RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus.
In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantations, water availability is a key factor limiting productivity. However, the molecular mechanisms underlying the adaptation of eucalyptus to water shortage remain unclear. In this study, we compared the molecular responses of two commercial eucalyptus hybrids during the dry season. Both hybrids differ in productivity when grown under water deficit. Pyrosequencing of RNA extracted from shoot apices provided extensive transcriptome coverage - a catalog of 129,993 unigenes (49,748 contigs and 80,245 singletons) was generated from 398 million base pairs, or 1.14 million reads. The pyrosequencing data enriched considerably existing Eucalyptus EST collections, adding 36,985 unigenes not previously represented. Digital analysis of read abundance in 14,460 contigs identified 1,280 that were differentially expressed between the two genotypes, 155 contigs showing differential expression between treatments (irrigated vs. non irrigated conditions during the dry season), and 274 contigs with significant genotype-by-treatment interaction. The more productive genotype displayed a larger set of genes responding to water stress. Moreover, stress signal transduction seemed to involve different pathways in the two genotypes, suggesting that water shortage induces distinct cellular stress cascades. Similarly, the response of functional proteins also varied widely between genotypes: the most productive genotype decreased expression of genes related to photosystem, transport and secondary metabolism, whereas genes related to primary metabolism and cell organisation were over-expressed. For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance of biomass growth during the dry season. Its strategy may involve a decrease of photosynthetic activity during the dry season associated with resources reallocation through major changes in the expression of primary metabolism associated genes. Further efforts will be needed to assess the adaptive nature of the genes highlighted in this study.


Signal-to-noise ratio and smallest detectable vibration amplitude in frequency-translated holography: an analysis.
The theoretical and experimental analysis of SNR in frequency-translated holography that is applied to the detection of small vibration amplitude is presented in this paper. The feature of the experiments lies on the usage of acoustic surface waves as the vibrating test object, since the acoustic surface waves give the reliable vibration amplitude and the easiness of the measurement of SNR. Furthermore the detectable smallest amplitude is estimated as 2.7 x 10(-4) lambda, which is several tenths smaller than the previously presented estimations, and the dependences of the detectable smallest vibration amplitude on the experimental arrangements are also made clear.


Developmental expression of the Drosophila melanogaster calmodulin gene.
The highly conserved, intracellular calcium binding protein calmodulin is present in all cells at all times. In addition to this constitutive level, the amount of calmodulin is highly regulated according to the tissue or stage of development. Since there are only a few genes or a single gene for this protein in most species, intricate regulatory elements may be necessary to effect its complex regulation. This report adds new information concerning the gene structure and outlines the developmental and spatial regulation of Drosophila melanogaster calmodulin transcripts. The gene contains five exons, including a 49 bp exon in the 5' untranslated region, and spans over 16 kb. Homologues to this small, 5' noncoding exon have not been found in other calmodulin genes. The combined level of the transcripts is developmentally regulated, and the relative amounts of the two transcript size classes (1.65 kb and 1.9 kb) are differentially regulated during development. Primer extension experiments and RNase protection mapping show that both size classes of Drosophila calmodulin transcripts initiate at the same site but undergo alternative termination within the final exon. The spatial distribution of calmodulin transcripts was examined by in situ hybridization to sections of adults and to developmentally staged whole mount embryos. Calmodulin transcripts are evenly distributed early in embryogenesis. In later stages of embryogenesis, higher levels accumulate in the developing nerve cord and other tissues. Elevated levels of calmodulin transcripts are seen quite distinctly in the adult neural tissues and in the photoreceptor region of the compound eye.


Neural markers of social and monetary rewards in children with Attention-Deficit/Hyperactivity Disorder and Autism Spectrum Disorder.
Recent theories of decision making propose a shared value-related brain mechanism for encoding monetary and social rewards. We tested this model in children with Attention-Deficit/Hyperactivity Disorder (ADHD), children with Autism Spectrum Disorder (ASD) and control children. We monitored participants' brain dynamics using high density-electroencephalography while they played a monetary and social reward tasks. Control children exhibited a feedback Error-Related Negativity (fERN) modulation and Anterior Cingulate Cortex (ACC) source activation during both tasks. Remarkably, although cooperation resulted in greater losses for the participants, the betrayal options generated greater fERN responses. ADHD subjects exhibited an absence of fERN modulation and reduced ACC activation during both tasks. ASD subjects exhibited normal fERN modulation during monetary choices and inverted fERN/ACC responses in social options than did controls. These results suggest that in neurotypicals, monetary losses and observed disloyal social decisions induced similar activity in the brain value system. In ADHD children, difficulties in reward processing affected early brain signatures of monetary and social decisions. Conversely, ASD children showed intact neural markers of value-related monetary mechanisms, but no brain modulation by prosociality in the social task. These results offer insight into the typical and atypical developments of neural correlates of monetary and social reward processing.


Morphological and molecular description of Ixodes woyliei n. sp. (Ixodidae) with consideration for co-extinction with its critically endangered marsupial host.
Taxonomic identification of ticks obtained during a longitudinal survey of the critically endangered marsupial, Bettongia penicillata Gray, 1837 (woylie, brush-tailed bettong) revealed a new species of Ixodes Latrielle, 1795. Here we provide morphological data for the female and nymphal life stages of this novel species (Ixodes woyliei n. sp.), in combination with molecular characterisation using the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). In addition, molecular characterisation was conducted on several described Ixodes species and used to provide phylogenetic context. Ixodes spp. ticks were collected from the two remaining indigenous B. penicillata populations in south-western Australia. Of 624 individual B. penicillata sampled, 290 (47%) were host to ticks of the genus Ixodes; specifically I. woyliei n. sp., I. australiensis Neumann, 1904, I. myrmecobii Roberts, 1962, I. tasmani Neumann, 1899 and I. fecialis Warburton & Nuttall, 1909. Of these, 123 (42%) were host to the newly described I. woyliei n. sp. In addition, 268 individuals from sympatric marsupial species (166 Trichosurus vulpecula hypoleucus Wagner, 1855 (brushtail possum), 89 Dasyurus geoffroii Gould, 1841 (Western quoll) and 13 Isoodon obesulus fusciventer Gray, 1841 (southern brown bandicoot)) were sampled for ectoparasites and of these, I. woyliei n. sp. was only found on two I. o. fusciventer. Morphological and molecular data have confirmed the first new Australian Ixodes tick species described in over 50 years, Ixodes woyliei n. sp. Based on the long-term data collected, it appears this tick has a strong predilection for B. penicillata, with 42% of Ixodes infections on this host identified as I. woyliei n. sp. The implications for this host-parasite relationship are unclear but there may be potential for a future co-extinction event. In addition, new molecular data have been generated for collected specimens of I. australiensis, I. tasmani and museum specimens of I. victoriensis Nuttall, 1916, which for the first time provides molecular support for the subgenus Endopalpiger Schulze, 1935 as initially defined. These genetic data provide essential information for future studies relying on genotyping for species identification or for those tackling the phylogenetic relationships of Australian Ixodes species.


Crystals of hexagonal ice with (2 0 2 3) Miller index faces explain exotic arcs in the Lascar halo display.
This article focuses on the 1997 Lascar halo display, during which very unusual arcs and halos were documented. Photographs have been analyzed with the aid of a specific image processing method developed by us. Using crystals of hexagonal ice with exotic (2 0 2 3) Miller index faces, it is possible to simulate all the features of the display with constant crystal populations and oriented crystals in plate orientation. The simulations perform better than the cubic ice explanation. The existence of (2 0 2 3) crystal faces is supported by a 1998 South Pole halo display.


APEX (Aqueous Photochemistry of Environmentally occurring Xenobiotics): a free software tool to predict the kinetics of photochemical processes in surface waters.
The APEX software predicts the photochemical transformation kinetics of xenobiotics in surface waters as a function of: photoreactivity parameters (direct photolysis quantum yield and second-order reaction rate constants with transient species, namely ˙OH, CO₃(-)˙, (1)O₂ and the triplet states of chromophoric dissolved organic matter, (3)CDOM*), water chemistry (nitrate, nitrite, bicarbonate, carbonate, bromide and dissolved organic carbon, DOC), and water depth (more specifically, the optical path length of sunlight in water). It applies to well-mixed surface water layers, including the epilimnion of stratified lakes, and the output data are average values over the considered water column. Based on intermediate formation yields from the parent compound via the different photochemical pathways, the software can also predict intermediate formation kinetics and overall yield. APEX is based on a photochemical model that has been validated against available field data of pollutant phototransformation, with good agreement between model predictions and field results. The APEX software makes allowance for different levels of knowledge of a photochemical system. For instance, the absorption spectrum of surface water can be used if known, or otherwise it can be modelled from the values of DOC. Also the direct photolysis quantum yield can be entered as a detailed wavelength trend, as a single value (constant or average), or it can be defined as a variable if unknown. APEX is based on the free software Octave. Additional applications are provided within APEX to assess the σ-level uncertainty of the results and the seasonal trend of photochemical processes.


Updates and Comparative Analysis of the Mitochondrial Genomes of Paracoccidioides spp. Using Oxford Nanopore MinION Sequencing.
The mitochondrial genome of the Paracoccidioides brasiliensis reference isolate Pb18 was first sequenced and described by Cardoso et al. (2007), as a circular genome with a size of 71.3 kb and containing 14 protein coding genes, 25 tRNAs, and the large and small subunits of ribosomal RNA. Later in 2011, Desjardins et al. (2011) obtained partial assemblies of mitochondrial genomes of P. lutzii (Pb01), P. americana (Pb03), and P. brasiliensis sensu stricto (Pb18), although with a size of only 43.1 kb for Pb18. Sequencing errors or other limitations resulting from earlier technologies, and the advantages of NGS (short and long reads), prompted us to improve and update the mtDNA sequences and annotations of two Paracoccidioides species. Using Oxford Nanopore and Illumina read sequencing, we generated high-quality complete de novo mitochondrial genome assemblies and annotations for P. brasiliensis (Pb18) and P. americana (Pb03). Both assemblies were characterized by an unusually long spacer or intron region (>50 kb) between exons 2 and 3 of the nad5 gene, which was moderately conserved between Pb03 and Pb18 but not similar to other reported sequences, except for an unassigned contig in the 2011 assembly of Pb03. The reliability of the insert missing from previous mtDNA genome assemblies was confirmed by inspection of the individual Nanopore read sequences containing nad5 coding DNA, and experimentally by PCR for Pb18. We propose that the insert may aid replication initiation and may be excised to produce a smaller structural variant. The updated mtDNA genomes should enable more accurate SNP and other comparative or evolutionary analyses and primer/probe designs. A comparative analysis of the mtDNA from 32 isolates of Paracoccidioides spp., using the SNPs of the aligned mitochondrial genomes, showed groupings within the brasiliensis species complex that were largely consistent with previous findings from only five mitochondrial loci.


