Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.
A cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste. Pseudomonas putida is an archetype of such microbes due to its metabolic versatility, stress resistance, amenability to genetic modifications, and vast potential for environmental and industrial applications. To address both the elucidation of the metabolic wiring in P. putida and its uses in biocatalysis, in particular for the production of non-growth-related biochemicals, we developed and present here a genome-scale constraint-based model of the metabolism of P. putida KT2440. Network reconstruction and flux balance analysis (FBA) enabled definition of the structure of the metabolic network, identification of knowledge gaps, and pin-pointing of essential metabolic functions, facilitating thereby the refinement of gene annotations. FBA and flux variability analysis were used to analyze the properties, potential, and limits of the model. These analyses allowed identification, under various conditions, of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. The model was validated with data from continuous cell cultures, high-throughput phenotyping data, (13)C-measurement of internal flux distributions, and specifically generated knock-out mutants. Auxotrophy was correctly predicted in 75% of the cases. These systematic analyses revealed that the metabolic network structure is the main factor determining the accuracy of predictions, whereas biomass composition has negligible influence. Finally, we drew on the model to devise metabolic engineering strategies to improve production of polyhydroxyalkanoates, a class of biotechnologically useful compounds whose synthesis is not coupled to cell survival. The solidly validated model yields valuable insights into genotype-phenotype relationships and provides a sound framework to explore this versatile bacterium and to capitalize on its vast biotechnological potential.


Autophagy differentially controls plant basal immunity to biotrophic and necrotrophic pathogens.
In plants, autophagy has been assigned 'pro-death' and 'pro-survival' roles in controlling programmed cell death associated with microbial effector-triggered immunity. The role of autophagy in basal immunity to virulent pathogens has not been addressed systematically, however. Using several autophagy-deficient (atg) genotypes, we determined the function of autophagy in basal plant immunity. Arabidopsis mutants lacking ATG5, ATG10 and ATG18a develop spreading necrosis upon infection with the necrotrophic fungal pathogen, Alternaria brassicicola, which is accompanied by the production of reactive oxygen intermediates and by enhanced hyphal growth. Likewise, treatment with the fungal toxin fumonisin B1 causes spreading lesion formation in atg mutant genotypes. We suggest that autophagy constitutes a 'pro-survival' mechanism that controls the containment of host tissue-destructive microbial infections. In contrast, atg plants do not show spreading necrosis, but exhibit marked resistance against the virulent biotrophic phytopathogen, Pseudomonas syringae pv. tomato. Inducible defenses associated with basal plant immunity, such as callose production or mitogen-activated protein kinase activation, were unaltered in atg genotypes. However, phytohormone analysis revealed that salicylic acid (SA) levels in non-infected and bacteria-infected atg plants were slightly higher than those in Col-0 plants, and were accompanied by elevated SA-dependent gene expression and camalexin production. This suggests that previously undetected moderate infection-induced rises in SA result in measurably enhanced bacterial resistance, and that autophagy negatively controls SA-dependent defenses and basal immunity to bacterial infection. We infer that the way in which autophagy contributes to plant immunity to different pathogens is mechanistically diverse, and thus resembles the complex role of this process in animal innate immunity.


In vitro assessment of triterpenoids NVX-207 and betulinyl-bis-sulfamate as a topical treatment for equine skin cancer.
Equine sarcoid (ES) is the most prevalent skin tumor in equids worldwide. Additionally, aging grey horses frequently suffer from equine malignant melanoma (EMM). Current local therapies targeting these skin tumors remain challenging. Therefore, more feasible topical treatment options should be considered. In order to develop a topical therapy against ES and EMM, betulinyl-bis-sulfamate and NVX-207, derivatives of the naturally occurring betulin and betulinic acid, respectively, were evaluated for their antiproliferative (crystal violet staining assay), cytotoxic (MTS assay) and apoptotic (AnnexinV staining, cell cycle investigations) effects on primary ES cells, EMM cells and equine dermal fibroblasts in vitro. The more potent derivative was assessed for its in vitro penetration and permeation on isolated equine skin within 30 min and 24 h using Franz-type diffusion cells and HPLC analysis. Betulinyl-bis-sulfamate and NVX-207 inhibited the proliferation and metabolism in ES cells, EMM cells and fibroblasts significantly (p < 0.001) in a time- and dose-dependent manner. NVX-207 had superior anticancer effects compared to betulinyl-bis-sulfamate. Both compounds led to the externalization of phosphatidylserines on the cell membrane and DNA fragmentation, demonstrating that the effective mode of action was apoptosis. After 48 h of treatment with NVX-207, the number of necrotic cells was less than 2% in all cell types. Detected amounts of NVX-207 in the different skin layers exceeded the half-maximal inhibitory concentrations calculated by far. Even though data obtained in vitro are auspicious, the results are not unconditionally applicable to the clinical situation. Consequently, in vivo studies are required to address the antitumoral effects of topically applied NVX-207 in ES and EMM patients.


Incidental Pulmonary Nodules Reported on CT Abdominal Imaging: Frequency and Factors Affecting Inclusion in the Hospital Discharge Summary.
Incidental imaging findings require an assessment of risk and clinical relevance, as well as consideration of further evaluation. Incidental findings are common on imaging obtained in the hospital, with pulmonary nodules being among the most frequent findings that may require additional evaluation. We conducted a retrospective study to determine the factors associated with documentation of incidental findings in the hospital discharge summary, using pulmonary nodules reported on abdominal computed tomography (CT) as an example of incidental findings with well-defined follow-up guidelines. Between January 1, 2012 and December 31, 2014, 7173 patients underwent in-patient abdominal CT without concurrent chest CT; of these patients, 62.2% were ≥60 years old, 50.6% were men, and 45.5% were current or former smokers. Incidental pulmonary nodules were reported in 402 patients (5.6%; 95% confidence interval [CI], 5.1%-6.2%). Based on nodule size, reported size stability, and patients' smoking status, 208 patients (2.9%; 95% CI, 2.5%-3.3%) required follow-up surveillance, per the 2005 Fleischner Society guidelines. Of these 208 patients, 48 (23%) received discharge summaries that included documentation of the incidental findings, with 34 summaries including a recommendation for nodule follow-up and 19 summaries including a time frame for repeat CT. Three factors were positively associated with the inclusion of the pulmonary nodule in the discharge summary: mention of the pulmonary nodule in the summary headings of the radiology report (P ≤ 0.001), radiologist recommendations for further surveillance (P ≤ 0.001), and medical discharging service (P = 0.016). These findings highlight the need for a multidisciplinary systems-based approach to incidental pulmonary nodule documentation and surveillance. Journal of Hospital Medicine 2017;12:454-457.


The interaction of aflatoxin B1 with vitamin K, phenylbutazone, and sulfamethoxine in rats.
The interactions of aflatoxin B1 (AFB1) with vitamin K, phenylbutazone, and sulfamethoxine were investigated in albino rats. Vitamin K (5 mg/kg) was able to completely suppress the increase in whole blood clotting time caused by AFB1 (25 micrograms/kg). Phenylbutazone (50 mg/kg) and sulfamethoxine (50 mg/kg) also significantly (P less than 0.05) lowered the increased clotting time caused by AFB1. Equilibrium dialysis was performed on rat plasma (4 mg/ml protein content) to investigate the displacement of AFB1 (3 micrograms) from its bound form by vitamin K (250 micrograms), phenylbutazone (2500 micrograms), and sulfamethoxine (2500 micrograms). Phenylbutazone and sulfamethoxine significantly (P less than 0.05) displaced AFB1 from rat plasma protein. Histopathological examinations performed on the liver, kidneys, and spleen of control and treated rats showed that none of the drugs used appeared to offer any significant organ protection against AFB1 except in the spleen.


Multisensory visuo-tactile context learning enhances the guidance of unisensory visual search.
Does multisensory distractor-target context learning enhance visual search over and above unisensory learning? To address this, we had participants perform a visual search task under both uni- and multisensory conditions. Search arrays consisted of one Gabor target that differed from three homogeneous distractors in orientation; participants had to discriminate the target's orientation. In the multisensory session, additional tactile (vibration-pattern) stimulation was delivered to two fingers of each hand, with the odd-one-out tactile target and the distractors co-located with the corresponding visual items in half the trials; the other half presented the visual array only. In both sessions, the visual target was embedded within identical (repeated) spatial arrangements of distractors in half of the trials. The results revealed faster response times to targets in repeated versus non-repeated arrays, evidencing 'contextual cueing'. This effect was enhanced in the multisensory session-importantly, even when the visual arrays presented without concurrent tactile stimulation. Drift-diffusion modeling confirmed that contextual cueing increased the rate at which task-relevant information was accumulated, as well as decreasing the amount of evidence required for a response decision. Importantly, multisensory learning selectively enhanced the evidence-accumulation rate, expediting target detection even when the context memories were triggered by visual stimuli alone.


Glycoarray Technologies: Deciphering Interactions from Proteins to Live Cell Responses.
Microarray technologies inspired the development of carbohydrate arrays. Initially, carbohydrate array technology was hindered by the complex structures of glycans and their structural variability. The first designs of glycoarrays focused on the HTP (high throughput) study of protein-glycan binding events, and subsequently more in-depth kinetic analysis of carbohydrate-protein interactions. However, the applications have rapidly expanded and now achieve successful discrimination of selective interactions between carbohydrates and, not only proteins, but also viruses, bacteria and eukaryotic cells, and most recently even live cell responses to immobilized glycans. Combining array technology with other HTP technologies such as mass spectrometry is expected to allow even more accurate and sensitive analysis. This review provides a broad overview of established glycoarray technologies (with a special focus on glycosaminoglycan applications) and their emerging applications to the study of complex interactions between glycans and whole living cells.


