3D structure of individual mammalian genomes studied by single cell Hi-C

The folding of genomic DNA from the beads-on-a-string like structure of nucleosomes into higher order assemblies is critically linked to nuclear processes. We have calculated the first 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. This has allowed us to study genome folding down to a scale of <100 kb and to validate the structures. We show that the structures of individual topological-associated domains and loops vary very substantially from cell-to-cell. By contrast, A/B compartments, lamin-associated domains and active enhancers/promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding. Through studying pluripotency factor- and NuRD-regulated genes, we illustrate how single cell genome structure determination provides a novel approach for investigating biological processes.We thank the Wellcome Trust (082010/Z/07/Z), the EC FP7 4DCellFate project (277899) and the MRC (MR/M010082/1) for financial support

A pilot study comparing two weight loss maintenance interventions among low-income, mid-life women

BACKGROUND: Despite high obesity prevalence rates, few low-income midlife women participate in weight loss maintenance trials. This pilot study aims to assess the effectiveness of two weight loss maintenance interventions in this under-represented population. METHODS: Low-income midlife women who completed a 16-week weight loss intervention and lost ≥ 8 lbs (3.6 kg) were eligible to enroll in one of two 12-month maintenance programs. The programs were similar in content and had the same number of total contacts, but were different in the contact modality (Phone + Face-to-Face vs. Face-to-Face Only). Two criteria were used to assess successful weight loss maintenance at 12 months: (1) retaining a loss of ≥ 5% of body weight from the start of the weight loss phase and (2) a change in body weight of < 3%, from the start to the end of the maintenance program. Outcome measures of changes in physiologic and psychosocial factors, and evaluations of process measures and program acceptability (measured at 12 months) are also reported. For categorical variables, likelihood ratio or Fisher’s Exact (for small samples) tests were used to evaluate statistically significant relationships; for continuous variables, t-tests or their equivalents were used to assess differences between means and also to identify correlates of weight loss maintenance. RESULTS: Overall, during the 12-month maintenance period, 41% (24/58) of participants maintained a loss of ≥ 5% of initial weight and 43% (25/58) had a <3% change in weight. None of the comparisons between the two maintenance programs were statistically significant. However, improvements in blood pressure and dietary behaviors remained significant at the end of the 12-month maintenance period for participants in both programs. Participant attendance and acceptability were high for both programs. CONCLUSIONS: The effectiveness of two pilot 12-month maintenance interventions provides support for further research in weight loss maintenance among high-risk, low-income women. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT0028830

Randomized trial of tapas acupressure technique for weight loss maintenance

<p>Abstract</p> <p>Background</p> <p>Obesity is an urgent public health problem, yet only a few clinical trials have systematically tested the efficacy of long-term weight-loss maintenance interventions. This randomized clinical trial tested the efficacy of a novel mind and body technique for weight-loss maintenance.</p> <p>Methods</p> <p>Participants were obese adults who had completed a six-month behavioral weight-loss program prior to randomization. Those who successfully lost weight were randomized into either an experimental weight-loss maintenance intervention, Tapas Acupressure Technique (TAT^®), or a control intervention comprised of social-support group meetings (SS) led by professional facilitators. TAT combines self-applied light pressure to specific acupressure points accompanied by a prescribed sequence of mental steps. Participants in both maintenance conditions attended eight group sessions over six months of active weight loss maintenance intervention, followed by an additional 6 months of no intervention. The main outcome measure was change in weight from the beginning of the weight loss maintenance intervention to 12 months later. Secondary outcomes were change in depression, stress, insomnia, and quality of life. We used analysis of covariance as the primary analysis method. Missing values were replaced using multiple imputation.</p> <p>Results</p> <p>Among 285 randomized participants, 79% were female, mean age was 56 (standard deviation (sd) = 11), mean BMI at randomization was 34 (sd = 5), and mean initial weight loss was 9.8 kg (sd = 5). In the primary outcome model, there was no significant difference in weight regain between the two arms (1.72 kg (se 0.85) weight regain for TAT and 2.96 kg (se 0.96) weight regain for SS, p < 0.097) Tests of between- arm differences for secondary outcomes were also not significant. A secondary analysis showed a significant interaction between treatment and initial weight loss (p < .036), with exploratory <it>post hoc </it>tests showing that greater initial weight loss was associated with more weight regain for SS but less weight regain for TAT.</p> <p>Conclusions</p> <p>The primary analysis showed no significant difference in weight regain between TAT and SS, while secondary and post hoc analyses indicate direction for future research.</p> <p>Trial Registration</p> <p>ClinicalTrials.gov: <a href="http://www.clinicaltrials.gov/ct2/show/NCT00526565">NCT00526565</a></p

Central synapses release a resource-efficient amount of glutamate.