Self-interaction corrected density functional theory for the study of intramolecular electron transfer dynamics in radical carbocations.
We derived an orbital dependent Kohn-Sham based scheme for the correction of the self-interaction error in DFT, which is particularly suited for the study of open shell molecular systems. Our approach is based on a weighted form of the Perdew and Zunger (PZ) self-interaction correction scheme, in which an empirical coefficient is introduced in front of the SIC term to remove overcorrections. The method is used to investigate the first principle molecular dynamics of the intramolecular electron transfer (IET) in bis(methylene) adamanthyl radical cation and allows the analysis of the free energy surface that governs the IET process at room temperature (300 K). Indeed, the thermal activation of all molecular degrees of freedom provides important additional information about the mechanisms involved in the IET process. Our study confirms and extends previous results obtained with CASSCF and shows that there is no predominant degeneracy-lifting mode even at room temperature. However, we also identified regions in the phase space for which there is a significant probability for a productive IET event. In addition, we performed thermodynamic integrations along selected reaction coordinates to determine an estimate of the activation free energy barrier for the IET process.


Berberine inhibits lipopolysaccharide-induced expression of inflammatory cytokines by suppressing TLR4-mediated NF-ĸB and MAPK signaling pathways in rumen epithelial cells of Holstein calves.
Subacute ruminal acidosis (SARA) can increase the level of inflammation and induce rumenitis in dairy cows. Berberine (BBR) is the major active component of Rhizoma Coptidis, which is a type of Chinese anti-inflammatory drug for gastrointestinal diseases. The purpose of this study was to investigate the anti-inflammatory effects of BBR on lipopolysaccharide (LPS)-stimulated rumen epithelial cells (REC) and the underlying molecular mechanisms. REC were cultured and stimulated with LPS in the presence or absence of different concentrations of BBR. The results showed that cell viability was not affected by BBR. Moreover, BBR markedly decreased the concentrations and mRNA expression of pro-inflammatory cytokines, including tumor necrosis factor-α, interleukin-1β, and interleukin-6 in the LPS-treated REC in a dose-dependent manner. Importantly, Western blotting analysis showed that BBR significantly suppressed the protein expression of toll-like receptor 4 (TLR4) and myeloid differentiation primary response protein (MyD88) and the phosphorylation of nuclear factor-κB (NF-κB), inhibitory kappa B (IκBα), p38 mitogen-activated protein kinase (MAPK), and c-Jun N-terminal kinase (JNK) in LPS-treated REC. Furthermore, the results of immunocytofluorescence showed that BBR significantly inhibited the nuclear translocation of NF-κB p65 induced by LPS treatment. In conclusion, the protective effects of BBR on LPS-induced inflammatory responses in REC may be due to its ability to suppress the TLR4-mediated NF-κB and MAPK signaling pathways. These findings suggest that BBR can be used as an anti-inflammatory drug to treat inflammation induced by SARA.


WebACT: an online genome comparison suite.
Comparison of related genomes is an enormously powerful technique for explaining phenotypic differences and revealing recent evolutionary events. Genomes evolve through a host of mechanisms including long- and short-range intragenomic rearrangements, insertion of laterally acquired DNA, gene loss, and single-nucleotide polymorphisms. The Artemis Comparison Tool (ACT) was developed to enable the intuitive visualization of the consequences of such events in the context of two or more aligned genomes. WebACT is an online resource designed to allow the alignment of up to five genomic sequences within the ACT environment without the need for local software installation. Comparisons can be carried out between uploaded sequences, or those selected from the EMBL or RefSeq databases, using BLASTZ, MUMmer, or Basic Local Alignment Search Tool (BLAST). Precomputed comparisons can be selected from a database covering all the completed bacterial chromosome and plasmid sequences in the Genome Reviews database (1). This allows the rapid visualization of regions of interest, without the need to handle the full genome sequences. Here, we describe the process of using WebACT to prepare comparisons for visualization, and the selection of precomputed comparisons from the database. The use of ACT to view the selected comparison is then explored using examples from bacterial genomes.


Cosmetologists and reproductive outcomes.
To test the hypothesis that cosmetologists are at increased risk of poor pregnancy outcomes compared with women of the same age who are not cosmetologists. Participants were recruited through mass mailing of questionnaires. To be included in the study, respondents to the survey had to be aged between 21 and 55 years and not have had a hysterectomy or oophorectomy. This analysis focused on 350 cosmetologists and 397 women in other occupations who met these inclusion criteria and who reported five or fewer singleton pregnancies. The main outcome measures were miscarriage, stillbirth, the occurrence of maternal health conditions during pregnancy (preeclampsia, high blood pressure, diabetes), hospitalization or physician-ordered bed rest during pregnancy, preterm labor, and premature delivery (before 37 weeks at delivery). There were no statistically significant associations between occupation and the pregnancy outcomes after adjustment for age, race, education, and smoking and alcohol use at the time of pregnancy. A statistically significant association was found between race and low birth weight such that nonwhite women were at increased risk of reporting a low birth weight neonate compared with white women (odds ratio [OR] 3.35, 95% confidence interval [CI] 1.53-7.26). Similarly, current smoking was found to be positively associated with miscarriage (OR 1.53, CI 1.09-2.16) and miscarriage or stillbirth (OR 1.64, 95% CI 1.18-2.28). Risk of adverse pregnancy outcomes among cosmetologists is not increased compared with women of the same age working in other occupations.


Receiving of emotional signal of pain from conspecifics in laboratory rats.
Though recent studies have shown that rodents express emotions with their face, whether emotional expression in rodents has a communicative function between conspecifics is still unclear. Here, we demonstrate the ability of visual recognition of emotional expressions in laboratory rats. We found that Long-Evans rats avoid images of pain expressions of conspecifics but not those of neutral expressions. The results indicate that rats use visual emotional signals from conspecifics to adjust their behaviour in an environment to avoid a potentially dangerous place. Therefore, emotional expression in rodents, rather than just a mere 'expression' of emotional states, might have a communicative function.


Quantification of the second-order nonlinear susceptibility of collagen I using a laser scanning microscope.
Characteristic changes in the organization of fibrillar collagen can potentially serve as an early diagnostic marker in various pathological processes. Tissue types containing collagen I can be probed by pulsed high-intensity laser radiation, thereby generating second harmonic light that provides information about the composition and structure at a microscopic level. A technique was developed to determine the essential second harmonic generation (SHG) parameters in a laser scanning microscope setup. A rat-tail tendon frozen section was rotated in the xy-plane with the pulsed laser light propagating along the z-axis. By analyzing the generated second harmonic light in the forward direction with parallel and crossed polarizer relative to the polarization of the excitation laser beam, the second-order nonlinear optical susceptibilities of the collagen fiber were determined. Systematic variations in SHG response between ordered and less ordered structures were recorded and evaluated. A 500 microm-thick z-cut lithiumniobate (LiNbO(3)) was used as reference. The method was applied on frozen sections of malignant melanoma and normal skin tissue. Significant differences were found in the values of d(22), indicating that this parameter has a potential role in differentiating between normal and pathological processes.


Limiting transplantation-related mortality following unrelated donor stem cell transplantation by using a nonmyeloablative conditioning regimen.
A nonmyeloablative conditioning regimen was investigated in 47 patients with hematological malignancy receiving allogeneic progenitor cells from matched, unrelated donors. The median patient age was 44 years. The majority of patients had high-risk features, including having failed a prior transplantation (29 individuals). Twenty of the transplants were mismatched for HLA class I and/or class II alleles. Recipient conditioning consisted of 20 mg CAMPATH-1H on days -8 to -4, 30 mg/m(2) fludarabine on days -7 to -3, and 140 mg/m(2) melphalan on day -2. Graft-versus-host disease (GVHD) prophylaxis was with cyclosporine A alone. Primary graft failure occurred in only 2 of 44 evaluable patients (4.5%). Chimerism studies in 34 patients indicated that the majority (85.3%) attained initial full donor chimerism. Only 3 patients developed grade III to IV acute GVHD, and no patients have yet developed chronic extensive GVHD. The estimated probability of nonrelapse mortality at day 100 was 14.9% (95% confidence interval [CI], 4.7%-25.1%). With a median follow-up of 344 days (range, 79-830), overall and progression-free survivals at 1 year were 75.5% (95% CI, 62.8%-88.2%) and 61.5% (95% CI, 46.1%-76.8%), respectively. In summary, a nonmyeloablative regimen incorporating in vivo CAMPATH-1H is effective in promoting durable engraftment in most patients and in reducing the risk of severe GVHD following matched unrelated donor transplantation.


