Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14048917_1.fastq.gz | Fastqsanger.gz | |||
| SRR14048917_2.fastq.gz | Fastqsanger.gz | |||
| SRR14048918_1.fastq.gz | Fastqsanger.gz | |||
| SRR14048918_2.fastq.gz | Fastqsanger.gz | |||
| SRR14048919_1.fastq.gz | Fastqsanger.gz |
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Project description:Organohalide-respiring Dehalococcoidia bacteria are one of the few microorganisms capable of transforming chlorinated solvents to benign ethene in anoxic environments. The tceA gene found in these bacteria, coding the trichloroethene-dechlorinating RDase TceA, is frequently detected in contaminated groundwater but not recognized as a biomarker for vinyl chloride detoxification. Here, we demonstrate that the tceA-carrying Dehalococcoides mccartyi (Dhc) strains FL2 and 195 grow with VC as electron acceptor when sufficient vitamin B12 is provided. Global proteomic profiling confirmed the predominant TceA expression in VC-grown Dhc FL2 cells, providing a line of evidence for the implication of TceA in respiratory VC reductive dechlorination.
2020-10-09 | MSV000086254 | MassIVE
Project description:A microarray targeting four sequenced strains in the Dehalococcoides (Dhc) genus was used to analyze gene expression in a robust long-term trichloroethene (TCE)-degrading microbial community (designated ANAS) during feeding cycles that involve conditions of periodic substrate supply. The Dhc transcriptome was examined at three time-points throughout a batch feeding cycle: T1 (27 h) when TCE, dichloroethene (DCE), and vinyl chloride (VC) were present; T2 (54 h) when only VC remained; and T3 (13 d) when Dhc had been starved of substrate for nine days. 90% of the Dhc ORFs that were detected in the ANAS DNA were found to be expressed as RNA sometime during the time course, demonstrating extraordinary utilization of the streamlined genome. 97% of these transcripts were differentially expressed during the time course, indicating efficiency of transcription through regulation in Dhc. Most Dhc genes were significantly down-regulated at T3, responding to a lack of substrate as would be expected. The tceA and vcrA genes, which code for proteins with known chlorinated ethene reduction functions, were highly expressed at both T1 and T2, whereas two other putative reductive dehalogenase genes (DET0173 and DET1545) were most highly expressed at T2, likely in response to the presence of VC. Hydrogenases were most highly expressed at T1, reflecting their important role in accumulating electrons used to initiate reductive dechlorination and other biosynthesis pathways. Cobalamin transport genes were preferentially expressed at T2, reflecting an increase in corrinoid transport as chloroethenes were degraded and a decrease in activity of the transport system after dehalogenation was complete. This is the first application of a microarray targeting a known genus, including both core genomes and identified strain-specific genes, applied to improve our understanding of transcriptional dynamics within an undefined microbial community. Replicate samples were independently collected, and simultaneously but individually extracted, fragmented, labeled, and hybridized to arrays. Three DNA samples (one from each of the three replicate cycles) and nine RNA samples (one from each of the three time-points in each of the three replicate cycles) were prepared for microarray analysis.
2013-03-01 | E-GEOD-42635 | biostudies-arrayexpress
Project description:A fundamental, evolutionarily conserved biological mechanism required for long-term memory formation is rapid induction of gene transcription upon learning in relevant brain areas. For episodic types of memories, two regions undergoing this transcription are the dorsal hippocampus (dHC) and prelimbic (PL) cortex. Whether and to what extent these regions regulate similar or distinct transcriptomic profiles upon learning remains to be understood. Here, we used RNA sequencing in the dHC and PL cortex of male rats to profile their transcriptomes in untrained conditions (baseline) and at 1 hour and 6 days after inhibitory avoidance learning. We found that, out of 33,713 transcripts, over 14,000 were significantly expressed at baseline in both regions and approximately 3,000 were selectively enriched in each region. Gene Ontology biological pathway analyses indicated that commonly expressed pathways included synapse organization, regulation of membrane potential, and vesicle localization. The enriched pathways in the dHC were gliogenesis, axon development, and lipid modification, while in the PL cortex included vesicle localization and synaptic vesicle cycle. At 1 hour after learning, 135 transcripts changed significantly in the dHC and 478 in the PL cortex; of these, only 34 were shared. Biological pathways most significantly regulated by learning in the dHC were protein dephosphorylation, glycogen and glucan metabolism, while in the PL cortex were axon development and axonogenesis. The transcriptome profiles returned to baseline by 6 days after training. Thus, a significant portion of dHC and PL cortex transcriptomic profiles is divergent and their regulation upon learning is largely distinct and transient.
