Community-wide plasmid gene mobilization and selection.

Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.

Stability and robustness of blood variables in an antidoping context.

Introduction:  With the setting up of the newly Athlete's Biological Passport antidoping programme, novel guidelines have been introduced to guarantee results beyond reproach. We investigated in this context, the effect of storage time on the variables commonly measured for the haematological passport. We also wanted to assess for these variables, the within and between analyzer variations. Methods:  Blood samples were obtained from top level male professional cyclists (27 samples for the first part of the study and 102 for the second part) taking part to major stage races. After collection, they were transported under refrigerated conditions (2 °C < T < 12 °C), delivered to the antidoping laboratory, analysed and then stored at approximately 4 °C to conduct analysis at different time points up to 72 h after delivery. A mixed-model procedure was used to determine the stability of the different variables. Results:  As expected haemoglobin concentration was not affected by storage and showed stability for at least 72 h. Under the conditions of our investigation, the reticulocytes percentage showed a much better stability than previous published data (> 48 h) and the technical comparison of the haematology analyzer demonstrated excellent results. Conclusion:  In conclusion, our data clearly demonstrate that as long as the World Anti-Doping Agency's guidelines are followed rigorously, all blood results reach the quality level required in the antidoping context.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-β signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.

Effects of exercise on the isoelectric patterns of erythropoietin.

OBJECTIVES: Recombinant erythropoietin has a strong impact on aerobic power and is therefore one of the most potent doping agents in endurance sports. The anti-doping control of this synthetic hormone relies on the detection, in the urine, of its isoelectric pattern, which differs from that of the corresponding natural hormone, the latter being typically more acidic than the former. However, a small number of natural urinary patterns, referred to as "atypical patterns," are less acidic than the dominant form. Based on anecdotal evidence, the occurrence of such patterns seems to be related to particular strenuous exercises. This study aimed to demonstrate this relation using a strenuous exercise protocol. DESIGN: Seven athletes took part in a training protocol including a series of supramaximal short-duration exercises. Urine and blood samples were collected throughout the protocols. SETTINGS: World Cycling Center, Aigle, Switzerland, and research laboratories. PARTICIPANTS: Seven top-level athletes (cyclists) were involved in this study. MAIN OUTCOME MEASURES: Erythropoietin (EPO) isoelectric patterns were obtained by submitting blood and urine samples to isoelectric focusing. Additional protein dosages were performed. RESULTS: Supramaximal short-duration exercises induced the transformation of typical urinary natural EPO patterns into atypical ones. None of the obtained atypical patterns fulfilled the 3 criteria mandatory for reporting an adverse analytical finding. Serum EPO patterns were not affected by the exercises that caused the transformation of urinary patterns. CONCLUSION: An exercise-induced transient renal dysfunction is proposed as a hypothetic explanation for these observations that rely on parallel investigations of proteinuria in the same samples.

Selectome update: quality control and computational improvements to a database of positive selection.

Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have benchmarked and implemented a thorough quality control procedure on multiple sequence alignments, aiming to provide minimum false-positive results. We have also improved the computational efficiency of the branch-site test implementation, allowing larger data sets and more frequent updates. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees. A total of 6810 gene trees have some evidence of positive selection. Finally, the web interface has been improved to be more responsive and to facilitate searches and browsing.

The carbon isotope composition of natural SiC (moissanite) from the Earth's mantle: New discoveries from ophiolites