Improved Survival for Rural Trauma Patients Transported by Helicopter to a Verified Trauma Center: A Propensity Score Analysis.
Recent studies using advanced statistical methods to control for confounders have demonstrated an association between helicopter transport (HT) versus ground ambulance transport (GT) in terms of improved survival for adult trauma patients. The aim of this study was to apply a methodologically vigorous approach to determine if HT is associated with a survival benefit for when trauma patients are transported to a verified trauma center in a rural setting. The ascertainment of trauma patients age ≥ 15 years (n = 469 cases) by HT and (n = 580 cases) by GT between 1999 and 2012 was restricted to the scene of injury in a rural area of 10 to 35 miles from the trauma center. The propensity score (PS) was determined using data including demographics, prehospital physiology, intubation, total prehospital time, and injury severity. The PS matching was performed with different calipers to select a higher percentage of matches of HT compared to GT patients. The outcome of interest was survival to discharge from hospital. Identical logistic regression analysis was done taking into account for each matched design to select an appropriate effect estimate and confidence interval (CI) controlling for initial vital signs in the emergency department, the need for urgent surgery, intensive care unit admission, and mechanical ventilation. Unadjusted mortalities for HT compared to GT were 7.7 and 5.3%, respectively (p > 0.05). The adjusted rates were 4.0% for HT and 7.6% for GT (p < 0.05). In a PS well-matched data set, HT was associated with a 2.69-fold increase in odds of survival compared to GT patients (adjusted odds ratio = 2.69; 95% CI = 1.21-5.97). In a rural setting, we demonstrated improved survival associated with HT compared to GT for scene transportation of adult trauma patients to a verified Level II trauma center using an advanced methodologic approach, which included adjustment for transport distance. The implication of survival benefit to rural population is discussed. We recommend larger studies with multiple trauma systems need to be repeated using similar study methodology to substantiate our findings.


Implant failure in bilateral metal-on-metal hip resurfacing arthroplasties: a clinical and pathological study.
Metal-on-metal hip resurfacing arthroplasties (MoMHRAs) have a high failure rate due to pseudotumour formation. It is not certain whether pseudotumours in bilateral MoMHRAs form on the basis of an adverse reaction to metal debris (ARMD) that is entirely due to a local innate and adaptive immune response to Cobalt-Chrome (Co-Cr) wear particles. To determine if there is a systemic component to ARMD in bilateral MoMHRAs, we examined the histology of ARMD in unilateral and bilateral MoMHRAs revised for pseudotumour and determined whether implant survival differed between these two groups. Periprosthetic tissue specimens from 119 hips revised for pseudotumour were examined. These were derived from 109 patients including 10 patients with bilateral MoMHRAs and 99 with sunilateral MoMHRAs including a cohort of 20 patients with bilateral MoMHRAs that had undergone only one MoMHRA revision for pseudotumour. The mean time to revision for pseudotumour of unilateral and bilateral MoMHRAs was determined. The histology of periprosthetic tissue was examined for evidence of the innate and adaptive immune response and scored semi-quantitatively. There was no significant difference in histological features of the innate / adaptive response between Group 1 bilateral pseudotumours and Group 2 and Group 3 unilateral pseudotumours. Histological features, including ALVAL scores, were similar in the periprosthetic tissues of right and left hips in Group 1 bilateral MoMHRAs. The mean time to first revision for pseudotumour of bilateral MoMHRAs (6.59 years) was not decreased compared with unilateral MoMHRAs (5.66 years) or bilateral MoMHRAs that had only one revision (7.05 years). Right and left hip pseudotumours in bilateral MoMHRAs exhibit similar histological features of the innate and adaptive immune response. Mean implant survival is not decreased in bilateral compared with unilateral MoMHRA cases. The findings suggest that pseudotumour formation is due more to a local than a systemic innate /adaptive immune response to components of metal wear.


Role of the genetic background of rats in infection by HTLV-I and HTLV-II and in the development of associated diseases.
Three aspects of the rat model of HTLV-I/II infection were investigated. (i) The efficacy of HTLV-I-transformed rat cell lines in infecting different strains of rats: WKY and Lewis HTLV-I-transformed cell lines were injected into adult WKY, Lewis and Brown Norway rats, representing syngeneic and allogeneic combinations. The HTLV-I provirus was not detected in peripheral-blood mononuclear cells (PBMC) from these rats 18 weeks after inoculation, showing that HTLV-I-transformed rat cells are not suitable for virus challenge in vaccination experiments. Rats inoculated with Lewis HTLV-I-transformed cells produced an antibody response to HTLV-I, which was higher in allogeneic (WKY and Brown Norway) than in syngeneic rats. (ii) The susceptibility of rats to HTLV-II infection: After human HTLV-II-producing cells (MO) were injected into adult WKY rats, the HTLV-II provirus was detected in PBMC 12 weeks later. Sequencing of a portion of this provirus confirmed its identity with the HTLV-II from MO cells. (iii) The role of MHC haplotype in susceptibility to neurological disease in rats inoculated as newborns with HTLV-I: The hypothesis that the RT-Ik haplotype confers susceptibility was tested by inoculating newborn OKA (RT-Ik), WKY (RT-Il), Lewis (RT-Il) and Fischer 344 (RT-I lvl) rats with human HTLV-I-producing cells (MT-2). Eighteen months later, only the WKY rats showed histological abnormality of the spinal cord, without clinical paralysis. Fischer 344 rats developed cutaneous tumors and OKA rats mammary tumors. The HTLV-I provirus was not detected in these tumors.


COP9 Signalosome Interaction with UspA/Usp15 Deubiquitinase Controls VeA-Mediated Fungal Multicellular Development.
COP9 signalosome (CSN) and Den1/A deneddylases physically interact and promote multicellular development in fungi. CSN recognizes Skp1/cullin-1/Fbx E3 cullin-RING ligases (CRLs) without substrate and removes their posttranslational Nedd8 modification from the cullin scaffold. This results in CRL complex disassembly and allows Skp1 adaptor/Fbx receptor exchange for altered substrate specificity. We characterized the novel ubiquitin-specific protease UspA of the mold Aspergillusnidulans, which corresponds to CSN-associated human Usp15 and interacts with six CSN subunits. UspA reduces amounts of ubiquitinated proteins during fungal development, and the uspA gene expression is repressed by an intact CSN. UspA is localized in proximity to nuclei and recruits proteins related to nuclear transport and transcriptional processing, suggesting functions in nuclear entry control. UspA accelerates the formation of asexual conidiospores, sexual development, and supports the repression of secondary metabolite clusters as the derivative of benzaldehyde (dba) genes. UspA reduces protein levels of the fungal NF-kappa B-like velvet domain protein VeA, which coordinates differentiation and secondary metabolism. VeA stability depends on the Fbx23 receptor, which is required for light controlled development. Our data suggest that the interplay between CSN deneddylase, UspA deubiquitinase, and SCF-Fbx23 ensures accurate levels of VeA to support fungal development and an appropriate secondary metabolism.


Validation of a Human Papillomavirus (HPV) DNA Cervical Screening Test That Provides Expanded HPV Typing.
As cervical cancer screening shifts from cytology to human papillomavirus (HPV) testing, a major question is the clinical value of identifying individual HPV types. We aimed to validate Onclarity (Becton Dickinson Diagnostics, Sparks, MD), a nine-channel HPV test recently approved by the FDA, by assessing (i) the association of Onclarity types/channels with precancer/cancer; (ii) HPV type/channel agreement between the results of Onclarity and cobas (Roche Molecular Systems, Pleasanton, CA), another FDA-approved test; and (iii) Onclarity typing for all types/channels compared to typing results from a research assay (linear array [LA]; Roche). We compared Onclarity to histopathology, cobas, and LA. We tested a stratified random sample (n = 9,701) of discarded routine clinical specimens that had tested positive by Hybrid Capture 2 (HC2; Qiagen, Germantown, MD). A subset had already been tested by cobas and LA (n = 1,965). Cervical histopathology was ascertained from electronic health records. Hierarchical Onclarity channels showed a significant linear association with histological severity. Onclarity and cobas had excellent agreement on partial typing of HPV16, HPV18, and the other 12 types as a pool (sample-weighted kappa value of 0.83); cobas was slightly more sensitive for HPV18 and slightly less sensitive for the pooled high-risk types. Typing by Onclarity showed excellent agreement with types and groups of types identified by LA (kappa values from 0.80 for HPV39/68/35 to 0.97 for HPV16). Onclarity typing results corresponded well to histopathology and to an already validated HPV DNA test and could provide additional clinical typing if such discrimination is determined to be clinically desirable.


Large-scale aerosol-assisted synthesis of biofriendly Fe₂O₃ yolk-shell particles: a promising support for enzyme immobilization.
Multiple-shelled Fe2O3 yolk-shell particles were synthesized using the spray drying method and intended as a suitable support for the immobilization of commercial enzymes such as glucose oxidase (GOx), horseradish peroxidase (HRP), and laccase as model enzymes. Yolk-shell particles have an average diameter of 1-3 μm with pore diameters in the range of 16 to 28 nm. The maximum immobilization of GOx, HRP, and laccase resulted in the enzyme loading of 292, 307 and 398 mg per g of support, respectively. After cross-linking of immobilized laccase by glutaraldehyde, immobilization efficiency was improved from 83.5% to 90.2%. K(m) and V(max) values were 41.5 μM and 1722 μmol min(-1) per mg protein for cross-linked laccase and those for free laccase were 29.3 μM and 1890 μmol min(-1) per mg protein, respectively. The thermal stability of the enzyme was enhanced up to 18-fold upon cross-linking, and the enzyme retained 93.1% of residual activity after ten cycles of reuse. The immobilized enzyme has shown up to 32-fold higher stability than the free enzyme towards different solvents and it showed higher efficiency than free laccase in the decolorization of dyes and degradation of bisphenol A. The synthesized yolk-shell particles have 3-fold higher enzyme loading efficiency and lower acute toxicity than the commercial Fe2O3 spherical particles. Therefore, the use of unique yolk-shell structure Fe2O3 particles with multiple-shells will be promising for the immobilization of various enzymes in biotechnological applications with improved electrochemical properties. To the best of our knowledge, this is the first report on the use of one pot synthesized Fe2O3 yolk-shell structure particles for the immobilization of enzymes.


Development of neuromuscular organization in the ctenophore Pleurobrachia bachei.
The phylogenetic position of the phylum Ctenophora and the nature of ctenphore nervous systems are highly debated topics in modern evolutionary biology. However, very little is known about the organization of ctenophore neural and muscular systems, and virtually nothing has been reported about their embryogenesis. Here we have characterized the neural and muscular development of the sea gooseberry, Pleurobrachia bachei, starting from the cleavage stages to posthatching larvae. Scanning electron microscopy and immunochemistry were used to describe the formation of the embryonic mouth, tentacles, combs, aboral organ, and putative sensory cells. The muscles started their specification at the end of the first day of Pleurobrachia development. In contrast, neurons appeared 2 days after myogenesis, just before the hatching of fully formed cydippid larvae. The first tubulin-immunoreactive neurons, a small group of four to six cells with neuronal processes, was initially recognized at the aboral pole during the third day of development. Surprisingly, this observed neurogenesis occurred after the emergence of distinct behavioral patterns in the embryos. Thus, the embryonic behavior associated with comb cilia beatings and initial muscle organization does not require morphologically defined neurons and their elongated neurites. This study provides the first description of neuromuscular development in the enigmatic ctenophores and establishes the foundation for future research using emerging genomic tools and resources.