Measuring improved targeting of health interventions to the poor in the context of a community-randomised trial in rural India.
In spite of growing interest in socioeconomic differentials in health outcomes and access to health services, little has been written about methodologies for assessing the impact of equity-enhancing policies or programs. This paper describes three methodological challenges involved in designing a randomised trial with an equity outcome, and how these were met in a trial of alternative strategies to improving the uptake of benefits of a health insurance scheme among its poorest members. The Vimo SEWA trial is nested within a community-based insurance scheme in rural India. While conducting this trial, three methodological problems were encountered: (i) measuring poverty (or "wealth", or "socioeconomic status") (ii) assessing beneficiaries against an appropriate reference standard population and (iii) settling on an appropriate equity measure as an outcome indicator. These problems are likely to arise in any policy or program assessment that has an equity outcome. In the Vimo SEWA trial, the socioeconomic status of beneficiaries (claimants) is assessed relative to that of all scheme members living in same sub-district by applying a rapid assessment questionnaire--which reduces to an integrated index of socioeconomic status--to both a random sample of members in each sub-district, and to all claimants. The results are used to estimate the full distribution of socioeconomic status of members in each sub-district, with each member given a rank score between 0 and 100. Interpolation is used to estimate the rank scores of claimants relative to the membership base. The primary outcome measure for the trial is the mean socioeconomic rank score of claimants. In developing country settings, using an index of socioeconomic status is simpler than assessing household income or the value of household consumption. It is also relatively straightforward to compare the socioeconomic status of health program beneficiaries with a relevant reference population, although two independent surveys are required. Expressing relative wealth on a scale from zero to 100 is conceptually appealing, and the mean value of this rank score provides an equity-specific outcome measure readily integrated into the usual analytic framework for cluster-randomised trials.


Impact of plain packaging of tobacco products on smoking in adults and children: an elicitation of international experts' estimates.
Governments sometimes face important decisions in the absence of direct evidence. In these cases, expert elicitation methods can be used to quantify uncertainty. We report the results of an expert elicitation study regarding the likely impact on smoking rates in adults and children of plain packaging of tobacco products. Thirty-three tobacco control experts were recruited from the UK (n = 14), Australasia (n = 12) and North America (n = 7). Experts' estimates were individually elicited via telephone interviews, and then linearly pooled. Elicited estimates consisted of (1) the most likely, (2) the highest possible, and (3) the lowest possible value for the percentage of (a) adult smokers and (b) children trying smoking, two years after the introduction of plain packaging (all other things being constant) in a target country in the expert's region of residence. The median estimate for the impact on adult smoking prevalence was a 1 percentage point decline (99% range 2.25 to 0), and for the percentage of children trying smoking was a 3 percentage point decline (99% range 6.1 to 0), the latter estimated impact being larger than the former (P < 0.001, sign test). There were no differences in either estimate by region (I2: Adults: 0; Children: 0) but there was considerable variability between experts' estimates within regions (I2: Adults: 0.91; Children: 0.89). In the absence of direct evidence for the impact of introducing plain packaging on smoking rates in adults and children, this study shows that tobacco control experts felt the most likely outcomes would be a reduction in smoking prevalence in adults, and a greater reduction in the numbers of children trying smoking, although there was substantial variability in the estimated size of these impacts. No experts judged an increase in smoking as a likely outcome.


Closing the Aboriginal child injury gap: targets for injury prevention.
To describe the leading mechanisms of hospitalised unintentional injury in Australian Aboriginal children and identify the injury mechanisms with the largest inequalities between Aboriginal and non-Aboriginal children. We used linked hospital and mortality data to construct a whole of population birth cohort including 1,124,717 children (1,088,645 non-Aboriginal and 35,749 Aboriginal) born in the state of New South Wales (NSW), Australia, between 1 July 2000 and 31 December 2012. Injury hospitalisation rates were calculated per person years at risk for injury mechanisms coded according to the ICD10-AM classification. The leading injury mechanisms in both groups of children were falls from playground equipment. For 66 of the 69 injury mechanisms studied, Aboriginal children had a higher rate of hospitalisation compared with non-Aboriginal children. The largest relative inequalities were observed for injuries due to exposure to fire and flame, and the largest absolute inequalities for injuries due to falls from playground equipment. Aboriginal children in NSW experience a significant higher burden of unintentional injury compared with their non-Aboriginal counterparts. Implications for Public Health: We suggest the implementation of targeted injury prevention measures aimed at injury mechanism and age groups identified in this study.


Effects of pH on Na+-Ca2+ exchange in canine cardiac sarcolemmal vesicles.
Using highly purified sarcolemmal vesicles isolated from dog ventricles, we examined the effects of pH on Na+-Ca2+ exchange. The initial rate of Nai+-dependent Ca2+ uptake is a sigmoid function of pH. The Ca2+ uptake is inhibited at pH 6 and stimulated at pH 9 (as compared with uptake at pH 7.4). This dependence on pH suggests that the ionization state of a histidine residue may be important in Na+-Ca2+ exchange. The effects of H+ on Nai+-dependent Ca2+ uptake are partially competitive with Ca2+, although this relationship is complex. Nao+-dependent Ca2+ efflux is also sensitive to H+ and increases monotonically with pH. These effects of pH appear to be due to intrinsic interactions with the Na+-Ca2+ exchange system and are not due to an alteration of Na+-H+ exchange or membrane permeability. The effects of pH on vesicular Na+-Ca2+ exchange are apparent only at low Ca2+ and Na+ concentrations. Thus modulation of vesicular Na+-Ca2+ exchange by pH is manifest only under ionic conditions which exist intracellularly in intact myocardium. Since the negative inotropy caused by acidosis is thought to reflect a fall in internal pH, these results suggest that alteration of sarcolemmal Ca2+ transport (medicated by Na+-Ca2+ exchange) by internal pH may contribute to the regulation of myocardial contractility by pH.


Upregulation of Epac-1 in Hepatic Stellate Cells by Prostaglandin E2 in Liver Fibrosis Is Associated with Reduced Fibrogenesis.
Exchange protein activated by cAMP (Epac-1) is an important signaling mechanism for cAMP-mediated effects, yet factors that change Epac-1 levels are unknown. Such factors are relevant because it has been postulated that Epac-1 directly affects fibrogenesis. Prostaglandin E2 (PGE2) is a well-known cAMP activator, and we therefore studied the effects of this cyclo-oxygenase product on Epac-1 expression and on fibrogenesis within the liver. Liver fibrosis was induced by 8 weeks carbon tetrachloride (CCL4) administration to mice. In the last 2 weeks, mice received vehicle, PGE2, the cyclo-oxygenase-2 inhibitor niflumic acid (NFA), or PGE2 coupled to cell-specific carriers to hepatocytes, Kupffer cells, or hepatic stellate cells (HSC). Results showed antifibrotic effects of PGE2 and profibrotic effects of NFA in CCL4 mice. Western blot analysis revealed reduced Epac-1 protein expression in fibrotic livers of mice and humans compared with healthy livers. PGE2 administration to fibrotic mice completely restored intrahepatic Epac-1 levels and also led to reduced Rho kinase activity, a downstream target of Epac-1. Cell-specific delivery of PGE2 to either hepatocytes, Kupffer cells, or HSC identified the latter cell as the key player in the observed effects on Epac-1 and Rho kinase. No significant alterations in protein kinase A expressions were found. In primary isolated HSC, PGE2 elicited Rap1 translocation reflecting Epac-1 activation, and Epac-1 agonists attenuated platelet-derived growth factor-induced proliferation and migration of these cells. These studies demonstrate that PGE2 enhances Epac-1 activity in HSC, which is associated with significant changes in (myo)fibroblast activities in vitro and in vivo. Therefore, Epac-1 is a potential target for antifibrotic drugs.


Distinguishing N-acetylneuraminic acid linkage isomers on glycopeptides by ion mobility-mass spectrometry.
Differentiating the structure of isobaric glycopeptides represents a major challenge for mass spectrometry-based characterisation techniques. Here we show that the regiochemistry of the most common N-acetylneuraminic acid linkages of N-glycans can be identified in a site-specific manner from individual glycopeptides using ion mobility-mass spectrometry analysis of diagnostic fragment ions.


Ketogenic Diet Acts on Body Remodeling and MicroRNAs Expression Profile.
The Ketogenic Diet (KD) promotes metabolic changes and optimizes energy metabolism. It is unknown if microRNAs (miRs) are influenced by KD in obese subjects. The screening of circulating miRs was performed with the FDA approved platform n-counter flex and blood biochemical parameters were dosed by ADVIA 1800. The aim of this study was to evaluate mir profile under 6 weeks of biphasic KD in obese subjects. We enrolled 36 obese subjects (18 females and 18 males) in stage 1 of Edmonton Obesity Staging System (EOSS) parameter. Any correlation was found between biochemical parameter and three miRs, hsa-let-7b-5p, hsa-miR-143-3p and hsa-miR-504-5p influenced in an equal manner in both sexes. The KD resulted safe and ameliorate both biochemical and anthropometric factors in obese subjects re-collocating them into stage 0 of EOSS parameters. The miRs herein identified under KD might be a useful tool to monitor low carbohydrate nutritional regimens which reflect indirectly the regulatory biochemical mechanisms and cell signaling that orchestrate metabolic and signaling pathways.


HR 720, a novel angiotensin receptor antagonist inhibits the angiotensin II-induced trophic effects, fibronectin release and fibronectin-EIIIA+ expression in rat aortic vascular smooth muscle cells in vitro.
The aim of this study was to evaluate the direct trophic effects of angiotensin II (AII) on rat vascular smooth muscle cells obtained from a single cellular isolate. Cell volume, protein synthesis, fibronectin (FN) release and FN-EIIIA+ mRNA isoform expression were analyzed in parallel. The effects of HR 720, a novel AT1 angiotensin receptor antagonist with some AT2 receptor affinity, were compared with those of selective AT1 antagonist EXP 3174. Both HR 720 and EXP 3174 inhibited in a concentration-dependent manner the maximum increase in cell volume induced by 10(-9) M Sar1-All (IC50 = 0.49 x 10(-9) M and 0.79 x 10(-9) M, respectively). Maximum [3H]leucine incorporation was also achieved at 10(-9) M All. HR 720 blocked the increase in protein synthesis with potency similar to EXP 3174; the respective IC50 values were 1.04 x 10(-9) M and 1.36 x 10(-9) M. All dose-dependently increased FN release, which was also equally inhibited by about 50% with both compounds at 10(-6) M. Furthermore, All enhanced FN-EIIIA+ mRNA in rat vascular smooth muscle cells (VSMC), which indicated a modulation of FN isoform expression which was inhibited by angiotensin II antagonists. In conclusion, All induced parallel and concentration-dependent increases in cell volume, protein synthesis, FN release and FN-EIIIA+ mRNA expression in vascular smooth muscle cells. These effects appeared to be essentially mediated by AT1 receptor stimulation as indicated by the equal inhibitory effects of HR 720 and EXP 3174.