Moissanite (natural SiC) has been recovered from podiform chromitites of several ophiolite complexes, including the Luobusa and Donqiao ophiolites in Tibet, the Semail ophiolite in Oman and the United Arab Emirates, and the Ray-Iz ophiolite of the Polar Urals, Russia. Taking these new occurrences with the numerous earlier reports of moissanite in diamondiferous kimberlites leads to the conclusion that natural SiC is a widespread mineral in the Earth's mantle, which implies at least locally extremely low redox conditions. The ophiolite moissanite grains are mostly fragments (20 to 150 mu m) with one or more crystal faces, but some euhedral hexagonal grains have also been recovered. Twinned crystals are common in chromitites from the Luobusa ophiolite. The moissanite is rarely colorless, more commonly light bluish-gray to blue or green. Many grains contain inclusions of native Si and Fe-Si alloys (FeSi(2), Fe(3)Si(7)). Secondary ion mass spectrometric (SIMS) analysis shows that the ophiolite-hosted moissanite has a distinctive (13)C-depleted isotopic composition (delta(13)C from -18 to -35 parts per thousand, n=36), much lighter than the main carbon reservoir in the upper mantle (delta(13)C near -5 parts per thousand). The compiled data from moissanite from kimberlites and other mantle settings share the characteristic of strongly (13)C-depleted isotopic composition. This suggests that moissanite originates from a separate carbon reservoir in the mantle or that its formation involved strong isotopic fractionation. The degree of fractionation needed to produce the observed moissanite compositions from the main C-reservoir would be unrealistically large at the high temperatures required for moissanite formation. Subduction of biogenic carbonaceous material could potentially satisfy both the unusual isotopic and redox constraints on moissanite formation, but this material would need to stay chemically isolated from the upper mantle until it reached the high-T stability field of moissanite. The origin of moissanite in the mantle is still unsolved, but all evidence from the upper mantle indicates that it cannot have formed there, barring special and local redox conditions. We suggest, alternatively, that moissanite may have formed in the lower mantle, where the existence of (13)C-depleted carbon is strongly supported by studies of extraterrestrial carbon (Mars, Moon, meteorites). (C) 2009 Elsevier B. V. All rights reserved.

Time for change: a roadmap to guide the implementation of the World Anti-Doping Code 2015

A medical and scientific multidisciplinary consensus meeting was held from 29 to 30 November 2013 on Anti-Doping in Sport at the Home of FIFA in Zurich, Switzerland, to create a roadmap for the implementation of the 2015 World Anti-Doping Code. The consensus statement and accompanying papers set out the priorities for the antidoping community in research, science and medicine. The participants achieved consensus on a strategy for the implementation of the 2015 World Anti-Doping Code. Key components of this strategy include: (1) sport-specific risk assessment, (2) prevalence measurement, (3) sport-specific test distribution plans, (4) storage and reanalysis, (5) analytical challenges, (6) forensic intelligence, (7) psychological approach to optimise the most deterrent effect, (8) the Athlete Biological Passport (ABP) and confounding factors, (9) data management system (Anti-Doping Administration & Management System (ADAMS), (10) education, (11) research needs and necessary advances, (12) inadvertent doping and (13) management and ethics: biological data. True implementation of the 2015 World Anti-Doping Code will depend largely on the ability to align thinking around these core concepts and strategies. FIFA, jointly with all other engaged International Federations of sports (Ifs), the International Olympic Committee (IOC) and World Anti-Doping Agency (WADA), are ideally placed to lead transformational change with the unwavering support of the wider antidoping community. The outcome of the consensus meeting was the creation of the ad hoc Working Group charged with the responsibility of moving this agenda forward.

Analytical progresses of the International Olympic Committee and World Anti-Doping Agency Olympic laboratories.

The Summer Olympic Games constitute the biggest concentration of human sports and activities in a particular place and time since 776 BCE, when the written history of the Olympic Games in Olympia began. Summer and Winter Olympic anti-doping laboratories, accredited by the International Olympic Committee in the past and the World Anti-Doping Agency in the present times, acquire worldwide interest to apply all new analytical advancements in the fight against doping in sports, hoping that this major human event will not become dirty by association with this negative phenomenon. This article summarizes the new analytical progresses, technologies and knowledge used by the Olympic laboratories, which for the vast majority of them are, eventually, incorporated into routine anti-doping analysis.

Recent advances in biocuration: meeting report from the fifth International Biocuration Conference.

The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration's (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions with journals. The conference is an essential part of the ISB's goal to support exchanges among members of the biocuration community. Next year's conference will be held in Cambridge, UK, from 7 to 10 April 2013. In the meanwhile, the ISB website provides information about the society's activities (http://biocurator.org), as well as related events of interest.

Prevalence, predictors, and consequences of long-term refusal of antipsychotic treatment in first-episode psychosis.

