Lake levels in the southern Bolivian Altiplano (19°-21°S) during the Late Glacial based on diatom studies

This study is focused on the endorheic Uyuni-Coipasa Basin located in the southern Bolivian Altiplano. Stratigraphical and fossil diatom studies based on a detailed radiocarbon chronology revealed six phases in water-level changes and paleosalinity variations. At 15,430 +- 80 yr B.P., lacustrine conditions settled in the southern Bolivian Altiplano. A saline lake, characterized by benthic meso-metasaline species, reached +4 m altitude above the present bottom of the basin. After 15,430 +- 80 yr B.P. the level rapidly rose to + 27 m, as suggested by a tychoplanktonic mesoline flora. Between 14,500 years and 13,000 years, finely lamited sediments at + 32 m contained successively a dominance of epiphytic mesosaline to hypersaline species and tychoplanktonic oligosaline diatoms, indicating weak fluctuations in water-level and salinity. At 13,000 years, strong changes in the diatom flora occurred: epiphytic oligo-hypersaline diatoms were replaced by planktonic meso-polysaline species. They indicate a deep salt lake (the lake level reached + 100 m). After 12,j000 yars, the lake level abruptly dropped, as suggested by fluviatile sediments with a benthic mesopolysaline diatom flora. The main lake was replaced by shallow saline ponds. A wet pulse occurred at 11,400 years, characterizad by low water level ( + 7 m) and high salinity. This lacustrine phase remained until 10,400 yr B.P. These data indicate changes in Precipitation minus Evaporation (P-E). Our regional interpretations are based on a comparison with the available data on the northern (Lake Titicaca) and southern (Lipez area) Bolivian Altiplano and on the northern Chilean Altiplano (Atacama Desert). (Résumé d'auteur)

La dernière transition glaciaire/interglaciaire des Andes tropicales sud (Bolivie) d'après l'étude des variations des niveaux lacustres et des fluctuations glaciaires

Une comparaison entre les variations des niveaux lacustres dans le bassin de Uyuni-Coipasa et les fluctuations glaciaires dans la Cordillère Orientale montre que les lacs et les glaciers ont simultanément enregistré les changements des précipitations. Un intense maximum lacustre (environ 13-12 14C ka BP) a eu lieu aux latitudes tropicales sud de la Bolivie, 4 000 à 6 000 ans avant le maximum lacustre de l'Afrique nord-équatoriale. (Résumé d'auteur

Goulphar: rapid access and expertise for standard two-color microarray normalization methods

BACKGROUND: Raw data normalization is a critical step in microarray data analysis because it directly affects data interpretation. Most of the normalization methods currently used are included in the R/BioConductor packages but it is often difficult to identify the most appropriate method. Furthermore, the use of R commands for functions and graphics can introduce mistakes that are difficult to trace. We present here a script written in R that provides a flexible means of access to and monitoring of data normalization for two-color microarrays. This script combines the power of BioConductor and R analysis functions and reduces the amount of R programming required. RESULTS: Goulphar was developed in and runs using the R language and environment. It combines and extends functions found in BioConductor packages (limma and marray) to correct for dye biases and spatial artifacts. Goulphar provides a wide range of optional and customizable filters for excluding incorrect signals during the pre-processing step. It displays informative output plots, enabling the user to monitor the normalization process, and helps adapt the normalization method appropriately to the data. All these analyses and graphical outputs are presented in a single PDF report. CONCLUSION: Goulphar provides simple, rapid access to the power of the R/BioConductor statistical analysis packages, with precise control and visualization of the results obtained. Complete documentation, examples and online forms for setting script parameters are available from

Livre blanc - Réussir avec un marketing responsable : les recettes gagnantes

Ce livre blanc synthétise les bonnes pratiques de marketing responsable : l’intégration des enjeux de la durabilité dans l’offre peut apporter une valeur ajoutée à la marque et/ou à l’entreprise, et permettre ainsi. de gagner en compétitivité dans un contexte où les consommateurs sont en attente d’actions sur ces sujets