Screening of potential a disintegrin and metalloproteinase with thrombospondin motifs-4 inhibitors using a collagen model fluorescence resonance energy transfer substrate.
The major components of the cartilage extracellular matrix are type II collagen and aggrecan. Type II collagen provides cartilage with its tensile strength, whereas the water-binding capacity of aggrecan provides compressibility and elasticity. Aggrecan breakdown leads to an increase in proteolytic susceptibility of articular collagen; hence, aggrecan may also have a protective effect on type II collagen. Given their role in aggrecan degradation and differing substrate specificity profiles, the pursuit of inhibitors for both aggrecanase 1 (a disintegrin and metalloproteinase with thrombospondin motifs-4 [ADAMTS-4]) and aggrecanase 2 (ADAMTS-5) is desirable. We previously described collagen model fluorescence resonance energy transfer (FRET) substrates for aggrecan-degrading members of the ADAMTS family. These FRET substrate assays are also fully compatible with multiwell formats. In the current study, a collagen model FRET substrate was examined for inhibitor screening of ADAMTS-4. ADAMTS-4 was screened against a small compound library (n=960) with known pharmacological activity. Five compounds that inhibited ADAMTS-4>60% at a concentration of 1muM were identified. A secondary screen using reversed-phase high-performance liquid chromatography (RP-HPLC) was developed and performed for verification of the five potential inhibitors. Ultimately, piceatannol was confirmed as a novel inhibitor of ADAMTS-4, with an IC(50) value of 1muM. Because the collagen model FRET substrates have distinct conformational features that may interact with protease secondary substrate sites (exosites), nonactive site-binding inhibitors can be identified via this approach. Selective inhibitors for ADAMTS-4 would allow a more definitive evaluation of this protease in osteoarthritis and also represent a potential next generation in metalloproteinase therapeutics.


Derivation of genetic biomarkers for cancer risk stratification in Barrett's oesophagus: a prospective cohort study.
The risk of developing adenocarcinoma in non-dysplastic Barrett's oesophagus is low and difficult to predict. Accurate tools for risk stratification are needed to increase the efficiency of surveillance. We aimed to develop a prediction model for progression using clinical variables and genetic markers. In a prospective cohort of patients with non-dysplastic Barrett's oesophagus, we evaluated six molecular markers: p16, p53, Her-2/neu, 20q, MYC and aneusomy by DNA fluorescence in situ hybridisation on brush cytology specimens. Primary study outcomes were the development of high-grade dysplasia or oesophageal adenocarcinoma. The most predictive clinical variables and markers were determined using Cox proportional-hazards models, receiver operating characteristic curves and a leave-one-out analysis. A total of 428 patients participated (345 men; median age 60 years) with a cumulative follow-up of 2019 patient-years (median 45 months per patient). Of these patients, 22 progressed; nine developed high-grade dysplasia and 13 oesophageal adenocarcinoma. The clinical variables, age and circumferential Barrett's length, and the markers, p16 loss, MYC gain and aneusomy, were significantly associated with progression on univariate analysis. We defined an 'Abnormal Marker Count' that counted abnormalities in p16, MYC and aneusomy, which significantly improved risk prediction beyond using just age and Barrett's length. In multivariate analysis, these three factors identified a high-risk group with an 8.7-fold (95% CI 2.6 to 29.8) increased HR when compared with the low-risk group, with an area under the curve of 0.76 (95% CI 0.66 to 0.86). A prediction model based on age, Barrett's length and the markers p16, MYC and aneusomy determines progression risk in non-dysplastic Barrett's oesophagus.


Light-Induced Translation of Motorized Molecules on a Surface.
Molecular machines are a key component in the vision of molecular nanotechnology and have the potential to transport molecular species and cargo on surfaces. The motion of such machines should be triggered remotely, ultimately allowing a large number of molecules to be propelled by a single source, with light being an attractive stimulus. Here, we report upon the photoinduced translation of molecular machines across a surface by characterizing single molecules before and after illumination. Illumination of molecules containing a motor unit results in an enhancement in the diffusion of the molecules. The effect vanishes if an incompatible photon energy is used or if the motor unit is removed from the molecule, revealing that the enhanced motion is due to the presence of the wavelength-sensitive motor in each molecule.


Phylogenetic analysis of the genus Plasmodium based on the gene encoding adenylosuccinate lyase.
Phylogenetic studies of the genus Plasmodium have been performed using sequences of the nuclear, mitochondrial and plastid genes. Here we have analyzed the adenylosuccinate lyase (ASL) gene, which encodes an enzyme involved in the salvage of host purines needed by malaria parasites for DNA synthesis. The ASL gene is present in several eukaryotic as well as prokaryotic organisms and does not have repeat regions, which facilitates the accuracy of the alignment. Furthermore, it has been shown that ASL is not subject to positive natural selection. We have sequenced the ASL gene of several different Plasmodium species infecting humans, rodents, monkeys and birds and used the obtained sequences along with the previously known P. falciparum ASL sequence, for structural and phylogenetic analysis of the genus Plasmodium. The genetic divergence of ASL is comparable with that observed in other nuclear genes such as cysteine proteinase, although ASL cannot be considered conserved when compared to aldolase or superoxide dismutase, which exhibit a slower rate of evolution. Nevertheless, a protein like ASL has a rate of evolution that provides enough information for elucidating evolutionary relationships. We modeled 3D structures of the ASL protein based on sequences used in the phylogenetic analysis and obtained a consistent structure for four different species despite the divergence observed. Such models would facilitate alignment in further studies with a greater number of plasmodial species or other Apicomplexa.


Clinico-epidemiological and sociodemographic profile of patients with hemophilia in the Brazilian Amazon: High prevalence of hepatitis C infection and its possible corrrelation with inhibitor development.
Hemophilia is a recessive genetic disease caused by a mutation on the X chromosome that has been linked to a high risk of transfusion-transmitted infections, especially sexually transmitted infections. The purpose of this retrospective study was to characterize the clinical and epidemiological profile and describe the prevalence of sexually transmitted viral infections in patients with hemophilia in the Northern Brazilian state of Amazonas. We assessed clinical, laboratory and sociodemographic data of hemophiliac patients (n = 311) for the period 2011-2019. The majority of the study population was composed of people with a low level of education aged 21-30 years old. The prevalence of HCV, HBV, and HTLV-1/2 infections among the study population were 10.52, 0.52, and 1.05%, respectively. No HIV infection was found among the patients. Between 2011 and 2015 the prevalence of HCV increased by over 100% and the incidence peaked in 2013. The severe hemophilia was associated with the presence of inhibitor factor (Odds Ratio [OD] 9.83; 95% IC: 3.41-27.62, p < 0.0001) or target joint (OD 6.59; 95% IC: 3.27-13.34, p < 0.0001). The presence of inhibitor was positive and significantly correlated with HCV infection (r = 1.00, p < 0.0001). Our results showed that HCV infection is highly prevalent in patients with hemophilia and might be involved in the development of inhibitors. Thus, these data provide new insights into the clinical and epidemiological profile of patients suffering from hemophilia in the Northern Brazilian state of Amazonas.


Dose-Escalated Robotic SBRT for Stage I-II Prostate Cancer.
Stereotactic body radiotherapy (SBRT) is the precise external delivery of very high-dose radiotherapy to targets in the body, with treatment completed in one to five fractions. SBRT should be an ideal approach for organ-confined prostate cancer because (I) dose-escalation should yield improved rates of cancer control; (II) the unique radiobiology of prostate cancer favors hypofractionation; and (III) the conformal nature of SBRT minimizes high-dose radiation delivery to immediately adjacent organs, potentially reducing complications. This approach is also more convenient for patients, and is cheaper than intensity-modulated radiotherapy (IMRT). Several external beam platforms are capable of delivering SBRT for early-stage prostate cancer, although most of the mature reported series have employed a robotic non-coplanar platform (i.e., CyberKnife). Several large studies report 5-year biochemical relapse rates which compare favorably to IMRT. Rates of late GU toxicity are similar to those seen with IMRT, and rates of late rectal toxicity may be less than with IMRT and low-dose rate brachytherapy. Patient-reported quality of life (QOL) outcomes appear similar to IMRT in the urinary domain. Bowel QOL may be less adversely affected by SBRT than with other radiation modalities. After 5 years of follow-up, SBRT delivered on a robotic platform is yielding outcomes at least as favorable as IMRT, and may be considered appropriate therapy for stage I-II prostate cancer.


Reversible control of assembly and disassembly of interlocked supermolecules.
Two kinds of interlocked supramolecular complexes that display stimulus-responsive assembly and disassembly have been described. One is a pseudorotaxane driven by hydrogen-bonding interactions between rings 2a and 2b and rods 1a and 1b. The rods contain a binding site for the ring as well as a stimulus-responsive diazo group, both of which are conformationally constrained in parallel by connecting them to a rigid xanthene skeleton. The trans isomer of 1a bearing a rigid binding site cannot form the pseudorotaxanes with the rings 2a and 2b because the neighboring diazophenyl group sterically shields the binding site. However, when trans-1a was converted to the corresponding cis-1a by UV light, the pseudorotaxanes are immediately formed with association constants of 70 +/- 10 M(-1) and (1.1 +/- 0.1) x 10(3) M(-1) for 2a and 2b, respectively, in CDCl3 at 24 +/- 1 degrees C. The pseudorotaxanes are completely disassembled into their molecular component when heated at 80-85 degrees C for 20 min. The assembly and disassembly processes can be reversibly cycled by repeating irradiation and heating alternatively. In the case of the rod 1b that possesses a flexible binding site, both cis and trans isomers can form the corresponding pseudorotaxanes with association constants of (2.0 +/- 0.3) x 10(2) M(-1) for 2a and trans-1b and of (7.4 +/- 0.5) x 10(2) M(-1) for 2a and cis-1b in CDCl3 at 24 +/- 1 degrees C. In this system, therefore, external stimuli can modulate the relative distribution of the pseudorotaxane and its components. Finally, the work was extended to the construction of a kinetically more stable molecular machine based on a rotaxane-like complex 10.11 between a metallocycle 11 and a dumbbell 10. In this system, the complex and its components showed separate sets of the signals, not the averaged, in 1H NMR spectroscopy as expected by the increased kinetic stability.


