Search

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Aging is a biological process characterized by the progressive functional decline of many interrelated physiological systems. In particular, aging is associated with the development of a systemic state of low-grade chronic inflammation (inflammaging), and with progressive deterioration of metabolic function. Systems biology has helped in identifying the mediators and pathways involved in these phenomena, mainly through the application of high-throughput screening methods, valued for their molecular comprehensiveness. Nevertheless, inflammation and metabolic regulation are dynamical processes whose behavior must be understood at multiple levels of biological organization (molecular, cellular, organ, and system levels) and on multiple time scales. Mathematical modeling of such behavior, with incorporation of mechanistic knowledge on interactions between inflammatory and metabolic mediators, may help in devising nutritional interventions capable of preventing, or ameliorating, the age-associated functional decline of the corresponding systems. © 2014 The Authors.

Nutrigenetic research examines the effects of inter-individual differences in genotype on responses to nutrients and other food components, in the context of health and of nutrient requirements. A practical application of nutrigenetics is the use of personal genetic information to guide recommendations for dietary choices that are more efficacious at the individual or genetic subgroup level relative to generic dietary advice. Nutrigenetics is unregulated, with no defined standards, beyond some commercially adopted codes of practice. Only a few official nutrition-related professional bodies have embraced the subject, and, consequently, there is a lack of educational resources or guidance for implementation of the outcomes of nutrigenetic research. To avoid misuse and to protect the public, personalised nutrigenetic advice and information should be based on clear evidence of validity grounded in a careful and defensible interpretation of outcomes from nutrigenetic research studies. Evidence requirements are clearly stated and assessed within the context of state-of-the-art 'evidence-based nutrition'. We have developed and present here a draft framework that can be used to assess the strength of the evidence for scientific validity of nutrigenetic knowledge and whether 'actionable'. In addition, we propose that this framework be used as the basis for developing transparent and scientifically sound advice to the public based on nutrigenetic tests. We feel that although this area is still in its infancy, minimal guidelines are required. Though these guidelines are based on semi-quantitative data, they should stimulate debate on their utility. This framework will be revised biennially, as knowledge on the subject increases. © 2017 The Author(s).

Pooled analysis of secondary data increases the power of research and enables scientific discovery in nutritional epidemiology. Information on study characteristics that determine data quality is needed to enable correct reuse and interpretation of data. This study aims to define essential quality characteristics for data from observational studies in nutrition. First, a literature review was performed to get an insight on existing instruments that assess the quality of cohort, case-control, and cross-sectional studies and dietary measurement. Second, 2 face-to-face workshops were organized to determine the study characteristics that affect data quality. Third, consensus on the data descriptors and controlled vocabulary was obtained. From 4884 papers retrieved, 26 relevant instruments, containing 164 characteristics for study design and 93 characteristics for measurements, were selected. The workshop and consensus process resulted in 10 descriptors allocated to "study design" and 22 to "measurement" domains. Data descriptors were organized as an ordinal scale of items to facilitate the identification, storage, and querying of nutrition data. Further integration of an Ontology for Nutrition Studies will facilitate interoperability of data repositories. © 2017 American Society for Nutrition.

