DaChuan; Sithithaworn, Paiboon; Yongvanit, Puangrat; Wongkham, Sopit; Khuntikeo, Narong; Bhudhisawasdi, Vajaraphongsa; Popescu, Irinel; Rozen, Steven G; Tan, Patrick; Teh, Bin Tean
How can Tissue Types be Identified? A Lesson on Identifying and Classifying Animal Tissues
NSDL National Science Digital Library
The purpose of this inquiry is for students to develop and test a scheme to identify the major types of tissues and to identify similarities and differences in animal tissue types. This is an advanced lab recommended for second year Biology students, 11th or 12th grade. Students should have knowledge of cells and cell organelles. Upon completion of this activity, students will be able to: discuss how tissues can be categorized and recognized, recognize the differences between major types of tissues, and develop a scheme to identify/categorize tissues into related groups. This teaching resource was developed by a K-12 science teacher in the American Physiological SocietyĂÂs 2006 Frontiers in Physiology Program. For more information on this program, please visit www.frontiersinphys.org.
Ramona Lundberg (Deuel High School)
DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia.
We hypothesized that DNA methylation distributes into specific patterns in cancer cells, which reflect critical biological differences. We therefore examined the methylation profiles of 344 patients with acute myeloid leukemia (AML). Clustering of these patients by methylation data segregated patients into 16 groups. Five of these groups defined new AML subtypes that shared no other known feature. In addition, DNA methylation profiles segregated patients with CEBPA aberrations from other subtypes of leukemia, defined four epigenetically distinct forms of AML with NPM1 mutations, and showed that established AML1-ETO, CBFb-MYH11, and PML-RARA leukemia entities are associated with specific methylation profiles. We report a 15 gene methylation classifier predictive of overall survival in an independent patient cohort (p < 0.001, adjusted for known covariates). PMID:20060365
Figueroa, Maria E; Lugthart, Sanne; Li, Yushan; Erpelinck-Verschueren, Claudia; Deng, Xutao; Christos, Paul J; Schifano, Elizabeth; Booth, James; van Putten, Wim; Skrabanek, Lucy; Campagne, Fabien; Mazumdar, Madhu; Greally, John M; Valk, Peter J M; Löwenberg, Bob; Delwel, Ruud; Melnick, Ari
Cell type-specific expression analysis to identify putative cellular mechanisms for neurogenetic disorders.
Recent advances have substantially increased the number of genes that are statistically associated with complex genetic disorders of the CNS such as autism and schizophrenia. It is now clear that there will likely be hundreds of distinct loci contributing to these disorders, underscoring a remarkable genetic heterogeneity. It is unclear whether this genetic heterogeneity indicates an equal heterogeneity of cellular mechanisms for these diseases. The commonality of symptoms across patients suggests there could be a functional convergence downstream of these loci upon a limited number of cell types or circuits that mediate the affected behaviors. One possible mechanism for this convergence would be the selective expression of at least a subset of these genes in the cell types that comprise these circuits. Using profiling data from mice and humans, we have developed and validated an approach, cell type-specific expression analysis, for identifying candidate cell populations likely to be disrupted across sets of patients with distinct genetic lesions. Using human genetics data and postmortem gene expression data, our approach can correctly identify the cell types for disorders of known cellular etiology, including narcolepsy and retinopathies. Applying this approach to autism, a disease where the cellular mechanism is unclear, indicates there may be multiple cellular routes to this disorder. Our approach may be useful for identifying common cellular mechanisms arising from distinct genetic lesions. PMID:24453331
Xu, Xiaoxiao; Wells, Alan B; O'Brien, David R; Nehorai, Arye; Dougherty, Joseph D
Porcine Skin-Derived Progenitor (SKP) Spheres and Neurospheres: Distinct "Stemness" Identified by Microarray Analysis
Abstract Skin-derived progenitors (SKP) are neural crest derived and can generate neural and mesodermal progeny in vitro, corresponding to the multipotency of neural crest stem cells. Likewise, neural stem/progenitor cells (displaying as neurospheres) have the capacity of self-renewing, and can produce most phenotypes in the nervous system. Both form spheres when cultured with epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF). Although the "stemness" of neural stem/progenitor cells has been extensively investigated, the molecular comparison of SKP spheres and neurospheres has not been elucidated. Here, SKP spheres and neurospheres from the same individual porcine fetuses were isolated with the same culture medium, and the multipotency was tested by in vitro differentiation assays. Microarray analysis was used to illustrate the "stemness" of SKP spheres and neurospheres. The upregulated genes that were in common in the SKP spheres and neurospheres are involved in ribosome, tight junction, gap junction, cell communication, calcium signaling, ErbB signaling, JAK–STAT signaling, MAPK signaling, etc. The differentially expressed genes between SKP spheres and neurospheres are mainly involved in ECM–receptor interaction and the transforming growth factor-beta (TGF-?) signaling pathway. Finally, treatment with leukemia inhibitory factor (LIF) or MEK inhibitor results in a distinctive impact on the "stemness" and differentiation genes of SKP spheres and neurospheres. Thus, the cell-intrinsic genetic program may contribute to the innate "stemness" of SKP spheres and neurospheres in a similar local microenvironment.
Zhao, Ming-Tao; Whitworth, Kristin M.; Lin, Hui; Zhang, Xia; Isom, S. Clay; Dobbs, Kyle B.; Bauer, Bethany; Zhang, Yong
Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites.
Histone acetylation has long been determined as a highly dynamic modification associated with open chromatin and transcriptional activation. Here we develop a metabolic labelling scheme using stable isotopes to study the kinetics of acetylation turnover at 19 distinct lysines on histones H3, H4 and H2A. Using human HeLa S3 cells, the analysis reveals 12 sites of histone acetylation with fast turnover and 7 sites stable over a 30 h experiment. The sites showing fast turnover (anticipated from classical radioactive measurements of whole histones) have half-lives between ~1-2 h. To support this finding, we use a broad-spectrum deacetylase inhibitor to verify that only fast turnover sites display 2-10-fold increases in acetylation whereas long-lived sites clearly do not. Most of these stable sites lack extensive functional studies or localization within global chromatin, and their role in non-genetic mechanisms of inheritance is as yet unknown. PMID:23892279
Zheng, Yupeng; Thomas, Paul M; Kelleher, Neil L
In silico molecular comparisons of C. elegans and mammalian pharmacology identify distinct targets that regulate feeding.
Phenotypic screens can identify molecules that are at once penetrant and active on the integrated circuitry of a whole cell or organism. These advantages are offset by the need to identify the targets underlying the phenotypes. Additionally, logistical considerations limit screening for certain physiological and behavioral phenotypes to organisms such as zebrafish and C. elegans. This further raises the challenge of elucidating whether compound-target relationships found in model organisms are preserved in humans. To address these challenges we searched for compounds that affect feeding behavior in C. elegans and sought to identify their molecular mechanisms of action. Here, we applied predictive chemoinformatics to small molecules previously identified in a C. elegans phenotypic screen likely to be enriched for feeding regulatory compounds. Based on the predictions, 16 of these compounds were tested in vitro against 20 mammalian targets. Of these, nine were active, with affinities ranging from 9 nM to 10 µM. Four of these nine compounds were found to alter feeding. We then verified the in vitro findings in vivo through genetic knockdowns, the use of previously characterized compounds with high affinity for the four targets, and chemical genetic epistasis, which is the effect of combined chemical and genetic perturbations on a phenotype relative to that of each perturbation in isolation. Our findings reveal four previously unrecognized pathways that regulate feeding in C. elegans with strong parallels in mammals. Together, our study addresses three inherent challenges in phenotypic screening: the identification of the molecular targets from a phenotypic screen, the confirmation of the in vivo relevance of these targets, and the evolutionary conservation and relevance of these targets to their human orthologs. PMID:24260022
Lemieux, George A; Keiser, Michael J; Sassano, Maria F; Laggner, Christian; Mayer, Fahima; Bainton, Roland J; Werb, Zena; Roth, Bryan L; Shoichet, Brian K; Ashrafi, Kaveh
In Silico Molecular Comparisons of C. elegans and Mammalian Pharmacology Identify Distinct Targets That Regulate Feeding
Phenotypic screens can identify molecules that are at once penetrant and active on the integrated circuitry of a whole cell or organism. These advantages are offset by the need to identify the targets underlying the phenotypes. Additionally, logistical considerations limit screening for certain physiological and behavioral phenotypes to organisms such as zebrafish and C. elegans. This further raises the challenge of elucidating whether compound-target relationships found in model organisms are preserved in humans. To address these challenges we searched for compounds that affect feeding behavior in C. elegans and sought to identify their molecular mechanisms of action. Here, we applied predictive chemoinformatics to small molecules previously identified in a C. elegans phenotypic screen likely to be enriched for feeding regulatory compounds. Based on the predictions, 16 of these compounds were tested in vitro against 20 mammalian targets. Of these, nine were active, with affinities ranging from 9 nM to 10 µM. Four of these nine compounds were found to alter feeding. We then verified the in vitro findings in vivo through genetic knockdowns, the use of previously characterized compounds with high affinity for the four targets, and chemical genetic epistasis, which is the effect of combined chemical and genetic perturbations on a phenotype relative to that of each perturbation in isolation. Our findings reveal four previously unrecognized pathways that regulate feeding in C. elegans with strong parallels in mammals. Together, our study addresses three inherent challenges in phenotypic screening: the identification of the molecular targets from a phenotypic screen, the confirmation of the in vivo relevance of these targets, and the evolutionary conservation and relevance of these targets to their human orthologs.
Lemieux, George A.; Keiser, Michael J.; Sassano, Maria F.; Laggner, Christian; Mayer, Fahima; Bainton, Roland J.; Werb, Zena; Roth, Bryan L.; Shoichet, Brian K.; Ashrafi, Kaveh
A serum response factor-dependent transcriptional regulatory program identifies distinct smooth muscle cell sublineages.
The SM22alpha promoter has been used as a model system to define the molecular mechanisms that regulate smooth muscle cell (SMC) specific gene expression during mammalian development. The SM22alpha gene is expressed exclusively in vascular and visceral SMCs during postnatal development and is transiently expressed in the heart and somites during embryogenesis. Analysis of the SM22alpha promoter in transgenic mice revealed that 280 bp of 5' flanking sequence is sufficient to restrict expression of the lacZ reporter gene to arterial SMCs and the myotomal component of the somites. DNase I footprint and electrophoretic mobility shift analyses revealed that the SM22alpha promoter contains six nuclear protein binding sites (designated smooth muscle elements [SMEs] -1 to -6, respectively), two of which bind serum response factor (SRF) (SME-1 and SME-4). Mutational analyses demonstrated that a two-nucleotide substitution that selectively eliminates SRF binding to SME-4 decreases SM22alpha promoter activity in arterial SMCs by approximately 90%. Moreover, mutations that abolish binding of SRF to SME-1 and SME-4 or mutations that eliminate each SME-3 binding activity totally abolished SM22alpha promoter activity in the arterial SMCs and somites of transgenic mice. Finally, we have shown that a multimerized copy of SME-4 (bp -190 to -110) when linked to the minimal SM22alpha promoter (bp -90 to +41) is necessary and sufficient to direct high-level transcription in an SMC lineage-restricted fashion. Taken together, these data demonstrate that distinct transcriptional regulatory programs control SM22alpha gene expression in arterial versus visceral SMCs. Moreover, these data are consistent with a model in which combinatorial interactions between SRF and other transcription factors that bind to SME-4 (and that bind directly to SRF) activate transcription of the SM22alpha gene in arterial SMCs.
Kim, S; Ip, H S; Lu, M M; Clendenin, C; Parmacek, M S
Distinct and conserved prominin-1/CD133-positive retinal cell populations identified across species.
Besides being a marker of various somatic stem cells in mammals, prominin-1 (CD133) plays a role in maintaining the photoreceptor integrity since mutations in the PROM1 gene are linked with retinal degeneration. In spite of that, little information is available regarding its distribution in eyes of non-mammalian vertebrates endowed with high regenerative abilities. To address this subject, prominin-1 cognates were isolated from axolotl, zebrafish and chicken, and their retinal compartmentalization was investigated and compared to that of their mammalian orthologue. Interestingly, prominin-1 transcripts--except for the axolotl--were not strictly restricted to the outer nuclear layer (i.e., photoreceptor cells), but they also marked distinct subdivisions of the inner nuclear layer (INL). In zebrafish, where the prominin-1 gene is duplicated (i.e., prominin-1a and prominin-1b), a differential expression was noted for both paralogues within the INL being localized either to its vitreal or scleral subdivision, respectively. Interestingly, expression of prominin-1a within the former domain coincided with Pax-6-positive cells that are known to act as progenitors upon injury-induced retino-neurogenesis. A similar, but minute population of prominin-1-positive cells located at the vitreal side of the INL was also detected in developing and adult mice. In chicken, however, prominin-1-positive cells appeared to be aligned along the scleral side of the INL reminiscent of zebrafish prominin-1b. Taken together our data indicate that in addition to conserved expression of prominin-1 in photoreceptors, significant prominin-1-expressing non-photoreceptor retinal cell populations are present in the vertebrate eye that might represent potential sources of stem/progenitor cells for regenerative therapies. PMID:21407811
Jászai, József; Fargeas, Christine A; Graupner, Sylvi; Tanaka, Elly M; Brand, Michael; Huttner, Wieland B; Corbeil, Denis
Distinct and Conserved Prominin-1/CD133-Positive Retinal Cell Populations Identified across Species
Besides being a marker of various somatic stem cells in mammals, prominin-1 (CD133) plays a role in maintaining the photoreceptor integrity since mutations in the PROM1 gene are linked with retinal degeneration. In spite of that, little information is available regarding its distribution in eyes of non-mammalian vertebrates endowed with high regenerative abilities. To address this subject, prominin-1 cognates were isolated from axolotl, zebrafish and chicken, and their retinal compartmentalization was investigated and compared to that of their mammalian orthologue. Interestingly, prominin-1 transcripts—except for the axolotl—were not strictly restricted to the outer nuclear layer (i.e., photoreceptor cells), but they also marked distinct subdivisions of the inner nuclear layer (INL). In zebrafish, where the prominin-1 gene is duplicated (i.e., prominin-1a and prominin-1b), a differential expression was noted for both paralogues within the INL being localized either to its vitreal or scleral subdivision, respectively. Interestingly, expression of prominin-1a within the former domain coincided with Pax-6–positive cells that are known to act as progenitors upon injury-induced retino-neurogenesis. A similar, but minute population of prominin-1–positive cells located at the vitreal side of the INL was also detected in developing and adult mice. In chicken, however, prominin-1–positive cells appeared to be aligned along the scleral side of the INL reminiscent of zebrafish prominin-1b. Taken together our data indicate that in addition to conserved expression of prominin-1 in photoreceptors, significant prominin-1–expressing non-photoreceptor retinal cell populations are present in the vertebrate eye that might represent potential sources of stem/progenitor cells for regenerative therapies.
Jaszai, Jozsef; Fargeas, Christine A.; Graupner, Sylvi; Tanaka, Elly M.; Brand, Michael; Huttner, Wieland B.; Corbeil, Denis
Heparan Sulfate Phage Display Antibodies Identify Distinct Epitopes with Complex Binding Characteristics
Heparan sulfate (HS) binds and modulates the transport and activity of a large repertoire of regulatory proteins. The HS phage display antibodies are powerful tools for the analysis of native HS structure in situ; however, their epitopes are not well defined. Analysis of the binding specificities of a set of HS antibodies by competitive binding assays with well defined chemically modified heparins demonstrates that O-sulfates are essential for binding; however, increasing sulfation does not necessarily correlate with increased antibody reactivity. IC50 values for competition with double modified heparins were not predictable from IC50 values with corresponding singly modified heparins. Binding assays and immunohistochemistry revealed that individual antibodies recognize distinct epitopes and that these are not single linear sequences but families of structurally similar motifs in which subtle variations in sulfation and conformation modify the affinity of interaction. Modeling of the antibodies demonstrates that they possess highly basic CDR3 and surrounding surfaces, presenting a number of possible orientations for HS binding. Unexpectedly, there are significant differences between the existence of epitopes in tissue sections and observed in vitro in dot blotted tissue extracts, demonstrating that in vitro specificity does not necessarily correlate with specificity in situ/vivo. The epitopes are therefore more complex than previously considered. Overall, these data have significance for structure-activity relationships of HS, because the model of one antibody recognizing multiple HS structures and the influence of other in situ HS-binding proteins on epitope availability are likely to reflect the selectivity of many HS-protein interactions in vivo.
Thompson, Sophie M.; Fernig, David G.; Jesudason, Edwin C.; Losty, Paul D.; van de Westerlo, Els M. A.; van Kuppevelt, Toin H.; Turnbull, Jeremy E.
Wilms tumour histology is determined by distinct types of precursor lesions and not epigenetic changes.
Current models of Wilms tumour development propose that histological features of the tumours are programmed by the underlying molecular aberrations. For example, tumours associated with WT1 mutations arise from intralobar nephrogenic rests (ILNR), concur with CTNNB1 mutations and have distinct histology, whereas tumours with IGF2 loss of imprinting (LOI) often arise from perilobar nephrogenic rests (PLNR). Intriguingly, ILNR and PLNR are found simultaneously in Wilms tumours in children with overgrowth who have constitutional IGF2 LOI. We therefore examined whether the precursor lesions or early epigenetic changes are the primary determinant of Wilms tumour histology. We examined the histological features and gene expression profiles of IGF2 LOI tumours and WT1-mutant tumours which are associated with PLNR and/or ILNR. Two distinct types of IGF2 LOI tumours were identified: the first type had a blastemal-predominant histology associated with PLNR, while the second subtype had a myogenic histology, increased expression of mesenchymal lineage genes and an association with ILNR, similar to WT1-mutant tumours. These ILNR-associated IGF2 LOI tumours also showed signatures of activation of the WNT signalling pathway: differential expression of beta-catenin targets (MMP2, RARG, DKK1) and WNT antagonist genes (DKK1, WIF1, SFRP4). Unexpectedly, the majority of these tumours had CTNNB1 mutations, which are normally only seen in WT1-mutant tumours. The absence of WT1 mutations in tumours with IGF2 LOI indicated that CTNNB1 mutations occur predominantly in tumours arising from ILNR independent of the presence or absence of WT1 mutations. Thus, even though these two classes of tumours with IGF2 LOI have the same underlying predisposing epigenetic error, the tumour histology and the gene expression profiles are determined by the nature of the precursor cells within the nephrogenic rests and subsequent CTNNB1 mutations. PMID:18484682
Fukuzawa, R; Anaka, M R; Heathcott, R W; McNoe, L A; Morison, I M; Perlman, E J; Reeve, A E
A Comparative Genome Analysis Identifies Distinct Sorting Pathways in Gram-Positive Bacteria
Surface proteins in gram-positive bacteria are frequently required for virulence, and many are attached to the cell wall by sortase enzymes. Bacteria frequently encode more than one sortase enzyme and an even larger number of potential sortase substrates that possess an LPXTG-type cell wall sorting signal. In order to elucidate the sorting pathways present in gram-positive bacteria, we performed a
David Comfort; Robert T. Clubb
Resolving Tumor Heterogeneity: Genes Involved in Chordoma Cell Development Identified by Low-Template Analysis of Morphologically Distinct Cells
The classical sacrococcygeal chordoma tumor presents with a typical morphology of lobulated myxoid tumor tissue with cords, strands and nests of tumor cells. The population of cells consists of small non-vacuolated cells, intermediate cells with a wide range of vacuolization and large heavily vacuolated (physaliferous) cells. To date analysis was only performed on bulk tumor mass because of its rare incidence, lack of suited model systems and technical limitations thereby neglecting its heterogeneous composition. We intended to clarify whether the observed cell types are derived from genetically distinct clones or represent different phenotypes. Furthermore, we aimed at elucidating the differences between small non-vacuolated and large physaliferous cells on the genomic and transcriptomic level. Phenotype-specific analyses of small non-vacuolated and large physaliferous cells in two independent chordoma cell lines yielded four candidate genes involved in chordoma cell development. UCHL3, coding for an ubiquitin hydrolase, was found to be over-expressed in the large physaliferous cell phenotype of MUG-Chor1 (18.7-fold) and U-CH1 (3.7-fold) cells. The mannosyltransferase ALG11 (695-fold) and the phosphatase subunit PPP2CB (18.6-fold) were found to be up-regulated in large physaliferous MUG-Chor1 cells showing a similar trend in U-CH1 cells. TMEM144, an orphan 10-transmembrane family receptor, yielded contradictory data as cDNA microarray analysis showed up- but RT-qPCR data down-regulation in large physaliferous MUG-Chor1 cells. Isolation of few but morphologically identical cells allowed us to overcome the limitations of bulk analysis in chordoma research. We identified the different chordoma cell phenotypes to be part of a developmental process and discovered new genes linked to chordoma cell development representing potential targets for further research in chordoma tumor biology.
Wagner, Karin; Meditz, Katharina; Kolb, Dagmar; Feichtinger, Julia; Thallinger, Gerhard G.; Quehenberger, Franz; Liegl-Atzwanger, Bernadette; Rinner, Beate
Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4
BACKGROUND: Human T-lymphotropic virus type 4 (HTLV-4) is a new deltaretrovirus recently identified in a primate hunter in Cameroon. Limited sequence analysis previously showed that HTLV-4 may be distinct from HTLV-1, HTLV-2, and HTLV-3, and their simian counterparts, STLV-1, STLV-2, and STLV-3, respectively. Analysis of full-length genomes can provide basic information on the evolutionary history and replication and pathogenic potential
William M Switzer; Marco Salemi; Shoukat H Qari; Hongwei Jia; Rebecca R Gray; Aris Katzourakis; Susan J Marriott; Kendle N Pryor; Nathan D Wolfe; Donald S Burke; Thomas M Folks; Walid Heneine
Nuclear Morphometry Identifies a Distinct Aggressive Cellular Phenotype in Cutaneous Squamous Cell Carcinoma
By identifying aggressive cutaneous squamous cell carcinoma (cSCC) in patients who are at high risk for recurrences or second primaries after resection, intensive surveillance and therapy may decrease morbidity and mortality. We investigated the role of nuclear morphometry (karyometry) in differentiating between aggressive and nonaggressive cSCC. We retrospectively analyzed cSCC lesions from 40 male patients. 22 patients had evidence of aggressive cSCC (local/regional recurrence or a second primary cSCC), and 18 patients were identified with similar ages and sites of disease as control patients with nonaggressive cSCC (no evidence of recurrence, metastasis, or second primary). We performed karyometric analysis to identify nuclear features that discriminate between aggressive and nonaggressive cSCC nuclei. We used statistically significant differences (Kruskal-Wallis test P < 0.0001) to compose a quantitative aggressive classification score (proportion of aggressive nuclei from 0% to 100%). For comparisons, we used Fisher's exact test or Student t test. The mean age was 79 ± 7 years for aggressive cSCC and 80 ± 9 years for nonaggressive cSCC (P = 0.66). We analyzed a mean of 96 nuclei in each group. The mean classification score for aggressive cSCC was significantly higher (69% ± 6%) than for nonaggressive cSCC (28% ± 5%, P = 0.00002). Overall, the classification score accurately categorized 80% of our patients (P = 0.0004). In most patients, karyometry differentiated between aggressive and nonaggressive cSCC. We found that classification scores, which provide information on individual lesions, could be used for risk stratification.
Glazer, Evan S.; Bartels, Peter H.; Prasad, Anil R.; Yozwiak, Michael L.; Bartels, Hubert G.; Einspahr, Janine G.; Alberts, David S.; Krouse, Robert S.
Novel 'phage display antibodies identify distinct heparan sulfate domains in developing mammalian lung.
Heparan sulfate proteoglycans (HSPGs) are essential to respiratory morphogenesis in species as diverse as Drosophila and mice; they play a role in the regulation of numerous HS-binding growth factors, e.g. fibroblast growth factors. Moreover, an HS analogue, heparin, modulates lung growth in vitro. However, it has been difficult to assess the roles of specific HS structures in lung development due to technical barriers to their spatial localisation. Lungs from Sprague-Dawley rats were harvested between E15.5 and E19.5 and immediately fixed in 4 % (w/v) paraformaldehyde (in 0.1 M phosphate-buffered saline (PBS), pH 7.4). Lungs were washed in PBS, cryoprotected with 20% (w/v) sucrose (in PBS), gelatin embedded [7.5% (w/v) gelatin, 15% (w/v) sucrose in PBS], before being covered in Cryo-M-Bed (Bright, Huntingdon, UK) and snap frozen at -40 degrees C. Cryosections were cut at 8 microm and stained with the HSPG core protein specific antibody 3G10 and a HS 'phage display antibody, EW4G2V. 3G10 and EW4G2V immunohistochemistry highlighted the presence of specific HS structures in lungs at all gestational ages examined. 3G10 strongly labelled airway basement membranes and the surrounding mesenchyme and showed weak staining of airway epithelial cells. EW4G2V, however, was far more selective, labelling the airway basement membranes only. Mesenchymal and epithelial cells did not appear to possess the HS epitope recognised by EW4G2V at these gestational ages. Novel 'phage display antibodies allow the spatial distribution of tissue HS to be analysed, and demonstrate in situ that distinct cellular compartments of a tissue possess different HS structures, possibly on the same proteoglycan core protein. These probes offer a new opportunity to determine the role of HS in the pathogenesis of congenital defects such as congenital diaphragmatic hernia (CDH), where lung development is aberrant, and the resulting pulmonary hypoplasia and hypertension are a primary cause of mortality. PMID:17216534
Thompson, S M; Connell, M G; Fernig, D G; Ten Dam, G B; van Kuppevelt, T H; Turnbull, J E; Jesudason, E C; Losty, P D
Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f
Background The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif. Results The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments. Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi. Conclusions The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.
A New Approach for Integration of Two Distinct Types of Nu merical Simulator
Electromagnetic transient simulation and electro- mechanical transient simulation are two distinct types of simulators, based on different modeling techniques. EMTP comprises a three-phase simulation engine which can ac- commodate phase unbalance and waveform distortion. TSP produces phasor solutions, usually only positive sequence, in the time domain. This paper presents a hybrid simulator, based on interfacing the two types of simulators.
Hongtian Su; L. A. Snider; K. W. Chan; Baorong Zhou
Maternal glutaric acidemia, type I identified by newborn screening.
We report two women with glutaric acidemia type I in whom the diagnosis was unsuspected until a low carnitine level was found in their newborn children. Both mothers had low carnitine in plasma. In the first, organic acid analysis was only done after fibroblast studies revealed normal carnitine uptake. Having learned from the first family, organic acid analysis was done immediately in the mother of family 2. In both, the plasma acylcarnitine profile was normal but both excreted the metabolites typical of their disorder. One of the women was a compound heterozygote for distinct mutations in the glutaric acid dehydrogenase gene, whereas the second was either homozygous or hemizygous for a mutation in Exon 6 of the gene. PMID:18304851
Crombez, Eric A; Cederbaum, Stephen D; Spector, Elaine; Chan, Erica; Salazar, Denise; Neidich, Julie; Goodman, Stephen
Maternal Glutaric Acidemia, Type I Identified by Newborn Screening*
We report two women with glutaric acidemia type I in whom the diagnosis was unsuspected until a low carnitine level was found in their newborn children. Both mothers had low carnitine in plasma. In the first, organic acid analysis was only done after fibroblast studies revealed normal carnitine uptake. Having learned from the first family, organic acid analysis was done immediately in the mother of family 2. In both, the plasma acylcarnitine profile was normal but both excreted the metabolites typical of their disorder. One of the women was a compound heterozygote for distinct mutations in the glutaric acid dehydrogenase gene, whereas the second was either homozygous or hemizygous for a mutation in Exon 6 of the gene.
Crombez, Eric A.; Cederbaum, Stephen D.; Spector, Elaine; Chan, Erica; Salazar, Denise; Neidich, Julie; Goodman, Stephen
Smooth muscle differentiation identifies two classes of poorly differentiated pleomorphic sarcomas with distinct outcome.
The clinical relevance of accurately diagnosing pleomorphic sarcomas has been shown, especially in cases of undifferentiated pleomorphic sarcomas with myogenic differentiation, which appear significantly more aggressive. To establish a new smooth muscle differentiation classification and to test its prognostic value, 412 sarcomas with complex genetics were examined by immunohistochemistry using four smooth muscle markers (calponin, h-caldesmon, transgelin and smooth muscle actin). Two tumor categories were first defined: tumors with positivity for all four markers and tumors with no or incomplete phenotypes. Multivariate analysis demonstrated that this classification method exhibited the strongest prognostic value compared with other prognostic factors, including histological classification. Secondly, incomplete or absent smooth muscle phenotype tumor group was then divided into subgroups by summing for each tumor the labeling intensities of all four markers for each tumors. A subgroup of tumors with an incomplete but strong smooth muscle differentiation phenotype presenting an intermediate metastatic risk was thus identified. Collectively, our results show that the smooth muscle differentiation classification method may be a useful diagnostic tool as well as a relevant prognostic tool for undifferentiated pleomorphic sarcomas. PMID:24287457
Pérot, Gaëlle; Mendiboure, Jean; Brouste, Véronique; Velasco, Valérie; Terrier, Philippe; Bonvalot, Sylvie; Guillou, Louis; Ranchčre-Vince, Dominique; Aurias, Alain; Coindre, Jean-Michel; Chibon, Frédéric
Development of a multiplex RT-PCR-ELISA to identify four distinct species of tospovirus.
In this study, a multiplex RT-PCR-ELISA was developed to detect and differentiate four tospovirus species found in Thailand, namely Capsicum chlorosis virus (CaCV), Melon yellow spot virus (MYSV), Tomato necrotic ringspot virus (TNRV), and Watermelon silver mottle virus (WSMoV). In this system, nucleocapsid (N) gene fragments of four tospoviruses were simultaneously amplified and labeled with digoxigenin (DIG) in a single RT-PCR reaction using a pair of degenerate primers binding to the same conserved regions in all four tospovirus N genes. The DIG-labeled amplicons were distinguished into species by four parallel hybridizations to species-specific biotinylated probes in streptavidin-coated microtiter wells followed by ELISA detection using a peroxidase-conjugated anti-DIG antibody. Results indicated that the multiplex RT-PCR-ELISA assay could specifically identify each of these four tospoviruses without cross-reactivity between species or reactivity to healthy plant negative controls. Assay sensitivity was 10- to 1000-fold higher than conventional RT-PCR. When applied to naturally infected plants, all samples yielded concordant results between RT-PCR-ELISA and the reference RT-PCR. In conclusion, the multiplex RT-PCR-ELISA developed in this study has superior specificity, sensitivity, and high-throughput capacity compared to conventional RT-PCR and is an attractive alternative for the identification of different tospovirus species. PMID:24642237
Charoenvilaisiri, Saengsoon; Seepiban, Channarong; Bhunchoth, Anjana; Warin, Nuchnard; Luxananil, Plearnpis; Gajanandana, Oraprapai
Functional characterization of Prickle2 and BBS7 identify overlapping phenotypes yet distinct mechanisms.
Ciliopathies are genetic disorders that are caused by dysfunctional cilia and affect multiple organs. One type of ciliopathy, Bardet-Biedl syndrome, is a rare disorder characterized by obesity, retinitis pigmentosa, polydactyly, mental retardation and susceptibility to cardiovascular diseases. The Wnt/Planar cell polarity (PCP) has been associated with cilia function and ciliogenesis in directing the orientation of cilia and basal bodies. Yet the exact relationship between PCP and ciliopathy is not well understood. Here, we examine interactions between a core PCP component, Prickle2 (Pk2), and a central BBS gene, Bbs7, using gene knockdown in the zebrafish. pk2 and bbs7 knockdown both disrupt the formation of a ciliated organ, the Kupffer?s vesicle (KV), but do not display a synergistic interaction. By measuring cell polarity in the neural tube, we find that bbs7 activity is not required for Pk asymmetric localization. Moreover, BBS protein complex formation is preserved in the Pk2-deficient (Pk2(-/-)) mouse. Previously we reported an intracellular melanosome transport delay as a cardinal feature of reduced bbs gene activity. We find that pk2 knockdown suppresses bbs7-related retrograde transport delay. Similarly, knockdown of ift22, an anterograde intraflagellar transport component, also suppresses the bbs7-related retrograde delay. Notably, we find that pk2 knockdown larvae show a delay in anterograde transport. These data suggest a novel role for Pk2 in directional intracellular transport and our analyses show that PCP and BBS function independently, yet result in overlapping phenotypes when knocked down in zebrafish. PMID:24938409
Mei, Xue; Westfall, Trudi A; Zhang, Qihong; Sheffield, Val C; Bassuk, Alexander G; Slusarski, Diane C
Two distinct human parainfluenza virus type 1 genotypes detected during the 1991 Milwaukee epidemic.
The extent of genetic and antigenic variation found in a population of human parainfluenza virus type 1 (HPIV-1) during a single local epidemic was investigated. Fifteen HPIV-1 strains isolated from children in 1991 were analyzed. Nucleotide sequence variation in the hemagglutinin-neuraminidase protein (HN) gene demonstrated two distinct genotypes (genotypes C and D). Unique patterns were identified involving 62 nucleotide and 10 amino acid positions. These patterns represented 40% of all mutations within the HN gene. The remaining mutations were randomly distributed, and 74% involved only one (55%) or two isolates. Genotypes were statistically different from each other at both the nucleotide (P = 0.001) and amino acid (P = 0.001) levels and demonstrated unique potential N-linked glycosylation patterns. Thirty-eight monoclonal antibodies (MAbs) made to four different viral proteins (22 HN, 2 fusion [F], 1 phosphoprotein, and 13 nucleoprotein) (originating from two different genotypes [genotypes A and D]) were compared for their ability to bind to the clinical isolates in enzyme-linked immunosorbent assays (ELISAs) and hemagglutinin-inhibition (HI) assays. Twenty-one MAbs bound well to all clinical isolates in ELISAs and HI assays. The remaining 17 MAbs showed variation in all four structural proteins. Three HN MAbs demonstrated genotype C- and D-specific antigenic and neutralization differences. Evolutionary analysis using parsimony methods confirmed the differences between the two genotypes. No differences in either clinical presentation or disease severity between the two genotypes were found. Geographically localized HPIV-1 epidemics can be caused by at least two distinct genotypes with minor but specific antigenic changes. The clinical and immunologic roles of HPIV-1 genotypes have not been determined.
Henrickson, K J; Savatski, L L
Identifying aquifer type in fractured rock aquifers using harmonic analysis.
Determining aquifer type, unconfined, semi-confined, or confined, by drilling or performing pumping tests has inherent problems (i.e., cost and complex field issues) while sometimes yielding inconclusive results. An improved method to cost-effectively determine aquifer type would be beneficial for hydraulic mapping of complex aquifer systems like fractured rock aquifers. Earth tides are known to influence water levels in wells penetrating confined aquifers or unconfined thick, low-porosity aquifers. Water-level fluctuations in wells tapping confined and unconfined aquifers are also influenced by changes in barometric pressure. Harmonic analyses of water-level fluctuations of a thick (~1000 m) carbonate aquifer located in south-central Oklahoma (Arbuckle-Simpson aquifer) were utilized in nine wells to identify aquifer type by evaluating the influence of earth tides and barometric-pressure variations using signal identification. On the basis of the results, portions of the aquifer responded hydraulically as each type of aquifer even though there was no significant variation in lithostratigraphy. The aquifer type was depth dependent with confined conditions becoming more prevalent with depth. The results demonstrate that harmonic analysis is an accurate and low-cost method to determine aquifer type. PMID:22463080
Rahi, Khayyun A; Halihan, Todd
Hippocampal pyramidal neurons comprise two distinct cell types that are countermodulated by metabotropic receptors
Summary Relating the function of neuronal cell types to information processing and behavior is a central goal of neuroscience. In the hippocampus, pyramidal cells in CA1 and the subiculum process sensory and motor cues to form a cognitive map encoding spatial, contextual, and emotional information, which they transmit throughout the brain. Do these cells constitute a single class, or are there multiple cell types with specialized functions? Using unbiased cluster analysis, we show that there are two morphologically and electrophysiologically distinct principal cell types that carry hippocampal output. We show further that these two cell types are inversely modulated by the synergistic action of glutamate and acetylcholine acting on metabotropic receptors that are central to hippocampal function. Combined with prior connectivity studies, our results support a model of hippocampal processing in which the two pyramidal cell types are predominantly segregated into two parallel pathways that process distinct modalities of information.
Graves, Austin R; Moore, Shannon J; Bloss, Erik B; Mensh, Brett D; Kath, William L; Spruston, Nelson
Two distinct CCR5 domains can mediate coreceptor usage by human immunodeficiency virus type 1.
The chemokine receptor CCR5 is the major fusion coreceptor for macrophage-tropic strains of human immunodeficiency virus type 1 (HIV-1). To define the structures of CCR5 that can support envelope (Env)-mediated membrane fusion, we analyzed the activity of homologs, chimeras, and mutants of human CCR5 in a sensitive gene reporter cell-cell fusion assay. Simian, but not murine, homologs of CCR5 were fully active as HIV-1 fusion coreceptors. Chimeras between CCR5 and divergent chemokine receptors demonstrated the existence of two distinct regions of CCR5 that could be utilized for Env-mediated fusion, the amino-terminal domain and the extracellular loops. Dual-tropic Env proteins were particularly sensitive to alterations in the CCR5 amino-terminal domain, suggesting that this domain may play a pivotal role in the evolution of coreceptor usage in vivo. We identified individual residues in both functional regions, Asp-11, Lys-197, and Asp-276, that contribute to coreceptor function. Deletion of a highly conserved cytoplasmic motif rendered CCR5 incapable of signaling but did not abrogate its ability to function as a coreceptor, implying the independence of fusion and G-protein-mediated chemokine receptor signaling. Finally, we developed a novel monoclonal antibody to CCR5 to assist in future studies of CCR5 expression.
Doranz, B J; Lu, Z H; Rucker, J; Zhang, T Y; Sharron, M; Cen, Y H; Wang, Z X; Guo, H H; Du, J G; Accavitti, M A; Doms, R W; Peiper, S C
ON IDENTIFYING THE PROGENITORS OF Type Ia SUPERNOVAE
We propose two new means of identifying the main class of progenitors of Type Ia supernovae-single or double degenerate: (1) if the range of supernova properties is significantly determined by the range of viewing angles of non-spherically symmetric explosions, then the nature of the correlation between polarization and another property (for example, the velocity gradient) can be used to determine the geometry of the asymmetry and hence the nature of the progenitor, and (2) in the double- but not in the single-degenerate case, the range in the observed properties (e.g., velocity gradients) is likely to increase with the amount of carbon seen in the ejecta.
Livio, Mario; Pringle, J. E., E-mail: email@example.com [Space Telescope Science Institute, Baltimore, MD (United States)
Genetic errors identified in 12 major cancer types
Examining 12 major types of cancer, scientists at Washington University School of Medicine in St. Louis (home of the Alvin J. Siteman Cancer Center) have identified 127 repeatedly mutated genes that appear to drive the development and progression of a range of tumors in the body. The discovery sets the stage for devising new diagnostic tools and more personalized cancer treatments. The research, published Oct. 17 in Nature, shows that some of the same genes commonly mutated in certain cancers also occur in seemingly unrelated tumors.
Two Types of Human Mast Cells That Have Distinct Neutral Protease Compositions
Two human mast cell types were identified by immunohistochemical techniques in skin, lung, and small intestine. One type contains the neutral proteases, tryptase and chymotryptic proteinase, and is termed the TC mast cell. The second type contains only tryptase and is termed the T mast cell. Both types are fixed better by Carnoy's fluid than by formalin. The percentage of
A. A. Irani; N. M. Schechter; S. S. Craig; G. Deblois; L. B. Schwartz
Identifying patients at risk of type 2 diabetes.
At present there are nearly 3 million people with diabetes in the UK. It is predicted that this number will almost double by 2025. Nine out of ten of these individuals will have type 2 diabetes. It is estimated that one in seven adults have impaired glucose regulation and up to 12% of these will develop type 2 diabetes each year. The impact of obesity on the development of type 2 diabetes cannot be overemphasised, with a 1 kg/m2 increase in BMI raising the risk of impaired fasting glycaemia by 9.5% and of developing new-onset type 2 diabetes by 8.4%. A 1 cm increase in waist circumference increases the risks by 3.2% and 3.5% respectively. NICE advises using a validated risk assessment tool to identify patients at risk of diabetes. Risk factors used by such tools include: age; ethnicity; weight; first-degree relative with type 2 diabetes; low birthweight and sedentary lifestyle. Certain comorbidities increase the risk of type 2 diabetes, these include: cardiovascular and cerebrovascular disease; polycystic ovary syndrome; a history of gestational diabetes; and mental health problems. The initial screening blood test could be a fasting plasma glucose, HbA1c, or an oral glucose tolerance test, according to WHO criteria. NICE recommends that high-risk patients should be offered a programme encouraging them to undertake a minimum of 150 minutes of moderate intensity physical activity a week, gradually lose weight to reach and maintain a BMI within the healthy range, increase consumption of whole grains, vegetables, and other foods that are high in dietary fibre, reduce the total amount of fat in their diet and eat less saturated fat. PMID:22988703
Savill, Peter
Burkholderia Type VI Secretion Systems Have Distinct Roles in Eukaryotic and Bacterial Cell Interactions
Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs) of Burkholderia thailandensis (B. thai) in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ?T6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans—leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections.
Schwarz, Sandra; West, T. Eoin; Boyer, Frederic; Chiang, Wen-Chi; Carl, Mike A.; Hood, Rachel D.; Rohmer, Laurence; Tolker-Nielsen, Tim; Skerrett, Shawn J.; Mougous, Joseph D.
Chemical similarities among physically distinct spring types in a karst terrain
NASA Astrophysics Data System (ADS)
In karst regions where correlations between physical characteristics of springs and temporal variations in spring water chemistry have been found, spring water chemistry has been used to infer physical attributes of karst systems. Possible correlations between chemical and physical characteristics of springs were tested in the Inner Bluegrass Karst Region of central Kentucky where previous dye-tracing studies have identified two physically distinct spring types: local high-level springs discharging from shallow flow paths and major low-level springs discharging from a deep integrated conduit system. Representative high-level and major springs were sampled over a 16-month period and analyzed for major dissolved components. Both spring types showed similar variations in temperature, calcium, magnesium, bicarbonate, and hardness. No systematic differences in ionic concentrations or in saturation indices with respect to calcite and dolomite were apparent between the two spring types. Chemical similarities between high-level and major springs during low flow are attributed to recharge of major springs by percolation and by high-level springs and to the occurrence of most chemical reactions near the recharge zone rather than in the deep conduit system. During high discharge, however, most recharge to the major springs is surface runoff which produces low ionic concentrations. Similarly low ionic concentrations in the high-level springs are thought to result from rapid flow through the soil-rock zone and short flow distances. These relationships indicate that spring water chemistry is not only a function of conduit size but also an indicator of recharge type and amount and flow path length. Differing flow path lengths to major and high-level springs counteract the effect of varying conduit size between the two spring types and result in similar ionic concentrations. These data indicate that spring water chemistry cannot be used to predict physical characteristics of karst aquifers in the Inner Bluegrass Region. The physical and chemical attributes of springs in the Inner Bluegrass were compared to those of springs in the Nittany Valley of Pennsylvania. A reported high correlation between physical and chemical characteristics of springs in the Pennsylvania karst system reflects geological and structural controls not present in the Inner Bluegrass Region.
Scanlon, B. R.; Thrailkill, J.
Type AB thymoma is not a mixed tumor of type A and type B thymomas, but a distinct type of thymoma.
Type AB thymoma is generally regarded to be a mixture of type A and type B thymomas, but has not been studied extensively. In this study, we precisely investigated the characteristics of type AB thymoma immunohistochemically and compared it with other types of thymoma, including type A, metaplastic, and type B1 thymoma. In type A thymoma, the tumor cells were composed solely of pan-cytokeratin (CK-AE1/AE3)(+) claudin-1(+) vimentin(-) epithelial membrane antigen (EMA)(-) short spindle cells. Metaplastic thymoma exhibited biphasic architecture of epithelial islands of short spindle cells, which were phenotypically almost identical to the tumor cells in type A thymoma, and anastomosing bundles of CK-AE1/AE3(-) claudin-1(-) vimentin(+) EMA(+) fibroblast-like long spindle-shaped epithelial cells. Interestingly, we found that there were two distinctive subtypes of cell in type AB thymoma: the conventional subtype and the metaplastic subtype. The conventional subtype is characterized by type A-like components resembling type A thymoma. The metaplastic subtype is characterized by type A-like components extensively resembling the anastomosing bundles of fibroblast-like long spindle epithelial cells. Interestingly, the metaplastic subtype was a major subtype (14/19 cases), while the conventional subtype was a minor one (5/19 cases). In contrast to the rarity of metaplastic thymoma, the metaplastic subtype of type AB thymoma appears to be a major subtype of type AB thymoma. PMID:24802113
Miki, Yukari; Hamada, Kana; Yoshino, Tadashi; Miyatani, Katsuya; Takahashi, Kiyoshi
X-linked intellectual disability type Nascimento is a clinically distinct, probably underdiagnosed entity.
X-linked intellectual disability type Nascimento (MIM #300860), caused by mutations in UBE2A (MIM *312180), is characterized by craniofacial dysmorphism (synophrys, prominent supraorbital ridges, deep-set, almond-shaped eyes, depressed nasal bridge, prominent columella, hypoplastic alae nasi, and macrostomia), skin anomalies (hirsutism, myxedematous appearance, onychodystrophy), micropenis, moderate to severe intellectual disability (ID), motor delay, impaired/absent speech, and seizures. Hitherto only five familial point mutations and four different deletions including UBE2A have been reported in the literature.We present eight additional individuals from five families with UBE2A associated ID - three males from a consanguineous family, in whom we identified a small deletion of only 7.1 kb encompassing the first three exons of UBE2A, two related males with a UBE2A missense mutation in exon 4, a patient with a de novo nonsense mutation in exon 6, and two sporadic males with larger deletions including UBE2A. All affected male individuals share the typical clinical phenotype, all carrier females are unaffected and presented with a completely skewed X inactivation in blood. We conclude that 1.) X-linked intellectual disability type Nascimento is a clinically very distinct entity that might be underdiagnosed to date. 2.) So far, all females carrying a familial UBE2A aberration have a completely skewed X inactivation and are clinically unaffected. This should be taken in to account when counselling those families. 3.) The coverage of an array should be checked carefully prior to analysis since not all arrays have a sufficient resolution at specific loci, or alternative quantitative methods should be applied not to miss small deletions. PMID:24053514
Czeschik, Johanna Christina; Bauer, Peter; Buiting, Karin; Dufke, Claudia; Guillén-Navarro, Encarna; Johnson, Diana S; Koehler, Udo; López-González, Vanesa; Lüdecke, Hermann-Josef; Male, Alison; Morrogh, Deborah; Rieß, Angelika; Tzschach, Andreas; Wieczorek, Dagmar; Kuechler, Alma
X-linked intellectual disability type Nascimento is a clinically distinct, probably underdiagnosed entity
X-linked intellectual disability type Nascimento (MIM #300860), caused by mutations in UBE2A (MIM *312180), is characterized by craniofacial dysmorphism (synophrys, prominent supraorbital ridges, deep-set, almond-shaped eyes, depressed nasal bridge, prominent columella, hypoplastic alae nasi, and macrostomia), skin anomalies (hirsutism, myxedematous appearance, onychodystrophy), micropenis, moderate to severe intellectual disability (ID), motor delay, impaired/absent speech, and seizures. Hitherto only five familial point mutations and four different deletions including UBE2A have been reported in the literature. We present eight additional individuals from five families with UBE2A associated ID - three males from a consanguineous family, in whom we identified a small deletion of only 7.1 kb encompassing the first three exons of UBE2A, two related males with a UBE2A missense mutation in exon 4, a patient with a de novo nonsense mutation in exon 6, and two sporadic males with larger deletions including UBE2A. All affected male individuals share the typical clinical phenotype, all carrier females are unaffected and presented with a completely skewed X inactivation in blood. We conclude that 1.) X-linked intellectual disability type Nascimento is a clinically very distinct entity that might be underdiagnosed to date. 2.) So far, all females carrying a familial UBE2A aberration have a completely skewed X inactivation and are clinically unaffected. This should be taken in to account when counselling those families. 3.) The coverage of an array should be checked carefully prior to analysis since not all arrays have a sufficient resolution at specific loci, or alternative quantitative methods should be applied not to miss small deletions.
Genetically distinct pathways guide effector export through the type VI secretion system.
Bacterial secretion systems often employ molecular chaperones to recognize and facilitate export of their substrates. Recent work demonstrated that a secreted component of the type VI secretion system (T6SS), haemolysin co-regulated protein (Hcp), binds directly to effectors, enhancing their stability in the bacterial cytoplasm. Herein, we describe a quantitative cellular proteomics screen for T6S substrates that exploits this chaperone-like quality of Hcp. Application of this approach to the Hcp secretion island I-encoded T6SS (H1-T6SS) of Pseudomonas aeruginosa led to the identification of a novel effector protein, termed Tse4 (type VI secretion exported 4), subsequently shown to act as a potent intra-specific H1-T6SS-delivered antibacterial toxin. Interestingly, our screen failed to identify two predicted H1-T6SS effectors, Tse5 and Tse6, which differ from Hcp-stabilized substrates by the presence of toxin-associated PAAR-repeat motifs and genetic linkage to members of the valine-glycine repeat protein G (vgrG) genes. Genetic studies further distinguished these two groups of effectors: Hcp-stabilized effectors were found to display redundancy in interbacterial competition with respect to the requirement for the two H1-T6SS-exported VgrG proteins, whereas Tse5 and Tse6 delivery strictly required a cognate VgrG. Together, we propose that interaction with either VgrG or Hcp defines distinct pathways for T6S effector export. PMID:24589350
Whitney, John C; Beck, Christina M; Goo, Young Ah; Russell, Alistair B; Harding, Brittany N; De Leon, Justin A; Cunningham, David A; Tran, Bao Q; Low, David A; Goodlett, David R; Hayes, Christopher S; Mougous, Joseph D
Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions
Transcription factors (TFs) regulate gene expression by binding to short DNA sequence motifs, yet their binding specificities alone cannot explain how certain TFs drive a diversity of biological processes. In order to investigate the factors that control the functions of the pleiotropic TF STAT3, we studied its genome-wide binding patterns in four different cell types: embryonic stem cells, CD4+ T cells, macrophages and AtT-20 cells. We describe for the first time two distinct modes of STAT3 binding. First, a small cell type-independent mode represented by a set of 35 evolutionarily conserved STAT3-binding sites that collectively regulate STAT3's own functions and cell growth. We show that STAT3 is recruited to sites with E2F1 already pre-bound before STAT3 activation. Second, a series of different transcriptional regulatory modules (TRMs) assemble around STAT3 to drive distinct transcriptional programs in the four cell types. These modules recognize cell type-specific binding sites and are associated with factors particular to each cell type. Our study illustrates the versatility of STAT3 to regulate both universal- and cell type-specific functions by means of distinct TRMs, a mechanism that might be common to other pleiotropic TFs.
Hutchins, Andrew Paul; Diez, Diego; Takahashi, Yoshiko; Ahmad, Shandar; Jauch, Ralf; Tremblay, Michel Lucien; Miranda-Saavedra, Diego
Fiber type composition of the architecturally distinct regions of human supraspinatus muscle: a cadaveric study.
The human supraspinatus muscle is clinically important as it is frequently injured in older adults and the elderly. We have previously shown that the supraspinatus has a complex architecture with two distinct regions each consisting of three parts. Further we have found dynamic changes in architectural parameters such as fiber bundle length markedly vary between these regions. Fiber types of the supraspinatus have not been thoroughly investigated throughout its volume and are of interest to clinicians treating supraspinatus pathologies. In this study we investigated the distribution of fiber types within the distinct regions and parts of supraspinatus. Samples of supraspinatus were excised from six distinct parts of each muscle from five formalin embalmed specimens (one male, four female; mean age 77±11.1 years) free of tendon pathology. Samples were frozen in liquid nitrogen and then cryosectioned. Serial sections were labeled using immunohistochemical techniques and antibodies against fast or slow myosin heavy chain isoforms. The mean percentage of Type I (slow) fibers ranged from 56.73% to 63.97%. Results demonstrated significant variations in fiber type distribution. The middle part of the anterior region has a significantly greater percentage of Type I fibers compared to that of the posterior. The superficial part of the anterior region has a greater percentage of Type II (fast) fibers compared to the middle and deep parts. Findings aid in highlighting the distinct functions of the anterior and posterior regions, and prompt the need to re-evaluate assessment and treatment techniques established on a limited understanding of the fiber type distribution. PMID:23463598
Kim, S Y; Lunn, D D; Dyck, R J; Kirkpatrick, L J; Rosser, B W C
Differential expression of vesicular glutamate transporters 1 and 2 may identify distinct modes of glutamatergic transmission in the macaque visual system
Glutamate is the primary neurotransmitter utilized by the mammalian visual system for excitatory neurotransmission. The sequestration of glutamate into synaptic vesicles, and the subsequent transport of filled vesicles to the presynaptic terminal membrane, is regulated by a family of proteins known as vesicular glutamate transporters (VGLUTs). Two VGLUT proteins, VGLUT1 and VGLUT2, characterize distinct sets of glutamatergic projections between visual structures in rodents and prosimian primates, yet little is known about their distributions in the visual system of anthropoid primates. We have examined the mRNA and protein expression patterns of VGLUT1 and VGLUT2 in the visual system of macaque monkeys, an Old World anthropoid primate, in order to determine their relative distributions in the superior colliculus, lateral geniculate nucleus, pulvinar complex, V1 and V2. Distinct expression patterns for both VGLUT1 and VGLUT2 identified architectonic boundaries in all structures, as well as anatomical subdivisions of the superior colliculus, pulvinar complex, and V1. These results suggest that VGLUT1 and VGLUT2 clearly identify regions of glutamatergic input in visual structures, and may identify common architectonic features of visual areas and nuclei across the primate radiation. Additionally, we find that VGLUT1 and VGLUT2 characterize distinct subsets of glutamatergic projections in the macaque visual system; VGLUT2 predominates in driving or feedforward projections from lower order to higher order visual structures while VGLUT1 predominates in modulatory or feedback projections from higher order to lower order visual structures. The distribution of these two proteins suggests that VGLUT1 and VGLUT2 may identify class 1 and class 2 type glutamatergic projections within the primate visual system (Sherman and Guillery, 2006).
Balaram, Pooja; Hackett, Troy A.; Kaas, Jon H.
Clonal Complexes of Campylobacter jejuni Identified by Multilocus Sequence Typing Correlate with Strain Associations Identified by Multilocus Enzyme Electrophoresis
Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) with SmaI were used to subtype 55 isolates of Campylobacter jejuni from a diverse range of human and animal sources previously characterized by multilocus enzyme electrophoresis (MEE). MEE and MLST targeted 11 and 7 loci, respectively, and all loci were unique to each method. MEE, MLST, and PFGE identified 40, 37, and 48 discrete subtypes, respectively, with many of the subtypes occurring only once within the data set. Simpson's indices of diversity were calculated to be 0.979, 0.966, and 0.994 for MEE, MLST, and PFGE, respectively, demonstrating that MEE and MLST had similar discriminatory powers but that PFGE was more discriminatory. Allele diversity was higher in the MLST loci; individual single-locus diversities for the 11 MEE loci and the 7 MLST loci were 0.491 and 0.854, respectively. The clonal complexes recognized by MLST correlated with the strain associations previously recognized by MEE and contained some isolates indistinguishable by PFGE. Many clusters contained isolates from diverse geographical regions and from both humans and animals. These results demonstrate the usefulness of MLST for investigation of the global epidemiology of this important pathogen and illustrate its potential to identify indistinguishable strains or clones in geographically distinct regions.
Sails, Andrew D.; Swaminathan, Bala; Fields, Patricia I.
GATA-3 expression identifies a high-risk subset of PTCL, NOS with distinct molecular and clinical features.
