Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis; insights for early bactericidal activity

ABSTRACT: Background: Pyrazinamide (PZA) plays an essential part in the shortened 6-month tuberculosis (TB) treatment course due to its activity against slow-growing, semi-dormant organisms. We tested the paradigm that PZA preferentially targets slow growing cells of Mycobacterium tuberculosis that remain after the initial kill by isoniazid, by observing the response of either slow growing or fast growing bacilli to differing concentrations of PZA. Methods: M. tuberculosis H37Rv was grown in continuous culture at either a constant fast growth rate (Mean Generation Time [MGT] of 23.1 h) or slow growth rate (69.3 h MGT) at a controlled dissolved oxygen tension of 10% and a controlled acidity at pH 6.3 Â± 0.1. The cultures were exposed to step-wise increases in the concentration of PZA (25 Âµg ml-1 to 250 Âµg ml-1) every 2 MGTs, and bacterial survival was measured. PZA-induced global gene expression was explored for each increase in PZA-concentration, using microarray.

ORGANISM(S): Mycobacterium tuberculosis H37Rv

SUBMITTER: Rose Elizabeth Jeeves

PROVIDER: E-MTAB-4093 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression data from polarized T helper cells isolated from mice with opticospinal (OSE) experimental autoimmune encephalomyelitis (EAE)

Project description:T cells from the spleen of a mixed-gender pool of four double-transgenic 2D2 (TCRMOG) x IgHMOG mice (OSE) mice, which spontaneously develop experimental autoimmune encephalomyelitis (EAE), were used to derive TH1- and TH17-polarized cells, as described in https://doi.org/10.1371/journal.pone.0015531. Here, expression was compared, first, between TH1 and naïve TH0 and, second, between TH17 and naïve TH0 cells.

2020-08-21 | E-MTAB-9133 | biostudies-arrayexpress

Pain-killer carprofen elicits pleiotropic modes of bactericidal action with potential to reverse antimicrobial resistance in tuberculosis.

Project description:The alarming rise of antimicrobial resistance in Mycobacterium tuberculosis coupled with the shortage of new antibiotics has made tuberculosis (TB) control a global health priority. Non-steroidal anti-inflammatory drugs (NSAIDs) inhibit the growth of multi-drug resistant isolates of M. tuberculosis. Repurposing NSAIDs, with known clinical properties and safety records, offers a direct route to clinical trials. Therefore we investigated the novel mechanisms of anti-mycobacterial action of the NSAID, carprofen. Integrative molecular and microbiological approaches revealed that carprofen, a bactericidal drug, inhibited bacterial drug efflux mechanisms. In addition, carprofen restricted mycobacterial biofilm-like growth, highlighting the requirement of efflux-mediated communicative systems for the formation of biofilms. Transcriptome profiling revealed that carprofen likely acts by inhibiting respiration through the disruption of membrane potential, which may explain why spontaneous drug-resistant mutants could not be raised due to the pleiotropic nature of carprofen’s anti-tubercular action. This immunomodulatory drug has the potential to reverse TB antimicrobial resistance by inhibiting drug efflux pumps and biofilm formation, and paves a new chemotherapeutic path for tackling tuberculosis.

2020-08-15 | E-MTAB-6191 | biostudies-arrayexpress

Pilot KOMP knockout mouse strains

Project description:This is a test case of D. West's RNA-seq from KOMP2 mutant strains

2015-12-28 | E-MTAB-3662 | biostudies-arrayexpress

RNA-seq of pancreatic cancer cells derived from a genetically engineered mouse model, which harbor the inducible KrasG12D allele

Project description:Pancreatic adenocarcinoma (PDAC) is a lethal disease and it is the most common type of pancreatic cancer. Majority of the pancreatic cancers harbor alterations in the Kras gene. Currently there are no approved drugs that target Kras directly and it's downstream effect on the epigenome remains unknown. In this study, we investigated the epigenetic landscape of pancreatic cancer cells which harbor the inducible KrasG12D allele. We performed RNA-seq, ChIP-seq against 6 different histone marks, ATAC-seq and RRBS to assess the changes in the epigenome after oncogenic KrasG12D induction.

2021-09-06 | E-MTAB-10896 | biostudies-arrayexpress

ΔNp63 promotes stem cell activity in mammary gland development and basal-like breast cancer by enhancing Fzd7 expression and Wnt signaling

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-08-19 | E-GEOD-47493 | biostudies-arrayexpress

IMPC (international mouse phenotyping consortium) high throughput RNA seq of 1143 samples from 106 IMPC knockout lines

Project description:A RNA Seq analysis of 7 tissues from 16 week old male knockout mice. A total of 106 IMPC knockout lines were analysed by David West's group at Children's Hospital Oakland Research Institute.

2017-12-01 | E-MTAB-5131 | biostudies-arrayexpress

RNAseq of coding RNA in the liver, spleen, kidney, abdominal muscle and gonadal adipose tissue of knock out mice and wild type controls as part of the KOMP2 project.

Project description:This is a pilot study from the Knockout Mouse Phenotyping Program (KOMP2). The program provides broad, standardized phenotyping of a genome-wide collection of mouse knockouts generated by the International Knockout Mouse Consortium (IKMC), funded by the NIH, European Union, Wellcome Trust, Canada, and the Texas Enterprise Fund. In this experiment RNAseq was performed to profile expression of coding RNA in the liver, spleen, kidney, abdominal muscle and gonadal adipose tissue of knock out mice (1810027O10Rik knockout, Sik1 knockout, 3110043O21Rik knockout, 3110043O21Rik knockout) compared with wild type controls.

2017-12-31 | E-MTAB-4035 | biostudies-arrayexpress

Composition of the mitoribosome of Diplonema papillatum

Project description:Biosynthesis of mitochondrial genome-encoded proteins is carried out by the mitoribosome, a specialized apparatus that has evolved and diverged dramatically since its bacterial origin. Recent studies across various eukaryotes have demonstrated widespread structural and compositional diversity of mitoribosomes. We used affinity pulldown of four mitoribosomal proteins to carry out a detailed analysis of mitoribosomes in Diplonema papillatum, the type species of diplonemids, a widespread group of single-celled marine flagellates. Using as baits mitoribosomal proteins integrating at distinct sites and phases during subunit maturation also allowed us to sample populations of mitoribosome assembly intermediates.

2023-05-19 | PXD039927 | Pride

Epigenetic profile of iPSC differentiation process by scRNA-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scRNA-seq.

2021-08-17 | E-MTAB-10220 | biostudies-arrayexpress

MetaNovo : an open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets

Project description:Results We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome database - but simultaneously identified proteins present in the samples that are derived from known gut organisms that were missed by the previous analyses. Finally, MetaNovo was benchmarked on samples of known microbial composition against matched metagenomic and whole genomic database workflows, yielding many more MS/MS for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and providing evidence for a known sample contaminant without prior expectation. Conclusions By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence search databases. We show that the MetaNovo approach to mass spectrometry metaproteomics can be more accurate than current gold standard approaches of tailored or matched genomic database searches, identify sample contaminants without prior expectation and that increases in assigned spectra from this approach can yield novel insights into previously unidentified metaproteomic signals - building on the potential for complex mass spectrometry metaproteomic data to speak for itself. The pipeline source code is available on GitHub and documentation is provided to run the software as a singularity-compatible docker image available from the Docker Hub.

2023-05-16 | PXD030708 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data