Background: The apolipoprotein E (APOE) risk allele (e4) is associated with higher total cholesterol (TC), amplified response to saturated fatty acid (SFA) reduction, and increased cardiovascular disease. Although knowledge of gene risk may enhance dietary change, it is unclear whether e4 carriers would benefit from gene-based personalized nutrition (PN). Objectives: The aims of this study were to 1) investigate interactions between APOE genotype and habitual dietary fat intake and modulations of fat intake on metabolic outcomes; 2) determine whether gene-based PN results in greater dietary change than do standard dietary advice (level 0) and nongene-based PN (levels 1-2); and 3) assess the impact of knowledge of APOE risk (risk: E4+, nonrisk: E42) on dietary change after gene-based PN (level 3). Design: Individuals (n = 1466) recruited into the Food4Me pan- European PN dietary intervention study were randomly assigned to 4 treatment arms and genotyped for APOE (rs429358 and rs7412). Diet and dried blood spot TC and v-3 (n-3) index were determined at baseline and after a 6-mo intervention. Data were analyzed with the use of adjusted general linear models. Results: Significantly higher TC concentrations were observed in E4+ participants than in E42 (P , 0.05). Although there were no significant differences in APOE response to gene-based PN (E4+ compared with E42), both groups had a greater reduction in SFA (percentage of total energy) intake than at level 0 (mean 6 SD: E4+, 20.72% 6 0.35% compared with 21.95% 6 0.45%, P = 0.035; E42, 20.31% 6 0.20% compared with 21.68% 6 0.35%, P = 0.029). Gene-based PN was associated with a smaller reduction in SFA intake than in nongene-based PN (level 2) for E42 participants (21.68% 6 0.35% compared with 22.56% 6 0.27%, P = 0.025). Conclusions: The APOE e4 allele was associated with higher TC. Although gene-based PN targeted to APOE was more effective in reducing SFA intake than standard dietary advice, there was no difference between APOE "risk" and "nonrisk" groups. Furthermore, disclosure of APOE nonrisk may have weakened dietary response to PN. This trial was registered at clinicaltrials.gov as NCT01530139. Am J Clin Nutr 2016;104:827-36. © 2016 American Society for Nutrition.

Managing paleoscience data is highly challenging to the multiplicity of actors in play, types of sampling, analysis, post-analysis treatments, statistics etc. However, a well-structured curating of data would permit innovative developments based on data and/or sample re-use, such as meta-analysis or the development of new proxies on previously studied cores. In this paper, we will present two recent initiatives that allowed us tackling this objective at a French national level: the “National Cyber Core Repository” (NCCR) and the “LTER-France retro-observatory” (ROZA).NCCR was developed under the umbrella of the French National Center fo Coring and Drilling (C2FN) thanks to the national excellence equipment project CLIMCOR. It aims at gathering on a unique website the locations and metadata of any scientific coring/drilling performed by French teams or using French facilities, whatever the type of archive it is (lake/marine sediment; ice etc.). It uses international standard, notably IGSN (for samples), ORCID (for persons) and DOI (for campaigns). NCC follows the INSPIRE ISO 19115 standard in order to catalogue the data. For continental sediment, NCCR may be fed directly on the field through a specifically developed mobile application.Based on NCCR, further initiatives may be led. In particular, under the umbrella of LTER-France (Long Term Ecological Research), we developed ROZA in order to facilitate the re-use of data and samples. Here the idea is to capitalise the knowledge on a given lake from which several sediment cores can be taken through time. In that aim we selected at least one lake from each of the 13 areas composing the network LTER-France. To enter the database, a set of mandatory data must be provided under a pre-determined format. In that case, the insertion of ROZA within the network LTER will favor to use of paleodata by non-paleodata scientists, in particular ecologists.

Recommended dietary allowances for micronutrients fluctuate noticeably within European Union countries. The Network of Excellence EURRECA (EURopean micronutrient RECommendations Aligned) aims at harmonising micronutrient intake recommendations through population groups. The lack of proper markers of status for some micronutrients limits progress in this area: metabolomics could help identifying such new markers. We developed an original metabolomic strategy in order to monitor the largest fraction of a list of >270 metabolites known to be influenced by the micronutrients of interest. To improve the coverage of these metabolites in plasma, a multi platform approach was performed using both liquid and gas chromatography coupled to mass spectrometry. A sample preparation protocol based on a three-step plasma fractionation has been set up, using both liquid and solid phase extractions. Four fractions were obtained containing respectively polar metabolites, neutral lipids, free fatty acids and polar lipids. Recoveries were determined using spiked plasma samples, and the advantages and drawbacks of the fractionation method compared to a commonly used single preparation step method were investigated in terms of metabolites detection and robustness. Fractionation improved coverage of the endogenous metabolome more than twice in terms of extracted features, allowing to identify 90 metabolites. © 2012 Springer Science+Business Media, LLC.