A new genomic resource dedicated to wood formation in Eucalyptus

<p>Abstract</p> <p>Background</p> <p>Renowned for their fast growth, valuable wood properties and wide adaptability, <it>Eucalyptus </it>species are amongst the most planted hardwoods in the world, yet they are still at the early stages of domestication because conventional breeding is slow and costly. Thus, there is huge potential for marker-assisted breeding programs to improve traits such as wood properties. To this end, the sequencing, analysis and annotation of a large collection of expressed sequences tags (ESTs) from genes involved in wood formation in <it>Eucalyptus </it>would provide a valuable resource.</p> <p>Results</p> <p>We report here the normalization and sequencing of a cDNA library from developing <it>Eucalyptus </it>secondary xylem, as well as the construction and sequencing of two subtractive libraries (juvenile <it>versus </it>mature wood and <it>vice versa</it>). A total of 9,222 high quality sequences were collected from about 10,000 cDNA clones. The EST assembly generated a set of 3,857 wood-related unigenes including 2,461 contigs (Cg) and 1,396 singletons (Sg) that we named 'EUCAWOOD'. About 65% of the EUCAWOOD sequences produced matches with poplar, grapevine, <it>Arabidopsis </it>and rice protein sequence databases. BlastX searches of the Uniref100 protein database allowed us to allocate gene ontology (GO) and protein family terms to the EUCAWOOD unigenes. This annotation of the EUCAWOOD set revealed key functional categories involved in xylogenesis. For instance, 422 sequences matched various gene families involved in biosynthesis and assembly of primary and secondary cell walls. Interestingly, 141 sequences were annotated as transcription factors, some of them being orthologs of regulators known to be involved in xylogenesis. The EUCAWOOD dataset was also mined for genomic simple sequence repeat markers, yielding a total of 639 putative microsatellites. Finally, a publicly accessible database was created, supporting multiple queries on the EUCAWOOD dataset.</p> <p>Conclusion</p> <p>In this work, we have identified a large set of wood-related <it>Eucalyptus </it>unigenes called EUCAWOOD, thus creating a valuable resource for functional genomics studies of wood formation and molecular breeding in this economically important genus. This set of publicly available annotated sequences will be instrumental for candidate gene approaches, custom array development and marker-assisted selection programs aimed at improving and modulating wood properties.</p

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes

The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes. Three main projects are used, InterPro, CluSTr and GO Slim, to give an overview on families, domains, sites, and functions of the proteins from each of the complete genomes. Complete proteome analysis is available for a total of 89 proteome sets. A specifically designed application enables InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the databas

Blood Bacterial Profiles Associated With Human Immunodeficiency Virus Infection and Immune Recovery

[EN] Human immunodeficiency virus (HIV) infection impairs mucosal immunity and leads to bacterial translocation, fueling chronic inflammation and disease progression. While this is well established, questions remain about the compositional profile of the translocated bacteria, and to what extent it is influenced by antiretroviral therapy (ART). Using 16S ribosomal DNA targeted sequencing and shotgun proteomics, we showed that HIV increases bacterial translocation from the gut to the blood. HIV increased alpha diversity in the blood, which was dominated by aerobic bacteria belonging to Micrococcaceae (Actinobacteria) and Pseudomonadaceae (Proteobacteria) families, and the number of circulating bacterial proteins was also increased. Forty-eight weeks of ART attenuated this phenomenon. We found that enrichment with Lactobacillales order, and depletion of Actinobacteria class and Moraxellaceae and Corynebacteriacae families, were significantly associated with greater immune recovery and correlated with several inflammatory markers. Our findings suggest that the molecular cross talk between the host and the translocated bacterial products could influence ART-mediated immune recovery.This work was supported by the Instituto de Salud Carlos III (Plan Estatal de I+D+i 2013–2016, projects PI15/00345 and PI18/00154); the Fundación Asociación Española Contra el Cáncer within the European Research Era-NET aligning national/regional translational cancer research programs and activities program (grant AC17/00019) and cofinanced by the European Development Regional Fund; and Plan Estatal de I+D+i 2013–2016 (grant PT17/0019 to the Proteomics Facility of the Spanish National Center for BIotechnology)

The Gut Microbiota Regulates Intestinal CD4 T Cells Expressing RORγt and Controls Metabolic Disease

SummaryA high-fat diet (HFD) induces metabolic disease and low-grade metabolic inflammation in response to changes in the intestinal microbiota through as-yet-unknown mechanisms. Here, we show that a HFD-derived ileum microbiota is responsible for a decrease in Th17 cells of the lamina propria in axenic colonized mice. The HFD also changed the expression profiles of intestinal antigen-presenting cells and their ability to generate Th17 cells in vitro. Consistent with these data, the metabolic phenotype was mimicked in RORγt-deficient mice, which lack IL17 and IL22 function, and in the adoptive transfer experiment of T cells from RORγt-deficient mice into Rag1-deficient mice. We conclude that the microbiota of the ileum regulates Th17 cell homeostasis in the small intestine and determines the outcome of metabolic disease

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology