Project description:Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in log-phase (6 h) Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in log-phase (6 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of phoU1 or phoU2 in log-phase (6 h). Results: The expression of 23 genes were significantly decreased and 69 genes was significantly increased in expression level due to the loss of phoU1 expression.The expression of 474 genes were significantly decreased and 471 genes were significantly increased in expression level due to the loss of phoU2 expression.
Project description:Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in stationary phase (10 h). Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in stationary phase (10 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of phoU1 or phoU2. Results: The expression of 2 genes were significantly decreased and no genes was significantly increased in expression level due to the loss of phoU1 expression.The expression of 279 genes were significantly decreased and 716 genes were significantly increased in expression level due to the loss of phoU2 expression.
Project description:We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent. To this end, gene expression data for a histone knock-out (?ura3?hpyA) strain versus parent (?ura3) were collected. The histone deletion mutant and parent strain, at log and stationary phase, were compared to the common reference strain NRC-1 (log). There are three biological replicates each, plus dye-flips, for a total of 24 arrays
Project description:We compared the expression profile of TTHA0118 deletion mutant strain of Thermus thermophils HB8 with that of wild-type. The mutant strain grown in minimum essential medium (CS medium) exhibited growth retardation. In early log phase, 29 genes were suppressed and 25 genes were activated for the mutant strain. The suppressed genes included genes of electron transport, and cell growth and division. The activated genes included genes of stress response. We suggested that these transcriptional alterations in the mutant cell were induced by the pAp accumulation and mononucleotides starvation. Keywords: cell type comparison Keywords: cell type comparison
Project description:Transcriptome Comparison of staphylococcus aureus phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (12 h)
Project description:Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in rich medium during growth to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complex medium (CM; 250g/L NaCl, 20g/L MgSO4.7H2O, 3g/L sodium citrate, 2g/L KCl, 10g/L peptone) at 37ºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, late log, and stationary phase to measure genome-wide transcription.
Project description:The custom-made S. epidermidis GeneChips(Shanghai Biochip Co., Ltd) included qualifiers representing open reading frame (ORF) sequences identified in the genomes of the S. epidermidis strain RP62A, as well as unique ORFs in S. epidermidis strain 12228. The GeneChips were composed of cDNA array containing PCR products of 2316 genes and oligonucleotide array containing 252 genes.Two-component regulatory systems (TCSs) play a pivotal role in bacterial adaptation, survival, and virulence by sensing changes in the external environment and modulating gene expression in response to a variety of stimuli.To investigate the regulatory role of LytSR, one of the TCSs identified in the genomes of S. epidermidis, we used the GeneChips to perform a transcriptional profile analysis of the wild strain and lytSR mutant.
Project description:Vancomycin-intermediate Staphylococcus aureus (VISA) evolve in a strain-specific manner and acquire mutations that lead to alterations in cell wall metabolism that reduce susceptibility to vancomycin. We had earlier isolated several VISA mutant strains of the clinical hVISA strain MM66. This study is aimed at analyzing the metabolome of these mutants in comparison to the parent strain.
Project description:Objective of the study is to find out the differentially regulated genes of Mycobacterium BCG strain in extended stationary phase comparison to log phase growth and resuscitation phase. Mycobacterium BCG culture was grown in Sauton medium at 37o C without shaking. Cells at A600 0.6-0.8 were harvested as log phase culture. The cells harvested after 5 months incubation at 37oC without shaking became non culturable and were harvested as extended stationary phase cells. The extended stationary phase cells were treated with resuscitation promoting factor (Rpf) from Micrococcus luteus and harvested after 8 days. Cells of this stage were treated as resuscitation phase cells. Gene expression profiling was carried out using Agilent microarray platform. Keywords: Extended stationary phase, Log phase growth and Resuscitation phase.