Why synapses release a certain amount of neurotransmitter is poorly understood. We combined patch-clamp electrophysiology with computer simulations to estimate how much glutamate is discharged at two distinct central synapses of the rat. We found that, regardless of some uncertainty over synaptic microenvironment, synapses generate the maximal current per released glutamate molecule while maximizing signal information content. Our result suggests that synapses operate on a principle of resource optimization

Risk factors for incident falls in older men and women:The English longitudinal study of ageing

Background: falls are a major cause of disability and death in older people, particularly women. Cross-sectional surveys suggest that some risk factors associated with a history of falls may be sex-specific, but whether risk factors for incident falls differ between the sexes is unclear. We investigated whether risk factors for incident falls differ between men and women.Methods: participants were 3298 people aged ≥60 who took part in the Waves 4-6 surveys of the English Longitudinal Study of Ageing. At Wave 4, they provided information about sociodemographic, lifestyle, behavioural and medical factors and had their physical and cognitive function assessed. Data on incident falls during the four-year follow-up period was collected from them at Waves 5 and 6. Poisson regression with robust variance estimation was used to derive relative risks (RR) for the association between baseline characteristics and incident falls.Results: in multivariable-adjusted models that also controlled for history of falls, older age was the only factor associated with increased risk of incident falls in both sexes. Some factors were only predictive of falls in one sex, namely more depressive symptoms (RR (95% CI) 1.03 (1.01,1.06)), incontinence (1.12 (1.00,1.24)) and never having married in women (1.26 (1.03,1.53)), and greater comorbidity (1.04 (1.00,1.08)), higher levels of pain (1.10 (1.04,1.17) and poorer balance, as indicated by inability to attempt a full-tandem stand, (1.23 (1.04,1.47)) in men. Of these, only the relationships between pain, balance and comorbidity and falls risk differed significantly by sex.Conclusions: there were some differences between the sexes in risk factors for incident falls. Our observation that associations between pain, balance and comorbidity and incident falls risk varied by sex needs further investigation in other cohorts. <br/

Infectious Offspring: How Birds Acquire and Transmit an Avian Polyomavirus in the Wild

Detailed patterns of primary virus acquisition and subsequent dispersal in wild vertebrate populations are virtually absent. We show that nestlings of a songbird acquire polyomavirus infections from larval blowflies, common nest ectoparasites of cavity-nesting birds, while breeding adults acquire and renew the same viral infections via cloacal shedding from their offspring. Infections by these DNA viruses, known potential pathogens producing disease in some bird species, therefore follow an ‘upwards vertical’ route of an environmental nature mimicking horizontal transmission within families, as evidenced by patterns of viral infection in adults and young of experimental, cross-fostered offspring. This previously undescribed route of viral transmission from ectoparasites to offspring to parent hosts may be a common mechanism of virus dispersal in many taxa that display parental care

Weekend admission to hospital has a higher risk of death in the elective setting than in the emergency setting: a retrospective database study of national health service hospitals in England