Balancing potency, metabolic stability and permeability in pyrrolopyrimidine-based EGFR inhibitors.
The present study describes our continuous effort to develop epidermal growth factor receptor (EGFR) inhibitors based on the 6-aryl-pyrrolo[2,3-d]pyrimidin-4-amine scaffold. The activity-ADME space has been evaluated by synthesizing 43 new structures, including four variations of the 4-amino group and 34 different substitution patterns in the 6-aryl moiety. Most of the new pyrrolopyrimidines were highly active, with twelve analogues possessing lower IC50 values than the commercial drug Erlotinib in enzymatic assays. Ten EGFR inhibitors were also profiled in cell studies using the Ba/F3-EGFRL858R reporter cells, and all revealed nanomolar activity. However, some of the privileged structures in terms of potency had ADME short-comings: compounds containing amides, sulfonamides, amine and hydroxymethyl substituents in the 6-aryl group had low permeability and high efflux, derivatives having (R)-3-amino-3-phenylpropan-1-ol at C-4 induced hERG inhibition properties, and metabolic lability was seen for compounds having (S)-2-methoxy-1-phenylethan-1-amine at C-4. Based on a trade-off between enzymatic activity, cellular potency and ADME properties, (S)-2-phenyl-2-((6-phenyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino)ethan-1-ol appeared as the most promising drug candidate. Cellular studies indicate this compound to have therapeutic use in EGFR driven diseases.


Mortality in Guillain-Barre syndrome.
To determine the frequency, timing, causes, and risk factors of death in Guillain-Barré syndrome (GBS). Prospectively collected data were reviewed from a cohort of 527 patients with GBS previously included in 1 observational and 3 therapeutic studies. Risk factors were identified by comparing deceased and surviving patients with GBS. Fifteen (2.8%) of 527 patients with GBS died within 6 months of follow-up at highly variable time points during the disease course, with a median time from onset of weakness to death of 76 days (interquartile range 23-152 days). In 356 patients with an extended follow-up of 12 months, the mortality rate was 3.9%. Only 3 patients (20%) died during the acute progressive phase and 2 patients (13%) died during the plateau phase. Ten patients (67%) died during the recovery phase after neurologic improvement, most frequently from respiratory or cardiovascular complications. Eleven patients (73%) were admitted to an intensive care unit during the course of disease, but only 7 patients (47%) died in the intensive care unit. Risk factors for death were age (p < 0.001), severity of weakness at entry (p = 0.02), mechanical ventilation (p < 0.001), delay from onset of weakness to entry (p = 0.035), and time to peak disability (p = 0.039). Death after GBS predominantly occurs in the elderly and severely affected patients, especially during the recovery phase. Future research is required to determine whether mortality of GBS can be reduced by intensified monitoring in patients with an increased risk profile.


Synthesis of optical pulses by use of similaritons.
We propose and demonstrate experimentally a novel method for synthesizing chirp-free pulses of any desired temporal shape by means of chirp compensation and spectral filtering of optical Raman similaritons. The synthesized pulse shape is independent of the waveform, wavelength and energy of the initial pulses that are used for the similariton generation. Pulses are fully characterized by means of different techniques including cross-correlation and spectrum measurements, and the PICASO technique.


Recall cues interfere with retrieval from visuospatial working memory.
Visuospatial working memory allows us to hold multiple visual objects over short delays. It is typically tested by presenting an array of objects, then after a delay showing a 'probe' indicating which memory item to recall or reproduce by adjusting a target feature. However, recent studies demonstrate that information at the time of probe can disrupt recall. Here, in three experiments we test whether traditional memory probes, which contain features that compete with the feature to be recalled, may themselves interfere with performance. We asked participants to report the direction of one of the several coloured arrows in memory, based on its colour. First, we demonstrate that recall is better when the probe is initially just a coloured dot, rather than a coloured arrow which has to be adjusted to match orientation memory, consistent with interference from features of the probe itself. Second, this interference is present even when a mask follows the memory array, suggesting that the interference does not work by degrading immediate or iconic memory. Finally, when items are shown sequentially, the first and last items are invulnerable to probe interference. Our findings support recent theories of associative recall, in which probes reactivate features in WM, retrieving information by pattern completion.


Clinical utility of the exercise ECG in patients with diabetes and chest pain.
The purpose of this study was to determine the characteristics of exercise treadmill testing in diabetic patients presenting with chest pain. The diagnosis of coronary artery disease (CAD) in diabetic patients is confounded by different manifestations of coronary disease than are seen in the general population. Because of the association of diabetes with accelerated CAD, it is critical to assess the diagnostic utility of the standard exercise test in diabetic patients with chest pain. This study was a retrospective analysis of standard exercise test results in 1,282 male patients without prior myocardial infarction who had undergone coronary angiography and were being evaluated for possible CAD at two Veterans' Administration institutions. In patients with diabetes, 38% had an abnormal exercise test result, and the prevalence of angiographic CAD was 69%; the sensitivity of the exercise test was 47% (95% confidence interval [CI], 41 to 58), and specificity was 81% (95% CI, 68 to 89). In patients without diabetes, 38% had an abnormal exercise test result, and the prevalence of angiographic CAD was 58%; the sensitivity of the exercise test was 52% (95% CI, 48 to 56), and specificity was 80% (95% CI, 76 to 83). The receiver operating characteristic curves were also similar in both diabetic and nondiabetic patients (0.67 and 0.68, respectively). These data demonstrate that the standard exercise test has similar diagnostic characteristics in diabetic as in nondiabetic patients.


The effects of supplemental carbohydrate ingestion on intermittent isokinetic leg exercise.
The purpose of this investigation was to examine the effects of carbohydrate (CHO) supplementation on isokinetic leg extension/flexion exercise performance, blood glucose responses, blood free fatty acid (FFA) responses, and blood lactate (La) responses. Eight resistance trained males (mean+/-SEM, age: 23.7+/-1.3 yrs, height: 180.0+/-3.5 cm, bodymass: 94.9+/-4.9 kg) participated in a randomized, double blind protocol with testing sessions separated by 7-d. Subjects were given CHO or placebo (P) while performing 16 sets of 10 repetitions at 120 degrees x s(-1) on a Cybex isokinetic dynamometer. Performance variables measured were; total work (TW), average work (AW), peak torque (PT) and average torque (AT). Plasma glucose (PG), FFA, and La were measured prior to testing (PRE), after set 8 (MID), and 16 (POST). Results indicated that the CHO treatment elicited significantly (p<0.05) more TW (CHO: 41.1+/-3.9 kJ; P: 38.1+/-3.9 kJ) and AW (CHO: 2.6+/-0.2 kJ; P: 2.4+/-0.2 kJ). There were no differences (p<0.05) between treatments for PT of the hamstrings (CHO: 91.6+/-6.5 Nm; P: 87.4+/-8.5 Nm) and quadriceps (CHO: 129.7+/-9.5 Nm; P: 123.0+/-10.6 Nm). The AT of the hamstrings (CHO: 77.8+/-5.2 Nm; P: 75.7+/-8.7 Nm) and quadriceps (CHO: 116.9+/-8.9 Nm; P: 110.0+/-8.5 Nm) were not statistically different (p>0.05) between the treatments. PG was significantly higher at the POST blood draw in the CHO treatment. No significant differences (p>0.05) were observed between the treatments for FFA and La concentrations. The data from this investigation indicate that the use of CHO supplementation during isokinetic leg exercise allows for the performance of more work.


Anti-CD20 Disrupts Meningeal B-Cell Aggregates in a Model of Secondary Progressive Multiple Sclerosis.
Therapies targeting B cells have been used in the clinic for multiple sclerosis (MS). In patients with relapsing MS, anti-CD20 therapy often suppresses relapse activity; yet, their effect on disease progression has been disappointing. Most anti-CD20 therapeutic antibodies are type I, but within the unique microenvironment of the brain, type II antibodies may be more beneficial, as type II antibodies exhibit reduced complement-dependent cytotoxicity and they have an increased capacity to induce direct cell death that is independent of the host immune response. We compared the effect of type I with type II anti-CD20 therapy in a new rodent model of secondary progressive MS (SPMS), which recapitulates the principal histopathologic features of MS including meningeal B-cell aggregates. Focal MS-like lesions were induced by injecting heat-killed Mycobacterium tuberculosis into the piriform cortex of MOG-immunized mice. Groups of mice were treated with anti-CD20 antibodies (type I [rituxumab, 10 mg/kg] or type II [GA101, 10 mg/kg]) 4 weeks after lesion initiation, and outcomes were evaluated by immunohistochemistry. Anti-CD20 therapy decreased the extent of glial activation, significantly decreased the number of B and T lymphocytes in the lesion, and resulted in disruption of the meningeal aggregates. Moreover, at the given dose, the type II anti-CD20 therapy was more efficacious than the type I and also protected against neuronal death. These results indicate that anti-CD20 may be an effective therapy for SPMS with B-cell aggregates and that the elimination of CD20+ B cells alone is sufficient to cause disruption of aggregates in the brain.