The cell of origin and the tumor microenvironment's role remain elusive for the most common peripheral T-cell lymphomas (PTCLs). As macrophages promote the growth and survival of malignant T cells and are abundant constituents of the tumor microenvironment, their functional polarization was examined in T-cell lymphoproliferative disorders. Cytokines that are abundant within the tumor microenvironment, particularly interleukin (IL)-10, were observed to promote alternative macrophage polarization. Macrophage polarization was signal transducer and activator of transcription 3 dependent and was impaired by the Janus kinase inhibitor ruxolitinib. In conventional T cells, the production of T helper (Th)2-associated cytokines and IL-10, both of which promote alternative macrophage polarization, is regulated by the T-cell transcription factor GATA-binding protein 3 (GATA-3). Therefore, its role in the T-cell lymphomas was examined. GATA-3 expression was observed in 45% of PTCLs, not otherwise specified (PTCL, NOS) and was associated with distinct molecular features, including the production of Th2-associated cytokines. In addition, GATA-3 expression identified a subset of PTCL, NOS with distinct clinical features, including inferior progression-free and overall survival. Collectively, these data suggest that further understanding the cell of origin and lymphocyte ontogeny among the T-cell lymphomas may improve our understanding of the tumor microenvironment's pathogenic role in these aggressive lymphomas. PMID:24497534
Wang, Tianjiao; Feldman, Andrew L; Wada, David A; Lu, Ye; Polk, Avery; Briski, Robert; Ristow, Kay; Habermann, Thomas M; Thomas, Dafydd; Ziesmer, Steven C; Wellik, Linda E; Lanigan, Thomas M; Witzig, Thomas E; Pittelkow, Mark R; Bailey, Nathanael G; Hristov, Alexandra C; Lim, Megan S; Ansell, Stephen M; Wilcox, Ryan A
Functional genomics identifies five distinct molecular subtypes with clinical relevance and pathways for growth control in epithelial ovarian cancer
Epithelial ovarian cancer (EOC) is hallmarked by a high degree of heterogeneity. To address this heterogeneity, a classification scheme was developed based on gene expression patterns of 1538 tumours. Five, biologically distinct subgroups — Epi-A, Epi-B, Mes, Stem-A and Stem-B — exhibited significantly distinct clinicopathological characteristics, deregulated pathways and patient prognoses, and were validated using independent datasets. To identify subtype-specific molecular targets, ovarian cancer cell lines representing these molecular subtypes were screened against a genome-wide shRNA library. Focusing on the poor-prognosis Stem-A subtype, we found that two genes involved in tubulin processing, TUBGCP4 and NAT10, were essential for cell growth, an observation supported by a pathway analysis that also predicted involvement of microtubule-related processes. Furthermore, we observed that Stem-A cell lines were indeed more sensitive to inhibitors of tubulin polymerization, vincristine and vinorelbine, than the other subtypes. This subtyping offers new insights into the development of novel diagnostic and personalized treatment for EOC patients.
Tan, Tuan Zea; Miow, Qing Hao; Huang, Ruby Yun-Ju; Wong, Meng Kang; Ye, Jieru; Lau, Jieying Amelia; Wu, Meng Chu; Bin Abdul Hadi, Luqman Hakim; Soong, Richie; Choolani, Mahesh; Davidson, Ben; Nesland, Jahn M; Wang, Ling-Zhi; Matsumura, Noriomi; Mandai, Masaki; Konishi, Ikuo; Goh, Boon-Cher; Chang, Jeffrey T; Thiery, Jean Paul; Mori, Seiichi
Carbon isotopic compositions identify four petroleum types in Northern California
On the basis of carbon isotopic compositions of saturated and aromatic hydrocarbons in 16 oil and 6condensate samples from fields and seeps in northern California, four pertroleum types have been identified. The isotopically heaviest type is represented by oils from the Petrolia, Petaluma, and Pinole Point fields with saturated hydrocarbon (SH){delta}{sup 13}C values of -22.9{+-}0.6{per_thousand} and aromatic hydrocarbon (AH) {delta}{sup 13}C values of -22.1{+-}0.5{per_thousand}. Oil seeps in the Clear Lake area and oil samples from the Arbuckle and Bunker gas fields have SH{delta}{sup 13}C values of -26.4{+-}0.9{per_thousand} and AR{delta}{sup 13}C values of -25.1{+-}1.1{per_thousand} and represent a second petroleum type. Condensate samples from Dutch Slough, Knightsen, Lindsey Slough, and Rio Vista gas fields are considered a third type and have a whole condensate {delta}{sup 13} value of -26.2{+-}0.5{per_thousand} and AH{delta}{sup 13}C value of -27.4{+-}0.3{per_thousand}, and represent the fourth type. Volumetrically, the amount of oil and condensate recovered from these fields is small when compared to the fields in southern California. However, the petroleum potential of northern California may be underestimated because the petroleum geology is poorly understood and source rocks are poorly documented. The geographic distribution of these four petroleum types in northern California, predominately a dry-gas province, suggest that the petroleum geology is complex. For example, the Petrolia field is 180 miles northwest of the Petaluma and Pinole Point fields, and the Brentwood and Livermore oil samples are isotopically similar but come from contrasting geologic settings. Although {delta}{sup 13}C values are similar, the relationship of the condensate in the Rio Vista area to the oil samples in the Clear Lake area is unclear. Their isotopic similarity but physical dissimilarity could be due to migration or to source facies variations.
Magoon, L.B.; Stanley, R.G. [Geological Survey, Menlo Park, CA (United States); Lillis, P.G.; Warden, A. [Geological Survey, Denver, CO (United States); MacKevett, N.H. [Consultant, Bakersfield, CA (United States); Castano, J. [DGSI, Houston, TX (United States)
Animal Models of GWAS-Identified Type 2 Diabetes Genes
More than 65 loci, encoding up to 500 different genes, have been implicated by genome-wide association studies (GWAS) as conferring an increased risk of developing type 2 diabetes (T2D). Whilst mouse models have in the past been central to understanding the mechanisms through which more penetrant risk genes for T2D, for example, those responsible for neonatal or maturity-onset diabetes of the young, only a few of those identified by GWAS, notably TCF7L2 and ZnT8/SLC30A8, have to date been examined in mouse models. We discuss here the animal models available for the latter genes and provide perspectives for future, higher throughput approaches towards efficiently mining the information provided by human genetics.
da Silva Xavier, Gabriela; Bellomo, Elisa A.; McGinty, James A.; French, Paul M.; Rutter, Guy A.
Distinction between auditory electrophysiological responses in type 1 and type 2 diabetic animal models.
Neurological research has focused recently on determining the molecular mechanisms of common causes of damage to the peripheral and central nervous systems. One of the metabolic systemic diseases that can result in sensorineural hearing loss is diabetic mellitus (DM). In this study, we aimed to compare the auditory electrophysiological responses present in animal models of type 1 and type 2 DM using auditory brainstem response (ABR), auditory middle latency response (AMLR), and transient evoked otoacoustic emission (TEOAE) in animal model. We found that ABR threshold shifts and latency delays were similar in both types of DM. On the other hand, we found that type 2 diabetic mice exhibited more severe dysfunction to the central auditory pathway, as measured AMLRs and the cochlear hair cells, as measured TEOAEs. These results together suggest that hyperglycemia associated with type 1 or type 2 DM causes auditory nerve dysfunction, while hyperinsulinemia associated with type 2 DM causes dysfunction to both the central auditory pathways and cochlear hair cells. PMID:24607932
Hong, Bin Na; Kang, Tong Ho
'Saviour Siblings'? The Distinction between PGD with HLA Tissue Typing and Preimplantation HLA Tissue Typing
One of the more controversial uses of preimplantation genetic diagnosis (PGD) involves selecting embryos with a specific tissue\\u000a type so that the child to be born can act as a donor to an existing sibling who requires a haematopoietic stem cell transplant.\\u000a PGD with HLA tissue typing is used to select embryos that are free of a familial genetic disease
Crystal K. Liu
Microarray comparative genomic hybridisation analysis of intraocular uveal melanomas identifies distinctive imbalances associated with loss of chromosome 3
Defining regions of genomic imbalance can identify genes involved in tumour development. Conventional cytogenetics has identified several nonrandom copy number alterations (CNA) in uveal melanomas (UVM), which include monosomy 3, chromosome 6 abnormalities and gain of 8q. To gain further insight into the CNAs and define the regions involved more precisely we analysed 18 primary UVMs using 1?Mb BAC microarray comparative genomic hybridisation (CGH). Our analysis showed that the most common genomic imbalances were 8q gain (78%), 6p gain (67%) and monosomy 3 (56%). Two distinct CGH profiles could be delineated on the basis of the chromosome 3 status. The most common genetic changes in monosomy 3 tumours, in our study, were gain of 8q11.21–q24.3, 6p25.1–p21.2, 21q21.2–q21.3 and 21q22.13–q22.3 and loss of 1p36.33–p34.3, 1p31.1–p21.2, 6q16.2–q25.3 and 8p23.3–p11.23. In contrast, disomy 3 tumours showed recurrent gains of only 6p25.3–p22.3 and 8q23.2–q24.3. Our approach allowed definition of the smallest overlapping regions of imbalance, which may be important in the development of UVM.
Hughes, S; Damato, B E; Giddings, I; Hiscott, P S; Humphreys, J; Houlston, R S
The effect of temperature stress on coral- Symbiodinium associations containing distinct symbiont types
NASA Astrophysics Data System (ADS)
Several studies have demonstrated that the temperature tolerance of scleractinian reef-building corals is controlled, in part, by hosting physiologically distinct symbiotic algae. We investigated the thermal tolerance of coral-algal associations within seven common species of reef-building corals hosting distinct Symbiodinium sub-clades collected from Heron Island during experimentally induced bleaching conditions. During experimental heating, photosynthetic fitness was assessed by the dark-adapted yield of PSII ( F v/ F m), and excitation pressure across PSII ( Q m) of each coral-algal association using pulse amplitude modulation fluorometry. The onset of bleaching was determined by the measurement of Symbiodinium cell density. Using the ribosomal internal transcribed spacer 2 (ITS-2) region, we showed that Symbiodinium type-coral host associations were temporally and spatially conserved in a high proportion of the colonies sampled within each species. Generally, the species Acropora millepora, Platygyra daedalea, Acropora aspera and Acropora formosa contained Symbiodinium ITS-2 type C3, whereas the species Montipora digitata, Porites cylindrica and Porites lutea contained Symbiodinium type C15. Bleaching susceptibility showed some association with Symbiodinium type, but further research is required to confirm this. Corals hosting C3 Symbiodinium displayed higher reductions in F v/ F m during heating compared to their C15 counterparts, irrespective of host species. However, a corresponding reduction in Symbiodinium density was not observed. Nonetheless, A. aspera and A. formosa showed significant reductions in Symbiodinium density relative to controls. This correlated with large increases in Q m and decreases in F v/ F m in heated explants. Our results suggest a range of bleaching susceptibilities for the coral species investigated, with A. aspera and A. formosa showing the greatest susceptibility to bleaching and M. digitata showing the lowest bleaching susceptibility. The data provide strong evidence for distinct differences in temperature tolerance between C3 and C15 Symbiodinium types when in- hospite; however, future studies addressing the confounding effect of host species would help to confirm this.
Fisher, P. L.; Malme, M. K.; Dove, S.
Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics
Introduction Breast cancer is a profoundly heterogeneous disease with respect to biologic and clinical behavior. Gene-expression profiling has been used to dissect this complexity and to stratify tumors into intrinsic gene-expression subtypes, associated with distinct biology, patient outcome, and genomic alterations. Additionally, breast tumors occurring in individuals with germline BRCA1 or BRCA2 mutations typically fall into distinct subtypes. Methods We applied global DNA copy number and gene-expression profiling in 359 breast tumors. All tumors were classified according to intrinsic gene-expression subtypes and included cases from genetically predisposed women. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was used to identify significant DNA copy-number aberrations and genomic subgroups of breast cancer. Results We identified 31 genomic regions that were highly amplified in > 1% of the 359 breast tumors. Several amplicons were found to co-occur, the 8p12 and 11q13.3 regions being the most frequent combination besides amplicons on the same chromosomal arm. Unsupervised hierarchical clustering with 133 significant GISTIC regions revealed six genomic subtypes, termed 17q12, basal-complex, luminal-simple, luminal-complex, amplifier, and mixed subtypes. Four of them had striking similarity to intrinsic gene-expression subtypes and showed associations to conventional tumor biomarkers and clinical outcome. However, luminal A-classified tumors were distributed in two main genomic subtypes, luminal-simple and luminal-complex, the former group having a better prognosis, whereas the latter group included also luminal B and the majority of BRCA2-mutated tumors. The basal-complex subtype displayed extensive genomic homogeneity and harbored the majority of BRCA1-mutated tumors. The 17q12 subtype comprised mostly HER2-amplified and HER2-enriched subtype tumors and had the worst prognosis. The amplifier and mixed subtypes contained tumors from all gene-expression subtypes, the former being enriched for 8p12-amplified cases, whereas the mixed subtype included many tumors with predominantly DNA copy-number losses and poor prognosis. Conclusions Global DNA copy-number analysis integrated with gene-expression data can be used to dissect the complexity of breast cancer. This revealed six genomic subtypes with different clinical behavior and a striking concordance to the intrinsic subtypes. These genomic subtypes may prove useful for understanding the mechanisms of tumor development and for prognostic and treatment prediction purposes.
Natural diversity in the model legume Medicago truncatula allows identifying distinct genetic mechanisms conferring partial resistance to Verticillium wilt
Verticillium wilt is a major threat to alfalfa (Medicago sativa) and many other crops. The model legume Medicago truncatula was used as a host for studying resistance and susceptibility to Verticillium albo-atrum. In addition to presenting well-established genetic resources, this wild plant species enables to investigate biodiversity of the response to the pathogen and putative crosstalk between disease and symbiosis. Symptom scoring after root inoculation and modelling of disease curves allowed assessing susceptibility levels in recombinant lines of three crosses between susceptible and resistant lines, in a core collection of 32 lines, and in mutants affected in symbiosis with rhizobia. A GFP-expressing V. albo-atrum strain was used to study colonization of susceptible plants. Symptoms and colonization pattern in infected M. truncatula plants were typical of Verticillium wilt. Three distinct major quantitative trait loci were identified using a multicross, multisite design, suggesting that simple genetic mechanisms appear to control Verticillium wilt resistance in M. truncatula lines A17 and DZA45.5. The disease functional parameters varied largely in lines of the core collection. This biodiversity with regard to disease response encourages the development of association genetics and ecological approaches. Several mutants of the resistant line, impaired in different steps of rhizobial symbiosis, were affected in their response to V. albo-atrum, which suggests that mechanisms involved in the establishment of symbiosis or disease might have some common regulatory control points.
Gentzbittel, Laurent
Signaling profiling at the single-cell level identifies a distinct signaling signature in murine hematopoietic stem cells
Hematopoietic stem cell (HSC) function is tightly regulated by cytokine signaling. Although phospho-flow cytometry allows us to study signaling in defined populations of cells, there has been tremendous hurdle to carry out this study in rare HSCs due to unrecoverable critical HSC markers, low HSC number, and poor cell recovery rate. Here, we overcame these difficulties and developed a "HSC phospho-flow" method to analyze cytokine signaling in murine HSCs at the single-cell level and compare HSC signaling profile to that of multipotent progenitors (MPPs), a cell type immediately downstream of HSCs, and commonly used Lin? cKit+ cells (LK cells, enriched for myeloid progenitors). We chose to study signaling evoked from three representative cytokines, stem cell factor (SCF) and thrombopoietin (TPO) that are essential for HSC function, and granulocyte macrophage-colony stimulating factor (GM-CSF) that is dispensable for HSCs. HSCs display a distinct TPO and GM-CSF signaling signature from MPPs and LK cells, which highly correlates with receptor surface expression. In contrast, although majority of LK cells express lower levels of cKit than HSCs and MPPs, SCF-evoked ERK1/2 activation in LK cells shows a significantly increased magnitude for a prolonged period. These results suggest that specific cellular context plays a more important role than receptor surface expression in SCF signaling. Our study of HSC signaling at the homeostasis stage paves the way to investigate signaling changes in HSCs under conditions of stress, aging, and hematopoietic diseases.
Du, Juan; Wang, Jinyong; Kong, Guangyao; Jiang, Jing; Zhang, Jingfang; Liu, Yangang; Tong, Wei; Zhang, Jing
An infant with human parechovirus type 3 infection with a distinctive rash on the extremities.
Human parechovirus type 3 (HPeV3) is known to cause sepsis-like syndrome and meningoencephalitis in neonates and young infants. We herein report a neonatal case of sepsis-like syndrome due to HPeV3 infection, diagnosed using polymerase chain reaction (PCR), with a distinctive erythematous rash present mainly on the soles and palms that helped in the diagnosis of the disease. Combining the unique characteristics of rash and confirmation by PCR at the early stage of the disease led to the diagnosis of HPeV3, distinguishing it from sepsis and other critical disease conditions, and allowing for appropriate, rapid management. PMID:22938181
Shoji, Kensuke; Komuro, Hisako; Kobayashi, Yoshinori; Shike, Tatsuhiko; Funaki, Takanori; Katsuta, Tomohiro; Miyata, Ippei; Saitoh, Akihiko
Identifying metabolic enzymes with multiple types of association evidence
Background: Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes. Results: We present a novel method for identifying genes encoding for a specific metabolic function based on a local structure
Peter Kharchenko; Lifeng Chen; Yoav Freund; Dennis Vitkup; George M. Church
Identifying Aerosol Type/Mixture from Aerosol Absorption Properties Using AERONET
NASA Technical Reports Server (NTRS)
Aerosols are generated in the atmosphere through anthropogenic and natural mechanisms. These sources have signatures in the aerosol optical and microphysical properties that can be used to identify the aerosol type/mixture. Spectral aerosol absorption information (absorption Angstrom exponent; AAE) used in conjunction with the particle size parameterization (extinction Angstrom exponent; EAE) can only identify the dominant absorbing aerosol type in the sample volume (e.g., black carbon vs. iron oxides in dust). This AAE/EAE relationship can be expanded to also identify non-absorbing aerosol types/mixtures by applying an absorption weighting. This new relationship provides improved aerosol type distinction when the magnitude of absorption is not equal (e.g, black carbon vs. sulfates). The Aerosol Robotic Network (AERONET) data provide spectral aerosol optical depth and single scattering albedo - key parameters used to determine EAE and AAE. The proposed aerosol type/mixture relationship is demonstrated using the long-term data archive acquired at AERONET sites within various source regions. The preliminary analysis has found that dust, sulfate, organic carbon, and black carbon aerosol types/mixtures can be determined from this AAE/EAE relationship when applying the absorption weighting for each available wavelength (Le., 440, 675, 870nm). Large, non-spherical dust particles absorb in the shorter wavelengths and the application of 440nm wavelength absorption weighting produced the best particle type definition. Sulfate particles scatter light efficiently and organic carbon particles are small near the source and aggregate over time to form larger less absorbing particles. Both sulfates and organic carbon showed generally better definition using the 870nm wavelength absorption weighting. Black carbon generation results from varying combustion rates from a number of sources including industrial processes and biomass burning. Cases with primarily black carbon showed improved definition in the 870nm wavelength absorption weighting due to the increased absorption in the near-infrared wavelengths, while the 440nm wavelength provided better definition when black carbon mixed with dust. Utilization of this particle type scheme provides necessary information for remote sensing applications, which needs a priori knowledge of aerosol type to model the retrieved properties especially over semi-bright surfaces. In fact, this analysis reveals that the aerosol types occurred in mixtures with varying magnitudes of absorption and requires the use of more than one assumed aerosol mixture model. Furthermore, this technique will provide the aerosol transport model community a data set for validating aerosol type.
Giles, D. M.; Holben, B. N.; Eck, T. F.; Sinyuk, A.; Dickerson, R. R.; Thompson, A. M.; Slutsker, I.; Li, Z.; Tripathi, S. N.; Singh, R. P.; Zibordi, G.
Myosin IIB isoform plays an essential role in the formation of two distinct types of macropinosomes.
The function and mechanism of macropinocytosis in cells outside of the immune system remain poorly understood. We used a neuroblastoma cell line, Neuro-2a, to study macropinocytosis in neuronal cells. We found that phorbol 12-myristate 13-acetate (PMA) and insulin-like growth factor 1 (IGF-1) induced two distinct types of macropinocytosis in the Neuro-2a cells. IGF-1-induced macropinocytosis occurs mostly around the cell bodies and requires phosphoinositide 3-kinase (PI3K), while PMA-induced macropinocytosis occurs predominantly in the neurites and is independent of PI3K activity. Both types of macropinocytosis were inhibited by a specific inhibitor of nonmuscle myosin II, blebbistatin. siRNA knockdown of nonmuscle myosin II isoforms, -IIA and -IIB, resulted in opposite effects on macropinocytosis induced by PMA or IGF. Myosin IIA knockdown significantly increased, whereas myosin IIB knockdown significantly decreased, macropinocytosis with correlating changes in membrane ruffle formation. PMID:19743471
Jiang, Jun; Kolpak, Adrianne L; Bao, Zheng-Zheng
Foraging Blainville's beaked whales (Mesoplodon densirostris) produce distinct click types matched to different phases of echolocation.
Blainville's beaked whales (Mesoplodon densirostris Blainville) echolocate for prey during deep foraging dives. Here we use acoustic tags to demonstrate that these whales, in contrast to other toothed whales studied, produce two distinct types of click sounds during different phases in biosonar-based foraging. Search clicks are emitted during foraging dives with inter-click intervals typically between 0.2 and 0.4 s. They have the distinctive form of an FM upsweep (modulation rate of about 110 kHz ms(-1)) with a -10 dB bandwidth from 26 to 51 kHz and a pulse length of 270 micros, somewhat similar to chirp signals in bats and Cuvier's beaked whales (Ziphius cavirostris Cuvier), but quite different from clicks of other toothed whales studied. In comparison, the buzz clicks, produced in short bursts during the final stage of prey capture, are short (105 micros) transients with no FM structure and a -10 dB bandwidth from 25 to 80 kHz or higher. Buzz clicks have properties similar to clicks reported from large delphinids and hold the potential for higher temporal resolution than the FM clicks. It is suggested that the two click types are adapted to the separate problems of target detection and classification versus capture of low target strength prey in a cluttered acoustic environment. PMID:17142692
Johnson, M; Madsen, P T; Zimmer, W M X; de Soto, N Aguilar; Tyack, P L
Distinction between Clock and Time, and a Suggested Experiment with Different Types of Clocks in GPS
NASA Astrophysics Data System (ADS)
The clock is an instrument for measuring the time, instrument that may not run perfectly (accurately) under certain conditions (like, say, in strong electromagnetic field, in strong gravitational field, in extremely high or low temperature, pressure, etc.), but this does not mean that time itself runs slower or faster as Einstein's Theory of Relativity asserts. We are referring to an absolute time, i.e. time measured not with respect to ether or non-ether, but with respect to an absolute mathematical reference frame. Several types of clocks could run at a more slowly rate in a moving frame of reference than other types of clocks; it depends on the construction material and functioning principle of each type of clock. Relativists say that ``gravity slows time''. This is incorrect, since actually gravity slows today's types of clocks. And one type of clock is slowed more or less than another type of clock. Not only gravity but other (electric, magnetic, etc.) fields or various medium composition elements or structures may slow or accelerate clocks that are in that medium. The clocks used today in the satellites for the GPS necessitate a correction with respect to the Earth clocks. But in the future, when new types of clocks will be built based on different construction material and functioning principle, the correction of the GPS clocks would be different. In order to make the distinction between ``clock'' and ``time'', we suggest a Experiment # 1 with different types of clocks for the GPS clocks, in order to prove that the resulted dilation and contraction factors are different from those obtained with today's cesium atomic clock.
Smarandache, Florentin
Distinct Pseudomonas type-III effectors use a cleavable transit peptide to target chloroplasts.
The pathogen Pseudomonas syringae requires a type-III protein secretion system and the effector proteins it injects into plant cells for pathogenesis. The primary role for P. syringae type-III effectors is the suppression of plant immunity. The P. syringae pv. tomato DC3000 HopK1 type-III effector was known to suppress the hypersensitive response (HR), a programmed cell death response associated with effector-triggered immunity. Here we show that DC3000 hopK1 mutants are reduced in their ability to grow in Arabidopsis, and produce reduced disease symptoms. Arabidopsis transgenically expressing HopK1 are reduced in PAMP-triggered immune responses compared with wild-type plants. An N-terminal region of HopK1 shares similarity with the corresponding region in the well-studied type-III effector AvrRps4; however, their C-terminal regions are dissimilar, indicating that they have different effector activities. HopK1 is processed in planta at the same processing site found in AvrRps4. The processed forms of HopK1 and AvrRps4 are chloroplast localized, indicating that the shared N-terminal regions of these type-III effectors represent a chloroplast transit peptide. The HopK1 contribution to virulence and the ability of HopK1 and AvrRps4 to suppress immunity required their respective transit peptides, but the AvrRps4-induced HR did not. Our results suggest that a primary virulence target of these type-III effectors resides in chloroplasts, and that the recognition of AvrRps4 by the plant immune system occurs elsewhere. Moreover, our results reveal that distinct type-III effectors use a cleavable transit peptide to localize to chloroplasts, and that targets within this organelle are important for immunity. PMID:24299018
Li, Guangyong; Froehlich, John E; Elowsky, Christian; Msanne, Joseph; Ostosh, Andrew C; Zhang, Chi; Awada, Tala; Alfano, James R
The co-expression pattern of odorant binding proteins and olfactory receptors identify distinct trichoid sensilla on the antenna of the malaria mosquito Anopheles gambiae.
The initial steps of odorant recognition in the insect olfactory system involve odorant binding proteins (OBPs) and odorant receptors (ORs). While large families of OBPs have been identified in the malaria vector A. gambiae, little is known about their expression pattern in the numerous sensory hairs of the female antenna. We applied whole mount fluorescence in Situ hybridization (WM-FISH) and fluorescence immunohistochemistry (WM-FIHC) to investigate the sensilla co-expression of eight A. gambiae OBPs (AgOBPs), most notably AgOBP1 and AgOBP4, which all have abundant transcripts in female antenna. WM-FISH analysis of female antennae using AgOBP-specific probes revealed marked differences in the number of cells expressing each various AgOBPs. Testing combinations of AgOBP probes in two-color WM-FISH resulted in distinct cellular labeling patterns, indicating a combinatorial expression of AgOBPs and revealing distinct AgOBP requirements for various functional sensilla types. WM-FIHC with antisera to AgOBP1 and AgOBP4 confirmed expression of the respective proteins by support cells and demonstrated a location of OBPs within sensilla trichodea. Based on the finding that AgOBP1 and AgOBP4 as well as the receptor type AgOR2 are involved in the recognition of indole, experiments were performed to explore if the AgOBP-types and AgOR2 are co-expressed in distinct olfactory sensilla. Applying two-color WM-FISH with AgOBP-specific probes and probes specific for AgOR2 revealed a close association of support cells bearing transcripts for AgOBP1 and AgOBP4 and neurons with a transcript for the receptor AgOR2. Moreover, combined WM-FISH/-FIHC approaches using an AgOR2-specific riboprobe and AgOBP-specific antisera revealed the expression of the "ligand-matched" AgOBP1, AgOBP4 and AgOR2 to single trichoid hairs. This result substantiates the notion that a specific response to indole is mediated by an interplay of the proteins. PMID:23861970
Schultze, Anna; Pregitzer, Pablo; Walter, Marika F; Woods, Daniel F; Marinotti, Osvaldo; Breer, Heinz; Krieger, Jürgen
The Co-Expression Pattern of Odorant Binding Proteins and Olfactory Receptors Identify Distinct Trichoid Sensilla on the Antenna of the Malaria Mosquito Anopheles gambiae
The initial steps of odorant recognition in the insect olfactory system involve odorant binding proteins (OBPs) and odorant receptors (ORs). While large families of OBPs have been identified in the malaria vector A. gambiae, little is known about their expression pattern in the numerous sensory hairs of the female antenna. We applied whole mount fluorescence in Situ hybridization (WM-FISH) and fluorescence immunohistochemistry (WM-FIHC) to investigate the sensilla co-expression of eight A. gambiae OBPs (AgOBPs), most notably AgOBP1 and AgOBP4, which all have abundant transcripts in female antenna. WM-FISH analysis of female antennae using AgOBP-specific probes revealed marked differences in the number of cells expressing each various AgOBPs. Testing combinations of AgOBP probes in two-color WM-FISH resulted in distinct cellular labeling patterns, indicating a combinatorial expression of AgOBPs and revealing distinct AgOBP requirements for various functional sensilla types. WM-FIHC with antisera to AgOBP1 and AgOBP4 confirmed expression of the respective proteins by support cells and demonstrated a location of OBPs within sensilla trichodea. Based on the finding that AgOBP1 and AgOBP4 as well as the receptor type AgOR2 are involved in the recognition of indole, experiments were performed to explore if the AgOBP-types and AgOR2 are co-expressed in distinct olfactory sensilla. Applying two-color WM-FISH with AgOBP-specific probes and probes specific for AgOR2 revealed a close association of support cells bearing transcripts for AgOBP1 and AgOBP4 and neurons with a transcript for the receptor AgOR2. Moreover, combined WM-FISH/-FIHC approaches using an AgOR2-specific riboprobe and AgOBP-specific antisera revealed the expression of the "ligand-matched" AgOBP1, AgOBP4 and AgOR2 to single trichoid hairs. This result substantiates the notion that a specific response to indole is mediated by an interplay of the proteins.
Schultze, Anna; Pregitzer, Pablo; Walter, Marika F.; Woods, Daniel F.; Marinotti, Osvaldo; Breer, Heinz; Krieger, Jurgen
IS3 profiling identifies the enterohaemorrhagic Escherichia coli O-island 62 in a distinct enteroaggregative E. coli lineage
Background Enteroaggregative Escherichia coli (EAEC) are important diarrhoeal pathogens that are defined by a HEp-2 adherence assay performed in specialist laboratories. Multilocus sequence typing (MLST) has revealed that aggregative adherence is convergent, providing an explanation for why not all EAEC hybridize with the plasmid-derived probe for this category, designated CVD432. Some EAEC lineages are globally disseminated or more closely associated with disease. Results To identify genetic loci conserved within significant EAEC lineages, but absent from non-EAEC, IS3-based PCR profiles were generated for 22 well-characterised EAEC strains. Six bands that were conserved among, or missing from, specific EAEC lineages were cloned and sequenced. One band corresponded to the aggR gene, a plasmid-encoded regulator that has been used as a diagnostic target but predominantly detects EAEC bearing the plasmid already marked by CVD432. The sequence from a second band was homologous to an open-reading frame within the cryptic enterohaemorrhagic E. coli (EHEC) O157 genomic island, designated O-island 62. Screening of an additional 46 EAEC strains revealed that the EHEC O-island 62 was only present in those EAEC strains belonging to the ECOR phylogenetic group D, largely comprised of sequence type (ST) complexes 31, 38 and 394. Conclusions The EAEC 042 gene orf1600, which lies within the EAEC equivalent of O-island 62 island, can be used as a marker for EAEC strains belonging to the ECOR phylogenetic group D. The discovery of EHEC O-island 62 in EAEC validates the genetic profiling approach for identifying conserved loci among phylogenetically related strains.
Expression of cadherins and catenins correlates with distinct histologic types of ovarian carcinomas.
Alterations in the cadherin-catenin expression and activation of the Wnt signaling have been related to the pathology of ovarian carcinomas. Here, we evaluated the immunoreactivity of cadherins (E-, P-, and N-cadherin and cadherin-11) and catenins (alpha-, beta-, and gamma-catenin and p120) in 86 ovarian tumors. We found significant differences in the expression of all cadherins and catenins among the distinct histologic tumor types. Clear cell tumors were rarely N-cadherin- and P-cadherin-positive and showed reduced membranous expression in all the catenins; Serous carcinomas were frequently N-cadherin- and P-cadherin-positive, mucinous tumors strongly expressed E-cadherin and the catenins in the membrane, and endometrioid tumors characteristically expressed nucleocytoplasmic beta-catenin in most of the cases. We next studied whether allelic losses in the chromosomal regions containing various cadherin genes (16q22) or APC gene (5q21) occurred in ovarian tumors and observed a high frequency of loss of heterozygosity in 16q22 (78%) and 5q21 (33%) regions, but there were no differences among the tumor types analyzed. Finally, we also assessed the molecular alterations responsible for beta-catenin nuclear accumulation in endometrioid tumors by screening for mutations in AXIN1, AXIN2, APC, and KRAS genes. Mutations in KRAS were observed in 2 of 19 tumors, but no mutations were detected in AXIN1, AXIN2, or APC genes. Only beta-catenin gene mutations were associated with nuclear beta-catenin staining in these tumors. In conclusion, different cadherin-catenin expression patterns are associated with distinct histologic types. Oncogenic Wnt signaling plays a role only in endometrioid tumors, where beta-catenin mutations seem to be the main cause of its aberrant expression. PMID:16867867
Sarrió, David; Moreno-Bueno, Gema; Sánchez-Estévez, Carolina; Bańón-Rodríguez, Inmaculada; Hernández-Cortés, Ginés; Hardisson, David; Palacios, José
Method for identifying type I diabetes mellitus in humans
A method and system for classifying subject populations utilizing predictive and diagnostic biomarkers for type I diabetes mellitus. The method including determining the levels of a variety of markers within the serum or plasma of a target organism and correlating this level to general populations as a screen for predisposition or progressive monitoring of disease presence or predisposition.
Metz, Thomas O [Kennewick, WA; Qian, Weijun [Richland, WA; Jacobs, Jon M [Pasco, WA
Array CGH identifies distinct DNA copy number profiles of oncogenes and tumor suppressor genes in chromosomal- and microsatellite-unstable sporadic colorectal carcinomas.
DNA copy number changes represent molecular fingerprints of solid tumors and are as such relevant for better understanding of tumor development and progression. In this study, we applied genome-wide array comparative genomic hybridization (aCGH) to identify gene-specific DNA copy number changes in chromosomal (CIN)- and microsatellite (MIN)-unstable sporadic colorectal cancers (sCRC). Genomic DNA was extracted from microdissected, matching normal colorectal epithelium and invasive tumor cells of formalin-fixed and paraffin-embedded tissues of 22 cases with colorectal cancer (CIN = 11, MIN = 11). DNA copy number changes were determined by aCGH for 287 target sequences in tumor cell DNAs, using pooled normal DNAs as reference. aCGH data of tumor cell DNAs was confirmed by fluorescence in situ hybridization (FISH) for three genes on serial tissues as those used for aCGH. aCGH revealed DNA copy number changes previously described by metaphase CGH (gains 7, 8q, 13q, and 20q; losses 8p, 15q, 18q, and 17p). However, chromosomal regions 20q, 13q, 7, and 17p were preferentially altered in CIN-type tumors and included DNA amplifications of eight genes on chromosome 20q (TOP1, AIB1, MYBL2, CAS, PTPN1, STK15, ZNF217, and CYP24), two genes on chromosome 13q (BRCA2 and D13S25), and three genes on chromosome 7 (IL6, CYLN2, and MET) as well as DNA deletions of two genes on chromosome 17p (HIC1 and LLGL1). Finally, additional CIN-tumor-associated DNA amplifications were identified for EXT1 (8q24.11) and MYC (8q24.12) as well as DNA deletions for MAP2K5 (15q23) and LAMA3 (18q11.2). In contrast, distinct MIN-tumor-associated DNA amplifications were detected for E2F5 (8p22-q21.3), GARP (11q13.5-q14), ATM (11q22.3), KAL (Xp22.3), and XIST (Xq13.2) as well as DNA deletions for RAF1 (3p25), DCC (18q21.3), and KEN (21q tel). aCGH revealed distinct DNA copy number changes of oncogenes and tumor suppressor genes in CIN- and MIN-type sporadic colorectal carcinomas. The identified candidate genes are likely to have distinct functional roles in the carcinogenesis and progression of CIN- and MIN-type sporadic CRCs and may be involved in the differential response of CIN- and MIN-type tumor cells to (adjuvant) therapy, such as 5-fluorouracil. PMID:17143621
Lassmann, Silke; Weis, Roland; Makowiec, Frank; Roth, Jasmine; Danciu, Mihai; Hopt, Ulrich; Werner, Martin
Distinct proliferative and transcriptional effects of the D-type cyclins in vivo
The D-type cyclins (D1, D2 and D3) are components of the cell cycle machinery and govern progression through G1 phase in response to extracellular signals. Although these proteins are highly homologous and conserved in evolution, they contain distinct structural motifs and are differentially regulated in various cell types. Cyclin D1 appears to play a role in many different types of cancer, whereas cyclins D2 and D3 are less frequently associated with malignancy. In this study, we transiently expressed cyclin D1, D2 or D3 in hepatocytes and analyzed transcriptional networks regulated by each. All three D-type cyclins promoted robust hepatocyte proliferation and marked liver growth, although cyclin D3 stimulated less DNA synthesis than D1 or D2. Accordingly, the three D-type cyclins similarly activated genes associated with cell division. Cyclin D1 regulated transcriptional pathways involved in the metabolism of carbohydrates, lipids, amino acids, and other substrates, whereas cyclin D2 did not regulate these pathways despite having an equivalent effect on proliferation. Comparison of transcriptional profiles following 70% partial hepatectomy and cyclin D1 transduction revealed a highly significant overlap, suggesting that cyclin D1 may regulate diverse cellular processes in the regenerating liver. In summary, these studies provide the first comparative analysis of the transcriptional networks regulated by the D-type cyclins and provide insight into novel functions of these key cell cycle proteins. Further study of the unique targets of cyclin D1 should provide further insight into its prominent role in proliferation, growth and cancer.
Mullany, Lisa K.; White, Peter; Hanse, Eric A.; Nelsen, Christopher J.; Goggin, Melissa M.; Mullany, Joseph E.; Anttila, Chelsea K.; Greenbaum, Linda E.; Kaestner, Klaus H.; Albrecht, Jeffrey H.
Differential Progression of Structural and Functional Alterations in Distinct Retinal Ganglion Cell Types in a Mouse Model of Glaucoma
Intraocular pressure (IOP) elevation is a principal risk factor for glaucoma. Using a microbead injection technique to chronically raise IOP for 15 or 30 d in mice, we identified the early changes in visual response properties of different types of retinal ganglion cells (RGCs) and correlated these changes with neuronal morphology before cell death. Microbead-injected eyes showed reduced optokinetic tracking as well as cell death. In such eyes, multielectrode array recordings revealed that four RGC types show diverse alterations in their light responses upon IOP elevation. OFF-transient RGCs exhibited a more rapid decline in both structural and functional organizations compared with other RGCs. In contrast, although the light-evoked responses of OFF-sustained RGCs were perturbed, the dendritic arbor of this cell type remained intact. ON-transient and ON-sustained RGCs had normal functional receptive field sizes but their spontaneous and light-evoked firing rates were reduced. ON- and OFF-sustained RGCs lost excitatory synapses across an otherwise structurally normal dendritic arbor. Together, our observations indicate that there are changes in spontaneous activity and light-evoked responses in RGCs before detectable dendritic loss. However, when dendrites retract, we found corresponding changes in receptive field center size. Importantly, the effects of IOP elevation are not uniformly manifested in the structure and function of diverse RGC populations, nor are distinct RGC types perturbed within the same time-frame by such a challenge.
Della Santina, Luca; Inman, Denise M.; Lupien, Caroline B.; Horner, Philip J.
Do female general practitioners have a distinctive type of medical practice?
Using data collected in 1983-84 for a representative sample of 736 general practitioners practising in Quebec, we compared the practice characteristics of the 296 female physicians and the 320 male physicians who agreed to participate. The female doctors were more likely than the male doctors to favour salaried practice in local community health centres, to practise in an urban setting and to have an office-based practice. The female physicians had a less diversified type of practice, being less involved in hospital care, emergency care, home care and administrative work. Sex differences were more marked for physicians in fee-for-service practice than for salaried physicians. Given the increasing numbers of women in the medical profession, these findings are of special interest since they indicate distinctive differences in medical practice between women and men.
Maheux, B; Dufort, F; Lambert, J; Berthiaume, M
The Cancer Genome Atlas Identifies Distinct Subtypes of Deadly Brain Cancer That May Lead to New Treatment Strategies
The most common form of malignant brain cancer in adults, glioblastoma multiforme, is not a single disease but appears to be four distinct molecular subtypes, according to a study by the Cancer Genome Atlas (TCGA) Research Network. The researchers of this study also found that response to aggressive chemotherapy and radiation differed by subtype.
The Cancer Genome Atlas Identifies Distinct Subtypes of Deadly Brain Cancer That May Lead to New Treatment Strategies
The most common form of malignant brain cancer in adults, glioblastoma multiforme (GBM), is not a single disease but appears to be four distinct molecular subtypes, according to a study by The Cancer Genome Atlas (TCGA) Research Network. The researchers of this study also found that response to aggressive chemotherapy and radiation differed by subtype.
Clericuzio type poikiloderma with neutropenia is distinct from Rothmund-Thomson syndrome.
Two siblings from a consanguineous family presented with a poikiloderma of limbs and face, plantar keratoderma, and toenail pachyonychia. Neutropenia and neutrophil dysfunction with impairment of the respiratory burst and bacterial killing resulted in frequent respiratory tract infections. A bronchocentric granulomatous pneumonia was a fatal complication. The clinical presentation is consistent with Clericuzio type poikiloderma with neutropenia. Literature review identified several additional probable patients. Genetic linkage analysis excluded the locus of the RECQL4 gene, mutations in which have been described in some patients with the Rothmund-Thomson poikiloderma syndrome. This report confirms the clinical and genetic identity of the Clericuzio type of poikiloderma with neutropenia syndrome. PMID:15558713
Van Hove, Johan L K; Jaeken, Jaak; Proesmans, Marijke; Boeck, Kris De; Minner, Kristin; Matthijs, Gert; Verbeken, Eric; Demunter, Anouk; Boogaerts, Marc
Gene Expression Profiling Reveals Distinct Cocaine-Responsive Genes in Human Fetal CNS Cell Types
Objectives Prenatal exposure to cocaine causes cytoarchitectural alterations in the developing neocortex. Previously, we reported that cocaine inhibits neural progenitor cell proliferation through oxidative endoplasmic reticulum stress and consequent down-regulation of cyclin A, whereas cyclin A expression was increased in astrocytes. In the present study, cell type-specific responses to cocaine were further explored. Methods Gene expression profiles were examined in five types of cells obtained from the human fetal cerebral cortex at 20 weeks gestation. Cells were treated with 100 µM cocaine in vitro for 24 hr, followed by gene expression analysis using a human neural/stem cell/drug abuse-focused cDNA array, with verification by quantitative real-time RT-PCR. Results Cocaine influenced transcription of distinct categories of genes in a cell type-specific manner. Cocaine down-regulated cytoskeleton-related genes including ezrin, ?2 actin, ?3d tubulin and ?8 tubulin in neural and/or A2B5+ progenitor cells. In contrast, cocaine modulated immune and cell death-related genes in microglia and astrocytes. In microglia, cocaine up-regulated the immunoregulatory and pro-apoptotic genes IL-1? and BAX. In astrocytes, cocaine down-regulated the immune response gene glucocorticoid receptor and up-regulated the anti-apoptotic genes 14-3-3 ? and HVEM. Therefore, cell types comprising the developing neocortex show differential responses to cocaine. Conclusions These data suggest that cocaine causes cytoskeletal abnormalities leading to disturbances in neural differentiation and migration in progenitor cells, while altering immune and apoptotic responses in glia. Understanding the mechanisms of cocaine's effects on human CNS cells may help in the development of therapeutic strategies to prevent or ameliorate cocaine-induced impairments in fetal brain development.
Lee, Chun-Ting; Lehrmann, Elin; Hayashi, Teruo; Amable, Rose; Tsai, Shang-Yi; Chen, Jia; Sanchez, Joseph F.; Shen, James; Becker, Kevin G.; Freed, William J.
Comparison of odor-active compounds from six distinctly different rice flavor types.
Using a dynamic headspace system with Tenax trap, GC-MS, GC-olfactometry (GC-O), and multivariate analysis, the aroma chemistry of six distinctly different rice flavor types (basmati, jasmine, two Korean japonica cultivars, black rice, and a nonaromatic rice) was analyzed. A total of 36 odorants from cooked samples were characterized by trained assessors. Twenty-five odorants had an intermediate or greater intensity (odor intensity >or= 3) and were considered to be major odor-active compounds. Their odor thresholds in air were determined using GC-O. 2-Acetyl-1-pyrroline (2-AP) had the lowest odor threshold (0.02 ng/L) followed by 11 aldehydes (ranging from 0.09 to 3.1 ng/L), guaiacol (1.5 ng/L), and 1-octen-3-ol (2.7 ng/L). On the basis of odor thresholds and odor activity values (OAVs), the importance of each major odor-active compound was assessed. OAVs for 2-AP, hexanal, ( E)-2-nonenal, octanal, heptanal, and nonanal comprised >97% of the relative proportion of OAVs from each rice flavor type, even though the relative proportion varied among samples. Thirteen odor-active compounds [2-AP, hexanal, ( E)-2-nonenal, octanal, heptanal, nonanal, 1-octen-3-ol, ( E)-2-octenal, ( E, E)-2,4-nonadienal, 2-heptanone, ( E, E)-2,4-decadienal, decanal, and guaiacol] among the six flavor types were the primary compounds explaining the differences in aroma. Multivariate analysis demonstrated that the individual rice flavor types could be separated and characterized using these compounds, which may be of potential use in rice-breeding programs focusing on flavor. PMID:18363355
Yang, Dong Sik; Shewfelt, Robert L; Lee, Kyu-Seong; Kays, Stanley J
Annular protofibrils are a structurally and functionally distinct type of amyloid oligomer.
Amyloid oligomers are believed to play causal roles in several types of amyloid-related neurodegenerative diseases. Several different types of amyloid oligomers have been reported that differ in morphology, size, or toxicity, raising the question of the pathological significance and structural relationships between different amyloid oligomers. Annular protofibrils (APFs) have been described in oligomer preparations of many different amyloidogenic proteins and peptides as ring-shaped or pore-like structures. They are interesting because their pore-like morphology is consistent with numerous reports of membrane-permeabilizing activity of amyloid oligomers. Here we report the preparation of relatively homogeneous preparations of APFs and an antiserum selective for APFs (alphaAPF) compared with prefibrillar oligomers (PFOs) and fibrils. PFOs appear to be precursors for APF formation, which form in high yield after exposure to a hydrophobic-hydrophilic interface. Surprisingly, preformed APFs do not permeabilize lipid bilayers, unlike the precursor PFOs. APFs display a conformation-dependent, generic epitope that is distinct from that of PFOs and amyloid fibrils. Incubation of PFOs with phospholipids vesicles results in a loss of PFO immunoreactivity with a corresponding increase in alphaAPF immunoreactivity, suggesting that lipid vesicles catalyze the conversion of PFOs into APFs. The annular anti-protofibril antibody also recognizes heptameric alpha-hemolysin pores, but not monomers, suggesting that the antibody recognizes an epitope that is specific for a beta barrel structural motif. PMID:19098006
Kayed, Rakez; Pensalfini, Anna; Margol, Larry; Sokolov, Yuri; Sarsoza, Floyd; Head, Elizabeth; Hall, James; Glabe, Charles
Quantitative Morphometry of Electrophysiologically Identified CA3b Interneurons Reveals Robust Local Geometry and Distinct Cell Classes
The morphological and electrophysiological diversity of inhibitory cells in hippocampal area CA3 may underlie specific computational roles and is not yet fully elucidated. In particular, interneurons with somata in strata radiatum (R) and lacunosum-moleculare (L-M) receive converging stimulation from the dentate gyrus and entorhinal cortex as well as within CA3. Although these cells express different forms of synaptic plasticity, their axonal trees and connectivity are still largely unknown. We investigated the branching and spatial patterns, plus the membrane and synaptic properties, of rat CA3b R and L-M interneurons digitally reconstructed after intracellular labeling. We found considerable variability within but no difference between the two layers, and no correlation between morphological and biophysical properties. Nevertheless, two cell types were identified based on the number of dendritic bifurcations, with significantly different anatomical and electrophysiological features. Axons generally branched an order of magnitude more than dendrites. However, interneurons on both sides of the R/L-M boundary revealed surprisingly modular axo-dendritic arborizations with consistently uniform local branch geometry. Both axons and dendrites followed a lamellar organization, and axons displayed a spatial preference towards the fissure. Moreover, only a small fraction of the axonal arbor extended to the outer portion of the invaded volume, and tended to return towards the proximal region. In contrast, dendritic trees demonstrated more limited but isotropic volume occupancy. These results suggest a role of predominantly local feedforward and lateral inhibitory control for both R and L-M interneurons. Such role may be essential to balance the extensive recurrent excitation of area CA3 underlying hippocampal autoassociative memory function.
Ascoli, Giorgio A.; Brown, Kerry M.; Calixto, Eduardo; Card, J. Patrick; Galvan, E. J.; Perez-Rosello, T.; Barrionuevo, German
Digital morphometry of rat cerebellar climbing fibers reveals distinct branch and bouton types
Cerebellar climbing fibers provide powerful excitatory input to Purkinje cells, which represent the sole output of the cerebellar cortex. Recent discoveries suggest that climbing fibers have information-rich signaling properties important for cerebellar function, beyond eliciting the well-known all-or-none Purkinje cell complex spike. Climbing fiber morphology has not been quantitatively analyzed at the same level of detail as their biophysical properties. Because morphology can greatly influence function, including the capacity for information processing, it is important to understand climbing fiber branching structure in detail, as well as its variability across and within arbors. We have digitally reconstructed 68 rat climbing fibers labeled using biotinylated dextran amine (BDA) injected into the inferior olive and comprehensively quantified their morphology. Climbing fiber structure was considerably diverse even within the same anatomical regions. Distinctly identifiable primary, tendril, and distal branches could be operationally differentiated by the relative size of the subtrees at their initial bifurcations. Additionally, primary branches were more directed toward the cortical surface and had fewer and less pronounced synaptic boutons, suggesting they prioritize efficient and reliable signal propagation. Tendril and distal branches were spatially segregated and bouton dense, indicating specialization in signal transmission. Furthermore, climbing fibers systematically targeted molecular layer interneuron cell bodies, especially at terminal boutons, potentially instantiating feed-forward inhibition on Purkinje cells. This study offers the most detailed and comprehensive characterization of climbing fiber morphology to date. The reconstruction files and metadata are publicly distributed at NeuroMorpho.Org.
Brown, Kerry M.; Sugihara, Izumi; Shinoda, Yoshikazu; Ascoli, Giorgio A.
BH3 Profiling Identifies Three Distinct Classes ofApoptoticBlockstoPredictResponsetoABT-737 and Conventional Chemotherapeutic Agents
SUMMARY Cancer cells exhibit many abnormal phenotypes that induce apoptotic signaling via the intrinsic, or mitochondrial, pathway. That cancer cells nonetheless survive implies that they select for blocks in apoptosis. Identifying cancer-specific apoptotic blocks is necessary to rationally target them. Using a panel of 18 lymphoma cell lines, we show that a strategy we have developed, BH3 profiling, can identify
Jing Deng; Nicole Carlson; Kunihiko Takeyama; Paola Dal Cin; Margaret Shipp; Anthony Letai
Invasive micropapillary carcinoma: A distinct type of adenocarcinomas in the gastrointestinal tract
Invasive micropapillary carcinoma (IMPC) is a rare histological type of tumor, first described in invasive ductal breast cancer, than in malignancies in other organs such as lungs, urinary bladder, ovaries or salivary glands. Recent literature data shows that this histological lesion has also been found in cancers of the gastrointestinal system. The micropapillary components are clusters of neoplastic cells that closely adhere to each other and are located in distinct empty spaces. Moreover, clusters of neoplastic cells do not have a fibrous-vascular core. The IMPC cells show reverse polarity resulting in typical ''inside-out'' structures that determines secretary properties, disturbs adhesion and conditions grade of malignancy in gastrointestinal (GI) tract. Invasive micropapillary carcinoma in this location is associated with metastases to local lymph nodes and lymphovascular invasion. IMPC can be a prognostic factor for patients with cancers of the stomach, pancreas and with colorectal cancer since it is related with disease-free and overall survival. The purpose of this review is to present the characterization of invasive micropapillary carcinoma in colon, rectum, stomach and others site of GI tract, and to determine the immunohistological indentification of IMPC in those localization.
Guzinska-Ustymowicz, Katarzyna; Niewiarowska, Katarzyna; Pryczynicz, Anna
Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers
Background Although prognostic biomarkers specific for particular cancers have been discovered, microarray analysis of gene expression profiles, supported by integrative analysis algorithms, helps to identify common factors in molecular oncology. Similarities of Ordered Gene Lists (SOGL) is a recently proposed approach to meta-analysis suitable for identifying features shared by two data sets. Here we extend the idea of SOGL to the detection of significant prognostic marker genes from microarrays of multiple data sets. Three data sets for leukemia and the other six for different solid tumors are used to demonstrate our method, using established statistical techniques. Results We describe a set of significantly similar ordered gene lists, representing outcome comparisons for distinct types of cancer. This kind of similarity could improve the diagnostic accuracies of individual studies when SOGL is incorporated into the support vector machine algorithm. In particular, we investigate the similarities among three ordered gene lists pertaining to mesothelioma survival, prostate recurrence and glioma survival. The similarity-driving genes are related to the outcomes of patients with lung cancer with a hazard ratio of 4.47 (p = 0.035). Many of these genes are involved in breakdown of EMC proteins regulating angiogenesis, and may be used for further research on prognostic markers and molecular targets of gene therapy for cancers. Conclusion The proposed method and its application show the potential of such meta-analyses in clinical studies of gene expression profiles.
Yang, Xinan; Sun, Xiao
Mesangial IgG glomerulonephritis: a distinct type of primary glomerulonephritis.
Fourteen cases of mesangial IgG glomerulonephritis characterized by exclusive or predominant mesangial IgG deposits are reported. The median age at onset was 19 yr (range, 13 to 47 yr). No patient exhibited evidence of systemic lupus erythematous or other systemic diseases. Proteinuria was present in all cases (median, 2.4 g/d; range, 1 to 13 g/d), microscopic hematuria in 12 cases, and macroscopic hematuria in two cases. Five patients were hypertensive at the time of referral. In all cases, renal biopsies revealed mesangial IgG deposits and varying degrees of mesangial matrix expansion, in the absence of significant mesangial cell proliferation. Complement component (mainly C3) deposits were present in virtually all cases. Subepithelial deposits were also noted in nine cases. IgG deposits were polyclonal and consisted mainly of IgG1 and IgG3 subclasses. In electron-microscopic analyses, deposits were electron dense and granular. Treatment was purely supportive. After a mean follow-up period of 11 yr, seven patients had experienced progression to chronic renal failure, including four who had reached end-stage renal failure. Three patients exhibited persistently normal renal function. For one patient, a symptomatic recurrence of mesangial IgG deposits in the renal graft was diagnosed 4 yr after renal transplantation. Such a recurrence highlights the specificity of this type of glomerulonephritis. Mesangial IgG glomerulonephritis is a distinct, albeit rare, type of glomerulonephritis that exhibits far from benign outcome and may recur in renal transplants. PMID:11805165
Fakhouri, Fadi; Darré, Silvina; Droz, Dominique; Lemaire, Matthieu; Nabarra, Bernadette; Machet, Marie-Christine; Chauveau, Dominique; Lesavre, Philippe; Grünfeld, Jean-Pierre; Noël, Laure-Hélčne; Knebelmann, Bertrand
Discovery of a Distinct Superfamily of Kunitz-Type Toxin (KTT) from Tarantulas
Background Kuntiz-type toxins (KTTs) have been found in the venom of animals such as snake, cone snail and sea anemone. The main ancestral function of Kunitz-type proteins was the inhibition of a diverse array of serine proteases, while toxic activities (such as ion-channel blocking) were developed under a variety of Darwinian selection pressures. How new functions were grafted onto an old protein scaffold and what effect Darwinian selection pressures had on KTT evolution remains a puzzle. Principal Findings Here we report the presence of a new superfamily of KTTs in spiders (Tarantulas: Ornithoctonus huwena and Ornithoctonus hainana), which share low sequence similarity to known KTTs and is clustered in a distinct clade in the phylogenetic tree of KTT evolution. The representative molecule of spider KTTs, HWTX-XI, purified from the venom of O. huwena, is a bi-functional protein which is a very potent trypsin inhibitor (about 30-fold more strong than BPTI) as well as a weak Kv1.1 potassium channel blocker. Structural analysis of HWTX-XI in 3-D by NMR together with comparative function analysis of 18 expressed mutants of this toxin revealed two separate sites, corresponding to these two activities, located on the two ends of the cone-shape molecule of HWTX-XI. Comparison of non-synonymous/synonymous mutation ratios (?) for each site in spider and snake KTTs, as well as PBTI like body Kunitz proteins revealed high Darwinian selection pressure on the binding sites for Kv channels and serine proteases in snake, while only on the proteases in spider and none detected in body proteins, suggesting different rates and patterns of evolution among them. The results also revealed a series of key events in the history of spider KTT evolution, including the formation of a novel KTT family (named sub-Kuntiz-type toxins) derived from the ancestral native KTTs with the loss of the second disulfide bridge accompanied by several dramatic sequence modifications. Conclusions/Significance These finding illustrate that the two activity sites of Kunitz-type toxins are functionally and evolutionally independent and provide new insights into effects of Darwinian selection pressures on KTT evolution, and mechanisms by which new functions can be grafted onto old protein scaffolds.