<p>Abstract</p> <p>Background</p> <p>Although acute hospitals offer a twenty-four hour seven day a week service levels of staffing are lower over the weekends and some health care processes may be less readily available over the weekend. Whilst it is thought that emergency admission to hospital on the weekend is associated with an increased risk of death, the extent to which this applies to elective admissions is less well known. We investigated the risk of death in elective and elective patients admitted over the weekend versus the weekdays.</p> <p>Methods</p> <p>Retrospective statistical analysis of routinely collected acute hospital admissions in England, involving all patient discharges from all acute hospitals in England over a year (April 2008-March 2009), using a logistic regression model which adjusted for a range of patient case-mix variables, seasonality and admission over a weekend separately for elective and emergency (but excluding zero day stay emergency admissions discharged alive) admissions.</p> <p>Results</p> <p>Of the 1,535,267 elective admissions, 91.7% (1,407,705) were admitted on the weekday and 8.3% (127,562) were admitted on the weekend. The mortality following weekday admission was 0.52% (7,276/1,407,705) compared with 0.77% (986/127,562) following weekend admission. Of the 3,105,249 emergency admissions, 76.3% (2,369,316) were admitted on the weekday and 23.7% (735,933) were admitted on the weekend. The mortality following emergency weekday admission was 6.53% (154,761/2,369,316) compared to 7.06% (51,922/735,933) following weekend admission. After case-mix adjustment, weekend admissions were associated with an increased risk of death, especially in the elective setting (elective Odds Ratio: 1.32, 95% Confidence Interval 1.23 to 1.41); vs emergency Odds Ratio: 1.09, 95% Confidence Interval 1.05 to 1.13).</p> <p>Conclusions</p> <p>Weekend admission appears to be an independent risk factor for dying in hospital and this risk is more pronounced in the elective setting. Given the planned nature of elective admissions, as opposed to the unplanned nature of emergency admissions, it would seem less likely that this increased risk in the elective setting is attributable to unobserved patient risk factors. Further work to understand the relationship between weekend processes of care and mortality, especially in the elective setting, is required.</p

CKD classification based on estimated GFR over three years and subsequent cardiac and mortality outcomes: a cohort study

<p>Abstract</p> <p>Background</p> <p>It is unknown whether defining chronic kidney disease (CKD) based on one versus two estimated glomerular filtration rate (eGFR) assessments changes the prognostic importance of reduced eGFR in a community-based population.</p> <p>Methods</p> <p>Participants in the Atherosclerosis Risk in Communities Study and the Cardiovascular Health Study were classified into 4 groups based on two eGFR assessments separated by 35.3 ± 2.5 months: sustained eGFR < 60 mL/min per 1.73 m²(1 mL/sec per 1.73 m²); eGFR increase (change from below to above 60); eGFR decline (change from above to below 60); and eGFR persistently ≥60. Outcomes assessed in stratified multivariable Cox models included cardiac events and a composite of cardiac events, stroke, and mortality.</p> <p>Results</p> <p>There were 891 (4.9%) participants with sustained eGFR < 60, 278 (1.5%) with eGFR increase, 972 (5.4%) with eGFR decline, and 15,925 (88.2%) with sustained eGFR > 60. Participants with eGFR sustained < 60 were at highest risk of cardiac and composite events [HR = 1.38 (1.15, 1.65) and 1.58 (1.41, 1.77)], respectively, followed by eGFR decline [HR = 1.20 (1.00, 1.45) and 1.32 (1.17, 1.49)]. Individuals with eGFR increase trended toward increased cardiac risk [HR = 1.25 (0.88, 1.77)] and did not significantly differ from eGFR decline for any outcome. Results were similar when estimating GFR with the CKD-EPI equation.</p> <p>Conclusion</p> <p>Individuals with persistently reduced eGFR are at highest risk of cardiovascular outcomes and mortality, while individuals with an eGFR < 60 mL/min per 1.73 m²at any time are at intermediate risk. Use of even a single measurement of eGFR to classify CKD in a community population appears to have prognostic value.</p

A novel evolutionary strategy revealed in the Phaeoviruses

Phaeoviruses infect the brown algae, which are major contributors to primary production of coastal waters and estuaries. They exploit a Persistent evolutionary strategy akin to a K- selected life strategy via genome integration and are the only known representatives to do so within the giant algal viruses that are typified by r- selected Acute lytic viruses. In screening the genomes of five species within the filamentous brown algal lineage, here we show an unprecedented diversity of viral gene sequence variants especially amongst the smaller phaeoviral genomes. Moreover, one variant shares features from both the two major sub-groups within the phaeoviruses. These phaeoviruses have exploited the reduction of their giant dsDNA genomes and accompanying loss of DNA proofreading capability, typical of an Acute life strategist, but uniquely retain a Persistent life strategy