Intracellular accumulation of glycerol is essential for yeast cells to survive hyperosmotic stress. Upon hyperosmotic stress the gene expression of enzymes in the glycerol pathway is strongly induced. Recently, however, it was shown that this gene-expression response is not essential for survival of an osmotic shock [Mettetal JT et al. (2008) Science 319: 482-484 and Westfall PJ et al. (2008) Proc Natl Acad Sci 105: 12212-12217]. Instead, pure metabolic adaptation can rescue the yeast. The existence of two alternative mechanisms urged the question which of these mechanisms dominates time-dependent adaptation of wild-type yeast to osmotic stress under physiological conditions. The regulation of the glycerol pathway was analysed in aerobic, glucose-limited cultures upon addition of 1 M of sorbitol, leading to a hyperosmotic shock. In agreement with earlier studies, the mRNA levels of the glycerol-producing enzymes as well as their catalytic capacities increased. Qualitatively this induction followed a similar time course to the increase of the glycerol flux. However, a quantitative regulation analysis of the data revealed an initial regulation by metabolism alone. After only a few minutes gene expression came into play, but even after an hour, 80% of the increase in the glycerol flux was explained by metabolic changes in the cell, and 20% by induction of gene expression. This demonstrates that the novel metabolic mechanism is not just a secondary rescue mechanism, but the most important mechanism to regulate the glycerol flux under physiological conditions. Copyright (C) 2010 John Wiley & Sons, Ltd.

In this study, the authors investigated how the glycolytic flux was regulated in time upon nitrogen starvation of cells with different growth histories. We have compared cells grown in glucose-limited chemostat cultures under respiratory conditions (low dilution rate of 0.1/h) to cells grown under respirofermentative conditions (high dilution rate of 0.35/h). The fermentative capacity was lower in cells grown under respiratory conditions than in cells grown under respirofermentative conditions, yet more resilient to prolonged nitrogen starvation. The time profiles revealed that the fermentative capacity even increased in cells grown under respiratory conditions during the first hours of nitrogen starvation. In cells grown under respirofermentative conditions the fermentative capacity decreased from the onset of nitrogen starvation. We have applied timedependent Regulation Analysis to follow the fermentative capacity during nitrogen starvation. In both experiments, diverse categories of regulation were found. However, in the cells grown under respiratory conditions regulation was predominantly metabolic, whereas in the cells grown under respirofermentative conditions hierarchical regulation was dominant. To study the metabolic regulation, concentrations of intracellular metabolites, including allosteric regulators, were measured. The obtained results can explain some aspects of the metabolic regulation, but not all. © The Institution of Engineering and Technology 2010.

Diet-quality scores (DQS), which are developed across the globe, are used to define adherence to specific eating patterns and have been associated with risk of coronary heart disease and type-II diabetes. We explored the association between five diet-quality scores (Healthy Eating Index, HEI; Alternate Healthy Eating Index, AHEI; MedDietScore, MDS; PREDIMED Mediterranean Diet Score, P-MDS; Dutch Healthy Diet-Index, DHDI) and markers of metabolic health (anthropometry, objective physical activity levels (PAL), and dried blood spot total cholesterol (TC), total carotenoids, and omega-3 index) in the Food4Me cohort, using regression analysis. Dietary intake was assessed using a validated Food Frequency Questionnaire. Participants (n = 1480) were adults recruited from seven European Union (EU) countries. Overall, women had higher HEI and AHEI than men (p < 0.05), and scores varied significantly between countries. For all DQS, higher scores were associated with lower body mass index, lower waist-to-height ratio and waist circumference, and higher total carotenoids and omega-3-index (p trends < 0.05). Higher HEI, AHEI, DHDI, and P-MDS scores were associated with increased daily PAL, moderate and vigorous activity, and reduced sedentary behaviour (p trend < 0.05). We observed no association between DQS and TC. To conclude, higher DQS, which reflect better dietary patterns, were associated with markers of better nutritional status and metabolic health. © 2018 by the authors. Licensee MDPI, Basel, Switzerland. Chemicals/CAS: cholesterol, 57-88-5

