DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer

Germline pathogenic mutations in BRCA1 increase risk of developing breast cancer. Screening for mutations in BRCA1 frequently identifies sequence variants of unknown pathogenicity and recent work has aimed to develop methods for determining pathogenicity. We previously observed that tumor DNA methylation can differentiate BRCA1-mutated from BRCA1-wild type tumors. We hypothesized that we could predict pathogenicity of variants based on DNA methylation profiles of tumors that had arisen in carriers of unclassified variants. We selected 150 FFPE breast tumor DNA samples [47 BRCA1 pathogenic mutation carriers, 65 BRCAx (BRCA1-wild type), 38 BRCA1 test variants] and analyzed a subset (n=54) using the Illumina 450K methylation platform, using the remaining samples for bisulphite pyrosequencing validation. Three validated markers (BACH2, C8orf31, and LOC654342) were combined with sequence bioinformatics in a model to predict pathogenicity of 27 variants (independent test set). Predictions were compared with standard multifactorial likelihood analysis. Prediction was consistent for c.5194-12G>A (IVS 19-12 G>A) (P>0.99); 13 variants were considered not pathogenic or likely not pathogenic using both approaches. We conclude that tumor DNA methylation data alone has potential to be used in prediction of BRCA1 variant pathogenicity but is not independent of estrogen receptor status and grade, which are used in current multifactorial models to predict pathogenicity

A pilot study evaluating the effects of a 12 week exergaming programme on body mass, size and composition in postpartum females

Introduction: Pregnancy is associated with weight gain, the retention of which contributes to the prevalence of obesity and overweight in adult females. Many new mothers do not achieve the recommendations for physical activity (PA), citing factors such as a lack of time and access to childcare. Exergaming may address some of the barriers to PA and offer an alternative to traditional exercise, thus aiding in weight management. The aim of this pilot study was to evaluate the effects of an exergaming intervention on body composition in postpartum females. Methods: Eight females who had given birth within 1 year completed a 12 week exergaming intervention, which required them to exercise at home for 45 minutes on alternate days, using the Wii Fit. Participants self-reported their pre-pregnancy body weight, and visited the laboratory prior to and following the intervention for evaluation of body weight, size (height, regional circumferences, body mass index [BMI]) and composition (fat mass [FM], lean mass [LM] and bone mineral content [BMC]). Body composition was evaluated via full body full-body dual-energy x-ray absorptiometry scan. Participants completed a three-day weighed food intake at three time-points. Results: Baseline body mass was 8.2 kg greater than self-reported pre-pregnancy values (56.8 ± 5.1 kg). Following the intervention, body mass was significantly lower than baseline values and was similar to pre-pregnancy levels (59.9 ± 7.9 kg). Reductions in BMI (~2 kg·m2 ), waist, hip and bust circumference (3-6%) accompanied the loss of body mass. Food diaries confirmed participants had not altered their energy intake. Discussion: The results of this pilot study indicate that exergaming may offer an alternative to traditional exercise for preventing the retention of gestational weight gain and reducing associated health risks, whilst also maintaining lean mass and bone mineral content

Effects of reduced energy availability on bone metabolism in women and men

Background: The short-term effects of low energy availability (EA) on bone metabolism in physically active women and men are currently unknown. Purpose: We evaluated the effects of low EA on bone turnover markers (BTMs) in a cohort of women and a cohort of men, and compared effects between sexes. Methods: These studies were performed using a randomised, counterbalanced, crossover design. Eleven eumenorrheic women and eleven men completed two 5-day protocols of controlled (CON; 45 kcal·kgLBM-1.d-1) and restricted (RES; 15 kcal.kgLBM-1·d-1) EAs. Participants ran daily on a treadmill at 70% of their peak aerobic capacity (VO2 peak) resulting in an exercise energy expenditure of 15 kcal·kgLBM-1·d-1 and consumed diets providing 60 and 30 kcal·kgLBM-1·d-1. Blood was analysed for BTMs [β-carboxyl-terminal cross-linked telopeptide of type I collagen (β-CTX) and amino-terminal propeptide of type 1 procollagen (P1NP)], markers of calcium metabolism [( parathyroid hormone (PTH), albumin-adjusted calcium (ACa), magnesium (Mg) and phosphate (PO4)] and regulatory hormones [sclerostin, insulin-like growth factor 1 (IGF-1), triiodothyronine (T3), insulin, leptin, glucagon-like- peptide-2 (GLP-2)]. Results: In women,β-CTX AUC was significantly higher P=0.03) and P1NP AUC was significantly lower (P=0.01) in RES compared to CON. In men, neither β-CTX (P=0.46) n or P1NP (P=0.12) AUCs were significantly different between CON and RES. There were no significant differences between sexes for any BTM AUCs (all P values>0.05). Insulin and leptin AUCs were significantly lower following RES in women only (for both P=0.01). There were no differences in any AUCs of regulatory hormones or markers of calcium metabolism between men and women following RES (all P values>0.05). Conclusions: When comparing within groups, five days of low EA (15 kcal·kgLBM-1·d-1) decreased bone formation and increased bone resorption in women, but not in men, and no sex specific differences were detected

