How Broken DNA Finds Its Template for Repair: A Computational Approach

Homologous recombination (HR) is the process by which a double-strand break in DNA is repaired using an identical donor template. Despite rapid progress in identifying the functions of the proteins that mediate HR, little is known about how broken DNA finds its homologous template. This process, coined homology search, has been difficult to monitor experimentally. Therefore, we present here a computational approach to model the effect of subnuclear positioning and chromatin dynamics on homology search. We found that, in our model, homology search occurs more efficiently if both the cut site and its template are at the nuclear periphery, whereas restricting the movement of the template or the break alone to the periphery markedly increases the time of the search. Immobilization of either component at any position slows down the search. Based on these results, we propose a new model for homology search, the facilitated random search model, which predicts that the search is random, but that nuclear organization and dynamics strongly influence its speed and efficiency

G-portal : A map-based digital library for distributed geospatial and georeferenced resources

SingAREN Projec

GBA mutations are associated with Rapid eye movement sleep behavior disorder

Rapid eye movement sleep behavior disorder and GBA mutations are both associated with Parkinson’s disease. The GBA gene was sequenced in idiopathic rapid eye movement sleep behavior disorder patients (n = 265), and compared to controls (n = 2240). Rapid eye movement sleep behavior disorder questionnaire was performed in an independent Parkinson’s disease cohort (n = 120). GBA mutations carriers had an OR of 6.24 (10.2% in patients vs. 1.8% in controls, P < 0.0001) for rapid eye movement sleep behavior disorder, and among Parkinson’s disease patients, the OR for mutation carriers to have probable rapid eye movement sleep behavior disorder was 3.13 (P = 0.039). These results demonstrate that rapid eye movement sleep behavior disorder is associated with GBA mutations, and that combining genetic and prodromal data may assist in identifying individuals susceptible to Parkinson’s disease

A Randomized Trial of Rofecoxib for the Chemoprevention of Colorectal Adenomas

BACKGROUND & AIMS: In human and animal studies, nonsteroidal anti-inflammatory drugs have been associated with a reduced risk of colorectal neoplasia. Although the underlying mechanisms are unknown, inhibition of cyclooxygenase (COX), particularly COX-2, is thought to play a role. We conducted a randomized, placebo-controlled, double-blind trial to assess whether use of the selective COX-2 inhibitor rofecoxib would reduce the risk of colorectal adenomas. METHODS: We randomized 2587 subjects with a recent history of histologically confirmed adenomas to receive daily placebo or 25 mg rofecoxib. Randomization was stratified by baseline use of cardioprotective aspirin. Colonoscopic follow-up evaluation was planned for 1 and 3 years after randomization. The primary end point was all adenomas diagnosed during 3 years' treatment. In a modified intent-to-treat analysis, we computed the relative risk of any adenoma after randomization, using Mantel-Haenszel statistics stratified by low-dose aspirin use at baseline. RESULTS: Adenoma recurrence was less frequent for rofecoxib subjects than for those randomized to placebo (41% vs 55%; P < .0001; relative risk [RR], 0.76; 95% confidence interval [CI], 0.69-0.83). Rofecoxib also conferred a reduction in risk of advanced adenomas (P < .01). The chemopreventive effect was more pronounced in the first year (RR, 0.65; 95% CI, 0.57-0.73) than in the subsequent 2 years (RR, 0.81; 95% CI, 0.71-0.93). As reported previously, rofecoxib was associated with increased risks of significant upper gastrointestinal events and serious thrombotic cardiovascular events. CONCLUSIONS: In this randomized trial, rofecoxib significantly reduced the risk of colorectal adenomas, but also had serious toxicity

The Orphan G Protein-coupled Receptors GPR41 and GPR43 Are Activated by Propionate and Other Short Chain Carboxylic Acids

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The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Trial outcomes and information for clinical decision-making: a comparative study of opinions of health professionals

Background: Trials are robust sources of data for clinical practice, however, trial outcomes may not reflect what is important to communicate for decision making. The study compared clinicians’ views of outcomes to include in a core outcome set for colorectal cancer (CRC) surgery, with what clinicians considered important information for clinical practice (core information). Methods: Potential outcomes/information domains were identified through systematic literature reviews, reviews of hospital information leaflets and interviews with patients. These were organized into 6 categories, and used to design a questionnaire survey that asked surgeons and nurses from a sample of CRC centers to rate the importance of each domain as an outcome or as information on a 9-point Likert scale. Respondents were re-surveyed (round 2) following group feedback (Delphi methods). Comparisons were made by calculating the difference in mean scores between the outcomes and information domains, and paired t-tests were used to explore the difference between mean scores of the 6 outcome/information categories. Results: Data sources identified 1216 outcomes/information of CRC surgery that informed a 94 item questionnaire. First round questionnaires were returned from 63/81 (78%) of centers. Clinicians rated 76/94 (84%) domains of higher importance to measure in trials than to information to communicate to patients in Round 1. This was reduced to 24/47 (51%) in Round 2. The greatest difference was evident in domains about survival, which was rated much more highly as a trial outcome than important piece of information for decision-making (mean difference 2.3, 95% CI 1.9-2.8, p<0.0001). Specific complications and quality-of-life domains were rated similarly (mean difference 0.18, 95% CI -0.1-0.4, p=0.2 and 0.2, 95% CI -0.1-0.5, p=0.2 respectively). Conclusions: Whilst clinicians want to measure key outcomes in trials, they rate these as less important to communicate in decision-making with patients. This discrepancy needs to be explored and addressed to maximize the impact of trials on clinical practice