M1T1 Streptococcus pyogenes (isolate 5448) WT and Animal-passaged variant in vitro and in vivo
Ontology highlight
ABSTRACT:
ORGANISM(S): Streptococcus pyogenes
SUBMITTER: Ramy Aziz
PROVIDER: E-GEOD-19103 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Microarray analysis was performed on in vivo-derived RNA from the well characterized GAS strain 5448 and its derivative 5448R-, containing the mutated ropB allele from 5628. We followed a cyclic design that allowed us to compare every condition to each other at least twice, and guaranteed dye swapping to eliminate effects of non-specific binding. This study consists of 4 replicates of 5448 and 3 replicates of 5448R-.
2010-05-15 | E-GEOD-13656 | biostudies-arrayexpress
Project description:Aflatoxins are carcinogenic fungal secondary metabolites. Levels of aflatoxins in agricultural commodities are stringently regulated by many countries. A cluster of genes is responsible for aflatoxin biosynthesis by Aspergillus flavus and other closely related species. Expression of the clustered aflatoxin genes is governed by a complex network of regulatory mechanisms. To better understand the molecular events that are associated with aflatoxin production, transcription profiling by microarray analyses which compared three independent aflatoxigenic A. flavus strains to individual isogenic progenies that no longer produced aflatoxins after serial transfers was carried out. Twenty-two significantly differentially expressed features were identified. After physical mapping using the A. oryzae genome sequence as the reference, the number of unique genes was reduced to 16. Compared to the parental strains, changes in the aflatoxin gene expression levels in the progenies were not significant, which suggests that the inability to produce aflatoxins is not caused by decreased expression. The only gene showing higher expression levels in the progenies is homologous to glutathione S-transferease genes. Overexpression of this gene, named hcc, at six- to nine-fold in an aflatoxigenic A. flavus did not cause discernible changes in colony morphology or aflatoxin production. Loss of aflatoxin production after serial transfers may not result from a single event but caused by multiple factors. Keywords: Compartiave hybridization toxigenic and atoxigenic lines of Aspergillus Aspergillus flavus NRRL 29459, NRRL 29474, and NRRL 29490 are aflatoxigenic strains originated from soil collection in a peanut field (Terrell Co., Georgia, USA). Strains 459B-20-2, 474A-20, and 499A-20 were nonaflatoxigenic isolates obtained after 20 serial transfers of the parental strains on potato dextrose agar slants (Horn and Dorner 2002). Comparsions in each experiment consisted of one aflatoxigenic parental strain and one nonaflatoxigenic progeny, compared after 48- or 72-hr growth. Each comparison was repeated with duplicate dye-flip.
2010-05-26 | E-GEOD-8185 | biostudies-arrayexpress
Project description:NIH 3T3 cells (mouse fibroblasts) were engineered such that the dominant negative ATPase-defective BRG-1 is expressed via the tet-off inducible expression system to inactivate the SWI-SNF chromatin remodeling complexes (Mol Cell Biol 20, 2839). These cell lines have been used for several studies to demonstrate the in vivo functions of the SWI-SNF complexes in transcription, differentiation and cell cycle control. We used one of those cell line designated as B05-1. B05-1 cells were cultured in the medium with tetracycline for routine maintenance, and cultured in the medium without tetracycline for four days to maximally induce the expression of the dominant negative BRG-1, which we designated as B05-1(+tet) and B05-1(-tet) cells, respectively. The aim of our microarray experiments was to determine the genes whose expression levels are changed by inactivation of the SWI-SNF complexes by analyzing the genes differentially expressed between B05-1(+tet) and B05-1(-tet) cells. It should be noted that, since the comparison was made between B05-1 cells cultured with and without tetracycline for four days, the genes differentially expressed between these two cells do not only represent the genes that are directly regulated by the SWI-SNF complexes but also include the genes that are secondarily affected by SWI-SNF inactivation as well as the genes whose expression is changed by tetracycline effect per se.
2006-01-01 | E-MEXP-434 | biostudies-arrayexpress
Project description:The objective of this study was to investigate which genes are important for Streptococcus pyogenes during intracellular survival in human macrophages. Streptococcus pyogenes is an important human pathogen, which has recently gained recognition as an intracellular microorganism during the course of severe invasive infections such as necrotizing fasciitis. Although the surface anchored M protein has been identified as a pivotal factor affecting phagosomal maturation and S. pyogenes survival within macrophages, the overall transcriptional profile required for the pathogen to adapt and persist intracellularly is yet unknown. To address this, gene expression profiles of S. pyogenes within human macrophages were determined and compared to those of extracellular bacteria using customized microarrays and real-time qRT-PCR. In order to model the early phase of infection involving adaptation to the intracellular compartment, samples were collected 2h post-infection and within 2 h post infection, the expression of 145 streptococcal genes was significantly altered in the intracellular environment. The majority of differentially regulated genes were associated with metabolic and energy-dependent processes. Key upregulated genes in early phase intracellular bacteria were ihk and irr, encoding a two-component gene regulatory system (TCS). We observed that an isogenic S. pyogenes mutant deficient in ihk/irr displayed significantly reduced bacterial counts as compared to wild-type bacteria following infection of macrophages. Comparison of gene expression of selected genes at 2h and 6h post-infection revealed a dramatic shift in response regulators over time with a down-regulation of ihk/irr genes concurrent with an upreguation of the well-studied covR/S two component regulator. In reinfection assays, intracellular bacteria from the 6h time point exhibited significantly greater survival within macrophages than did bacteria collected at the 2h time point. The findings illustrate how gene expression of S. pyogenes during the intracellular life cycle is fine-tuned by temporal expression of specific two-component systems. Five samples with three biological replicates are analysed. Each open reading frame in triplicate (three technical replicas per sample). Resulting in 6-9 data points per gene per condition. The extracellular bacteria are control samples and the internal control is the house-keeping gene gyrase.