Diao, Jian-Bo; Jiang, Li-Ping; Tang, Xing; Liang, Song-Ping
Integrated Genotypic Analysis of Hedgehog-Related Genes Identifies Subgroups of Keratocystic Odontogenic Tumor with Distinct Clinicopathological Features
Keratocystic odontogenic tumor (KCOT) arises as part of Gorlin syndrome (GS) or as a sporadic lesion. Gene mutations and loss of heterozygosity (LOH) of the hedgehog receptor PTCH1 plays an essential role in the pathogenesis of KCOT. However, some KCOT cases lack evidence for gene alteration of PTCH1, suggesting that other genes in the hedgehog pathway may be affected. PTCH2 and SUFU participate in the occurrence of GS-associated tumors, but their roles in KCOT development are unknown. To elucidate the roles of these genes, we enrolled 36 KCOT patients in a study to sequence their entire coding regions of PTCH1, PTCH2 and SUFU. LOH and immunohistochemical expression of these genes, as well as the downstream targets of hedgehog signaling, were examined using surgically-excised KCOT tissues. PTCH1 mutations, including four novel ones, were found in 9 hereditary KCOT patients, but not in sporadic KCOT patients. A pathogenic mutation of PTCH2 or SUFU was not found in any patients. LOH at PTCH1 and SUFU loci correlated with the presence of epithelial budding. KCOT harboring a germline mutation (Type 1) showed nuclear localization of GLI2 and frequent histological findings such as budding and epithelial islands, as well as the highest recurrence rate. KCOT with LOH but without a germline mutation (Type 2) less frequently showed these histological features, and the recurrence rate was lower. KCOT with neither germline mutation nor LOH (Type 3) consisted of two subgroups, Type 3A and 3B, which were characterized by nuclear and cytoplasmic GLI2 localization, respectively. Type 3B rarely exhibited budding and recurrence, behaving as the most amicable entity. The expression patterns of CCND1 and BCL2 tended to correlate with these subgroups. Our data indicates a significant role of PTCH1 and SUFU in the pathogenesis of KCOT, and the genotype-oriented subgroups constitute entities with different potential aggressiveness.
Shimada, Yasuyuki; Katsube, Ken-ichi; Kabasawa, Yuji; Morita, Kei-ichi; Omura, Ken; Yamaguchi, Akira; Sakamoto, Kei
Heparan sulfate phage display antibodies identify distinct epitopes with complex binding characteristics: insights into protein binding specificities.
Heparan sulfate (HS) binds and modulates the transport and activity of a large repertoire of regulatory proteins. The HS phage display antibodies are powerful tools for the analysis of native HS structure in situ; however, their epitopes are not well defined. Analysis of the binding specificities of a set of HS antibodies by competitive binding assays with well defined chemically modified heparins demonstrates that O-sulfates are essential for binding; however, increasing sulfation does not necessarily correlate with increased antibody reactivity. IC50 values for competition with double modified heparins were not predictable from IC50 values with corresponding singly modified heparins. Binding assays and immunohistochemistry revealed that individual antibodies recognize distinct epitopes and that these are not single linear sequences but families of structurally similar motifs in which subtle variations in sulfation and conformation modify the affinity of interaction. Modeling of the antibodies demonstrates that they possess highly basic CDR3 and surrounding surfaces, presenting a number of possible orientations for HS binding. Unexpectedly, there are significant differences between the existence of epitopes in tissue sections and observed in vitro in dot blotted tissue extracts, demonstrating that in vitro specificity does not necessarily correlate with specificity in situ/vivo. The epitopes are therefore more complex than previously considered. Overall, these data have significance for structure-activity relationships of HS, because the model of one antibody recognizing multiple HS structures and the influence of other in situ HS-binding proteins on epitope availability are likely to reflect the selectivity of many HS-protein interactions in vivo. PMID:19837661
Thompson, Sophie M; Fernig, David G; Jesudason, Edwin C; Losty, Paul D; van de Westerlo, Els M A; van Kuppevelt, Toin H; Turnbull, Jeremy E
IS3 profiling identifies the enterohaemorrhagic Escherichia coli O-island 62 in a distinct enteroaggregative E. coli lineage
Background Enteroaggregative Escherichia coli (EAEC) are important diarrhoeal pathogens that are defined by a HEp-2 adherence assay performed in specialist laboratories.\\u000a Multilocus sequence typing (MLST) has revealed that aggregative adherence is convergent, providing an explanation for why\\u000a not all EAEC hybridize with the plasmid-derived probe for this category, designated CVD432. Some EAEC lineages are globally\\u000a disseminated or more closely associated with
Iruka N Okeke; Louissa R Macfarlane-Smith; Jonathan N Fletcher; Anna M Snelling
Capillary cerebral amyloid angiopathy identifies a distinct APOE ?4-associated subtype of sporadic Alzheimer's disease
The deposition of amyloid ?-protein (A?) in the vessel wall, i.e., cerebral amyloid angiopathy (CAA), is associated with Alzheimer's\\u000a disease (AD). Two types of CAA can be differentiated by the presence or absence of capillary A?-deposits. In addition, as\\u000a in Alzheimer's disease, risk for capillary CAA is associated with the apolipoprotein E (APOE) ?4-allele. Because these morphological and genetic differences
Dietmar Rudolf Thal; Andreas Papassotiropoulos; Takaomi C. Saido; W. Sue T. Griffin; Robert E. Mrak; Heike Kölsch; Kelly Del Tredici; Johannes Attems; Estifanos Ghebremedhin
Soil Characteristics as an Aid to Identifying Forest Habitat Types in Northern Idaho.
National Technical Information Service (NTIS)
Vegetation and soil physical characteristics were analyzed to identify numerical patterns within the soils data, relationships between soils and habitat types, and soil characteristics related to specific habitat types. Ordination and discriminant analysi...
K. E. Neiman
Genomic profiling reveals distinctive molecular relapse patterns in IDH1/2 wild-type glioblastoma.
Molecular changes associated with the progression of glioblastoma after standard radiochemotherapy remain poorly understood. We compared genomic profiles of 27 paired primary and recurrent IDH1/2 wild-type glioblastomas by genome-wide array-based comparative genomic hybridization. By bioinformatic analysis, primary and recurrent tumor profiles were normalized and segmented, chromosomal gains and losses identified taking the tumor cell content into account, and difference profiles deduced. Seven of 27 (26%) pairs lacked DNA copy number differences between primary and recurrent tumors (equal pairs). The recurrent tumors in 9/27 (33%) pairs contained all chromosomal imbalances of the primary tumors plus additional ones, suggesting a sequential acquisition of and/or selection for aberrations during progression (sequential pairs). In 11/27 (41%) pairs, the profiles of primary and recurrent tumors were divergent, i.e., the recurrent tumors contained additional aberrations but had lost others, suggesting a polyclonal composition of the primary tumors and considerable clonal evolution (discrepant pairs). Losses on 9p21.3 harboring the CDKN2A/B locus were significantly more common in primary tumors from sequential and discrepant (nonequal) pairs. Nonequal pairs showed ten regions of recurrent genomic differences between primary and recurrent tumors harboring 46 candidate genes associated with tumor recurrence. In particular, copy numbers of genes encoding apoptosis regulators were frequently changed at progression. In summary, approximately 25% of IDH1/2 wild-type glioblastoma pairs have stable genomic imbalances. In contrast, approximately 75% of IDH1/2 wild-type glioblastomas undergo further genomic aberrations and alter their clonal composition upon recurrence impacting their genomic profile, a process possibly facilitated by 9p21.3 loss in the primary tumor. © 2014 Wiley Periodicals, Inc. PMID:24706357
Riehmer, Vera; Gietzelt, Jens; Beyer, Ulrike; Hentschel, Bettina; Westphal, Manfred; Schackert, Gabriele; Sabel, Michael C; Radlwimmer, Bernhard; Pietsch, Torsten; Reifenberger, Guido; Weller, Michael; Weber, Ruthild G; Loeffler, Markus
Two distinct types of inwardly rectifying K+ channels in bull-frog atrial myocytes.
1. Single atrial myocytes were enzymatically isolated from the bull-frog as previously described (Hume & Giles, 1981), and patch-clamp techniques were used in an attempt to identify and separate two inwardly rectifying K+ channels in this tissue. 2. Single-channel measurements consistently demonstrated the existence of two different resting K+ channels, which both exhibited strong inward rectification. The unitary conductances of these K+ channels were 34 +/- 4 and 22 +/- 3 pS (mean +/- S.D., at 22-24 degrees C) when measured with 110 mM-K+ in the pipette solution, and their mean open times were 0.87 +/- 0.33 and 129.9 +/- 49.4 ms, respectively. 3. In the absence of acetylcholine (ACh) in the pipette, openings of the larger channels with the shorter open times occurred at a very low frequency. When ACh was present in the patch pipette, the activity of this channel increased significantly, although the single-channel conductance and gating behaviour were very similar either with or without ACh in the pipette. 4. The zero-current voltage (extrapolated from the inward currents through these types of channels) depended on the extracellular K+ concentration. [K+]o, in the fashion expected for a predominantly K(+)-selective channel: it shifted by 58 mV for a tenfold change in [K+]o. Very similar results were obtained from whole-cell voltage-clamp measurements (53 mV for a tenfold change in [K+]o). 5. The conductance of both types of K+ channels depended on [K+]o. The single-channel conductances were 25 +/- 3 and 13 +/- 2 pS with 50 mM [K+]o, and 19 +/- 4 and 9 +/- 2 pS with 20 mM [K+]o, respectively. 6. These results demonstrate that two types of resting inwardly rectifying K+ channels can be identified in single atrial myocytes. One of these is an inwardly rectifying K+ channel (IK1) previously identified in whole-cell voltage-clamp experiments (Hume & Giles, 1983). The second channel is the muscarinic receptor-regulated K+ channel (IK(ACh) which was first described in mammalian nodal and atrial cells. 7. N-Ethylmaleimide (NEM), a reagent which alkylates sulphydryl groups, affects these two types of K+ channels differentially. In the cell-attached patch configuration, bath application of NEM (50 microM) completely abolished the activity of IK(ACh), without affecting the IK1 channel activity. 8. To obtain further evidence that these two currents, IK1 and IK(ACh), were different, the inside-out patch-clamp technique was used.(ABSTRACT TRUNCATED AT 400 WORDS)
Clark, R B; Nakajima, T; Giles, W; Kanai, K; Momose, Y; Szabo, G
A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease.
As part of a study to determine the diversity of whitefly-transmitted viruses (genus Begomovirus, family Geminiviridae) associated with cotton leaf curl disease in Pakistan, leaf samples from cotton plants showing typical leaf curl disease symptoms were collected in various locations of Punjab province. Sequence analysis of full-length virus clones (~2.7 kb) showed plants to be infected with the begomovirus cotton leaf curl Burewala virus, the only virus identified in cotton in the Punjab since 2001. Surprisingly, a second virus, the leafhopper-transmitted chickpea chlorotic dwarf virus (CpCDV) of the genus Mastrevirus (family Geminiviridae), was identified in a small number of plants. The sequences of four CpCDV isolates from cotton originating from geographically distinct areas in Punjab were obtained. Analysis of the sequences showed them to represent a distinct, newly identified strain of CpCDV with the highest levels of nucleotide sequence identity to isolates of CpCDV strains C and D that have been identified previously in Pakistan. CpCDV has not been identified previously in cotton. The significance of this finding is discussed. PMID:24212888
Manzoor, Muhammad Tariq; Ilyas, Muhammad; Shafiq, Muhammad; Haider, Muhammad Saleem; Shahid, Ahmad Ali; Briddon, Rob W
The influence of distinct types of aquatic vegetation on the flow field
NASA Astrophysics Data System (ADS)
The Sustainable management of fluvial systems dealing with flood prevention, erosion protection and restoration of rivers and estuaries requires implementation of soft/green-engineering methods. In-stream aquatic vegetation can be regarded as one of these as it plays an important role for both river ecology (function) and geomorphology (form). The goal of this research is to offer insight gained from pilot experimental studies on the effects of a number of different elements modeling instream, aquatic vegetation on the local flow field. It is hypothesized that elements of the same effective "blockage" area but of distinct characteristics (structure, porosity and flexibility), will affect both the mean and fluctuating levels of the turbulent flow to a different degree. The above hypothesis is investigated through a set of rigorous set of experimental runs which are appropriately designed to assess the variability between the interaction of aquatic elements and flow, both quantitatively and qualitatively. In this investigation three elements are employed to model aquatic vegetation, namely a rigid cylinder, a porous but rigid structure and a flexible live plant (Cupressus Macrocarpa). Firstly, the flow field downstream each of the mentioned elements was measured under steady uniform flow conditions employing acoustic Doppler velocimetry. Three-dimensional flow velocities downstream the vegetation element are acquired along a measurement grid extending about five-fold the element's diameter. These measurements are analyzed to develop mean velocity and turbulent intensity profiles for all velocity components. A detailed comparison between the obtained results is demonstrative of the validity of the above hypothesis as each of the employed elements affects in a different manner and degree the flow field. Then a flow visualization technique, during which fluorescent dye is injected upstream of the element and images are captured for further analysis and comparison, was employed to visualize the flow structures shed downstream the aquatic elements. This method allows to further observe qualitatively and visually identify the different characteristics of the eddies advected downstream, conclusively confirming the results of the aforementioned experimental campaign.
Valyrakis, Manousos; Barcroft, Stephen; Yagci, Oral
Segregated Expression of AMPA-Type Glutamate Receptors and Glutamate Transporters Defines Distinct Astrocyte Populations in the Mouse Hippocampus
Recent data have suggested the existence of direct signaling pathways between glial cells and neurons. Here we report the coexistence of distinct types of cells expressing astrocyte-specific markers within the hippocampus that display diverse morphological, molecular, and functional profiles. Usage of transgenic mice with GFAP promoter-controlled enhanced green fluorescent protein (EGFP) expression allowed the identification of astroglial cells after fresh
Katja Matthias; Frank Kirchhoff; Gerald Seifert; Kerstin Huttmann; Marina Matyash; Helmut Kettenmann; Christian Steinhauser
Essential role of EBF1 in the generation and function of distinct mature B cell types
The transcription factor EBF1 is essential for lineage specification in early B cell development. In this study, we demonstrate by conditional mutagenesis that EBF1 is required for B cell commitment, pro–B cell development, and subsequent transition to the pre–B cell stage. Later in B cell development, EBF1 was essential for the generation and maintenance of several mature B cell types. Marginal zone and B-1 B cells were lost, whereas follicular (FO) and germinal center (GC) B cells were reduced in the absence of EBF1. Activation of the B cell receptor resulted in impaired intracellular signaling, proliferation and survival of EBF1-deficient FO B cells. Immune responses were severely reduced upon Ebf1 inactivation, as GCs were formed but not maintained. ChIP- and RNA-sequencing of FO B cells identified EBF1-activated genes that encode receptors, signal transducers, and transcriptional regulators implicated in B cell signaling. Notably, ectopic expression of EBF1 efficiently induced the development of B-1 cells at the expense of conventional B cells. These gain- and loss-of-function analyses uncovered novel important functions of EBF1 in controlling B cell immunity.
Vilagos, Bojan; Hoffmann, Mareike; Souabni, Abdallah; Sun, Qiong; Werner, Barbara; Medvedovic, Jasna; Bilic, Ivan; Minnich, Martina; Axelsson, Elin; Jaritz, Markus
Two Types of Morphologically Distinct Fibers Comprising Gallionella ferruginea Twisted Stalks
Two morphologically distinct extracellular stalk fibers produced by Gallionella ferruginea were compared by electron microscopy and elemental analysis. The thick- and fine-fiber stalks were different in structure on a micrometer scale and in the site on the mother cell to which they were attached, but on a nanometer scale they were similar in ultrastructure and in the elemental composition of their basic fiber matrix.
Suzuki, Tomoko; Hashimoto, Hideki; Ishihara, Hiromichi; Matsumoto, Nobuyuki; Kunoh, Hitoshi; Takada, Jun
Cytology by Infrared Micro-Spectroscopy: Automatic Distinction of Cell Types in Urinary Cytology
We report microscopically collected infrared spectra of cells found in human urine in an effort to develop automatic methods for bladder cancer screening. Unsupervised multivariate analysis of the observed spectral patterns reveals distinct spectral classes, which correlated very well with visual cytology. Therefore, we believe that spectral analysis of individual cells can aid cytology in rendering reliable diagnoses based on objective measurements and discriminant algorithms.
Bird, Benjamin; Romeo, Melissa J.; Diem, Max; Bedrossian, Kristi; Laver, Nora; Naber, Stephen
Restriction Fragment Length Polymorphisms Detected with Novel DNA Probes Differentiate among Diverse Lineages of Serogroup 4 Listeria monocytogenes and Identify Four Distinct Lineages in Serotype 4b
Listeria monocytogenes of serotype 4b has been implicated in numerous outbreaks of food-borne listeriosis and in ca. 40% of sporadic cases. Strains of this serotype appear to be relatively homogeneous genetically, and molecular markers specific for distinct serotype 4b lineages have not been frequently identified. Here we show that DNA fragments derived from the putative mannitol permease locus of Listeria monocytogenes had an unexpectedly high potential to differentiate among different strains of serotype 4b when used as probes in Southern blotting of EcoRI-digested genomic DNA, yielding four distinct restriction fragment length polymorphism (RFLP) patterns. Strains of two epidemic-associated lineages, including the major epidemic clone implicated in several outbreaks in Europe and North America, had distinct RFLPs which differed from those of all other serotype 4b strains that we screened but which were encountered among strains of serotypes 1/2b and 3b. In addition, three serogroup 4 lineages were found to have unique RFLPs that were not encountered among any other L. monocytogenes strains. One was an unusual lineage of serotype 4b, and the other two were members of the serotype 4a and 4c group. The observed polymorphisms may reflect evolutionary relationships among lineages of L. monocytogenes and may facilitate detection and population genetic analysis of specific lineages.
Tran, Huyen L.; Kathariou, Sophia
Aping expressions? Chimpanzees produce distinct laugh types when responding to laughter of others.
Humans have the ability to replicate the emotional expressions of others even when they undergo different emotions. Such distinct responses of expressions, especially positive expressions, play a central role in everyday social communication of humans and may give the responding individuals important advantages in cooperation and communication. The present work examined laughter in chimpanzees to test whether nonhuman primates also use their expressions in such distinct ways. The approach was first to examine the form and occurrence of laugh replications (laughter after the laughter of others) and spontaneous laughter of chimpanzees during social play and then to test whether their laugh replications represented laugh-elicited laugh responses (laughter triggered by the laughter of others) by using a quantitative method designed to measure responses in natural social settings. The results of this study indicated that chimpanzees produce laugh-elicited laughter that is distinct in form and occurrence from their spontaneous laughter. These findings provide the first empirical evidence that nonhuman primates have the ability to replicate the expressions of others by producing expressions that differ in their underlying emotions and social implications. The data further showed that the laugh-elicited laugh responses of the subjects were closely linked to play maintenance, suggesting that chimpanzees might gain important cooperative and communicative advantages by responding with laughter to the laughter of their social partners. Notably, some chimpanzee groups of this study responded more with laughter than others, an outcome that provides empirical support of a socialization of expressions in great apes similar to that of humans. PMID:21355640
Davila-Ross, Marina; Allcock, Bethan; Thomas, Chris; Bard, Kim A
IL-25 simultaneously elicits distinct populations of innate lymphoid cells and multipotent progenitor type 2 (MPPtype2) cells
The predominantly epithelial cell–derived cytokines IL-25, IL-33, and thymic stromal lymphopoietin (TSLP) can promote CD4+ Th2 cell–dependent immunity, inflammation, and tissue repair at barrier surfaces through the induction of multiple innate immune cell populations. IL-25 and IL-33 were previously shown to elicit four innate cell populations, named natural helper cells, nuocytes, innate type 2 helper cells, and multipotent progenitor type 2 (MPPtype2) cells, now collectively termed group 2 innate lymphoid cells (ILC2). In contrast to other types of ILC2, MPPtype2 cells exhibit multipotent potential and do not express T1/ST2 or IL-7R?, suggesting that MPPtype2 cells may be a distinct population. Here, we show that IL-33 elicits robust ILC2 responses, whereas IL-25 predominantly promotes MPPtype2 cell responses at multiple tissue sites with limited effects on ILC2 responses. MPPtype2 cells were distinguished from ILC2 by their differential developmental requirements for specific transcription factors, distinct genome-wide transcriptional profile, and functional potential. Furthermore, IL-25–induced MPPtype2 cells promoted Th2 cytokine–associated inflammation after depletion of ILC2. These findings indicate that IL-25 simultaneously elicits phenotypically and functionally distinct innate lymphoid– and nonlymphoid-associated cell populations and implicate IL-25–elicited MPPtype2 cells and extramedullary hematopoiesis in the promotion of Th2 cytokine responses at mucosal surfaces.
Saenz, Steven A.; Siracusa, Mark C.; Monticelli, Laurel A.; Ziegler, Carly G.K.; Kim, Brian S.; Brestoff, Jonathan R.; Peterson, Lance W.; Wherry, E. John; Goldrath, Ananda W.; Bhandoola, Avinash
Cytokinetic nodes in fission yeast arise from two distinct types of nodes that merge during interphase.
We investigated the assembly of cortical nodes that generate the cytokinetic contractile ring in fission yeast. Observations of cells expressing fluorescent fusion proteins revealed two types of interphase nodes. Type 1 nodes containing kinase Cdr1p, kinase Cdr2p, and anillin Mid1p form in the cortex around the nucleus early in G2. Type 2 nodes with protein Blt1p, guanosine triphosphate exchange factor Gef2p, and kinesin Klp8p emerge from contractile ring remnants. Quantitative measurements and computer simulations showed that these two types of nodes come together by a diffuse-and-capture mechanism: type 2 nodes diffuse to the equator and are captured by stationary type 1 nodes. During mitosis, cytokinetic nodes with Mid1p and all of the type 2 node markers incorporate into the contractile ring, whereas type 1 nodes with Cdr1p and Cdr2p follow the separating nuclei before dispersing into the cytoplasm, dependent on septation initiation network signaling. The two types of interphase nodes follow parallel branches of the pathway to prepare nodes for cytokinesis. PMID:24637325
Akamatsu, Matthew; Berro, Julien; Pu, Kai-Ming; Tebbs, Irene R; Pollard, Thomas D
Distinct functional connectivity of limbic network in the washing type obsessive-compulsive disorder.
Neurobiological models of obsessive-compulsive disorder (OCD) emphasize disturbances of the corticostriatal circuit, but it remains unclear as to how these complex network dysfunctions correspond to heterogeneous OCD phenotypes. We aimed to investigate corticostriatal functional connectivity alterations distinct to OCD characterized predominantly by contamination/washing symptoms. Functional connectivity strengths of the striatal seed regions with remaining brain regions during the resting condition and the contamination symptom provocation condition were compared among 13 OCD patients with predominant contamination/washing symptoms (CON), 13 OCD patients without these symptoms (NCON), and 18 healthy controls. The CON group showed distinctively altered functional connectivity between the ventral striatum and the insula during both the resting and symptom-provoking conditions. Also, the connectivity strength between the ventral striatum and the insula significantly correlated with contamination/washing symptom severity. As common connectivity alterations of the whole OCD subjects, corticostriatal circuits involving the orbitofrontal and temporal cortices were again confirmed. To our knowledge, this is the first study that examined specific abnormalities in functional connectivity of contamination/washing symptom dimension OCD. The findings suggest limbic network dysfunctions to play a pivotal role in contamination/washing symptoms, possibly associated with emotionally salient error awareness. Our study sample allowed us to evaluate the corticostriatal network dysfunction underlying the contamination/washing symptom dimension, which leaves other major symptom dimensions to be explored in the future. PMID:24768985
Jhung, Kyungun; Ku, Jeonghun; Kim, Se Joo; Lee, Hyeongrae; Kim, Kyung Ran; An, Suk Kyoon; Kim, Sun I; Yoon, Kang-Jun; Lee, Eun
Adenylyl cyclases (ACs) convert ATP to cAMP and therefore, subserve multiple regulatory functions in the nervous system. AC1 and AC8 are the only cyclases stimulated by calcium and calmodulin, making them uniquely poised to regulate neuronal development and neuronal processes such as learning and memory. Here, we detail the production and application of a novel antibody against mouse AC1. Along with AC8 immunohistochemistry, these data reveal distinct and partially overlapping patterns of protein expression in brain during development and adulthood. AC1 protein increased in abundance in the neonatal hippocampus from postnatal day 7 to 14. By adulthood, abundant AC1 protein expression was observed in the mossy fiber tract in the hippocampus and the molecular layer in the cerebellum, with diffuse expression in the cortex and thalamus. AC8 protein levels were abundant during development, with diffuse and increasing expression in the hippocampus that intensified in the CA1/CA2 region by adulthood. AC8 expression was weak in the cerebellum at postnatal day 7 and decreased further by postnatal day 14. Analysis of synaptosome fractions from the adult brain demonstrated robust expression of AC1 in the postsynaptic density and extrasynaptic regions, while expression of AC8 was observed in the presynaptic active zone and extrasynaptic fractions. These findings were confirmed with localization of AC1 and/or AC8 with PSD-95, Tau, synaptophysin and MAP-2 expression throughout the brain. Together, these data provide insight into the functional roles of AC1 and AC8 as reflected by their distinct localization in cellular and subcellular compartments.
Conti, Alana C.; Maas, James W.; Muglia, Lisa M.; Dave, Bhumy A.; Vogt, Sherri K.; Tran, Timothy T.; Rayhel, Elizabeth J.; Muglia, Louis J.
Distinct AMPA-Type Glutamatergic Synapses in Developing Rat CA1 Hippocampus
We assessed synaptic ?-amino-3-hydroxy-5-methyl-4-isoxazole propionate receptor (AMPAR) properties during synaptogenesis to describe the development of individual glutamatergic synapses on rat hippocampal CA1 principal neurons. Pharmacologically isolated AMPAR-mediated glutamatergic synaptic currents [evoked by stimulation of the Schaffer Collateral pathway, excitatory postsynaptic currents (EPSCs)], had significantly greater inward-rectification at ages P5–7 compared with P8–18. These inward rectifying EPSCs demonstrated paired-pulse dependent unblocking at positive holding potentials, consistent with voltage-dependent internal polyamine block. Measurements of paired-pulse facilitation did not support altered presynaptic properties associated with inward rectification. Using asynchronous EPSCs (aEPSCs) to analyze populations of individual synapses, we found that quantal amplitudes (Q) increased across early postnatal development (P5-P18) and were directly modulated by increases in the number of activated receptors. Quantal AMPAR decay kinetics (aEPSC ?decays) exhibited the highest coefficient of variation (CV) from P5 to 7 and became markedly less variable at P8–18. At P5–7, faster quantal kinetics coexisted with much slower kinetics; only slower quantal kinetics were found at P8–18. This supports diverse quantal synaptic properties limited to P5–7. Multivariate cluster analysis of Q, CV?decay, and median ?decay supported a segregation of neurons into two distinct age groups of P5–7 and P8–18, similar to the age-related segregation suggested by inward rectification. Taken together, these findings support synaptic, calcium permeable AMPARs at a subset of synapses onto CA1 pyramidal neurons exclusively at P5–7. These distinct synapses coexist with those sharing the properties of more mature synapses. These synapses disappear after P7 as activated receptor numbers increase with age.
Stubblefield, Elizabeth A.
Functional genomics identifies neural stem cell sub-type expression profiles and genes regulating neuroblast homeostasis
The Drosophila larval central brain contains about 10,000 differentiated neurons and 200 scattered neural progenitors (neuroblasts), which can be further subdivided into ~95 type I neuroblasts and eight type II neuroblasts per brain lobe. Only type II neuroblasts generate self-renewing intermediate neural progenitors (INPs), and consequently each contributes more neurons to the brain, including much of the central complex. We characterized six different mutant genotypes that lead to expansion of neuroblast numbers; some preferentially expand type II or type I neuroblasts. Transcriptional profiling of larval brains from these mutant genotypes versus wild-type allowed us to identify small clusters of transcripts enriched in type II or type I neuroblasts, and we validated these clusters by gene expression analysis. Unexpectedly, only a few genes were found to be differentially expressed between type I/II neuroblasts, suggesting that these genes play a large role in establishing the different cell types. We also identified a large group of genes predicted to be expressed in all neuroblasts but not neurons. We performed a neuroblast-specific, RNAi-based functional screen and identified 84 genes that are required to maintain proper neuroblast numbers; all have conserved mammalian orthologs. These genes are excellent candidates for regulating neural progenitor self-renewal in Drosophila and mammals.
Carney, Travis D.; Miller, Michael R.; Robinson, Kristin J.; Bayraktar, Omer A.; Osterhout, Jessica A.; Doe, Chris Q.
Activation of Type I Interferon Pathway in Systemic Lupus Erythematosus: Association with Distinct Clinical Phenotypes
Growing evidence over the last few years suggests a central role of type I IFN pathway in the pathogenesis of systemic autoimmune disorders. Data from clinical and genetic studies in patients with systemic lupus erythematosus (SLE) and lupus-prone mouse models, indicates that the type I interferon system may play a pivotal role in the pathogenesis of several lupus and associated clinical features, such as nephritis, neuropsychiatric and cutaneous lupus, premature atherosclerosis as well as lupus-specific autoantibodies particularly against ribonucleoproteins. In the current paper, our aim is to summarize the latest findings supporting the association of type I IFN pathway with specific clinical manifestations in the setting of SLE providing insights on the potential use of type I IFN as a therapeutic target.
Karageorgas, Theophanis P.; Tseronis, Dimitrios D.; Mavragani, Clio P.
Multilocus Sequence Typing of Mycoplasma hyorhinis Strains Identified by a Real-Time TaqMan PCR Assay.
A real-time TaqMan PCR assay based on the gene encoding the protein p37 was developed to detect Mycoplasma hyorhinis. Its specificity was validated with 29 epidemiologically unrelated M. hyorhinis strains (28 field strains and one reference strain) and other mycoplasma species or with other microorganisms commonly found in pigs. The estimated detection limit of this qPCR assay was 125 microorganism equivalents/?l. The same 29 epidemiologically unrelated M. hyorhinis strains and four previously fully sequenced strains were typed by two portable typing methods, the sequencing of the p37 gene and a multilocus sequence typing (MLST) scheme. The first method revealed 18 distinct nucleotide sequences and insufficient discriminatory power (0.934). The MLST scheme was developed with the sequenced genomes of the M. hyorhinis strains HUB-1, GDL-1, MCLD, and SK76 and based on the genes dnaA, rpoB, gyrB, gltX, adk, and gmk. In total, 2,304 bp of sequence was analyzed for each strain. MLST was capable of subdividing the 33 strains into 29 distinct sequence types. The discriminatory power of the method was >0.95, which is the threshold value for interpreting typing results with confidence (D = 0.989). Population analysis showed that recombination in M. hyorhinis occurs and that strains are diverse but with a certain clonality (one unique clonal complex was identified). The new qPCR assay and the robust MLST scheme are available for the acquisition of new knowledge on M. hyorhinis epidemiology. A web-accessible database has been set up for the M. hyorhinis MLST scheme at http://pubmlst.org/mhyorhinis/. PMID:24622092
Tocqueville, Véronique; Ferré, Séverine; Nguyen, Ngoc Hong Phuc; Kempf, Isabelle; Marois-Créhan, Corinne
Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing
Intrinsically disordered regions have been associated with various cellular processes and are implicated in several human diseases, but their exact roles remain unclear. We previously defined two classes of conserved disordered regions in budding yeast, referred to as "flexible" and "constrained" conserved disorder. In flexible disorder, the property of disorder has been positionally conserved during evolution, whereas in constrained disorder, both the amino acid sequence and the property of disorder have been conserved. Here, we show that flexible and constrained disorder are widespread in the human proteome, and are particularly common in proteins with regulatory functions. Both classes of disordered sequences are highly enriched in regions of proteins that undergo tissue-specific (TS) alternative splicing (AS), but not in regions of proteins that undergo general (i.e., not tissue-regulated) AS. Flexible disorder is more highly enriched in TS alternative exons, whereas constrained disorder is more highly enriched in exons that flank TS alternative exons. These latter regions are also significantly more enriched in potential phosphosites and other short linear motifs associated with cell signaling. We further show that cancer driver mutations are significantly enriched in regions of proteins associated with TS and general AS. Collectively, our results point to distinct roles for TS alternative exons and flanking exons in the dynamic regulation of protein interaction networks in response to signaling activity, and they further suggest that alternatively spliced regions of proteins are often functionally altered by mutations responsible for cancer.
Michaut, Magali; Sun, Mark; Irimia, Manuel; Bellay, Jeremy; Myers, Chad L.; Blencowe, Benjamin J.; Kim, Philip M.
Distinct Neural Correlates for Two Types of Inhibition in Bilinguals: Response Inhibition versus Interference Suppression
ERIC Educational Resources Information Center
To examine the effects of bilingualism on cognitive control, we studied monolingual and bilingual young adults performing a flanker task with functional MRI. The trial types of primary interest for this report were incongruent and no-go trials, representing interference suppression and response inhibition, respectively. Response times were similar…
Luk, Gigi; Anderson, John A. E.; Craik, Fergus I. M.; Grady, Cheryl; Bialystok, Ellen
Pathologically and Biologically Distinct Types of Epithelium in Intraductal Papillary Mucinous Neoplasms Delineation of an \\
Although general characteristics of intraductal papillary mucinous neoplasms (IPMNs) and their delineation from other pan- creatic tumors have been well established, several issues regarding their biology and management remain unresolved. It has been noted briefly by us and other authors that there are different types of papillae in IPMNs; however, their frequency, biologic significance, and clini- cal relevance are unknown.
N. Volkan Adsay; Kambiz Merati; Olca Basturk; Christine Iacobuzio-Donahue; Edi Levi; Jeanette D. Cheng; Fazlul H. Sarkar; Ralph H. Hruban; David S. Klimstra
A de novo interstitial deletion of 8p11.2 including ANK1 identified in a patient with spherocytosis, psychomotor developmental delay, and distinctive facial features.
The contiguous gene syndrome involving 8p11.2 is recognized as a combined phenotype of both Kallmann syndrome and hereditary spherocytosis, because the genes responsible for these 2 clinical entities, the fibroblast growth factor receptor 1 (FGFR1) and ankyrin 1 (ANK1) genes, respectively, are located in this region within a distance of 3.2Mb. We identified a 3.7Mb deletion of 8p11.2 in a 19-month-old female patient with hereditary spherocytosis. The identified deletion included ANK1, but not FGFR1, which is consistent with the absence of any phenotype or laboratory findings of Kallmann syndrome. Compared with the previous studies, the deletion identified in this study was located on the proximal end of 8p, indicating a pure interstitial deletion of 8p11.21. This patient exhibited mild developmental delay and distinctive facial findings in addition to hereditary spherocytosis. Thus, some of the genes included in the deleted region would be related to these symptoms. PMID:22771917
Miya, Kazushi; Shimojima, Keiko; Sugawara, Midori; Shimada, Shino; Tsuri, Hiroyuki; Harai-Tanaka, Tomomi; Nakaoka, Sachiko; Kanegane, Hirokazu; Miyawaki, Toshio; Yamamoto, Toshiyuki
Myosin IIB isoform plays an essential role in the formation of two distinct types of macropinosomes
The function and mechanism of macropinocytosis in cells outside of the immune system remain poorly understood. We used a neuroblastoma cell line, Neuro-2a, to study macropinocytosis in neuronal cells. We found phorbol 12-myristate 13-acetate (PMA) and insulin-like growth factor 1 (IGF-1) induced two dinstinct types of macropinocytosis in the Neuro-2a cells. IGF-1-induced macropinocytosis occurs mostly around the cell bodies and requires phosphoinositide 3-kinase (PI3K), while PMA-induced macropinocytosis occurs predominantly in the neurites and is independent of PI3K. Both types of macropinocytosis were inhibited by a specific inhibitor of non-muscle myosin II, blebbistatin. siRNA knock-down of nonmuscle myosin II isoforms, -IIA and –IIB, resulted in opposite effects on macropinocytosis induced by PMA or IGF. Myosin IIA knock-down significantly increased, whereas myosin IIB knock-down significantly decreased, macropinocytosis with correlating changes in membrane ruffle formation.
Jiang, Jun; Kolpak, Adrianne L.; Bao, Zheng-Zheng
Biased Signaling of the Angiotensin II Type 1 Receptor Can Be Mediated through Distinct Mechanisms
BackgroundSeven transmembrane receptors (7TMRs) can adopt different active conformations facilitating a selective activation of either G protein or ?-arrestin-dependent signaling pathways. This represents an opportunity for development of novel therapeutics targeting selective biological effects of a given receptor. Several studies on pathway separation have been performed, many of these on the Angiotensin II type 1 receptor (AT1R). It has been
Marie Mi Bonde; Jonas Tind Hansen; Samra Joke Sanni; Stig Haunsř; Steen Gammeltoft; Christina Lyngsř; Jakob Lerche Hansen; Karl-Wilhelm Koch
Ancient, independent evolution and distinct molecular features of the novel human T-lymphotropic virus type 4
Background Human T-lymphotropic virus type 4 (HTLV-4) is a new deltaretrovirus recently identified in a primate hunter in Cameroon. Limited sequence analysis previously showed that HTLV-4 may be distinct from HTLV-1, HTLV-2, and HTLV-3, and their simian counterparts, STLV-1, STLV-2, and STLV-3, respectively. Analysis of full-length genomes can provide basic information on the evolutionary history and replication and pathogenic potential of new viruses. Results We report here the first complete HTLV-4 sequence obtained by PCR-based genome walking using uncultured peripheral blood lymphocyte DNA from an HTLV-4-infected person. The HTLV-4(1863LE) genome is 8791-bp long and is equidistant from HTLV-1, HTLV-2, and HTLV-3 sharing only 62–71% nucleotide identity. HTLV-4 has a prototypic genomic structure with all enzymatic, regulatory, and structural proteins preserved. Like STLV-2, STLV-3, and HTLV-3, HTLV-4 is missing a third 21-bp transcription element found in the long terminal repeats of HTLV-1 and HTLV-2 but instead contains unique c-Myb and pre B-cell leukemic transcription factor binding sites. Like HTLV-2, the PDZ motif important for cellular signal transduction and transformation in HTLV-1 and HTLV-3 is missing in the C-terminus of the HTLV-4 Tax protein. A basic leucine zipper (b-ZIP) region located in the antisense strand of HTLV-1 and believed to play a role in viral replication and oncogenesis, was also found in the complementary strand of HTLV-4. Detailed phylogenetic analysis shows that HTLV-4 is clearly a monophyletic viral group. Dating using a relaxed molecular clock inferred that the most recent common ancestor of HTLV-4 and HTLV-2/STLV-2 occurred 49,800 to 378,000 years ago making this the oldest known PTLV lineage. Interestingly, this period coincides with the emergence of Homo sapiens sapiens during the Middle Pleistocene suggesting that early humans may have been susceptible hosts for the ancestral HTLV-4. Conclusion The inferred ancient origin of HTLV-4 coinciding with the appearance of Homo sapiens, the propensity of STLVs to cross-species into humans, the fact that HTLV-1 and -2 spread globally following migrations of ancient populations, all suggest that HTLV-4 may be prevalent. Expanded surveillance and clinical studies are needed to better define the epidemiology and public health importance of HTLV-4 infection.
Switzer, William M; Salemi, Marco; Qari, Shoukat H; Jia, Hongwei; Gray, Rebecca R; Katzourakis, Aris; Marriott, Susan J; Pryor, Kendle N; Wolfe, Nathan D; Burke, Donald S; Folks, Thomas M; Heneine, Walid
We present R-band light curves of Type II supernovae (SNe) from the Caltech Core-Collapse Project (CCCP). With the exception of interacting (Type IIn) SNe and rare events with long rise times, we find that most light curve shapes belong to one of three apparently distinct classes: plateau, slowly declining, and rapidly declining events. The last class is composed solely of Type IIb SNe which present similar light curve shapes to those of SNe Ib, suggesting, perhaps, similar progenitor channels. We do not find any intermediate light curves, implying that these subclasses are unlikely to reflect variance of continuous parameters, but rather might result from physically distinct progenitor systems, strengthening the suggestion of a binary origin for at least some stripped SNe. We find a large plateau luminosity range for SNe IIP, while the plateau lengths seem rather uniform at approximately 100 days. As analysis of additional CCCP data goes on and larger samples are collected, demographic studies of core-collapse SNe will likely continue to provide new constraints on progenitor scenarios.
Arcavi, Iair; Gal-Yam, Avishay; Yaron, Ofer [Department of Particle Physics and Astrophysics, Weizmann Institute of Science, Rehovot 76100 (Israel); Cenko, S. Bradley; Becker, Adam B. [Department of Astronomy, University of California, Berkeley, CA 94720-3411 (United States); Fox, Derek B. [Department of Astronomy and Astrophysics, Pennsylvania State University, University Park, PA 16802 (United States); Leonard, Douglas C. [Department of Astronomy, San Diego State University, San Diego, CA 92182 (United States); Moon, Dae-Sik [Department of Astronomy and Astrophysics, University of Toronto, Toronto, ON M5S 3H4 (Canada); Sand, David J. [Las Cumbres Observatory Global Telescope Network, Santa Barbara, CA 93117 (United States); Soderberg, Alicia M. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Kiewe, Michael [Department of Physics, University of Wisconsin, Madison, WI 53706 (United States); Scheps, Raphael [King's College, University of Cambridge, Cambridge CB2 1ST (United Kingdom); Birenbaum, Gali [12 Amos St, Ramat Chen, Ramat Gan 52233 (Israel); Chamudot, Daniel [20 Chen St, Petach Tikvah 49520 (Israel); Zhou, Jonathan, E-mail: firstname.lastname@example.com [101 Dunster Street, Box 398, Cambridge, MA 02138 (United States)
Mutations at Ser331 in the HSN type I gene SPTLC1 are associated with a distinct syndromic phenotype.
Mutations in the serine palmitoyltransferase subunit 1 (SPTLC1) gene are the most common cause of hereditary sensory neuropathy type 1 (HSN1). Here we report the clinical and molecular consequences of a particular mutation (p.S331Y) in SPTLC1 affecting a patient with severe, diffuse muscle wasting and hypotonia, prominent distal sensory disturbances, joint hypermobility, bilateral cataracts and considerable growth retardation. Normal plasma sphingolipids were unchanged but 1-deoxy-sphingolipids were significantly elevated. In contrast to other HSN patients reported so far, our findings strongly indicate that mutations at amino acid position Ser331 of the SPTLC1 gene lead to a distinct syndrome. PMID:23454272
Auer-Grumbach, Michaela; Bode, Heiko; Pieber, Thomas R; Schabhüttl, Maria; Fischer, Dirk; Seidl, Rainer; Graf, Elisabeth; Wieland, Thomas; Schuh, Reinhard; Vacariu, Gerda; Grill, Franz; Timmerman, Vincent; Strom, Tim M; Hornemann, Thorsten
Distinct Functional Properties of Isoamylase-Type Starch Debranching Enzymes in Monocot and Dicot Leaves1[C][W][OPEN
Isoamylase-type starch debranching enzymes (ISA) play important roles in starch biosynthesis in chloroplast-containing organisms, as shown by the strict conservation of both catalytically active ISA1 and the noncatalytic homolog ISA2. Functional distinctions exist between species, although they are not understood yet. Numerous plant tissues require both ISA1 and ISA2 for normal starch biosynthesis, whereas monocot endosperm and leaf exhibit nearly normal starch metabolism without ISA2. This study took in vivo and in vitro approaches to determine whether organism-specific physiology or evolutionary divergence between monocots and dicots is responsible for distinctions in ISA function. Maize (Zea mays) ISA1 was expressed in Arabidopsis (Arabidopsis thaliana) lacking endogenous ISA1 or lacking both native ISA1 and ISA2. The maize protein functioned in Arabidopsis leaves to support nearly normal starch metabolism in the absence of any native ISA1 or ISA2. Analysis of recombinant enzymes showed that Arabidopsis ISA1 requires ISA2 as a partner for enzymatic function, whereas maize ISA1 was active by itself. The electrophoretic mobility of recombinant and native maize ISA differed, suggestive of posttranslational modifications in vivo. Sedimentation equilibrium measurements showed recombinant maize ISA1 to be a dimer, in contrast to previous gel permeation data that estimated the molecular mass as a tetramer. These data demonstrate that evolutionary divergence between monocots and dicots is responsible for the distinctions in ISA1 function.
Facon, Maud; Lin, Qiaohui; Azzaz, Abdelhamid M.; Hennen-Bierwagen, Tracie A.; Myers, Alan M.; Putaux, Jean-Luc; Roussel, Xavier; D'Hulst, Christophe; Wattebled, Fabrice
Phenotypic Variation of Helicobacter pylori Isolates from Geographically Distinct Regions Detected by Lectin Typing
A total of 309 Helicobacter pylori isolates from 18 different countries were analyzed with a previously developed lectin typing system. The system was developed by using a proteolytic pretreatment to enhance the carbohydrate fraction of the sample. Four lectins from Ulex europaeus, Lotus tetragonolobus, Erythrina cristigali, and Triticum vulgaris were used to type the strains. The lectins were chosen for their specificities for sugars commonly encountered in the lipopolysaccharide of H. pylori. The isolates were received from their parent institutions as pellets of biomass and were typed at one of three centers (in Ireland, Sweden, and Estonia). All 16 possible lectin reaction patterns were observed in the study, with the isolates with the predominant pattern exhibiting reactions with all the lectins in the panel. For European patients suffering from gastritis, an association was noted between lectin reaction pattern MH4 and atrophic chronic gastritis; isolates with lectin reaction pattern MH4 were isolated from patients with atrophic chronic gastritis, whereas isolates with this pattern were not isolated from patients with chronic gastritis (P = 0.0006). In addition, statistically significant relationships were noted between the lectin reaction pattern and the associated pathology of isolates from the Swedish population. Isolates with patterns MH13 and MH16, which had low lectin reactivities, correlated with nonulcer disease (P = 0.0025 and P = 0.0002, respectively), and all four isolates from adenocarcinoma patients were characterized as possessing reaction pattern MH16. In contrast, isolates with lectin reaction patterns MH1 and MH10, which had high lectin reactivities, were associated with ulcer disease (P = 0.046 and P = 0.0022, respectively).
Hynes, Sean O.; Broutet, Nathalie; Wadstrom, Torkel; Mikelsaar, Marika; O'Toole, Paul W.; Telford, John; Engstrand, Lars; Kamiya, Shigeru; Mentis, Andreas F.; Moran, Anthony P.
Characterization of Staphylococcus aureus from Distinct Geographic Locations in China: An Increasing Prevalence of spa-t030 and SCCmec Type III
Staphylococcus aureus belongs to one of the most common bacteria causing healthcare and community associated infections in China, but their molecular characterization has not been well studied. From May 2011 to June 2012, a total of 322 non-duplicate S. aureus isolates were consecutively collected from seven tertiary care hospitals in seven cities with distinct geographical locations in China, including 171 methicillin sensitive S. aureus (MSSA) and 151 MRSA isolates. All isolates were characterized by spa typing. The presence of virulence genes was tested by PCR. MRSA were further characterized by SCCmec typing. Seventy four and 16 spa types were identified among 168 MSSA and 150 MRSA, respectively. One spa type t030 accounted for 80.1% of all MRSA isolates, which was higher than previously reported, while spa-t037 accounted for only 4.0% of all MRSA isolates. The first six spa types (t309, t189, t034, t377, t078 and t091) accounted for about one third of all MSSA isolates. 121 of 151 MRSA isolates (80.1%) were identified as SCCmec type III. pvl gene was found in 32 MSSA (18.7%) and 5 MRSA (3.3%) isolates, with ST22-MSSA-t309 as the most commonly identified strain. Compared with non-epidemic MRSA clones, epidemic MRSA clones (corresponding to ST239) exhibited a lower susceptibility to rifampin, ciprofloxacin, gentamicin and trimethoprim-sulfamethoxazole, a higher prevalence of sea gene and a lower prevalence of seb, sec, seg, sei and tst genes. The increasing prevalence of multidrug resistant spa-t030 MRSA represents a major public health problem in China.
Duo, Libo; Xiong, Jie; Gong, Yanwen; Yang, Jiyong; Wang, Zhanke; Wu, Xuqin; Lu, Zhongyi; Meng, Xiangzhao; Zhao, Jingya; Zhang, Changjian; Wang, Fang; Zhang, Yulong; Zhang, Mengqiang; Han, Li
Cloning and biochemical characterization of Staphylococcus aureus type IA DNA topoisomerase comprised of distinct five domains.
DNA topoisomerases play critical roles in regulating DNA topology and are essential enzymes for cell survival. In this study, a gene encoding type IA DNA topoisomerase was cloned from Staphylococcus aureus (S. aureus) sp. strain C-66, and the biochemical properties of recombinant enzyme was characterized. The nucleotide sequence analysis showed that the cloned gene contained an open reading frame (2070 bp) that could encode a polypeptide of 689 amino acids. The cloned gene actually produced 79.1 kDa functional enzyme (named Sau-TopoI) in Escherichia coli (E. coli). Sau-TopoI enzyme purified from E. coli showed ATP-independent and Mg(2+)-dependent manners for relaxing negatively supercoiled DNA. The relaxation activity of Sau-TopoI was inhibited by camptothecin, but not by nalidixic acid and etoposide. Cleavage site mapping showed that the enzyme could preferentially bind to and cleave the sequence GGNN?CAT (N and ? represent any nucleotide and cleavage site, respectively). All these results suggest that the purified enzyme is type IA DNA topoisomerase. In addition, domain mapping analysis showed that the enzyme was composed of conserved four domains (I through IV), together with a variable C-terminal region containing a unique domain V. PMID:21281597
Park, Jung Eun; Kim, Hyun Ik; Park, Jong Woo; Park, Jong Kun; Lee, Jung Sup
Satellite tracking reveals distinct movement patterns for Type B and Type C killer whales in the southern Ross Sea, Antarctica
During January\\/February 2006, we satellite-tracked two different ecotypes of killer whales (Orcinus orca) in McMurdo Sound, Ross Sea, Antarctica, using surface-mounted tags attached with sub-dermal darts. A single Type B whale\\u000a (pinniped prey specialist), tracked for 27 days, traveled an average net distance of 56.8 ± 32.8 km day?1, a maximum of 114 km day?1, and covered an estimated area of 49,351 km2. It spent several days near
Russel D. Andrews; Robert L. Pitman; Lisa T. Ballance
Isolation of an adenovirus antigenically distinct from equine adenovirus type 1 from diarrheic foal feces.
Adenovirus was isolated in equine fetal kidney cell cultures from the feces of 2 foals with diarrhea that also had large numbers (greater than 10(6)/g) of rotavirus particles in their feces. Unlike equine adenovirus type 1 (EAdV1), the fecal EAdV did not hemagglutinate human O, rhesus macaque, or equine RBC. By serum neutralization, the fecal viruses were identical with each other, but showed no relationship to EAdV1. Antiserum prepared against the fecal viruses did not contain hemagglutination-inhibiting antibody to EAdV1. It is proposed that the fecal viruses be considered prototypic of EAdV2. The frequency of neutralizing antibody to EAdV2 in 339 equine serum samples was 77%. Neither EAdV1 nor EAdV2 is related by serum neutralization to any of 30 human adenovirus serotypes. PMID:6176153
Studdert, M J; Blackney, M H
iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels.
Conotoxins are small disulfide-rich neurotoxic peptides, which can bind to ion channels with very high specificity and modulate their activities. Over the last few decades, conotoxins have been the drug candidates for treating chronic pain, epilepsy, spasticity, and cardiovascular diseases. According to their functions and targets, conotoxins are generally categorized into three types: potassium-channel type, sodium-channel type, and calcium-channel types. With the avalanche of peptide sequences generated in the postgenomic age, it is urgent and challenging to develop an automated method for rapidly and accurately identifying the types of conotoxins based on their sequence information alone. To address this challenge, a new predictor, called iCTX-Type, was developed by incorporating the dipeptide occurrence frequencies of a conotoxin sequence into a 400-D (dimensional) general pseudoamino acid composition, followed by the feature optimization procedure to reduce the sample representation from 400-D to 50-D vector. The overall success rate achieved by iCTX-Type via a rigorous cross-validation was over 91%, outperforming its counterpart (RBF network). Besides, iCTX-Type is so far the only predictor in this area with its web-server available, and hence is particularly useful for most experimental scientists to get their desired results without the need to follow the complicated mathematics involved. PMID:24991545
Ding, Hui; Deng, En-Ze; Yuan, Lu-Feng; Liu, Li; Lin, Hao; Chen, Wei; Chou, Kuo-Chen
iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels
Conotoxins are small disulfide-rich neurotoxic peptides, which can bind to ion channels with very high specificity and modulate their activities. Over the last few decades, conotoxins have been the drug candidates for treating chronic pain, epilepsy, spasticity, and cardiovascular diseases. According to their functions and targets, conotoxins are generally categorized into three types: potassium-channel type, sodium-channel type, and calcium-channel types. With the avalanche of peptide sequences generated in the postgenomic age, it is urgent and challenging to develop an automated method for rapidly and accurately identifying the types of conotoxins based on their sequence information alone. To address this challenge, a new predictor, called iCTX-Type, was developed by incorporating the dipeptide occurrence frequencies of a conotoxin sequence into a 400-D (dimensional) general pseudoamino acid composition, followed by the feature optimization procedure to reduce the sample representation from 400-D to 50-D vector. The overall success rate achieved by iCTX-Type via a rigorous cross-validation was over 91%, outperforming its counterpart (RBF network). Besides, iCTX-Type is so far the only predictor in this area with its web-server available, and hence is particularly useful for most experimental scientists to get their desired results without the need to follow the complicated mathematics involved.
Ding, Hui; Deng, En-Ze; Liu, Li; Chou, Kuo-Chen
Intermediate-Type Vancomycin Resistance (VISA) in Genetically-Distinct Staphylococcus aureus Isolates Is Linked to Specific, Reversible Metabolic Alterations
Intermediate (VISA-type) vancomycin resistance in Staphylococcus aureus has been associated with a range of physiologic and genetic alterations. Previous work described the emergence of VISA-type resistance in two clonally-distinct series of isolates. In both series (the first belonging to MRSA clone ST8-USA300, and the second to ST5-USA100), resistance was conferred by a single mutation in yvqF (a negative regulator of the vraSR two-component system associated with vancomycin resistance). In the USA300 series, resistance was reversed by a secondary mutation in vraSR. In this study, we combined systems-level metabolomic profiling with statistical modeling techniques to discover specific, reversible metabolic alterations associated with the VISA phenotype.
Alexander, Elizabeth L.; Gardete, Susana; Bar, Haim Y.; Wells, Martin T.; Tomasz, Alexander; Rhee, Kyu Y.
Distinct magnetic properties of one novel type of nanoscale cobalt-iron Prussian blue analogues synthesized in microemulsion
NASA Astrophysics Data System (ADS)
One novel type of nanoscale cobalt-iron Prussian blue analogues (PBA) in the form of mixed nanorods and nanocubes were synthesized using cetyltrimethyl ammonium bromide (CTAB) as the surfactant in microemulsion at low temperature. The generated products were characterized by SQUID, XRD and IR techniques, etc. The effects of potassium contents, cobalt-to-iron ratios, reaction temperatures on the properties of the nanoscale cobalt-iron PBA were systematically explored. The results showed that the novel type of nanomaterials possessed distinct magnetic properties in that their coercivities were intensely dependent on cobalt-to-iron ratios and potassium contents. Furthermore, it was observed that low reaction temperature not only affected the morphologies of the products, but also had influence on their magnetic properties. Additionally, the cobalt-iron Prussian blue analogues were strongly influenced by CTAB around their surface, which led to higher Curie temperatures.
Liu, Hui; long Du, Xian; Gao, Peiyuan; Zhao, Ji hua; Fang, Jian; Shen, Weiguo
Analysis of Moraxella catarrhalis by DNA typing: evidence for a distinct subpopulation associated with virulence traits.
Two DNA typing methods, probe-generated restriction fragment length polymorphism analysis and single-adapter amplified fragment length polymorphism analysis, were used to study the genetic relationships among 90 Moraxella catarrhalis strains. Both methods were found to be highly concordant, generating a dendrogram with 2 main branches. The division of the M. catarrhalis population into 2 subspecies was supported by analysis of the 16S rRNA sequences. Both beta-lactamase-positive and beta-lactamase-negative strains were found in all main branches, suggesting horizontal transfer of the beta-lactamase gene. In contrast, 2 virulence traits, complement resistance and adherence to epithelial cells, were strongly associated with 1 of the 2 subspecies. The branch depth suggested that complement-resistant adherent strains diverged from a common ancestor more recently than did complement-sensitive nonadherent strains. These findings suggest the existence of subpopulations of M. catarrhalis that differ in virulence, and they may have implications for vaccine development. PMID:10762569
Bootsma, H J; van der Heide, H G; van de Pas, S; Schouls, L M; Mooi, F R
Narrow-host-range bacteriophages that infect Rhizobium etli associate with distinct genomic types.
