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Association between chlorinated pesticides in the serum of prepubertal Russian boys and longitudinal biomarkers of metabolic function

Tue, 07/14/2015 - 4:04pm

Organochlorine pesticides (OCPs) have been linked to adult metabolic disorders; however, few studies have examined these associations in childhood. We prospectively evaluated the associations of baseline serum OCPs (hexachlorobenzene, beta-hexachlorocyclohexane, and p,p'-dichlorodiphenyldichloroethylene) in Russian boys with subsequent repeated measurements of serum glucose, insulin, lipids, leptin, and calculated homeostatic model assessment of insulin resistance (IR). During 2003-2005, we enrolled 499 boys aged 8-9 years in a prospective cohort; 318 had baseline serum OCPs and serum biomarkers measured at ages 10-13 years. Multivariable generalized estimating equation and mediation regression models were used to examine associations and direct and indirect (via body mass index (BMI) (weight (kg)/height (m)(2))) effects of prepubertal OCP tertiles and quintiles with biomarkers. In multivariable models, higher p,p'-dichlorodiphenyldichloroethylene (quintile 5 vs. quintile 1) was associated with lower leptin, with relative mean decreases of 61.8% (95% confidence interval: 48.4%, 71.7%) in models unadjusted for BMI and 22.2% (95% confidence interval: 7.1%, 34.9%) in models adjusted for BMI; the direct effect of p,p'-dichlorodiphenyldichloroethylene on leptin accounted for 27% of the total effect. IR prevalence was 6.6% at ages 12-13 years. Higher hexachlorobenzene (tertile 3 vs. tertile 1) was associated with higher odds of IR in models adjusted for BMI (odds ratio = 4.37, 95% confidence interval: 1.44, 13.28). These results suggest that childhood OCPs may be associated with IR and lower leptin.

Individual differences in aversion to ambiguity regarding medical tests and treatments: association with cancer screening cognitions

Tue, 07/14/2015 - 4:04pm

BACKGROUND: Aversion to "ambiguity"-uncertainty about the reliability, credibility, or adequacy of information-about medical tests and treatments is an important psychological response that varies among individuals, but little is known about its nature and extent. The purpose of this study was to examine how individual-level ambiguity aversion relates to important health cognitions related to different cancer screening tests.

METHODS: A survey of 1,074 adults, ages 40 to 70 years, was conducted in four integrated U.S. healthcare systems. The Ambiguity Aversion in Medicine (AA-Med) scale, a measure of individual differences in aversion to ambiguity (AA) about medical tests and treatments, was administered along with measures of several cancer screening-related cognitions: perceived benefits and harms of colonoscopy, mammography, and PSA screening, and ambivalence and future intentions regarding these tests. Multivariable analyses were conducted to assess the associations between AA-Med scores and cancer screening cognitions.

RESULTS: Individual-level AA as assessed by the AA-Med scale was significantly associated (P < 0.05) with lower perceived benefits, greater perceived harms, and greater ambivalence about all three screening tests, and lower intentions for colonoscopy but not mammography or PSA screening.

CONCLUSION: Individual-level AA is broadly and simultaneously associated with various pessimistic cognitive appraisals of multiple cancer screening tests. The breadth of these associations suggests that the influence of individual-level AA is insensitive to the degree and nonspecific with respect to the causes of ambiguity.

IMPACT: Individual-level AA constitutes a measurable, wide-ranging cognitive bias against medical intervention, and more research is needed to elucidate its mechanisms and effects.

Screening Questions for Nonsteroidal Anti-inflammatory Drug Risk Knowledge

Tue, 07/14/2015 - 4:04pm

OBJECTIVE: The aim of this study was to evaluate screening questions for estimating nonsteroidal anti-inflammatory drug (NSAID) risk knowledge.

METHODS: Cross-sectional data from a telephone interview of NSAID users 50 years or older from 39 physician practices in Alabama were used. Patient-reported awareness of prescription NSAID risk and health literacy were the independent variables, and a cumulative index score of objectively tested knowledge of 4 prominent NSAID risks was the dependent variable. General linearized latent and mixed model ordered logistic regression was used to estimate associations among the independent variables, covariates, and objectively tested NSAID risk knowledge. Population-averaged probabilities for levels of objectively tested NSAID risk knowledge were subsequently estimated.

RESULTS: Subjective awareness of any prescription NSAID risk (adjusted odds ratio [AOR], 2.40; 95% confidence interval [CI], 1.55-3.74), adequate health literacy (AOR, 1.71; 95% CI, 1.04-2.83), and physician counseling about 1 or more NSAID risks (AOR, 1.69; 95% CI, 1.09-2.61) were significantly and positively associated with NSAID risk knowledge. The probability of correctly answering at least 1 of the 4 NSAID risk knowledge questions was 70% in the absence of any subjective risk awareness and in less than adequate health literacy. Whereas the probability of correctly answering at least 1 of the 4 NSAID risk knowledge questions increased to 86% in the presence of subjective awareness of any prescription NSAID risk and adequate health literacy.