In e-health intervention studies, there are concerns about the reliability of internet-based, self-reported (SR) data and about the potential for identity fraud. This study introduced and tested a novel procedure for assessing the validity of internet-based, SR identity and validated anthropometric and demographic data via measurements performed face-to-face in a validation study (VS). Participants (n = 140) from seven European countries, participating in the Food4Me intervention study which aimed to test the efficacy of personalised nutrition approaches delivered via the internet, were invited to take part in the VS. Participants visited a research centre in each country within 2 weeks of providing SR data via the internet. Participants received detailed instructions on how to perform each measurement. Individual’s identity was checked visually and by repeated collection and analysis of buccal cell DNA for 33 genetic variants. Validation of identity using genomic information showed perfect concordance between SR and VS. Similar results were found for demographic data (age and sex verification). We observed strong intra-class correlation coefficients between SR and VS for anthropometric data (height 0.990, weight 0.994 and BMI 0.983). However, internet-based SR weight was under-reported (Δ −0.70 kg [−3.6 to 2.1], p

International audience; Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative ‘coordination of standards in metabolomics’ (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities’ participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

International audience; The development of a chronic, low grade, inflammatory status named "inflammaging" is a major characteristic of ageing, which plays a critical role in the pathogenesis of age-related diseases. Inflammaging is both local and systemic, and a variety of organs and systems contribute inflammatory stimuli that accumulate lifelong. The NU-AGE rationale is that a one year Mediterranean whole diet (considered by UNESCO a heritage of humanity), newly designed to meet the nutritional needs of the elderly, will reduce inflammaging in fully characterized subjects aged 65-79 years of age, and will have systemic beneficial effects on health status (physical and cognitive). Before and after the dietary intervention a comprehensive set of analyses, including omics (transcriptomics, epigenetics, metabolomics and metagenomics) will be performed to identify the underpinning molecular mechanisms. NU-AGE will set up a comprehensive database as a tool for a systems biology approach to inflammaging and nutrition. NU-AGE is highly interdisciplinary, includes leading research centres in Europe on nutrition and ageing, and is complemented by EU multinational food industries and SMEs, interested in the production of functional and enriched/advanced traditional food tailored for the elderly market, and European Federations targeting policy makers and major stakeholders, from consumers to EU Food & Drink Industries.

BACKGROUND: Causes and consequences of the complex changes in lipids occurring in the metabolic syndrome are only partly understood. Several interconnected processes are deteriorating, which implies that multi-target approaches might be more successful than strategies based on a limited number of surrogate markers. Preparations from Chinese Medicine (CM) systems have been handed down with documented clinical features similar as metabolic syndrome, which might help developing new intervention for metabolic syndrome. The progress in systems biology and specific animal models created possibilities to assess the effects of such preparations. Here we report the plasma and liver lipidomics results of the intervention effects of a preparation SUB885C in apolipoprotein E3 Leiden cholesteryl ester transfer protein (ApoE*3Leiden.CETP) mice. SUB885C was developed according to the principles of CM for treatment of metabolic syndrome. The cannabinoid receptor type 1 blocker rimonabant was included as a general control for the evaluation of weight and metabolic responses. METHODOLOGY/PRINCIPAL FINDINGS: ApoE*3Leiden.CETP mice with mild hypercholesterolemia were divided into SUB885C-, rimonabant- and non-treated control groups. SUB885C caused no weight loss, but significantly reduced plasma cholesterol (-49%, p CONCLUSIONS: SUB885C, a multi-components preparation, is able to produce anti-atherogenic changes in lipids of the ApoE*3Leiden.CETP mice, which are comparable to those obtained with compounds belonging to known drugs (e.g. rimonabant, atorvastatin, niacin). This study successfully illustrated the power of lipidomics in unraveling intervention effects and to help finding new targets or ingredients for lifestyle-related metabolic abnormality

Obesity is a risk factor for cardiovascular diseases and type 2 diabetes especially when the fat is accumulated to central depots. Novel biomarkers are crucial to develop diagnostics for obesity and related metabolic disorders. We evaluated the associations between metabolite profiles (136 lipid components, 12 lipoprotein subclasses, 17 low-molecular-weight metabolites, 12 clinical markers) and 28 phenotype parameters (including different body fat distribution parameters such as android (A), gynoid (G), abdominal visceral (VAT), subcutaneous (SAT) fat) in 215 plasma/serum samples from healthy overweight men (n=32) and women (n=83) with central obesity. (Partial) correlation analysis and partial least squares (PLS) regression analysis showed that only specific metabolites were associated to A:G ratio, VAT, and SAT, respectively. These association patterns were gender dependent. For example, insulin, cholesterol, VLDL, and certain triacylglycerols (TG 54:1-3) correlated to VAT in women, while in men VAT was associated with TG 50:1-5, TG 55:1, phosphatidylcholine (PC 32:0), and VLDL ((X)L). Moreover, multiple regression analysis revealed that waist circumference and total fat were sufficient to predict VAT and SAT in women. In contrast, only VAT but not SAT could be predicted in men and only when plasma metabolites were included, with PC 32:0 being most strongly associated with VAT. These findings collectively highlight the potential of metabolomics in obesity and that gender differences need to be taken into account for novel biomarker and diagnostic discovery for obesity and metabolic disorders. © Copyright 2012 Mary Ann Liebert, Inc.

The field of systems biology is often held back by difficulties in obtaining comprehensive, high-quality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae, a widely used model organism that is also used in the production of fuels, chemicals, food ingredients and pharmaceuticals. With the current focus on biofuels and sustainability, there is much interest in harnessing this species as a general cell factory. In this study, we characterized two yeast strains, under two standard growth conditions. We ensured the high quality of the experimental data by evaluating a wide range of sampling and analytical techniques. Here we show significant differences in the maximum specific growth rate and biomass yield between the two strains. On the basis of the integrated analysis of the high-throughput data, we hypothesize that differences in phenotype are due to differences in protein metabolism. © 2010 Macmillan Publishers Limited. All rights reserved.

Background: Lipids are known to play crucial roles in the development of life-style related risk factors such as obesity, dyslipoproteinemia, hypertension and diabetes. The first selective cannabinoid-1 receptor blocker rimonabant, an anorectic anti-obesity drug, was frequently used in conjunction with diet and exercise for patients with a body mass index greater than 30 kg/m2 with associated risk factors such as type II diabetes and dyslipidaemia in the past. Less is known about the impact of this drug on the regulation of lipid metabolism in plasma and liver in the early stage of obesity. Methodology/Principal Findings: We designed a four-week parallel controlled intervention on apolipoprotein E3 Leiden cholesteryl ester transfer protein (ApoE&z.ast;3Leiden.CETP) transgenic mice with mild overweight and hypercholesterolemia. A liquid chromatography-linear ion trap-Fourier transform ion cyclotron resonance-mass spectrometric approach was employed to investigate plasma and liver lipid responses to the rimonabant intervention. Rimonabant was found to induce a significant body weight loss (9.4%, p

Background Being able to visualize multivariate biological treatment effects can be insightful. However the axes in visualizations are often solely defined by variation and thus have no biological meaning. This makes the effects of treatment difficult to interpret. Methods A statistical visualization method is presented, which analyses and visualizes the effects of treatment in individual subjects. The visualization is based on predefined biological processes as determined by systems-biological datasets (metabolomics proteomics and transcriptomics). This allows one to evaluate biological effects depending on shifts of either groups or subjects in the space predefined by the axes, which illustrate specific biological processes. We built validated multivariate models for each axis to represent several biological processes. In this space each subject has his or her own score on each axis/process, indicating to which extent the treatment affects the related process. Results The health space model was applied to visualize the effects of a nutritional intervention, with the goal of applying diet to improve health. The model was therefore named the 'health space' model. The 36 study subjects received a 5-week dietary intervention containing several anti-inflammatory ingredients. Plasma concentrations of 79 proteins and 145 metabolites were quantified prior to and after treatment. The principal processes modulated by the intervention were oxidative stress, inflammation, and metabolism. These processes formed the axes of the 'health space'. The approach distinguished the treated and untreated groups, as well as two different response subgroups. One subgroup reacted mainly by modulating its metabolic stress profile, while a second subgroup showed a specific inflammatory and oxidative response to treatment. Conclusions The 'health space' model allows visualization of multiple results and to interpret them. The model presents treatment group effects, subgroups and individual responses.