Antimony mine site- microbial communities
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ABSTRACT:
PROVIDER: PRJEB64667 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microbial communities at the Mogalakwena mine site - Raw sequence reads
| PRJNA941860 | ENA
Project description:The mRNA expression of antimony resistant strains of Leishmania donovani was compared to the expression of the sensitive Leishmania donovani. The antimony resistant and sensitive Leishmania donovani were grown in complete M199 medium with 10% FCS and Penicillin streptomycin mixture. At stationary phase (5 day culture) cells were harvested in sterile Phosphate buffered saline and used for RNA isolation.
2016-07-03 | E-GEOD-62468 | biostudies-arrayexpress
Project description:The aim of the experiment is to detect any gene expression modulation in an antimony resistant L.infantum Sb2000.1 strain compared to an antimony sensitive L.infantum WT strain. We want to identify the modulated genes associated with an antimony resistant phenotype. The Sb2000.1 resistant strain used is about 1000 times more resistant to SbIII than the WT sensitive strain. The full-genome DNA microarrays includes one 70-oligonucleotide probe for each gene of L. infantum. Keywords: drug resistance
2009-08-15 | GSE16965 | GEO
Project description:The pyrite mine of Lousal, Grândola, Portugal, was discovered in 1882 and extensively exploited from 1900 until its closure in 1988 when the mining ores were not viable economically. Aiming at becoming a cultural-touristic center, the mining area was rehabilitated raising a Mining Museum and a Science Centre along with the reopening of a mining gallery for public access. In recent times, aerobiological studies on subterranean environments such as caves, mines and archeological necropolis revealed to be an important source of novel bacteria, from which their biotechnological potential are under study. Here we present a Pseudomonas sp. isolated from the mine air with potential secondary metabolite biosynthesis, resistance to antibiotics and virulence factors.
2021-11-05 | GSE186946 | GEO
Project description:The aim of the experiment is to detect any gene expression modulation in an antimony resistant L.infantum Sb2000.1 strain compared to an antimony sensitive L.infantum WT strain. We want to identify the modulated genes associated with an antimony resistant phenotype. The Sb2000.1 resistant strain used is about 1000 times more resistant to SbIII than the WT sensitive strain. The full-genome DNA microarrays includes one 70-oligonucleotide probe for each gene of L. infantum. Keywords: drug resistance Two-condition experiment, resistant strain Sb2000.1 vs wild-type. Five biological replicates for each strain, independently grown and harvested. One replicate per array
2009-08-15 | E-GEOD-16965 | biostudies-arrayexpress
Project description:Background: Drug resistance is a major problem in leishmaniasis chemotherapy. RNA expression profiling using DNA microarrays is a suitable approach to study simultaneous events leading to a drug-resistance phenotype. Genomic analysis has been performed primarily with Old World Leishmania species and here we investigate molecular alterations in antimony resistance in the New World species L. amazonensis. Methods/Principal Findings: We selected populations of L. amazonensis for resistance to antimony by step-wise drug pressure. Gene expression of highly resistant mutants was studied using DNA microarrays. RNA expression profiling of antimony-resistant L. amazonensis revealed the overexpression of genes involved in drug resistance including the ABC transporter MRPA and several genes related to thiol metabolism. The MRPA overexpression was validated by quantitative real-time PCR and further analysis revealed that this increased expression was correlated to gene amplification as part of extrachromosomal linear amplicons in some mutants and as part of supernumerary chromosomes in other mutants. The expression of several other genes encoding hypothetical proteins but also nucleobase and glucose transporter encoding genes were found to be modulated. Conclusions/Significance: Mechanisms classically found in Old World antimony resistant Leishmania were also highlighted in New World antimony-resistant L. amazonensis. These studies were useful to the identification of resistance molecular markers.
2011-06-11 | GSE26159 | GEO
Project description:The mRNA expression of antimony resistant strains of Leishmania donovani was compared to the expression of the sensitive Leishmania donovani.