Loop-mediated isothermal amplification applied to filarial parasites detection in the mosquito vectors: Dirofilaria immitis as a study model.
Despite recent advances in our understanding of the basic biology behind transmission of zoonotic infectious diseases harbored by arthropod vectors these diseases remain threatening public health concerns. For effective control of vector and treatment, precise sampling indicating the prevalence of such diseases is essential. With an aim to develop a quick and simple method to survey zoonotic pathogen-transmitting vectors, LAMP (loop-mediated isothermal amplification) was applied to the detection of filarial parasites using a filarial parasite-transmitting experimental model that included one of the mosquito vectors, Aedes aegypti, and the canine heartworm, Dirofilaria immitis. LAMP reactions amplifying the cytochrome oxidase subunit I gene demonstrated high sensitivity when a single purified D. immitis microfilaria was detected. Importantly, the robustness of the LAMP reaction was revealed upon identification of an infected mosquito carrying just a single parasite, a level easily overlooked using conventional microscopic analysis. Furthermore, successful detection of D. immitis in wild-caught mosquitoes demonstrated its applicability to field surveys. Due to its simplicity, sensitivity, and reliability, LAMP is suggested as an appropriate diagnostic method for routine diagnosis of mosquito vectors carrying filarial parasites. This method can be applied to the survey of not only canine filariasis but also lymphatic filariasis, another major public health problem. Therefore, this method offers great promise as a useful diagnostic method for filarial parasite detection in endemic filariasis regions.


Optimally Repeatable Kinetic Model Variant for Myocardial Blood Flow Measurements with 82Rb PET.
Purpose. Myocardial blood flow (MBF) quantification with 82Rb positron emission tomography (PET) is gaining clinical adoption, but improvements in precision are desired. This study aims to identify analysis variants producing the most repeatable MBF measures. Methods. 12 volunteers underwent same-day test-retest rest and dipyridamole stress imaging with dynamic 82Rb PET, from which MBF was quantified using 1-tissue-compartment kinetic model variants: (1) blood-pool versus uptake region sampled input function (Blood/Uptake-ROI), (2) dual spillover correction (SOC-On/Off), (3) right blood correction (RBC-On/Off), (4) arterial blood transit delay (Delay-On/Off), and (5) distribution volume (DV) constraint (Global/Regional-DV). Repeatability of MBF, stress/rest myocardial flow reserve (MFR), and stress/rest MBF difference (ΔMBF) was assessed using nonparametric reproducibility coefficients (RPCnp = 1.45 × interquartile range). Results. MBF using SOC-On, RVBC-Off, Blood-ROI, Global-DV, and Delay-Off was most repeatable for combined rest and stress: RPCnp = 0.21 mL/min/g (15.8%). Corresponding MFR and ΔMBF RPCnp were 0.42 (20.2%) and 0.24 mL/min/g (23.5%). MBF repeatability improved with SOC-On at stress (p < 0.001) and tended to improve with RBC-Off at both rest and stress (p < 0.08). DV and ROI did not significantly influence repeatability. The Delay-On model was overdetermined and did not reliably converge. Conclusion. MBF and MFR test-retest repeatability were the best with dual spillover correction, left atrium blood input function, and global DV.


Association between Federally Qualified Health Center usage and emergency department utilization among California's HIV-infected Medicaid beneficiaries, 2009.
Federally Qualified Health Centers (FQHCs) have long been important sources of care for publicly insured people living with HIV. FQHC users have historically used emergency departments (EDs) at a higher-than-average rate. This paper examines whether this greater use relates to access difficulties in FQHCs or to characteristics of FQHC users. Zero-inflated Poisson models were used to estimate how FQHC use related to the odds of being an ED user and annual number of ED visits, using claims data on 6,284 HIV-infected California Medicaid beneficiaries in 2008-2009. FQHC users averaged significantly greater numbers of annual ED visits than non-FQHC users and those with no outpatient usage (1.89, 1.59, and 1.70, respectively; P = 0.043). FQHC users had higher odds of being ED users (OR = 1.14; 95%CI 1.02-1.27). In multivariable analyses, FQHC clients had higher odds of ED usage controlling for demographic and service characteristics (OR = 1.15; 95%CI 1.02-1.30) but not when medical characteristics were included (OR = 1.08; 95%CI 0.95-1.24). Among ED users, FQHC use was not significantly associated with the number of ED visits in our models (rate ratio (RR) = 1.00; 95%CI 0.87-1.15). The overall difference in mean annual ED visits observed between FQHC and non-FQHC groups was reduced to insignificance (1.75; 95% CI 1.59-1.92 vs 1.70; 95%CI 1.54-1.85) after adjusting for demographic, service, and medical characteristics. Overall, FQHC users had higher ED utilization than non-FQHC users, but the disparity was largely driven by differences in underlying medical characteristics.


Current status of ABL tyrosine kinase inhibitors stop studies for chronic myeloid leukemia.
ABL tyrosine kinase inhibitors (TKIs) dramatically improves chronic myeloid leukemia (CML) prognosis and most CML patients are now able to lead lives that are equivalent to those of healthy individuals. However, high cost to CML patients of long-term treatment and adverse effects (AEs) remain problems. At the setout, a clinical study involving the discontinuation of imatinib was conducted in France. Then, several stop studies of first-generation (imatinib) and second-generation ABL TKIs (dasatinib, nilotinib), which induce earlier response than imatinib, have also been started. These studies revealed that almost half of CML patients who are treated with ABL TKIs and achieve a certain period of sustained deep molecular response can stop ABL TKIs safely and obtain treatment free remission (TFR). AEs of ABL TKIs withdrawal and predicting factors for successful discontinuation including immunity are becoming clear gradually through these studies. It is important to conduct a comprehensive examination of the results of studies with a wide variety of protocols in order to determine which discontinuation method results in the highest probability of TFR in clinical settings.


Role of amylase, mucin, IgA and albumin on salivary protein buffering capacity: a pilot study.
It has been suggested that proteins serve as major salivary buffers below pH5. It remains unclear, however, which salivary proteins are responsible for these buffering properties. The aim of this pilot study was to evaluate the correlation between salivary concentration of total protein, amylase, mucin, immunoglobulin A (IgA), albumin and total salivary protein buffering capacity at a pH range of 4-5. In addition, the buffering capacity and the number of carboxylic acid moieties of single proteins were assessed. Stimulated saliva samples were collected at 9:00, 13:00 and 17:00 from 4 healthy volunteers on 3 successive days. The buffering capacities were measured for total salivary protein or for specific proteins. Also, the concentration of total protein, amylase, mucin, IgA and albumin were analysed. Within the limits of the current study, it was found that salivary protein buffering capacity was highly positively correlated with total protein, amylase and IgA concentrations. A weak correlation was observed for both albumin and mucin individually. Furthermore, the results suggest that amylase contributed to 35 percent of the salivary protein buffering capacity in the pH range of 4-5.


Methods for studying the physiology of kidney oxygenation.
1. An improved understanding of the regulation of kidney oxygenation has the potential to advance preventative, diagnostic and therapeutic strategies for kidney disease. Here, we review the strengths and limitations of available and emerging methods for studying kidney oxygen status. 2. To fully characterize kidney oxygen handling, we must quantify multiple parameters, including renal oxygen delivery (DO2) and consumption (VO2), as well as oxygen tension (Po2). Ideally, these parameters should be quantified both at the whole-organ level and within specific vascular, tubular and interstitial compartments. 3. Much of our current knowledge of kidney oxygen physiology comes from established techniques that allow measurement of global kidney DO2 and VO2, or local tissue Po2. When used in tandem, these techniques can help us understand oxygen mass balance in the kidney. Po2 can be resolved to specific tissue compartments in the superficial cortex, but not deep below the kidney surface. We have limited ability to measure local kidney tissue DO2 and VO2. 4. Mathematical modelling has the potential to provide new insights into the physiology of kidney oxygenation, but is limited by the quality of the information such models are based on. 5. Various imaging techniques and other emerging technologies have the potential to allow Po2 mapping throughout the kidney and/or spatial resolution of Po2 in specific renal tissues, even in humans. All currently available methods have serious limitations, but with further refinement should provide a pathway through which data obtained from experimental animal models can be related to humans in the clinical setting.


Meta-analysis: implications of interleukin-28B polymorphisms in spontaneous and treatment-related clearance for patients with hepatitis C.
Since 2009, several studies have identified single-nucleotide polymorphisms (SNPs) near the gene encoding for interleukin (IL)-28 (IL28B) that are strongly associated with spontaneous and treatment-induced hepatitis C virus (HCV) clearance. Because this large amount of data includes some inconsistencies, we consider assessment of the global estimate for each SNP to be essential. Relevant studies assessing IL28B polymorphisms associated with sustained virologic response (SVR) and spontaneous clearance (SC) were identified from a literature search of PubMed up to 9 July, 2012. Studies were eligible studies if they included patients infected with HCV or HCV/HIV, or assessed any SNP located within or near the IL28B gene, SVR data available under standard treatment, and/or SC data in patients with acute HCV infection. Pooled odds ratios were estimated by fixed or random effects models when appropriate. Variables such as HCV genotype, ethnicity, and type of co-infection were studied. Of 282 screened studies, 67 were selected for SVR and 10 for SC. In total, 20,163 patients were studied for SVR and 3,554 for SC. For SVR, we found that all SNPs showed strong associations in patients with HCV genotypes 1 and 4, whereas the pooled ORs were almost three times lower for genotypes 2 and 3 (rs12979860 and rs8099917). Regarding ethnicity, the SNP most associated with SVR was rs12979860 in white patients, whereas in East Asians it seemed to be rs8099917. The most studied SNP (rs12979860) showed similar results for patients co-infected with HCV/HIV, as for those infected with HCV only. Finally, rs12979860 and rs8099917 both appeared to be associated with SC. IL28B polymorphisms influence both the outcome of interferon treatment and the natural clearance of HCV. However we did not identify a universal predictor SNP, as the best genetic markers differed depending on patient ethnicity, genotype, and type of infection. Nevertheless, our results may be useful for more precise treatment decision-making.