Disability outcomes of early cerebellar and brainstem symptoms in multiple sclerosis.
Cerebellar and brainstem symptoms are common in early stages of multiple sclerosis (MS) yet their prognostic values remain unclear. The aim of this study was to investigate long-term disability outcomes in patients with early cerebellar and brainstem symptoms. This study used data from MSBase registry. Patients with early cerebellar/brainstem presentations were identified as those with cerebellar/brainstem relapse(s) or functional system score ⩾ 2 in the initial 2 years. Early pyramidal presentation was chosen as a comparator. Andersen-Gill models were used to compare cumulative hazards of (1) disability progression events and (2) relapses between patients with and without early cerebellar/brainstem symptoms. Mixed effect models were used to estimate the associations between early cerebellar/brainstem presentations and expanded disability status scale (EDSS) scores. The study cohort consisted of 10,513 eligible patients, including 2723 and 3915 patients with early cerebellar and brainstem symptoms, respectively. Early cerebellar presentation was associated with greater hazard of progression events (HR = 1.37, p < 0.001) and EDSS (β = 0.16, p < 0.001). Patients with early brainstem symptoms had lower hazard of progression events (HR = 0.89, p = 0.01) and EDSS (β = -0.06, p < 0.001). Neither presentation was associated with changes in relapse risk. Early cerebellar presentation is associated with unfavourable outcomes, while early brainstem presentation is associated with favourable prognosis. These presentations may be used as MS prognostic markers and guide therapeutic approach.


Easing of suffering in children with cancer at the end of life: is care changing?
In the past decade studies have documented substantial suffering among children dying of cancer, prompting national attention on the quality of end-of-life care and the development of a palliative care service in our institutions. We sought to determine whether national and local efforts have led to changes in patterns of care, advanced care planning, and symptom control among children with cancer at the end of life. Retrospective cohort study from a US tertiary level pediatric institution. Parent survey and chart review data from 119 children who died between 1997 and 2004 (follow-up cohort) were compared with 102 children who died between 1990 and 1997 (baseline cohort). In the follow-up cohort, hospice discussions occurred more often (76% v 54%; adjusted risk difference [RD], 22%; P < .001) and earlier (adjusted geometric mean 52 days v 28 days before death; P = .002) compared with the baseline cohort. Do-not-resuscitate orders were also documented earlier (18 v 12 days; P = .031). Deaths in the intensive care unit or other hospitals decreased significantly (RD, 16%; P = .024). Parents reported less child suffering from pain (RD, 19%; P = .018) and dyspnea (RD, 21%; P = .020). A larger proportion of parents felt more prepared during the child's last month of life (RD, 29%; P < .001) and at the time of death (RD, 24%; P = .002). Children dying of cancer are currently receiving care that is more consistent with optimal palliative care and according to parents, are experiencing less suffering. With ongoing growth of the field of hospice and palliative medicine, further advancements are likely.


Francisella tularensis infection in cats: ABCD guidelines on prevention and management.
Disease in cats after infection with the zoonotic bacterium Francisella tularensis has been reported only from North America; rodents and lagomorphs are the more susceptible hosts. Tularaemia is transmitted by ticks, but also acquired by direct contact, bite, scratch, ingestion or inhalation. Clinical signs range from mild chronic localised infections to fatal acute disease; antibiotic therapy is efficient. Acquiring the infection from cats is a risk for owners of outdoor cats, veterinarians and technicians.


Bias and sensitivity to task constraints in spontaneous relational attention.
Two experiments examined factors that predicted children's tendencies to match objects versus relations across scenes when no instruction was given. Specifically, we assessed the presence of higher relational responding in children by (a) age, (b) greater presumed experience in generating relations through socialization in China versus the United States, and (c) in children with greater manipulated experience via a relational priming task. Experiment 1 showed that Chinese and U.S. children across all ages showed an initial bias to match objects versus relations across scenes. However, older children in both regions were more likely to notice features of the task that indicated attending to relational matches was a more reliable solution, and shifted their responding toward relations over the course of the task. Experiment 2 replicated the object-mapping bias and age effects within U.S. children while also examining the impact of directly manipulating children's relational experiences to test the malleability of the bias. Before the main scene-mapping task, children did a relation generation task known to prime attention to relations. This did not override the initial bias toward object mapping, but it magnified the role of age, making older children increasingly sensitive to task features that prompted relational matches, further shifting their responding toward relations over the course of the task.


Soil Bacterial and Fungal Communities Exhibit Distinct Long-Term Responses to Disturbance in Temperate Forests.
In Appalachian ecosystems, forest disturbance has long-term effects on microbially driven biogeochemical processes such as nitrogen (N) cycling. However, little is known regarding long-term responses of forest soil microbial communities to disturbance in the region. We used 16S and ITS sequencing to characterize soil bacterial (16S) and fungal (ITS) communities across forested watersheds with a range of past disturbance regimes and adjacent reference forests at the Coweeta Hydrologic Laboratory in the Appalachian mountains of North Carolina. Bacterial communities in previously disturbed forests exhibited consistent responses, including increased alpha diversity and increased abundance of copiotrophic (e.g., Proteobacteria) and N-cycling (e.g., Nitrospirae) bacterial phyla. Fungal community composition also showed disturbance effects, particularly in mycorrhizal taxa. However, disturbance did not affect fungal alpha diversity, and disturbance effects were not consistent at the fungal class level. Co-occurrence networks constructed for bacteria and fungi showed that disturbed communities were characterized by more connected and tightly clustered network topologies, indicating that disturbance alters not only community composition but also potential ecological interactions among taxa. Although bacteria and fungi displayed different long-term responses to forest disturbance, our results demonstrate clear responses of important bacterial and fungal functional groups (e.g., nitrifying bacteria and mycorrhizal fungi), and suggest that both microbial groups play key roles in the long-term alterations to biogeochemical processes observed following forest disturbance in the region.


Probing the Relationship Between Latent Linear Dynamical Systems and Low-Rank Recurrent Neural Network Models.
A large body of work has suggested that neural populations exhibit low-dimensional dynamics during behavior. However, there are a variety of different approaches for modeling low-dimensional neural population activity. One approach involves latent linear dynamical system (LDS) models, in which population activity is described by a projection of low-dimensional latent variables with linear dynamics. A second approach involves low-rank recurrent neural networks (RNNs), in which population activity arises directly from a low-dimensional projection of past activity. Although these two modeling approaches have strong similarities, they arise in different contexts and tend to have different domains of application. Here we examine the precise relationship between latent LDS models and linear low-rank RNNs. When can one model class be converted to the other, and vice versa? We show that latent LDS models can only be converted to RNNs in specific limit cases, due to the non-Markovian property of latent LDS models. Conversely, we show that linear RNNs can be mapped onto LDS models, with latent dimensionality at most twice the rank of the RNN. A surprising consequence of our results is that a partially observed RNN is better represented by an LDS model than by an RNN consisting of only observed units.


No interaction between competition and herbivory in limiting introduced Cirsium vulgare rosette growth and reproduction.
Both competition and herbivory have been shown to reduce plant survival, growth, and reproduction. Much less is known about whether competition and herbivory interact in determining plant performance, especially for introduced, weedy plant species in the invaded habitat. We simultaneously evaluated both the main and interactive effects of plant neighbors and insect herbivory on rosette growth and seed reproduction in the year of flowering for Cirsium vulgare (bull thistle, spear thistle), an introduced Eurasian species, in tallgrass prairie in 2 years. Effects of insect herbivory were strong and consistent in both years, causing reduced plant growth and seed production, whereas the effects of competition with established vegetation were weak. The amount of herbivore damage inflicted on rosettes did not depend on the presence of neighbor plants. We also found no interaction between competition and herbivory on key parameters of plant growth and fitness. The results of this study contradict the hypothesis that competitive context interacts with insect herbivory in limiting the invasiveness of this introduced thistle. Further, the results provide additional, experimental evidence that high levels of herbivory on established rosettes by native insects exert significant biotic resistance to the invasiveness of C. vulgare in western tallgrass prairie.


Single snap-shot double field optical zoom.
In this paper we present a new approach providing super resolved imaging at the center of the field of view and yet allowing seeing the remaining of the original field of view with the original resolution. This operation resembles optical zooming while the zoomed and the non zoomed images are obtained simultaneously. This is obtained by taking a single snap shot and using a single imaging lens. The technique utilizes a special static/still coding element and a post processing algorithmic, without any mechanical movements.


Ancient DNA and human history.
We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.


Crosstalk between Wnt Signaling and RNA Processing in Colorectal Cancer.
RNA processing involves a variety of processes affecting gene expression, including the removal of introns through RNA splicing, as well as 3' end processing (cleavage and polyadenylation). Alternative RNA processing is fundamentally important for gene regulation, and aberrant processing is associated with the initiation and progression of cancer. Deregulated Wnt signaling, which is the initiating event in the development of most cases of human colorectal cancer (CRC), has been linked to modified RNA processing, which may contribute to Wnt-mediated colonic carcinogenesis. Crosstalk between Wnt signaling and alternative RNA splicing with relevance to CRC includes effects on the expression of Rac1b, an alternatively spliced gene associated with tumorigenesis, which exhibits alternative RNA splicing that is influenced by Wnt activity. In addition, Tcf4, a crucial component of Wnt signaling, also exhibits alternative splicing, which is likely involved in colonic tumorigenesis. Modulation of 3' end formation, including of the Wnt target gene COX-2, also can influence the neoplastic process, with implications for CRC. While many human genes are dependent on introns and splicing for normal levels of gene expression, naturally intronless genes exist with a unique metabolism that allows for intron-independent gene expression. Effects of Wnt activity on the RNA metabolism of the intronless Wnt-target gene c-jun is a likely contributor to cancer development. Further, butyrate, a breakdown product of dietary fiber and a histone deacetylase inhibitor, upregulates Wnt activity in CRC cells, and also modulates RNA processing; therefore, the interplay between Wnt activity, the modulation of this activity by butyrate, and differential RNA metabolism in colonic cells can significantly influence tumorigenesis. Determining the role played by altered RNA processing in Wnt-mediated neoplasia may lead to novel interventions aimed at restoring normal RNA metabolism for therapeutic benefit. Therefore, this minireview presents a brief overview of several aspects of RNA processing of relevance to cancer, which potentially influence, or are influenced by, Wnt signaling activity.