OBJECTIVE: Studies investigating medication adherence in psychosis are limited by the need of a certain degree of medication adherence and the inclusion of mostly multiple-episode patients. By contrast, noninformed consent, epidemiological studies in first-episode psychosis (FEP) allow the assessment of an important subgroup of patients who persistently refuse antipsychotic medication and thereby never receive an adequate antipsychotic trial. The present study aims to assess the prevalence and predictors of such a "medication refusal" subgroup and its association with illness outcome. METHODS: The present file audit study assessed medication adherence in an epidemiological cohort of 605 FEP patients who were treated within the Early Psychosis Prevention and Intervention Centre for up to 18 months. Medication adherence was categorized into full adherence, nonadherence, and persistent medication refusal. Predictors were analyzed using logistic regression models. RESULTS: During the 18-month treatment period, 204 patients (33.7%) were fully adherent, 287 (47.4%) displayed at least 1 phase of nonadherence, and 114 patients (18.8%) were persistent medication refusers. Poor premorbid functioning, comorbid substance use, and poor insight predicted both medication refusal and nonadherence; a forensic history and no previous contact to psychiatric care were specifically predictive of medication refusal. With respect to illness outcome, nonadherent patients were worse off when compared with fully adherent patients, and medication refusers were even worse off compared with nonadherent patients. CONCLUSIONS: Within a nonselected epidemiological FEP cohort, almost 20% of patients are persistent medication refusers. The found predictors may help to identify the individual risk of persistent medication refusal and may enable an early (preventive) treatment adaptation.

Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals.

This short perspective explores some ways in which new genomic methodologies impact the study of endocrine signaling. Emphasis is put on the impact of studying species which are not molecular biology models. This opens the door to using knowledge molecular endocrinology in areas of biology as distant as conservation biology, as well as enriching endocrinology with information from biodiversity and natural variation.

Comparative modular analysis of gene expression in vertebrate development

The focus of my PhD research was the concept of modularity. In the last 15 years, modularity has become a classic term in different fields of biology. On the conceptual level, a module is a set of interacting elements that remain mostly independent from the elements outside of the module. I used modular analysis techniques to study gene expression evolution in vertebrates. In particular, I identified ``natural'' modules of gene expression in mouse and human, and I showed that expression of organ-specific and system-specific genes tends to be conserved between such distance vertebrates as mammals and fishes. Also with a modular approach, I studied patterns of developmental constraints on transcriptome evolution. I showed that none of the two commonly accepted models of the evolution of embryonic development (``evo-devo'') are exclusively valid. In particular, I found that the conservation of the sequences of regulatory regions is highest during mid-development of zebrafish, and thus it supports the ``hourglass model''. In contrast, events of gene duplication and new gene introduction are most rare in early development, which supports the ``early conservation model''. In addition to the biological insights on transcriptome evolution, I have also discussed in detail the advantages of modular approaches in large-scale data analysis. Moreover, I re-analyzed several studies (published in high-ranking journals), and showed that their conclusions do not hold out under a detailed analysis. This demonstrates that complex analysis of high-throughput data requires a co-operation between biologists, bioinformaticians, and statisticians.

Circulating miRNAs: a new generation of anti-doping biomarkers

MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. Cell-free miRNAs detected in blood plasma are used as specific and sensitive markers of physiological processes and some diseases. Circulating miRNAs are highly stable in body fluids, for example plasma. Therefore, profiles of circulating miRNAs have been investigated for potential use as novel, non-invasive anti-doping biomarkers. This review describes the biological mechanisms underlying the variation of circulating miRNAs, revealing that they have great potential as a new class of biomarker for detection of doping substances. The latest developments in extraction and profiling technology, and the technical design of experiments useful for anti-doping, are also discussed. Longitudinal measurements of circulating miRNAs in the context of the athlete biological passport are proposed as an efficient strategy for the use of these new markers. The review also emphasizes potential challenges for the translation of circulating miRNAs from research into practical anti-doping applications.

2011 lAAF World Championships in Daegu: blood tests for all athletes in the framework of the Athlete Biological Passport.

The 2011 International Association of Athletics Federation (IAAF) World Championships took place in Daegu, Korea. For the first time, all athletes were blood tested prior to the competition in order to give a clear signal to the world athletic community of the wish to enter into the era of the Athlete Biological Passport and fight against doping in their sport. The hematological parameters were measured on site. Thus, a mobile-accredited laboratory for blood testing was created in Daegu. Two serum tubes were collected for clinical chemistry and hormonal analyses in order to build the bases of the endocrine and the androgen (steroid) modules of the Athlete Biological Passport in blood. This paper describes some of the main challenges the project faced with regard to the large number of athletes, competing in different disciplines, and the logistic problems that had to be solved for smart implementation of one of the most complex operations organized in the last decade in the fight against doping.