CONCLUSIONS: Screening questions for subjective NSAID risk awareness and health literacy are predictive of objectively tested NSAID knowledge and can be used to triage patients as well as subsequently initiate and direct a conversation about NSAID risk.

Neighborhood socioeconomic status and food environment: a 20-year longitudinal latent class analysis among CARDIA participants

Tue, 07/14/2015 - 4:04pm

Cross-sectional studies suggest that neighborhood socioeconomic (SES) disadvantage is associated with obesogenic food environments. Yet, it is unknown how exposure to neighborhood SES patterning through adulthood corresponds to food environments that also change over time. We used latent class analysis (LCA) to classify participants in the U.S.-based Coronary Artery Risk Development in Young Adults study [n=5,114 at baseline 1985-1986 to 2005-2006] according to their longitudinal neighborhood SES residency patterns (upward, downward, stable high and stable low). For most classes of residents, the availability of fast food and non-fast food restaurants and supermarkets and convenience stores increased (p < 0.001). Yet, socioeconomically disadvantaged neighborhood residents had fewer fast food and non-fast food restaurants, more convenience stores, and the same number of supermarkets in their neighborhoods than the advantaged residents. In addition to targeting the pervasive fast food restaurant and convenient store retail growth, improving neighborhood restaurant options for disadvantaged residents may reduce food environment disparities.

The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs

Tue, 07/14/2015 - 2:36pm

PIWI-interacting RNAs (piRNAs) silence transposons in animal germ cells. PIWI proteins bind and amplify piRNAs via the "Ping-Pong" pathway. Because PIWI proteins cleave RNAs between target nucleotides t10 and t11-the nucleotides paired to piRNA guide positions g10 and g11-the first ten nucleotides of piRNAs participating in the Ping-Pong amplification cycle are complementary. Drosophila piRNAs bound to the PIWI protein Aubergine typically begin with uridine (1U), while piRNAs bound to Argonaute3, which are produced by Ping-Pong amplification, often have adenine at position 10 (10A). The Ping-Pong model proposes that the 10A is a consequence of 1U. We find that 10A is not caused by 1U. Instead, fly Aubergine as well as its homologs, Siwi in silkmoth and MILI in mice, have an intrinsic preference for adenine at the t1 position of their target RNAs; during Ping-Pong amplification, this t1A subsequently becomes the g10A of a piRNA bound to Argonaute3.

Data from: A Randomized, Double-Blind, Placebo-Controlled Trial of Adjunctive Metformin Therapy in Overweight/Obese Youth with Type 1 Diabetes

Mon, 07/06/2015 - 12:25am

This dataset is the primary data source for a manuscript submitted for publication.

An integrated encyclopedia of DNA elements in the human genome

Sun, 06/28/2015 - 5:06pm

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Functional analysis of transcription factor binding sites in human promoters

Sun, 06/28/2015 - 5:06pm

BACKGROUND: The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1.

RESULTS: In each cell line, between 36% and 49% of binding sites made a functional contribution to the promoter activity; the overall rate for observing function in any of the cell lines was 70%. Transcription factor binding resulted in transcriptional repression in more than a third of functional sites. When compared with predicted binding sites whose function was not experimentally verified, the functional binding sites had higher conservation and were located closer to transcriptional start sites (TSSs). Among functional sites, repressive sites tended to be located further from TSSs than were activating sites. Our data provide significant insight into the functional characteristics of YY1 binding sites, most notably the detection of distinct activating and repressing classes of YY1 binding sites. Repressing sites were located closer to, and often overlapped with, translational start sites and presented a distinctive variation on the canonical YY1 binding motif.

CONCLUSIONS: The genomic properties that we found to associate with functional TF binding sites on promoters -- conservation, TSS proximity, motifs and their variations -- point the way to improved accuracy in future TFBS predictions.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

Sun, 06/28/2015 - 5:06pm

Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict the effects of mutations on protein-protein interactions. Twenty-two groups predicted the effects of comprehensive saturation mutagenesis for two designed influenza hemagglutinin binders and the results were compared with experimental yeast display enrichment data obtained using deep sequencing. The most successful methods explicitly considered the effects of mutation on monomer stability in addition to binding affinity, carried out explicit side-chain sampling and backbone relaxation, evaluated packing, electrostatic, and solvation effects, and correctly identified around a third of the beneficial mutations. Much room for improvement remains for even the best techniques, and large-scale fitness landscapes should continue to provide an excellent test bed for continued evaluation of both existing and new prediction methodologies.

Evaluating template-based and template-free protein-protein complex structure prediction

Sun, 06/28/2015 - 5:06pm

We compared the performance of template-free (docking) and template-based methods for the prediction of protein-protein complex structures. We found similar performance for a template-based method based on threading (COTH) and another template-based method based on structural alignment (PRISM). The template-based methods showed similar performance to a docking method (ZDOCK) when the latter was allowed one prediction for each complex, but when the same number of predictions was allowed for each method, the docking approach outperformed template-based approaches. We identified strengths and weaknesses in each method. Template-based approaches were better able to handle complexes that involved conformational changes upon binding. Furthermore, the threading-based and docking methods were better than the structural-alignment-based method for enzyme-inhibitor complex prediction. Finally, we show that the near-native (correct) predictions were generally not shared by the various approaches, suggesting that integrating their results could be the superior strategy.