The OPERA trial : a protocol for the process evaluation of a randomised trial of an exercise intervention for older people in residential and nursing accommodation

Background: The OPERA trial is large cluster randomised trial testing a physical activity intervention to address depression amongst people living in nursing and residential homes for older people. A process evaluation was commissioned alongside the trial and we report the protocol for this process evaluation. Challenges included the cognitive and physical ability of the participants, the need to respect the privacy of all home residents, including study non-participants, and the physical structure of the homes. Evaluation activity had to be organised around the structured timetable of homes, leaving limited opportunities for data collection. The aims of this process evaluation are to provide findings that will assist in the interpretation of the clinical trial results, and to inform potential implementation of the physical activity intervention on a wider scale. Methods/design: Quantitative data on recruitment of homes and individuals is being collected. For homes in the intervention arm, data on dose and fidelity of the intervention delivered; including individual rates of participation in exercise classes are collected. In the control homes, uptake and delivery of depression awareness training is monitored. These data will be combined with qualitative data from an in-depth study of a purposive sample of eight homes (six intervention and two control). Discussion: Although process evaluations are increasingly funded alongside trials, it is still rare to see the findings published, and even rarer to see the protocol for such an evaluation published. Process evaluations have the potential to assist in interpreting and understanding trial results as well as informing future roll-outs of interventions. If such evaluations are funded they should also be reported and reviewed in a similar way to the trial outcome evaluation

Survey of the quality of experimental design, statistical analysis and reporting of research using animals

For scientific, ethical and economic reasons, experiments involving animals should be appropriately designed, correctly analysed and transparently reported. This increases the scientific validity of the results, and maximises the knowledge gained from each experiment. A minimum amount of relevant information must be included in scientific publications to ensure that the methods and results of a study can be reviewed, analysed and repeated. Omitting essential information can raise scientific and ethical concerns. We report the findings of a systematic survey of reporting, experimental design and statistical analysis in published biomedical research using laboratory animals. Medline and EMBASE were searched for studies reporting research on live rats, mice and non-human primates carried out in UK and US publicly funded research establishments. Detailed information was collected from 271 publications, about the objective or hypothesis of the study, the number, sex, age and/or weight of animals used, and experimental and statistical methods. Only 59% of the studies stated the hypothesis or objective of the study and the number and characteristics of the animals used. Appropriate and efficient experimental design is a critical component of high-quality science. Most of the papers surveyed did not use randomisation (87%) or blinding (86%), to reduce bias in animal selection and outcome assessment. Only 70% of the publications that used statistical methods described their methods and presented the results with a measure of error or variability. This survey has identified a number of issues that need to be addressed in order to improve experimental design and reporting in publications describing research using animals. Scientific publication is a powerful and important source of information; the authors of scientific publications therefore have a responsibility to describe their methods and results comprehensively, accurately and transparently, and peer reviewers and journal editors share the responsibility to ensure that published studies fulfil these criteria

Marine microalgae as a potential source of single cell protein (SCP)

[Abstract] The marine microalgae Tetraselmis suecica, Isochrysis galbana, Dunaliella tertiolecta and Chlorella stigmatophora are good biological sources of single cell protein (SCP). Protein content accounts for 39.12%–54.20% of the dry matter, D. tertiolecta having the highest. Lysine values are between 3.67 and 4.52 g/100 g of protein, and thus are higher than those for freshwater species. The total nucleic acid content is less than 7% of the dry matter; this value is definitely lower than that for yeasts or bacteria, commonly used as SCP sources. Amino acid profiles of the four species are very similar and comparable to the FAO reference protein, buth with a low content of methionine and cystine and a high content of lysine. The MEAA indices are between 81 and 84.98, without significant differences among the four species. Marine microalgae can be used as a potential SCP source

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species

Genes in durophage intersection set at 15 dpf. This is a comma separated table of the genes in the 15 dpf durophage intersection set. Given are edgeR results for each pairwise comparison. Columns indicating whether a gene is included in the intersection set at a threshold of 1.5 or 2 fold are provided. (CSV 13 kb