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ABSTRACT: Tuberculosis caused by Mycobacterium orygis in wild ungulates in Chennai, South India

PROVIDER: PRJNA789714 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17254975_1.fastq.gz	Fastqsanger.gz
	SRR17254975_2.fastq.gz	Fastqsanger.gz
	SRR17254976_1.fastq.gz	Fastqsanger.gz
	SRR17254976_2.fastq.gz	Fastqsanger.gz
	SRR17254977_1.fastq.gz	Fastqsanger.gz

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Project description:Bovine tuberculosis caused by Mycobacterium orygis

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The influence of reduced oxygen availability on gene expression in Laboratory (H37Rv) and clinical strains (S7 and S10) of Mycobacterium tuberculosis

Project description:Mycobacterium tuberculosis has the ability to persist within the host in a clinically latent stage. One important condition believed to contribute to latency is reduced access to oxygen but the response of M. tuberculosis to hypoxia is partially characterized. Virtually all dormant models against tuberculosis the vaccine tested in animals used laboratory strains H37Rv or Erdman strains. But major outbreaks of TB occur with the strains that have widely different genotypes and phenotypes compare to H37Rv. In this study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of lab strain (H37Rv) and most prevalent strains of Mycobacterium tuberculosis from South India S7 and S10 to hypoxia. Analysis of microarray results revealed that a total of 1161 genes are differentially regulated in H37Rv, among them 659 genes are upregulated and 502 genes are down regulated when > 1.5 fold change was taken as cut off. Microarray data of clinical isolates showed total of 790 genes are differentially regulated in S7 clinical isolates among which 453 are upregulated and 337 are down regulated. Interestingly numerous genes are differentially regulated in S10 clinical isolates (total of 2805 genes) and 1463 are upregulated and 1342 genes are down regulated during reduced oxygen model (Wayne’s model). Real-time quantitative RT-PCR was performed for few genes to validate the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of South Indian prevalent clinical strains of M. tuberculosis when exposed to reduced oxygen stress.

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Heterogeneous Gene Expression Patterns of Tuberculosis-Diabetes Interaction in Diverse Cohorts

Project description:Background. Diabetes mellitus (DM) increases tuberculosis (TB) severity. We previously reported baseline blood microarray data in a South Indian pulmonary TB cohort with or without DM, finding no qualitative or quantitative differences in immune pathway gene expression. To extend those observations, we compared baseline and longitudinal blood gene expression in TB patients from South India and Brazil. Methods. Adults with pulmonary TB, with or without DM, were enrolled at two sites in India and one site in Brazil. Blood RNA sequencing (RNAseq) was performed at baseline and treatment months 2 and 6. Differentially expressed genes (DEGs) and pathway activation were compared by group and site. Comparison was also made with published RNAseq data from the TANDEM study South African and Romanian cohorts. Findings. No consistent pattern of DEGs discriminated TB from TBDM in India or Brazil. Pathway analysis also showed little commonality between sites, although a shared profile of complement activation and matrix degradation was identified in TBDM. Indian participants showed marked longitudinal changes in DEGs and pathways at 2 and 6 months of treatment, whereas these were stable in Brazilian participants. High variability in gene expression was observed between sites at baseline and during treatment. Interpretation. DM exacerbates matrix degradation in TB but is not associated with major immune gene expression or pathway differences compared to TB without DM. Comparison between cohorts in India, Brazil, Romania, and South Africa revealed an unexpectedly high degree of site-specific variation that may reflect population differences in TB pathobiology.

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MntR(Rv2788): a transcriptional regulator that controls manganese homeostasis in Mycobacterium tuberculosis.

Project description:Transcriptional profiling of SirR and manganese regulated expression of genes in Mycobacterium tuberculosis strains comparing high manganese vs. low manganese in Rv (wild type Mycobacterium tuberculosis) and ST70 (mntR mutant strain of Mycobacterium tuberculosis) Two strains each with two conditions experiment, Rv (Mycobacterium tuberculosis wild type strain) high manganese vs. low manganese and ST70 (mntR mutant strain of Mycobacterium tuberculosis) high manganese vs. low manganese. Number of biological replicates is 3 for each condition for each strain.

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