Blind prediction of interfacial water positions in CAPRI

Sun, 06/28/2015 - 5:06pm

We report the first assessment of blind predictions of water positions at protein-protein interfaces, performed as part of the critical assessment of predicted interactions (CAPRI) community-wide experiment. Groups submitting docking predictions for the complex of the DNase domain of colicin E2 and Im2 immunity protein (CAPRI Target 47), were invited to predict the positions of interfacial water molecules using the method of their choice. The predictions-20 groups submitted a total of 195 models-were assessed by measuring the recall fraction of water-mediated protein contacts. Of the 176 high- or medium-quality docking models-a very good docking performance per se-only 44% had a recall fraction above 0.3, and a mere 6% above 0.5. The actual water positions were in general predicted to an accuracy level no better than 1.5 A, and even in good models about half of the contacts represented false positives. This notwithstanding, three hotspot interface water positions were quite well predicted, and so was one of the water positions that is believed to stabilize the loop that confers specificity in these complexes. Overall the best interface water predictions was achieved by groups that also produced high-quality docking models, indicating that accurate modelling of the protein portion is a determinant factor. The use of established molecular mechanics force fields, coupled to sampling and optimization procedures also seemed to confer an advantage. Insights gained from this analysis should help improve the prediction of protein-water interactions and their role in stabilizing protein complexes.

Backbone flexibility of CDR3 and immune recognition of antigens

Sun, 06/28/2015 - 5:06pm

Conformational entropy is an important component of protein-protein interactions; however, there is no reliable method for computing this parameter. We have developed a statistical measure of residual backbone entropy in folded proteins by using the varphi-psi distributions of the 20 amino acids in common secondary structures. The backbone entropy patterns of amino acids within helix, sheet or coil form clusters that recapitulate the branching and hydrogen bonding properties of the side chains in the secondary structure type. The same types of residues in coil and sheet have identical backbone entropies, while helix residues have much smaller conformational entropies. We estimated the backbone entropy change for immunoglobulin complementarity-determining regions (CDRs) from the crystal structures of 34 low-affinity T-cell receptors and 40 high-affinity Fabs as a result of the formation of protein complexes. Surprisingly, we discovered that the computed backbone entropy loss of only the CDR3, but not all CDRs, correlated significantly with the kinetic and affinity constants of the 74 selected complexes. Consequently, we propose a simple algorithm to introduce proline mutations that restrict the conformational flexibility of CDRs and enhance the kinetics and affinity of immunoglobulin interactions. Combining the proline mutations with rationally designed mutants from a previous study led to 2400-fold increase in the affinity of the A6 T-cell receptor for Tax-HLAA2. However, this mutational scheme failed to induce significant binding changes in the already-high-affinity C225-Fab/huEGFR interface. Our results will serve as a roadmap to formulate more effective target functions to design immune complexes with improved biological functions.

Endogenous U2.U5.U6 snRNA complexes in S. pombe are intron lariat spliceosomes

Sun, 06/28/2015 - 5:06pm

Excision of introns from pre-mRNAs is mediated by the spliceosome, a multi-megadalton complex consisting of U1, U2, U4/U6, and U5 snRNPs plus scores of associated proteins. Spliceosome assembly and disassembly are highly dynamic processes involving multiple stable intermediates. In this study, we utilized a split TAP-tag approach for large-scale purification of an abundant endogenous U2.U5.U6 complex from Schizosaccharomyces pombe. RNAseq revealed this complex to largely contain excised introns, indicating that it is primarily ILS (intron lariat spliceosome) complexes. These endogenous ILS complexes are remarkably resistant to both high-salt and nuclease digestion. Mass spectrometry analysis identified 68, 45, and 43 proteins in low-salt-, high-salt-, and micrococcal nuclease-treated preps, respectively. The protein content of a S. pombe ILS complex strongly resembles that previously reported for human spliced product (P) and Saccharomyces cerevisiae ILS complexes assembled on single pre-mRNAs in vitro. However, the ATP-dependent RNA helicase Brr2 was either substoichiometric in low-salt preps or completely absent from high-salt and MNase preps. Because Brr2 facilitates spliceosome disassembly, its relative absence may explain why the ILS complex accumulates logarithmically growing cultures and the inability of S. pombe extracts to support in vitro splicing.

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

Sun, 06/28/2015 - 5:06pm

SUMMARY: Protein-protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers. With a goal of providing an accessible and intuitive interface, we provide options for users to guide the scoring and the selection of output models, in addition to dynamic visualization of input structures and output docking models. This server enables the research community to easily and quickly produce structural models of protein-protein complexes and symmetric multimers for their own analysis.

AVAILABILITY: The ZDOCK server is freely available to all academic and non-profit users at: http://zdock.umassmed.edu. No registration is required.