Ultrastructural and cytochemical aspects of female gametophyte development in Sedum hispanicum L. (Crassulaceae).
Until now, development of the female gametophyte has been investigated only in some species of Crassulaceae using a light microscope. To the best of our knowledge, this is the first report that describes the process of megasporogenesis and megagametogenesis in Crassulaceae in detail. To achieve this, we performed embryological studies on Sedum hispanicum L. (Crassulaceae). Cytochemical analysis detected the presence of proteins, lipids, and insoluble polysaccharides in individual cells of the gametophyte. The development of the embryo sac conforms to the monosporic or Polygonum-type in anatropous, crassinucellate, and bitegmic ovules. One megaspore mother cell initiates the process of megasporogenesis. Prior to the first meiotic division, the nucleus is centrally located within the meiocyte. Other organelles seem to be distributed evenly over the micropylar and chalazal parts during the development. Most storage reserves detected during megasporogenesis were observed in the megaspore mother cell. Three mitotic divisions within the chalazal functional megaspore resulted in the enlargement of the eight-nucleated embryo sac. In the seven-celled gametophyte, three chalazally located antipodes degenerated. A mature embryo sac was formed by the egg apparatus and central cell. When the antipodes degenerated, both synergids became organelle-rich and more active. The concentration of lipid droplets, starch grains, and proteins increased during megagametogenesis in the growing gametophyte. In the cellular embryo sac, the central cell can be distinguished by its largest accumulation. Our data confirm the hypothesis that plasmodesmata with electron-dense dome are formed during development of the female gametophyte in S. hispanicum and not just during the stages of embryogenesis. We observed these structures in megaspores and coenocytic embryo sac walls. Functions of observed plasmodesmata are discussed.


Submillimetre galaxies reside in dark matter haloes with masses greater than 3 × 10(11) solar masses.
The extragalactic background light at far-infrared wavelengths comes from optically faint, dusty, star-forming galaxies in the Universe with star formation rates of a few hundred solar masses per year. These faint, submillimetre galaxies are challenging to study individually because of the relatively poor spatial resolution of far-infrared telescopes. Instead, their average properties can be studied using statistics such as the angular power spectrum of the background intensity variations. A previous attempt at measuring this power spectrum resulted in the suggestion that the clustering amplitude is below the level computed with a simple ansatz based on a halo model. Here we report excess clustering over the linear prediction at arcminute angular scales in the power spectrum of brightness fluctuations at 250, 350 and 500 μm. From this excess, we find that submillimetre galaxies are located in dark matter haloes with a minimum mass, M(min), such that log(10)[M(min)/M(⊙)] = 11.5(+0.7)(-0.2) at 350 μm, where M(⊙) is the solar mass. This minimum dark matter halo mass corresponds to the most efficient mass scale for star formation in the Universe, and is lower than that predicted by semi-analytical models for galaxy formation.


Tissue microarrays from bone marrow aspirates for high-throughput assessment of immunohistologic markers in pediatric acute leukemia.
Gene expression profiling studies have been employed to investigate prognostic subgroups in pediatric acute leukemia. Tissue microarrays (TMAs) are useful for high-throughput analysis of protein expression of target genes in acute leukemia samples and for validation of gene microarray analysis. Using cryopreserved samples of pediatric acute leukemia bone marrow aspirates, we constructed TMA from as few as 1 million cells. Bone marrow core biopsies from the same patients were included on the same TMA for comparison. A panel of 15 immunohistochemical markers typically used for diagnosis as well as those targeting recently characterized, prognostically relevant molecules of interest in pediatric acute leukemia was used to evaluate protein expression. Staining results confirm that suspension cells from bone marrow aspirates can be effectively used to derive protein expression data from multiple cases simultaneously with comparable efficacy to that of biopsy tissue. This method allows for new markers of diagnostic, prognostic, or therapeutic importance to be screened on large numbers of study patients. Furthermore, this technique may facilitate the inclusion of small samples, aspirates, and body fluids in large-scale studies of protein expression in clinical trials and protocols in which tissue biopsies are often unavailable.


A preliminary investigation into the acquisition of fingerprints on food.
The potential for enhancement and recovery of latent fingerprints on a variety of foodstuffs has been investigated. In general, black magnetic powder and black powder suspensions appear to be the most successful enhancement techniques with a high number of ridge detail-developed prints over a selected time scale. Banana, apple and tomato surfaces showed enhancement of latent prints but potato and egg surfaces proved to be less successful.


Magnetic Switching in Granular FePt Layers Promoted by Near-Field Laser Enhancement.
Light-matter interaction at the nanoscale in magnetic materials is a topic of intense research in view of potential applications in next-generation high-density magnetic recording. Laser-assisted switching provides a pathway for overcoming the material constraints of high-anisotropy and high-packing density media, though much about the dynamics of the switching process remains unexplored. We use ultrafast small-angle X-ray scattering at an X-ray free-electron laser to probe the magnetic switching dynamics of FePt nanoparticles embedded in a carbon matrix following excitation by an optical femtosecond laser pulse. We observe that the combination of laser excitation and applied static magnetic field, 1 order of magnitude smaller than the coercive field, can overcome the magnetic anisotropy barrier between "up" and "down" magnetization, enabling magnetization switching. This magnetic switching is found to be inhomogeneous throughout the material with some individual FePt nanoparticles neither switching nor demagnetizing. The origin of this behavior is identified as the near-field modification of the incident laser radiation around FePt nanoparticles. The fraction of not-switching nanoparticles is influenced by the heat flow between FePt and a heat-sink layer.


LONI MiND: metadata in NIfTI for DWI.
A wide range of computational methods have been developed for reconstructing white matter geometry from a set of diffusion-weighted images (DWIs), and many clinical studies rely on publicly-available implementations of these methods for analyzing DWI datasets. Unfortunately, the poor interoperability between DWI analysis tools often effectively restricts users to the algorithms provided by a single software suite, which may be suboptimal relative to those in other packages, or outdated given recent developments in the field. A major barrier to data portability and the interoperability between DWI analysis tools is the lack of a standard format for representing and communicating essential DWI-related metadata at various stages of post-processing. In this report, we address this issue by developing a framework for storing metadata in NIfTI for DWI (MiND). We utilize the standard NIfTI format extension mechanism to store essential DWI metadata in an extended header for multiple commonly-encountered DWI data structures. We demonstrate the utility of this approach by implementing a full suite of tools for DWI analysis workflows which communicate solely through the MiND mechanism. We also show that the MiND framework allows for simple, direct DWI data visualization, and we illustrate its effectiveness by constructing a group atlas for 330 subjects using solely MiND-centric tools for DWI processing. Our results indicate that the MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users.


Rapid and tunable control of protein stability in Caenorhabditis elegans using a small molecule.
Destabilizing domains are conditionally unstable protein domains that can be fused to a protein of interest resulting in degradation of the fusion protein in the absence of stabilizing ligand. These engineered protein domains enable rapid, reversible and dose-dependent control of protein expression levels in cultured cells and in vivo. To broaden the scope of this technology, we have engineered new destabilizing domains that perform well at temperatures of 20-25°C. This raises the possibility that our technology could be adapted for use at any temperature. We further show that these new destabilizing domains can be used to regulate protein concentrations in C. elegans. These data reinforce that DD can function in virtually any organism and temperature.


Does the Side Onset of Parkinson's Disease Influence the Time to Develop Levodopa-Induced Dyskinesia?
Aberrant plasticity is closely linked to the development of levodopa-induced dyskinesia (LID) in Parkinson's disease (PD). This study investigated whether dominant-side patients with PD exhibit a shorter time to LID development, based on the hypothesis that the dominant hemisphere may have greater plasticity than non-dominant-side patients. We analyzed data from 387 right-handed patients with PD who exhibited asymmetric motor deficits and received PD medications for ≥2 years (191 dominant-side and 196 non-dominant-side patients). The influence of side onset on time for LID development was assessed by Kaplan-Meier estimates and time-dependent Cox regression models based on the 5-year time point, after adjusting for age at PD onset, dopamine transporter activity in the posterior putamen, and daily levodopa dose. LID developed in 46 (23.4%) patients with non-dominant-side PD and in 35 (18.1%) patients with dominant-side PD. The Kaplan-Meier analyses revealed that non-dominant-side patients developed LID earlier than dominant-side patients (p = 0.027). The time-dependent Cox regression models showed that the risk of LID within 5 years of treatment was significantly higher in non-dominant-side than in dominant-side patients (hazard ratio 1.954; p = 0.034), whereas the risk after 5 years was similar between groups (p = 0.528). The present study demonstrated that LID developed earlier in non-dominant-side than in dominant-side patients with PD. These results suggested a greater potential of synaptic plasticity in the dominant hemisphere that may exert a protective role for the development of LID compared to the non-dominant hemisphere.


Early viral replication in the brain of SIV-infected rhesus monkeys.
To investigate the mechanism of simian immunodeficiency virus (SIV) entry into the central nervous system (CNS) and the initial events leading to neuropathogenesis, SIV replication was studied by in situ hybridization in the CNS of 5 Rhesus macaques at 7 days, 1, 2, and 3 months after SIV intravenous inoculation. CNS infection was found to be a frequent and early event, as SIV was detected in the CNS of all the animals studied and as early as 7 days postinoculation. At the earliest stage, the infection localized mainly to perivascular cells. Using combined immunohistochemistry and in situ hybridization, infected cells were shown to express the CD68 marker, suggesting that infected mononuclear phagocytes crossing the blood-brain barrier represent the main source of virus in the CNS. Early viral replication coincided with neuropathologic changes, consisting in gliosis, perivascular infiltrates and rare glial nodules. Immunophenotyping of brain tissue showed that increased macrophage infiltration, microglial reactivity and MHC class II induction occurred within the first week of infection, indicating a possible immunopathologic mechanism in early CNS pathogenesis.