Behavioural interactions selecting for symmetry and asymmetry in sexual reproductive systems of eusocial species.
Understanding the life-history complex of eusociality has remained an enduring problem in evolutionary ecology, partially because natural selection models have considered traits in relative isolation. I aim for a more inclusive model that uses ecological interactions to predict the evolutionary existence of sexual reproduction, sexual reproduction asymmetry, and sex ratios in eusocial species. Using a two-level selection process, with within-population selection on the sex ratio of the sexual caste and between-population selection on the worker sex ratio and the degree of sexual reproduction asymmetry, it is found that a male-haploid genome and a worker caste of pure females is the evolutionary optimum of most initial conditions when, like in eusocial hymenoptera, there is no pair bond between the sexual male and female. That a diploid genome and a worker caste with both males and females is the evolutionary optimum of most initial conditions when, like in eusocial termites, there is a pair bond. That sex-linked genomes may evolve in diploid eusocials, and that the model will not generally maintain sexual reproduction by itself. These results hold for ploidy-levels that behave as quantitative or discrete traits, over a relatively wide range of the relative investment in a sexual male versus sexual female, and for partial sexual systems where the genomic portion with diploid inheritance is either fixed or random.


In vitro cytotoxicity of TCDD on SPC-A1 cells.
The toxicology of TCDD (2,3,7,8-tetrachlorodibenzo-p-dioxin) has been studied mainly with regard to the carcinogenicity of its metabolites, but its phototoxicity is not well understood. Although some studies have indicated the lethal phototoxicity of TCDD, this study was designed to investigate its effect on SPC-A1 cells. SPC-A1 cells were cultured in 1640 medium and treated with 10 nmol/L, 0.1 micromol/L, 1 micromol/L TCDD for either 24 h or 96 h at each concentration. SPC-A1 cells were co-cultured with TCDD at different concentrations. Then the cell morphology, DNA fragment electrophoresis, and cell cycle were analyzed by flow cytometry, and enzyme assays were used to observe the effect of TCDD on the morphology, growth rate, and enxyme change of SPC-A1 cells. With the increasing concentrations of TCDD and prolongation of culture time, the morphology of SPC-A1 cells was changed from round shape to spindle, and the ability of SPC-A1 cells to adhere to wall was decreased. With debris emitted around the cells, the morphologic changes included reduction in cell volume. Nuclear chromatin condensation and PI were observed. With the increasing concentrations of TCDD, DNA ladder occurred. After treatment with TCDD, extraction of cancer cells exhibited typical DNA fragmentation, and flow cytometry analysis showed apoptosis in a dose-dependent manner. As the concentration of TCDD rose from 10 nmol/L to 1 micromol/L, the ratio of apoptotic cells increased from 10.76% to 21.82%. TCDD has in vitro cytotoxicity on SPC-A1 cells, and the cytotoxicity is positively related to its concentration and culture time. TCDD may inhibit the growth and proliferation of SPC-A1 cells through the pathway of apoptosis introduction.


Age Deficits in Facial Affect Recognition: The Influence of Dynamic Cues.
Older adults have difficulties in identifying most facial expressions of emotion. However, most aging studies have presented static photographs of intense expressions, whereas in everyday experience people see emotions that develop and change. The present study was designed to assess whether age-related difficulties with emotion recognition are reduced when more ecologically valid (i.e., dynamic) stimuli are used. We examined the effect of stimuli format (i.e., static vs. dynamic) on facial affect recognition in two separate studies that included independent samples and distinct stimuli sets. In addition to younger and older participants, a middle-aged group was included in Study 1 and eye gaze patterns were assessed in Study 2. Across both studies, older adults performed worse than younger adults on measures of facial affect recognition. In Study 1, older and-middle aged adults benefited from dynamic stimuli, but only when the emotional displays were subtle. Younger adults gazed more at the eye region of the face relative to older adults (Study 2), but dynamic presentation increased attention towards the eye region for younger adults only. Together, these studies provide important and novel insights into the specific circumstances in which older adults may be expected to experience difficulties in perceiving facial emotions.


Histiocytic malignancies. Morphologic, immunologic, and enzymatic heterogeneity.
We have studied 14 hematopoietic malignancies with histologic features of histiocytic differentiation, using frozen section immunologic stains, plastic section enzyme histochemistry, and paraffin section immunocytochemistry. There was morphologic, immunologic, and enzymatic heterogeneity, including findings in seven cases that suggested differentiation toward specialized subsets of histiocytes. Four cases expressed a mature monocyte/macrophage phenotype by frozen section monoclonal antibody staining and three of these had histologic patterns diagnostic of malignant histiocytosis; two other cases had ATPase and S100 protein reactivity and morphologic features consistent with interdigitating (reticulum) cell proliferations; and one case was alkaline phosphatase positive, suggestive of differentiation toward fibroblastic reticulum cells. Four cases had histologic findings consistent with malignant histiocytosis, but weak or unreactive staining patterns and were considered poorly differentiated histiocytic or primitive hematopoietic malignancies. Three other cases, also morphologically consistent with malignant histiocytosis, were identified as probably T-cell lymphomas. The morphologic and phenotypic characteristics of non-neoplastic histiocytes and dendritic cell types and their related neoplasms are discussed. Histiocytic malignancies comprise a diverse group that can be identified and subclassified by immunologic and enzymatic techniques.


Joint Hypermobility Syndrome Affects Response to a Low Fermentable Oligosaccharide, Disaccharide, Monosaccharide and Polyol Diet in Irritable Bowel Syndrome Patients: A Retrospective Study.
The low fermentable oligosaccharide, disaccharide, monosaccharide and polyol (FODMAP) diet causes significant clinical improvement in patients with irritable bowel syndrome (IBS). Joint hypermobility syndrome (JHS), defined as musculoskeletal symptoms in a hypermobile individual in the absence of systemic rheumatological disease, may be associated with functional gastrointestinal symptoms, including IBS. The aim of this study is to examine whether JHS can affect the response to the low FODMAP diet in patients with IBS. In this retrospective study, we included patients with IBS according to Rome III criteria who had followed a low FODMAP diet. Symptoms scores were measured before and after the low FODMAP diet. A total of 165 patients (130 females, age 44 ± 14 years) were included. Diarrhea predominant IBS (IBS-D) was present in 40.6% of our patients while JHS was present in 21.2%. The score for abdominal pain was higher for JHS compared to non-JHS prior to intervention (P = 0.011). Symptoms improved in both groups of patients after a low FODMAP diet (P < 0.0001). The largest effects were shown with significant decreases of the average score and bloating. When broken down by JHS and IBS type, a low FODMAP diet significantly improved pain, bloating, diarrhea, constipation, and the average score with the largest effect in JHS/constipation predominant IBS (IBS-C), JHS/mixed IBS and unclassified IBS (IBS-M), JHS/IBS-D, non-JHS/IBS-C and JHS/IBS-M, respectively. Our study suggests that a low FODMAP diet has a greater effect on IBS symptoms in JHS than non-JHS patients.


Nest use dynamics of an undisturbed population of bald eagles.
Management or conservation targets based on demographic rates should be evaluated within the context of expected population dynamics of the species of interest. Wild populations can experience stable, cyclical, or complex dynamics, therefore undisturbed populations can provide background needed to evaluate programmatic success. Many raptor species have recovered from large declines caused by environmental contaminants, making them strong candidates for ongoing efforts to understand population dynamics and ecosystem processes in response to human-caused stressors. Dynamic multistate occupancy models are a useful tool for analyzing species dynamics because they leverage the autocorrelation inherent in long-term monitoring datasets to obtain useful information about the dynamic properties of population or reproductive states. We analyzed a 23-year bald eagle monitoring dataset in a dynamic multistate occupancy modeling framework to assess long-term nest occupancy and reproduction in Lake Clark National Park and Preserve, Alaska. We also used a hierarchical generalized linear model to understand changes in nest productivity in relation to environmental factors. Nests were most likely to remain in the same nesting state between years. Most notably, successful nests were likely to remain in use (either occupied or successful) and had a very low probability of transitioning to an unoccupied state in the following year. There was no apparent trend in the proportion of nests used by eagles through time, and the probability that nests transitioned into or out of the successful state was not influenced by temperature or salmon availability. Productivity was constant over the course of the study, although warm April minimum temperatures were associated with increased chick production. Overall our results demonstrate the expected nesting dynamics of a healthy bald eagle population that is largely free of human disturbance and can be used as a baseline for the expected dynamics for recovering bald eagle populations in the contiguous 48 states.


Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems.
Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.


Phosphorus runoff during four years following composted manure application.
Repeated manure application can lead to excessive soil test P (STP) levels and increased P concentration in runoff, but also to improved water infiltration and reduced runoff. Research was conducted to evaluate soil P tests in prediction of P concentration in runoff and to determine the residual effects of composted manure on runoff P loss and leaching of P. The research was conducted from 2001 to 2004 under natural runoff events with plots of 11-m length. Low-P and high-P compost had been applied during the previous 3 yr, resulting in total applications of 750 and 1150 kg P ha(-1). Bray-P1 in the surface 5 cm of soil was increased from 16 to 780 mg kg(-1) with application of high-P compost. Runoff and sediment losses were 69 and 120% greater with no compost than with residual compost treatments. Runoff P concentration increased as STP increased, but much P loss occurred with the no-compost treatment as well. Agronomic soil tests were predictive of mean runoff P concentration, but increases in STP resulted in relatively small increases in runoff P concentration. Downward movement of P was not detected below 0.3 m. In conclusion, agronomic soil tests are useful in predicting long-term runoff P concentration, and risk of P loss may be of concern even at moderate soil P levels. The residual effect of compost application in reducing sediment and runoff loss was evident more than 3 yr after application and should be considered in P indices.


Differentiation and morphogenesis in pellet cultures of developing rat retinal cells.
We previously developed a reaggregate cell culture system (pellet cultures) in which retinal neuroepithelial cells proliferate and give rise to rod photoreceptor cells (rods) in vitro (Watanabe and Raff, 1990, Neuron 4:461-467). In the present study, we analyzed cell differentiation and morphogenesis in pellet cultures by using both cell-type-specific markers with immunofluorescence and electron microscopy. We demonstrated that, in addition to rods, the other major retinal cell types, including amacrine cells, bipolar cells, Müller cells, and ganglion cells were all present in the pellets, where most were able to develop from dividing precursor cells in vitro. The different cell types in the pellets became organized into two distinct structures: dark rosettes and pale rosettes. The cellular composition of these structures indicated that the dark rosettes correspond to the outer nuclear layer and the pale rosettes to the inner nuclear layer of the normal retina. Ultrastructural studies have indicated that the thin layer of neuronal processes surrounding the dark rosettes correspond to the outer plexiform layer, and the central region of the pale rosettes correspond to the inner plexiform layer of the normal retina. Other features of normal retinal development also occurred in the pellets, including programmed cell death and the formation of inner and outer rod cell segments and synapses. Thus, pellet cultures provide a convenient way to study different aspects of retinal development where one can control the size and the cellular composition of the initial reaggregate.