In this work, we isolated and characterized 14 bacteriophages that infect Rhizobium etli. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48 R. etli strains. We obtained the complete genome sequence of nine phages. Four phages were resistant to several restriction enzymes and in vivo cloning, probably due to nucleotide modifications. The genome size of the sequenced phages varied from 43 kb to 115 kb, with a median size of ? 45 to 50 kb. A large proportion of open reading frames of these phage genomes (65 to 70%) consisted of hypothetical and orphan genes. The remainder encoded proteins needed for phage morphogenesis and DNA synthesis and processing, among other functions, and a minor percentage represented genes of bacterial origin. We classified these phages into four genomic types on the basis of their genomic similarity, gene content, and host range. Since there are no reports of similar sequences, we propose that these bacteriophages correspond to novel species. PMID:24185856
Santamaría, Rosa Isela; Bustos, Patricia; Sepúlveda-Robles, Omar; Lozano, Luis; Rodríguez, César; Fernández, José Luis; Juárez, Soledad; Kameyama, Luis; Guarneros, Gabriel; Dávila, Guillermo; González, Víctor
Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types
In this work, we isolated and characterized 14 bacteriophages that infect Rhizobium etli. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48 R. etli strains. We obtained the complete genome sequence of nine phages. Four phages were resistant to several restriction enzymes and in vivo cloning, probably due to nucleotide modifications. The genome size of the sequenced phages varied from 43 kb to 115 kb, with a median size of ?45 to 50 kb. A large proportion of open reading frames of these phage genomes (65 to 70%) consisted of hypothetical and orphan genes. The remainder encoded proteins needed for phage morphogenesis and DNA synthesis and processing, among other functions, and a minor percentage represented genes of bacterial origin. We classified these phages into four genomic types on the basis of their genomic similarity, gene content, and host range. Since there are no reports of similar sequences, we propose that these bacteriophages correspond to novel species.
Santamaria, Rosa Isela; Bustos, Patricia; Sepulveda-Robles, Omar; Lozano, Luis; Rodriguez, Cesar; Fernandez, Jose Luis; Juarez, Soledad; Kameyama, Luis; Guarneros, Gabriel; Davila, Guillermo
Distinctive features of degenerating Purkinje cells in spinocerebellar ataxia type 31.
Spinocerebellar ataxia type 31 (SCA31) is an autosomal dominant form of pure cerebellar ataxia that is caused by a disease-specific insertion containing penta-nucleotide repeats (TGGAA)n . Neuropathologically, cerebellar Purkinje cells are preferentially affected and reduced in number in SCA31, and they are often surrounded by halo-like amorphous materials. In the present study, we performed neuropathological analyses on two SCA31 brains, and discussed the serial morphological changes of Purkinje cells in SCA31.We found that bent, elongated, often folded nuclei were observed frequently in degenerating Purkinje cells with the halo-like structure. Conversely, Purkinje cells without this structure developed marked atrophy with severely slender and condensed nuclei. On the basis of these pathological findings, we propose two different processes for Purkinje cell degeneration in SCA31, namely, shrinkage of Purkinje cells with or without the halo-like amorphous materials. The former, but not the latter, was considered to be specific to SCA31. Correspondingly, fragmentation of the Golgi apparatus was observed more frequently in Purkinje cells with the halo-like structure than in those without this structure. We consider that the profound nuclear deformity and fragmentation of the Golgi apparatus are closely linked with the formation of the halo-like structure in SCA31. PMID:24344778
Yoshida, Kunihiro; Asakawa, Mika; Suzuki-Kouyama, Emi; Tabata, Kenichi; Shintaku, Masayuki; Ikeda, Shu-Ichi; Oyanagi, Kiyomitsu
A distinct type of heterochromatin at the telomeric region of the Drosophila melanogaster Y chromosome.
Heterochromatin assembly and its associated phenotype, position effect variegation (PEV), provide an informative system to study chromatin structure and genome packaging. In the fruit fly Drosophila melanogaster, the Y chromosome is entirely heterochromatic in all cell types except the male germline; as such, Y chromosome dosage is a potent modifier of PEV. However, neither Y heterochromatin composition, nor its assembly, has been carefully studied. Here, we report the mapping and characterization of eight reporter lines that show male-specific PEV. In all eight cases, the reporter insertion sites lie in the telomeric transposon array (HeT-A and TART-B2 homologous repeats) of the Y chromosome short arm (Ys). Investigations of the impact on the PEV phenotype of mutations in known heterochromatin proteins (i.e., modifiers of PEV) show that this Ys telomeric region is a unique heterochromatin domain: it displays sensitivity to mutations in HP1a, EGG and SU(VAR)3-9, but no sensitivity to Su(z)2 mutations. It appears that the endo-siRNA pathway plays a major targeting role for this domain. Interestingly, an ectopic copy of 1360 is sufficient to induce a piRNA targeting mechanism to further enhance silencing of a reporter cytologically localized to the Ys telomere. These results demonstrate the diversity of heterochromatin domains, and the corresponding variation in potential targeting mechanisms. PMID:24475122
Wang, Sidney H; Nan, Ruth; Accardo, Maria C; Sentmanat, Monica; Dimitri, Patrizio; Elgin, Sarah C R
Calcium-permeable AMPA receptors provide a common mechanism for LTP in glutamatergic synapses of distinct hippocampal interneuron types.
Glutamatergic synapses on some hippocampal GABAergic interneurons exhibit activity-induced long-term potentiation (LTP). Interneuron types within the CA1 area expressing mutually exclusive molecular markers differ in LTP responses. Potentiation that depends on calcium-permeable (CP) AMPA receptors has been characterized in oriens-lacunosum moleculare (O-LM) interneurons, which express parvalbumin and somatostatin (SM). However, it is unknown how widely CP-AMPAR-dependent plasticity is expressed among different GABAergic interneuron types. Here we examine synaptic plasticity in rat hippocampal O-LM cells and two other interneuron types expressing either nitric oxide synthase (NOS) or cholecystokinin (CCK), which are known to be physiologically and developmentally distinct. We report similar CP-AMPAR-dependent LTP in NOS-immunopositive ivy cells and SM-expressing O-LM cells to afferent fiber theta burst stimulation. The potentiation in both cell types is induced at postsynaptic membrane potentials below firing threshold, and induction is blocked by intense spiking simultaneously with afferent stimulation. The strong inward rectification and calcium permeability of AMPARs is explained by a low level of GluA2 subunit mRNA expression. LTP is not elicited in CCK-expressing Schaffer collateral-associated cells, which lack CP-AMPARs and express high levels of the GluA2 subunit. The results show that CP-AMPAR-mediated synaptic potentiation is common in hippocampal interneuron types and occurs in interneurons of both feedforward and feedback inhibitory pathways. PMID:22573673
Szabo, Andras; Somogyi, Jozsef; Cauli, Bruno; Lambolez, Bertrand; Somogyi, Peter; Lamsa, Karri P
Sinonasal undifferentiated carcinoma and nasopharyngeal-type undifferentiated carcinoma: two clinically, biologically, and histopathologically distinct entities.
Sinonasal undifferentiated carcinoma (SNUC) is a rare aggressive neoplasm arising in the nasal cavity and paranasal sinuses. Primary sinonasal nasopharyngeal-type undifferentiated carcinoma (PSNPC) is an even rarer tumor that has not been adequately reported. Both tumors have been reported to be associated with Epstein-Barr virus (EBV). We studied the clinicopathologic features and EBV status of 36 SNUC and 13 PSNPC patients from Taiwan, an EBV endemic area. The median age of SNUC patients was 53 years (range 20-76 years), with a male/female ratio of approximately 2:1. Five patients had histories of previous nasopharyngeal carcinoma treated with irradiation 6-26 years earlier. The most common locations were nasal cavity and ethmoid sinus. Orbital and intracranial invasion and distant metastasis were frequent findings. The median survival was 10 months. All 36 tumors were negative for EBER-1 by in situ hybridization. The median age of PSNPC patients was 58 years (range 36-75 years), with a male/female ratio of approximately 2:1. The most common location is nasal cavity. Eight patients achieved disease-free survival. Eight tumors had the morphology of lymphoepithelioma, whereas significant inflammatory infiltrate was not detected in the other five tumors. All 13 tumors were positive for EBER-1 by in situ hybridization. Because of the difference in the relation with EBV, prognosis, and response to radiotherapy, SNUC and PSNPC should be considered as two entirely different entities. The most important criteria for PSNPC are vesicular nuclei, syncytial pattern, spindle cells, and absence of necrosis. PMID:11859210
Jeng, Yung-Ming; Sung, Ming-Tse; Fang, Chia-Lang; Huang, Hsuan-Ying; Mao, Tsui-Lien; Cheng, Wei; Hsiao, Cheng-Hsiang
Kernel Mixture Survival Models for Identifying Cancer Subtypes, Predicting Patient's Cancer Types and Survival Probabilities
One important application of microarray gene expression data is to study the relationship between the clinical phenotype of cancer patients and gene expression profiles on the whole-genome scale. The clinical phenotype includes several different types of cancers, survival times, relapse times, drug responses and so on. Under the situation that the subtypes of cancer have not been previously identified or
Tomohiro Ando; Seiya Imoto; Satoru Miyano
Biased Signaling of the Angiotensin II Type 1 Receptor Can Be Mediated through Distinct Mechanisms
Background Seven transmembrane receptors (7TMRs) can adopt different active conformations facilitating a selective activation of either G protein or ?-arrestin-dependent signaling pathways. This represents an opportunity for development of novel therapeutics targeting selective biological effects of a given receptor. Several studies on pathway separation have been performed, many of these on the Angiotensin II type 1 receptor (AT1R). It has been shown that certain ligands or mutations facilitate internalization and/or recruitment of ?-arrestins without activation of G proteins. However, the underlying molecular mechanisms remain largely unresolved. For instance, it is unclear whether such selective G protein-uncoupling is caused by a lack of ability to interact with G proteins or rather by an increased ability of the receptor to recruit ?-arrestins. Since uncoupling of G proteins by increased ability to recruit ?-arrestins could lead to different cellular or in vivo outcomes than lack of ability to interact with G proteins, it is essential to distinguish between these two mechanisms. Methodology/Principal Findings We studied five AT1R mutants previously published to display pathway separation: D74N, DRY/AAY, Y292F, N298A, and Y302F (Ballesteros-Weinstein numbering: 2.50, 3.49–3.51, 7.43, 7.49, and 7.53). We find that D74N, DRY/AAY, and N298A mutants are more prone to ?-arrestin recruitment than WT. In contrast, receptor mutants Y292F and Y302F showed impaired ability to recruit ?-arrestin in response to Sar1-Ile4-Ile8 (SII) Ang II, a ligand solely activating the ?-arrestin pathway. Conclusions/Significance Our analysis reveals that the underlying conformations induced by these AT1R mutants most likely represent principally different mechanisms of uncoupling the G protein, which for some mutants may be due to their increased ability to recruit ?-arrestin2. Hereby, these findings have important implications for drug discovery and 7TMR biology and illustrate the necessity of uncovering the exact molecular determinants for G protein-coupling and ?-arrestin recruitment, respectively.
Bonde, Marie Mi; Hansen, Jonas Tind; Sanni, Samra Joke; Hauns?, Stig; Gammeltoft, Steen; Lyngs?, Christina; Hansen, Jakob Lerche
Use of fission gas release characteristics to identify type of fuel element failure in LMRs
The performance of liquid-metal reactor (LMR) metal fuel elements has been studied at the Experimental Breeder Reactor II (EBR-II) for >25 yr and valuable fission gas (FG) data have been accumulated from the very occasional fuel element failure. In addition, the run-beyond-clad-breach (RBCB) performance of metal fuel has been specifically studied since 1986. From May 1986 to the present, archived data were obtained from the data acquisition system at EBR-II with the specific intention of studying the FG release behavior of different types of metal fuel breaches. The slope of natural logarithm of release to birth ratio versus the logarithm of decay constant of seven FG isotopes (i.e., {sup 85m}Kr, {sup 87}Kr, {sup 88}Kr, {sup 133}Xe, {sup 135}Xe, {sup 135m}Xe, {sup 138}Xe) as a function of time along with their activity were calculated and plotted and distinct characteristics were observed for different types of failure, e.g., upper plenum versus fuel column failures. A description of the analytical methods used and a comparison of the FG release behavior of these type types of breach are presented in this paper.
Mikaili, R.; Beck, W.N.; Lambert, J.D.B. (Argonne National Lab., IL (United States))
Implications for the Petrogenesis of Distinct Silicic Magma Types from the Lower Pleistocene Guachipelin Caldera, NW Costa Rica
NASA Astrophysics Data System (ADS)
Lower Pleistocene pyroclastic ash-flow deposits in NW Costa Rica represent sequential eruptions of high-silica (69-79%\\ SiO2) magmas from the Guachipelin Caldera. These high silica eruptions are not common in areas void of continental crust. The stratigraphic order of seven distinct units is identified by primary mineralogy and bulk chemical composition. Initial distinctions among separate stratigraphic units are defined based on pumice size, mineralogy, physical breaks, and color. First, six major units are identified based on field observations including mineralogy: glomerophyric plagioclase-amphibole (GPA), white biotite (WB), pink biotite (PB), amphibole (A), green unit rich in amphibole (GA), and plagioclase (PR). Further subdivisions are characterized by discrete chemical heterogeneities of trace elements within the macroscopic units. Most of the units identified in the field also have discrete ratios of trace elements (e.g. Nb/Ta): GPA (13.3-19.3), WB (7.6-14.6), PB (3.8-5.0), GA: (23.4-29.4); PR: (7.2-10.4). The amphibole unit (A) is the only one that presents two discrete ranges (6.5-9.5 and 11.5-13.0), which can be interpreted as an indication that the pumice fragments belong to two distinct units instead of one. These collective variations within the sequence provide the basis for petrogenetic interpretation. Differences in the incompatible element ratios behavior are consistent with partial melting (or melt segregation) of several different sources and/or partial melting of same source crust at varying degrees. Melt segregation (partial melting) from several different sources would require a complex plumbing system linking spatially distant crustal sources to a single shallow magma chamber or multiple magma chambers in the same area. In contrast, varying degrees of partial melting from a single crustal source could provide magma for recharge into a shallow chamber from a central conduit re-tapping the same source periodically. Considering the temporal (<0.5Ma) and spatial (single caldera) constraints of this sequence of eruptions, significant chemical variations of the magmas have occurred, which require processes to operate on relatively short time scales.
Deering, C. D.; Vogel, T. A.; Patino, L. C.; Alvarado, G. E.
Potential of infrared spectroscopy in combination with extended canonical variate analysis for identifying different paper types
NASA Astrophysics Data System (ADS)
The increasing use of secondary fiber in papermaking has led to the production of paper containing a wide range of contaminants. Wastepaper mills need to develop quality control methods for evaluating the incoming wastepaper stock as well as testing the specifications of the final product. The goal of this work is to present a fast and successful methodology for identifying different paper types. In this way, undesirable paper types can be refused, thus improving the runnability of the paper machine and the quality of the paper manufactured. In this work we examine various types of paper using information obtained by an appropriate chemometric treatment of infrared spectral data. For this purpose, we studied a large number of paper sheets of three different types (namely coated, offset and cast-coated) supplied by several paper manufacturers. We recorded Fourier transform infrared (FTIR) spectra with the aid of an attenuated total reflectance (ATR) module and near-infrared (NIR) reflectance spectra by means of fiber optics. Both techniques proved expeditious and required no sample pretreatment. The primary objective of this work was to develop a methodology for the accurate identification of samples of different paper types. For this purpose, we used the chemometric discrimination technique extended canonical variate analysis (ECVA) in combination with the k nearest neighbor (kNN) method to classify samples in the prediction set. Use of the NIR and FTIR techniques under these conditions allowed paper types to be identified with 100% success in prediction samples.
Riba, Jordi-Roger; Canals, Trini; Cantero, Rosa; Iturriaga, Hortensia
Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Microarray data from cell lines of Non-Small Cell Lung Carcinoma (NSCLC) can be used to look for differences in gene expression between the cell lines derived from different tumour samples, and to investigate if these differences can be used to cluster the cell lines into distinct groups. Dividing the cell lines into classes can help to improve diagnosis and the development of screens for new drug candidates. The micro-array data is first subjected to quality control analysis and then subsequently normalised using three alternate methods to reduce the chances of differences being artefacts resulting from the normalisation process. The final clustering into sub-classes was carried out in a conservative manner such that sub-classes were consistent across all three normalisation methods. If there is structure in the cell line population it was expected that this would agree with histological classifications, but this was not found to be the case. To check the biological consistency of the sub-classes the set of most strongly differentially expressed genes was be identified for each pair of clusters to check if the genes that most strongly define sub-classes have biological functions consistent with NSCLC.
Dalby, Andrew R.; Emam, Ibrahim; Franke, Raimo
Integrated Genome-wide DNA Copy Number and Expression Analysis Identifies Distinct Mechanisms of Primary Chemo-resistance in Ovarian Carcinomas
Purpose A significant number of women with serous ovarian cancer are intrinsically refractory to platinum-taxol based treatment. We analyzed somatic DNA copy number variation (CNV) and gene expression data to identify key mechanisms associated with primary resistance in advanced-stage serous cancers. Experimental Design Genome-wide CNV was measured in 118 ovarian tumors using high-resolution oligonucleotide microarrays. A well-defined subset of 85 advanced-stage serous tumors was then used to relate CNV to primary resistance to treatment. The discovery-based approach was complemented by quantitative-PCR copy number analysis of twelve candidate genes as independent validation of previously reported associations with clinical outcome. Likely CNV targets and tumor molecular subtypes were further characterized by gene expression profiling. Results Amplification of 19q12, containing Cyclin E (CCNE1) and 20q11.22-q13.12, mapping immediately adjacent to the steroid receptor co-activator NCOA3, were significantly associated with poor response to primary treatment. Other genes previously associated with CNV and clinical outcome in ovarian cancer were not associated with primary treatment resistance. Chemoresistant tumors with high CCNE1 copy number and protein expression were associated with increased cellular proliferation but so too were a subset of treatment responsive patients, suggesting a cell-cycle independent role for CCNE1 in modulating chemoresponse. Patients with a poor clinical outcome without CCNE1 amplification over expressed genes involved in extracellular matrix deposition. Conclusions We have identified two distinct mechanisms of primary treatment failure in serous ovarian cancer, involving CCNE1 amplification and enhanced extracellular matrix deposition. CCNE1 copy number is validated as a dominant marker of patient outcome in ovarian cancer.
Etemadmoghadam, Dariush; deFazio, Anna; Beroukhim, Rameen; Mermel, Craig; George, Joshy; Getz, Gaddy; Tothill, Richard; Okamoto, Aikou; Raeder, Maria B; Harnett, Paul; Lade, Stephen; Akslen, Lars A; Tinker, Anna; Locandro, Bianca; Alsop, Kathryn; Chiew, Yoke-Eng; Traficante, Nadia; Fereday, Sian; Johnson, Daryl; Fox, Stephen; Sellers, William; Urashima, Mitsuyoshi; Salvesen, Helga B; Meyerson, Matthew; Bowtell, David
Fourier Transform Infrared Imaging and Infrared Fiber Optic Probe Spectroscopy Identify Collagen Type in Connective Tissues
Hyaline cartilage and mechanically inferior fibrocartilage consisting of mixed collagen types are frequently found together in repairing articular cartilage. The present study seeks to develop methodology to identify collagen type and other tissue components using Fourier transform infrared (FTIR) spectral evaluation of matrix composition in combination with multivariate analyses. FTIR spectra of the primary molecular components of repair cartilage, types I and II collagen, and aggrecan, were used to develop multivariate spectral models for discrimination of the matrix components of the tissues of interest. Infrared imaging data were collected from bovine bone, tendon, normal cartilage, meniscus and human repair cartilage tissues, and composition predicted using partial least squares analyses. Histology and immunohistochemistry results were used as standards for validation. Infrared fiber optic probe spectral data were also obtained from meniscus (a tissue with mixed collagen types) to evaluate the potential of this method for identification of collagen type in a minimally-invasive clinical application. Concentration profiles of the tissue components obtained from multivariate analysis were in excellent agreement with histology and immunohistochemistry results. Bone and tendon showed a uniform distribution of predominantly type I collagen through the tissue. Normal cartilage showed a distribution of type II collagen and proteoglycan similar to the known composition, while in repair cartilage, the spectral distribution of both types I and II collagen were similar to that observed via immunohistochemistry. Using the probe, the outer and inner regions of the meniscus were shown to be primarily composed of type I and II collagen, respectively, in accordance with immunohistochemistry data. In summary, multivariate analysis of infrared spectra can indeed be used to differentiate collagen type I and type II, even in the presence of proteoglycan, in connective tissues, using both imaging and fiber optic methodology. This has great potential for clinical in situ applications for monitoring tissue repair.
Hanifi, Arash; McCarthy, Helen; Roberts, Sally; Pleshko, Nancy
Characterization of a Newly Identified Mycoplasma (Mycoplasma orale Type 3) from the Human Oropharynx
Six mycoplasma strains, isolated under anaerobic conditions from the human oropharynx, were studied by biologic and serologic means. The strains produced nippled colonies with weak hemolytic activity for guinea pig erythrocytes on agar medium. In addition, the strains metabolized arginine with a concomitant alkaline shift in the pH of the medium but did not produce a pH shift when grown in the presence of glucose or urea. The strains failed to reduce 2–3–5 triphenyl tetrazolium and were inhibited by 0.001% methylene blue. In addition, they required fresh yeast extract for growth. When compared by several serologic methods, the strains were found to be related to each other but distinct from 23 serotypes of human, animal, and avian origin. However, one-way serologic relationships between one of the new strains and Mycoplasma orale type 1 and M. salivarium were observed when they were tested by complement fixation. Furthermore, partial relationship of one of the new strains to all of the arginine-utilizing mycoplasma species of human origin was demonstrated with the agar gel diffusion technique. Thus, the new strains appear to constitute a new mycoplasma species, for which the name M. orale type 3 is tentatively proposed. M. orale type 3 accounted for 1.4% of 437 mycoplasma isolates from the oropharynx of adults. The new species probably is a rare member of the normal mycoplasmal flora of man. Images
Fox, H.; Purcell, R. H.; Chanock, R. M.
Localization of GABA-A receptor alpha subunits on neurochemically distinct cell types in the rat locus coeruleus.
The locus coeruleus (LC) provides the major source of noradrenaline to the central nervous system and is modulated by neurochemically diverse afferents. LC function is central to arousal, memory, cognition and the stress response, with dysfunction of the LC-noradrenergic axis implicated in debilitating psychiatric disorders. The precise targeting of neurotransmitter receptors within the LC is essential for processing the information contained in diverse afferents and thus LC output. The inhibitory modulation of LC neurons is thought to be effected mainly through GABA-A receptors (GABA(A)Rs). Diverse GABA(A)Rs are pentameric complexes assembled from a repertoire of subunits resulting in substantial diversity in their molecular, functional and pharmacological properties throughout the brain. The precise location of distinct GABA(A) R subunits in subregions of the LC, and the neurochemical identity of the cells that express them, remains to be determined. Here, we show that the GABA(A)R alpha1 subunit is expressed exclusively in neurochemically and morphologically diverse non-noradrenergic cell types within the LC, which may innervate the principal noradrenergic cells. Thus, the GABA(A)R alpha1 subunit could provide a neurochemical signature for a pool of local circuit interneurons in the LC. In contrast, non-overlapping GABA(A)R alpha2 and alpha3 subunit-immunoreactive puncta were enriched on noradrenergic dendrites and, to a lesser extent, on somata. The study reveals a cell-type- and domain-specific expression pattern of distinct GABA(A)R subunits in the LC. These data will serve as a template for understanding inhibitory modulation of this region and facilitate more directed pharmacological strategies for disorders arising from the impairment of LC function. PMID:21692880
Corteen, Nicole L; Cole, Tomilola M; Sarna, Ayshia; Sieghart, Werner; Swinny, Jerome D
The LIM and POU homeobox genes ttx-3 and unc-86 act as terminal selectors in distinct cholinergic and serotonergic neuron types
Transcription factors that drive neuron type-specific terminal differentiation programs in the developing nervous system are often expressed in several distinct neuronal cell types, but to what extent they have similar or distinct activities in individual neuronal cell types is generally not well explored. We investigate this problem using, as a starting point, the C. elegans LIM homeodomain transcription factor ttx-3, which acts as a terminal selector to drive the terminal differentiation program of the cholinergic AIY interneuron class. Using a panel of different terminal differentiation markers, including neurotransmitter synthesizing enzymes, neurotransmitter receptors and neuropeptides, we show that ttx-3 also controls the terminal differentiation program of two additional, distinct neuron types, namely the cholinergic AIA interneurons and the serotonergic NSM neurons. We show that the type of differentiation program that is controlled by ttx-3 in different neuron types is specified by a distinct set of collaborating transcription factors. One of the collaborating transcription factors is the POU homeobox gene unc-86, which collaborates with ttx-3 to determine the identity of the serotonergic NSM neurons. unc-86 in turn operates independently of ttx-3 in the anterior ganglion where it collaborates with the ARID-type transcription factor cfi-1 to determine the cholinergic identity of the IL2 sensory and URA motor neurons. In conclusion, transcription factors operate as terminal selectors in distinct combinations in different neuron types, defining neuron type-specific identity features.
Zhang, Feifan; Bhattacharya, Abhishek; Nelson, Jessica C.; Abe, Namiko; Gordon, Patricia; Lloret-Fernandez, Carla; Maicas, Miren; Flames, Nuria; Mann, Richard S.; Colon-Ramos, Daniel A.; Hobert, Oliver
The LIM and POU homeobox genes ttx-3 and unc-86 act as terminal selectors in distinct cholinergic and serotonergic neuron types.
Transcription factors that drive neuron type-specific terminal differentiation programs in the developing nervous system are often expressed in several distinct neuronal cell types, but to what extent they have similar or distinct activities in individual neuronal cell types is generally not well explored. We investigate this problem using, as a starting point, the C. elegans LIM homeodomain transcription factor ttx-3, which acts as a terminal selector to drive the terminal differentiation program of the cholinergic AIY interneuron class. Using a panel of different terminal differentiation markers, including neurotransmitter synthesizing enzymes, neurotransmitter receptors and neuropeptides, we show that ttx-3 also controls the terminal differentiation program of two additional, distinct neuron types, namely the cholinergic AIA interneurons and the serotonergic NSM neurons. We show that the type of differentiation program that is controlled by ttx-3 in different neuron types is specified by a distinct set of collaborating transcription factors. One of the collaborating transcription factors is the POU homeobox gene unc-86, which collaborates with ttx-3 to determine the identity of the serotonergic NSM neurons. unc-86 in turn operates independently of ttx-3 in the anterior ganglion where it collaborates with the ARID-type transcription factor cfi-1 to determine the cholinergic identity of the IL2 sensory and URA motor neurons. In conclusion, transcription factors operate as terminal selectors in distinct combinations in different neuron types, defining neuron type-specific identity features. PMID:24353061
Zhang, Feifan; Bhattacharya, Abhishek; Nelson, Jessica C; Abe, Namiko; Gordon, Patricia; Lloret-Fernandez, Carla; Maicas, Miren; Flames, Nuria; Mann, Richard S; Colón-Ramos, Daniel A; Hobert, Oliver
A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene
Type 1 diabetes (T1D) in children results from autoimmune destruction of pancreatic beta cells, leading to insufficient production of insulin. A number of genetic determinants of T1D have already been established through candidate gene studies, primarily within the major histocompatibility complex but also within other loci. To identify new genetic factors that increase the risk of T1D, we performed a
Hakon Hakonarson; Struan F. A. Grant; Jonathan P. Bradfield; Luc Marchand; Cecilia E. Kim; Joseph T. Glessner; Rosemarie Grabs; Tracy Casalunovo; Shayne P. Taback; Edward C. Frackelton; Margaret L. Lawson; Luke J. Robinson; Robert Skraban; Yang Lu; Rosetta M. Chiavacci; Charles A. Stanley; Susan E. Kirsch; Eric F. Rappaport; Jordan S. Orange; Dimitri S. Monos; Marcella Devoto; Hui-Qi Qu; Constantin Polychronakos
The use of four band multispectral photography to identify forest cover types
NASA Technical Reports Server (NTRS)
Four-band multispectral aerial photography and a color additive viewer were employed to identify forest cover types in Northern Alabama. The multispectral photography utilized the blue, green, red and near-infrared spectral regions and was made with black and white infrared film. On the basis of color differences alone, a differentiation between conifers and hardwoods was possible; however, supplementary information related to forest ecology proved necessary for the differentiation of various species of pines and hardwoods.
Downs, S. W., Jr.
Transcriptome Profiling Identifies Candidate Genes Associated with the Accumulation of Distinct Sulfur ?-Glutamyl Dipeptides in Phaseolus vulgaris and Vigna mungo Seeds.
Common bean (Phaseolus vulgaris) and black gram (Vigna mungo) accumulate ?-Glutamyl-S-methylcysteine and ?-Glutamyl-methionine in seed, respectively. Transcripts were profiled by 454 pyrosequencing data at a similar developmental stage coinciding with the beginning of the accumulation of these metabolites. Expressed sequence tags were assembled into Unigenes, which were assigned to specific genes in the early release chromosomal assembly of the P. vulgaris genome. Genes involved in multiple sulfur metabolic processes were expressed in both species. Expression of Sultr3 members was predominant in P. vulgaris, whereas expression of Sultr5 members predominated in V. mungo. Expression of the cytosolic SERAT1;1 and -1;2 was approximately fourfold higher in P. vulgaris while expression of the plastidic SERAT2;1 was twofold higher in V. mungo. Among BSAS family members, BSAS4;1, encoding a cytosolic cysteine desulfhydrase, and BSAS1;1, encoding a cytosolic O-acetylserine sulphydrylase were most highly expressed in both species. This was followed by BSAS3;1 encoding a plastidic ?-cyanoalanine synthase which was more highly expressed by 10-fold in P. vulgaris. The data identify BSAS3;1 as a candidate enzyme for the biosynthesis of S-methylcysteine through the use of methanethiol as substrate instead of cyanide. Expression of GLC1 would provide a complete sequence leading to the biosynthesis of ?-Glutamyl-S-methylcysteine in plastids. The detection of S-methylhomoglutathione in P. vulgaris suggested that homoglutathione synthetase may accept, to some extent, ?-Glutamyl-S-methylcysteine as substrate, which might lead to the formation of S-methylated phytochelatins. In conclusion, 454 sequencing was effective at revealing differences in the expression of sulfur metabolic genes, providing information on candidate genes for the biosynthesis of distinct sulfur amino acid ?-Glutamyl dipeptides between P. vulgaris and V. mungo. PMID:23532826
Liao, Dengqun; Cram, Dustin; Sharpe, Andrew G; Marsolais, Frédéric
Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans
Candida albicans is the most common human fungal pathogen causing mucosal and systemic infections. However, human antifungal immunity remains poorly defined. Here, by integrating transcriptional analysis and functional genomics, we identified Candida-specific host defense mechanisms in humans. Candida induced significant expression of genes from the type I interferon (IFN) pathway in human peripheral blood mononuclear cells. This unexpectedly prominent role of type I IFN pathway in anti-Candida host defense was supported by additional evidence. Polymorphisms in type I IFN genes modulated Candida-induced cytokine production and were correlated with susceptibility to systemic candidiasis. In in-vitro experiments, type I IFNs skewed Candida-induced inflammation from a Th17-response toward a Th1-response. Patients with chronic mucocutaneaous candidiasis displayed defective expression of genes in the type I IFN pathway. These findings indicate that the type I IFN pathway is a main signature of Candida-induced inflammation and plays a crucial role in anti-Candida host defense in humans.
Smeekens, Sanne P.; Ng, Aylwin; Kumar, Vinod; Johnson, Melissa D.; Plantinga, Theo S.; van Diemen, Cleo; Arts, Peer; Verwiel, Eugene T.P.; Gresnigt, Mark S.; Fransen, Karin; van Sommeren, Suzanne; Oosting, Marije; Cheng, Shih-Chin; Joosten, Leo A.B.; Hoischen, Alexander; Kullberg, Bart-Jan; Scott, William K.; Perfect, John R.; van der Meer, Jos W.M.; Wijmenga, Cisca; Netea, Mihai G.; Xavier, Ramnik J.
On Identifying Clusters Within the C-type Asteroids of the Sloan Digital Sky Survey
NASA Astrophysics Data System (ADS)
We applied AutoClass, a data mining technique based upon Bayesian Classification, to C-group asteroid colors in the Sloan Digital Sky Survey (SDSS). Previous taxonomic studies relied mostly on Principal Component Analysis (PCA) to differentiate asteroids within the C-group (e.g. B, G, F, Ch, Cg and Cb). AutoClass's advantage is that it calculates the most probable classification for us, removing the human factor from this part of the analysis. In our results, AutoClass divided the C-groups into two large classes and six smaller classes. The two large classes (n=4974 and 2033, respectively) display distinct regions with some overlap in color-vs-color plots. Each cluster's average spectrum is compared to 'typical' spectra of the C-group subtypes as defined by Tholen (1989) and each cluster's members are evaluated for consistency with previous taxonomies. Of the 117 asteroids classified as B-type in previous taxonomies, only 12 were found with SDSS colors that matched our criteria of having less than 0.1 magnitude error in u and 0.05 magnitude error in g, r, i, and z colors. Although this is a relatively small group, 11 of the 12 B-types were placed by AutoClass in the same cluster. By determining the C-group sub-classifications in the large SDSS database, this research furthers our understanding of the stratigraphy and composition of the main-belt.
Poole, Renae; Ziffer, J.; Harvell, T.
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features
Gene expression is determined by genomic elements called enhancers, which contain short motifs bound by different transcription factors (TFs). However, how enhancer sequences and TF motifs relate to enhancer activity is unknown, and general sequence requirements for enhancers or comprehensive sets of important enhancer sequence elements have remained elusive. Here, we computationally dissect thousands of functional enhancer sequences from three different Drosophila cell lines. We find that the enhancers display distinct cis-regulatory sequence signatures, which are predictive of the enhancers' cell type-specific or broad activities. These signatures contain transcription factor motifs and a novel class of enhancer sequence elements, dinucleotide repeat motifs (DRMs). DRMs are highly enriched in enhancers, particularly in enhancers that are broadly active across different cell types. We experimentally validate the importance of the identified TF motifs and DRMs for enhancer function and show that they can be sufficient to create an active enhancer de novo from a nonfunctional sequence. The function of DRMs as a novel class of general enhancer features that are also enriched in human regulatory regions might explain their implication in several diseases and provides important insights into gene regulation.
Yanez-Cuna, J. Omar; Arnold, Cosmas D.; Stampfel, Gerald; Boryn, Lukasz M.; Gerlach, Daniel; Rath, Martina; Stark, Alexander
Proteomic alterations of distinct mitochondrial subpopulations in the type 1 diabetic heart: contribution of protein import dysfunction.
Diabetic cardiomyopathy is associated with increased risk of heart failure in type 1 diabetic patients. Mitochondrial dysfunction is suggested as an underlying contributor to diabetic cardiomyopathy. Cardiac mitochondria are characterized by subcellular spatial locale, including mitochondria located beneath the sarcolemma, subsarcolemmal mitochondria (SSM), and mitochondria situated between the myofibrils, interfibrillar mitochondria (IFM). The goal of this study was to determine whether type 1 diabetic insult in the heart influences proteomic make-up of spatially distinct mitochondrial subpopulations and to evaluate the role of nuclear encoded mitochondrial protein import. Utilizing multiple proteomic approaches (iTRAQ and two-dimensional-differential in-gel electrophoresis), IFM proteomic make-up was impacted by type 1 diabetes mellitus to a greater extent than SSM, as evidenced by decreased abundance of fatty acid oxidation and electron transport chain proteins. Mitochondrial phosphate carrier and adenine nucleotide translocator, as well as inner membrane translocases, were decreased in the diabetic IFM (P < 0.05 for both). Mitofilin, a protein involved in cristae morphology, was diminished in the diabetic IFM (P < 0.05). Posttranslational modifications, including oxidations and deamidations, were most prevalent in the diabetic IFM. Mitochondrial heat shock protein 70 (mtHsp70) was significantly decreased in diabetic IFM (P < 0.05). Mitochondrial protein import was decreased in the diabetic IFM with no change in the diabetic SSM (P < 0.05). Taken together, these results indicate that mitochondrial proteomic alterations in the type 1 diabetic heart are more pronounced in the IFM. Further, proteomic alterations are associated with nuclear encoded mitochondrial protein import dysfunction and loss of an essential mitochondrial protein import constituent, mtHsp70, implicating this process in the pathogenesis of the diabetic heart. PMID:21048079
Baseler, Walter A; Dabkowski, Erinne R; Williamson, Courtney L; Croston, Tara L; Thapa, Dharendra; Powell, Matthew J; Razunguzwa, Trust T; Hollander, John M
Insulin resistance in skeletal muscle and adipose tissue in polycystic ovary syndrome: are the molecular mechanisms distinct from type 2 diabetes?
The association of polycystic ovary syndrome (PCOS) with insulin resistance was recognized almost three decades ago. Despite the pivotal role of insulin resistance in the pathogenesis of PCOS, the precise cellular and molecular mechanisms of impaired insulin action remain elusive. This review has two aims: 1) to review the mechanisms of insulin resistance, specifically impaired insulin-stimulated glucose transport, in skeletal muscle and adipose tissue in PCOS, and 2) to assess whether mechanisms of insulin resistance in PCOS are distinct from those in type 2 diabetes. As in type 2 diabetes, studies in skeletal muscle in PCOS support the existence of intrinsic defects in insulin signalling but also underscore the importance of in vivo environmental factors for the development of insulin resistance. In PCOS and type 2 diabetes, similar insulin signalling defects in muscle have been described i.e. impaired signalling via IRS-1 and up-regulation of ERK signalling. Similar defects in insulin signalling have also been described in adipose tissue in PCOS and type 2 diabetes, but data are limited. As for type 2 diabetes, PCOS is characterized by chronic inflammation, mitochondrial dysfunction and cellular stress. Androgen excess, a key feature of PCOS, has a genetic component: the relationship of hyperandrogenemia to the development of insulin resistance requires further study. In conclusion, although similar insulin signalling defects have been identified in muscle and adipose tissue in PCOS and type 2 diabetes, these defects probably reflect a common final pathway resulting from genetic and environmental influences on insulin action that are unique to each disorder. PMID:19078869
Corbould, A
Distinct cell types control lymphoid subset development by means of IL-15 and IL-15 receptor ? expression
IL-15 and the IL-15 receptor (IL-15R)? chain are essential for normal development of naive CD8 T cells, intestinal intraepithelial lymphocytes (IEL), and natural killer (NK)/NK/T cells. However, whether IL-15R? expression by these subsets is necessary for their production and which cell type needs to produce IL-15 to drive development are unknown. We analyzed the requirements for IL-15 and IL-15R? expression by bone marrow-derived or parenchymal cells for mediating lymphocyte subset development. Naive CD8 T cell development required IL-15R? expression by both bone marrow-derived and parenchymal cells, whereas memory-phenotype CD8 T cells required IL-15R? expression only by hematopoietic cells. In contrast and surprisingly, the development of IEL subsets, particularly CD8??Thy1–V?5+ T cell antigen receptor ?? and the CD8?? Thy1– T cell antigen receptor ?? IEL populations, depended completely on parenchymal cell expression of IL-15R? and IL-15 but not IL-15R?. In the case of NK and NK/T cell generation and maturation, expression of IL-15 and IL-15R? by both parenchymal and hematopoietic cells was important, although the latter played the greatest role. These results demonstrated dichotomous mechanisms by which IL-15 regulated lymphoid development, interacting with distinct cell types depending on the developmental pathway.
Schluns, Kimberly S.; Nowak, Elizabeth C.; Cabrera-Hernandez, Arturo; Puddington, Lynn; Lefrancois, Leo; Aguila, Hector L.
Expression of hepatocyte growth factor activator inhibitor type 2 (HAI-2) in human testis: identification of a distinct transcription start site for the HAI-2 gene in testis.
Hepatocyte growth factor activator inhibitor type 1 (HAI-1) and type 2 (HAI-2) are recently identified integral membrane Kunitz-type proteinase inhibitors. They have important regulatory roles in pericellular activation of hepatocyte growth factor/scatter factor (HGF/SF) which is critically involved in the development and regeneration of various tissues. Recent reports suggest that HGF/SF is also involved in testicular development and spermatogenesis. In this study, we analyzed the expression of HAIs in the testis. In human testis, HAI-2 was strongly expressed whereas HAI-1 mRNA was hardly detectable. Of interest was the observation that the mRNA size of HAI-2 was shorter in the testis (1.2 kb) than those in the other tissues such as placenta (1.5 kb). Subsequent experiments revealed that there are two major transcription start sites of the HAI-2 gene, which are -30 bp and -360 bp upstream from the translation initiation ATG codon. Although the latter site appeared to be mainly used in the placenta and other non-testicular organs, only the former site is used in testis, resulting in the -300 bp shorter mRNA. An immunohistochemical study using a specific monoclonal antibody raised against human HAI-2 protein indicated that HAI-2 is expressed exclusively in primary spermatocytes. These results suggest a distinct regulation of HAI-2 gene expression in testis and that HAI-2 may play a role in the process of spermatogenesis. PMID:12553733
Yamauchi, Masamichi; Itoh, Hiroshi; Naganuma, Seiji; Koono, Masashi; Hasui, Yoshihiro; Osada, Yukio; Kataoka, Hiroaki
Toward a theory of distinct types of "impulsive" behaviors: A meta-analysis of self-report and behavioral measures.
Impulsivity is considered a personality trait affecting behavior in many life domains, from recreational activities to important decision making. When extreme, it is associated with mental health problems, such as substance use disorders, as well as with interpersonal and social difficulties, including juvenile delinquency and criminality. Yet, trait impulsivity may not be a unitary construct. We review commonly used self-report measures of personality trait impulsivity and related constructs (e.g., sensation seeking), plus the opposite pole, control or constraint. A meta-analytic principal-components factor analysis demonstrated that these scales comprise 3 distinct factors, each of which aligns with a broad, higher order personality factor-Neuroticism/Negative Emotionality, Disinhibition versus Constraint/Conscientiousness, and Extraversion/Positive Emotionality/Sensation Seeking. Moreover, Disinhibition versus Constraint/Conscientiousness comprise 2 correlated but distinct subfactors: Disinhibition versus Constraint and Conscientiousness/Will versus Resourcelessness. We also review laboratory tasks that purport to measure a construct similar to trait impulsivity. A meta-analytic principal-components factor analysis demonstrated that these tasks constitute 4 factors (Inattention, Inhibition, Impulsive Decision-Making, and Shifting). Although relations between these 2 measurement models are consistently low to very low, relations between both trait scales and laboratory behavioral tasks and daily-life impulsive behaviors are moderate. That is, both independently predict problematic daily-life impulsive behaviors, such as substance use, gambling, and delinquency; their joint use has incremental predictive power over the use of either type of measure alone and furthers our understanding of these important, problematic behaviors. Future use of confirmatory methods should help to ascertain with greater precision the number of and relations between impulsivity-related components. PMID:24099400
Sharma, Leigh; Markon, Kristian E; Clark, Lee Anna
ISCCP Cloud Properties Associated with Standard Cloud Types Identified in Individual Surface Observations
NASA Technical Reports Server (NTRS)
Individual surface weather observations from land stations and ships are compared with individual cloud retrievals of the International Satellite Cloud Climatology Project (ISCCP), Stage C1, for an 8-year period (1983-1991) to relate cloud optical thicknesses and cloud-top pressures obtained from satellite data to the standard cloud types reported in visual observations from the surface. Each surface report is matched to the corresponding ISCCP-C1 report for the time of observation for the 280x280-km grid-box containing that observation. Classes of the surface reports are identified in which a particular cloud type was reported present, either alone or in combination with other clouds. For each class, cloud amounts from both surface and C1 data, base heights from surface data, and the frequency-distributions of cloud-top pressure (p(sub c) and optical thickness (tau) from C1 data are averaged over 15-degree latitude zones, for land and ocean separately, for 3-month seasons. The frequency distribution of p(sub c) and tau is plotted for each of the surface-defined cloud types occurring both alone and with other clouds. The average cloud-top pressures within a grid-box do not always correspond well with values expected for a reported cloud type, particularly for the higher clouds Ci, Ac, and Cb. In many cases this is because the satellites also detect clouds within the grid-box that are outside the field of view of the surface observer. The highest average cloud tops are found for the most extensive cloud type, Ns, averaging 7 km globally and reaching 9 km in the ITCZ. Ns also has the greatest average retrieved optical thickness, tau approximately equal 20. Cumulonimbus clouds may actually attain far greater heights and depths, but do not fill the grid-box. The tau-p(sub c) distributions show features that distinguish the high, middle, and low clouds reported by the surface observers. However, the distribution patterns for the individual low cloud types (Cu, Sc, St) occurring alone overlap to such an extent that it is not possible to distinguish these cloud types from each other on the basis of tau-p(sub c) values alone. Other cloud types whose tau-p(sub c) distributions are indistinguishable are Cb, Ns, and thick As. However, the tau-p(sub c) distribution patterns for the different low cloud types are nevertheless distinguishable when all occurrences of a low cloud type are included, indicating that the different low types differ in their probabilities of co-occurrence with middle and high clouds.
Hahn, Carole J.; Rossow, William B.; Warren, Stephen G.
Laterally projecting cerebrospinal fluid-contacting cells in the lamprey spinal cord are of two distinct types.
Cerebrospinal fluid-contacting (CSF-c) cells are found in all vertebrates, but their function remains elusive. In the lamprey spinal cord, they surround the central canal and some have processes passing the gray matter to the lateral edge of the flattened spinal cord. Stimulation of CSF-c cells at the central canal elicits GABAergic inhibitory postsynaptic potentials (IPSPs) in intraspinal stretch receptor neurons (edge cells). Here, we characterize laterally projecting CSF-c cells according to their morphology, phenotype, and neuronal properties by using immunohistochemistry, retrograde tracing, calcium imaging, and whole-cell recordings. We identify two types of CSF-c cells. Type 1 cells have a bulb-like ending that protrudes into the central canal and a lateral process that ramifies ventrolaterally and laterally with a dense plexus surrounding the mechanosensitive dendrites of the edge cells. Most type 1 cells fire spontaneous action potentials that are abolished by tetrodotoxin, and all display spontaneous excitatory postsynaptic potentials and IPSPs that remain in the presence of tetrodotoxin. GABA and somatostatin are colocalized in type 1 cells, and they express both GABA and glutamate receptors. Type 2 cells, on the other hand, have a flat ending protruding into the central canal and a laterally projecting process that ramifies only at the lateral edge. These cells show immunoreactivity to taurine, but they do not express GABA or somatostatin, nor do they have any active neuronal properties. Type 2 cells might be a form of glia. Type 1 CSF-c cells are neurons and may play a modulatory role by influencing edge cells and thus the locomotor-related sensory feedback. J. Comp. Neurol. 522:1753-1768, 2014. © 2014 Wiley Periodicals, Inc. PMID:24723248
Jalalvand, Elham; Robertson, Brita; Wallén, Peter; Hill, Russell H; Grillner, Sten
Laterally projecting cerebrospinal fluid-contacting cells in the lamprey spinal cord are of two distinct types.
Cerebrospinal fluid-contacting (CSF-c) cells are found in all vertebrates, but their function remains elusive. In the lamprey spinal cord, they surround the central canal and some have processes passing the gray matter to the lateral edge of the flattened spinal cord. Stimulation of CSF-c cells at the central canal elicits GABAergic inhibitory postsynaptic potentials (IPSPs) in intraspinal stretch receptor neurons (edge cells). Here, we characterize laterally projecting CSF-c cells according to their morphology, phenotype, and neuronal properties by using immunohistochemistry, retrograde tracing, calcium imaging, and whole-cell recordings. We identify two types of CSF-c cells. Type 1 cells have a bulb-like ending that protrudes into the central canal and a lateral process that ramifies ventrolaterally and laterally with a dense plexus surrounding the mechanosensitive dendrites of the edge cells. Most type 1 cells fire spontaneous action potentials that are abolished by tetrodotoxin, and all display spontaneous excitatory postsynaptic potentials and IPSPs that remain in the presence of tetrodotoxin. GABA and somatostatin are colocalized in type 1 cells, and they express both GABA and glutamate receptors. Type 2 cells, on the other hand, have a flat ending protruding into the central canal and a laterally projecting process that ramifies only at the lateral edge. These cells show immunoreactivity to taurine, but they do not express GABA or somatostatin, nor do they have any active neuronal properties. Type 2 cells might be a form of glia. Type 1 CSF-c cells are neurons and may play a modulatory role by influencing edge cells and thus the locomotor-related sensory feedback. J. Comp. Neurol. 522:1753-1768, 2014. © 2014 Wiley Periodicals, Inc. PMID:24436002
Jalalvand, Elham; Robertson, Brita; Wallén, Peter; Hill, Russell H; Grillner, Sten
Mating type idiomorphs from a French population of the wheat pathogen Mycosphaerella graminicola: widespread equal distribution and low but distinct levels of molecular polymorphism.
Septoria tritici blotch caused by the heterothallic ascomycete Mycosphaerella graminicola is currently the most frequent and the most economically damaging disease on wheat worldwide. Five hundred and ten strains of this fungus were sampled from 16 geographical locations representing the major wheat producing areas in France. Multiplex PCR amplification, PCR-RFLP-SSCP screening and sequencing of parts of mating type encoding sequences were performed in order to assess the distribution and molecular polymorphism of the mating type idiomorphs. The two idiomorphs were scored at similar frequencies within all sampled locations. Both mating types were also identified at the leaf spatial scale, on 42% of leaves from which two or three strains were isolated. No correlation was found between distribution of mating types and either host cultivars from which the sampling was carried out or in vitro colony phenotypes observed during the culture of strains on potato dextrose agar (PDA) medium. PCR-RFLP-SSCP assay highlighted only one MAT1-1 strain exhibiting a profile distinct from all other MAT1-1 strains, whereas ten MAT1-2 strains (among which two and four with same profiles, respectively) showed profiles differing from the other MAT1-2 strains. Sequencing revealed that all polymorphisms corresponded to single nucleotide variations and all strains displaying the same single strand conformation polymorphism (SSCP) profiles showed identical nucleotide sequences, thereby confirming the high sensitivity of SSCP. Only two out of the disclosed nucleotide variations were nonsynonymous. This study strongly suggests a large potential for sexual reproduction in the French population of M. graminicola and reports a high conservation of mating type sequences in the fungus at both nucleotide and population levels, with a great difference in molecular variability between the two idiomorphs. PMID:21036342
Siah, Ali; Tisserant, Benoit; El Chartouni, Léa; Duyme, Florent; Deweer, Caroline; Roisin-Fichter, Céline; Sanssené, Jean; Durand, Roger; Reignault, Philippe; Halama, Patrice
Oncomodulin Identifies Different Hair Cell Types in the Mammalian Inner Ear
The tight regulation of Ca2+ is essential for inner ear function, and yet the role of Ca2+ binding proteins (CaBPs) remains elusive. Using immunofluorescence and RT-PCR, we investigated the expression of oncomodulin (Ocm), a member of the parvalbumin family, relative to other EF-hand CaBPs in cochlear and vestibular organs in the mouse. In the mouse cochlea, Ocm is found only in outer hair cells and is localized preferentially to the basolateral outer hair cell membrane and to the base of the hair bundle. Developmentally, Ocm immunoreactivity begins as early as postnatal day (P) 2 and shows preferential localization to the basolateral wall and hair bundle after P8. Unlike the cochlea, Ocm expression is substantially reduced in vestibular tissues at older adult ages. In vestibular organs, Ocm is found in type I striolar or central hair cells, and has a more diffuse subcellular localization throughout the hair cell body. Additionally, Ocm immunoreactivity in vestibular hair cells is present as early as E18 and is not obviously affected by mutations that cause a disruption of hair bundle polarity. We also find Ocm expression in striolar hair cells across mammalian species. These data suggest that Ocm may have distinct functional roles in cochlear and vestibular hair cells.
Simmons, Dwayne D.; Tong, Benton; Schrader, Angela D.; Hawkes, Aubrey J.
A Visual Screen of a GFP-fusion Library Identifies a New Type of Nuclear Envelope Membrane Protein
The nuclear envelope (NE) is a distinct sub- domain of the ER, but few membrane components have been described that are specific to it. We per- formed a visual screen in tissue culture cells to identify proteins targeted to the NE. This approach does not re- quire assumptions about the nature of the association with the NE or the physical
Melissa M. Rolls; Pascal A. Stein; Stephen S. Taylor; Edward Ha; Frank McKeon; Tom A. Rapoport
Distinct roles for the catalytic and hemopexin domains of membrane type 1-matrix metalloproteinase in substrate degradation and cell migration.
Substrate degradation and cell migration are key steps in cancer metastasis. Membrane-type 1-matrix metalloproteinase (MT1-MMP) has been linked with these processes. Using the fluorescein isothiocyanate (FITC)-labeled fibronectin degradation assay combined with the phagokinetic cell migration assay, structure-function relationships of MT1-MMP were studied. Our data indicate that MT1-MMP initiates substrate degradation and enhances cell migration; cell migration occurs as a concurrent but independent event. Using recombinant DNA approaches, we demonstrated that the hemopexin-like domain and a nonenzymatic component of the catalytic domain of MT1-MMP are essential for MT1-MMP-mediated cell migration. Because the cytoplasmic domain of MT1-MMP was not required for MT1-MMP-mediated fibronectin degradation and cell migration, it is proposed that cross-talk between the hemopexin domain of MT1-MMP and adjacent cell surface molecules is responsible for outside-in signaling. Employing cDNAs encoding dominant negative mutations, we demonstrated that Rac1 participates in the MT1-MMP signal transduction pathway. These data demonstrated that each domain of MT1-MMP plays a distinct role in substrate degradation and cell migration. PMID:14729674
Cao, Jian; Kozarekar, Pallavi; Pavlaki, Maria; Chiarelli, Christian; Bahou, Wadie F; Zucker, Stanley
Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain
To characterize gene expression patterns in the regional subdivisions of the mammalian brain, we integrated spatial gene expression patterns from the Allen Brain Atlas for the adult mouse with panels of cell type-specific genes for neurons, astrocytes, and oligodendrocytes from previously published transcriptome profiling experiments. We found that the combined spatial expression patterns of 170 neuron-specific transcripts revealed strikingly clear and symmetrical signatures for most of the brain's major subdivisions. Moreover, the brain expression spatial signatures correspond to anatomical structures and may even reflect developmental ontogeny. Spatial expression profiles of astrocyte- and oligodendrocyte-specific genes also revealed regional differences; these defined fewer regions and were less distinct but still symmetrical in the coronal plane. Follow-up analysis suggested that region-based clustering of neuron-specific genes was related to (i) a combination of individual genes with restricted expression patterns, (ii) region-specific differences in the relative expression of functional groups of genes, and (iii) regional differences in neuronal density. Products from some of these neuron-specific genes are present in peripheral blood, raising the possibility that they could reflect the activities of disease- or injury-perturbed networks and collectively function as biomarkers for clinical disease diagnostics.
Ko, Younhee; Ament, Seth A.; Eddy, James A.; Caballero, Juan; Earls, John C.; Hood, Leroy; Price, Nathan D.
Multilocus Sequence Typing Reveals a Lack of Diversity among Escherichia coli O157:H7 Isolates That Are Distinct by Pulsed-Field Gel Electrophoresis
Escherichia coli O157:H7 is a major cause of foodborne illness in the United States. Pulsed-field gel electrophoresis (PFGE) is the molecular epidemiologic method mostly commonly used to identify food-borne outbreaks. Although PFGE is a powerful epidemiologic tool, it has disadvantages that make a DNA sequence-based approach potentially attractive. Multilocus sequence typing (MLST) analyzes the internal fragments of housekeeping genes to establish genetic relatedness between isolates. We sequenced selected portions of seven housekeeping genes and two membrane protein genes (ompA and espA) of 77 isolates that were diverse by PFGE to determine whether there was sufficient sequence variation to be useful as an epidemiologic tool. There was no DNA sequence diversity in the sequenced portions of the seven housekeeping genes and espA. For ompA, all but five isolates had sequence identical to that of the reference strains. E. coli O157:H7 has a striking lack of genetic diversity in the genes we explored, even among isolates that are clearly distinct by PFGE. Other approaches to identify improved molecular subtyping methods for E. coli 0157:H7 are needed.
Noller, Anna C.; McEllistrem, M. Catherine; Stine, O. Colin; Morris, Jr., J. Glenn; Boxrud, David J.; Dixon, Bruce; Harrison, Lee H.