2021-02-03 | GSE150950 | GEO
Project description:Microbial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non-toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1-DCE, cis-DCE, trans-DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16S rRNA gene sequence identity with previously sequenced Dhc strains BAV1 and CBDB1, placing it within the Pinellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom-designed microarray targeting four sequenced Dhc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional Dhc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of Dhc strains is likely driven by the horizontal transfer of key reductive dehalogenase-encoding genes.
2013-03-01 | GSE27611 | GEO
Project description:A microarray targeting four sequenced strains in the Dehalococcoides (Dhc) genus was used to analyze gene expression in a robust long-term trichloroethene (TCE)-degrading microbial community (designated ANAS) during feeding cycles that involve conditions of periodic substrate supply. The Dhc transcriptome was examined at three time-points throughout a batch feeding cycle: T1 (27 h) when TCE, dichloroethene (DCE), and vinyl chloride (VC) were present; T2 (54 h) when only VC remained; and T3 (13 d) when Dhc had been starved of substrate for nine days. 90% of the Dhc ORFs that were detected in the ANAS DNA were found to be expressed as RNA sometime during the time course, demonstrating extraordinary utilization of the streamlined genome. 97% of these transcripts were differentially expressed during the time course, indicating efficiency of transcription through regulation in Dhc. Most Dhc genes were significantly down-regulated at T3, responding to a lack of substrate as would be expected. The tceA and vcrA genes, which code for proteins with known chlorinated ethene reduction functions, were highly expressed at both T1 and T2, whereas two other putative reductive dehalogenase genes (DET0173 and DET1545) were most highly expressed at T2, likely in response to the presence of VC. Hydrogenases were most highly expressed at T1, reflecting their important role in accumulating electrons used to initiate reductive dechlorination and other biosynthesis pathways. Cobalamin transport genes were preferentially expressed at T2, reflecting an increase in corrinoid transport as chloroethenes were degraded and a decrease in activity of the transport system after dehalogenation was complete. This is the first application of a microarray targeting a known genus, including both core genomes and identified strain-specific genes, applied to improve our understanding of transcriptional dynamics within an undefined microbial community.
2013-03-01 | GSE42635 | GEO
Project description:The experiment was designed to identify the genes which get altered after over-expression and depletion of hsa-miR-195 levels in MCF7 and HEK 293T cells. Recent research has established that microRNAs (miRNAs) are key regulators of many cell processes including those often deregulated in cancer such as apoptosis. In our previous work we have shown that hsa-miR-195 targets the key anti-apoptotic molecule BCL2 and its over-expression induces apoptosis and augments sensitivity of cancer cells towards chemotherapeutic drug. These results suggested a possible anticancer role of miR-195 and therefore oblige its complete functional characterization. In this study global effect of alterations in cellular miR-195 levels on transcriptome was analysed in order to identify the regulatory functions of miR-195. Together our findings highlight a novel and important role of hsa-miR-195 potentially opening new avenues for the treatment of various diseases.
2016-02-01 | GSE43656 | GEO
Project description:Smith-Lemli-Opitz Syndrome (SLOS) is a developmental disorder caused by autosomal recessive mutations in the Dhcr7 gene. SLOS patients present clinically with multiple dysmorphologies, neurological, behavioral and cognitive defects, and demonstrate impaired cholesterol biosynthesis resulting in markedly elevated 7-DHC in all bodily tissues and fluids. Previous rodent models of SLOS suffered from neonatal mortality or variation in the biochemical phenotype over time. We generated a viable murine model bearing a conditional flosed allele of the Dhcr7 gene, and validated it by generating a mice with liver-specific deletion of Dhcr7 by breeding with a strain expressing Cre recombinase driven by an albumin promoter . These mice demonstrated elevated circulatory and liver 7-DHC levels, but phenotypic characterization of the knockout mice revealed no significant changes in viability, fertility, growth curves, liver architecture, hepatic triglyceride secretion, and parameters of systemic glucose homeostasis. Investigation in to changes in the liver transcriptome were investigated withe RNAseq, and identified enrichment in various pathways, including steroid hormone biosynthesis and various cell signaling and metabolism pathways. Most notably missing from the list are the genes related to cholesterol biosynthesis. Generation of this Dhcr7 conditional knockout model will allow for better studies into the post natal effects of blocking cholesterol biosynthesis, accumulation of 7-DHC, and the role of DHCR7 in specific tissues.