Enhanced recruitment of endosomal Na+/H+ exchanger NHE6 into Dendritic spines of hippocampal pyramidal neurons during NMDA receptor-dependent long-term potentiation.
Postsynaptic endosomal trafficking has emerged as a principal regulatory mechanism of structural and functional plasticity of glutamatergic synapses. Recycling endosomes perform activity-dependent transport of AMPA receptors (AMPARs) and lipids to the postsynaptic membrane, activities that are known to contribute to long-term synaptic potentiation and hypothesized to subserve learning and memory processes in the brain. Recently, genetic defects in a widely expressed vesicular pH-regulating transporter, the Na(+)/H(+) exchanger NHE6 isoform, have been implicated in neurodevelopmental disorders including severe X-linked mental retardation and autism. However, little information is available regarding the cellular properties of this transporter in the CNS. Here, we show by quantitative light microscopy that the protein abundance of NHE6 is developmentally regulated in area CA1 of the mouse hippocampus. Within pyramidal neurons, NHE6 was found to localize to discrete puncta throughout the soma and neurites, with noticeable accumulation at dendritic spines and presynaptic terminals. Dual immunolabeling of dendritic spines revealed that NHE6 partially colocalizes with typical markers of early and recycling endosomes as well as with the AMPAR subunit GluA1. Significantly, NHE6-containing vesicles exhibited enhanced translocation to dendritic spine heads during NMDA receptor (NMDAR)-dependent long-term potentiation. These data suggest that NHE6 may play a unique, previously unrecognized, role at glutamatergic synapses that are important for learning and memory.


Contribution of facet joints, axial compression, and composition to human lumbar disc torsion mechanics.
Stresses applied to the spinal column are distributed between the intervertebral disc and facet joints. Structural and compositional changes alter stress distributions within the disc and between the disc and facet joints. These changes influence the mechanical properties of the disc joint, including its stiffness, range of motion, and energy absorption under quasi-static and dynamic loads. There have been few studies evaluating the role of facet joints in torsion. Furthermore, the relationship between biochemical composition and torsion mechanics is not well understood. Therefore, the first objective of this study was to investigate the role of facet joints in torsion mechanics of healthy and degenerated human lumbar discs under a wide range of compressive preloads. To achieve this, each disc was tested under four different compressive preloads (300-1200 N) with and without facet joints. The second objective was to develop a quantitative structure-function relationship between tissue composition and torsion mechanics. Facet joints have a significant contribution to disc torsional stiffness (∼60%) and viscoelasticity, regardless of the magnitude of axial compression. The findings from this study demonstrate that annulus fibrosus GAG content plays an important role in disc torsion mechanics. A decrease in GAG content with degeneration reduced torsion mechanics by more than an order of magnitude, while collagen content did not significantly influence disc torsion mechanics. The biochemical-mechanical and compression-torsion relationships reported in this study allow for better comparison between studies that use discs of varying levels of degeneration or testing protocols and provide important design criteria for biological repair strategies. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.


Robust and stable transcriptional repression in Giardia using CRISPRi.
Giardia lamblia is a binucleate protistan parasite causing significant diarrheal disease worldwide. An inability to target Cas9 to both nuclei, combined with the lack of nonhomologous end joining and markers for positive selection, has stalled the adaptation of CRISPR/Cas9-mediated genetic tools for this widespread parasite. CRISPR interference (CRISPRi) is a modification of the CRISPR/Cas9 system that directs catalytically inactive Cas9 (dCas9) to target loci for stable transcriptional repression. Using a Giardia nuclear localization signal to target dCas9 to both nuclei, we developed efficient and stable CRISPRi-mediated transcriptional repression of exogenous and endogenous genes in Giardia. Specifically, CRISPRi knockdown of kinesin-2a and kinesin-13 causes severe flagellar length defects that mirror defects with morpholino knockdown. Knockdown of the ventral disk MBP protein also causes severe structural defects that are highly prevalent and persist in the population more than 5 d longer than defects associated with transient morpholino-based knockdown. By expressing two guide RNAs in tandem to simultaneously knock down kinesin-13 and MBP, we created a stable dual knockdown strain with both flagellar length and disk defects. The efficiency and simplicity of CRISPRi in polyploid Giardia allows rapid evaluation of knockdown phenotypes and highlights the utility of CRISPRi for emerging model systems.


On the validity of retrospective assessments of pregnancy intention.
Information on pregnancy intention is often gathered retrospectively (after the birth of a child). This article investigates whether the retrospective assessment of pregnancy intention leads to biased estimates of the extent or consequences of unintended fertility. Comparisons are made between pregnancy intentions ascertained during pregnancy and after birth using data from the National Longitudinal Survey of Youth. To address the bias caused by selective recognition or acknowledgment of pregnancy, we used the longitudinal feature of the data to determine actual pregnancy status at the time of interviews, which, in turn, was used as an instrumental variable for the retrospective (versus prospective) reporting of pregnancy intention. After correction for selective pregnancy recognition, we found no evidence that the retrospective assessment of pregnancy intention produces misleading estimates of either the number or the consequences of unintended births. This finding is supported by additional analyses of a small subsample of women for whom information on pregnancy intention was collected both during pregnancy and after birth.


Assessing the Electrode-Neuron Interface with the Electrically Evoked Compound Action Potential, Electrode Position, and Behavioral Thresholds.
Variability in speech perception scores among cochlear implant listeners may largely reflect the variable efficacy of implant electrodes to convey stimulus information to the auditory nerve. In the present study, three metrics were applied to assess the quality of the electrode-neuron interface of individual cochlear implant channels: the electrically evoked compound action potential (ECAP), the estimation of electrode position using computerized tomography (CT), and behavioral thresholds using focused stimulation. The primary motivation of this approach is to evaluate the ECAP as a site-specific measure of the electrode-neuron interface in the context of two peripheral factors that likely contribute to degraded perception: large electrode-to-modiolus distance and reduced neural density. Ten unilaterally implanted adults with Advanced Bionics HiRes90k devices participated. ECAPs were elicited with monopolar stimulation within a forward-masking paradigm to construct channel interaction functions (CIF), behavioral thresholds were obtained with quadrupolar (sQP) stimulation, and data from imaging provided estimates of electrode-to-modiolus distance and scalar location (scala tympani (ST), intermediate, or scala vestibuli (SV)) for each electrode. The width of the ECAP CIF was positively correlated with electrode-to-modiolus distance; both of these measures were also influenced by scalar position. The ECAP peak amplitude was negatively correlated with behavioral thresholds. Moreover, subjects with low behavioral thresholds and large ECAP amplitudes, averaged across electrodes, tended to have higher speech perception scores. These results suggest a potential clinical role for the ECAP in the objective assessment of individual cochlear implant channels, with the potential to improve speech perception outcomes.


Suppressor cell induction in vitro. I. Kinetics of induction of antigen-specific suppressor cells.
The induction of antigen-specific suppressor cells in vitro, using high concentrations (100 mug/ml) of keyhole limpet hemocyanin (KLH) in Marbrook flasks is described. Spleen and cortisone-resistant thymocytes were the richest source of suppressor cell precursors, compared to lymph node cells, peripheral blood lymphocytes or thoracic duct lymphocytes. Suppressor cells induced with KLH only suppressed KLH-reactive helper cells, and not B cells or helper cells of other specificity. The suppressor cells were T cells, as judged by their sensitivity to anti-Thy-1.2, heterologous anti-T, but not anti-B antisera.


Mycosins Are Required for the Stabilization of the ESX-1 and ESX-5 Type VII Secretion Membrane Complexes.
Pathogenic mycobacteria contain up to five type VII secretion (T7S) systems, ESX-1 to ESX-5. One of the conserved T7S components is the serine protease mycosin (MycP). Strikingly, whereas MycP is essential for secretion, the protease activity of MycP1 in Mycobacterium tuberculosis has been shown to be dispensable for secretion. The essential role of MycP therefore remains unclear. Here we show that MycP1 and MycP5 of M. marinum have similar phenotypes, confirming that MycP has a second unknown function that is essential for its T7S system. To investigate whether this role is related to proper functioning of the T7S membrane complex, we first analyzed the composition of the ESX-1 membrane complex and showed that this complex consists of EccBCDE1, similarly to what was previously shown for ESX-5. Surprisingly, while mycosins are not an integral part of these purified core complexes, we noticed that the stability of both the ESX-1 complex and the ESX-5 complex is compromised in the absence of their MycP subunit. Additional interaction studies showed that, although mycosins are not part of the central ESX membrane complex, they loosely associate with this complex. We hypothesize that this MycP association with the core membrane complex is crucial for the integrity and functioning of the T7S machinery. Among the major virulence factors of pathogenic mycobacteria are the type VII secretion (T7S) systems. Three of these systems, ESX-1, ESX-3, and ESX-5, have been shown to be crucial for virulence or viability. Here we describe the function of mycosin proteases, which are conserved components within these systems. We show that MycP1 and MycP5 have a second, proteolytic-independent function which is essential for the T7S system. We additionally found that this second essential role is related to the stabilization and proper functioning of their respective ESX membrane core complexes. Finally, we found that this is mediated by a loose association of MycP with the complex. Understanding the essential role of mycosins in type VII secretion systems, which play central roles in the virulence and viability of pathogenic mycobacteria, may provide new intervention strategies to treat tuberculosis.


Pathogenesis of giant cell arteritis: new insight into the implication of CD161+ T cells.
Giant cell arteritis (GCA) is a granulomatous large-vessel vasculitis that usually affects the aorta and/or its major branches, especially the branches of the carotid arteries. Histo-pathological lesions are observed in all layers of the artery leading to segmental and focal panarteritis with a polymorphic cell infiltrate that includes T cells, macrophages and multinucleated giant cells, a fragmented internal elastic lamina and intimal hyperplasia. The pathophysiology of GCA is complex and not fully understood. In this review, we discuss the immunological aspects of GCA pathogenesis with a particular emphasis on T cell responses. Upon dendritic cell activation in the adventitia, CD4 T cells co-expressing CD161 are recruited in the arterial wall and polarised into Th1 and Th17 cells that produce IFN-γ and IL-17, respectively. These cytokines activate macrophages, giant cells and vascular smooth muscle cells, thus inducing vascular remodelling which leads to the ischaemic manifestations of GCA. Macrophages infiltrating the adventitia produce IL-1β and IL-6, which are responsible for the general symptoms encountered in GCA.