2011-09-14 | E-GEOD-32130 | biostudies-arrayexpress
Project description:The overall gene expression of a CvfA- mutant of Streptococcus pyogenes grown in C medium was compared to that of the wild type (HSC5spc). Stationary phase cells (8 hrs post-inoculation) were used because the gene expression of the CvfA- mutant was most different from that of the wild type at stationary phase, while the difference of gene expression between the CvfA- mutant and the wild type was negligible at exponential phase. Two biological replicates (two different RNA sets extracted from the CvfA- mutant and the wild type at different day were used): 399773,399887,399888 vs. 399889,399890,399891 Technical replicates (Microarrays were hybridized with the same RNA with the same dye): 399773 and 399887; 399889 and 399890 Dye swap (Microarrays were hybridized with the same RNA but Cy3 and Cy5 dyes were swapped): 399773, 399887 vs. 399888; 399889, 399890 vs. 399891
2010-06-25 | E-GEOD-15938 | biostudies-arrayexpress
Project description:Changes in gene expression of the serotype A pre-passage wild-type strain H99W with two mouse-passaged strains were examined during log-phase growth at 37 ºC. Analysis included two replicates of each comparison with a Cy3-Cy5 dye swap
2016-08-11 | E-GEOD-59581 | biostudies-arrayexpress
Project description:Transcriptome changes were measured in S. pyogenes strain HSC5 in response to glucose availability, taking samples from the wild type strain (HSC5) grown in carbohydrate poor medium (C medium) versus this same medium with 1% (w/v) Glucose added. Furthermore, the effects of deletion of glucose responsive regulators CcpA and LacD.1 were measured by using isogenic mutants in these genes (Delta CcpA and Delta LacD.1 respectively) compared to the wild type parent strain (HSC5), both grown in C medium with 1% glucose. Experiments were carried out using two biological replicates for each variable tested (ie two independent RNA samples gathered on separate days), and dye exchange experiments for each RNA sample tested were carried out.
2011-02-27 | E-GEOD-25253 | biostudies-arrayexpress
Project description:Microarray was performed on RNA extracted from mid-logarithmic phase in vitro grown non-M1 Streptococcus pyogenes isolates, with either intact or mutant covRS operons. These isolates were compared with corresponding M1 covRS intact and mutant forms to link the expression prolfiles of these non-M1 isolates with invasive pathogenesis. A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=4 peplicates for each strain.
2010-08-27 | E-GEOD-23825 | biostudies-arrayexpress
Project description:Group A streptococci (GAS) may engage different sets of virulence strategies, depending on the site of infection and host context. We previously isolated 2 phenotypic variants of a globally disseminated M1T1 GAS clone: a virulent wild-type (WT) strain, characterized by a SpeB(+)/SpeA(-)/Sda1(low) phenotype, and a hypervirulent animal-passaged (AP) strain, better adapted to survive in vivo, with a SpeB(-)/SpeA(+)/Sda1(high) phenotype. This AP strain arises in vivo due to the selection of bacteria with mutations in covS, the sensor part of a key 2-component regulatory system, CovR/S. To determine whether covS mutations explain the hypervirulence of the AP strain, we deleted covS from WT bacteria (DeltaCovS) and were able to simulate the hypervirulence and gene expression phenotype of naturally selected AP bacteria. Correction of the covS mutation in AP bacteria reverted them back to the WT phenotype. Our data confirm that covS plays a direct role in regulating GAS virulence. A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=10 peplicates for each strain.
2010-09-22 | E-GEOD-24246 | biostudies-arrayexpress
Project description:These arrays measure gene expression across eight Y introgression lines in Drosophila simulans. Four lines (Ya19, Ya23, Ya24, Ya26) carry a D. simulans Y chromosome (from a Cameroon population) and four lines (Sec01, Sec03, Sec08, Sec27) carry a D. sechellia Y chromosome. All lines are otherwise identical with a D. simulans background (UCSD stock center line 14021-0251.092). Four biological replicates of each of eight lines, plus two technical replicates (dye swap), for a total of 32 arrays. Full methods are described in the accompanying publication.
2011-09-29 | E-GEOD-31907 | biostudies-arrayexpress