Molecular biodiversity
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB43928 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A collection of MS/MS data 112 microbial species. #BiodiversityLibrary
2015-02-26 | MSV000079053 | MassIVE
Project description:<p>Functional ecology and biodiversity lack integrative reference data that combine the assessment of traits at different levels. Here, we integrate data from 16 field samples of complex thallose liverworts (order Marchantiales) collected from biological soil crust communities in Southern Sweden and Germany at three levels: (1) bioimaging (morphometric measurements from macro- and microscopy), (2) metabolomics (molecular computations performed on liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) data) and (3) DNA marker sequencing. These data are used to construct a reference framework including a proposed naming scheme for the estimation of molecular traits and for demonstrating the systematic and standardized extraction of phenotypic and molecular traits for integration into the plant trait database TRY. Phylogenetic trees and partitioning around medoids are used to demonstrate the assessment of evolutionary relationships and the trait space connecting ecological hypotheses and documenting knowledge gains across domains. With our reference framework we want to encourage the combined assessment, reuse and integration of phenotypic and molecular traits into functional biodiversity research and related disciplines.</p>
2024-06-05 | MTBLS2239 | MetaboLights
Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks. 3 different drinking water samples (Orly, Ivry, Joinville drinking water sample)
2009-01-07 | E-GEOD-14318 | biostudies-arrayexpress
Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks.
2009-01-08 | GSE14318 | GEO
Project description:We performed aCGH analysis using a custom Agilent oligonucleotide array to analyze 288 probands with idiopathic autism spectrum disorder (ASD) from the Simons Simplex Collection (SSC) of autism samples. The array is customized to high resolution coverage of exons for genes identified as encoding proteins included in a detailed protein interaction network for autism.
2011-06-08 | GSE29576 | GEO
Project description:Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.
| S-EPMC3656639 | biostudies-other
Project description:Ophiocordyceps sinensis (Berk.) Sacc., a complex of larval carcass (sclerotium) and stroma formed by the fungus of Hirsutella sinensis infecting Hepialidae insect larvae, whose fruiting body is also the main fungal structure used for taxonomic identification. However, the induction of fruiting body is still inefficient and the high cost resulting in the large-scale artificial cultivation of this fungus has been unsuccessful in China.In this study,important factors and target genes associated with the fruiting body induction during the development of O. sinensis were identified, providing a basic molecular mechanism for facilitating the large-scale artificial cultivation of O. sinensis.
2021-06-30 | GSE160505 | GEO
Project description:Breast cancer cell lines have been used widely to investigate breast cancer pathobiology and new therapies. Breast cancer is a molecularly heterogeneous disease, and it is important to understand how well and which cell lines best model that diversity. In particular, microarray studies have identified molecular subtypes - luminal A, luminal B, ERBB2-associated, basal-like and normal-like - with characteristic gene-expression patterns and underlying DNA copy number alterations (CNAs). Here, we studied a collection of breast cancer cell lines to catalog molecular profiles and to assess their relation to breast cancer subtypes. Whole-genome DNA microarrays were used to profile gene expression and CNAs in a collection of 52 widely-used breast cancer cell lines, and comparisons were made to existing profiles of primary breast tumors. Hierarchical clustering was used to identify gene-expression subtypes, and Gene Set Enrichment Analysis (GSEA) to discover biological features of those subtypes. Genomic and transcriptional profiles were integrated to discover within high-amplitude CNAs candidate cancer genes with coordinately altered gene copy number and expression. Transcriptional profiling of breast cancer cell lines identified one luminal and two basal-like (A and B) subtypes. Luminal lines displayed an estrogen receptor (ER) signature and resembled luminal-A/B tumors, basal-A lines were associated with ETS-pathway and BRCA1 signatures and resembled basal-like tumors, and basal-B lines displayed mesenchymal and stem-cell characteristics. Compared to tumors, cell lines exhibited similar patterns of CNA, but an overall higher complexity of CNA (genetically simple luminal-A tumors were not represented), and only partial conservation of subtype-specific CNAs. We identified 80 high-level DNA amplifications and 13 presumptive homozygous deletions, and the resident genes with concomitantly altered gene-expression, highlighting known and novel candidate breast cancer genes. Overall, breast cancer cell lines were genetically more complex than tumors, but retained expression patterns with relevance to the luminal-basal subtype distinction. The compendium of molecular profiles defines cell lines suitable for investigations of subtype-specific pathobiology, biomarkers and therapies, and provides a resource for discovery of new breast cancer genes.
2009-07-10 | GSE13914 | GEO