The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes (Zosterops lateralis).
Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.


Genetic divergence of enterovirus D68 in China and the United States.
The largest outbreak of human enterovirus 68 (EV-D68) infections associated with severe respiratory illness and neurological complications emerged from the United States in 2014. China reported the circulation of EV-D68 since 2006, but these cases were sporadic and did not display neurological symptoms. Yet viral determinants responsible for the difference in prevalence between China and the U.S. were not clear. We analyzed the genome of 64 reported Chinese EV-D68 strains and found that genogroup replacement has occurred in China since 2006. The six coding mutations (M291T, V341A, T860N, D927N, S1108G and R2005K) associated with neurovirulence reported in American strains were not found in Chinese strains. Moreover, 2014 Chinese strains had a unique R220A mutation in the puff region of VP2 while R220E mutation occurred in other strains. Like other enteroviruses, the loop sequences of the domain X and Y in the 3'-UTR of the Chinese strains are complementary. However, the X loop sequences of the 2014 American strains were not complementary but identical to Y loop sequences. These results indicate that different EV-D68 strains circulated in China and America and the mutations might be responsible for different prevalence. Our findings also provide new evidence for the sequence diversity of EV-D68.


Determinants of social inequalities in stroke incidence across Europe: a collaborative analysis of 126 635 individuals from 48 cohort studies.
Knowledge on the origins of the social gradient in stroke incidence in different populations is limited. This study aims to estimate the burden of educational class inequalities in stroke incidence and to assess the contribution of risk factors in determining these inequalities across Europe. The MORGAM (MOnica Risk, Genetics, Archiving and Monograph) Study comprises 48 cohorts recruited mostly in the 1980s and 1990s in four European regions using standardised procedures for baseline risk factor assessment and fatal and non-fatal stroke ascertainment and adjudication during follow-up. Among the 126 635 middle-aged participants, initially free of cardiovascular diseases, generating 3788 first stroke events during a median follow-up of 10 years, we estimated differences in stroke rates and HRs for the least versus the most educated individuals. Compared with their most educated counterparts, the overall age-adjusted excess hazard for stroke was 1.54 (95% CI 1.25 to 1.91) and 1.41 (95% CI 1.16 to 1.71) in least educated men and women, respectively, with little heterogeneity across populations. Educational class inequalities accounted for 86-413 and 78-156 additional stroke events per 100 000 person-years in the least compared with most educated men and women, respectively. The additional events were equivalent to 47%-130% and 40%-89% of the average incidence rates. Inequalities in risk factors accounted for 45%-70% of the social gap in incidence in the Nordic countries, the UK and Lithuania-Kaunas (men), but for no more than 17% in Central and South Europe. The major contributors were cigarette smoking, alcohol intake and body mass index. Social inequalities in stroke incidence contribute substantially to the disease rates in Europe. Healthier lifestyles in the most disadvantaged individuals should have a prominent impact in reducing both inequalities and the stroke burden.


Exploring the translational disconnect between the murine and human inflammatory response: analysis of LPS dose-response relationship in murine versus human cell lines and implications for translation into murine models of sepsis.
Inflammation forms an important part of the human innate immune system and is largely dependent on the activation of the "classical" NF-κB pathway through Toll-like receptors (TLRs). Understanding this has allowed researchers to explore roles of therapeutic targets in managing conditions such as sepsis. Recapitulating an inflammatory response using lipopolysaccharide (LPS), a "sterile" technique, can provide information that is dissimilar to the clinical condition. By examining NF-κB activation (through immunoblotting of the p65 subunit) in two separate cell lines (murine and human) and analyzing two murine models of sepsis (intraperitoneal [IP] LPS and IP stool inoculation), an evaluation of the translational disconnect between experimental and clinical sepsis can be made. THP-1 (human) cells and RAW 264.7 (murine) cells were dosed with concentrations of LPS (human, 1 pg/mL to 100 ng/mL; murine, 30 pg/mL to 1,000 ng/mL) and nuclear actin and p65 were immunoblotted to measure changes in nuclear density. In vivo, C57BL/6 mice received either IP injection of stool suspension (5 µL/g) or LPS (25 mg/kg) or saline (1 mL/kg). Animals were culled at 6 hours and tissues were analyzed. An increase in basal p65:actin density in THP-1 cells (mean 0.214, standard error of the mean 0.024) was seen at doses as small as 0.1 ng/mL (0.519±0.064). In contrast to RAW 264.7 cells, basal increases (0.170±0.025) were only seen when a dose of 3 ng/mL (0.387±0.078) was used. Dose-response analysis of p65:actin ratio showed that THP-1 cells respond to lower doses of LPS than RAW 264.7 cells and lower doses produce a greater fold increase in the nuclear p65 density. Both in vivo models showed evidence of neutrophil (NL) recruitment into tissues (which was more intense after LPS treatment). IP stool inoculation resulted in an acute suppurative peritonitis and more substantial evidence of NL recruitment into adipose tissue and skeletal muscle. Our results support previous observations that translation of murine models into the human clinical setting suffers from considerable limitations including species-associated differences in LPS response seen at a molecular level. Furthermore, the histopathological changes during clinical sepsis cannot be adequately reproduced by injection of LPS. Therefore, the so-called translational disconnect that exists between murine LPS models and human sepsis involves NF-κB activation at a molecular level and is further augmented by the use of LPS as a stimulus for infectious responses in vivo.


Pneumocystosis in patients with acquired immunodeficiency syndrome.
Nurses need to be aware that pneumocystosis is one of the most common and lethal opportunistic infections among AIDS patients. They are extremely susceptible because HIV impairs physiological mechanisms for microbial defense. Patients exhibit only minor symptomatology while the unchecked P carinii organisms accumulate and replicate. Eventually as the sporozoans create a physical barrier between the alveolar-capillary membranes, ventilation becomes impaired and severe hypoxemia develops. Early clinical and diagnostic studies mimic the findings characteristic of ARDS. Unless correct staining techniques are used on sputum specimens, the organism often escapes identification. Thus, the diagnosis and specific treatment of PCP is often delayed. While supporting ventilation, the treatment of choice is administration of antimetabolite drugs, either trimethoprim-sulfame-thoxazole or pentamidine isethionate. The search for more effective, as well as safer, treatment of PCP continues. Life-threatening nursing diagnoses such as impaired gas exchange urgently require priority attention. Besides physical care, the severe hypoxemia demands nursing approaches to help the critically ill patient deal with fear and powerlessness. The nurse also assumes a surrogate role to patients abandoned by family and friends. The psychosocial aspects of nursing care require enormous skill and finesse, because the blood and respiratory isolation precautions can communicate mixed messages to lonely, frightened patients.


Information technology strategy and alignment issues in health care organizations.
Information technology (IT) plays a key role in public health care management because it could improve quality, efficiency, and patient care. Researchers and practitioners repeatedly contend that a health care organization's information systems strategy should be aligned with its objectives and strategies, a notion commonly known as IT alignment. Actor-related IT alignment issues in health care institutions were explored in this study. More specifically, it explores the possibility of moving beyond the current IT alignment perspective and, in so doing, explores whether IT alignment-as currently conceptualized in the dominant body of research-is sufficient for attaining improved quality, efficiency, and patient care in health care organizations. The findings are based on a qualitative and longitudinal study of six health care organizations in the Stockholm metropolitan area. The empirical data were gathered over the 2005-2011 period from interviews, a focus group, observations, and archival material. The data suggest recurrent misalignments between IT strategy and organizational strategy and operations due to the failure to deconstruct the IT artifact and to the existence of various levels of IT maturity. A more complex picture of IT alignment in health care that goes beyond the current perspective is being offered by this study. It argues that the previously common way of handling IT as a single artifact and applying one IT strategy to the entire organizational system is obsolete. MANAGERIAL IMPLICATIONS: The article suggests that considerable benefits can be gained by assessing IT maturity and its impact on IT alignment. The article also shows that there are different kinds of IT in medical care that requires diverse decisions, investments, prioritizations, and implementation approaches.


Large-scale phenotyping links adult hippocampal neurogenesis to the reaction to novelty.
The discovery of adult-born neurons in the hippocampus has triggered a wide range of studies that link the new neurons to various behavioral functions. However, the role of new neurons in behavior is still equivocal. Conflicting results may be due to the difficulty in manipulating neurogenesis without off-target effects as well as the statistical approach used, which fail to account for neurogenesis-independent effects of experimental manipulations on behavior. In this study, we apply a more comprehensive statistical and conceptual approach. Instead of between-group analyses, we consider the within-group relationships between neurogenesis and behavior (ANCOVA and mediation analysis) in a large-scale experiment, in which distinct age- (3 and 5 months) and strain- (DBA and C57) related differences in basal levels of neurogenesis in mice are compared with a large number (∼1,500) of behavioral read outs. The analysis failed to detect any association between anxiety and motor impulsivity with neurogenesis. However, within-group adult hippocampal neurogenesis is associated with the reaction to novelty. Specifically, more neurogenesis is associated with a longer latency to explore and a lower frequency of exploratory actions, overall indicative of a phenotype where animals with more neurogenesis were slower to explore a novel environment. This effect is observed in 5-months-old, but not in 3-months-old mice of both strains. An association between the reaction to novelty and adult neurogenesis can have a major impact on results from previous studies using classical behavioral experiments, in which animals are tested in a--for the animal--novel experimental set-up. The neurogenesis-novelty association found here is also a necessary link in the relation that has been suggested to exist between neurogenesis and psychiatric disorders marked by a failure to cope with novelty.


The Effect of Caffeic Acid on Spermatogonial Stem Cell-type A Cryopreservation.
Cancer treatment methods can lead to male infertility .in this regard, cryopreservation of spermatogonial stem cells (SSC) and cell-to-person transplantation after the course of treatment to resolve the problem of infertility is a good one. The cryopreservation of SSC is an important process as it can help on the return of spermatogenesis. However, during this process, the stem cells often become damaged which degrades their value for experiments and treatments. Caffeic acid (CA) is an antioxidant that has been shown to increase the viability of cells under stress. The aim of this study was to investigate the effect of CA has on spermatogonial stem cell (SSC) cryopreservation. Spermatogonial stem cells isolated from the testes of Balb/c mice pups were cultured in laminincoated dishes, purified using CD90.1 microbeads, then cryopreserved in vitrification media supplemented with 10 µM CA either through a slow or rapid freezing process. After thawing, cell viability was evaluated. Expression of Bax, Fas, Bcl-2 and P53 genes was determined by real-time PCR. Gel electrophoresis was used to confirm the results of the real-time PCR. The viability of the SSCs that were rapidly frozen and treated with CA was observed to be significantly reduced compared to the control group (p < 0.003). The viability SSCs that received CA and underwent the slow freezing treatment was significantly reduced compared to controls (p < 0.002). The expression levels of BAX, BCL-2, and Fas in the rapid freeze-thaw group didn't significantly change. However, the levels of P53 expression were shown to increase. In the group of SSCs that underwent the slow freezing process, the BAX gene expression levels increased, while the levels of BCL-2 gene expression decreased. No significant changes in the level of Fas and P53 expression were detected. When comparing the groups that received CA treatment, SSCs that were rapidly frozen showed an up-regulation of Fas and P53 expression and a down-regulation of Bcl-2 and Bax expression. Caffeic acid may protect intact SCCs during the cryopreservation process through stimulating the induction of apoptosis in injured SSCs. Supplementing the vitrification media with CA has a superior effect on the preservation of SSCs.


Genomic organization and single-nucleotide polymorphism map of desmuslin, a novel intermediate filament protein on chromosome 15q26.3.
Desmuslin is an alpha-dystrobrevin-interacting protein expressed primarily in heart and skeletal muscle. The desmuslin protein interacts with and is closely related to desmin, a protein encoded by a locus mutated in some forms of hereditary distal myopathy. As a muscle-specific intermediate filament protein, desmuslin is also a candidate for myopathies of unknown etiology. The desmuslin gene was localized to chromosome 15q26.3 by electronic screening of the human DNA sequence database. Primer pairs were designed to amplify the 5 exons of the desmuslin gene in 11 overlapping DNA segments. The desmuslin gene was screened for mutations in 71 patients with various forms of myopathy for which there was no known cause. In this analysis, 10 common and 2 rare amino acid altering single-nucleotide polymorphisms were identified, all of which were seen in a control population of individuals thus making these unlikely causes of the phenotype. Interestingly, one of the single-nucleotide polymorphisms found in a patient resulted in a premature stop codon in the first exon. The nonsense mutation was also detected in the patient's unaffected father and one unaffected control; it was detected in 0.44% (2/454) of unrelated chromosomes and is therefore predicted to have a homozygous frequency of 0.002%. No causative mutations were found in the desmuslin gene. However, the single-nucleotide polymorphisms mapped in this study represent a well-mapped group that can be used for disequilibrium studies of this region of chromosome 15q26.3.


Transcription factor YB-1 mediates DNA polymerase alpha gene expression.
Y-box protein-1 involvement in cyclin A and B1 gene regulation has recently been demonstrated. A more generalized role of this protein for cell replication is hypothesized as numerous regulatory sequences of cell cycle-related genes contain putative binding sites. In the present study the DNA polymerase alpha (DPA) gene is identified as another YB-1-responsive gene with a Y-box and 3' inverted repeat sequence, designated DPA RE-1, in the serum-responsive promoter region. Overexpressed YB-1 concentration-dependently trans-activated DPA gene expression in reporter assays and Southwestern blotting as well as DNA binding analyses revealed binding of distinct endogenous proteins to the RE-1 with molecular sizes of 26, 32 and 52 kDa. Among these, YB-1 binding was confirmed using recombinant as well as endogenous proteins, with preferential single-stranded DNA binding. Early serum growth response in mesangial cells was accompanied by a nuclear YB-1 shift and nucleocomplex formation at the RE-1. Fine mapping of the DPA RE-1 sequence unraveled a dependence on co-factors for trans-regulation with gene activation in the context of a heterologous SV40 promoter but suppression in the context of the abbreviated homologous promoter sequence. A YB-1 knock down resulted in decreased DPA transcription rates and abrogated the serum-dependent induction of DPA transcription. These results link YB-1 with serum responsiveness of DPA gene expression and provide insight into the required sequence and protein binding context.


Characterization of natural and induced variation in the LOV1 gene, a CC-NB-LRR gene conferring victorin sensitivity and disease susceptibility in Arabidopsis.
The fungus Cochliobolus victoriae, the causal agent of Victoria blight, produces a compound called victorin that is required for pathogenicity of the fungus. Victorin alone reproduces disease symptoms on sensitive plants. Victorin sensitivity and susceptibility to C. victoriae were originally described on oats but have since been identified on Arabidopsis thaliana. Victorin sensitivity and disease susceptibility in Arabidopsis are conferred by LOV1, a coiled-coil-nucleotide-binding-leucine-rich repeat (CC-NB-LRR) protein. We sequenced the LOV1 gene from 59 victorin-insensitive mutants and found that the spectrum of mutations causing LOV1 loss of function was similar to that found to cause loss of function of RPM1, a CC-NB-LRR resistance protein. Also, many of the mutated residues in LOV1 are in conserved motifs required for resistance protein function. These data indicate that LOV1 may have a mechanism of action similar to resistance proteins. Victorin sensitivity was found to be the prevalent phenotype in a survey of 30 Arabidopsis ecotypes, and we found very little genetic variation among LOV1 alleles. As selection would not be expected to preserve a functional LOV1 gene to confer victorin sensitivity and disease susceptibility, we propose that LOV1 may function as a resistance gene to a naturally-occurring pathogen of Arabidopsis.


[Characterization and photocatalytic activity of Ni-doped tiO2 nano photocatalysts prepared by low temperature combustion synthesis].
Ni-doped TiO2 photocatalysts were prepared by low temperature combustion synthesis and some properties, such as optical absorption, crystal type, grain size distribution and chemistry transformation during temperature rising were characterized by UV-Vis DRS, X-ray diffraction (XRD), laser light dispersion grain size measurement machine and TG-DSC respectively. The photocatalytic activities of the prepared photocatalysts under visible light irradiation were evaluated by monitoring the degradation of methylene blue dye, a probe pollutant. The results indicate that the Ni-doped TiO2 photocatalysts prepared by low temperature combustion synthesis shift the optical absorption threshold to visible light, the band gap of 0.4 Ni-TiO2 (atomic ratio) is 2.3 eV, which corresponds to a 564 nm threshold in the visible light range. The crystal type of photocatalyst is anatase TiO2 and the content of NiTiO3 rise with the increase of Ni dopant. The grain size of photocatalyst distributes from 50 to 150nm, which account for 96.9% of entire quantity. During temperature rising, the TiO2 phase in photocatalyst transforms from amorphous structure to anatase and NiTiO3 crystallites appear at 445.2 degrees C. After 150 min visible light irradiation, 93.9% of methylene blue dye are degraded over 0.4 Ni-TiO2 photocatalyst. The photocatalytic activity of Ni doped TiO2 is higher than that of P25 under identical conditions.


Substance use disorders and racial/ethnic minorities matter: a meta-analytic examination of the relation between alliance and outcome.
The purpose of this meta analysis was to examine the moderating impact of substance use disorder as inclusion/exclusion criterion as well as the percentage of racial/ethnic minorities on the strength of the alliance-outcome relationship in psychotherapy. It was hypothesized that the presence of a Diagnostic and Statistical Manual of Mental Disorders (DSM) Axis I substance use disorder as a criterion and the presence of racial/ethnic minorities as a sociocultural indicator are moderately correlated client factors reducing the relationship between alliance and outcome. A random effects restricted maximum-likelihood estimator was used for omnibus and moderator models (k = 94). The presence of (a) substance use disorder and (b) racial/ethnic minorities (overall and specific to African Americans) partially moderated the alliance-outcome correlation. The percentage of substance use disorders and racial/ethnic minority status was unexpectedly highly correlated in the present treatment research samples. Sociocultural contextual variables should be considered along with a DSM Axis I diagnosis of substance use disorders in analyzing and interpreting therapy process variables such as the alliance.


Two classes of single-stranded regions in DNA from sea urchin embryos.
Native DNA from sea urchin embryos contains single-stranded regions (gaps) of up to 3000 nucleotides. The longer gaps (more than 1400 nucleotides) are nonrandomly distributed and are rich in histone gene sequences, other moderately repetitive sequences, and polypyrimidines. The shorter gaps are associated with DNA replication. A method for isolation of the two classes of single-stranded DNA pieces is reported.


Inflammatory cause of metabolic syndrome via brain stress and NF-κB.
Metabolic syndrome, a network of medical disorders that greatly increase the risk for developing metabolic and cardiovascular diseases, has reached epidemic levels in many areas of today's world. Despite this alarming medicare situation, scientific understandings on the root mechanisms of metabolic syndrome are still limited, and such insufficient knowledge contributes to the relative lack of effective treatments or preventions for related diseases. Recent interdisciplinary studies from neuroendocrinology and neuroimmunology fields have revealed that overnutrition can trigger intracellular stresses to cause inflammatory changes mediated by molecules that control innate immunity. This type of nutrition-related molecular inflammation in the central nervous system, particularly in the hypothalamus, can form a common pathogenic basis for the induction of various metabolic syndrome components such as obesity, insulin resistance, and hypertension. Proinflammatory NF-κB pathway has been revealed as a key molecular system for pathologic induction of brain inflammation, which translates overnutrition and resulting intracellular stresses into central neuroendocrine and neural dysregulations of energy, glucose, and cardiovascular homeostasis, collectively leading to metabolic syndrome. This article reviews recent research advances in the neural mechanisms of metabolic syndrome and related diseases from the perspective of pathogenic induction by intracellular stresses and NF-κB pathway of the brain.