2016-01-01 | GSE62468 | GEO
Project description:Purpose: In this study, we have used a translatomic approach by coupling polysome profiling and deep RNA-sequencing to estimate changes in the translatome of antimony-resistant Leishmania parasites Methods: Leishmania tropica promastigotes were stepwise selected for resistance to trivalent antimony. Two different strains were studied, the L. tropica SbIII-sensitive or wildtype strain (WT) and the derived highly resistant strain (HR). After polysome profiling four types of samples were evaluated by deep RNAseq: total mRNA used as input, monosomes (MS), light polysomes (LP), and heavy polysomes (HP). The DESeq2 algorithm was used for differential expression analysis to identify translational changes at the basal level (HR Vs. WT), translational changes to combat the drug (HR+SbIII Vs. HR), and to compare translatomic Vs. transcriptomic changes (HP Vs. Total input) [see overall design section below]. Results: Differential translational analysis (cutoff of fold change ≥ 1.5 and p-value corrected by Benjamini-Hochberg FDR ≤ 0.05) showed that transcripts composition per polysome fraction was different in the resistant strain. It included several upregulated (Up) and downregulated (Down) transcripts. At the basal level, 2431 different transcripts were differentially translated: monosome (Down: 4, Up: 0), light polysomes (Down: 906, Up: 951), and heavy polysomes (Down: 1096, Up: 1064). Under the antimony challenge, 189 different transcripts were differentially translated: monosome (Down: 0, Up: 2), light polysomes (Down: 9, Up: 57), and heavy polysomes (Down: 30, Up: 134). Overall, most of the changes were identified in polysome fraction when compared with monosomes or total transcriptome. Conclusions: Our study shows evidence that translational control has a main role in coordinating the resistance to antimony in Leishmania parasites. We propose a novel model that establishes translational control as a major driver of antimony-resistant phenotypes in Leishmania parasites.
2023-04-04 | GSE173848 | GEO
Project description:To identify transcripts differentially expressed between control samples and spontaneous tumors, or control samples and antimony treated lung tumors, we collected RNA from male and female B6C3F1 mice from a 2-year inhalation NTP bioassay exposed to 0 to 30 mg/m3 antimony trioxide. These samples were interrogated with the Affymetrix Mouse Genome 430 2.0 GeneChip Array. A total of 9941 gene transcripts were differentially expressed between control samples and spontaneous tumors, and 12441 gene transcripts were differentially expressed between control samples and treated antimony tumors (false discovery rate (FDR) < 0.05).
2022-12-31 | GSE152629 | GEO
Project description:Antimony (Sb) and arsenic (As) are two hazardous metalloid elements, and the biogeochemical cycle of Sb and As can be better understood by studying plant rhizosphere microorganisms associated with Sb mine waste. In the current study, samples of three types of mine waste-Sb mine tailing, waste rocks, and smelting slag-and associated rhizosphere microorganisms of adapted plants were collected from Qinglong Sb mine, southwest China. 16S rRNA was sequenced and used to study the composition of the mine waste microbial community. The most abundant phylum in all samples was Proteobacteria, followed by Bacteroidota, Acidobacteriota, and Actinobacteriota. The community composition varied among different mine waste types. Gammaproteobacteria was the most abundant microorganism in tailings, Actinobacteria was mainly distributed in waste rock, and Saccharimonadia, Acidobacteriae, and Ktedonobacteria were mainly present in slag. At the family level, the vast majority of Hydrogenophilaceae were found in tailings, Ktedonobacteraceae, Chthoniobacteraceae, and Acidobacteriaceae (Subgroup 1) were mostly found in slag, and Pseudomonadaceae and Micrococcaceae were mainly found in waste rock. Actinobacteriota and Arthrobacter are important taxa for reducing heavy metal(loid) mobility, vegetation restoration, and self-sustaining ecosystem construction on antimony mine waste. The high concentrations of Sb and As reduce microbial diversity.
| S-EPMC9330434 | biostudies-literature