Simple rules for an efficient use of geographic information systems in molecular ecology

Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages

Neighbourhood socioeconomic deprivation and allostatic load : a multi-cohort study

Living in deprived neighbourhoods may have biological consequences, but few studies have assessed this empirically. We examined the association between neighbourhood deprivation and allostatic load, a biological marker of wear and tear, taking into account individual's socioeconomic position. We analysed data from three cohort studies (CoLaus-Switzerland; EPIPorto-Portugal; Whitehall II-UK) comprising 16,364 participants. We defined allostatic load using ten biomarkers of dysregulated metabolic, cardiovascular, and inflammatory systems (body mass index; waist circumference; total, high and low density lipoprotein cholesterol; trig lycerides; glucose; systolic and diastolic blood pressure; C-reactive protein). Mixed Poisson regression models were fitted to examine associations with neighbourhood deprivation (in quintiles, Q1-least deprived as reference). After adjustment for confounding variables, participants living in the most deprived quintile had 1.13 times higher allostatic load than those living in the least deprived quintile (Relative Risk, RR, for Q2 RR = 1.06, 95%CI 1.03-1.09; Q3 = 1.06, 1.03-1.10; Q4 = 1.09, 1.06-1.12; Q5 = 1.13, 1.09-1.16). This association was partially modified by individual's socioeconomic position, such that the relative risk was higher in participants with low socioeconomic position (Q5 vs Q11.16, 1.11-1.22) than those with high socioeconomic position (Q5 vs Q1 1.07, 1.11-1.13). Neighbourhood deprivation is associated with biological wear and tear, suggesting that neighbourhood-level interventions may yield health gains.Peer reviewe

Characterization of 37 Breed-Specific Single-Nucleotide Polymorphisms in Sheep

We identified 37 single-nucleotide polymorphisms (SNPs) in sheep and screened 16 individuals from 8 different sheep breeds selected throughout Europe. Population genetic measures based on the genotyping of about 30 sheep from the same 8 breeds are reported. To date, there are no sheep SNPs documented in the National Center for Biotechnology Information dbSNP database. Therefore, the markers presented here contribute significantly to those currently availabl

EMbaRC - A European Consortium of Microbial Resource Centres for Science & lnnovation

EMbaRC is an EU project funded under the Seventh Framework Programme, Research lnfrastructures action. lt aims to improve, coordinate and validate microbial Biological Resource Centres (BRC) delivery to European and lnternational researchers from both public and private sectors. Apart from the networking and research activities, EMbaRC offers EU-supported grants for Trans-national Access opportunities. Scientists who carry out research in Europe or Associated Countries can use EMbaRC infrastructures to support part of their research project. ln this presentation, the main achievements of the first year will be summarized. Networking activities allow i) an estimation of overlapping/uniqueness between the consortium holdings, ii) a deep analysis of strain deposit after publication, iii) a review of the training offered by the consortium in the collection management and associated tools (identification, data management, etc.), iv) an harmonisation of the quality manual, v) a first draft for a biosecurity code, and vi) establish the basis of a common strategy to increase the sustainability of BRCs. Joint Research activities focused in particular on storage of recalcitrant strains, DNA storage and species identification by new methods like mass spectrometry ... ln parallel, success stories are being gathered to support the idea that microbial collections contribute to the bioeconomy. Such achievements can be a way to increase the sustainability of collections, and some of them will be presented

Grants for trans-national access to leading European Microbial Biological Resource Centres (BRCs) - EMbaRC training and outreach programme

The EMbaRC Training and Outreach Programme (TOP) is an opportunity for scientists to stay atone of the EMbaRC centres to benefit from expert advice and to use advanced equipment to support part of their research project. EMbaRC will cover the bench fees, travel and subsistence costs. This unique opportunity for training in collection management, identification of bacteria and fungi by stateof-the-art techniques or phenotypic screening of a collection of strains is organised with the support of the Seventh Framework Programme, Research lnfrastructures Action

Industrial chicory genome gives insights into the molecular timetable of anther development and male sterility

Industrial chicory (Cichorium intybus var. sativum) is a biannual crop mostly cultivated for extraction of inulin, a fructose polymer used as a dietary fiber. F1 hybrid breeding is a promising breeding strategy in chicory but relies on stable male sterile lines to prevent self-pollination. Here, we report the assembly and annotation of a new industrial chicory reference genome. Additionally, we performed RNA-Seq on subsequent stages of flower bud development of a fertile line and two cytoplasmic male sterile (CMS) clones. Comparison of fertile and CMS flower bud transcriptomes combined with morphological microscopic analysis of anthers, provided a molecular understanding of anther development and identified key genes in a range of underlying processes, including tapetum development, sink establishment, pollen wall development and anther dehiscence. We also described the role of phytohormones in the regulation of these processes under normal fertile flower bud development. In parallel, we evaluated which processes are disturbed in CMS clones and could contribute to the male sterile phenotype. Taken together, this study provides a state-of-the-art industrial chicory reference genome, an annotated and curated candidate gene set related to anther development and male sterility as well as a detailed molecular timetable of flower bud development in fertile and CMS lines

A database of naturally occurring human urinary peptides and proteins for use in clinical applications

Owing to its availability, ease of collection and correlation with (patho-) physiology, urine is an attractive source for clinical proteomics. However, the lack of comparable datasets from large cohorts has greatly hindered development in this field. Here we report the establishment of a high resolution proteome database of naturally occurring human urinary peptides and proteins - ranging from 800-17,000 Da - from over 3,600 individual samples using capillary electrophoresis coupled to mass spectrometry, yielding an average of 1,500 peptides per sample. All processed data were deposited in an SQL database, currently containing 5,010 relevant unique urinary peptides that serve as classifiers for diagnosis and monitoring of diseases, including kidney and vascular diseases. Of these, 352 have been sequenced to date. To demonstrate the applicability of this database, two examples of disease diagnosis were provided: For renal damage diagnosis, patients with a specific renal disease were identified with high specificity and sensitivity in a blinded cohort of 131 individuals. We further show definition of biomarkers specific for immunosuppression and complications after transplantation (Kaposi's sarcoma). Due to its high information content, this database will be a powerful tool for the validation of biomarkers for both renal and non-renal diseases

AdaptMap: exploring goat diversity and adaptation

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