Ontology highlight
ABSTRACT:
PROVIDER: PRJNA765926 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16085950_1.fastq.gz | Fastqsanger.gz | |||
| SRR16085950_2.fastq.gz | Fastqsanger.gz | |||
| SRR16085951_1.fastq.gz | Fastqsanger.gz | |||
| SRR16085951_2.fastq.gz | Fastqsanger.gz | |||
| SRR16085952_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:Whole genome metagenomics of river sediments of India
| PRJEB48704 | ENA
Project description:Toxicity of river sediments are assessed using whole sediment toxicity tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. Moreover, natural sediment properties, such as grain size distribution and organic carbon content, can influence the test parameters by masking pollutant toxicity. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bioavailable fraction of pollutants. The nematode Caenorhabditis elegans is ideally suited for these purposes, as (i) it can be exposed to whole sediments, and (ii) its genome is fully sequenced and widely annotated. In this pilot study we exposed C. elegans for 48 h to three sediments varying in degree of contamination with e.g. heavy metals and organic pollutants. Following the exposure period, gene expression was profiled using a whole genome DNA-microarray approach. Whole genome DNA microarray experiments were performed using a common reference design to identify differentially expressed genes in nematodes exposed to one of three river sediments of differing pollution level. Each sample consists of the 5 “biological replicates”.
2008-06-25 | E-GEOD-11837 | biostudies-arrayexpress
Project description:Toxicity of river sediments are assessed using whole sediment toxicity tests with benthic organisms. The challenge, however, is the differentiation between multiple effects caused by complex contaminant mixtures and the unspecific toxicity endpoints such as survival, growth or reproduction. Moreover, natural sediment properties, such as grain size distribution and organic carbon content, can influence the test parameters by masking pollutant toxicity. The use of gene expression profiling facilitates the identification of transcriptional changes at the molecular level that are specific to the bioavailable fraction of pollutants. The nematode Caenorhabditis elegans is ideally suited for these purposes, as (i) it can be exposed to whole sediments, and (ii) its genome is fully sequenced and widely annotated. In this pilot study we exposed C. elegans for 48 h to three sediments varying in degree of contamination with e.g. heavy metals and organic pollutants. Following the exposure period, gene expression was profiled using a whole genome DNA-microarray approach.
2008-06-25 | GSE11837 | GEO
Project description:Evaluation of different strategies to interpret metaproteomics data acquired on soil samples from a floodplain along the Seine River (France) incorporating sample-specific metagenomics data, soil genome catalogue database, and generic sequence database.
2022-02-17 | PXD026798 | Pride
Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5α and Sphingomonas sp. strain NM-05 (involved in the biodegradation of γ-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of γ-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHα, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems.
2011-04-15 | GSE24353 | GEO
Project description:Integrative proteo-trnascriptomics analysis of MDR abd drug sensitive E. coli strains isolated from river Yamuna, Delhi, India to identify novel drug targets against Multi drug Resistant E. coli
2025-02-10 | PXD048998 | Pride
Project description:In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut and oral microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.
2025-09-15 | PXD057056 | Pride
Project description:We have developed a 60-mer oligonucleotide multibacterial microarray for detection and expression profiling of biodegradative genes and bacterial diversity (16S rRNA gene) in different habitats contaminated with varieties of hazardous chemicals. The genes selected were involved in biodegradation and biotransformation of various groups of compounds viz. nitroaromatic compounds (148 genes), chloroaromatic compounds (75 genes), monoaromatic compounds (373 genes), polyaromatic hydrocarbons (174 genes), pesticides/ herbicides (34 genes), alkanes/aliphatics (185 genes) and heavy metals (68 genes), which covered a total number of 133 chemicals. The efficiency (specificity, detection sensitivity) of the developed array was evaluated using the labeled genomic DNA of pure bacterial strains, Escherichia coli DH5M-NM-1 and Sphingomonas sp. strain NM-05 (involved in the biodegradation of M-NM-3-hexachlorohexane isolated from IPL, Lucknow) at different concentrations of 300ng, 500ng, 800ng, 1000ng and 1250ng. The specificity of the developed array was further validated using mixed cultures containing three strains (Sphingomonas sp. strain NM-05, Rhodococcus sp. strain RHA1 and Bordetella sp. strain IITR-02) involved in biodegradation of M-NM-3-hexachlorohexane, biphenyl and chlorobenzenes respectively. The mixed culture also contained non-target/non-degrader strains (E. coli DHM-NM-1, E.coli BL21 and E.coli K12 NCTC50192). The developed array was applied for profiling using the total soil DNA in five contaminated habitats of north India, viz. chloroaromatic chemicals contaminated site (India Pesticide Limited, Chinhat, Lucknow), a river sediments (Gomti river sediment, Lucknow), heavy metal industry dump site (Jajmau industrial area Kanpur), a effluent treatment plant (CETP along Ganges river near Kanpur), and an oil refinery (Mathura oil refinery). Hybridization of 16S rRNA probes revealed the presence of bacteria similar to well characterized genera involved in biodegradation of pollutants. Genes involved in complete degradation pathways for hexachlorocyclohexane (lin), 1,2,4-trichlorobenzene (tcb), naphthalene (nah), phenol (mph), biphenyl (bph), benzene (ben), toluene (tbm), xylene (xyl), phthalate (pht), Salicylate (sal) and resistance to mercury (mer) were detected with highest intensity. The most abundant genes belonged to hydroxylases, monooxygenases and dehydrogenases which were present in all the five samples. Many compound specific genes which initiate the degradation pathway were also detected. Thus, the array developed and validated here may be useful in assessing the biodegradative potential and composition of environmentally useful bacteria in hazardous ecosystems. Agilent one-color CGH experiment,Organism: Genotypic designed Agilent-17159 Genotypic designed Agilent Multibacterial 8x15k Array , Labeling kit: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)
2011-04-15 | E-GEOD-24353 | biostudies-arrayexpress
Project description:Metaproteomic data for Rodriguez-Ramos, et al. interrogating microbial and viral communities of hyporheic river sediments within the Columbia River. Samples were digested with trypsin, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.
2021-04-28 | MSV000087330 | MassIVE
Project description:Desulfurella amilsii is an acidotolerant sulfur-reducing bacterium isolated from sediments of an acidic river. It can grow in a broad range of pH and can obtain energy via respiring elemental sulfur or thiosulfate, as well as by disproportionating elemental sulfur. Its genome encodes the enzyme sulfur reductase, and several rhodanese-like proteins, possibly playing a role in sulfur respiration and disproportionation. Thiosulfate reductase and dissimilatory sulfite reductase are encoded and might play a role during the respiration of thiosulfate. The involvement of these enzymes in the reductive routes of sulfur metabolism is not yet clearly understood. Desulfurella amilsii was used in this study to combine strategies for sulfur metabolism research on the protein level to shed some light on the pathways involved in the metabolism of this microorganism.
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