Targeting surface nucleolin with multivalent HB-19 and related Nucant pseudopeptides results in distinct inhibitory mechanisms depending on the malignant tumor cell type
Background Nucleolin expressed at the cell surface is a binding protein for a variety of ligands implicated in tumorigenesis and angiogenesis. By using a specific antagonist that binds the C-terminal RGG domain of nucleolin, the HB-19 pseudopeptide, we recently reported that targeting surface nucleolin with HB-19 suppresses progression of established human breast tumor cells in the athymic nude mice, and delays development of spontaneous melanoma in the RET transgenic mice. Methods By the capacity of HB-19 to bind stably surface nucleolin, we purified and identified nucleolin partners at the cell surface. HB-19 and related multivalent Nucant pseudopeptides, that present pentavalently or hexavalently the tripeptide Lys?(CH2N)-Pro-Arg, were then used to show that targeting surface nucleolin results in distinct inhibitory mechanisms on breast, prostate, colon carcinoma and leukemia cells. Results Surface nucleolin exists in a 500-kDa protein complex including several other proteins, which we identified by microsequencing as two Wnt related proteins, Ku86 autoantigen, signal recognition particle subunits SRP68/72, the receptor for complement component gC1q-R, and ribosomal proteins S4/S6. Interestingly, some of the surface-nucleolin associated proteins are implicated in cell signaling, tumor cell adhesion, migration, invasion, cell death, autoimmunity, and bacterial infections. Surface nucleolin in the 500-kDa complex is highly stable. Surface nucleolin antagonists, HB-19 and related multivalent Nucant pseudopeptides, exert distinct inhibitory mechanisms depending on the malignant tumor cell type. For example, in epithelial tumor cells they inhibit cell adhesion or spreading and induce reversion of the malignant phenotype (BMC cancer 2010, 10:325) while in leukemia cells they trigger a rapid cell death associated with DNA fragmentation. The fact that these pseudopeptides do not cause cell death in epithelial tumor cells indicates that cell death in leukemia cells is triggered by a specific signaling mechanism, rather than nonspecific cellular injury. Conclusions Our results suggest that targeting surface nucleolin could change the organization of the 500-kDa complex to interfere with the proper functioning of surface nucleolin and the associated proteins, and thus lead to distinct inhibitory mechanisms. Consequently, HB-19 and related Nucant pseudopeptides provide novel therapeutic opportunities in treatment of a wide variety of cancers and related malignancies.
It has recently been shown that a significant fraction of late-type members of nearby, very young associations (age {approx}<10 Myr) display excess emission at mid-IR wavelengths indicative of dusty circumstellar disks. We demonstrate that the detection of mid-IR excess emission can be utilized to identify new nearby, young, late-type stars including two definite new members ('TWA 33' and 'TWA 34') of the TW Hydrae Association (TWA). Both new TWA members display mid-IR excess emission in the Wide-field Infrared Survey Explorer catalog and they show proper motion and youthful spectroscopic characteristics-namely, H{alpha} emission, strong lithium absorption, and low surface gravity features consistent with known TWA members. We also detect mid-IR excess-the first unambiguous evidence of a dusty circumstellar disk-around a previously identified UV-bright, young, accreting star (2M1337) that is a likely member of the Lower-Centaurus Crux region of the Scorpius-Centaurus Complex.
Schneider, Adam; Song, Inseok [Department of Physics and Astronomy, University of Georgia, Athens, GA 30602 (United States); Melis, Carl [Center for Astrophysics and Space Sciences, University of California, San Diego, CA 92093 (United States); Zuckerman, B. [Department of Physics and Astronomy, University of California, Los Angeles, CA, 90095 (United States); Bessell, Mike, E-mail: firstname.lastname@example.com, E-mail: email@example.com, E-mail: email@example.com, E-mail: email@example.com, E-mail: email@example.com [Research School of Astronomy and Astrophysics, The Australian National University, Weston Creek, ACT 2611 (Australia)
Genome-Wide Expression Profiling Identifies Type 1 Interferon Response Pathways in Active Tuberculosis
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), remains the leading cause of mortality from a single infectious agent. Each year around 9 million individuals newly develop active TB disease, and over 2 billion individuals are latently infected with M.tb worldwide, thus being at risk of developing TB reactivation disease later in life. The underlying mechanisms and pathways of protection against TB in humans, as well as the dynamics of the host response to M.tb infection, are incompletely understood. We carried out whole-genome expression profiling on a cohort of TB patients longitudinally sampled along 3 time-points: during active infection, during treatment, and after completion of curative treatment. We identified molecular signatures involving the upregulation of type-1 interferon (?/?) mediated signaling and chronic inflammation during active TB disease in an Indonesian population, in line with results from two recent studies in ethnically and epidemiologically different populations in Europe and South Africa. Expression profiles were captured in neutrophil-depleted blood samples, indicating a major contribution of lymphocytes and myeloid cells. Expression of type-1 interferon (?/?) genes mediated was also upregulated in the lungs of M.tb infected mice and in infected human macrophages. In patients, the regulated gene expression-signature normalized during treatment, including the type-1 interferon mediated signaling and a concurrent opposite regulation of interferon-gamma. Further analysis revealed IL15RA, UBE2L6 and GBP4 as molecules involved in the type-I interferon response in all three experimental models. Our data is highly suggestive that the innate immune type-I interferon signaling cascade could be used as a quantitative tool for monitoring active TB disease, and provide evidence that components of the patient's blood gene expression signature bear similarities to the pulmonary and macrophage response to mycobacterial infection.
Ottenhoff, Tom H. M.; Zhang, Mingzi M.; Wong, Hazel E. E.; Sahiratmadja, Edhyana; Khor, Chiea Chuen; Alisjahbana, Bachti; van Crevel, Reinout; Marzuki, Sangkot; Seielstad, Mark; van de Vosse, Esther; Hibberd, Martin L.
Jaffe-Campanacci syndrome, revisited: detailed clinical and molecular analyses determine whether patients have neurofibromatosis type 1, coincidental manifestations, or a distinct disorder.
Purpose:"Jaffe-Campanacci syndrome" describes the complex of multiple nonossifying fibromas of the long bones, mandibular giant cell lesions, and café-au-lait macules in individuals without neurofibromas. We sought to determine whether Jaffe-Campanacci syndrome is a distinct genetic entity or a variant of neurofibromatosis type 1.Methods:We performed germline NF1, SPRED1, and GNAS1 (exon 8) mutation testing on patients with Jaffe-Campanacci syndrome or Jaffe-Campanacci syndrome-related features. We also performed somatic NF1 mutation testing on nonossifying fibromas and giant cell lesions.Results:Pathogenic germline NF1 mutations were identified in 13 of 14 patients with multiple café-au-lait macules and multiple nonossifying fibromas or giant cell lesions ("classical" Jaffe-Campanacci syndrome); all 13 also fulfilled the National Institutes of Health diagnostic criteria for neurofibromatosis type 1. Somatic NF1 mutations were detected in two giant cell lesions but not in two nonossifying fibromas. No SPRED1 or GNAS1 (exon 8) mutations were detected in the seven NF1-negative patients with Jaffe-Campanacci syndrome, nonossifying fibromas, or giant cell lesions.Conclusion:In this study, the majority of patients with café-au-lait macules and nonossifying fibromas or giant cell lesions harbored a pathogenic germline NF1 mutation, suggesting that many Jaffe-Campanacci syndrome cases may actually have neurofibromatosis type 1. We provide the first proof of specific somatic second-hit mutations affecting NF1 in two giant cell lesions from two unrelated patients, establishing these as neurofibromatosis type 1-associated tumors.Genet Med 16 6, 448-459. PMID:24232412
Stewart, Douglas R; Brems, Hilde; Gomes, Alicia G; Ruppert, Sarah L; Callens, Tom; Williams, Jennifer; Claes, Kathleen; Bober, Michael B; Hachen, Rachel; Kaban, Leonard B; Li, Hua; Lin, Angela; McDonald, Marie; Melancon, Serge; Ortenberg, June; Radtke, Heather B; Samson, Ignace; Saul, Robert A; Shen, Joseph; Siqveland, Elizabeth; Toler, Tomi L; van Maarle, Merel; Wallace, Margaret; Williams, Misti; Legius, Eric; Messiaen, Ludwine
The plasmid R64 thin pilus identified as a type IV pilus.
The entire nucleotide sequence of the pil region of the IncI1 plasmid R64 was determined. Analysis of the sequence indicated that 14 genes, designated pilI through pilV, are involved in the formation of the R64 thin pilus. Protein products of eight pil genes were identified by the maxicell procedure. The pilN product was shown to be a lipoprotein by an experiment using globomycin. A computer search revealed that several R64 pil genes have amino acid sequence homology with proteins involved in type IV pilus biogenesis, protein secretion, and transformation competence. The pilS and pilV products were suggested to be prepilins for the R64 thin pilus, and the pilU product appears to be a prepilin peptidase. These results suggest that the R64 thin pilus belongs to the type IV family, specifically group IVB, of pili. The requirement of the pilR and pilU genes for R64 liquid mating was demonstrated by constructing their frameshift mutations. Comparison of three type IVB pilus biogenesis systems, the pil system of R64, the toxin-coregulated pilus (tcp) system of Vibrio cholerae, and the bundle-forming pilus (bfp) system of enteropathogenic Escherichia coli, suggests that they have evolved from a common ancestral gene system.
Kim, S R; Komano, T
Alpha-7 nicotinic receptor expression by two distinct cell types in the dorsal raphe nucleus and locus coeruleus of rat.
The alpha 7 nicotinic acetylcholine receptor (nAChR) subunit can be assembled to form a homomeric-pentamer with high permeability to calcium. Although the expression of the alpha 7-nAChR has been demonstrated throughout the CNS, the neurochemical phenotype of neurons expressing alpha 7 remains to a large extent unknown. Using an antibody against the alpha 7 nAChR subunit, immunohistochemical staining was observed in rat dorsal raphe nucleus (DRN) and locus coeruleus (LC), serotonergic and noradrenergic brainstem nuclei, respectively. In both the DRN and LC, there appeared to be two histologically distinct alpha 7-expressing cell types as distinguished by size, i.e. large versus small diameter. In rats treated with either a serotonergic (5,7-dihydroxytryptamine) or noradrenergic (anti-dopamine-beta-hydroxylase saporin) neurotoxin, tryptophan hydroxylase and tyrosine hydroxylase immunostaining was abolished, respectively. Similarly, the alpha 7-positive large-diameter cells were no longer detectable, suggesting that these cells were serotonergic DRN and noradrenergic LC neurons. Indeed, double-labeling experiments revealed in the large cell types coexpression of alpha 7 with tryptophan hydroxylase in the DRN and with tyrosine hydroxylase in the LC of saline-treated rats. In contrast to the large-diameter cells, the alpha 7-positive small-diameter cells were neither serotonergic nor adrenergic, and were still detected in both the DRN and LC of lesioned rats. Moreover, cell counts revealed an increase number of these cells in lesioned rats with expression of alpha 7 in somal processes not seen in non-lesioned controls. Double labeling revealed coexpression of alpha 7 and GABA within the majority, but not all, of the toxin-resistant cells. The results of these studies suggest that both serotonergic and noradrenergic neurons express alpha 7 nAChRs. In addition, there appears to be a small-diameter cell-type in both the DRN and LC, possibly a GABAergic interneuron, expressing alpha 7 that may be regulated by neurotoxic injury. PMID:12031534
Bitner, R S; Nikkel, A L
Cell-Type-Specific Transcriptional Profiles of the Dimorphic Pathogen Penicillium marneffei Reflect Distinct Reproductive, Morphological, and Environmental Demands
Penicillium marneffei is an opportunistic human pathogen endemic to Southeast Asia. At 25° P. marneffei grows in a filamentous hyphal form and can undergo asexual development (conidiation) to produce spores (conidia), the infectious agent. At 37° P. marneffei grows in the pathogenic yeast cell form that replicates by fission. Switching between these growth forms, known as dimorphic switching, is dependent on temperature. To understand the process of dimorphic switching and the physiological capacity of the different cell types, two microarray-based profiling experiments covering approximately 42% of the genome were performed. The first experiment compared cells from the hyphal, yeast, and conidiation phases to identify "phase or cell-state–specific" gene expression. The second experiment examined gene expression during the dimorphic switch from one morphological state to another. The data identified a variety of differentially expressed genes that have been organized into metabolic clusters based on predicted function and expression patterns. In particular, C-14 sterol reductase–encoding gene ergM of the ergosterol biosynthesis pathway showed high-level expression throughout yeast morphogenesis compared to hyphal. Deletion of ergM resulted in severe growth defects with increased sensitivity to azole-type antifungal agents but not amphotericin B. The data defined gene classes based on spatio-temporal expression such as those expressed early in the dimorphic switch but not in the terminal cell types and those expressed late. Such classifications have been helpful in linking a given gene of interest to its expression pattern throughout the P. marneffei dimorphic life cycle and its likely role in pathogenicity.
Pasricha, Shivani; Payne, Michael; Canovas, David; Pase, Luke; Ngaosuwankul, Nathamon; Beard, Sally; Oshlack, Alicia; Smyth, Gordon K.; Chaiyaroj, Sansanee C.; Boyce, Kylie J.; Andrianopoulos, Alex
The evolution of three types of indoleamine 2,3 dioxygenases in fungi with distinct molecular and biochemical characteristics.
Indoleamine 2,3-dioxygenase (IDO) is a tryptophan-degrading enzyme and known as a mammalian immunosuppressive molecule. In fungi, the primary role of IDO is to supply nicotinamide adenine dinucleotide (NAD(+)) via the kynurenine pathway. We previously reported that the koji-mold, Aspergillus oryzae has two IDO genes, IDO? and IDO?. In the present study, we found that A. oryzae also has the third IDO, IDO?. These three-types of IDOs are widely distributed among the Pezizomycotina fungi, although the black truffle, Tuber melanosporum has only one corresponding gene to IDO?/IDO?. The yeast, Saccharomyces cerevisiae has a single IDO gene. Generally, Pezizomycotina IDO? showed similar enzymatic properties to the yeast IDO, suggesting that the IDO? is a functional homologue of the S. cerevisiae IDO. In contrast to IDO?, the K(m) value of IDO? is higher. However, the reaction velocity of IDO? is very fast, resulting in comparable or higher catalytic efficiency than IDO?. Thus IDO? may functionally substitute for IDO? in fungal L-Trp metabolism. The enzymatic activity of IDO? was comparatively very low with the values of enzymatic parameters comparable to vertebrate IDO2 enzymes. IDO? and IDO? have similar gene structures, suggesting that they were generated by gene duplication which occurred rather early in Pezizomycotina evolution, although the timing of the duplication remains debatable. In contrast, the phylogenetic trees suggest that IDO?s form an evolutionarily distinct group of IDO enzymes, with a closer relationship to group I bacterial IDOs than other fungal IDOs. The ancestor of the IDO? family is likely to have diverged from other eukaryotic IDOs at a very early stage of eukaryotic evolution. PMID:22564706
Yuasa, Hajime J; Ball, Helen J
Quantitative MRD monitoring identifies distinct GVL response patterns after allogeneic stem cell transplantation for chronic lymphocytic leukemia: results from the GCLLSG CLL3X trial
The purpose of this study was to prospectively analyze minimal residual disease(MRD) kinetics after reduced-intensity allogeneic stem cell transplantation (allo-SCT) in high-risk chronic lymphocytic leukemia (CLL). Subjects were the first 30 consecutive patients from a prospective clinical trial, and seven pilot patients treated identically. Using real-time quantitative-PCR (RQ-PCR) and\\/or flow-based MRD monitoring (sensitivity ?10?4), five distinct patterns of MRD kinetics
M Ritgen; S Böttcher; S Stilgenbauer; D Bunjes; J Schubert; S Cohen; A Humpe; M Hallek; M Kneba; N Schmitz; H Döhner; P Dreger
Significant Deregulated Pathways in Diabetes Type II Complications Identified through Expression Based Network Biology
NASA Astrophysics Data System (ADS)
Type 2 Diabetes is a complex multifactorial disease, which alters several signaling cascades giving rise to serious complications. It is one of the major risk factors for cardiovascular diseases. The present research work describes an integrated functional network biology approach to identify pathways that get transcriptionally altered and lead to complex complications thereby amplifying the phenotypic effect of the impaired disease state. We have identified two sub-network modules, which could be activated under abnormal circumstances in diabetes. Present work describes key proteins such as P85A and SRC serving as important nodes to mediate alternate signaling routes during diseased condition. P85A has been shown to be an important link between stress responsive MAPK and CVD markers involved in fibrosis. MAPK8 has been shown to interact with P85A and further activate CTGF through VEGF signaling. We have traced a novel and unique route correlating inflammation and fibrosis by considering P85A as a key mediator of signals. The next sub-network module shows SRC as a junction for various signaling processes, which results in interaction between NF-kB and beta catenin to cause cell death. The powerful interaction between these important genes in response to transcriptionally altered lipid metabolism and impaired inflammatory response via SRC causes apoptosis of cells. The crosstalk between inflammation, lipid homeostasis and stress, and their serious effects downstream have been explained in the present analyses.
Ukil, Sanchaita; Sinha, Meenakshee; Varshney, Lavneesh; Agrawal, Shipra
Genome-wide association study identifies three novel loci for type 2 diabetes.
Although over 60 loci for type 2 diabetes (T2D) have been identified, there still remains a large genetic component to be clarified. To explore unidentified loci for T2D, we performed a genome-wide association study (GWAS) of 6 209 637 single-nucleotide polymorphisms (SNPs), which were directly genotyped or imputed using East Asian references from the 1000 Genomes Project (June 2011 release) in 5976 Japanese patients with T2D and 20 829 nondiabetic individuals. Nineteen unreported loci were selected and taken forward to follow-up analyses. Combined discovery and follow-up analyses (30 392 cases and 34 814 controls) identified three new loci with genome-wide significance, which were MIR129-LEP [rs791595; risk allele = A; risk allele frequency (RAF) = 0.080; P = 2.55 × 10(-13); odds ratio (OR) = 1.17], GPSM1 [rs11787792; risk allele = A; RAF = 0.874; P = 1.74 × 10(-10); OR = 1.15] and SLC16A13 (rs312457; risk allele = G; RAF = 0.078; P = 7.69 × 10(-13); OR = 1.20). This study demonstrates that GWASs based on the imputation of genotypes using modern reference haplotypes such as that from the 1000 Genomes Project data can assist in identification of new loci for common diseases. PMID:23945395
Hara, Kazuo; Fujita, Hayato; Johnson, Todd A; Yamauchi, Toshimasa; Yasuda, Kazuki; Horikoshi, Momoko; Peng, Chen; Hu, Cheng; Ma, Ronald C W; Imamura, Minako; Iwata, Minoru; Tsunoda, Tatsuhiko; Morizono, Takashi; Shojima, Nobuhiro; So, Wing Yee; Leung, Ting Fan; Kwan, Patrick; Zhang, Rong; Wang, Jie; Yu, Weihui; Maegawa, Hiroshi; Hirose, Hiroshi; Kaku, Kohei; Ito, Chikako; Watada, Hirotaka; Tanaka, Yasushi; Tobe, Kazuyuki; Kashiwagi, Atsunori; Kawamori, Ryuzo; Jia, Weiping; Chan, Juliana C N; Teo, Yik Ying; Shyong, Tai E; Kamatani, Naoyuki; Kubo, Michiaki; Maeda, Shiro; Kadowaki, Takashi
Comparative Genetics: Synergizing Human and NOD Mouse Studies for Identifying Genetic Causation of Type 1 Diabetes
Although once widely anticipated to unlock how human type 1 diabetes (T1D) develops, extensive study of the nonobese diabetic (NOD) mouse has failed to yield effective treatments for patients with the disease. This has led many to question the usefulness of this animal model. While criticism about the differences between NOD and human T1D is legitimate, in many cases disease in both species results from perturbations modulated by the same genes or different genes that function within the same biological pathways. Like in humans, unusual polymorphisms within an MHC class II molecule contributes the most T1D risk in NOD mice. This insight supports the validity of this model and suggests the NOD has been improperly utilized to study how to cure or prevent disease in patients. Indeed, clinical trials are far from administering T1D therapeutics to humans at the same concentration ranges and pathological states that inhibit disease in NOD mice. Until these obstacles are overcome it is premature to label the NOD mouse a poor surrogate to test agents that cure or prevent T1D. An additional criticism of the NOD mouse is the past difficulty in identifying genes underlying T1D using conventional mapping studies. However, most of the few diabetogenic alleles identified to date appear relevant to the human disorder. This suggests that rather than abandoning genetic studies in NOD mice, future efforts should focus on improving the efficiency with which diabetes susceptibility genes are detected. The current review highlights why the NOD mouse remains a relevant and valuable tool to understand the genes and their interactions that promote autoimmune diabetes and therapeutics that inhibit this disease. It also describes a new range of technologies that will likely transform how the NOD mouse is used to uncover the genetic causes of T1D for years to come.
Driver, John P.; Chen, Yi-Guang; Mathews, Clayton E.
Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology.
The virulence properties of human immunodeficiency virus type 2 (HIV-2) are known to vary significantly and to range from relative attenuation in certain individuals to high-level pathogenicity in others. These differences in clinical manifestations may, at least in part, be determined by genetic differences among infecting virus strains. Evaluation of the full spectrum of HIV-2 genetic diversity is thus a necessary first step towards understanding its molecular epidemiology, natural history of infection, and biological diversity. In this study, we have used nested PCR techniques to amplify viral sequences from the DNA of uncultured peripheral blood mononuclear cells from 12 patients with HIV-2 seroreactivity. Sequence analysis of four nonoverlapping genomic regions allowed a comprehensive analysis of HIV-2 phylogeny. The results revealed (i) the existence of five distinct and roughly equidistant evolutionary lineages of HIV-2 which, by analogy with HIV-1, have been termed sequence subtypes A to E; (ii) evidence for a mosaic HIV-2 genome, indicating that coinfection with genetically divergent strains and recombination can occur in HIV-2-infected individuals; and (iii) evidence supporting the conclusion that some of the HIV-2 subtypes may have arisen from independent introductions of genetically diverse sooty mangabey viruses into the human population. Importantly, only a subset of HIV-2 strains replicated in culture: all subtype A viruses grew to high titers, but attempts to isolate representatives of subtypes C, D, and E, as well as the majority of subtype B viruses, remained unsuccessful. Infection with all five viral subtypes was detectable by commercially available serological (Western immunoblot) assays, despite intersubtype sequence differences of up to 25% in the gag, pol, and env regions. These results indicate that the genetic and biological diversity of HIV-2 is far greater than previously appreciated and suggest that there may be subtype-specific differences in virus biology. Systematic natural history studies are needed to determine whether this heterogeneity has clinical relevance and whether the various HIV-2 subtypes differ in their in vivo pathogenicity. PMID:7933127
Gao, F; Yue, L; Robertson, D L; Hill, S C; Hui, H; Biggar, R J; Neequaye, A E; Whelan, T M; Ho, D D; Shaw, G M
Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology.
The virulence properties of human immunodeficiency virus type 2 (HIV-2) are known to vary significantly and to range from relative attenuation in certain individuals to high-level pathogenicity in others. These differences in clinical manifestations may, at least in part, be determined by genetic differences among infecting virus strains. Evaluation of the full spectrum of HIV-2 genetic diversity is thus a necessary first step towards understanding its molecular epidemiology, natural history of infection, and biological diversity. In this study, we have used nested PCR techniques to amplify viral sequences from the DNA of uncultured peripheral blood mononuclear cells from 12 patients with HIV-2 seroreactivity. Sequence analysis of four nonoverlapping genomic regions allowed a comprehensive analysis of HIV-2 phylogeny. The results revealed (i) the existence of five distinct and roughly equidistant evolutionary lineages of HIV-2 which, by analogy with HIV-1, have been termed sequence subtypes A to E; (ii) evidence for a mosaic HIV-2 genome, indicating that coinfection with genetically divergent strains and recombination can occur in HIV-2-infected individuals; and (iii) evidence supporting the conclusion that some of the HIV-2 subtypes may have arisen from independent introductions of genetically diverse sooty mangabey viruses into the human population. Importantly, only a subset of HIV-2 strains replicated in culture: all subtype A viruses grew to high titers, but attempts to isolate representatives of subtypes C, D, and E, as well as the majority of subtype B viruses, remained unsuccessful. Infection with all five viral subtypes was detectable by commercially available serological (Western immunoblot) assays, despite intersubtype sequence differences of up to 25% in the gag, pol, and env regions. These results indicate that the genetic and biological diversity of HIV-2 is far greater than previously appreciated and suggest that there may be subtype-specific differences in virus biology. Systematic natural history studies are needed to determine whether this heterogeneity has clinical relevance and whether the various HIV-2 subtypes differ in their in vivo pathogenicity. Images
Gao, F; Yue, L; Robertson, D L; Hill, S C; Hui, H; Biggar, R J; Neequaye, A E; Whelan, T M; Ho, D D; Shaw, G M
Evaluating the Usefulness of High-Temporal Resolution Vegetation Indices to Identify Crop Types
NASA Astrophysics Data System (ADS)
The National Aeronautical and Space Agency (NASA) and the United States Department of Agriculture (USDA) jointly sponsored research covering the 2004 to 2006 South American crop seasons that focused on developing methods for the USDA's Foreign Agricultural Service's (FAS) Production Estimates and Crop Assessment Division (PECAD) to identify crop types using MODIS-derived, hyper-temporal Normalized Difference Vegetation Index (NDVI) images. NDVI images were composited in 8 day intervals from daily NDVI images and aggregated to create a hyper-termporal NDVI layerstack. This NDVI layerstack was used as input to image classification algorithms. Research results indicated that creating high-temporal resolution Normalized Difference Vegetation Index (NDVI) composites from NASA's MODerate Resolution Imaging Spectroradiometer (MODIS) data products provides useful input to crop type classifications as well as potential useful input for regional crop productivity modeling efforts. A current NASA-sponsored Rapid Prototyping Capability (RPC) experiment will assess the utility of simulated future Visible Infrared Imager / Radiometer Suite (VIIRS) imagery for conducting NDVI-derived land cover and specific crop type classifications. In the experiment, methods will be considered to refine current MODIS data streams, reduce the noise content of the MODIS, and utilize the MODIS data as an input to the VIIRS simulation process. The effort also is being conducted in concert with an ISS project that will further evaluate, verify and validate the usefulness of specific data products to provide remote sensing-derived input for the Sinclair Model a semi-mechanistic model for estimating crop yield. The study area encompasses a large portion of the Pampas region of Argentina--a major world producer of crops such as corn, soybeans, and wheat which makes it a competitor to the US. ITD partnered with researchers at the Center for Surveying Agricultural and Natural Resources (CREAN) of the National University of Cordoba, Argentina, and CREAN personnel collected and continue to collect field-level, GIS-based in situ information. Current efforts involve both developing and optimizing software tools for the necessary data processing. The software includes the Time Series Product Tool (TSPT), Leica's ERDAS Imagine, and Mississippi State University's Temporal Map Algebra computational tools.
Hilbert, K.; Lewis, D.; O'Hara, C. G.
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: email@example.com
Ison, Jon; Kalas, Matus; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter
A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach.
Sophisticated mechanisms are employed to facilitate information exchange between interfacing bacteria. A type VI secretion system (T6SS) of Pseudomonas aeruginosa was shown to deliver cell wall-targeting effectors to neighboring cells. However, the generality of bacteriolytic effectors and, moreover, of antibacterial T6S remained unknown. Using parameters derived from experimentally validated bacterial T6SS effectors we identified a phylogenetically disperse superfamily of T6SS-associated peptidoglycan-degrading effectors. The effectors separate into four families composed of peptidoglycan amidase enzymes of differing specificities. Effectors strictly co-occur with cognate immunity proteins, indicating that self-intoxication is a general property of antibacterial T6SSs and effector delivery by the system exerts a strong selective pressure in nature. The presence of antibacterial effectors in a plethora of organisms, including many that inhabit or infect polymicrobial niches in the human body, suggests that the system could mediate interbacterial interactions of both environmental and clinical significance. PMID:22607806
Russell, Alistair B; Singh, Pragya; Brittnacher, Mitchell; Bui, Nhat Khai; Hood, Rachel D; Carl, Mike A; Agnello, Danielle M; Schwarz, Sandra; Goodlett, David R; Vollmer, Waldemar; Mougous, Joseph D
A widespread bacterial type VI secretion effector superfamily identified using a heuristic approach
Summary Sophisticated mechanisms are employed to facilitate information exchange between interfacing bacteria. A type VI secretion system (T6SS) of Pseudomonas aeruginosa was shown to deliver cell wall-targeting effectors to neighboring cells. However, the generality of bacteriolytic effectors, and moreover, of antibacterial T6S, remained unknown. Using parameters derived from experimentally validated bacterial T6SS effectors and informatics, we identified a phylogenetically disperse superfamily of T6SS-associated peptidoglycan-degrading effectors. The effectors separate into four families composed of peptidoglycan amidase enzymes of differing specificities. Effectors strictly co-occur with cognate immunity proteins, indicating that self-intoxication is a general property of antibacterial T6SSs and effector delivery by the system exerts a strong selective pressure in nature. The presence of antibacterial effectors in a plethora of organisms, including many that inhabit or infect polymicrobial niches in the human body, suggests that the system could mediate interbacterial interactions of both environmental and clinical significance.
Russell, Alistair B.; Singh, Pragya; Brittnacher, Mitchell; Bui, Nhat Khai; Hood, Rachel D.; Carl, Mike A.; Agnello, Danielle M.; Schwarz, Sandra; Goodlett, David R.; Vollmer, Waldemar; Mougous, Joseph D.
Probing cell type-specific functions of Gi in vivo identifies GPCR regulators of insulin secretion.
The in vivo roles of the hundreds of mammalian G protein-coupled receptors (GPCRs) are incompletely understood. To explore these roles, we generated mice expressing the S1 subunit of pertussis toxin, a known inhibitor of G(i/o) signaling, under the control of the ROSA26 locus in a Cre recombinase-dependent manner (ROSA26(PTX)). Crossing ROSA26(PTX) mice to mice expressing Cre in pancreatic beta cells produced offspring with constitutive hyperinsulinemia, increased insulin secretion in response to glucose, and resistance to diet-induced hyperglycemia. This phenotype underscored the known importance of G(i/o) and hence of GPCRs for regulating insulin secretion. Accordingly, we quantified mRNA for each of the approximately 373 nonodorant GPCRs in mouse to identify receptors highly expressed in islets and examined the role of several. We report that 3-iodothyronamine, a thyroid hormone metabolite, could negatively and positively regulate insulin secretion via the G(i)-coupled alpha(2A)-adrenergic receptor and the G(s)-coupled receptor Taar1, respectively, and protease-activated receptor-2 could negatively regulate insulin secretion and may contribute to physiological regulation of glucose metabolism. The ROSA26(PTX) system used in this study represents a new genetic tool to achieve tissue-specific signaling pathway modulation in vivo that can be applied to investigate the role of G(i/o)-coupled GPCRs in multiple cell types and processes. PMID:17992256
Regard, Jean B; Kataoka, Hiroshi; Cano, David A; Camerer, Eric; Yin, Liya; Zheng, Yao-Wu; Scanlan, Thomas S; Hebrok, Matthias; Coughlin, Shaun R
Probing cell type-specific functions of Gi in vivo identifies GPCR regulators of insulin secretion
The in vivo roles of the hundreds of mammalian G protein–coupled receptors (GPCRs) are incompletely understood. To explore these roles, we generated mice expressing the S1 subunit of pertussis toxin, a known inhibitor of Gi/o signaling, under the control of the ROSA26 locus in a Cre recombinase–dependent manner (ROSA26PTX). Crossing ROSA26PTX mice to mice expressing Cre in pancreatic ? cells produced offspring with constitutive hyperinsulinemia, increased insulin secretion in response to glucose, and resistance to diet-induced hyperglycemia. This phenotype underscored the known importance of Gi/o and hence of GPCRs for regulating insulin secretion. Accordingly, we quantified mRNA for each of the approximately 373 nonodorant GPCRs in mouse to identify receptors highly expressed in islets and examined the role of several. We report that 3-iodothyronamine, a thyroid hormone metabolite, could negatively and positively regulate insulin secretion via the Gi-coupled ?2A-adrenergic receptor and the Gs-coupled receptor Taar1, respectively, and protease-activated receptor–2 could negatively regulate insulin secretion and may contribute to physiological regulation of glucose metabolism. The ROSA26PTX system used in this study represents a new genetic tool to achieve tissue-specific signaling pathway modulation in vivo that can be applied to investigate the role of Gi/o-coupled GPCRs in multiple cell types and processes.
Regard, Jean B.; Kataoka, Hiroshi; Cano, David A.; Camerer, Eric; Yin, Liya; Zheng, Yao-Wu; Scanlan, Thomas S.; Hebrok, Matthias; Coughlin, Shaun R.
Identifying contributors of DNA mixtures by means of quantitative information of STR typing.
Estimating the weight of evidence in forensic genetics is often done in terms of a likelihood ratio, LR. The LR evaluates the probability of the observed evidence under competing hypotheses. Most often, probabilities used in the LR only consider the evidence from the genomic variation identified using polymorphic genetic markers. However, modern typing techniques supply additional quantitative data, which contain very important information about the observed evidence. This is particularly true for cases of DNA mixtures, where more than one individual has contributed to the observed biological stain. This article presents a method for including the quantitative information of short tandem repeat (STR) DNA mixtures in the LR. Also, an efficient algorithmic method for finding the best matching combination of DNA mixture profiles is derived and implemented in an on-line tool for two- and three-person DNA mixtures. Finally, we demonstrate for two-person mixtures how this best matching pair of profiles can be used in estimating the likelihood ratio using importance sampling. The reason for using importance sampling for estimating the likelihood ratio is the often vast number of combinations of profiles needed for the evaluation of the weight of evidence. Online tool is available at http://people.math.aau.dk/~tvede/dna/. PMID:21210742
Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt; Morling, Niels
Classification of distinct subtypes of peripheral T-cell lymphoma unspecified, identified by chemokine and chemokine receptor expression: Analysis of prognosis.
WHO classification for malignant lymphoma was recently proposed. However, PTCL is heterogeneous. Chemokines and its receptors are closely associated with the T-cell subtypes. To clarify the T-cell subtype in PTCL, we conducted DNA chips of chemokine, its receptor (R) and cytokines. Angioimmunoblastic T-cell lymphoma (AILD, n=4), anaplastic large cell lymphoma (ALCL, n=4), adult T-cell leukemia lymphoma (ATLL, n=7), NK-cell lymphoma (NKL, n=2) and PTCL, unspecified (PTCL-U, n=6) were analyzed using DNA chips. In addition, immunological stainings were performed in 280 cases. In DNA chip, AILD, ALCL, NKL and ATLL showed a tendency for respective clusters, otherwise, PTCL-U clustered with AILD, ALCL and ATLL. From the gene expression profiling, CCR4, CCR3, MIG, CXCR3 and BLC were selected for immunohistochemistry. ATLL (n=48) expressed CCR4. ALCL (n=26) expressed CCR3, NKL (n=20) expressed MIG, and AILD (n=29) expressed CXCR3 and/or BLC. From the expression patterns, PTCL-U (n=134) were classified into three groups; CCR4 type (CCR4(+), n=42), CCR3 type (CCR3(+), n=31) and CXCR3 type (CXCR3(+) BLC(+/-), n=54). The prognosis was poor for ATLL, intermediate for AILD and favorable for ALCL (P=0.0014). Among PTCL-U, CCR4 type, CXCR3 type and CCR3 type had prognoses equivalent to ATLL, AILD and ALCL, respectively (P<0.0001). PMID:15289861
Ohshima, Koichi; Karube, Kennosuke; Kawano, Riko; Tsuchiya, Takeshi; Suefuji, Hiroaki; Yamaguchi, Takahiro; Suzumiya, Junji; Kikuchii, Masahiro
QChIPat: a quantitative method to identify distinct binding patterns for two biological ChIP-seq samples in different experimental conditions
Background Many computational programs have been developed to identify enriched regions for a single biological ChIP-seq sample. Given that many biological questions are often asked to compare the difference between two different conditions, it is important to develop new programs that address the comparison of two biological ChIP-seq samples. Despite several programs designed to address this question, these programs suffer from some drawbacks, such as inability to distinguish whether the identified differential enriched regions are indeed significantly enriched, lack of distinguishing binding patterns, and neglect of the normalization between samples. Results In this study, we developed a novel quantitative method for comparing two biological ChIP-seq samples, called QChIPat. Our method employs a new global normalization method: nonparametric empirical Bayes (NEB) correction normalization, utilizes pre-defined enriched regions identified from single-sample peak calling programs, uses statistical methods to define differential enriched regions, then defines binding (histone modification) pattern information for those differential enriched regions. Our program was tested on a benchmark data: histone modifications data used by ChIPDiffs. It was then applied on two study cases: one to identify differential histone modification sites for ChIP-seq of H3K27me3 and H3K9me2 data in AKT1-transfected MCF10A cells; the other to identify differential binding sites for ChIP-seq of TCF7L2 data in MCF7 and PANC1 cells. Conclusions Several advantages of our program include: 1) it considers a control (or input) experiment; 2) it incorporates a novel global normalization strategy: nonparametric empirical Bayes correction normalization; 3) it provides the binding pattern information among different enriched regions. QChIPat is implemented in R, Perl and C++, and has been tested under Linux. The R package is available at http://motif.bmi.ohio-state.edu/QChIPat.
Array CGH identifies distinct DNA copy number profiles of oncogenes and tumor suppressor genes in chromosomal- and microsatellite-unstable sporadic colorectal carcinomas
DNA copy number changes represent molecular fingerprints of solid tumors and are as such relevant for better understanding\\u000a of tumor development and progression. In this study, we applied genome-wide array comparative genomic hybridization (aCGH)\\u000a to identify gene-specific DNA copy number changes in chromosomal (CIN)- and microsatellite (MIN)-unstable sporadic colorectal\\u000a cancers (sCRC). Genomic DNA was extracted from microdissected, matching normal colorectal
Silke Lassmann; Roland Weis; Frank Makowiec; Jasmine Roth; Mihai Danciu; Ulrich Hopt; Martin Werner
Type X collagen is colocalized with a proteoglycan epitope to form distinct morphological structures in bovine growth cartilage
Using antibodies raised against type X collagen, isolated from deer antler, we have immunolocalized type X collagen in growth plate and epiphyseal cartilage from fetal and ambulatory calves. In ambulatory calf growth plate, type X collagen was demonstrated to be present in longitudinal septa that extend from the resting zone into the underlying trabecular bone. The much more restricted distribution
G. Gibson; D.-L. Lin; K. Francki; B. Caterson; B. Foster
Identifying and investigating pesticide application types to promote a more sustainable pesticide use. The case of smallholders in Boyacá, Colombia
The present paper investigates pesticide application types adopted by smallholder potato producers in the Department of Boyacá, Colombia. In this region, environmental, health and adverse economic effects due to pesticide mis- or over-use respectively have been observed. Firstly, pesticide application types were identified based on input-effectiveness. Secondly, their determinants of adoption were investigated. Finally suggestions were given to develop intervention
Giuseppe Feola; Claudia R. Binder
Insertion element IS1296 in Mycoplasma mycoides subsp. mycoides small colony identifies a European clonal line distinct from African and Australian strains.
Strains of Mycoplasma mycoides subsp. mycoides small colony (SC) type, the agent of contagious bovine pleuropneumonia (CBPP), were analysed with respect to the polymorphism of distribution of a newly discovered insertion element, IS1296, on the chromosome. Analysis of 64 strains isolated from Europe, Africa and Australia, including four vaccine strains and the type strain PG1, revealed ten different IS patterns, forming two main clusters. The European strains originated from outbreaks of CBPP in different countries, and from various other sources such as semen and preputial washings from cattle, lungs from goats and buffalo, and milk from sheep. They showed identical IS1296 patterns, except one strain which had an additional IS1296 element, but the pattern belonged to the same cluster. This shows that the strains from Europe form a clonal lineage. The strains originating from different geographical parts of the African continent and from Australia showed four closely related IS1296 patterns which belong to a separate cluster. This indicates that strains from Africa and Australia form a clonal lineage different from that of the European strains, suggesting that the sporadic cases of CBPP that have re-emerged in Europe almost 15 years after the last declared endemic case in 1967 arose from an established reservoir within Europe rather than being the result of repeated importation from Africa and Australia. While most strains from Africa and Australia had the same IS1296 pattern, all vaccine strains could be distinguished by an individual pattern. The type strain PG1 also had a particular IS1296 pattern which belongs to the cluster of the strains from Africa and Australia. The molecular definition of clonality of M. mycoides subsp. mycoides SC strains with IS1296 represents a rapid and reproducible method for subtyping and differentiation of vaccine strains. It permits at the present time the definition of two main clonal lines, one including the strains from the European continent and a second with strains from Africa and Australia. PMID:8574413
Cheng, X; Nicolet, J; Poumarat, F; Regalla, J; Thiaucourt, F; Frey, J
Type X collagen is colocalized with a proteoglycan epitope to form distinct morphological structures in bovine growth cartilage.
Using antibodies raised against type X collagen, isolated from deer antler, we have immunolocalized type X collagen in growth plate and epiphyseal cartilage from fetal and ambulatory calves. In ambulatory calf growth plate, type X collagen was demonstrated to be present in longitudinal septa that extend from the resting zone into the underlying trabecular bone. The much more restricted distribution of type X collagen seen in fetal growth plate, both here and previously, suggested that prominent localization of type X collagen to the longitudinal septa was stimulated by weight bearing. The location of type X collagen has been compared with that of an epitope (7D4), composed of specific sulfation patterns in chondroitin sulfate of some aggrecan molecules. Colocalization of type X collagen with the 7D4 epitope in longitudinal septa of growth plates from ambulatory calves suggested these molecules contribute to the formation and function of longitudinal septa. Immunolocalization of type X collagen and 7D4 in calf epiphyseal cartilage demonstrated colocalization at an interface that appears to represent the junction of articular cartilage and cartilage associated with formation of the secondary ossification center. Immunolocalization of type X collagen and the 7D4 proteoglycan epitope in these structures suggested that type X collagen and the 7D4 epitope form structures with important mechanical roles and capacity to influence the morphology of associated bony structures. PMID:8894136
Gibson, G; Lin, D L; Francki, K; Caterson, B; Foster, B
Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers
Background: Although prognostic biomarkers specific for particular cancers have been discovered, microarray analysis of gene expression profiles, supported by integrative analysis algorithms, helps to identify common factors in molecular oncology. Similarities of Ordered Gene Lists (SOGL) is a recently proposed approach to meta-analysis suitable for identifying features shared by two data sets. Here we extend the idea of SOGL to
Xinan Yang; Xiao Sun
The 'blue-on' opponent pathway in primate retina originates from a distinct bistratified ganglion cell type
COLOUR vision in humans and Old World monkeys begins with the differential activation of three types of cone photoreceptor which are maximally sensitive to short (S), medium (M) and long (L) wavelengths. Signals from the three cone types are relayed to the retinal ganglion cells via cone-specific bipolar cell types1-4. Colour-coding ganglion cells fall into two major physiological classes: the
Dennis M. Dacey; Barry B. Lee
Multilocus Sequence Typing Supports the Hypothesis that Cow and Human-Associated Salmonella Isolates Represent Distinct and Overlapping Populations
A collection of 179 human and 156 bovine clinical Salmonella isolates obtained from across New York state over the course of 1 year was characterized using serotyping and a multilocus sequence typing (MLST) scheme based on the sequencing of three genes (fimA, manB, and mdh). The 335 isolates were differentiated into 52 serotypes and 72 sequence types (STs). Analyses of
S. D. Alcaine; Y. Soyer; L. D. Warnick; W.-L. Su; S. Sukhnanand; J. Richards; E. D. Fortes; P. McDonough; T. P. Root; N. B. Dumas; Y. Grohn; M. Wiedmann
Proteome and metabolome profiling of cytokinin action in Arabidopsis identifying both distinct and similar responses to cytokinin down- and up-regulation
In plants, numerous developmental processes are controlled by cytokinin (CK) levels and their ratios to levels of other hormones. While molecular mechanisms underlying the regulatory roles of CKs have been intensely researched, proteomic and metabolomic responses to CK deficiency are unknown. Transgenic Arabidopsis seedlings carrying inducible barley cytokinin oxidase/dehydrogenase (CaMV35S>GR>HvCKX2) and agrobacterial isopentenyl transferase (CaMV35S>GR>ipt) constructs were profiled to elucidate proteome- and metabolome-wide responses to down- and up-regulation of CK levels, respectively. Proteome profiling identified >1100 proteins, 155 of which responded to HvCKX2 and/or ipt activation, mostly involved in growth, development, and/or hormone and light signalling. The metabolome profiling covered 79 metabolites, 33 of which responded to HvCKX2 and/or ipt activation, mostly amino acids, carbohydrates, and organic acids. Comparison of the data sets obtained from activated CaMV35S>GR>HvCKX2 and CaMV35S>GR>ipt plants revealed unexpectedly extensive overlaps. Integration of the proteomic and metabolomic data sets revealed: (i) novel components of molecular circuits involved in CK action (e.g. ribosomal proteins); (ii) previously unrecognized links to redox regulation and stress hormone signalling networks; and (iii) CK content markers. The striking overlaps in profiles observed in CK-deficient and CK-overproducing seedlings might explain surprising previously reported similarities between plants with down- and up-regulated CK levels.
Hoehenwarter, Wolfgang; Brzobohaty, Bretislav
Proteomic Profile Identifies Dysregulated Pathways in Cornelia de Lange Syndrome Cells With Distinct Mutations in SMC1A and SMC3 Genes
Mutations in cohesin genes have been identified in Cornelia de Lange syndrome (CdLS), but its etiopathogenetic mechanisms are still poorly understood. To define biochemical pathways that are affected in CdLS we analyzed the proteomic profile of CdLS cell lines carrying mutations in the core cohesin genes, SMC1A and SMC3. Dysregulated protein expression was found in CdLS probands compared to controls. The proteomics analysis was able to discriminate between probands harboring mutations in the different domains of the SMC proteins. In particular, proteins involved in the response to oxidative stress were specifically down-regulated in hinge mutated probands. In addition, the finding that CdLS cell lines show an increase in global oxidative stress argues that it could contribute to some CdLS phenotypic features such as premature physiological aging and genome instability. Finally, the c-MYC gene represents a convergent hub lying at the center of dysregulated pathways, and is down-regulated in CdLS. This study allowed us to highlight, for the first time, specific biochemical pathways that are affected in CdLS, providing plausible causal evidence for some of the phenotypic features seen in CdLS.
Gimigliano, Anna; Mannini, Linda; Bianchi, Laura; Puglia, Michele; Deardorff, Matthew A.; Menga, Stefania; Krantz, Ian D; Musio, Antonio; Bini, Luca
Proteomic profile identifies dysregulated pathways in Cornelia de Lange syndrome cells with distinct mutations in SMC1A and SMC3 genes.
Mutations in cohesin genes have been identified in Cornelia de Lange syndrome (CdLS), but its etiopathogenetic mechanisms are still poorly understood. To define biochemical pathways that are affected in CdLS, we analyzed the proteomic profile of CdLS cell lines carrying mutations in the core cohesin genes, SMC1A and SMC3. Dysregulated protein expression was found in CdLS probands compared to controls. The proteomics analysis was able to discriminate between probands harboring mutations in the different domains of the SMC proteins. In particular, proteins involved in the response to oxidative stress were specifically down-regulated in hinge mutated probands. In addition, the finding that CdLS cell lines show an increase in global oxidative stress argues that it could contribute to some CdLS phenotypic features such as premature physiological aging and genome instability. Finally, the c-MYC gene represents a convergent hub lying at the center of dysregulated pathways, and is down-regulated in CdLS. This study allowed us to highlight, for the first time, specific biochemical pathways that are affected in CdLS, providing plausible causal evidence for some of the phenotypic features seen in CdLS. PMID:23106691
Gimigliano, Anna; Mannini, Linda; Bianchi, Laura; Puglia, Michele; Deardorff, Matthew A; Menga, Stefania; Krantz, Ian D; Musio, Antonio; Bini, Luca
Analysis of the Arabidopsis Shoot Meristem Transcriptome during Floral Transition Identifies Distinct Regulatory Patterns and a Leucine-Rich Repeat Protein That Promotes Flowering[C][W][OA
Flowering of Arabidopsis thaliana is induced by exposure to long days (LDs). During this process, the shoot apical meristem is converted to an inflorescence meristem that forms flowers, and this transition is maintained even if plants are returned to short days (SDs). We show that exposure to five LDs is sufficient to commit the meristem of SD-grown plants to flower as if they were exposed to continuous LDs. The MADS box proteins SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) and FRUITFULL (FUL) play essential roles in this commitment process and in the induction of flowering downstream of the transmissible FLOWERING LOCUS T (FT) signal. We exploited laser microdissection and Solexa sequencing to identify 202 genes whose transcripts increase in the meristem during floral commitment. Expression of six of these transcripts was tested in different mutants, allowing them to be assigned to FT-dependent or FT-independent pathways. Most, but not all, of those dependent on FT and its paralog TWIN SISTER OF FT (TSF) also relied on SOC1 and FUL. However, this dependency on FT and TSF or SOC1 and FUL was often bypassed in the presence of the short vegetative phase mutation. FLOR1, which encodes a leucine-rich repeat protein, was induced in the early inflorescence meristem, and flor1 mutations delayed flowering. Our data contribute to the definition of LD-dependent pathways downstream and in parallel to FT.
Torti, Stefano; Fornara, Fabio; Vincent, Coral; Andres, Fernando; Nordstrom, Karl; Gobel, Ulrike; Knoll, Daniela; Schoof, Heiko; Coupland, George
Study Identifies Novel Genomic Changes in the Most Common Type of Lung Cancer
... genomic changes in the most common type of lung cancer TCGA finds mutations in a key cancer- ... in a well-known cancer-causing pathway in lung adenocarcinoma, the most common subtype of lung cancer. ...
Use of Genome Scans to Identify Susceptibility Genes for Type 2 Diabetes
\\u000a Heredity has long been regarded as a risk factor for type 2 diabetes. Familial aggregation of type 2 diabetes is consistently\\u000a observed across populations worldwide. The concordance rates for diabetes in monozygotic twins are 50% or higher, whereas\\u000a those for dizygotic twins are substantially lower, at 10 to 17% (1–3). It is estimated that siblings of diabetic individuals are 1.2
Wen-Chi Hsueh; Braxton D. Mitchell; Alan R. Shuldiner
Potential of infrared spectroscopy in combination with extended canonical variate analysis for identifying different paper types
The increasing use of secondary fiber in papermaking has led to the production of paper containing a wide range of contaminants. Wastepaper mills need to develop quality control methods for evaluating the incoming wastepaper stock as well as testing the specifications of the final product. The goal of this work is to present a fast and successful methodology for identifying
Jordi-Roger Riba; Trini Canals; Rosa Cantero; Hortensia Iturriaga
Description of the georeferenced digital database produced by the U.S. EPA/MED along with the U.S. FWS for a R-EMAP project funded by EPA/ORD for Region 5 that produced an inventory of the coastal wetlands of the Great Lakes was described. The process used to identify and classif...
Researchers Identify Novel Type of Antibody that Potently Inhibits HIV Infection
A small antibody fragment that is highly effective in neutralizing the human immunodeficiency virus (HIV) by preventing the virus from entering cells has been identified by researchers at NCI. This finding may provide insight into the development of new treatments against HIV and other viruses, hopefully in the not too distant future.
Spatial Relationships between GABAergic and Glutamatergic Synapses on the Dendrites of Distinct Types of Mouse Retinal Ganglion Cells across Development
Neuronal output requires a concerted balance between excitatory and inhibitory (I/E) input. Like other circuits, inhibitory synaptogenesis in the retina precedes excitatory synaptogenesis. How then do neurons attain their mature balance of I/E ratios despite temporal offset in synaptogenesis? To directly compare the development of glutamatergic and GABAergic synapses onto the same cell, we biolistically transfected retinal ganglion cells (RGCs) with PSD95CFP, a marker of glutamatergic postsynaptic sites, in transgenic Thy1YFP?2 mice in which GABAA receptors are fluorescently tagged. We mapped YFP?2 and PSD95CFP puncta distributions on three RGC types at postnatal day P12, shortly before eye opening, and at P21 when robust light responses in RGCs are present. The mature IGABA/E ratios varied among ON-Sustained (S) A-type, OFF-S A-type, and bistratified direction selective (DS) RGCs. These ratios were attained at different rates, before eye-opening for ON-S and OFF-S A-type, and after eye-opening for DS RGCs. At both ages examined, the IGABA/E ratio was uniform across the arbors of the three RGC types. Furthermore, measurements of the distances between neighboring PSD95CFP and YFP?2 puncta on RGC dendrites indicate that their local relationship is established early in development, and cannot be predicted by random organization. These close spatial associations between glutamatergic and GABAergic postsynaptic sites appear to represent local synaptic arrangements revealed by correlative light and EM reconstructions of a single RGC's dendrites. Thus, although RGC types have different IGABA/E ratios and establish these ratios at separate rates, the local relationship between excitatory and inhibitory inputs appear similarly constrained across the RGC types studied.
Bleckert, Adam; Parker, Edward D.; Kang, YunHee; Pancaroglu, Raika; Soto, Florentina; Lewis, Renate; Craig, Ann Marie; Wong, Rachel O. L.
IL10 and the Dangers of Immune Polarization: Excessive Type 1 and Type 2 Cytokine Responses Induce Distinct Forms of Lethal Immunopathology in Murine Schistosomiasis
To dissect the controversial roles of type 1 and type 2 cytokines to the pathogenesis of schistosomiasis, we generated IL-10\\/IL-4- and IL-10\\/IL-12-deficient mice that develop highly polarized type 1 and type 2 cytokine responses, respectively. Interestingly, the Th1-polarized IL-10\\/IL-4-deficient mice rapidly lost weight at the onset of egg-laying and displayed 100% mortality by wk 9 postinfection. This acute mortality was
Karl F. Hoffmann; Allen W. Cheever; Thomas A. Wynn
PKscan: a program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length
A computer program written in C++ has been developed which can detect all potential H-type RNA pseudoknots within any given RNA sequence. There is no limit on the length of the input sequence. A validation run of the program using the full-length (8173 nt) genomic mRNA of simian retrovirus type-1 (SRV-1) identifies the established -1 frameshift stimulating pseudokont at the gagpro junction as the most stable pseudoknot within the genomic mRNA.
Huang, Xiaolan; Du, Zhihua; Cheng, Jie; Cheng, Qiang
PKscan: a program to identify H-type RNA pseudoknots in any RNA sequence with unlimited length.
A computer program written in C++ has been developed which can detect all potential H-type RNA pseudoknots within any given RNA sequence. There is no limit on the length of the input sequence. A validation run of the program using the full-length (8173 nt) genomic mRNA of simian retrovirus type-1 (SRV-1) identifies the established -1 frameshift stimulating pseudokont at the gagpro junction as the most stable pseudoknot within the genomic mRNA. PMID:23847396
Huang, Xiaolan; Du, Zhihua; Cheng, Jie; Cheng, Qiang
Using genome-context data to identify specific types of functional associations in pathway\\/genome databases
Background: Hundreds of genes lacking homology to any protein of known function are sequenced every day. Genome-context methods have proved useful in providing clues about functional annotations for many proteins. However, genome-context methods detect many biological types of functional associations, and do not identify which type of functional association they have found. Results: We have developed two new genome-context-based algorithms.
Michelle L. Green; Peter D. Karp
Analysis of Pax6 Contiguous Gene Deletions in the Mouse, Mus musculus, Identifies Regions Distinct from Pax6 Responsible for Extreme Small-Eye and Belly-Spotting Phenotypes
In the mouse Pax6 function is critical in a dose-dependent manner for proper eye development. Pax6 contiguous gene deletions were shown to be homozygous lethal at an early embryonic stage. Heterozygotes express belly spotting and extreme microphthalmia. The eye phenotype is more severe than in heterozygous Pax6 intragenic null mutants, raising the possibility that deletions are functionally different from intragenic null mutations or that a region distinct from Pax6 included in the deletions affects eye phenotype. We recovered and identified the exact regions deleted in three new Pax6 deletions. All are homozygous lethal at an early embryonic stage. None express belly spotting. One expresses extreme microphthalmia and two express the milder eye phenotype similar to Pax6 intragenic null mutants. Analysis of Pax6 expression levels and the major isoforms excluded the hypothesis that the deletions expressing extreme microphthalmia are directly due to the action of Pax6 and functionally different from intragenic null mutations. A region distinct from Pax6 containing eight genes was identified for belly spotting. A second region containing one gene (Rcn1) was identified for the extreme microphthalmia phenotype. Rcn1 is a Ca+2-binding protein, resident in the endoplasmic reticulum, participates in the secretory pathway and expressed in the eye. Our results suggest that deletion of Rcn1 directly or indirectly contributes to the eye phenotype in Pax6 contiguous gene deletions.
Favor, Jack; Bradley, Alan; Conte, Nathalie; Janik, Dirk; Pretsch, Walter; Reitmeir, Peter; Rosemann, Michael; Schmahl, Wolfgang; Wienberg, Johannes; Zaus, Irmgard
Short and Long-term memory in Drosophila require cAMP signaling in distinct neuron types
Summary Background A common feature of memory and its underlying synaptic plasticity is that each can be dissected into short-lived forms involving modification or trafficking of existing proteins and long-term forms that require new gene expression. An underlying assumption of this cellular view of memory consolidation is that these different mechanisms occur within a single neuron. At the neuro-anatomical level, however, different temporal stages of memory can engage distinct neural circuits, a notion that has not been conceptually integrated with the cellular view. Results We have investigated this issue in the context of aversive Pavlovian olfactory memory in Drosophila. Previous studies have demonstrated a central role for cAMP signaling in the mushroom body (MB). The Ca++ responsive adenylyl cyclase rutabaga is believed to be a coincidence detector in ? neurons, one of the three principle classes of MB Kenyon cells. We are able to separately restore short-term or long-term memory to a rutabaga mutant with expression of rutabaga in different subsets of MB neurons. Conclusions Our findings suggest a model in which the learning experience initiates two parallel associations: a short-lived trace in MB ? neurons, and a long-lived trace in ?/? neurons.
Blum, Allison L.; Li, Wanhe; Cressy, Mike; Dubnau, Josh
Colon cancer molecular subtypes identified by expression profiling and associated to stroma, mucinous type and different clinical behavior
Background Colon cancer patients with the same stage show diverse clinical behavior due to tumor heterogeneity. We aimed to discover distinct classes of tumors based on microarray expression patterns, to analyze whether the molecular classification correlated with the histopathological stages or other clinical parameters and to study differences in the survival. Methods Hierarchical clustering was performed for class discovery in 88 colon tumors (stages I to IV). Pathways analysis and correlations between clinical parameters and our classification were analyzed. Tumor subtypes were validated using an external set of 78 patients. A 167 gene signature associated to the main subtype was generated using the 3-Nearest-Neighbor method. Coincidences with other prognostic predictors were assesed. Results Hierarchical clustering identified four robust tumor subtypes with biologically and clinically distinct behavior. Stromal components (p?0.001), nuclear ?-catenin (p?=?0.021), mucinous histology (p?=?0.001), microsatellite-instability (p?=?0.039) and BRAF mutations (p?0.001) were associated to this classification but it was independent of Dukes stages (p?=?0.646). Molecular subtypes were established from stage I. High-stroma-subtype showed increased levels of genes and altered pathways distinctive of tumour-associated-stroma and components of the extracellular matrix in contrast to Low-stroma-subtype. Mucinous-subtype was reflected by the increased expression of trefoil factors and mucins as well as by a higher proportion of MSI and BRAF mutations. Tumor subtypes were validated using an external set of 78 patients. A 167 gene signature associated to the Low-stroma-subtype distinguished low risk patients from high risk patients in the external cohort (Dukes B and C:HR?=?8.56(2.53-29.01); Dukes B,C and D:HR?=?1.87(1.07-3.25)). Eight different reported survival gene signatures segregated our tumors into two groups the Low-stroma-subtype and the other tumor subtypes. Conclusions We have identified novel molecular subtypes in colon cancer with distinct biological and clinical behavior that are established from the initiation of the tumor. Tumor microenvironment is important for the classification and for the malignant power of the tumor. Differential gene sets and biological pathways characterize each tumor subtype reflecting underlying mechanisms of carcinogenesis that may be used for the selection of targeted therapeutic procedures. This classification may contribute to an improvement in the management of the patients with CRC and to a more comprehensive prognosis.
A novel type III crustin (CrusEs2) identified from Chinese mitten crab Eriocheir sinensis.
Antimicrobial peptides are important effectors in the host innate immune response against microbial invasion. In the present study, the cDNA encoding a crustin (designated CrusEs2) was cloned from Chinese mitten crab Eriocheir sinensis by using EST analysis and rapid amplification of cDNA ends (RACE) approach. The full-length cDNA of CrusEs2 was of 1237 bp, containing a 5' untranslated region (UTR) of 12 bp, a 3' UTR of 886 bp with a poly (A) tail, and an open reading frame (ORF) of 339 bp encoding a polypeptide of 112 amino acids with a signal peptide of 19 amino acids. The CrusEs2 contained a typical WAP domain, but lacked the Gly-rich domain of the type II crustin and the Cys-rich region present in both type I and type II crustin, suggesting that CrusEs2 should be classified as a type III crustin. The mRNA transcripts of CrusEs2 could be detected in haemocytes and gill, and its expression level in haemocytes was up-regulated after Listonella anguillarum challenge, while decreased after Micrococcus luteus challenge. The mature peptide coding region of CrusEs2 was cloned into pET-21a+ and expressed in Escherichia coli. The purified recombinant CrusEs2 inhibited the growth of Gram-positive bacteria at MIC of 0.093-0.37 ?M. The results indicated that CrusEs2 was involved in immune response of E. sinensis against bacterial challenge. PMID:21549196
Mu, Changkao; Zheng, Peilin; Zhao, Jianmin; Wang, Lingling; Qiu, Limei; Zhang, Huan; Gai, Yunchao; Song, Linsheng
A case of type IV solar urticaria identified by reverse in vitro serum test.
We had a 17-year-old male patient with solar urticaria diagnosed as type IV of modified Harber's classification. The action spectrum of this case was estimated to be 433-499 nm and the inhibition spectrum was 533 nm. Both in vitro serum test and tentatively designated "reverse in vitro serum test" were positive. The patient was prescribed 20 mg/day epinastine hydrochloride (Alesion) orally for 49 weeks with improvement of the symptoms. PMID:14714829
Ozaki, Hirotake; Matsuyama, Takashi; Kawakubo, Yo; Miyahara, Motomi; Ozawa, Akira
Cytotoxic T cells kill influenza virus infected cells but do not distinguish between serologically distinct type A viruses
THE molecular basis of recognition and target cell killing by cytotoxic T cells is still unknown. Doherty and Zinkernagel showed that mouse cells infected with lymphocytic choriomeningitis virus can be lysed by immune cytotoxic T cells but only if both cell types share at least part of the major histocompatibility (H-2) region (see ref. 1). H-2 compatibility is also required
H. J. Zweerink; S. A. Courtneidge; J. J. Skehel; M. J. Crumpton; Brigitte A. Askonas
No increase in bleeding identified in type 1 VWD subjects with D1472H sequence variation.
The diagnosis of von Willebrand disease (VWD) is complicated by issues with current laboratory testing, particularly the ristocetin cofactor activity assay (VWF:RCo). We have recently reported a sequence variation in the von Willebrand factor (VWF) A1 domain, p.D1472H (D1472H), associated with a decrease in the VWF:RCo/VWF antigen (VWF:Ag) ratio but not associated with bleeding in healthy control subjects. This report expands the previous study to include subjects with symptoms leading to the diagnosis of type 1 VWD. Type 1 VWD subjects with D1472H had a significant decrease in the VWF:RCo/VWF:Ag ratio compared with those without D1472H, similar to the findings in the healthy control population. No increase in bleeding score was observed, however, for VWD subjects with D1472H compared with those without D1472H. These results suggest that the presence of the D1472H sequence variation is not associated with a significant increase in bleeding symptoms, even in type 1 VWD subjects. PMID:23520336
Flood, Veronica H; Friedman, Kenneth D; Gill, Joan Cox; Haberichter, Sandra L; Christopherson, Pamela A; Branchford, Brian R; Hoffmann, Raymond G; Abshire, Thomas C; Dunn, Amy L; Di Paola, Jorge A; Hoots, W Keith; Brown, Deborah L; Leissinger, Cindy; Lusher, Jeanne M; Ragni, Margaret V; Shapiro, Amy D; Montgomery, Robert R
No increase in bleeding identified in type 1 VWD subjects with D1472H sequence variation
The diagnosis of von Willebrand disease (VWD) is complicated by issues with current laboratory testing, particularly the ristocetin cofactor activity assay (VWF:RCo). We have recently reported a sequence variation in the von Willebrand factor (VWF) A1 domain, p.D1472H (D1472H), associated with a decrease in the VWF:RCo/VWF antigen (VWF:Ag) ratio but not associated with bleeding in healthy control subjects. This report expands the previous study to include subjects with symptoms leading to the diagnosis of type 1 VWD. Type 1 VWD subjects with D1472H had a significant decrease in the VWF:RCo/VWF:Ag ratio compared with those without D1472H, similar to the findings in the healthy control population. No increase in bleeding score was observed, however, for VWD subjects with D1472H compared with those without D1472H. These results suggest that the presence of the D1472H sequence variation is not associated with a significant increase in bleeding symptoms, even in type 1 VWD subjects.
Friedman, Kenneth D.; Gill, Joan Cox; Haberichter, Sandra L.; Christopherson, Pamela A.; Branchford, Brian R.; Hoffmann, Raymond G.; Abshire, Thomas C.; Dunn, Amy L.; Di Paola, Jorge A.; Hoots, W. Keith; Brown, Deborah L.; Leissinger, Cindy; Lusher, Jeanne M.; Ragni, Margaret V.; Shapiro, Amy D.; Montgomery, Robert R.
Distinct phases of cryogenic tissue damage in the cerebral cortex of wild-type and c-fos deficient mice.
To characterize the development of tissue damage following cryogenic injury to the mouse cortex, the time course of histopathological changes, transcriptional responses and DNA strand breaks following application of a liquid nitrogen-cooled probe to the surface of the parietal bone were assessed. Distinct phases of tissue damage were observed: after 30 min, there was demarcation of a core lesion followed by mainly necrotic cell death starting 2 h after injury. At 12 hours, progressive apoptotic death of scattered cells in the periphery of the core lesion was detected, resembling the penumbra observed in ischaemic stroke. In situ hybridization for c-fos revealed an absence of expression in the core region, suggesting early cessation of transcription. There was strong induction of c-fos in the penumbra 30 min after the lesion, which had spread over the ipsilateral hemisphere at 2 h, possibly caused by peri-infarction depolarization. At later time points, sustained expression of c-fos was observed in some cells in the penumbra. Since a role for c-fos has been postulated in the initiation or execution of apoptotic pathways, the susceptibility of c-fos deficient mice was explored (n=4) in this model. Cryoinjury-induced tissue injury was markedly attenuated in c-fos deficient mice. A model of the phases and mechanisms of cryogenic injury is proposed, which discriminates an early phase characterized by physical changes caused by hypothermia and their immediate consequences (i.e. transcriptional block), an intermediate phase where secondary changes lead to necrosis in the core region, and a final phase of delayed apoptotic cell death in the penumbra. PMID:10632897
Steinbach, J P; Weissenberger, J; Aguzzi, A
A distinct type of glycerol-3-phosphate acyltransferase with sn-2 preference and phosphatase activity producing 2-monoacylglycerol.
The first step in assembly of membrane and storage glycerolipids is acylation of glycerol-3-phosphate (G3P). All previously characterized membrane-bound, eukaryotic G3P acyltransferases (GPATs) acylate the sn-1 position to produce lysophosphatidic acid (1-acyl-LPA). Cutin is a glycerolipid with omega-oxidized fatty acids and glycerol as integral components. It occurs as an extracellular polyester on the aerial surface of all plants, provides a barrier to pathogens and resistance to stress, and maintains organ identity. We have determined that Arabidopsis acyltransferases GPAT4 and GPAT6 required for cutin biosynthesis esterify acyl groups predominantly to the sn-2 position of G3P. In addition, these acyltransferases possess a phosphatase domain that results in sn-2 monoacylglycerol (2-MAG) rather than LPA as the major product. Such bifunctional activity has not been previously described in any organism. The possible roles of 2-MAGs as intermediates in cutin synthesis are discussed. GPAT5, which is essential for the accumulation of suberin aliphatics, also exhibits a strong preference for sn-2 acylation. However, phosphatase activity is absent and 2-acyl-LPA is the major product. Clearly, plant GPATs can catalyze more reactions than the sn-1 acylation by which they are currently categorized. Close homologs of GPAT4-6 are present in all land plants, but not in animals, fungi or microorganisms (including algae). Thus, these distinctive acyltransferases may have been important for evolution of extracellular glycerolipid polymers and adaptation of plants to a terrestrial environment. These results provide insight into the biosynthetic assembly of cutin and suberin, the two most abundant glycerolipid polymers in nature. PMID:20551224
Yang, Weili; Pollard, Mike; Li-Beisson, Yonghua; Beisson, Fred; Feig, Michael; Ohlrogge, John
A new point mutation in the ND1 mitochondrial gene identified in a type II diabetic patient
A novel mutation in a mitochondrial gene was identified in a patient with type II diabetes mellitus. G-to-A transition was localized at the nt3316 position of gene ND1 and resulted in alanine threonine replacement at position 4 of mitochondrial NAD-H-dehydrogenase. 6 refs., 2 figs.
Kalinin, V.N. [Research Center of Medical Genetics, Moscow (Russian Federation); Schmidt, W.; Olek, K. [Institut fuer Molekularbiologische Diagnostik, Bonn (Germany)] [and others
Definition of Genetic Events Directing the Development of Distinct Types of Brain Tumors from Postnatal Neural Stem/Progenitor Cells
Although brain tumors are classified and treated based upon their histology, the molecular factors involved in the development of various tumor types remain unknown. In this study, we show that the type and order of genetic events directs the development of gliomas, central nervous system primitive neuroectodermal tumors, and atypical teratoid/rhabdoid-like tumors from postnatal mouse neural stem/progenitor cells (NSC/NPC). We found that the overexpression of specific genes led to the development of these three different brain tumors from NSC/NPCs, and manipulation of the order of genetic events was able to convert one established tumor type into another. In addition, loss of the nuclear chromatin-remodeling factor SMARCB1 in rhabdoid tumors led to increased phosphorylation of eIF2?, a central cytoplasmic unfolded protein response (UPR) component, suggesting a role for the UPR in these tumors. Consistent with this, application of the proteasome inhibitor bortezomib led to an increase in apoptosis of human cells with reduced SMARCB1 levels. Taken together, our findings indicate that the order of genetic events determines the phenotypes of brain tumors derived from a common precursor cell pool, and suggest that the UPR may represent a therapeutic target in atypical teratoid/rhabdoid tumors.
Hertwig, Falk; Meyer, Katharina; Braun, Sebastian; Ek, Sara; Spang, Rainer; Pfenninger, Cosima V.; Artner, Isabella; Prost, Gaelle; Chen, Xinbin; Biegel, Jaclyn A.; Judkins, Alexander R.; Englund, Elisabet; Nuber, Ulrike A.
Two phenotypically distinct T cells are involved in ultraviolet-irradiated urocanic acid-induced suppression of the efferent delayed-type hypersensitivity response to herpes simplex virus, type 1 in vivo
When UVB-irradiated urocanic acid, the putative photoreceptor/mediator for UVB suppression, is administered to mice it induces a dose-dependent suppression of the delayed-type hypersensitivity response to herpes simplex virus, type 1 (HSV-1), of similar magnitude to that induced by UV irradiation of mice. In this study, the efferent suppression of delayed-type hypersensitivity by UV-irradiated urocanic acid is demonstrated to be due to 2 phenotypically distinct T cells, (Thy1+, L3T4-, Ly2+) and (Thy1+, L3T4+, Ly2-). The suppression is specific for HSV-1. This situation parallels the generation of 2 distinct T-suppressor cells for HSV-1 by UV irradiation of mice and provides further evidence for the involvement of urocanic acid in the generation of UVB suppression.
Ross, J.A.; Howie, S.E.; Norval, M.; Maingay, J.
The N-terminal region of Pseudomonas type III effector AvrPtoB elicits Pto-dependent immunity and has two distinct virulence determinants.
Resistance to bacterial speck disease in tomato is activated by the physical interaction of the host Pto kinase with either of the sequence-dissimilar type III effector proteins AvrPto or AvrPtoB (HopAB2) from Pseudomonas syringae pv. tomato. Pto-mediated immunity requires Prf, a protein with a nucleotide-binding site and leucine-rich repeats. The N-terminal 307 amino acids of AvrPtoB were previously reported to interact with the Pto kinase, and we show here that this region (AvrPtoB(1-307)) is sufficient for eliciting Pto/Prf-dependent immunity against P. s. pv. tomato. AvrPtoB(1-307) was also found to be sufficient for a virulence activity that enhances ethylene production and increases growth of P. s. pv. tomato and severity of speck disease on susceptible tomato lines lacking either Pto or Prf. Moreover, we found that residues 308-387 of AvrPtoB are required for the previously reported ability of AvrPtoB to suppress pathogen-associated molecular patterns-induced basal defenses in Arabidopsis. Thus, the N-terminal region of AvrPtoB has two structurally distinct domains involved in different virulence-promoting mechanisms. Random and targeted mutagenesis identified five tightly clustered residues in AvrPtoB(1-307) that are required for interaction with Pto and for elicitation of immunity to P. s. pv. tomato. Mutation of one of the five clustered residues abolished the ethylene-associated virulence activity of AvrPtoB(1-307). However, individual mutations of the other four residues, despite abolishing interaction with Pto and avirulence activity, had no effect on AvrPtoB(1-307) virulence activity. None of these mutations affected the basal defense-suppressing activity of AvrPtoB(1-387). Based on sequence alignments, estimates of helical propensity, and the previously reported structure of AvrPto, we hypothesize that the Pto-interacting domains of AvrPto and AvrPtoB(1-307) have structural similarity. Together, these data support a model in which AvrPtoB(1-307) promotes ethylene-associated virulence by interaction not with Pto but with another unknown host protein. PMID:17764515
Xiao, Fangming; He, Ping; Abramovitch, Robert B; Dawson, Jennifer E; Nicholson, Linda K; Sheen, Jen; Martin, Gregory B
Differential Expression Profiling of Spleen MicroRNAs in Response to Two Distinct Type II Interferons in Tetraodon nigroviridis
MicroRNAs are endogenous, small non-coding RNAs approximately 18–26 nucleotides in length that regulate target gene expression at the post-transcription level. Interferon-? (IFN-?) is a Th1 cytokine that is involved in both the innate and adaptive immune responses. We previously identified two IFN-? genes in green-spotted puffer fish (Tetraodon nigroviridis). To determine whether miRNAs participate in IFN-?-related immune responses, T. nigroviridis spleen cells were treated with recombinant IFN-? isoforms, and a Solexa high-throughput sequencing method was used to identify miRNAs. In total, 1,556, 1,538 and 1,573 miRNAs were found in the three samples, and differentially expressed miRNAs were determined. In total, 398 miRNAs were differentially expressed after rIFN-?1 treatment, and 438 miRNAs were differentially expressed after rIFN-?2 treatment; additionally, 403 miRNAs were differentially expressed between the treatment groups. Ten differentially expressed miRNAs were chosen for validation using qRT-PCR. Target genes for the differentially expressed miRNAs were predicted, and GO and KEGG analyses were performed. This study provides basic knowledge regarding fish IFN-?-induced miRNAs and offers clues for further studies into the mechanisms underlying fish IFN-?-mediated immune responses.
Peng, Wan; Wang, Ting; Zhang, Yong; Lin, Haoran
Two distinct ferroelectric phases in the multiferroic Y -type hexaferrite Ba2Mg2Fe12O22
NASA Astrophysics Data System (ADS)
The magnetic phase diagram of the Y -type hexaferrite Ba2Mg2Fe12O22 has been studied using single-crystal neutron diffraction. The result indicates successive phase transitions where the magnetic modulation wave number changed discontinuously when a magnetic field is applied and the temperature is varied. For the low-temperature spin-driven ferroelectric state, we have found a sixfold structure with q=(001/2) in weak magnetic fields and a twofold structure with q=(003/2) in strong magnetic fields between which a first-order transition intervenes accompanied by a hysteresis.
Sagayama, Hajime; Taniguchi, Kouji; Abe, Nobuyuki; Arima, Taka-Hisa; Nishikawa, Yusaku; Yano, Shin-Ichiro; Kousaka, Yusuke; Akimitsu, Jun; Matsuura, Masato; Hirota, Kazuma
Levels of three distinct p75 neurotrophin receptor forms found in human plasma are altered in type 2 diabetic patients
Aims\\/hypothesis The p75 neurotrophin receptor (p75NTR) has been shown to appear in the plasma of diabetic rats, possibly indicating diabetic\\u000a neuropathy. The aim of this study was to use a semi-quantitative assay for human plasma p75NTR to investigate whether this\\u000a receptor is a marker of peripheral diabetic neuropathy (DPN) and autonomic cardiovascular neuropathy (CAN) in type 2 diabetic\\u000a patients.\\u000a \\u000a \\u000a \\u000a Subjects and
P. M. Humpert; S. Kopf; Z. Djuric; K. Laine; G. Korosoglou; G. Rudofsky Jr; A. Hamann; M. Morcos; M. von Eynatten; P. P. Nawroth; A. Bierhaus
Ultrastructural characteristics of novel epithelial cell types identified in human pathologic liver specimens with chronic ductular reaction.
Previous immunohistochemical studies on human liver biopsies with chronic ductular reaction revealed the presence of "small cells" with bile-duct type cytokeratin profile in the periportal area. This study identified similar cells by electron microscopy. The authors studied 13 human liver specimens with various liver diseases, but all characterized by chronic ductular reaction. In all specimens, variable numbers of "small cells" with common epithelial characteristics were identified in the periportal area. They could be classified into three types. Type I cells showed an oval cell shape and oval nucleus, early or established formation of junctional complexes with adjacent cells, a full assortment of cytoplasmic organelles, and bundles of tonofilaments. Type II cells showed features of bile-duct cell differentiation, including lateral interdigitations, apical microvilli, basal pinocytotic vacuoles, and basement membrane formation. In contrast, type III cells displayed additional features indicating hepatocellular differentiation, such as a more prominent nucleus, formation of a hemicanaliculus, and glycogen rosettes. It is concluded that these small cells of epithelial nature display variable differentiation characteristics of either bile-duct type cells or hepatocytes. These findings support the existence of bipotential progenitor epithelial cells in human liver. They may have implications for liver regeneration and carcinogenesis. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9
De Vos, R.; Desmet, V.
Distinct and Atypical Intrinsic and Extrinsic Cell Death Pathways between Photoreceptor Cell Types upon Specific Ablation of Ranbp2 in Cone Photoreceptors
Non-autonomous cell-death is a cardinal feature of the disintegration of neural networks in neurodegenerative diseases, but the molecular bases of this process are poorly understood. The neural retina comprises a mosaic of rod and cone photoreceptors. Cone and rod photoreceptors degenerate upon rod-specific expression of heterogeneous mutations in functionally distinct genes, whereas cone-specific mutations are thought to cause only cone demise. Here we show that conditional ablation in cone photoreceptors of Ran-binding protein-2 (Ranbp2), a cell context-dependent pleiotropic protein linked to neuroprotection, familial necrotic encephalopathies, acute transverse myelitis and tumor-suppression, promotes early electrophysiological deficits, subcellular erosive destruction and non-apoptotic death of cones, whereas rod photoreceptors undergo cone-dependent non-autonomous apoptosis. Cone-specific Ranbp2 ablation causes the temporal activation of a cone-intrinsic molecular cascade highlighted by the early activation of metalloproteinase 11/stromelysin-3 and up-regulation of Crx and CoREST, followed by the down-modulation of cone-specific phototransduction genes, transient up-regulation of regulatory/survival genes and activation of caspase-7 without apoptosis. Conversely, PARP1+-apoptotic rods develop upon sequential activation of caspase-9 and caspase-3 and loss of membrane permeability. Rod photoreceptor demise ceases upon cone degeneration. These findings reveal novel roles of Ranbp2 in the modulation of intrinsic and extrinsic cell death mechanisms and pathways. They also unveil a novel spatiotemporal paradigm of progression of neurodegeneration upon cell-specific genetic damage whereby a cone to rod non-autonomous death pathway with intrinsically distinct cell-type death manifestations is triggered by cell-specific loss of Ranbp2. Finally, this study casts new light onto cell-death mechanisms that may be shared by human dystrophies with distinct retinal spatial signatures as well as with other etiologically distinct neurodegenerative disorders.
Cho, Kyoung-in; Yu, Minzhong; Hao, Ying; Qiu, Sunny; Pillai, Indulekha C. L.; Peachey, Neal S.; Ferreira, Paulo A.
Ticking Stellar Time Bomb Identified - Astronomers find prime suspect for a Type Ia supernova
NASA Astrophysics Data System (ADS)
Using ESO's Very Large Telescope and its ability to obtain images as sharp as if taken from space, astronomers have made the first time-lapse movie of a rather unusual shell ejected by a "vampire star", which in November 2000 underwent an outburst after gulping down part of its companion's matter. This enabled astronomers to determine the distance and intrinsic brightness of the outbursting object. It appears that this double star system is a prime candidate to be one of the long-sought progenitors of the exploding stars known as Type Ia supernovae, critical for studies of dark energy. "One of the major problems in modern astrophysics is the fact that we still do not know exactly what kinds of stellar system explode as a Type Ia supernova," says Patrick Woudt, from the University of Cape Town and lead author of the paper reporting the results. "As these supernovae play a crucial role in showing that the Universe's expansion is currently accelerating, pushed by a mysterious dark energy, it is rather embarrassing." The astronomers studied the object known as V445 in the constellation of Puppis ("the Stern") in great detail. V445 Puppis is the first, and so far only, nova showing no evidence at all for hydrogen. It provides the first evidence for an outburst on the surface of a white dwarf [1] dominated by helium. "This is critical, as we know that Type Ia supernovae lack hydrogen," says co-author Danny Steeghs, from the University of Warwick, UK, "and the companion star in V445 Pup fits this nicely by also lacking hydrogen, instead dumping mainly helium gas onto the white dwarf." In November 2000, this system underwent a nova outburst, becoming 250 times brighter than before and ejecting a large quantity of matter into space. The team of astronomers used the NACO adaptive optics instrument [2] on ESO's Very Large Telescope (VLT) to obtain very sharp images of V445 Puppis over a time span of two years. The images show a bipolar shell, initially with a very narrow waist, with lobes on each side. Two knots are also seen at both the extreme ends of the shell, which appear to move at about 30 million kilometres per hour. The shell - unlike any previously observed for a nova - is itself moving at about 24 million kilometres per hour. A thick disc of dust, which must have been produced during the last outburst, obscures the two central stars. "The incredible detail that we can see on such small scales - about hundred milliarcseconds, which is the apparent size of a one euro coin seen from about forty kilometres - is only possible thanks to the adaptive optics technology available on large ground-based telescopes such as ESO's VLT," says Steeghs. A supernova is one way that a star can end its life, exploding in a display of grandiose fireworks. One family of supernovae, called Type Ia supernovae, are of particular interest in cosmology as they can be used as "standard candles" to measure distances in the Universe [3] and so can be used to calibrate the accelerating expansion that is driven by dark energy. One defining characteristic of Type Ia supernovae is the lack of hydrogen in their spectrum. Yet hydrogen is the most common chemical element in the Universe. Such supernovae most likely arise in systems composed of two stars, one of them being the end product of the life of sun-like stars, or white dwarfs. When such white dwarfs, acting as stellar vampires that suck matter from their companion, become heavier than a given limit, they become unstable and explode [4]. The build-up is not a simple process. As the white dwarf cannibalises its prey, matter accumulates on its surface. If this layer becomes too dense, it becomes unstable and erupts as a nova. These controlled, mini-explosions eject part of the accumulated matter back into space. The crucial question is thus to know whether the white dwarf can manage to gain weight despite the outburst, that is, if some of the matter taken from the companion stays on the white dwarf, so that it will eventual
Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies.
CD20 is a cell-surface marker of normal and malignant B cells. Rituximab, a monoclonal antibody targeting CD20, has improved the treatment of malignant lymphomas. Therapeutic CD20 antibodies are classified as either type I or II based on different mechanisms of killing malignant B cells. To reveal the molecular basis of this distinction, we fine-mapped the epitopes recognized by both types. We also determined the first X-ray structure of a type II antibody by crystallizing the obinutuzumab (GA101) Fab fragment alone and in complex with a CD20 cyclopeptide. Despite recognizing an overlapping epitope, GA101 binds CD20 in a completely different orientation than type I antibodies. Moreover, the elbow angle of GA101 is almost 30° wider than in type I antibodies, potentially resulting in different spatial arrangements of 2 CD20 molecules bound to a single GA101 or rituximab molecule. Using protein tomography, different CD20 complexes were found to be associated with the 2 antibodies, and confocal microscopy showed different membrane compartmentalization of these subpopulations of the cellular CD20 pool. Our findings offer a possible molecular explanation for the different cellular responses elicited by type I and II antibodies. PMID:21444918
Niederfellner, Gerhard; Lammens, Alfred; Mundigl, Olaf; Georges, Guy J; Schaefer, Wolfgang; Schwaiger, Manfred; Franke, Andreas; Wiechmann, Kornelius; Jenewein, Stefan; Slootstra, Jerry W; Timmerman, Peter; Brännström, Annika; Lindstrom, Frida; Mössner, Ekkehard; Umana, Pablo; Hopfner, Karl-Peter; Klein, Christian
Generation and characterization of yeast two-hybrid cDNA libraries derived from two distinct mouse pluripotent cell types.
Pluripotent stem cells have the therapeutic potential in future regenerative medicine applications. Therefore, it is highly important to understand the molecular mechanisms governing the pluripotency and differentiation potential of these cells. Our current knowledge of pluripotent cells is largely limited owing to the candidate gene/protein approach rather than studying the complex interactions of the proteins. Experimentally, yeast two-hybrid system (Y2H) is by far the most useful and widely used method to detect the protein-protein interactions in high-throughput screenings. Unfortunately, currently there is no GAL4-based pluripotent stem cell-specific cDNA library available for screening the interaction proteins impeding the large-scale studies. In this study, we report the construction of Y2H cDNA libraries derived from mouse pluripotent embryonic stem cells (ESCs) and multipotent adult germ-line stem cells (maGSCs) in GAL4-based Y2H vector system with very high transformation efficiency. Furthermore, we have constructed two different baits and screened for interaction partners in an effort to characterize the libraries and also as a part of our ongoing studies. Consequently, many putative interaction proteins were identified in both cases and their interaction was further validated by direct-Y2H. The observed interactions between bait proteins and their respective analyzed putative interaction proteins were further confirmed using two independent approaches in mammalian cells, thus highlighting the biological significance of the identified interactor (s). Finally, we would like to make these cDNA libraries as a resource that can be distributed to the research community. PMID:22674187
Zheng, Ying; Tan, Xiaoying; Pyczek, Joanna; Nolte, Jessica; Pantakani, D V Krishna; Engel, Wolfgang
A New Type of Signal Peptidase Cleavage Site Identified in an RNA Virus Polyprotein*
Pestiviruses, a group of enveloped positive strand RNA viruses belonging to the family Flaviviridae, express their genes via a polyprotein that is subsequently processed by proteases. The structural protein region contains typical signal peptidase cleavage sites. Only the site at the C terminus of the glycoprotein Erns is different because it does not contain a hydrophobic transmembrane region but an amphipathic helix functioning as the Erns membrane anchor. Despite the absence of a hydrophobic region, the site between the C terminus of Erns and E1, the protein located downstream in the polyprotein, is cleaved by signal peptidase, as demonstrated by mutagenesis and inhibitor studies. Thus, ErnsE1 is processed at a novel type of signal peptidase cleavage site showing a different membrane topology. Prevention of glycosylation or introduction of mutations into the C-terminal region of Erns severely impairs processing, presumably by preventing proper membrane interaction or disturbing a conformation critical for the protein to be accepted as a substrate by signal peptidase.
Bintintan, Ioana; Meyers, Gregor
Use of Ribotyping and Hemolysin Activity To Identify Highly Virulent Streptococcus suis Type 2 Isolates†
Nineteen Streptococcus suis type 2 isolates were evaluated for their virulence in pigs and mice. Of these, seven were determined to be highly virulent in pigs on the basis of clinical sign scores and gross pathology and histopathology results. Clinical sign scores correlated with gross pathology and histopathology scores at P equal to 0.004 and P equal to 0.009, respectively. The virulence of highly virulent isolates in pigs compared somewhat with virulence in mice, but the correlation was not significant. No correlation of virulence was noted among the moderately virulent and avirulent isolates in pigs and mice. Chromosomal DNAs from all S. suis isolates were evaluated by PstI, PvuII, EcoRI, and HaeIII restriction enzyme digestion followed by hybridization with a digoxigenin-11-dUTP-labeled cDNA probe transcribed from 16S and 23S rRNAs from Escherichia coli. The hybridization patterns (ribotypes) varied depending upon the enzyme used, but a significant number of isolates determined to be highly virulent in pigs had unique hybridization patterns compared with those of the moderately virulent and avirulent isolates (P = 0.002). In addition, hemolysin activity showed a high correlation to virulence (P = 0.00008) and ribotype (P = 0.002).
Staats, Jacque J.; Plattner, Brandon L.; Nietfeld, Jerome; Dritz, Steve; Chengappa, M. M.
DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients
In addition to genetic predisposition, environmental and lifestyle factors contribute to the pathogenesis of type 2 diabetes (T2D). Epigenetic changes may provide the link for translating environmental exposures into pathological mechanisms. In this study, we performed the first comprehensive DNA methylation profiling in pancreatic islets from T2D and non-diabetic donors. We uncovered 276 CpG loci affiliated to promoters of 254 genes displaying significant differential DNA methylation in diabetic islets. These methylation changes were not present in blood cells from T2D individuals nor were they experimentally induced in non-diabetic islets by exposure to high glucose. For a subgroup of the differentially methylated genes, concordant transcriptional changes were present. Functional annotation of the aberrantly methylated genes and RNAi experiments highlighted pathways implicated in ?-cell survival and function; some are implicated in cellular dysfunction while others facilitate adaptation to stressors. Together, our findings offer new insights into the intricate mechanisms of T2D pathogenesis, underscore the important involvement of epigenetic dysregulation in diabetic islets and may advance our understanding of T2D aetiology.
Volkmar, Michael; Dedeurwaerder, Sarah; Cunha, Daniel A; Ndlovu, Matladi N; Defrance, Matthieu; Deplus, Rachel; Calonne, Emilie; Volkmar, Ute; Igoillo-Esteve, Mariana; Naamane, Najib; Del Guerra, Silvia; Masini, Matilde; Bugliani, Marco; Marchetti, Piero; Cnop, Miriam; Eizirik, Decio L; Fuks, Francois
Type A and B monoamine oxidase in age-related neurodegenerative disorders: their distinct roles in neuronal death and survival.
In neurodegenerative disorders, including Parkinson's and Alzheimer's diseases, type B monoamine oxidase (MAO-B) has been proposed to play a primary role though generating reactive oxygen species in oxidation of monoamine substrates. MAO-B oxidizes MPTP into MPP+, and an MAO-B inhibitor, deprenyl, prevents the MPTP oxidation and also MPP+neutotoxicity. These results suggest the association of MAO-B with neuronal death in neurodegenerative disorders. On the other hand, deprenyl and rasagiline, selective MAO-B inhibitors, have been proved to protect neuronal cells in cellular and animal models of neurodegeneration. These inhibitors decrease oxidation of the substrates, scavenge oxygen radicals, intervene apoptosis signal pathway in mitochondria and induce pro-survival genes coding anti-apoptotic Bcl-2 and neurotrophic factors. However, the association of MAO-B itself with the neuroprotective function of MAO-B inhibitors remains enigmatic. Recently, the involvement of type A MAO (MAO-A) in neuronal death has been shown by upregulation MAO-A expression in cellular models. MAO-A is a target of an endogenous neurotoxin, Nmethyl( R)salsolinol, and MAO-A knockdown (KO) with short interfering (si)RNA protects neuronal death from apoptosis. In addition, MAO-A mediates the increased expression of genes for anti-apoptotic, pro-survival Bcl-2 and neurotrophic factors by MAO-B inhibitors, whereas MAO-B doe not. In this review, we present our recent results on the novel role of MAO-A and MAO-B in neuronal death and also in the neuroprotective gene induction by MAO inhibitors. The future development of new series of neuroprotective drugs is discussed among compounds, which have high affinity to MAO-A and can induce pro-survival genes. MAO-A is expected to play a role in disease-modifying therapy for neurodegenerative disorders. PMID:23231395
Naoi, Makoto; Maruyama, Wakako; Inaba-Hasegawa, Keiko
A-type and B-type lamins initiate layer assembly at distinct areas of the nuclear envelope in living cells
To investigate nuclear lamina re-assembly in vivo, Drosophila A-type and B-type lamins were artificially expressed in Drosophila lamin Dm{sub 0}null mutant brain cells. Both exogenous lamin C (A-type) and Dm{sub 0} (B-type) formed sub-layers at the nuclear periphery, and efficiently reverted the abnormal clustering of the NPC. Lamin C initially appeared where NPCs were clustered, and subsequently extended along the nuclear periphery accompanied by the recovery of the regular distribution of NPCs. In contrast, lamin Dm{sub 0} did not show association with the clustered NPCs during lamina formation and NPC spacing recovered only after completion of a closed lamin Dm{sub 0} layer. Further, when lamin Dm{sub 0} and C were both expressed, they did not co-polymerize, initiating layer formation in separate regions. Thus, A and B-type lamins reveal differing properties during lamina assembly, with A-type having the primary role in organizing NPC distribution. This previously unknown complexity in the assembly of the nuclear lamina could be the basis for intricate nuclear envelope functions.
Furukawa, Kazuhiro, E-mail: firstname.lastname@example.com [Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181 (Japan)] [Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181 (Japan); Ishida, Kazuya; Tsunoyama, Taka-aki; Toda, Suguru; Osoda, Shinichi; Horigome, Tsuneyoshi [Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181 (Japan)] [Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181 (Japan); Fisher, Paul A. [Department of Pharmacological Sciences, School of Medicine, University Medical Center, State University of New York at Stony Brook, Stony Brook, NY 11794-8651 (United States)] [Department of Pharmacological Sciences, School of Medicine, University Medical Center, State University of New York at Stony Brook, Stony Brook, NY 11794-8651 (United States); Sugiyama, Shin [Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602 (Japan)] [Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602 (Japan)
Identifying risk factors for clinically significant diabetic macula edema in patients with type 2 diabetes mellitus.
It is known that clinic blood pressure (BP), gender, cigarette smoking, dyslipidemia, anemia and thiazolidenediones (TZD) treatment are predictors for clinically significant diabetic macula edema (CSDME). We examined a most risky factor for CSDME in Japanese patients with type 2 diabetes mellitus (T2DM) and diabetic retinopathy (DR) confirmed using optical coherence tomography by multiple regression analysis (MRA). As the risk factors, wakening-up BP was added to such factors. Seven diabetic Japanese patients with CSDME (group 1) and 124 subjects without CSDME (group 2) assonated with DR using optical coherence tomography were studied. The durations of T2DM in groups 1 and 2 were 15±10 years and 20±15 years, respectively. There was no statistically difference in means of gender, duration, age, body mass index (BMI), HbA1c, TC, LDL and TC/HDL, serum creatinine, urinary albumin excretion rate, and clinic BP between two groups. Morning systolic home BP (MSHBP), cigarette smoking and foveal thickness were significantly (p<0.001) higher in group 1 than group 2, whereas visual acuity was significantly (p<0.00?) lower in group 1 than in group 2. The patients in both groups had received various kinds of drugs for hyperglycemia, hypertension and others. There were no significant differences in the variables in both groups. MRA revealed that MSHBP, cigarette smoking and pioglitazone as TZD treatment were significantly positive predictors for CSDME, while BMI had a significantly negative predictor. Other variables were not significantly correlated to CSDME. The review summarizes a multiple regression analysis revealed that MSHBP makes an addition to predictive factors for CSDME among risk factors reported previously in patient with T2DM. PMID:23363297
Kamoi, Kyuzi; Takeda, Keiji; Hashimoto, Kaoru; Tanaka, Reiko; Okuyama, Shinya
Identifying and meeting the challenges of insulin therapy in type 2 diabetes
Type 2 diabetes mellitus (T2DM) is a chronic illness that requires clinical recognition and treatment of the dual pathophysiologic entities of altered glycemic control and insulin resistance to reduce the risk of long-term micro- and macrovascular complications. Although insulin is one of the most effective and widely used therapeutic options in the management of diabetes, it is used by less than one-half of patients for whom it is recommended. Clinician-, patient-, and health care system-related challenges present numerous obstacles to insulin use in T2DM. Clinicians must remain informed about new insulin products, emerging technologies, and treatment options that have the potential to improve adherence to insulin therapy while optimizing glycemic control and mitigating the risks of therapy. Patient-related challenges may be overcome by actively listening to the patient's fears and concerns regarding insulin therapy and by educating patients about the importance, rationale, and evolving role of insulin in individualized self-treatment regimens. Enlisting the services of Certified Diabetes Educators and office personnel can help in addressing patient-related challenges. Self-management of diabetes requires improved patient awareness regarding the importance of lifestyle modifications, self-monitoring, and/or continuous glucose monitoring, improved methods of insulin delivery (eg, insulin pens), and the enhanced convenience and safety provided by insulin analogs. Health care system-related challenges may be improved through control of the rising cost of insulin therapy while making it available to patients. To increase the success rate of treatment of T2DM, the 2012 position statement from the American Diabetes Association and the European Association for the Study of Diabetes focused on individualized patient care and provided clinicians with general treatment goals, implementation strategies, and tools to evaluate the quality of care.
Sorli, Christopher; Heile, Michael K
Frequent Intratype Neutralization by Plasma Immunoglobulin A Identified in HIV Type 2 Infection
Abstract Human immunodeficiency virus type 2 (HIV-2) is less transmissible and less pathogenic compared to HIV-1 and, when matched for CD4+ T cell count, the plasma viral load in HIV-2-infected individuals is approximately one log lower than in HIV-1-infected individuals. The explanation for these observations is elusive, but differences in virus controlling immunity generated in the two infections may be contributing factors. In the present study, we investigated neutralization by immunoglobulin A (IgA), in parallel with IgG, purified from plasma of HIV-1, HIV-2, and HIV-1/HIV-2 dually (HIV-D) infected individuals. Neutralization was analyzed against HIV-1 and HIV-2 isolates using a plaque reduction assay. In HIV-2 infection, intratype-specific neutralization by IgA was frequently detected, although at a lesser magnitude then the corresponding IgG neutralizing titers. In contrast, neutralization by IgA could rarely be demonstrated in HIV-1 infection despite similar plasma IgA levels in both infections. In addition, IgA and IgG of HIV-D plasma neutralized the HIV-2 isolate more potently than the HIV-1 isolate, suggesting that the difference between neutralizing activity of plasma IgA and IgG depends on the virus itself. Taken together, these findings suggest that both IgA and IgG add to the potent intratype neutralizing activity detected in HIV-2 plasma, which may contribute to virus control in HIV-2 infection.
Mansson, Fredrik; Palm, Angelica A.; Vincic, Elzbieta; da Silva, Zacarias; Medstrand, Patrik; Norrgren, Hans; Fenyo, Eva Maria; Jansson, Marianne
Particular Candida albicans Strains in the Digestive Tract of Dyspeptic Patients, Identified by Multilocus Sequence Typing
Background Candida albicans is a human commensal that is also responsible for chronic gastritis and peptic ulcerous disease. Little is known about the genetic profiles of the C. albicans strains in the digestive tract of dyspeptic patients. The aim of this study was to evaluate the prevalence, diversity, and genetic profiles among C. albicans isolates recovered from natural colonization of the digestive tract in the dyspeptic patients. Methods and Findings Oral swab samples (n?=?111) and gastric mucosa samples (n?=?102) were obtained from a group of patients who presented dyspeptic symptoms or ulcer complaints. Oral swab samples (n?=?162) were also obtained from healthy volunteers. C. albicans isolates were characterized and analyzed by multilocus sequence typing. The prevalence of Candida spp. in the oral samples was not significantly different between the dyspeptic group and the healthy group (36.0%, 40/111 vs. 29.6%, 48/162; P > 0.05). However, there were significant differences between the groups in the distribution of species isolated and the genotypes of the C. albicans isolates. C. albicans was isolated from 97.8% of the Candida-positive subjects in the dyspeptic group, but from only 56.3% in the healthy group (P < 0.001). DST1593 was the dominant C. albicans genotype from the digestive tract of the dyspeptic group (60%, 27/45), but not the healthy group (14.8%, 4/27) (P < 0.001). Conclusions Our data suggest a possible link between particular C. albicans strain genotypes and the host microenvironment. Positivity for particular C. albicans genotypes could signify susceptibility to dyspepsia.
Gong, Yan-Bing; Zheng, Jian-Ling; Jin, Bo; Zhuo, De-Xiang; Huang, Zhu-Qing; Qi, He; Zhang, Wei; Duan, Wei; Fu, Ji-Ting; Wang, Chui-Jie; Mao, Ze-Bin
Distinct motor impairments of dopamine D1 and D2 receptor knockout mice revealed by three types of motor behavior
Both D1R and D2R knock out (KO) mice of the major dopamine receptors show significant motor impairments. However, there are some discrepant reports, which may be due to the differences in genetic background and experimental procedures. In addition, only few studies directly compared the motor performance of D1R and D2R KO mice. In this paper, we examined the behavioral difference among N10 congenic D1R and D2R KO, and wild type (WT) mice. First, we examined spontaneous motor activity in the home cage environment for consecutive 5 days. Second, we examined motor performance using the rota-rod task, a standard motor task in rodents. Third, we examined motor ability with the Step-Wheel task in which mice were trained to run in a motor-driven turning wheel adjusting their steps on foothold pegs to drink water. The results showed clear differences among the mice of three genotypes in three different types of behavior. In monitoring spontaneous motor activities, D1R and D2R KO mice showed higher and lower 24 h activities, respectively, than WT mice. In the rota-rod tasks, at a low speed, D1R KO mice showed poor performance but later improved, whereas D2R KO mice showed a good performance at early days without further improvement. When first subjected to a high speed task, the D2R KO mice showed poorer rota-rod performance at a low speed than the D1R KO mice. In the Step-Wheel task, across daily sessions, D2R KO mice increased the duration that mice run sufficiently close to the spout to drink water, and decreased time to touch the floor due to missing the peg steps and number of times the wheel was stopped, which performance was much better than that of D1R KO mice. These incongruent results between the two tasks for D1R and D2R KO mice may be due to the differences in the motivation for the rota-rod and Step-Wheel tasks, aversion- and reward-driven, respectively. The Step-Wheel system may become a useful tool for assessing the motor ability of WT and mutant mice.
Nakamura, Toru; Sato, Asako; Kitsukawa, Takashi; Momiyama, Toshihiko; Yamamori, Tetsuo; Sasaoka, Toshikuni
Distinct pattern of antibody reactivity with oligomeric or polymeric forms of the capsular polysaccharide of Haemophilus influenzae type b.
The chain length of oligosaccharides required for antibody binding has been studied by using the capsular polysaccharide from Haemophilus influenzae type b or oligosaccharides derived from it. The concentration of competing antigens required to achieve a 50% inhibition of antibody binding by human polyclonal antisera in an in vitro competition enzyme-linked immunosorbent assay decreased progressively from greater than 10(-3) to 5 x 10(-7) M as the inhibiting saccharide chain length increased from 1 to 262 repeat units. Even small oligosaccharides (one or two repeat units) are potentially capable of competing to a significant level if a high enough concentration of saccharides is used. A similar pattern of reactivity was seen with a monoclonal anti-polyribosyl ribitol phosphate antibody, suggesting that the differences in the avidity of the antibody subpopulations in the polyclonal antisera do not contribute to the binding patterns observed. The binding reaction was specific as evaluated with pneumococcal saccharides. Furthermore, an oligosaccharide-protein conjugate binds antibody better than the free oligosaccharides do. Such a difference in binding was not observed between the polysaccharide and a polysaccharide-protein conjugate. Overall, the data suggest that identical epitopes are expressed by oligomeric and polymeric forms of the antigen and that a particularly more stable conformation in polysaccharides is preferred by antibodies. Covalent coupling of oligomers to protein increases the expression of stable conformation of epitopes. The data further suggest that this kind of antigenic analysis may be important for the design and synthesis of glycoconjugate vaccines.
Pillai, S; Ciciriello, S; Koster, M; Eby, R
Single nucleotide polymorphisms in the interferon gamma gene are associated with distinct types of retinochoroidal scar lesions presumably caused by Toxoplasma gondii infection
The association of single nucleotide polymorphisms (SNPs) in the interferon (IFN)-? gene ( IFNG ) with different types of retinal scar lesions presumably caused by toxoplasmosis were investigated in a cross-sectional population-based genetic study. Ten SNPs were investigated and after Bonferroni correction, only the associations between SNPs rs2069718 and rs3181035 with retinal/retinochoroidal scar lesions type A (most severe scar lesions) and C (least severe scar lesions), respectively, remained significant. The associations of two different IFNG SNPs with two different types of retinal lesions attributable to toxoplasmosis support the hypothesis that different inflammatory mechanisms underlie the development of these lesions. The in vitro analysis of IFN-? secretion by peripheral blood mononuclear cells stimulated with Toxoplasma gondii antigens was also investigated. The association between SNP rs2069718 and type A scar lesions revealed that differential IFN-? levels are correlated with distinct genotypes. However, no correlation was observed with IFN-? secretion levels and the SNP rs3181035 , which was significantly associated with type C scar lesions. Our findings strongly suggest that immunogenetic studies of individuals with congenital or postnatally acquired infection are needed to better understand the role of IFN-? and its polymorphisms in the pathogenesis of ocular toxoplasmosis.
Peixe, Ricardo Guerra; Boechat, Marcela Santana Bastos; Rangel, Alba Lucinia Peixoto; Rosa, Rhonia Franca Gomes; Petzl-Erler, Maria Luiza; Bahia-Oliveira, Lilian MG
Distinct potentiation of L-type currents and secretion by cAMP in rat chromaffin cells.
We have investigated the potentiating action of cAMP on L-currents of rat chromaffin cells and the corresponding increase of Ca(2+)-evoked secretory responses with the aim of separating the action of cAMP on Ca(2+) entry through L-channels and the downstream effects of cAMP/protein kinase A (PKA) on exocytosis. In omega-toxin-treated rat chromaffin cells, exposure to the permeable cAMP analog 8-(4-chlorophenylthio)-adenosine 3',5'-monophosphate (pCPT-cAMP; 1 mM, 30 min) caused a moderate increase of Ca(2+) charge carried through L-channels (19% in 10 mM Ca(2+) at +10 mV) and a drastic potentiation of secretion ( approximately 100%), measured as membrane capacitance increments (deltaC). The apparent Ca(2+) dependency of exocytosis increased with pCPT-cAMP and was accompanied by 83% enhancement of the readily releasable pool of vesicles with no significant change of the probability of release, as evaluated with paired-pulse stimulation protocols. pCPT-cAMP effects could be mimicked by stimulation of beta(1)-adrenoreceptors and reversed by the PKA inhibitor H89, suggesting strict PKA dependence. For short pulses to +10 mV (100 ms), potentiation of exocytosis by pCPT-cAMP was proportional to the quantity of charge entering the cell and occurred independently of whether L, N, or P/Q channels were blocked, suggesting that cAMP acts as a constant amplification factor for secretion regardless of the channel type carrying Ca(2+). Analysis of statistical variations among depolarization-induced capacitance increments indicates that pCPT-cAMP acts downstream of Ca(2+) entry by almost doubling the mean size of unitary exocytic events, most likely as a consequence of an increased granule-to-granule rather than a granule-to-membrane fusion. PMID:12885675
Carabelli, V; Giancippoli, A; Baldelli, P; Carbone, E; Artalejo, A R
Distinct Potentiation of L-Type Currents and Secretion by cAMP in Rat Chromaffin Cells
We have investigated the potentiating action of cAMP on L-currents of rat chromaffin cells and the corresponding increase of Ca2+-evoked secretory responses with the aim of separating the action of cAMP on Ca2+ entry through L-channels and the downstream effects of cAMP/protein kinase A (PKA) on exocytosis. In ?-toxin-treated rat chromaffin cells, exposure to the permeable cAMP analog 8-(4-chlorophenylthio)-adenosine 3?,5?-monophosphate (pCPT-cAMP; 1 mM, 30 min) caused a moderate increase of Ca2+ charge carried through L-channels (19% in 10 mM Ca2+ at +10 mV) and a drastic potentiation of secretion (?100%), measured as membrane capacitance increments (?C). The apparent Ca2+ dependency of exocytosis increased with pCPT-cAMP and was accompanied by 83% enhancement of the readily releasable pool of vesicles with no significant change of the probability of release, as evaluated with paired-pulse stimulation protocols. pCPT-cAMP effects could be mimicked by stimulation of ?1-adrenoreceptors and reversed by the PKA inhibitor H89, suggesting strict PKA dependence. For short pulses to +10 mV (100 ms), potentiation of exocytosis by pCPT-cAMP was proportional to the quantity of charge entering the cell and occurred independently of whether L, N, or P/Q channels were blocked, suggesting that cAMP acts as a constant amplification factor for secretion regardless of the channel type carrying Ca2+. Analysis of statistical variations among depolarization-induced capacitance increments indicates that pCPT-cAMP acts downstream of Ca2+ entry by almost doubling the mean size of unitary exocytic events, most likely as a consequence of an increased granule-to-granule rather than a granule-to-membrane fusion.
Carabelli, V.; Giancippoli, A.; Baldelli, P.; Carbone, E.; Artalejo, A. R.
Novel sequences encoding venom C-type lectins are conserved in phylogenetically and geographically distinct Echis and Bitis viper species.
Envenoming by Echis saw scaled vipers and Bitis arietans puff adders is the leading cause of death and morbidity in Africa due to snake bite. Despite their medical importance, the composition and constituent functionality of venoms from these vipers remains poorly understood. Here, we report the cloning of cDNA sequences encoding seven clusters or isoforms of the haemostasis-disruptive C-type lectin (CTL) proteins from the venom glands of Echis ocellatus, E. pyramidum leakeyi, E. carinatus sochureki and B. arietans. All these CTL sequences encoded the cysteine scaffold that defines the carbohydrate-recognition domain of mammalian CTLs. All but one of the Echis and Bitis CTL sequences showed greater sequence similarity to the beta than alpha CTL subunits in venoms of related Asian and American vipers. Four of the new CTL clusters showed marked inter-cluster sequence conservation across all four viper species which were significantly different from that of previously published viper CTLs. The other three Echis and Bitis CTL clusters showed varying degrees of sequence similarity to published viper venom CTLs. Because viper venom CTLs exhibit a high degree of sequence similarity and yet exert profoundly different effects on the mammalian haemostatic system, no attempt was made to assign functionality to the new Echis and Bitis CTLs on the basis of sequence alone. The extraordinary level of inter-specific and inter-generic sequence conservation exhibited by the Echis and Bitis CTLs leads us to speculate that antibodies to representative molecules should neutralise the biological function of this important group of venom toxins in vipers that are distributed throughout Africa, the Middle East and the Indian subcontinent. PMID:14557069
Harrison, R A; Oliver, J; Hasson, S S; Bharati, K; Theakston, R D G
Distinctive mechanism for sustained TGF-? signaling and growth inhibition: MEK1 activation-dependent stabilization of type II TGF-? receptors.
There are multiple mechanisms by which cells evade TGF-?-mediated growth inhibitory effects. In this report, we describe a novel mechanism by which cells become resistant to TGF-?-mediated growth suppression. Although having all the components of the TGF-? signaling pathway, different cell lines, RL, HaCaT, and BJAB, have different sensitivities toward TGF-?-induced growth suppression. The TGF-? resistance of RL, a B-cell lymphoma cell line, was due to ligand-induced downregulation of TGF-? receptor II (T?RII) and only transient TGF-? induced nuclear translocation of Smad2 and Smad3. With low-dose phorbol 12-myristate 13-acetate (PMA) or anti-IgM treatment, TGF-? sensitivity was restored by stabilizing T?RII expression and sustaining TGF-? signaling. The MEK inhibitor, U0126, blocked both PMA- and anti-IgM-induced upregulation of T?RII. In HaCaT and BJAB, two TGF-?-sensitive cell lines, which had higher basal levels of phospho-MEK and T?RII compared with RL, U0126 induced downregulation of T?RII and blocked subsequent TGF-? signaling. Similar results were also obtained with normal B cells, where MEK1 inhibitor downregulated T?RII and subsequent TGF-? signaling. Constitutively active MEK1, but not constitutively active ERK2, induced upregulation of T?RII. Furthermore, T?RII physically interacted with the constitutively active MEK1, but not with wild-type MEK1, indicating involvement of active MEK1 in stabilizing T?RII. Collectively, our data suggest a novel mechanism for MEK1 in regulating the sensitivity to TGF-? signaling by stabilizing T?RII. PMID:21131601
Chen, Gang; Ghosh, Paritosh; Longo, Dan L
Identification of a 95 kDa putative adhesin from Actinomyces serovar WVA963 strain PK1259 that is distinct from type 2 fimbrial subunits.
The species Actinomyces serovar WVA963 is among the 20 bacteria most frequently isolated from human subgingival plaque. The interactions of this species with streptococci are inhibited by lactose, a function associated with type 2 fimbrial surface structures in Actinomyces naeslundii. Type 1 fimbriae mediate binding of cells to salivary proline-rich proteins. Specific polyclonal antisera against type 1 and type 2 fimbriae of A. naeslundii T14V revealed both types of fimbriae on Actinomyces serovar WVA963 strain PK1259. To investigate the role of type 2 fimbriae of strain PK1259 in Actinomyces-Streptococcus lactose-inhibitable coaggregations, spontaneous coaggregation-defective (Cog-) mutants that failed to coaggregate with streptococci were isolated; three were chosen for study. All three mutant strains synthesized type 1 fimbriae and a 59 kDa protein; mutant strains PK2415 and PK3092 synthesized type 2 fimbriae and a 57 kDa protein. In contrast, the Cog- strain PK2407 did not agglutinate with anti-type 2 antibodies or show the 57 kDa band, suggesting that the 57 kDa protein was the type 2 fimbrial subunit. Polyclonal antiserum raised against the Actinomyces serovar WVA963 strain PK2399, an antibiotic-resistant derivative of wild-type PK1259, blocked coaggregation between this strain and streptococci. Anti-PK2399 serum absorbed with mutant strain PK3092 bearing type 2 fimbriae retained its blocking ability. Surface sonicates of the parent and mutant strains were adsorbed to streptococcal cells and to lactose-agarose beads. Lactose eluates from both the streptococcal cells and the affinity beads were characterized by SDS-PAGE and corresponding immunoblots using anti-PK2399 serum absorbed with Cog- mutant PK3092. These blots revealed a 95 kDa putative adhesin in the parent strain PK2399 that was absent in the Cog- mutant strain PK3092. These results suggest the presence of a putative 95 kDa actinomyces adhesin distinct from the 57 kDa type 2 fimbrial subunit and that this adhesin mediates lactose-inhibitable coaggregation with streptococci. PMID:9084167
Klier, C M; Kolenbrander, P E; Roble, A G; Marco, M L; Cross, S; Handley, P S
Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci.
Christopher G. Bell; Sarah Finer; Cecilia M. Lindgren; Gareth A. Wilson; Vardhman K. Rakyan; Andrew E. Teschendorff; Pelin Akan; Elia Stupka; Thomas A. Down; Inga Prokopenko; Ian M. Morison; Jonathan Mill; Ruth Pidsley; Panos Deloukas; Timothy M. Frayling; Andrew T. Hattersley; Mark I. McCarthy; Stephan Beck; Graham A. Hitman; Thorkild I. A. Sorensen
Drug-repurposing identified the combination of Trolox C and Cytisine for the treatment of type 2 diabetes
Background Drug-induced gene expression dataset (for example Connectivity Map, CMap) represent a valuable resource for drug-repurposing, a class of methods for identifying novel indications for approved drugs. Recently, CMap-based methods have successfully applied to identifying drugs for a number of diseases. However, currently few gene expression based methods are available for the repurposing of combined drugs. Increasing evidence has shown that the combination of drugs may valid for novel indications. Method Here, for this purpose, we presented a simple CMap-based scoring system to predict novel indications for the combination of two drugs. We then confirmed the effectiveness of the predicted drug combination in an animal model of type 2 diabetes. Results We applied the presented scoring system to type 2 diabetes and identified a candidate combination of two drugs, Trolox C and Cytisine. Finally, we confirmed that the predicted combined drugs are effective for the treatment of type 2 diabetes. Conclusion The presented scoring system represents one novel method for drug repurposing, which would provide helps for greatly extended the space of drugs.
A sodium channel mutation identified in Aedes aegypti selectively reduces cockroach sodium channel sensitivity to type I, but not type II pyrethroids
Voltage-gated sodium channels are the primary target of pyrethroid insecticides. Numerous point mutations in sodium channel genes have been identified in pyrethroid-resistant insect species, and many have been confirmed to reduce or abolish sensitivity of channels expressed in Xenopus oocytes to pyrethroids. Recently, several novel mutations were reported in sodium channel genes of pyrethroid-resistant Aedes mosquito populations. One of the mutations is a phenylalanine (F) to cysteine (C) change in segment 6 of domain III (IIIS6) of the Aedes mosquito sodium channel. Curiously, a previous study showed that alanine substitution of this F did not alter the action of deltamethrin, a type II pyrethroid, on a cockroach sodium channel. In this study, we changed this F to C in a pyrethroid-sensitive cockroach sodium channel and examined mutant channel sensitivity to permethrin as well as five other type I or type II pyrethroids in Xenopus oocytes. Interestingly, the F to C mutation drastically reduced channel sensitivity to three type I pyrethroids, permethrin, NRDC 157 (a deltamethrin analogue lacking the ?-cyano group) and bioresemthrin, but not to three type II pyrethroids, cypermethrin, deltamethrin and cyhalothrin. These results confirm the involvement of the F to C mutation in permethrin resistance, and raise the possibility that rotation of type I and type II pyrethroids might be considered in the control of insect pest populations where this particular mutation is present.
Hu, Zhaonong; Du, Yuzhe; Nomura, Yoshiko; Dong, Ke
Envelope Variants from Women Recently Infected with Clade A Human Immunodeficiency Virus Type 1 Confer Distinct Phenotypes That Are Discerned by Competition and Neutralization Experiments
Women infected with clade A human immunodeficiency virus type 1 harbor a virus population that is genetically diverse in the envelope gene, a fact that contrasts with the homogeneous virus population identified in newly infected men. It is not known whether viral genetic diversity at this early stage of infection is manifested as phenotypic diversity. This is a significant question
Sally L. Painter; Roman Biek; David C. Holley; Mary Poss
A strategy to find gene combinations that identify children who progress rapidly to type 1 diabetes after islet autoantibody seroconversion.
We recently developed a novel approach capable of identifying gene combinations to obtain maximal disease risk stratification. Type 1 diabetes has a preclinical phase including seroconversion to autoimmunity and subsequent progression to diabetes. Here, we applied our gene combination approach to identify combinations that contribute either to islet autoimmunity or to the progression from islet autoantibodies to diabetes onset. We examined 12 type 1 diabetes susceptibility genes (INS, ERBB3, PTPN2, IFIH1, PTPN22, KIAA0350, CD25, CTLA4, SH2B3, IL2, IL18RAP, IL10) in a cohort of children of parents with type 1 diabetes and prospectively followed from birth. The most predictive combination was subsequently applied to a smaller validation cohort. The combinations of genes only marginally contributed to the risk of developing islet autoimmunity, but could substantially modify risk of progression to diabetes in islet autoantibody-positive children. The greatest discrimination was provided by risk allele scores of five genes, INS, IFIH1, IL18RAP, CD25, and IL2 genes, which could identify 80 % of islet autoantibody-positive children who progressed to diabetes within 6 years of seroconversion and discriminate high risk (63 % within 6 years; 95 % CI 45-81 %) and low risk (11 % within 6 years; 95 % CI 0.1-22 %; p = 4 × 10(-5)) antibody-positive children. Risk stratification by these five genes was confirmed in a second cohort of islet autoantibody children. These findings highlight genes that may affect the rate of the beta-cell destruction process once autoimmunity has initiated and may help to identify islet autoantibody-positive subjects with rapid progression to diabetes. PMID:24249616
Bonifacio, Ezio; Krumsiek, Jan; Winkler, Christiane; Theis, Fabian J; Ziegler, Anette-Gabriele
Damage-induced cell-cell communication in different cochlear cell types via two distinct ATP-dependent Ca2+ waves
Intercellular Ca2+ waves can coordinate the action of large numbers of cells over significant distances. Recent work in many different systems has indicated that the release of ATP is fundamental for the propagation of most Ca2+ waves. In the organ of hearing, the cochlea, ATP release is involved in critical signalling events during tissue maturation. ATP-dependent signalling is also implicated in the normal hearing process and in sensing cochlear damage. Here, we show that two distinct Ca2+ waves are triggered during damage to cochlear explants. Both Ca2+ waves are elicited by extracellular ATP acting on P2 receptors, but they differ in their source of Ca2+, their velocity, their extent of spread and the cell type through which they propagate. A slower Ca2+ wave (14 ?m/s) communicates between Deiters' cells and is mediated by P2Y receptors and Ca2+ release from IP3-sensitive stores. In contrast, a faster Ca2+ wave (41 ?m/s) propagates through sensory hair cells and is mediated by Ca2+ influx from the external environment. Using inhibitors and selective agonists of P2 receptors, we suggest that the faster Ca2+ wave is mediated by P2X4 receptors. Thus, in complex tissues, the expression of different receptors determines the propagation of distinct intercellular communication signals. Electronic supplementary material The online version of this article (doi:10.1007/s11302-010-9193-8) contains supplementary material, which is available to authorized users.
Lahne, Manuela
The C-type lectin receptor Endo180 displays internalization and recycling properties distinct from other members of the mannose receptor family.
Endo180/urokinase plasminogen activator receptor-associated protein together with the mannose receptor, the phospholipase A(2) receptor, and DEC-205/MR6-gp200 comprise the four members of the mannose receptor family. These receptors have a unique structural composition due to the presence of multiple C-type lectin-like domains within a single polypeptide backbone. In addition, they are all constitutively internalized from the plasma membrane via clathrin-mediated endocytosis and recycled back to the cell surface. Endo180 is a multifunctional receptor displaying Ca(2+)-dependent lectin activity, collagen binding, and association with the urokinase plasminogen activator receptor, and it has a proposed role in extracellular matrix degradation and remodeling. Within their short cytoplasmic domains, all four receptors contain both a conserved tyrosine-based and dihydrophobic-based putative endocytosis motif. Unexpectedly, Endo180 was found to be distinct within the family in that the tyrosine-based motif is not required for efficient delivery to and recycling from early endosomes. By contrast, receptor internalization is completely dependent on the dihydrophobic motif and modulated by a conserved upstream acidic residue. Furthermore, unlike the mannose receptor, Endo180 does not function as a phagocytic receptor in vitro. These findings demonstrate that despite an overall structural similarity, members of this receptor family employ distinct trafficking mechanisms that may reflect important differences in their physiological functions. PMID:12068012
Howard, Matthew J; Isacke, Clare M
An artificial neural network to estimate physical activity energy expenditure and identify physical activity type from an accelerometer.
The aim of this investigation was to develop and test two artificial neural networks (ANN) to apply to physical activity data collected with a commonly used uniaxial accelerometer. The first ANN model estimated physical activity metabolic equivalents (METs), and the second ANN identified activity type. Subjects (n = 24 men and 24 women, mean age = 35 yr) completed a menu of activities that included sedentary, light, moderate, and vigorous intensities, and each activity was performed for 10 min. There were three different activity menus, and 20 participants completed each menu. Oxygen consumption (in ml x kg(-1) x min(-1)) was measured continuously, and the average of minutes 4-9 was used to represent the oxygen cost of each activity. To calculate METs, activity oxygen consumption was divided by 3.5 ml x kg(-1) x min(-1) (1 MET). Accelerometer data were collected second by second using the Actigraph model 7164. For the analysis, we used the distribution of counts (10th, 25th, 50th, 75th, and 90th percentiles of a minute's second-by-second counts) and temporal dynamics of counts (lag, one autocorrelation) as the accelerometer feature inputs to the ANN. To examine model performance, we used the leave-one-out cross-validation technique. The ANN prediction of METs root-mean-squared error was 1.22 METs (confidence interval: 1.14-1.30). For the prediction of activity type, the ANN correctly classified activity type 88.8% of the time (confidence interval: 86.4-91.2%). Activity types were low-level activities, locomotion, vigorous sports, and household activities/other activities. This novel approach of applying ANNs for processing Actigraph accelerometer data is promising and shows that we can successfully estimate activity METs and identify activity type using ANN analytic procedures. PMID:19644028
Staudenmayer, John; Pober, David; Crouter, Scott; Bassett, David; Freedson, Patty
A New Means To Identify Type 3 Secreted Effectors: Functionally Interchangeable Class IB Chaperones Recognize a Conserved Sequence
ABSTRACT Many Gram-negative bacteria utilize specialized secretion systems to inject proteins (effectors) directly into host cells. Little is known regarding how bacteria ensure that only small subsets of the thousands of proteins they encode are recognized as substrates of the secretion systems, limiting their identification through bioinformatic analyses. Many of these proteins require chaperones to direct their secretion. Here, using the newly described protein interaction platform assay, we demonstrate that type 3 secretion system class IB chaperones from one bacterium directly bind their own effectors as well as those from other species. In addition, we observe that expression of class IB homologs from seven species, including pathogens and endosymbionts, mediate the translocation of effectors from Shigella directly into host cells, demonstrating that class IB chaperones are often functionally interchangeable. Notably, class IB chaperones bind numerous effectors. However, as previously proposed, they are not promiscuous; rather they recognize a defined sequence that we designate the conserved chaperone-binding domain (CCBD) sequence [(LMIF)1XXX(IV)5XX(IV)8X(N)10]. This sequence is the first defined amino acid sequence to be identified for any interspecies bacterial secretion system, i.e., a system that delivers proteins directly into eukaryotic cells. This sequence provides a new means to identify substrates of type III secretion systems. Indeed, using a pattern search algorithm for the CCBD sequence, we have identified the first two probable effectors from an endosymbiont, Sodalis glossinidius.
Costa, Sonia C. P.; Schmitz, Alexa M.; Jahufar, Fathima F.; Boyd, Justin D.; Cho, Min Y.; Glicksman, Marcie A.; Lesser, Cammie F.
A Rule-Based Prognostic Model for Type 1 Diabetes by Identifying and Synthesizing Baseline Profile Patterns
Objective To identify the risk-predictive baseline profile patterns of demographic, genetic, immunologic, and metabolic markers and synthesize these patterns for risk prediction. Research Design and Methods RuleFit is used to identify the risk-predictive baseline profile patterns of demographic, immunologic, and metabolic markers, using 356 subjects who were randomized into the control arm of the prospective Diabetes Prevention Trial-Type 1 (DPT-1) study. A novel latent trait model is developed to synthesize these baseline profile patterns for disease risk prediction. The primary outcome was Type 1 Diabetes (T1D) onset. Results We identified ten baseline profile patterns that were significantly predictive to the disease onset. Using these ten baseline profile patterns, a risk prediction model was built based on the latent trait model, which produced superior prediction performance over existing risk score models for T1D. Conclusion Our results demonstrated that the underlying disease progression process of T1D can be detected through some risk-predictive patterns of demographic, immunologic, and metabolic markers. A synthesis of these patterns provided accurate prediction of disease onset, leading to more cost-effective design of prevention trials of T1D in the future.
Lin, Ying; Qian, Xiaoning; Krischer, Jeffrey; Vehik, Kendra; Lee, Hye-Seung; Huang, Shuai
In vitro inhibition of SKOV-3 cell migration as a distinctive feature of progesterone receptor membrane component type 2 versus type 1.
Progesterone receptor membrane component type 2 (PGRMC2) is strongly homologous to PGRMC1 which is highly expressed in ovarian cancer and other cancer cells and was claimed to play an important role in chemotherapy resistance. Whereas PGRMC1 has been extensively characterized in in vitro studies, comparably little is known about PGRMC2. To determine PGRMC2's role in ovarian cancer cell proliferation and mobility PGRMC1- and 2-depleted and -overexpressing SKOV-3 cells were generated. In electric cell-substrate impedance sensing studies, PGRMC2 negatively affects SKOV-3 migration rate if overexpressed; oppositely, depletion was associated with an increased migration rate. PGRMC1 had no effect in this assay. These effects were not associated with f-actin regulation or actin cytoskeleton reorganization. Yet, these highly homologous proteins share many properties. Both PGRMC1 and 2 are localized to the endoplasmic reticulum. As PGRMC1 was reported to interact with cytochrome P450 proteins (CYP) binding of two different CYPs to PGRMC2 was tested; a stable interaction of PGRMC2 with CYP3A4 and CYP21A2 was found in human embryonic kidney cells. For both PGRMC types, cell viability assays revealed no significant differences of SKOV-3 survival in overexpressing and depleted cells. PGRMC2 also does not seem to have any influence on the apoptotic effect of cisplatin or the antiapoptotic effect of progesterone which had been reported for PGRMC1. In contrast to PGRMC1, protein levels of PGRMC2 in SKOV-3 cells are reduced by treatment with cisplatin (30-60?M). In conclusion, we show for the first time that PGRMC2 inhibits migration of SKOV-3 ovarian cancer cells in vitro. PMID:23064006
Albrecht, Christian; Huck, Volker; Wehling, Martin; Wendler, Alexandra
An Optimized Histochemical Method to Assess Skeletal Muscle Glycogen and Lipid Stores Reveals Two Metabolically Distinct Populations of Type I Muscle Fibers
Skeletal muscle energy metabolism has been a research focus of physiologists for more than a century. Yet, how the use of intramuscular carbohydrate and lipid energy stores are coordinated during different types of exercise remains a subject of debate. Controversy arises from contradicting data from numerous studies, which used different methodological approaches. Here we review the "pros and cons" of previously used histochemical methods and describe an optimized method to ensure the preservation and specificity of detection of both intramyocellular carbohydrate and lipid stores. For optimal preservation of muscle energy stores, air drying cryosections or cycles of freezing-thawing need to be avoided. Furthermore, optimization of the imaging settings in order to specifically image intracellular lipid droplets stained with oil red O or Bodipy-493/503 is shown. When co-staining lipid droplets with associated proteins, Bodipy-493/503 should be the dye of choice, since oil red O creates precipitates on the lipid droplets blocking the light. In order to increase the specificity of glycogen stain, an antibody against glycogen is used. The resulting method reveals the existence of two metabolically distinct myosin heavy chain I expressing fibers: I-1 fibers have a smaller crossectional area, a higher density of lipid droplets, and a tendency to lower glycogen content compared to I-2 fibers. Type I-2 fibers have similar lipid content than IIA. Exhaustive exercise lead to glycogen depletion in type IIA and IIX fibers, a reduction in lipid droplets density in both type I-1 and I-2 fibers, and a decrease in the size of lipid droplets exclusively in type I-1 fibers.
Prats, Clara; Gomez-Cabello, Alba; Nordby, Pernille; Andersen, Jesper L.; Helge, J?rn W.; Dela, Flemming; Baba, Otto; Ploug, Thorkil
JAK2-Centered Interactome Hotspot Identified by an Integrative Network Algorithm in Acute Stanford Type A Aortic Dissection
The precise mechanisms underlying dissections, especially those without connective tissue diseases or congenital vascular diseases, are incompletely understood. This study attempted to identify both the expression profile of the dissected ascending aorta and the interactome hotspots associated with the disease, using microarray technology and gene regulatory network analysis. There were 2,737 genes differentially expressed between patients with acute Stanford type A aortic dissection and controls. Eight interactome hotspots significantly associated with aortic dissection were identified by an integrative network algorithm. In particular, we identified a JAK2-centered expression module, which was validated in an independent gene expression microarray data set, and which was characterized by over-expressed cytokines and receptors in acute aortic dissection cases, indicating that JAK2 may play a key role in the inflammatory process, which potentially contributes to the occurrence of acute aortic dissection. Overall, the analytical strategy used in this study offered the possibility to identify functional relevant network modules and subsequently facilitated the biological interpretation in the complicated disease.
Teschendorff, Andrew E.; Hong, Tao; Wang, Linyan; Qian, Mengjia; Wang, Chunsheng; Wang, Xiangdong
Homozygosity of the Polymorphism MICA5.1 Identifies Extreme Risk of Progression to Overt Adrenal Insufficiency among 21-Hydroxylase Antibody-Positive Patients with Type 1 Diabetes
Context: Autoimmunity associated with Addison's disease (AD) can be detected by measuring 21-hydroxylase (21OH) autoantibodies. Subjects with type 1 diabetes (T1D) are at increased risk for AD. Genetic factors including HLA-DRB1*0404 and MICA have been associated with AD in populations with and without T1D. Objective: The objective of the study was to examine the effect of the MICA5.1 allele in subjects with 21OH autoantibodies on progression to AD. Design: Two components were used: 1) a cross-sectional study with subjects with AD identified and enrolled from September 1993 to November 2008 and 2) a cohort study prospectively following up patients with T1D who screened positive for 21OH autoantibodies. Setting: Subjects were identified from the Barbara Davis Center and through the National Adrenal Diseases Foundation. Patients: Sixty-three subjects with AD were referred through the National Adrenal Diseases Foundation (AD referrals). Sixty-three subjects with positive 21OH antibodies from the Barbara Davis Center were followed up for progression to AD, and 11 were diagnosed with AD (progressors). Results: Seventy-three percent of progressors (eight of 11) and 57% of AD referrals (36 of 63) were MICA5.1 homozygous (P = ns). Overall, 59% of patients with AD (44 of 74) were MICA5.1/5.1 compared with 17% of nonprogressors (nine of 52) (P < 0.0001) and 19% of normal DR3/4-DQB1*0302 controls (64 of 336) (P < 0.0001). Conclusions: Identifying extreme risk should facilitate monitoring of progression from 21OH antibody positivity to overt AD. The HLA-DR3/0404 genotype defines high-risk subjects for adrenal autoimmunity. MICA5.1/5.1 may define those at highest risk for progression to overt AD, a feature unique to AD and distinct from T1D.
Triolo, Taylor M.; Baschal, Erin E.; Armstrong, Taylor K.; Toews, Carrie S.; Fain, Pamela R.; Rewers, Marian J.; Yu, Liping; Miao, Dongmei; Eisenbarth, George S.; Gottlieb, Peter A.; Barker, Jennifer M.
MxA as a clinically applicable biomarker for identifying systemic interferon type I in primary Sj?gren's syndrome
Objective To establish an easy and practical assay for identifying systemic interferon (IFN) type I bioactivity in patients with primary Sjögren's syndrome (pSS). The IFN type I signature is present in over half of the pSS patients and identifies a subgroup with a higher disease activity. This signature is currently assessed via laborious expression profiles of multiple IFN type I-inducible genes. Methods In a cohort of 35 pSS patients, myxovirus-resistance protein A (MxA) was assessed as a potential biomarker for type I IFN activity, using an enzyme immunoassay (EIA) on whole-blood and flow cytometric analyses (fluorescence-activated cell sorting, FACS) of isolated CD14 monocytes. In addition, potential biomarkers such as CD64, CD169 and B cell-activating factor (BAFF) were simultaneously analysed in CD14 monocytes using FACS. The IFNscore, a measure for total type I IFN bioactivity, was calculated using expression values of the IFN type I signature genes—IFI44, IFI44L, IFIT3, LY6E and MX1—in CD14 monocytes, determined by real-time quantitative PCR. Results IFNscores correlated the strongest with monocyte MxA protein (r=0.741, p<0.001) and whole-blood MxA levels (r=0.764, p<0.001), weaker with CD169 (r=0.495, p<0.001) and CD64 (r=0.436, p=0.007), and not at all with BAFF protein. In particular, whole blood MxA levels correlated with EULAR Sjögren's Syndrome Disease Activity Index scores and numerous clinical pSS parameters. Interestingly, patients on hydroxychloroquine showed reduced MxA levels (EIA, p=0.04; FACS p=0.001). Conclusions The MxA assays were excellent tools to assess IFN type I activity in pSS, MxA-EIA being the most practical. MxA levels associate with features of active disease and are reduced in hydroxychloroquine-treated patients, suggesting the clinical applicability of MxA in stratifying patients according to IFN positivity.
Maria, Naomi I; Brkic, Zana; Waris, Matti; van Helden-Meeuwsen, Cornelia G; Heezen, Kim; van de Merwe, Joop P; van Daele, Paul L; Dalm, Virgil A S H; Drexhage, Hemmo A; Versnel, Marjan A
Genotypic characterization of Toxoplasma gondii in sheep from Brazilian slaughterhouses: new atypical genotypes and the clonal type II strain identified.
Toxoplasma gondii strains are genetically diverse in South America. To date, hundreds of T. gondii isolates from different animal hosts were genotyped in Brazil, most of them are different from those identified around the world. This study aimed to determine T. gondii infection rate in sheep from Brazilian slaughterhouses, as well as the genotype of these isolates. T. gondii antibodies were detected in 66/602 (10.96%) serum samples through modified agglutination test (MAT) and indirect fluorescent antibody test (IFAT). MAT-HS and IFAT-IgG presented high concordance (0.95) and strong correlation (r=0.79). T. gondii DNA was detected in tissue samples of 33% (22/66) serum positive sheep by PCR of the 529 bp repetitive element. In the bioassay in mice, T. gondii were detected in mice brain or muscle tissues in 30% (20/66) of serum positive sheep. Positive samples were typed through Restriction Fragment Length Polymorphism (RFLP-PCR) using 11 markers: SAG1, SAG2 (5'-3'SAG2 and alt.SAG2), SAG3, BTUB, GRA6, L358, c22-8, c29-6, PK1, Apico and CS3. Of 22 samples, 13 were positive and 9 genotypes were identified. Four of these 9 genotypes are unique. Nine samples had negative results in RFLP-PCR typing, which may be due to low DNA concentration. Six isolates were virulent killing mice between 12 and 25 days postinfection. Two non-virulent isolates belonged to clonal type II genotype, which were not observed in Brazil previously. These findings confirm the high diversity and high frequency of virulent genotypes among Brazilian animals. This study also proved the presence of type II T. gondii in Brazil. PMID:20970257
da Silva, Rodrigo Costa; Langoni, Helio; Su, Chunlei; da Silva, Aristeu Vieira
A unique enhancer element for the trans activator (p40 sup tax ) of human T-cell leukemia virus type I that is distinct from cyclic AMP- and 12-O-tetradecanoylphobol-13-acetate-responsive elements
The trans activator (p40{sup tax}) of human T-cell leukemia virus type I (HTLV-I) is a transcriptional factor that activates the long terminal repeat (LTR) of HTLV-I and interleukin-2 receptor {alpha}. The authors examined the HTLV-I enhancer responsible for tax-mediated trans activation and identified (A/T)(G/C)(G/C)CNNTGACG(T/A) as a plausible tax-responsive element (TRE). The putative TRE in the LTR was found to be different from the elements required for activation by cyclic AMP and 12-O-tetradecanoylphorbol-13-acetate, although these elements overlapped each other. The TRE was also different from a binding site of N-{kappa}B-like factor that was identified was identified in the interleukin-2 receptor {alpha} promoter and human immunodeficiency virus LTR as a TRE. The latter result was further demonstrated by the failure of the NF-{kappa}B sequence to compete with the TRE of the LTR in a protein-binding assay. These findings indicate that tax function and its cascade can modulate activities of various enhancer sequences, which are probably regulated by distinct DNA-binding factors.
Fujisawa, Junichi; Toita, Masami; Yoshida, Mitsuaki (Cancer Institute, Tokyo (Japan))
[Type A aortic dissection: the role of angiography in identifying morphologic features in comparison with autopsy and surgical findings].
To evaluate the reliability of cineangiography in identifying some morphologic characteristics of type A aortic dissection, the angiograms of 36 consecutive patients were retrospectively revised and compared with the surgical of necropsy findings. The following features were examined: site and extension of intimal tear (s); extension of the wall dissection; coronary and brachiocephalic arteries involvement; coexisting anuloaortic ectasia; aortic valve state. The angiographic diagnosis of site and extension of the intimal tear was correct in 97 (35/36) and 100% of cases respectively. In one case the presence of an intimal tear at the level of the aortic arch was missed because of the superimposition of the innominate artery. The extension of the wall dissection was correctly identified in 24 out of 25 patients. In one case the presence of distal false lumen thrombosis made the correct diagnosis impossible. The brachiocephalic arteries involvement was always correctly stated while the coronary involvement was suspected in 6 and confirmed in 5 (1 false positive). Anuloectasia was suspected in 12 and confirmed in 10 (2 false positives). In our experience the most challenging diagnosed were the presence of aortic arch tears and the aortic arch and coronary arteries involvement in the dissection. This study confirms that many morphologic features of type A aortic dissection can be adequately assessed by cineangiography. PMID:2055376
Giommi, L; Cavallini, C; Franceschini, E; Marton, F; Risica, G; Olivari, Z; Cuzzato, V
Distinct and additive effects of sodium bicarbonate and continuous mild heat stress on fiber type shift via calcineurin/NFAT pathway in human skeletal myoblasts.
Ingestion of sodium bicarbonate (NaHCO3) is known to enhance athletic performance, probably via increased extracellular buffering capacity. At present, little is known about the direct effects of NaHCO3 on myogenesis, especially in vitro. Here, we examined the effects of NaHCO3 and the combined effects of NaHCO3 and continuous mild heat stress (CMHS) at 39°C on the differentiation of human skeletal muscle myoblasts (HSMMs). Levels of myosin heavy chain (MyHC) type I mRNA increased with increasing NaHCO3 concentrations; in contrast, those of MyHC IIx decreased. The NaHCO3-induced fast-to-slow shift was additively enhanced by CMHS. Likewise, intracellular calcium levels and expression of three factors, nuclear factor of activated T cells c2 (NFATc2), NFATc4, and peroxisome-proliferator-activated receptor-? coactivator-1?, were upregulated with increasing NaHCO3 concentrations; moreover, these effects of NaHCO3 were additively enhanced by CMHS. Overexpression experiments and small interfering RNA-mediated knockdown experiments confirmed that NFATc2 and NFATc4 were involved in MyHC I regulation. The present study provided evidence that NaHCO3 and CMHS distinctly and additively induced a fast-to-slow fiber type shift through changes in intracellular calcium levels and the modulation of calcium signaling. PMID:23703530
Yamaguchi, Tetsuo; Omori, Maiko; Tanaka, Nobuho; Fukui, Naoshi
Large identified pyramidal cells in macaque motor and premotor cortex exhibit "thin spikes": implications for cell type classification
Recent studies have suggested that extracellular recordings of putative cortical interneurons have briefer spikes that those of pyramidal neurons, providing a means of identifying cortical cell types in recordings from awake monkeys. To test this, we investigated the spike duration of antidromically identified pyramidal tract neurons (PTNs) recorded from primary motor (M1) or ventral premotor cortex (F5) in 4 awake macaque monkeys. M1 antidromic latencies (ADLs) were skewed towards short ADLs (151 PTNs; 0.5-5.5 ms, median 1.1 ms) and significantly different from that of F5 ADLs (54 PTNs; 1.0-6.9 ms, median 2.6 ms). The duration of PTN spikes, recorded with a high pass filter of 300 Hz and measured from the negative trough to the positive peak of the spike waveform, ranged from 0.15 to 0.71 ms. Importantly, we found a positive linear correlation between ADL and spike duration in both M1 (R2=0.40, p<0.001) and F5 (R2=0.57, p<0.001). Thus PTNs with the shortest ADL (fastest axons) had the briefest spikes, and since PTN soma size is correlated with axon size and conduction velocity, it is likely that the largest pyramidal neurons (Betz cells in M1) have spikes with short durations (0.15 to 0.45 ms), which overlap heavily with those reported for putative interneurons in previous studies in non-primates. In summary, one class of physiologically identified cortical pyramidal neuron exhibits a wide variety of spike durations and the results suggest that spike duration alone may not be a reliable indicator of cell type.
Vigneswaran, G.; Kraskov, A.; Lemon, R. N.
Functional genomics identified a novel protein tyrosine phosphatase receptor type F-mediated growth inhibition in hepatocarcinogenesis.
It is unclear how proliferating cells elicit suppression on cell proliferation and how cancer cells evade this growth suppression. Using a loss-of-function screening of the human kinome and phosphatome to identify genes suppressing tumor initiation in human hepatocellular carcinoma (HCC), we identified 19 genes and characterized one of the top-scoring tumor suppressor candidates, protein tyrosine phosphatase receptor type F (PTPRF). We found that PTPRF was induced during cell proliferation by cell-cell contact. Ectopic expression of wild-type PTPRF, but not the phosphatase-inactive mutant, suppressed cell proliferation and colony formation in soft-agar assays. In contrast, PTPRF silencing led to cell hyperproliferation, enhanced tumor colony formation in soft agar, and increased xenograft tumor growth in nude mice. Mechanistically, PTPRF silencing showed aberrant ERK-dependent signaling including the phosphorylation/stabilization of v-myc avian myelocytomatosis viral oncogene homolog (MYC) through the direct activation of v-src avian sarcoma viral oncogene homolog (SRC) and suppression of PP2A. This PTPRF-mediated growth suppression during cell proliferation functioned independently of the Hippo-Yap pathway. Clinically, PTPRF was down-regulated in 42% HCC (37/89), 67% gastric cancer (27/40), and 100% colorectal cancer (40/40). PTPRF up-regulation was found in 24% HCC (21/89) and associated with better clinical outcomes. Conclusion: A novel PTPRF-mediated growth suppression pathway was identified by way of a functional genomics screening in human hepatoma cells. Induction of PTPRF by cell-cell contact during cell proliferation quenched the activated ERK-dependent proliferation signaling to prevent cell hyperproliferation and tumor initiation. PTPRF down-regulation in HCC facilitated tumor development. Our findings shed light on how cancer cells can evade growth suppression and open a new avenue for future development of anticancer therapies. PMID:24470239
Bera, Rabindranath; Chiou, Chih-Yung; Yu, Ming-Chin; Peng, Jei-Ming; He, Chung-Ru; Hsu, Chih-Yun; Huang, Hsiao-Ling; Ho, Uda Y; Lin, Shi-Ming; Lin, Yu-Jr; Hsieh, Sen-Yung
Role of T-type calcium current in identified D-hair mechanoreceptor neurons studied in vitro.
Different subsets of dorsal root ganglion (DRG) mechanoreceptors transduce low- and high-intensity mechanical stimuli. It was shown recently that, in vivo, neurotrophin-4 (NT-4)-dependent D-hair mechanoreceptors specifically express a voltage-activated T-type calcium channel (Ca(v)3.2) that may be required for their mechanoreceptive function. Here we show that D-hair mechanoreceptors can be identified in vitro by a rosette-like morphology in the presence of NT-4 and that these rosette neurons are almost all absent in DRG cultures taken from NT-4 knock-out mice. In vitro identification of the D-hair mechanoreceptor allowed us to explore the electrophysiological properties of these cells. We demonstrate that the T-type Ca(v)3.2 channel induced slow membrane depolarization that contributes to lower the voltage threshold for action potential generation and controls spike latency after stimulation of D-hair mechanoreceptors. Indeed, the properties of the T-type amplifier are particularly well suited to explain the high sensitivity of D-hair mechanoreceptors to slowly moving stimuli. PMID:15456821
Dubreuil, Anne-Sophie; Boukhaddaoui, Hassan; Desmadryl, Gilles; Martinez-Salgado, Carlos; Moshourab, Rabih; Lewin, Gary R; Carroll, Patrick; Valmier, Jean; Scamps, Frédérique
Strategy to control type I error increases power to identify genetic variation using the full biological trajectory.
Genome-wide association studies have been successful in identifying loci that underlie continuous traits measured at a single time point. To additionally consider continuous traits longitudinally, it is desirable to look at SNP effects at baseline and over time using linear-mixed effects models. Estimation and interpretation of two coefficients in the same model raises concern regarding the optimal control of type I error. To investigate this issue, we calculate type I error and power under an alternative for joint tests, including the two degree of freedom likelihood ratio test, and compare this to single degree of freedom tests for each effect separately at varying alpha levels. We show which joint tests are the optimal way to control the type I error and also illustrate that information can be gained by joint testing in situations where either or both SNP effects are underpowered. We also show that closed form power calculations can approximate simulated power for the case of balanced data, provide reasonable approximations for imbalanced data, but overestimate power for complicated residual error structures. We conclude that a two degree of freedom test is an attractive strategy in a hypothesis-free genome-wide setting and recommend its use for genome-wide studies employing linear-mixed effects models. PMID:23633177
Benke, K S; Wu, Y; Fallin, D M; Maher, B; Palmer, L J
SLoWPoKES-II: Identifying Ultra-wide Binaries to the Late-M and L Spectral Types
NASA Astrophysics Data System (ADS)
The Sloan Low-mass Wide Pairs of Kinematically Equivalent Stars (SLoWPoKES) catalog identified over 1300 bona fide, common proper motion binary systems. While SLoWPoKES was the largest ever sample of wide low-mass binaries, some of the most interesting and valuable systems—those with very low-mass components and therefore the most fragile systems—do not have proper motion data available. To find these interesting systems, we have extended our techniques: we present the SLoWPoKES-II catalog of low-mass visual binaries identified from the Sloan Digital Sky Survey by matching photometric distances and without the need for proper motion information. We vetted the candidate pairs by comparing their Galactic positions to Monte Carlo realizations of a simulated Milky Way. Over 41,000 visual binaries (including over 400 very low-mass pairs) with angular separations of 0.?4-10?, were identified, each with a probability of chance alignment of ? 5%. The catalog contains a diversity of systems—in mass, mass ratios, metallicity, and evolutionary states—that should facilitate follow-up studies to characterize the properties of low-mass stars and brown dwarfs. The identified SLoWPoKES-II systems are at distance up to 250 pc, which allows us to study the (wide) binary properties as a function of their position in the Galaxy. For example, the wide binary fraction shows a decline as a function of Galactic height (a proxy for age), suggesting dynamical processing of wide pairs with age. The trend is evident across the mid-K to mid-M spectral types and is accentuated at larger separations. The mass ratio, as estimated from their colors, distribution is significantly skewed towards unity. The data are publicly available on our data visualization portal at http://slowpokes.vanderbilt.edu.
Dhital, Saurav; West, A. A.; Stassun, K.; Schluns, K.; Massey, A. P.
Distinct Cell Clusters Touching Islet Cells Induce Islet Cell Replication in Association with Over-Expression of Regenerating Gene (REG) Protein in Fulminant Type 1 Diabetes
Background Pancreatic islet endocrine cell-supporting architectures, including islet encapsulating basement membranes (BMs), extracellular matrix (ECM), and possible cell clusters, are unclear. Procedures The architectures around islet cell clusters, including BMs, ECM, and pancreatic acinar-like cell clusters, were studied in the non-diabetic state and in the inflamed milieu of fulminant type 1 diabetes in humans. Result Immunohistochemical and electron microscopy analyses demonstrated that human islet cell clusters and acinar-like cell clusters adhere directly to each other with desmosomal structures and coated-pit-like structures between the two cell clusters. The two cell-clusters are encapsulated by a continuous capsule composed of common BMs/ECM. The acinar-like cell clusters have vesicles containing regenerating (REG) I? protein. The vesicles containing REG I? protein are directly secreted to islet cells. In the inflamed milieu of fulminant type 1 diabetes, the acinar-like cell clusters over-expressed REG I? protein. Islet endocrine cells, including beta-cells and non-beta cells, which were packed with the acinar-like cell clusters, show self-replication with a markedly increased number of Ki67-positive cells. Conclusion The acinar-like cell clusters touching islet endocrine cells are distinct, because the cell clusters are packed with pancreatic islet clusters and surrounded by common BMs/ECM. Furthermore, the acinar-like cell clusters express REG I? protein and secrete directly to neighboring islet endocrine cells in the non-diabetic state, and the cell clusters over-express REG I? in the inflamed milieu of fulminant type 1 diabetes with marked self-replication of islet cells.
Aida, Kaoru; Saitoh, Sei; Nishida, Yoriko; Yokota, Sadanori; Ohno, Shinichi; Mao, Xiayang; Akiyama, Daiichiro; Tanaka, Shoichiro; Awata, Takuya; Shimada, Akira; Oikawa, Youichi; Shimura, Hiroki; Furuya, Fumihiko; Takizawa, Soichi; Ichijo, Masashi; Ichijo, Sayaka; Itakura, Jun; Fujii, Hideki; Hashiguchi, Akinori; Takasawa, Shin; Endo, Toyoshi; Kobayashi, Tetsuro
Prospective study of low-dose ristocetin-induced platelet aggregation to identify type 2B von Willebrand disease (VWD) and platelet-type VWD in children.
Type 2B von Willebrand disease (VWD2B) and platelet-type von Willebrand disease (PT-VWD) are rare bleeding disorders characterised by an increased ristocetin-induced platelet aggregation (RIPA) at low dose of ristocetin. It was the objective of this study to detect children with VWD2B and PT-VWD using RIPA at low dose of ristocetin (0.5 mg/ml) in the screening evaluation of bleeding disorders, and to analyse the phenotypic data along with the molecular findings. Over a 14-year period, 641 children with personal and family bleeding symptoms or bleeding from birth with previously uncharacterised haemostatic disorders were prospectively studied. Six unrelated patients (0.93%) showed RIPA at low dose of ristocetin. RIPA-based mixing studies identified that the plasma of the six probands and at least one parent from five unrelated families induced aggregation of normal platelets with the addition of low-dose ristocetin. None of the probands' platelets showed aggregation with cryoprecipitate. Low ristocetin cofactor activity/VWF antigen ratio with absent collagen binding activity or thrombocytopenia were detected respectively in only two patients. Molecular analysis of exon 28 of the VWF gene identified mutations in only three patients. No mutation in the GP1BA gene was found. In this large prospective paediatric study, the screening approach including RIPA at low dose of ristocetin permitted the detection of patients with VWD2B that would otherwise have been missed. No patient with phenotype or genotype of PT-VWD was identified. Heterogeneity of bleeding symptoms and phenotypic parameters were found among members of the same family. PMID:20941465
Frontroth, Juan Pablo; Hepner, Mirta; Sciuccati, Gabriela; Feliú Torres, Aurora; Pieroni, Graciela; Bonduel, Mariana
Quantitative Proteomic Analysis of Niemann-Pick Disease, Type C1 Cerebellum Identifies Protein Biomarkers and Provides Pathological Insight
Niemann-Pick disease, type C1 (NPC1) is a fatal, neurodegenerative disorder for which there is no definitive therapy. In NPC1, a pathological cascade including neuroinflammation, oxidative stress and neuronal apoptosis likely contribute to the clinical phenotype. While the genetic cause of NPC1 is known, we sought to gain a further understanding into the pathophysiology by identifying differentially expressed proteins in Npc1 mutant mouse cerebella. Using two-dimensional gel electrophoresis and mass spectrometry, 77 differentially expressed proteins were identified in Npc1 mutant mice cerebella compared to controls. These include proteins involved in glucose metabolism, detoxification/oxidative stress and Alzheimer disease-related proteins. Furthermore, members of the fatty acid binding protein family, including FABP3, FABP5 and FABP7, were found to have altered expression in the Npc1 mutant cerebellum relative to control. Translating our findings from the murine model to patients, we confirm altered expression of glutathione s-transferase ?, superoxide dismutase, and FABP3 in cerebrospinal fluid of NPC1 patients relative to pediatric controls. A subset of NPC1 patients on miglustat, a glycosphingolipid synthesis inhibitor, showed significantly decreased levels of FABP3 compared to patients not on miglustat therapy. This study provides an initial report of dysregulated proteins in NPC1 which will assist with further investigation of NPC1 pathology and facilitate implementation of therapeutic trials.
Cologna, Stephanie M.; Jiang, Xiao-Sheng; Backlund, Peter S.; Cluzeau, Celine V. M.; Dail, Michelle K.; Yanjanin, Nicole M.; Siebel, Stephan; Toth, Cynthia L.; Jun, Hyun-sik; Wassif, Christopher A.; Yergey, Alfred L.; Porter, Forbes D.
Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.
We carried out a genome-wide association study of type-2 diabetes (T2D) in individuals of South Asian ancestry. Our discovery set included 5,561 individuals with T2D (cases) and 14,458 controls drawn from studies in London, Pakistan and Singapore. We identified 20 independent SNPs associated with T2D at P < 10(-4) for testing in a replication sample of 13,170 cases and 25,398 controls, also all of South Asian ancestry. In the combined analysis, we identified common genetic variants at six loci (GRB14, ST6GAL1, VPS26A, HMG20A, AP3S2 and HNF4A) newly associated with T2D (P = 4.1 × 10(-8) to P = 1.9 × 10(-11)). SNPs at GRB14 were also associated with insulin sensitivity (P = 5.0 × 10(-4)), and SNPs at ST6GAL1 and HNF4A were also associated with pancreatic beta-cell function (P = 0.02 and P = 0.001, respectively). Our findings provide additional insight into mechanisms underlying T2D and show the potential for new discovery from genetic association studies in South Asians, a population with increased susceptibility to T2D. PMID:21874001
Kooner, Jaspal S; Saleheen, Danish; Sim, Xueling; Sehmi, Joban; Zhang, Weihua; Frossard, Philippe; Been, Latonya F; Chia, Kee-Seng; Dimas, Antigone S; Hassanali, Neelam; Jafar, Tazeen; Jowett, Jeremy B M; Li, Xinzhong; Radha, Venkatesan; Rees, Simon D; Takeuchi, Fumihiko; Young, Robin; Aung, Tin; Basit, Abdul; Chidambaram, Manickam; Das, Debashish; Grundberg, Elin; Hedman, Asa K; Hydrie, Zafar I; Islam, Muhammed; Khor, Chiea-Chuen; Kowlessur, Sudhir; Kristensen, Malene M; Liju, Samuel; Lim, Wei-Yen; Matthews, David R; Liu, Jianjun; Morris, Andrew P; Nica, Alexandra C; Pinidiyapathirage, Janani M; Prokopenko, Inga; Rasheed, Asif; Samuel, Maria; Shah, Nabi; Shera, A Samad; Small, Kerrin S; Suo, Chen; Wickremasinghe, Ananda R; Wong, Tien Yin; Yang, Mingyu; Zhang, Fan; Abecasis, Goncalo R; Barnett, Anthony H; Caulfield, Mark; Deloukas, Panos; Frayling, Timothy M; Froguel, Philippe; Kato, Norihiro; Katulanda, Prasad; Kelly, M Ann; Liang, Junbin; Mohan, Viswanathan; Sanghera, Dharambir K; Scott, James; Seielstad, Mark; Zimmet, Paul Z; Elliott, Paul; Teo, Yik Ying; McCarthy, Mark I; Danesh, John; Tai, E Shyong; Chambers, John C
Integrated Genetic and Epigenetic Analysis Identifies Haplotype-Specific Methylation in the FTO Type 2 Diabetes and Obesity Susceptibility Locus
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p?=?9.40×10?4, permutation p?=?1.0×10?3). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p?=?1.13×10?7). Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM), encapsulates a Highly Conserved Non-Coding Element (HCNE) that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA) SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases.
Wilson, Gareth A.; Rakyan, Vardhman K.; Teschendorff, Andrew E.; Akan, Pelin; Stupka, Elia; Down, Thomas A.; Prokopenko, Inga; Morison, Ian M.; Mill, Jonathan; Pidsley, Ruth; Deloukas, Panos; Frayling, Timothy M.; Hattersley, Andrew T.; McCarthy, Mark I.; Beck, Stephan; Hitman, Graham A.
Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.
Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D), focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip) and absolute methylation values were estimated using a Bayesian algorithm (BATMAN). Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p?=?9.40×10(-4), permutation p?=?1.0×10(-3)). Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p?=?1.13×10(-7)). Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM), encapsulates a Highly Conserved Non-Coding Element (HCNE) that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA) SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases. PMID:21124985
Bell, Christopher G; Finer, Sarah; Lindgren, Cecilia M; Wilson, Gareth A; Rakyan, Vardhman K; Teschendorff, Andrew E; Akan, Pelin; Stupka, Elia; Down, Thomas A; Prokopenko, Inga; Morison, Ian M; Mill, Jonathan; Pidsley, Ruth; Deloukas, Panos; Frayling, Timothy M; Hattersley, Andrew T; McCarthy, Mark I; Beck, Stephan; Hitman, Graham A
The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
Background Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders. Results We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation. Conclusions We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
The A- and B-type cyclins of Drosophila are accumulated and destroyed in temporally distinct events that define separable phases of the G2-M transition.
We show that the sequence of Drosophila cyclin B has greater identity with B-type cyclins from other animal phyla than with Drosophila cyclin A, suggesting that the two cyclins have distinct roles that have been maintained in evolution. Cyclin A is not detectable in unfertilized eggs and is present at low levels prior to cellularization of the syncytial embryo. In contrast, the levels of cyclin B remain uniformly high throughout these developmental stages. In cells within cellularized embryos and the larval brain, cyclin A accumulates to peak levels in prophase and is degraded throughout the period in which chromosomes are becoming aligned on the metaphase plate. The degradation of cyclin B, on the other hand, does not occur until the metaphase-anaphase transition. In cells arrested at c-metaphase by treating with microtubule destabilizing drugs to prevent spindle formation, cyclin A has been degraded in the arrested cells, whereas cyclin B is maintained at high levels. These observations suggest that cyclin A has a role in the G2-M transition that is independent of spindle formation, and that entry into anaphase is a key requirement for the degradation of cyclin B. Images Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7.
Whitfield, W G; Gonzalez, C; Maldonado-Codina, G; Glover, D M
Redox regulation of T-cell turnover by the p13 protein of human T-cell leukemia virus type 1: distinct effects in primary versus transformed cells.
The present study investigated the function of p13, a mitochondrial protein of human T-cell leukemia virus type 1 (HTLV-1). Although necessary for viral propagation in vivo, the mechanism of function of p13 is incompletely understood. Drawing from studies in isolated mitochondria, we analyzed the effects of p13 on mitochondrial reactive oxygen species (ROS) in transformed and primary T cells. In transformed cells (Jurkat, HeLa), p13 did not affect ROS unless the cells were subjected to glucose deprivation, which led to a p13-dependent increase in ROS and cell death. Using RNA interference we confirmed that expression of p13 also influences glucose starvation-induced cell death in the context of HTLV-1-infected cells. ROS measurements showed an increasing gradient from resting to mitogen-activated primary T cells to transformed T cells (Jurkat). Expression of p13 in primary T cells resulted in their activation, an effect that was abrogated by ROS scavengers. These findings suggest that p13 may have a distinct impact on cell turnover depending on the inherent ROS levels; in the context of the HTLV-1 propagation strategy, p13 could increase the pool of "normal" infected cells while culling cells acquiring a transformed phenotype, thus favoring lifelong persistence of the virus in the host. PMID:20395415
Silic-Benussi, Micol; Cavallari, Ilaria; Vajente, Nicola; Vidali, Silvia; Chieco-Bianchi, Luigi; Di Lisa, Fabio; Saggioro, Daniela; D'Agostino, Donna M; Ciminale, Vincenzo
Spectroscopic Distinctions between Two Types of Ce(3+) Ions in X2-Y2SiO5: A Theoretical Investigation.
The Ce(3+) ions occupying the two crystallographically distinct Y(3+) sites both with C1 point group symmetry in the X2-Y2SiO5 (X2-YSO) crystal are discriminated by their spectroscopic properties calculated with ab initio approaches and phenomenological model analyses. Density functional theory (DFT) calculations with the supercell approach are performed to obtain the local structures of Ce(3+), based on which the wave function-based embedded cluster calculations at the CASSCF/CASPT2 level are carried out to derive the 4f ? 5d transition energies. From the ab initio calculated energy levels and wave functions, the crystal-field parameters (CFPs) and the anisotropic g-factor tensors of Ce(3+) are extracted. The theoretical results agree well with available experimental data. The structural and spectroscopic properties for the two types of Ce(3+) ions in X2-YSO are thus distinguished in terms of the calculated local atomic structures, 4f ? 5d transition energies, and spectral parameters. PMID:24953347
Wen, Jun; Duan, Chang-Kui; Ning, Lixin; Huang, Yucheng; Zhan, Shengbao; Zhang, Jie; Yin, Min
Purification and characterization of three distinct types of phospholipase A2 inhibitors from the blood plasma of the Chinese mamushi, Agkistrodon blomhoffii siniticus.
Three distinct types of phospholipase A2 (PLA2) inhibitory proteins (PLIalpha, PLIbeta, and PLIgamma) were isolated from the blood plasma of the Chinese mamushi, Agkistrodon blomhoffii siniticus. PLIalpha is an inhibitor that we have already purified and whose amino acid sequence we have already determined [Ohkura, Inoue, Ikeda and Hayashi (1993) J. Biochem. (Tokyo) 113, 413-419]. It inhibited selectively the group-II acidic PLA2s from Crotalidae venom. PLIbeta was a 160-kDa glycoprotein having a trimeric structure composed of 50-kDa subunits. The amino acid sequence of the first 30 amino acids of the N-terminal part of the 50-kDa subunit was determined and found to have no significant homology to that of known proteins. PLIbeta was a selective inhibitor against the group-II basic PLA2s from Crotalidae venom. Some amino acid residues located in or close to the interfacial binding surface of the group-II basic PLA2s were suggested to be involved in selective binding to PLIbeta. PLIgamma was a 100-kDa glycoprotein containing 25-kDa and 20-kDa subunits and inhibited all of the PLA2s investigated equally, including Elapidae venom PLA2s (group I), Crotalidae and Viperidae venom PLA2s (group II) and honey-bee PLA2 (group III). From the N-terminal sequences of the two subunits, PLIgamma was found to be the same type of PLI that had been purified from Thailand cobra plasma. PMID:9230137
Ohkura, N; Okuhara, H; Inoue, S; Ikeda, K; Hayashi, K
Colorectal cancers show distinct mutation spectra in members of the canonical WNT signaling pathway according to their anatomical location and type of genetic instability.
It is unclear whether the mutation spectra in WNT genes vary among distinct types of colorectal tumors. We have analyzed mutations in specific WNT genes in a cohort of 52 colorectal tumors and performed a meta-analysis of previous studies. Notably, significant differences were found among the mutation spectra. We have previously shown that in familial adenomatous polyposis, APC somatic mutations are selected to provide the "just-right" level of WNT signaling for tumor formation. Here, we found that APC mutations encompassing at least two beta-catenin down-regulating motifs (20 a.a. repeats) are significantly more frequent in microsatellite unstable (MSI-H) than in microsatellite stable (MSS) tumors where truncations retaining less than two repeats are more frequent (P = 0.0009). Moreover, in cases where both APC hits are detected, selection for mutations retaining a cumulative number of two 20 a.a. repeats became apparent in MSI-H tumors (P = 0.001). This type of mutations were also more frequent in proximal versus distal colonic tumors, regardless of MSI status (P = 0.0008). Among MSI-H tumors, CTNNB1 mutations were significantly more frequent in HNPCC than in sporadic lesions (28% versus 6%, P < 10-6) and were preferentially detected in the proximal colon, independently of MSI status (P = 0.017). In conclusion, the observed spectra of WNT gene mutations in colorectal tumors are likely the result from selection of specific levels of beta-catenin signaling, optimal for tumor formation in the context of specific anatomical locations and forms of genetic instability. We suggest that this may underlie the preferential location of MMR deficient tumors in the proximal colon. PMID:20544848
Albuquerque, Cristina; Baltazar, Célia; Filipe, Bruno; Penha, Filipa; Pereira, Teresa; Smits, Ron; Cravo, Marília; Lage, Pedro; Fidalgo, Paulo; Claro, Isabel; Rodrigues, Paula; Veiga, Isabel; Ramos, José Silva; Fonseca, Isabel; Leităo, Carlos Nobre; Fodde, Riccardo
Alternative splicing of VWFA modules generates variants of type VI collagen alpha 3 chain with a distinctive expression pattern in embryonic chicken tissues and potentially different adhesive function.
Type VI collagen, a ubiquitous extracellular cell adhesion molecule, is formed by heterotrimeric monomers which associate into dimers and tetramers and assemble into larger oligomers constituting the 100 nm-long periodic microfilaments of connective tissues. One distinctive structural characteristic of type VI collagen is represented by an alpha 3 chain with a much larger molecular mass compared to the other two chains and with an extensive size heterogeneity, exemplified by the separation into up to five polypeptides in SDS-PAGE. There is evidence that the alpha 3(VI) mRNA can undergo alternative splicing of three VWFA modules at the 5'-end, potentially resulting in the expression of protein variants. Here we report that alternative splicing of alpha 3(VI) mRNA in chicken embryo did not result in the absolute predominance of a particular alpha 3(VI) form in any tissue; instead, the expression of variants including exons A9, A8 and A6 increased with age. In addition, these variants had a more restricted tissue distribution pattern compared to variants including only constitutive exons: A9+ were the rarest and were present almost exclusively in skin and skeletal muscle; A6+ were expressed in several of the examined tissues with local variations; A8+ had intermediate levels and were less widely distributed than A6+ variants. Quantitative densitometric scanning of immunoblots of type VI collagen purified from gizzard and stained with VWFA module-specific antibodies indicated that the polymorphic migration pattern of alpha 3(VI) polypeptides is contributed by concurrent or independent splicing of two exons (A8 and A6) and probably by processing and/or proteolysis at the N- and C-terminus. Three exon-specific recombinant polypeptides were examined in cell adhesion assays, and A6 appeared to be the most active, particularly at low substrate concentrations. The adhesion to the recombinant modules was not abrogated by EDTA nor by mAbs against the integrin beta 1 or alpha 2 subunits. Over all, these results suggest that the splicing of the alpha 3(VI) mRNA and the tissue distribution pattern of type VI collagen variants, apart from promoting cell adhesion to different extents, might also affect additional structural as well as functional properties of this molecule, including microfilament formation and interaction with other extracellular matrix molecules. PMID:9524362
Doliana, R; Mucignat, M T; Segat, D; Zanussi, S; Fabbro, C; Lakshmi, T R; Colombatti, A
Identifying postpartum intervention approaches to prevent type 2 diabetes in women with a history of gestational diabetes
Background Women who develop gestational diabetes mellitus (GDM) have an increased risk for the development of type 2 diabetes. Despite this "window of opportunity," few intervention studies have targeted postpartum women with a history of GDM. We sought perspectives of women with a history of GDM to identify a) barriers and facilitators to healthy lifestyle changes postpartum, and b) specific intervention approaches that would facilitate participation in a postpartum lifestyle intervention program. Methods We used mixed methods to gather data from women with a prior history of GDM, including focus groups and informant interviews. Analysis of focus groups relied on grounded theory and used open-coding to categorize data by themes, while frequency distributions were used for the informant interviews. Results Of 38 women eligible to participate in focus groups, only ten women were able to accommodate their schedules to attend a focus group and 15 completed informant interviews by phone. We analyzed data from 25 women (mean age 35, mean pre-pregnancy BMI 28, 52% Caucasian, 20% African American, 12% Asian, 8% American Indian, 8% refused to specify). Themes from the focus groups included concern about developing type 2 diabetes, barriers to changing diet, and barriers to increasing physical activity. In one focus group, women expressed frustration about feeling judged by their physicians during their GDM pregnancy. Cited barriers to lifestyle change were identified from both methods, and included time and financial constraints, childcare duties, lack of motivation, fatigue, and obstacles at work. Informants suggested facilitators for lifestyle change, including nutrition education, accountability, exercise partners/groups, access to gyms with childcare, and home exercise equipment. All focus group and informant interview participants reported access to the internet, and the majority expressed interest in an intervention program delivered primarily via the internet that would include the opportunity to work with a lifestyle coach. Conclusion Time constraints were a major barrier. Our findings suggest that an internet-based lifestyle intervention program should be tested as a novel approach to prevent type 2 diabetes in postpartum women with a history of GDM. Trial Registration ClinicalTrials.gov: NCT01102530
A distinct type of sialyl Lewis X antigen defined by a novel monoclonal antibody is selectively expressed on helper memory T cells.