Adaptive finite element based tomography for fluorescence optical imaging in tissue.
A three-dimensional fluorescence-enhanced optical tomography scheme based upon an adaptive finite element formulation is developed and employed to reconstruct fluorescent targets in turbid media from frequency-domain measurements made in reflectance geometry using area excitation illumination. The algorithm is derived within a Lagrangian framework by treating the photon diffusion model as a constraint to the optimization problem. Adaptively refined meshes are used to separately discretize maps of the forward/adjoint variables and the unknown parameter of fluorescent yield. A truncated Gauss-Newton method with simple bounds is used as the optimization method. Fluorescence yield reconstructions from simulated measurement data with added Gaussian noise are demonstrated for one and two fluorescent targets embedded within a 512ml cubical tissue phantom. We determine the achievable resolution for the area-illumination/area-detection reflectance measurement geometry by reconstructing two 0.4cm diameter spherical targets placed at at a series of decreasing lateral spacings. The results show that adaptive techniques enable the computationally efficient and stable solution of the inverse imaging problem while providing the resolution necessary for imaging the signals from molecularly targeting agents.


Convergent phylogenetic and functional responses to altered fire regimes in mesic savanna grasslands of North America and South Africa.
The importance of fire in the creation and maintenance of mesic grassland communities is well recognized. Improved understanding of how grasses--the dominant clade in these important ecosystems--will respond to alterations in fire regimes is needed in the face of anthropogenically driven climate and land-use change. Here, we examined how grass communities shift in response to experimentally manipulated fire regimes at multiple levels of community diversity--taxonomic, phylogenetic and functional--in C4-dominanted mesic savanna grassland sites with similar structure and physiognomy, yet disparate biogeographic histories. We found that the grass communities were similar in their phylogenetic response and aspects of their functional response to high fire frequency. Both sites exhibited phylogenetic clustering of highly abundant species in annually burned plots, driven by species of the Andropogoneae, and a narrow range of functional strategies associated with rapid post-fire regeneration in a high-light, nitrogen-limited environment. By examining multiple facets of diversity in a comparative context, we identified convergent phylogenetic and functional responses to altered fire regimes in two mesic savanna grasslands. Our results highlight the importance of a common filtering process associated with fire that is consistent across grasslands of disparate biogeographic histories and taxonomic representation.


Interaction of four soybean cultivars with subsoiling and a nematicide.
Yields of four soybean, Glycine max, cultivars were increased with subsoiling under the row and application of the nematicide, DBCP i 1,2-dibromo-3-chloropropane) in Tiflon sandy loam heavily infested with the root-knot nematode Meloidogyne incognita. These cultivars represent four maturity groups: very early (V), "Essex', early (VI), "Davis': medium (VII), 'Ransom'; and late (VIII), ' Hutton '. The average increase for the four cullivars was about the same for subsoiling or DBCP. When the treatmcnts were used together, the increase was greater than when either was used alone, but the effects were not additive. Increased yields were obtained with subsoiling and DBCP for the most nematode resistant cultivar, Hutton, as well as for the most susccptiblc, Davis. Subsoiling reduced root-knot galling in nonfumigated plots but did not affect it in fumigated plots. On 12 September, M. incognita larvae were most numerous at the 0- to 20 cm depth, intermediate at 20 to 33 cm depth and least numerous at 33 to 46 cm depth, Subsoiling did not affect larval populations at the three levels.


First Report of Cucumber vein yellowing virus on Cucumber in Lebanon.
In a 2-year (2008 to 2009) wide-scale survey of viruses infecting cucurbits, a limited number of greenhouse-grown cucumber (Cucumis sativus) plants showed vein-yellowing symptoms. Greenhouses were infested with whiteflies and infection with Cucumber vein yellowing virus (CVYV) was suspected. CVYV is widely distributed in southern Europe in both open field and protected cucurbit crops (2). Total RNA was extracted from seven plants with vein yellowing symptoms using TRI Reagent (Sigma-Aldrich, St Louis, MO). RT-PCR tests using CVYV-specific primers (CV+/CV-) targeting the coat protein of CVYV (2) gave amplicons of the expected size from seven plants. The sequence of one representative isolate, CVYV-LB3 (GenBank Accession No. JF289167), showed 97, 95.6, and 95.2% pairwise nucleotide identity with isolates from Tunisia (EF538680), Israel (AF233429), and Jordan (JF460793), respectively. In 2012, CVYV like symptoms were not observed in greenhouses in the same areas. In early spring 2013, a total of 16 leaf samples with vein-yellowing symptoms were collected from the northern coastal areas (Jbeil, Amshit, Tabarja) and 11 samples showing only yellowing on older leaves from the southern coast (Jiyeh). CVYV was detected in all samples from the northern coast and in four samples from the southern coast. Four isolates from the North and two from the South were sequenced (KC990497 to KC990502) and showed high sequence variation. The pairwise nucleotide and amino acid identities between these isolates ranged from 95.1 to 100% and 98.5 to 100%, respectively. Pairwise nucleotide and amino acid identities of the isolates with CVYV-LB3 showed variable homology between 93.7 to 98.2% and 94.6 to 96.6%, respectively. The inter-population structure of CVYV in Lebanon showed high variability as compared to the homogenous Spanish population (4). For transmission tests, non-viruliferous whiteflies (Bemisia tabaci) were exposed for an 18-h acquisition access period on vein-yellowed leaves followed by a 24-h inoculation access period to healthy cucumber plants (5-leaf stage). In addition, leaves with vein-yellowing symptoms were ground in 0.1 M phosphate buffer (pH 7.0) and sap-inoculated on carborundum-dusted cucumber (cv. Delta) and squash (Cucurbita pepo cv. FarajF1) plants. Vein yellowing symptoms developed 9 to 11 days post-inoculation on all whitefly inoculated plants, while symptoms were delayed till 3 weeks post inoculation on seven out of eight sap-inoculated plants. All symptomatic plants were positive for CVYV by RT-PCR. Furthermore, surveyed plants were also tested for Cucurbit chlorotic yellows virus (CCYV) and Cucurbit yellow stunting disorder virus (CYSDV), two criniviruses reported previously in Lebanon, by RT-PCR (1). Double or triple infection of CCYV and CYSDV occurred in 18 out of 20 of the CVYV-infected plants. During the past 5 years, a limited number of cucumber plants showed CVYV symptoms. This indicates that CVYV occurrence is sporadic. However, its occurrence in mixed infection with criniviruses may have damaging economic implications to cucurbit production (3). To our knowledge, this is the first report of CVYV on cucurbits in Lebanon and its occurrence in co-infection with CCYV. References: (1) P. E. Abrahamian et al. Plant Dis. 96: 1704, 2012. (2) I. M. Cuadrado et al. Plant Dis. 85:336, 2001. (3) F. M. Gil-Salas et al. Plant Pathol. 61:468, 2011. (4) D. Janssen et al. Virus Genes 34:367, 2007.


The co-repressor mSin3A is a functional component of the REST-CoREST repressor complex.
The repressor REST/NRSF restricts expression of a large set of genes to neurons by suppressing their expression in non-neural tissues. We find that REST repression involves two distinct repressor proteins. One of these, CoREST, interacts with the COOH-terminal repressor domain of REST (Andres, M. E., Burger, C., Peral-Rubio, M. J., Battaglioli, E., Anderson, M. E., Grimes, J., Dallmanm J., Ballas, N. , and Mandel, G. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 9873-9878). Here we show that the co-repressor mSin3A also interacts with REST. The REST-mSin3A association involves the NH(2)-terminal repressor domain of REST and the paired amphipathic helix 2 domain of mSin3A. REST forms complexes with endogenous mSin3A in mammalian cells, and both mSin3A and CoREST interact with REST in intact mammalian cells. REST repression is blocked in yeast lacking Sin3 and rescued in its presence. In mammalian cells, repression by REST is reduced when binding to mSin3A is inhibited. In mouse embryos, the distribution of mSin3A and REST transcripts is largely coincident. The pattern of CoREST gene expression is more restricted, suggesting that mSin3A is required constitutively for REST repression, whereas CoREST is recruited for more specialized repressor functions.


Desulfination by 2'-hydroxybiphenyl-2-sulfinate desulfinase proceeds via electrophilic aromatic substitution by the cysteine-27 proton.
Biodesulfurization is an attractive option for enzymatically removing sulfur from the recalcitrant thiophenic derivatives that comprise the majority of organosulfur compounds remaining in hydrotreated petroleum products. Desulfurization in the bacteria Rhodococcus erythropolis follows a four-step pathway culminating in C-S bond cleavage in the 2'-hydroxybiphenyl-2-sulfinate (HBPS) intermediate to yield 2-hydroxybiphenyl and bisulfite. The reaction, catalyzed by 2'-hydroxybiphenyl-2-sulfinate desulfinase (DszB), is the rate-limiting step and also the least understood, as experimental evidence points to a mechanism unlike that of other desulfinases. On the basis of structural and biochemical evidence, two possible mechanisms have been proposed: nucleophilic addition and electrophilic aromatic substitution. Density functional theory calculations showed that electrophilic substitution by a proton is the lower energy pathway and is consistent with previous kinetic and site-directed mutagenesis studies. C27 transfers its proton to HBPS, leading directly to the release of SO2 without the formation of a carbocation intermediate. The H60-S25 dyad stabilizes the transition state by withdrawing the developing negative charge on cysteine. Establishing the desulfination mechanism and specific role of active site residues, accomplished in this study, is essential to protein engineering efforts to increase DszB catalytic activity, which is currently too low for industrial-scale application.