2020-09-04 | GSE146523 | GEO
Project description:Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by Dehalococcoides organisms. A Dehalococcoides-containing microbial consortium (ANAS) with the ability to degrade TCE to ethene, an innocuous end-product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of Dehalococcoides ethenogenes 195 (strain 195). This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray revealed that the genes associated with central metabolism including an apparently incomplete carbon fixation pathway, cobalamin salvaging system, nitrogen fixation pathway, and five hydrogenase complexes are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase tceA was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria which is essential in developing effective strategies for bioremediation of PCE and TCE in the environment. Keywords: comparative genomic hybridization
2008-09-01 | GSE9612 | GEO
Project description:Increased intestinal permeability is associated to the onset of inflammatory bowel disease (IBD) since the exposition to luminal content causes an immunological response that promotes intestinal inflammation. Several studies have been shown that microRNAs (miRNAs) are involved in IBD pathogenesis. Here, we aimed to functionally characterize the role of miRNAs in the regulation of intestinal permeability. miRNA profile of intestinal epithelial cells (IECs) isolated by colon of a UC mice model were identified using microarray. To predict the target genes of modulated miRNAs, we performed a bioinformatic analysis. To validate biologically miRNA targets, we performed transient transfection experiments in HT-29, Caco2 and T84 cell lines. To assess their role in barrier function, trans-epithelial electrical resistance and dextran flux assays were used. To investigate the in vivo effect of miR-195-5p, we employed a DSS-induced colitis model in mice. We identified 18 deregulated miRNAs in IECs from UC mice model and control mice. Among them, down-regulated miR-195-5p targeted CLDN2 and are involved in altered intestinal permeability. CLDN2 expression levels were increased in UC mice models and negatively correlated with the miR-195-5p expression. We demonstrated that the gain-of-function of miR-195-5p in colonic epithelial cell lines decreased the CLDN2 levels. We in vitro confirmed that miR-195-5p was able to control the intestinal barrier integrity. We also in vivo demonstrated that miR-195-5p attenuated the colonic inflammatory response in DSS-induced colitis and reduced the colonic permeability. All together our data support a previously unreported role of miR-195-5p in intestinal permeability and provide a potential pharmacological target for new therapeutic approaches in IBD.
2022-04-27 | GSE183896 | GEO
Project description:To explore functionally crucial tumor-suppressive (TS)-miRNAs in hepatocellular carcinoma (HCC), we performed integrative function- and expression-based screenings of TS-miRNAs in six HCC cell lines. The screenings identified seven miRNAs, which showed growth-suppressive activities through the overexpression of each miRNA and were endogenously downregulated in HCC cell lines. Further expression analyses using a large panel of HCC cell lines and primary tumors demonstrated four miRNAs, miR-101, -195, -378 and -497, as candidate TS-miRNAs frequently silenced in HCCs. Among them, two clustered miRNAs miR-195 and miR-497 showed significant growth-suppressive activity with induction of G1 arrest. Comprehensive exploration of their targets using Argonute2-immunoprecipitation-deep-sequencing (Ago2-IP-seq) and genome-wide expression profiling after their overexpression, successfully identified a set of cell-cycle regulators, including CCNE1, CDC25A, CCND3, CDK4, and BTRC. Our results suggest the molecular pathway regulating cell cycle progression to be integrally altered by downregulation of miR-195 and miR-497 expression, leading to aberrant cell proliferation in hepatocarcinogenesis. Identification of miR-195 and miR-497 target genes by sequencing Ago2-binding mRNAs and total mRNAs of miR-195 or miR-497 overexpressed, or non-treated Hep G2 cell.
2013-05-31 | GSE41074 | GEO