A subset of human helper memory T cells is known to adhere to E-selectin expressed on cytokine-activated endothelial cells. However, sialyl Lex antigen, the carbohydrate ligand for E-selectin, has been hardly detectable on these cells, at least when typical anti-sialyl Lex antibodies were used for detection. One of the MoAbs (2F3, IgM), which we raised against a chemically synthesized sialyl Lex glycolipid preparation, is found to react selectively to CD4+ CD45RObright+ CD45RA- helper memory T cells among peripheral lymphocytes in healthy individuals. The specificity of the antibody is in clear contrast to that of the hitherto reported typical anti-sialyl Lex antibodies FH-6 and SNH-3. These classical anti-sialyl Lex antibodies were known to react to a subset of natural killer (NK) cells, but were not reactive with any particular subset of resting peripheral T or B cells of healthy individuals if the cells were not activated. On the other hand, the newly generated 2F3 antibody specifically reacted to helper memory T cells, and did not react to NK cells, B cells, or any T cells other than helper memory T cells. When tested against the sialyl Lex-active glycolipid antigen, the reactivity of 2F3 was not significantly different from that of the classical anti-sialyl Lex antibodies. But when tested against oligosaccharides prepared from cellular glycoproteins, 2F3 detected a distinct set of O-linked oligosaccharides, which were not reactive to the classical anti-sialyl Lex antibodies. Our results suggest that various molecular species of sialyl Lex antigens are present on carbohydrate side chains of cellular glycoproteins, and that helper memory T cells express a distinct type of sialyl Lex antigen that is defined by 2F3 but is not efficiently detected by other typical anti-sialyl Lex antibodies. Among cultured lymphocytic leukemia cells, the adult T-cell leukemia (ATL) cells preferentially expressed the 2F3-defined antigen, and acute lymphocytic leukemia cells rarely expressed the antigen. The cultured ATL cells expressing the 2F3-defined antigen showed a clear E-selectin-dependent adhesion to cytokin-activated endothelial cells, and the 2F3-defined sialyl Lex antigen served as a ligand for E-selectin as ascertained by the clear inhibition of adhesion with the 2F3 antibody.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:7693048
Ohmori, K; Takada, A; Ohwaki, I; Takahashi, N; Furukawa, Y; Maeda, M; Kiso, M; Hasegawa, A; Kannagi, M; Kannagi, R
Chronic human immunodeficiency virus type 1 infection stimulates distinct NF-kappa B/rel DNA binding activities in myelomonoblastic cells.
The relationship between human immunodeficiency virus type 1 (HIV-1) infection and the induction of NF-kappa B binding activity was examined in a myeloid cell model of HIV-1 infection derived from the PLB-985 cell line. Chronic infection of PLB-985 cells led to increased monocyte-specific surface marker expression, increased c-fms gene transcription, and morphological alterations consistent with differentiation along the monocytic pathway. PLB-IIIB cells displayed a constitutive NF-kappa B-like binding activity that was distinct from that induced by tumor necrosis factor alpha or phorbol 12-myristate 13-acetate treatment of the parental PLB-985 cell line. This unique DNA binding activity consisted of proteins of 70, 90, and 100 kDa with a high degree of binding specificity for the NF-kappa B site within the PRDII domain of beta interferon. In this report, we characterize the nature of these proteins and demonstrate that binding of these proteins is also induced following Sendai paramyxovirus infection. The 70-kDa protein corresponds to the NF-kappa B RelA (p65) subunit, which is activated in response to an acute paramyxovirus infection or a chronic HIV-1 infection. Virus infection does not appear to alter the amount of RelA (p65) or NFKB1 (p50) but rather affects the capacity of I kappa B alpha to sequester RelA (p65), therefore leading to constitutive levels of RelA DNA binding activity and to increased levels of NF-kappa B-dependent gene activity. The virally induced 90- to 100-kDa proteins have a distinct binding specificity for the PRDII domain and an AT-rich sequence but do not cross-react with NF-kappa B subunit-specific antisera directed against NFKB1 (p105 or p50), NFKB2 (p100 or p52), RelA (p65), or c-rel. DNA binding of the 90- to 100-kDa proteins was not inhibited by recombinant I kappa B alpha/MAD-3 and was resistant to tryptic digestion, suggesting that these proteins may not be NF-kappa B related. Transient cotransfection experiments demonstrated that RelA and NFKB1 expression maximally stimulated HIV-1 LTR- and NF-kappa B-dependent reporter genes; differences in NF-kappa B-like binding activity were also reflected in higher constitutive levels of NF-kappa B-regulated gene expression in HIV-1-infected myeloid cells. Images
Roulston, A; Beauparlant, P; Rice, N; Hiscott, J
Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci
To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom ?50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with ?2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and clinical trials totaling 17,418 cases and 70,298 controls. First, meta-analysis of 25 studies comprising 14,073 cases and 57,489 controls of European descent confirmed eight established T2D loci at genome-wide significance. In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium identified a T2D locus at genome-wide significance (GATAD2A/CILP2/PBX4; p = 5.7 × 10?9) and two loci exceeding study-wide significance (SREBF1, and TH/INS; p < 2.4 × 10?6). Second, meta-analyses of 1,986 cases and 7,695 controls from eight African-American studies identified study-wide-significant (p = 2.4 × 10?7) variants in HMGA2 and replicated variants in TCF7L2 (p = 5.1 × 10?15). Third, conditional analysis revealed multiple known and novel independent signals within five T2D-associated genes in samples of European ancestry and within HMGA2 in African-American samples. Fourth, a multiethnic meta-analysis of all 39 studies identified T2D-associated variants in BCL2 (p = 2.1 × 10?8). Finally, a composite genetic score of SNPs from new and established T2D signals was significantly associated with increased risk of diabetes in African-American, Hispanic, and Asian populations. In summary, large-scale meta-analysis involving a dense gene-centric approach has uncovered additional loci and variants that contribute to T2D risk and suggests substantial overlap of T2D association signals across multiple ethnic groups.
Saxena, Richa; Elbers, Clara C.; Guo, Yiran; Peter, Inga; Gaunt, Tom R.; Mega, Jessica L.; Lanktree, Matthew B.; Tare, Archana; Castillo, Berta Almoguera; Li, Yun R.; Johnson, Toby; Bruinenberg, Marcel; Gilbert-Diamond, Diane; Rajagopalan, Ramakrishnan; Voight, Benjamin F.; Balasubramanyam, Ashok; Barnard, John; Bauer, Florianne; Baumert, Jens; Bhangale, Tushar; Bohm, Bernhard O.; Braund, Peter S.; Burton, Paul R.; Chandrupatla, Hareesh R.; Clarke, Robert; Cooper-DeHoff, Rhonda M.; Crook, Errol D.; Davey-Smith, George; Day, Ian N.; de Boer, Anthonius; de Groot, Mark C.H.; Drenos, Fotios; Ferguson, Jane; Fox, Caroline S.; Furlong, Clement E.; Gibson, Quince; Gieger, Christian; Gilhuijs-Pederson, Lisa A.; Glessner, Joseph T.; Goel, Anuj; Gong, Yan; Grant, Struan F.A.; Grobbee, Diederick E.; Hastie, Claire; Humphries, Steve E.; Kim, Cecilia E.; Kivimaki, Mika; Kleber, Marcus; Meisinger, Christa; Kumari, Meena; Langaee, Taimour Y.; Lawlor, Debbie A.; Li, Mingyao; Lobmeyer, Maximilian T.; Maitland-van der Zee, Anke-Hilse; Meijs, Matthijs F.L.; Molony, Cliona M.; Morrow, David A.; Murugesan, Gurunathan; Musani, Solomon K.; Nelson, Christopher P.; Newhouse, Stephen J.; O'Connell, Jeffery R.; Padmanabhan, Sandosh; Palmen, Jutta; Patel, Sanjey R.; Pepine, Carl J.; Pettinger, Mary; Price, Thomas S.; Rafelt, Suzanne; Ranchalis, Jane; Rasheed, Asif; Rosenthal, Elisabeth; Ruczinski, Ingo; Shah, Sonia; Shen, Haiqing; Silbernagel, Gunther; Smith, Erin N.; Spijkerman, Annemieke W.M.; Stanton, Alice; Steffes, Michael W.; Thorand, Barbara; Trip, Mieke; van der Harst, Pim; van der A, Daphne L.; van Iperen, Erik P.A.; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Wolffenbuttel, Bruce H.R.; Young, Taylor; Zafarmand, M. Hadi; Zmuda, Joseph M.; Boehnke, Michael; Altshuler, David; McCarthy, Mark; Kao, W.H. Linda; Pankow, James S.; Cappola, Thomas P.; Sever, Peter; Poulter, Neil; Caulfield, Mark; Dominiczak, Anna; Shields, Denis C.; Bhatt, Deepak L.; Zhang, Li; Curtis, Sean P.; Danesh, John; Casas, Juan P.; van der Schouw, Yvonne T.; Onland-Moret, N. Charlotte; Doevendans, Pieter A.; Dorn, Gerald W.; Farrall, Martin; FitzGerald, Garret A.; Hamsten, Anders; Hegele, Robert; Hingorani, Aroon D.; Hofker, Marten H.; Huggins, Gordon S.; Illig, Thomas; Jarvik, Gail P.; Johnson, Julie A.; Klungel, Olaf H.; Knowler, William C.; Koenig, Wolfgang; Marz, Winfried; Meigs, James B.; Melander, Olle; Munroe, Patricia B.; Mitchell, Braxton D.; Bielinski, Susan J.; Rader, Daniel J.; Reilly, Muredach P.; Rich, Stephen S.; Rotter, Jerome I.; Saleheen, Danish; Samani, Nilesh J.; Schadt, Eric E.; Shuldiner, Alan R.; Silverstein, Roy; Kottke-Marchant, Kandice; Talmud, Philippa J.; Watkins, Hugh; Asselbergs, Folkert W.; de Bakker, Paul I.W.; McCaffery, Jeanne; Wijmenga, Cisca; Sabatine, Marc S.; Wilson, James G.; Reiner, Alex; Bowden, Donald W.; Hakonarson, Hakon; Siscovick, David S.; Keating, Brendan J.
'Snake River (SR)-type' volcanism at the Yellowstone hotspot track: Distinctive products from unusual, high-temperature silicic super-eruptions
A new category of large-scale volcanism, here termed Snake River (SR)-type volcanism, is defined with reference to a distinctive volcanic facies association displayed by Miocene rocks in the central Snake River Plain area of southern Idaho and northern Nevada, USA. The facies association contrasts with those typical of silicic volcanism elsewhere and records unusual, voluminous and particularly environmentally devastating styles of eruption that remain poorly understood. It includes: (1) large-volume, lithic-poor rhyolitic ignimbrites with scarce pumice lapilli; (2) extensive, parallel-laminated, medium to coarse-grained ashfall deposits with large cuspate shards, crystals and a paucity of pumice lapilli; many are fused to black vitrophyre; (3) unusually extensive, large-volume rhyolite lavas; (4) unusually intense welding, rheomorphism, and widespread development of lava-like facies in the ignimbrites; (5) extensive, fines-rich ash deposits with abundant ash aggregates (pellets and accretionary lapilli); (6) the ashfall layers and ignimbrites contain abundant clasts of dense obsidian and vitrophyre; (7) a bimodal association between the rhyolitic rocks and numerous, coalescing low-profile basalt lava shields; and (8) widespread evidence of emplacement in lacustrine-alluvial environments, as revealed by intercalated lake sediments, ignimbrite peperites, rhyolitic and basaltic hyaloclastites, basalt pillow-lava deltas, rhyolitic and basaltic phreatomagmatic tuffs, alluvial sands and palaeosols. Many rhyolitic eruptions were high mass-flux, large volume and explosive (VEI 6-8), and involved H2O-poor, low-??18O, metaluminous rhyolite magmas with unusually low viscosities, partly due to high magmatic temperatures (900-1,050??C). SR-type volcanism contrasts with silicic volcanism at many other volcanic fields, where the fall deposits are typically Plinian with pumice lapilli, the ignimbrites are low to medium grade (non-welded to eutaxitic) with abundant pumice lapilli or fiamme, and the rhyolite extrusions are small volume silicic domes and coule??es. SR-type volcanism seems to have occurred at numerous times in Earth history, because elements of the facies association occur within some other volcanic fields, including Trans-Pecos Texas, Etendeka-Paran, Lebombo, the English Lake District, the Proterozoic Keewanawan volcanics of Minnesota and the Yardea Dacite of Australia. ?? Springer-Verlag 2007.
Branney, M. J.; Bonnichsen, B.; Andrews, G. D. M.; Ellis, B.; Barry, T. L.; McCurry, M.
ZnT8-Specific CD4+ T Cells Display Distinct Cytokine Expression Profiles between Type 1 Diabetes Patients and Healthy Adults
Determination of antigen-specific T cell repertoires in human blood has been a challenge. Here, we show a novel integrated approach that permits determination of multiple parameters of antigen-specific T cell repertoires. The approach consists of two assays: the Direct assay and the Cytokine-driven assay. Briefly, human PBMCs are first stimulated with overlapping peptides encoding a given antigen for 48 hours to measure cytokine secretion (Direct assay). Peptide-reactive T cells are further expanded by IL-2 for 5 days; and after overnight starvation, expanded cells are stimulated with the same peptides from the initial culture to analyze cytokine secretion (Cytokine-driven assay). We first applied this integrated approach to determine the type of islet-antigen-specific T cells in healthy adults. Out of ten donors, the Direct assay identified GAD65-specific CD4+ T cells in three adults and zinc transporter 8 (ZnT8)-specific CD4+ T cells in five adults. The intracytoplasmic cytokine staining assay showed that these islet-antigen-specific CD4+ T cells belonged to the CD45RO+ memory compartment. The Cytokine-driven assay further revealed that islet-antigen-specific CD4+ T cells in healthy adults were capable of secreting various types of cytokines including type 1 and type 2 cytokines as well as IL-10. We next applied our integrated assay to determine whether the type of ZnT8-specific CD4+ T cells is different between Type 1 diabetes patients and age/gender/HLA-matched healthy adults. We found that ZnT8-specific CD4+ T cells were skewed towards Th1 cells in T1D patients, while Th2 and IL-10-producing cells were prevalent in healthy adults. In conclusion, the Direct assay and the Cytokine-driven assay complement each other, and the combination of the two assays provides information of antigen-specific T cell repertoires on the breadth, type, and avidity. This strategy is applicable to determine the differences in the quality of antigen-specific T cells between health and disease.
Chujo, Daisuke; Foucat, Emile; Nguyen, Thien-Son; Chaussabel, Damien; Banchereau, Jacques; Ueno, Hideki
Early region 3 of adenovirus type 19 (subgroup D) encodes an HLA-binding protein distinct from that of subgroups B and C.
Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host. For example, the most abundant E3 protein, E3/19K, inhibits the transport of newly synthesized class I major histocompatibility molecules to the cell surface, thereby interfering with antigen presentation. So far, the E3 regions of Ad subgroups A, B, C, and F have been characterized. We have cloned the E3A region of Ad type 19a (Ad19a), which belongs to the largest subgroup, D, and causes epidemic keratoconjunctivitis in humans. The sequence reveals five open reading frames (ORFs) with the potential to encode the Ad19 equivalent of pVIII, as well as proteins 12.2K, 16.2K, and 18.6K. The last ORF predicts a novel 49K protein which has no counterpart in other subgroups. Both the sequence and the overall organization of the E3 region from Ad19a shows a closer relationship to group B than to group C Ads. The 18.6K ORF represents the Ad19 homolog of the Ad2 E3/19K protein. By using 293 cells stably transfected with the Adl9a E3A region, we showed by immunoprecipitation, pulse-chase experiments, and fluorescence-activated cell sorter analysis that the Ad19 E3/19K protein binds to and prevents the transport of major histocompatibility complex molecules to the cell surface. The similar but distinct functional activity of the Ad19 E3/19K protein, combined with the new sequence which differs from those of subgroup B and C proteins, allows a more precise definition of amino acids essential for HLA binding.
Deryckere, F; Burgert, H G
An "Exacerbate-reverse" Strategy in Yeast Identifies Histone Deacetylase Inhibition as a Correction for Cholesterol and Sphingolipid Transport Defects in Human Niemann-Pick Type C Disease*?
Niemann-Pick type C (NP-C) disease is a fatal lysosomal lipid storage disorder for which no effective therapy exists. A genome-wide, conditional synthetic lethality screen was performed using the yeast model of NP-C disease during anaerobiosis, an auxotrophic condition that requires yeast to utilize exogenous sterol. We identified 12 pathways and 13 genes as modifiers of the absence of the yeast NPC1 ortholog (NCR1) and quantified the impact of loss of these genes on sterol metabolism in ncr1? strains grown under viable aerobic conditions. Deletion of components of the yeast NuA4 histone acetyltransferase complex in ncr1? strains conferred anaerobic inviability and accumulation of multiple sterol intermediates. Thus, we hypothesize an imbalance in histone acetylation in human NP-C disease. Accordingly, we show that the majority of the 11 histone deacetylase (HDAC) genes are transcriptionally up-regulated in three genetically distinct fibroblast lines derived from patients with NP-C disease. A clinically approved HDAC inhibitor (suberoylanilide hydroxamic acid) reverses the dysregulation of the majority of the HDAC genes. Consequently, three key cellular diagnostic criteria of NP-C disease are dramatically ameliorated as follows: lysosomal accumulation of both cholesterol and sphingolipids and defective esterification of LDL-derived cholesterol. These data suggest HDAC inhibition as a candidate therapy for NP-C disease. We conclude that pathways that exacerbate lethality in a model organism can be reversed in human cells as a novel therapeutic strategy. This "exacerbate-reverse" approach can potentially be utilized in any model organism for any disease.
Munkacsi, Andrew B.; Chen, Fannie W.; Brinkman, Matthew A.; Higaki, Katsumi; Gutierrez, Giselle Dominguez; Chaudhari, Jagruti; Layer, Jacob V.; Tong, Amy; Bard, Martin; Boone, Charles; Ioannou, Yiannis A.; Sturley, Stephen L.
Whole-exome sequencing identifies mutations of KIF22 in spondyloepimetaphyseal dysplasia with joint laxity, leptodactylic type.
Spondyloepimetaphyseal dysplasia with joint laxity (SEMDJL), leptodactylic (lepto-SEMDJL) or Hall type, is an autosomal-dominant skeletal dysplasia manifesting with short stature, joint laxity with dislocation(s), limb malalignment, and spinal deformity. Its causative gene mutation has not yet been discovered. We captured and sequenced the exomes of eight affected individuals in six unrelated kindreds (three individuals in a family and five simplex individuals). Five novel sequence variants in KIF22, which encodes a member of the kinesin-like protein family, were identified in seven individuals. Sanger sequencing of KIF22 confirmed that c.443C>T (p.Pro148Ser) cosegregated with the phenotype in the affected individuals in the family; c.442C>T (p.Pro148Leu) or c.446G>A (p.Arg149Gln) was present in four of five simplex individuals, but was absent in unaffected individuals in their family and 505 normal cohorts. KIF22 mRNA was detected in human bone, cartilage, joint capsule, ligament, skin, and primary cultured chondrocytes. In silico analysis of KIF22 protein structure indicates that Pro148 and Arg149 are important in maintaining hydrogen bonds in the ATP binding and motor domains of KIF22. We conclude that these mutations in KIF22 cause lepto-SEMDJL. PMID:22152677
Min, Byung-Joo; Kim, Namshin; Chung, Taesu; Kim, Ok-Hwa; Nishimura, Gen; Chung, Chin Youb; Song, Hae Ryong; Kim, Hyun Woo; Lee, Hye Ran; Kim, Jiwoong; Kang, Tae-Hoon; Seo, Myung-Eui; Yang, San-Deok; Kim, Do-Hwan; Lee, Seung-Bok; Kim, Jong-Il; Seo, Jeong-Sun; Choi, Ji-Yeob; Kang, Daehee; Kim, Dongsup; Park, Woong-Yang; Cho, Tae-Joon
Whole-Exome Sequencing Identifies Mutations of KIF22 in Spondyloepimetaphyseal Dysplasia with Joint Laxity, Leptodactylic Type
Spondyloepimetaphyseal dysplasia with joint laxity (SEMDJL), leptodactylic (lepto-SEMDJL) or Hall type, is an autosomal-dominant skeletal dysplasia manifesting with short stature, joint laxity with dislocation(s), limb malalignment, and spinal deformity. Its causative gene mutation has not yet been discovered. We captured and sequenced the exomes of eight affected individuals in six unrelated kindreds (three individuals in a family and five simplex individuals). Five novel sequence variants in KIF22, which encodes a member of the kinesin-like protein family, were identified in seven individuals. Sanger sequencing of KIF22 confirmed that c.443C>T (p.Pro148Ser) cosegregated with the phenotype in the affected individuals in the family; c.442C>T (p.Pro148Leu) or c.446G>A (p.Arg149Gln) was present in four of five simplex individuals, but was absent in unaffected individuals in their family and 505 normal cohorts. KIF22 mRNA was detected in human bone, cartilage, joint capsule, ligament, skin, and primary cultured chondrocytes. In silico analysis of KIF22 protein structure indicates that Pro148 and Arg149 are important in maintaining hydrogen bonds in the ATP binding and motor domains of KIF22. We conclude that these mutations in KIF22 cause lepto-SEMDJL.
Min, Byung-Joo; Kim, Namshin; Chung, Taesu; Kim, Ok-Hwa; Nishimura, Gen; Chung, Chin Youb; Song, Hae Ryong; Kim, Hyun Woo; Lee, Hye Ran; Kim, Jiwoong; Kang, Tae-Hoon; Seo, Myung-Eui; Yang, San-Deok; Kim, Do-Hwan; Lee, Seung-Bok; Kim, Jong-Il; Seo, Jeong-Sun; Choi, Ji-Yeob; Kang, Daehee; Kim, Dongsup; Park, Woong-Yang; Cho, Tae-Joon
Genome-wide association study in people of South Asian ancestry identifies six novel susceptibility loci for type 2 diabetes
We carried out a genome wide association study of type-2 diabetes (T2D) amongst 20,119 people of South Asian ancestry (5,561 with T2D); we identified 20 independent SNPs associated with T2D at P<10?4 for testing amongst a further 38,568 South Asians (13,170 with T2D). In combined analysis, common genetic variants at six novel loci (GRB14, ST6GAL1, VPS26A, HMG20A, AP3S2 and HNF4A) were associated with T2D (P=4.1×10?8 to P=1.9×10?11); SNPs at GRB14 were also associated with insulin sensitivity, and at ST6GAL1 and HNF4A with pancreatic beta-cell function respectively. Our findings provide additional insight into mechanisms underlying T2D, and demonstrate the potential for new discovery from genetic association studies in South Asians who have increased susceptibility to T2D.
Kooner, Jaspal S; Saleheen, Danish; Sim, Xueling; Sehmi, Joban; Zhang, Weihua; Frossard, Philippe; Been, Latonya F; Chia, Kee-Seng; Dimas, Antigone S; Hassanali, Neelam; Jafar, Tazeen; Jowett, Jeremy BM; Li, Xinzhing; Radha, Venkatesan; Rees, Simon D; Takeuchi, Fumihiko; Young, Robin; Aung, Tin; Basit, Abdul; Chidambaram, Manickam; Das, Debashish; Grunberg, Elin; Hedman, Asa K; Hydrie, Zafar I; Islam, Muhammed; Khor, Chiea-Chuen; Kowlessur, Sudhir; Kristensen, Malene M; Liju, Samuel; Lim, Wei-Yen; Matthews, David R; Liu, Jianjun; Morris, Andrew P; Nica, Alexandra C; Pinidiyapathirage, Janani M; Prokopenko, Inga; Rasheed, Asif; Samuel, Maria; Shah, Nabi; Shera, A Samad; Small, Kerrin S; Suo, Chen; Wickremasinghe, Ananda R; Wong, Tien Yin; Yang, Mingyu; Zhang, Fan; Abecasis, Goncalo R; Barnett, Anthony H; Caulfield, Mark; Deloukas, Panos; Frayling, Tim; Froguel, Philippe; Kato, Norihiro; Katulanda, Prasad; Kelly, M Ann; Liang, Junbin; Mohan, Viswanathan; Sanghera, Dharambir K; Scott, James; Seielstad, Mark; Zimmet, Paul Z; Elliott, Paul; Teo, Yik Ying; McCarthy, Mark I; Danesh, John; Tai, E Shyong; Chambers, John C
Measurement of time in oligodendrocyte-type-2 astrocyte (O-2A) progenitors is a cellular process distinct from differentiation or division.
When stimulated by platelet-derived growth factor (PDGF), oligodendrocyte-type-2 astrocyte (O-2A) progenitors derived from perinatal rat optic nerves undergo a limited number of cell divisions before clonally related cells synchronously and symmetrically differentiate into nondividing oligodendrocytes. The duration of this mitotic period is thought to be controlled by a cell-intrinsic biological clock. Thus, in the presence of PDGF, the measurement of time by the biological clock is intimately coupled to the control of division and differentiation. In contrast, O-2A progenitors grown in the presence of PDGF plus basic fibroblast growth factor (bFGF) divide indefinitely in the absence of differentiation and so do not exhibit a limited period of division. We have tested whether growth in PDGF plus bFGF alters the duration of the limited period of division O-2A progenitors exhibit in response to PDGF alone. Accordingly, O-2A progenitors were grown in the presence of PDGF plus bFGF for varying lengths of time, before being switched to conditions that promote timed differentiation (PDGF but not bFGF). Increasing duration of culture in PDGF plus bFGF led to a gradual shortening of the period for which O-2A progenitors were subsequently responsive to PDGF alone, until eventually all cells differentiated without dividing after switching. In contrast, a short exposure to bFGF was not sufficient to cause a similar alteration in the pattern of differentiation. These results indicate that O-2A progenitors prevented from undergoing timed differentiation nevertheless retain the ability to measure elapsed time, implying that the biological clock in this cell type can be uncoupled from differentiation. Furthermore, they demonstrate that the biological clock does not impose an absolute limit on the number of divisions that an O-2A progenitor can undergo. In contrast with existing hypotheses, our observations suggest that the molecular mechanism that controls timed differentiation must consist of at least two components, with the clock itself being in some manner distinct from mechanisms that limit cell division and/or directly regulate differentiation. PMID:8150211
Bögler, O; Noble, M
Genotypically defined lissencephalies show distinct pathologies.
Lissencephaly is traditionally divided into 2 distinct pathologic forms: classic (type I) and cobblestone (type II). To date, mutations in 4 genes, LIS1, DCX, RELN, and ARX, have been associated with distinct type I lissencephaly syndromes. Each of these genes has been shown to play a role in normal cell migration, consistent with the presumed pathogenesis of type I lissencephaly. Based on these data, we hypothesized that all forms of radiographically defined type I lissencephaly independent of genotype would be pathologically similar. To test this hypothesis, we examined brains from 16 patients, including 15 lissencephalic patients and one patient with subcortical band heterotopia. Of these 16 patients, 6 had LIS1 deletions, 2 had DCX mutations, and 2 had ARX mutations. In addition, 6 patients had no defined genetic defect, although the patient with subcortical band heterotopia exhibited the same pattern of malformation expected with an XLIS mutation. In all cases, the cortex was thickened; however, the topographic distribution of the cortical pathology varied, ranging from frontal- to occipital-biased pathology to diffuse involvement of the neocortex. Although brains with LIS1 deletions exhibited the classic 4-layer lissencephalic architecture, patients with DCX and ARX mutations each had unique cytoarchitectural findings distinct from LIS1. Furthermore, 2 of the 5 patients with no known genetic defect showed a fourth type of histopathology characterized by a 2-layered cortex. Interestingly, the 2 brains with the fourth type of lissencephaly showed profound brainstem and cerebellar abnormalities. In summary, we identified at least 4 distinct histopathologic subtypes of lissencephaly that stratify with the underlying genetic defect. Based on these data, a new classification for lissencephaly is proposed that incorporates both pathologic and genetic findings. PMID:16215456
Forman, Mark S; Squier, Waney; Dobyns, William B; Golden, Jeffrey A
The cribriform pattern identifies a subset of acinar predominant tumors with poor prognosis in patients with stage I lung adenocarcinoma: a conceptual proposal to classify cribriform predominant tumors as a distinct histologic subtype.
The 2011 International Association for the Study of Lung Cancer (IASLC)/American Thoracic Society (ATS)/European Respiratory Society (ERS) lung adenocarcinoma classification emphasizes the prognostic significance of histologic subtypes. However, one limitation of this classification is that the highest percentage of patients (?40%) is classified as acinar predominant tumors, and these patients display a spectrum of favorable and unfavorable clinical behaviors. We investigated whether the cribriform pattern can further stratify prognosis by histologic subtype. Tumor slides from 1038 patients with stage I lung adenocarcinoma (1995-2009) were reviewed. Tumors were classified according to the IASLC/ATS/ERS classification. The percentage of cribriform pattern was recorded, and the cribriform predominant subtype was considered as a subtype for analysis. The log-rank test was used to analyze the association between histologic variables and recurrence-free probability. The 5-year recurrence-free probability for patients with cribriform predominant tumors (n=46) was 70%. The recurrence-free probability for patients with cribriform predominant tumors was significantly lower than that for patients with acinar (5-year recurrence-free probability, 87%; P=0.002) or papillary predominant tumors (83%; P=0.020) but was comparable to that for patients with micropapillary (P=0.34) or solid predominant tumors (P=0.56). The recurrence-free probability for patients with ?10% cribriform pattern tumors (n=214) was significantly lower (5-year recurrence-free probability, 73%) than that for patients with <10% cribriform pattern tumors (n=824; 84%; P<0.001). In multivariate analysis, patients with acinar predominant tumors with ?10% cribriform pattern remained at significantly increased risk of recurrence compared with those with <10% cribriform pattern (P=0.042). Cribriform predominant tumors should be considered a distinct subtype with a high risk of recurrence, and presence (?10%) of the cribriform pattern is an independent predictor of recurrence, identifying a poor prognostic subset of acinar predominant tumors. Our findings highlight the important prognostic value of comprehensive histologic subtyping and recording the percentage of each histologic pattern, according to the IASLC/ATS/ERS classification with the addition of the cribriform subtype. PMID:24186133
Kadota, Kyuichi; Yeh, Yi-Chen; Sima, Camelia S; Rusch, Valerie W; Moreira, Andre L; Adusumilli, Prasad S; Travis, William D
A Genome-Wide Association Study Identifies GRK5 and RASGRP1 as Type 2 Diabetes Loci in Chinese Hans
Substantial progress has been made in identification of type 2 diabetes (T2D) risk loci in the past few years, but our understanding of the genetic basis of T2D in ethnically diverse populations remains limited. We performed a genome-wide association study and a replication study in Chinese Hans comprising 8,569 T2D case subjects and 8,923 control subjects in total, from which 10 single nucleotide polymorphisms were selected for further follow-up in a de novo replication sample of 3,410 T2D case and 3,412 control subjects and an in silico replication sample of 6,952 T2D case and 11,865 control subjects. Besides confirming seven established T2D loci (CDKAL1, CDKN2A/B, KCNQ1, CDC123, GLIS3, HNF1B, and DUSP9) at genome-wide significance, we identified two novel T2D loci, including G-protein–coupled receptor kinase 5 (GRK5) (rs10886471: P = 7.1 × 10?9) and RASGRP1 (rs7403531: P = 3.9 × 10?9), of which the association signal at GRK5 seems to be specific to East Asians. In nondiabetic individuals, the T2D risk-increasing allele of RASGRP1-rs7403531 was also associated with higher HbA1c and lower homeostasis model assessment of ?-cell function (P = 0.03 and 0.0209, respectively), whereas the T2D risk-increasing allele of GRK5-rs10886471 was also associated with higher fasting insulin (P = 0.0169) but not with fasting glucose. Our findings not only provide new insights into the pathophysiology of T2D, but may also shed light on the ethnic differences in T2D susceptibility.
Li, Huaixing; Gan, Wei; Lu, Ling; Dong, Xiao; Han, Xueyao; Hu, Cheng; Yang, Zhen; Sun, Liang; Bao, Wei; Li, Pengtao; He, Meian; Sun, Liangdan; Wang, Yiqin; Zhu, Jingwen; Ning, Qianqian; Tang, Yong; Zhang, Rong; Wen, Jie; Wang, Di; Zhu, Xilin; Guo, Kunquan; Zuo, Xianbo; Guo, Xiaohui; Yang, Handong; Zhou, Xianghai; Zhang, Xuejun; Qi, Lu; Loos, Ruth J.F.; Hu, Frank B.; Wu, Tangchun; Liu, Ying; Liu, Liegang; Yang, Ze; Hu, Renming; Jia, Weiping; Ji, Linong; Li, Yixue; Lin, Xu
Modified Needle-Tip PcrV Proteins Reveal Distinct Phenotypes Relevant to the Control of Type III Secretion and Intoxication by Pseudomonas aeruginosa
The type III secretion system (T3SS) is employed to deliver effector proteins to the cytosol of eukaryotic hosts by multiple species of Gram-negative bacteria, including Pseudomonas aeruginosa. Translocation of effectors is dependent on the proteins encoded by the pcrGVHpopBD operon. These proteins form a T3S translocator complex, composed of a needle-tip complex (PcrV), translocons (PopB and PopD), and chaperones (PcrG and PcrH). PcrV mediates the folding and insertion of PopB/PopD in host plasmic membranes, where assembled translocons form a translocation channel. Assembly of this complex and delivery of effectors through this machinery is tightly controlled by PcrV, yet the multifunctional aspects of this molecule have not been defined. In addition, PcrV is a protective antigen for P. aeruginosa infection as is the ortholog, LcrV, for Yersinia. We constructed PcrV derivatives containing in-frame linker insertions and site-specific mutations. The expression of these derivatives was regulated by a T3S-specific promoter in a pcrV-null mutant of PA103. Nine derivatives disrupted the regulation of effector secretion and constitutively released an effector protein into growth medium. Three of these regulatory mutants, in which the linker was inserted in the N-terminal globular domain, were competent for the translocation of a cytotoxin, ExoU, into eukaryotic host cells. We also isolated strains expressing a delayed-toxicity phenotype, which secrete translocators slowly despite the normal level of effector secretion. Most of the cytotoxic translocation-competent strains retained the protective epitope of PcrV derivatives, and Mab166 was able to protect erythrocytes during infection with these strains. The use of defined PcrV derivatives possessing distinct phenotypes may lead to a better understanding of the functional aspects of T3 needle-tip proteins and the development of therapeutic agents or vaccines targeting T3SS-mediated intoxication.
Sato, Hiromi; Hunt, Meredith L.; Weiner, Joshua J.; Hansen, Andrew T.; Frank, Dara W.
Distinctive characteristics of MALDI-Q/TOF and TOF/TOF tandem mass spectrometry for sequencing of permethylated complex type N-glycans.
Concerted MALDI-MS profiling and CID MS/MS sequencing of permethylated glycans is one of the most effective approaches for high throughput glycomics applications. In essence, the identification of larger complex type N-glycans necessitates an unambiguous definition of any modification on the trimannosyl core and the complement of non-reducing terminal sequences which constitute the respective antennary structures. Permethylation not only affords analyses of both neutral and sialylated glycans at comparable ease and sensitivity but also yields more sequence-informative fragmentation pattern. Facile glycosidic cleavages directed mostly at N-acetylglucosamine under low energy CID, as implemented on a quadrupole/time-of-flight (Q/TOF) instrument, often afford multiple losses of the attached antenna resulting in characteristic ions related to the number of antennary branches on the trimannosyl core. Non-reducing terminal epitopes can be easily deduced but information on the linkage specific substituent on the terminal units is often missing. The high energy CID MS/MS afforded by TOF/TOF instrument can fill in the gap by giving an array of additional cross-ring and satellite ions. Glycosidic cleavages occurring specifically in concert with loss of 2-linked or 3-linked substituents provide an effective way to identify the branch-specific antennary extension. These characteristics are shown here to be effective in deriving the sequences of additionally galactosylated, sialylated and fucosylated terminal N-acetyllactosamine units and their antennary location. Together, a highly reproducible fragmentation pattern can be formulated to simplify spectral assignment. This work also provides first real examples of sequencing multiply sialylated complex type N-glycans by high energy CID on a TOF/TOF instrument. PMID:16897178
Yu, Shin-Yi; Wu, Sz-Wei; Khoo, Kay-Hooi
Complexes between tissue-type plasminogen activator and proteinase inhibitors in human plasma, identified with an immunoradiometric assay
Extrinsic (tissue-type) plasminogen activator antigen in human plasma, as measured by a two-site immunoradiometric assay, is composed of a fibrin-adsorbable and a nonadsorbable fraction. Gel filtration on Ultrogel AcA 44 in 1.6M KSCN of the fibrin-adsorbable fraction showed a peak with M/sub r/ approx. =70,000, which contained plasminogen activator activity and was assumed to represent free extrinsic plasminogen activator. The nonadsorbable fraction showed a broad peak with M/sub r/ approx. =140,000 without plasminogen activator activity. Overnight incubation at 37/sup 0/C of postexercise plasma revealed a shift of the M/sub r/ approx. =70,000 peak to the M/sub r/ approx. =140,000 position, suggesting that the M/sub r/ approx. =140,000 peak consists of extrinsic plasminogen activator-protease inhibitor complex(es). ..cap alpha../sub 2/-Antiplasmin is the main inhibitor of extrinsic plasminogen activator in plasma and is probably responsible for the generation of the M/sub r/ approx. =140,000 component. A possible involvement of other plasma proteinase inhibitors was explored by incubation of /sup 125/I-labeled extrinsic plasminogen activator in ..cap alpha../sub 2/-antiplasmin-depleted plasma. A complex was formed with a t1/2 of about 1 hr, which was identified by immunoprecipitation as extrinsic plasminogen activator-..cap alpha../sub 2/-antiplasmin complex. Additional evidence for the presence of extrinsic plasminogen activator complexes with ..cap alpha../sub 2/-antiplasmin and ..cap alpha../sub 1/-antitrypsin in plasma was obtained from two-site immunoradiometric assays. It was concluded that plasma contains both free extrinsic plasminogen activator and plasminogen activator complexes with ..cap alpha../sub 2/-antiplasmin and ..cap alpha../sub 1/-antitrypsin. These complexes are also present in plasma collected on the active site inhibitor, D-Phe-Pro-Arg-CH/sub 2/Cl, at rest and after exercise and are therefore assumed to circulate in vivo. (JMT)
Rijken, D.C. (Univ. of Leuven, Belgium); Juhan-Vague, I.; Collen, D.
High frequency of abnormal glucose tolerance in DQA1 * 0102\\/DQB1 * 0602 relatives identified as part of the Diabetes Prevention Trial—Type 1 Diabetes
Aims\\/hypothesis Immunological and genetic markers can be used to assess risk of developing type 1 diabetes prior to the onset of clinical symptoms. Autoantibody-positive relatives of patients with type 1 diabetes are at increased risk for disease, while the presence of HLA DQA1*0102\\/DQB1*0602 is thought to confer protection. Using the unique population identified by the Diabetes Prevention Trial—Type Diabetes (DPT-1), our
C. J. Greenbaum; G. Eisenbarth; M. Atkinson; L. Yu; S. Babu; D. Schatz; A. Zeidler; T. Orban; C. Wasserfall; D. Cuthbertson; J. Krischer
Heritability of nociception IV: neuropathic pain assays are genetically distinct across methods of peripheral nerve injury.
Prior genetic correlation analysis of 22 heritable behavioral measures of nociception and hypersensitivity in the mouse identified 5 genetically distinct pain types. In the present study, we reanalyzed that dataset and included the results of an additional 9 assays of nociception and hypersensitivity, with the following goals: to replicate the previously identified 5 pain types; to test whether any of the newly added pain assays represent novel genetically distinct pain types; and to test the level of genetic relatedness among 9 commonly used neuropathic pain assays. Multivariate analysis of pairwise correlations between assays shows that the newly added zymosan-induced heat hypersensitivity assay does not conform to the 2 previously identified groups of heat hypersensitivity assays and cyclophosphamide-induced cystitis, the first organ-specific visceral pain model examined, is genetically distinct from other inflammatory assays. The 4 included mechanical hypersensitivity assays are genetically distinct and do not comprise a single pain type as previously reported. Among the 9 neuropathic pain assays including autotomy, chemotherapy, nerve ligation and spared nerve injury assays, at least 4 genetically distinct types of neuropathic sensory abnormalities were identified, corresponding to differences in nerve injury method. In addition, 2 itch assays and Comt genotype were compared to the expanded set of nociception and hypersensitivity assays. Comt genotype was strongly related only to spontaneous inflammatory nociception assays. These results indicate the priority for continued investigation of genetic mechanisms in several assays newly identified to represent genetically distinct pain types. PMID:24071598
Young, Erin E; Costigan, Michael; Herbert, Teri A; Lariviere, William R
Two classes of the CDh1-type activators of the anaphase-promoting complex in plants: novel functional domains and distinct regulation.
The Cdc20 and Cdh1/Fzr proteins are the substrate-specific activators of the anaphase-promoting complex (APC). In Medicago truncatula, the MtCcs52A and MtCcs52B proteins represent two subgroups of the Cdh1-type activators, which display differences in their cell cycle regulation, structure, and function. The ccs52A transcripts are present in all phases of the cell cycle. By contrast, expression of ccs52B is restricted to late G2-phase and M-phase, and its induced overexpression in BY2 cells inhibited mitosis. MtCcs52A is active in Schizosaccharomyces pombe and binds to the S. pombe APC, whereas MtCcs52B does not because of differences in the N-terminal region. We identified a new functional domain, the Cdh1-specific motif conserved in the Cdh1 proteins that, in addition to the C-box and the terminal Ile and Arg residues, was essential for the activity and required for efficient binding to the APC. Moreover, we demonstrate that cyclin-dependent kinase phosphorylation sites adjacent to the C-box may regulate the interaction with the APC. In the different plant organs, the expression of Mtccs52A and Mtccs52B displayed differences and indicated the involvement of the APC in differentiation processes. PMID:14742878
Tarayre, Sylvie; Vinardell, José Maria; Cebolla, Angel; Kondorosi, Adam; Kondorosi, Eva
Genomic analyses across six cancer types identify basal-like breast cancer as a unique molecular entity.
To improve our understanding of the biological relationships among different types of cancer, we have characterized variation in gene expression patterns in a set of 1,707 samples representing 6 human cancer types (breast, ovarian, brain, colorectal, lung adenocarcinoma and squamous cell lung cancer). In the unified dataset, breast tumors of the Basal-like subtype were found to represent a unique molecular entity as any other cancer type, including the rest of breast tumors, while showing striking similarities with squamous cell lung cancers. Moreover, gene signatures tracking various cancer- and stromal-related biological processes such as proliferation, hypoxia and immune activation were found expressed similarly in different proportions of tumors across the various cancer types. These data suggest that clinical trials focusing on tumors with common profiles and/or biomarker expression rather than their tissue of origin are warranted with a special focus on Basal-like breast cancer and squamous cell lung carcinoma. PMID:24384914
Prat, Aleix; Adamo, Barbara; Fan, Cheng; Peg, Vicente; Vidal, Maria; Galván, Patricia; Vivancos, Ana; Nuciforo, Paolo; Palmer, Héctor G; Dawood, Shaheenah; Rodón, Jordi; Cajal, Santiago Ramony; Del Campo, Josep Maria; Felip, Enriqueta; Tabernero, Josep; Cortés, Javier
Genomes of Ashbya fungi isolated from insects reveal four mating-type loci, numerous translocations, lack of transposons, and distinct gene duplications.
The filamentous fungus Ashbya gossypii is a cotton pathogen transmitted by insects. It is readily grown and manipulated in the laboratory and is commercially exploited as a natural overproducer of vitamin B2. Our previous genome analysis of A. gossypii isolate ATCC10895, collected in Trinidad nearly 100 years ago, revealed extensive synteny with the Saccharomyces cerevisiae genome, leading us to use it as a model organism to understand the evolution of filamentous growth. To further develop Ashbya as a model system, we have investigated the ecological niche of A. gossypii and isolated additional strains and a sibling species, both useful in comparative analysis. We isolated fungi morphologically similar to A. gossypii from different plant-feeding insects of the suborder Heteroptera, generated a phylogenetic tree based on rDNA-ITS sequences, and performed high coverage short read sequencing with one A. gossypii isolate from Florida, a new species, Ashbya aceri, isolated in North Carolina, and a genetically marked derivative of ATCC10895 intensively used for functional studies. In contrast to S. cerevisiae, all strains carry four not three mating type loci, adding a new puzzle in the evolution of Ashbya species. Another surprise was the genome identity of 99.9% between the Florida strain and ATCC10895, isolated in Trinidad. The A. aceri and A. gossypii genomes show conserved gene orders rearranged by eight translocations, 90% overall sequence identity, and fewer tandem duplications in the A. aceri genome. Both species lack transposable elements. Finally, our work identifies plant-feeding insects of the suborder Heteroptera as the most likely natural reservoir of Ashbya, and that infection of cotton and other plants may be incidental to the growth of the fungus in its insect host. PMID:23749448
Dietrich, Fred S; Voegeli, Sylvia; Kuo, Sidney; Philippsen, Peter
Genomes of Ashbya Fungi Isolated from Insects Reveal Four Mating-Type Loci, Numerous Translocations, Lack of Transposons, and Distinct Gene Duplications
The filamentous fungus Ashbya gossypii is a cotton pathogen transmitted by insects. It is readily grown and manipulated in the laboratory and is commercially exploited as a natural overproducer of vitamin B2. Our previous genome analysis of A. gossypii isolate ATCC10895, collected in Trinidad nearly 100 years ago, revealed extensive synteny with the Saccharomyces cerevisiae genome, leading us to use it as a model organism to understand the evolution of filamentous growth. To further develop Ashbya as a model system, we have investigated the ecological niche of A. gossypii and isolated additional strains and a sibling species, both useful in comparative analysis. We isolated fungi morphologically similar to A. gossypii from different plant-feeding insects of the suborder Heteroptera, generated a phylogenetic tree based on rDNA-ITS sequences, and performed high coverage short read sequencing with one A. gossypii isolate from Florida, a new species, Ashbya aceri, isolated in North Carolina, and a genetically marked derivative of ATCC10895 intensively used for functional studies. In contrast to S. cerevisiae, all strains carry four not three mating type loci, adding a new puzzle in the evolution of Ashbya species. Another surprise was the genome identity of 99.9% between the Florida strain and ATCC10895, isolated in Trinidad. The A. aceri and A. gossypii genomes show conserved gene orders rearranged by eight translocations, 90% overall sequence identity, and fewer tandem duplications in the A. aceri genome. Both species lack transposable elements. Finally, our work identifies plant-feeding insects of the suborder Heteroptera as the most likely natural reservoir of Ashbya, and that infection of cotton and other plants may be incidental to the growth of the fungus in its insect host.
Dietrich, Fred S.; Voegeli, Sylvia; Kuo, Sidney; Philippsen, Peter
Multiplex single-base extension typing to identify nuclear genes required for RNA editing in plant organelles
We developed a multiplex single-base extension single-nucleotide polymorphism-typing procedure for screening large numbers of plants for mutations in mitochondrial RNA editing. The high sensitivity of the approach detects changes in the RNA editing status generated in total cellular cDNA from pooled RNA preparations of up to 50 green plants. The method has been employed to tag several nuclear encoded genes required for RNA editing at specific sites in mitochondria of Arabidopsis thaliana. This approach will allow large-scale screening for mutations in genes encoding trans-factors for many types of RNA editing as well as for other RNA modifications.
Takenaka, Mizuki; Brennicke, Axel
Genetics of Kidneys in Diabetes (GoKinD) Study: A Genetics Collection Available for Identifying Genetic Susceptibility Factors for Diabetic Nephropathy in Type 1 Diabetes
The Genetics of Kidneys in Diabetes (GoKinD) study is an initiative that aims to identify genes that are involved in diabetic nephropathy. A large number of individuals with type 1 diabetes were screened to identify two subsets, one with clear-cut kidney disease and another with normal renal status despite long-term diabetes. Those who met additional entry criteria and consented to
Patricia W. Mueller; John J. Rogus; Patricia A. Cleary; Yuan Zhao; Adam M. Smiles; Michael W. Steffes; Jean Bucksa; Therese B. Gibson; Suzanne K. Cordovado; Andrzej S. Krolewski; Concepcion R. Nierras; James H. Warram
Assay of the von Willebrand factor (VWF) propeptide to identify patients with type 1 von Willebrand disease with decreased VWF survival
Type 1 von Willebrand disease (VWD) is characterized by a partial quantitative deficiency of von Willebrand factor (VWF). Few VWF gene mutations have been identified that cause dominant type 1 VWD. The decreased survival of VWF in plasma has recently been identified as a novel mechanism for type 1 VWD. We report 4 families with moderately severe type 1 VWD characterized by low plasma VWF:Ag and FVIII:C levels, proportionately low VWF:RCo, and dominant inheritance. A decreased survival of VWF in affected individuals was identified with VWF half-lives of 1 to 3 hours, whereas the half-life of VWF propeptide (VWFpp) was normal. DNA sequencing revealed a single (heterozygous) VWF mutation in affected individuals, S2179F in 2 families, and W1144G in 2 families, neither of which has been previously reported. We show that the ratio of steady-state plasma VWFpp to VWF:Ag can be used to identify patients with a shortened VWF half-life. An increased ratio distinguished affected from unaffected individuals in all families. A significantly increased VWFpp/VWF:Ag ratio together with reduced VWF:Ag may indicate the presence of a true genetic defect and decreased VWF survival phenotype. This phenotype may require an altered clinical therapeutic approach, and we propose to refer to this phenotype as type-1C VWD.
Haberichter, Sandra L.; Balistreri, Michael; Christopherson, Pamela; Morateck, Patricia; Gavazova, Stefana; Bellissimo, Daniel B.; Manco-Johnson, Marilyn J.; Gill, Joan Cox; Montgomery, Robert R.
Evidence for Identifying Children at Risk for Being Overweight, Cardiovascular Disease, and Type 2 Diabetes in Primary Care
IntroductionPractitioners have noted the escalating risk for children being overweight and having cardiovascular disease and type 2 diabetes. The purpose of this study was to apply current recommendations in examining children and to test an expanded model of assessment to predict risk.
Ruth McGillis Bindler; Margaret Auld Bruya
A mutation unique in serine protease inhibitors (serpins) identified in a family with type II hereditary angioneurotic edema.
BACKGROUND: Hereditary angioneurotic edema (HANE) is an autosomal dominant disease due to genetic alterations at the C1 inhibitor gene. Mutations within the C1 inhibitor gene are responsible for the molecular defect in type II HANE. Most of the dysfunctional proteins result from mutations involving the Arg-444 (the P-1 site of the reactive center) or amino acids NH2-terminal to the reactive center. MATERIALS AND METHODS: We have studied a Spanish family with type II HANE by using polymerase chain reaction (PCR) to amplify the exon eight of the C1 inhibitor gene. The purified 338-bp PCR product was subcloned and transformed into competent cells. After overnight cultures, we extracted the cloning vector from the positive colonies and sequenced both strands of the PCR product from each patient and healthy members of the family. RESULTS: We show that affected individuals in this family have a missense mutation, changing an adenine to cytosine in the codon 445. This substitution changes threonine at the P-1' site of the reactive center to a proline. This mutation generates a new restriction site, recognized by Bsi YI. CONCLUSIONS: To our knowledge, this is the first molecular defect characterized in a Spanish family with type II HANE, and to date, this is the first reported mutation at the P-1' site of the reactive center in individuals with type II HANE. This new mutation located at the reactive center emphasizes once more time the enormous heterogeneity of this gene. Images FIG. 1 FIG. 2 FIG. 3
Ocejo-Vinyals, J. G.; Leyva-CobiA?n, F.; FernA?ndez-Luna, J. L.
Inhibitors of the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib] identified by in silico molecular docking.
AAC(6')-Ib is an important aminoglycoside resistance enzyme to target with enzymatic inhibitors. An in silico screening approach was used to identify potential inhibitors from the ChemBridge library. Several compounds were identified, of which two of them, 4-[(2-{[1-(3-methylphenyl)-4,6-dioxo-2-thioxotetrahydro-5(2H)-pyrimidinylidene]methyl}phenoxy)methyl]benzoic acid and 2-{5-[(4,6-dioxo-1,3-diphenyl-2-thioxotetrahydro-5(2H)-pyrimidinylidene)methyl]-2-furyl}benzoic acid, showed micromolar activity in inhibiting acetylation of kanamycin A. These compounds are predicted to bind the aminoglycoside binding site of AAC(6')-Ib and exhibited competitive inhibition against kanamycin A. PMID:24011645
Lin, David L; Tran, Tung; Adams, Christina; Alam, Jamal Y; Herron, Steven R; Tolmasky, Marcelo E
Mimotopes identified by phage display for the monoclonal antibody CII-C1 to type II collagen.
The characterization of B cell epitopes has been advanced by the use of random peptide libraries displayed within the coat protein of bacteriophage. This technique was applied to the monoclonal antibody (mAb) C1 to type II collagen (CII-C1). CII-C1 is known to react with a conformational epitope on type II collagen that includes residues 359-363. Three rounds of selection were used to screen two random nonameric phage libraries and 18 phagotopes were isolated. CII-C1 reacted by ELISA with 17 of the 18 phagotopes: one phagotope contained a stop codon. Of the eight most reactive phage, seven inhibited the reactivity by ELISA of CII-C1 with type II collagen. Of the 18 phage isolated, 11 encoded the motif F-G-x-Q with the sequence F-G-S-Q in 6, 2 encoded F-G-Q, and one the reverse motif Q-x-y-F. Most phagotopes that inhibited the reactivity of CII-C1 encoded two particular motifs consisting of two basic amino acid residues and a hydrophobic residue in the first part of the insert and the F-G-x-Q or F-G-Q motif in the second part; phagotopes which contained only one basic residue in the first part of the sequence were less reactive. These motifs are not represented in the linear sequence of type II collagen and thus represent mimotopes of the epitope for CII-C1 on type II collagen. There were five phagotopes with peptide inserts containing the sequence RLPFG occurring in the Epstein-Barr virus nuclear antigen, EBNA-1. This is of interest because EBV has been implicated in the initiation of rheumatoid arthritis (RA) by reason of increased reactivity to EBNA-1 in RA sera. In conclusion, the phage display technique disclosed mimotopes for a conformational epitope of type II collagen, and revealed an interesting homology with a sequence of the EBNA-1 antigen from Epstein Barr virus. PMID:9693968
Cook, A D; Davies, J M; Myers, M A; Mackay, I R; Rowley, M J
Two rare aneutriploids in the unisexual Ambystoma (Amphibia, Caudata) identified by GISH indicating two different types of meiotic errors.
We report two types of aneutriploids in unisexual salamanders Ambystomalaterale-2jeffersonianum (LJJ) and Ambystoma 2 laterale-jeffersonianum (LLJ). One karyotype has 3n = 42: L27 (L8-); J15 (J8p+), and we suggest that it was induced by homoeologous pairing after premeiotic endomitosis followed by an unequal L8;J8 segregation. The second karyotype has 3n = 43: L14 (L10q); J29 (J12+), which can be explained by meiotic nondisjunction followed by unbalanced segregation. These two rare aneutriploids demonstrate two different types of meiotic errors that might help to explain the high mortality observed in this complex. Case one also indicates that contemporary intergenomic exchanges and homoeologous recombinations may occur after a premeiotic chromosome doubling event. Our study provides additional evidence for the extremely flexible reproduction of unisexual Ambystoma. PMID:18160791
Bi, K; Bogart, J P; Fu, J
Follow-Up Analysis of Genome-Wide Association Data Identifies Novel Loci for Type 1 Diabetes
OBJECTIVE—Two recent genome-wide association (GWA) studies have revealed novel loci for