Improvement of H5N1 influenza vaccine viruses: influence of internal gene segments of avian and human origin on production and hemagglutinin content.
The H5N1-clade 1 influenza vaccine strain NIBRG-14 produces exceptionally low amounts of antigen, a problem recently encountered also for initial pandemic H1N1-2009 vaccine seeds. Here, we report on a strategy that may contribute to overcome this obstacle. Influenza vaccine viruses usually consist of two segments coding for the antigenic HA and NA proteins of a wild-type strain and the six residual internal gene segments of the vaccine donor strain A/PR/8/34 (PR8). To enhance the antigen yield from H5N1 vaccine virus we generated by reverse genetics a set of PR8-based reassortant viruses expressing the HA and NA segments of the prototypic strain A/Vietnam/1203/2004 and additional replacements of the internal M or PB1 genes of PR8. The reassortants were compared to the parental PR8 and H5N1 viruses in terms of growth in embryonated chicken eggs and the amount of incorporated antigenic HA protein. Compared to NIBRG-14, three out of six viruses displayed an increased replication in embryonated chicken eggs and higher HA content that was also maintained after ether/detergent extraction of virions. Electron microscopic analysis showed that the reassortment hardly affected particle shape and size. Two selected H5N1 reassortant viruses were investigated concerning their pathogenicity in ferrets and found to behave as low pathogenic as the PR8 donor strain. In conclusion, this study shows that replication and antigen content of PR8-derived H5N1 influenza vaccine viruses can be improved by incorporation of heterologous internal gene segments without compromising their attenuated character.


Characterization of the in vitro glucuronidation of flurbiprofen enantiomers.
To investigate the glucuronidation of the R- and S-enantiomers of the nonsteroidal antiinflammatory drug, flurbiprofen, by liver microsomes of several mammals, including humans, a new and reliable HPLC method for the separation and quantification of the corresponding diastereoisomeric glucuronides has been developed. Interspecies comparison revealed that the glucuronidation of flurbiprofen was highly efficient with liver microsomes of humans, monkeys, rats, and guinea pigs (in decreasing ranking order). Gunn rats, which present a genetic defect in the bilirubin UDP-glucuronosyltransferase (UGT) isoforms, were still able to glucuronidate the drug. The R-enantiomer was glucuronidated faster than the S-form by liver microsomes of rats and humans. Although the KM of glucuronidation of R- and S-enantiomers by rat liver UGT were in same order of magnitude (apparent KM 0.52 and 0.57 mM, respectively), the apparent Vmax's were significantly different (9.34 and 5.48 nmol/min.mg of protein). Regardless of the enantiomer considered, the glucuronidation of flurbiprofen was strongly increased up to 5-fold by treatment of rats with phenobarbital and, at a lower extent, by 3-methylcholanthrene. In contrast, the treatment of rats with ciprofibrate markedly decreased the activity. Glucuronidation of R-flurbiprofen was more enhanced by phenobarbital than that of the S-antipode. Each flurbiprofen enantiomer could weakly inhibit the glucuronidation of its antipode in a noncompetitive way. The apparent Ki was 0.51 mM with R-flurbiprofen as a substrate, and 0.37 mM with S-enantiomer. On the other hand, the rat liver UGT2B1 isoform, stably expressed in V79 cells, could glucuronidate flurbiprofen in an appreciable amount.(ABSTRACT TRUNCATED AT 250 WORDS)


Aging impairs contraction-induced human skeletal muscle mTORC1 signaling and protein synthesis.
Sarcopenia, the loss of skeletal muscle mass during aging, increases the risk for falls and dependency. Resistance exercise (RE) training is an effective treatment to improve muscle mass and strength in older adults, but aging is associated with a smaller amount of training-induced hypertrophy. This may be due in part to an inability to stimulate muscle-protein synthesis (MPS) after an acute bout of RE. We hypothesized that older adults would have impaired mammalian target of rapamycin complex (mTORC)1 signaling and MPS response compared with young adults after acute RE. We measured intracellular signaling and MPS in 16 older (mean 70 ± 2 years) and 16 younger (27 ± 2 years) subjects. Muscle biopsies were sampled at baseline and at 3, 6 and 24 hr after exercise. Phosphorylation of regulatory signaling proteins and MPS were determined on successive muscle biopsies by immunoblotting and stable isotopic tracer techniques, respectively. Increased phosphorylation was seen only in the younger group (P< 0.05) for several key signaling proteins after exercise, including mammalian target of rapamycin (mTOR), ribosomal S6 kinase (S6K)1, eukaryotic initiation factor 4E-binding protein (4E-BP)1 and extracellular signal-regulated kinase (ERK)1/2, with no changes seen in the older group (P >0.05). After exercise, MPS increased from baseline only in the younger group (P< 0.05), with MPS being significantly greater than that in the older group (P <0.05). We conclude that aging impairs contraction-induced human skeletal muscle mTORC1 signaling and protein synthesis. These age-related differences may contribute to the blunted hypertrophic response seen after resistance-exercise training in older adults, and highlight the mTORC1 pathway as a key therapeutic target to prevent sarcopenia.


The Ethics of Deep Brain Stimulation for the Treatment of Anorexia Nervosa.
There is preliminary evidence, from case reports and investigational studies, to suggest that Deep Brain Stimulation (DBS) could be used to treat some patients with Anorexia Nervosa (AN). Although this research is at an early stage, the invasive nature of the intervention and the vulnerability of the potential patients are such that anticipatory ethical analysis is warranted. In this paper, we first show how different treatment mechanisms raise different philosophical and ethical questions. We distinguish three potential mechanisms alluded to in the neuroscientific literature, relating to desire, control, and emotion, respectively. We explain why the precise nature of the mechanism has important implications for the patient's autonomy and personal identity. In the second part of the paper, we consider practical dimensions of offering DBS to patients with AN in certain cases. We first discuss some limited circumstances where the mere offering of the intervention might be perceived as exerting a degree of coercive pressure that could serve to undermine the validity of the patient's consent. Finally, we consider the implications of potential effects of DBS for the authenticity of the patient's choice to continue using stimulation to ameliorate their condition.


Using qualitative comparative analysis in a systematic review of a complex intervention.
Systematic reviews evaluating complex interventions often encounter substantial clinical heterogeneity in intervention components and implementation features making synthesis challenging. Qualitative comparative analysis (QCA) is a non-probabilistic method that uses mathematical set theory to study complex phenomena; it has been proposed as a potential method to complement traditional evidence synthesis in reviews of complex interventions to identify key intervention components or implementation features that might explain effectiveness or ineffectiveness. The objective of this study was to describe our approach in detail and examine the suitability of using QCA within the context of a systematic review. We used data from a completed systematic review of behavioral interventions to improve medication adherence to conduct two substantive analyses using QCA. The first analysis sought to identify combinations of nine behavior change techniques/components (BCTs) found among effective interventions, and the second analysis sought to identify combinations of five implementation features (e.g., agent, target, mode, time span, exposure) found among effective interventions. For each substantive analysis, we reframed the review's research questions to be designed for use with QCA, calibrated sets (i.e., transformed raw data into data used in analysis), and identified the necessary and/or sufficient combinations of BCTs and implementation features found in effective interventions. Our application of QCA for each substantive analysis is described in detail. We extended the original review findings by identifying seven combinations of BCTs and four combinations of implementation features that were sufficient for improving adherence. We found reasonable alignment between several systematic review steps and processes used in QCA except that typical approaches to study abstraction for some intervention components and features did not support a robust calibration for QCA. QCA was suitable for use within a systematic review of medication adherence interventions and offered insights beyond the single dimension stratifications used in the original completed review. Future prospective use of QCA during a review is needed to determine the optimal way to efficiently integrate QCA into existing approaches to evidence synthesis of complex interventions.


Positive correlation between cytochrome P450 2E1 mRNA level and serum estradiol level in human uterine endometrium.
Most carcinogens are bioactivated by cytochrome P450s (CYPs) and these enzymes within target cells are closely related to susceptibility to cancer. Since extrahepatic CYPs occur typically at much lower levels, the existence and the role of CYP in extrahepatic tissues have been difficult to assess. In this study, we modified the reverse transcriptase-polymerase chain reaction (RT-PCR) to evaluate the relative quantities of CYP 2E1 mRNA in human endometrium. Total RNA from human endometrium was reverse-transcribed and co-amplified by PCR in the same tube containing both primer pairs of CYP 2E1 and beta-actin. The CYP 2E1 and beta-actin PCR products were 298 and 600 bp, respectively. The restriction enzyme MboI digested these two products to the predicted size for DNA fragments, demonstrating that both PCR products were specific and CYP 2E1 mRNA exists in human endometrium. CYP 1A1 mRNA was also examined, but could not be detected clearly. Adding [alpha-32P]dCTP to the reaction mixture made it possible to quantify the relative yield of the CYP 2E1 PCR product in comparison with the beta-actin product. The ratio of the yield of the CYP 2E1 PCR product to the beta-actin PCR product could be calculated at a point of 25 cycles of amplification. This ratio and serum estradiol levels were correlated positively (r = 0.654; p < 0.05), but no relationship to serum progesterone levels was observed.


Centromere evolution and CpG methylation during vertebrate speciation.
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.


Magnetoreception of Photoactivated Cryptochrome 1 in Electrochemistry and Electron Transfer.
Cryptochromes are flavoproteins whose photochemistry is important for crucial functions associated with phototropism and circadian clocks. In this report, we, for the first time, observed a magnetic response of the cryptochrome 1 (CRY1) immobilized at a gold electrode with illumination of blue light. These results present the magnetic field-enhanced photoinduced electron transfer of CRY1 to the electrode by voltammetry, exhibiting magnetic responsive rate constant and electrical current changes. A mechanism of the electron transfer, which involves photoinduced radicals in the CRY, is sensitive to the weak magnetic field; and the long-lived free radical FAD•- is responsible for the detected electrochemical Faradaic current. As a photoreceptor, the finding of a 5.7% rate constant change in electron transfer corresponding to a 50 μT magnetic field may be meaningful in regulation of magnetic field signaling and circadian clock function under an electromagnetic field.