Identification of Gene Products Involved in the Oxidative Stress Response of Moraxella catarrhalis: Evaluation of OxyR dependent Genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Moraxella catarrhalis
SUBMITTER: Todd Hoopman
PROVIDER: E-GEOD-24351 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Identification of gene products involved in the oxidative stress response of Moraxella catarrhalis.
Hoopman Todd C TC Liu Wei W Joslin Stephanie N SN Pybus Christine C Brautigam Chad A CA Hansen Eric J EJ
Infection and immunity 20101122 2
Moraxella catarrhalis is subjected to oxidative stress from both internal and environmental sources. A previous study (C. D. Pericone, K. Overweg, P. W. Hermans, and J. N. Weiser, Infect. Immun. 68:3990-3997, 2000) indicated that a wild-type strain of M. catarrhalis was very resistant to killing by exogenous hydrogen peroxide (H₂O₂). The gene encoding OxyR, a LysR family transcriptional regulator, was identified and inactivated in M. catarrhalis strain O35E, resulting in an increase in sensitivi ...[more]
Similar Datasets
Project description:Series of DNA microarrays (4) comparing the M. catarrhalis strain 035E response to 50 mM hydrogen peroxide relative to a water-only control. Wild-type cells were exposed to either 50 mM hydrogen peroxide or a water-only control for 15 minutes. RNA was extracted and DNA microarray analysis performed. 4 biologic replicates were studied. One dye swap was included in this series analysis.
2010-12-07 | E-GEOD-24331 | biostudies-arrayexpress
Project description:Analysis of the gene expression pattern of a znuA mutant constructed in the O35E background. It's pattern of expression was compared to that of O35E. 3 biological replicates were prepared. Each replicate was grown in BHI broth and RNA extracted with the Ambion Ribopure bacterial kit.
2014-03-16 | E-GEOD-28027 | biostudies-arrayexpress
Project description:M. catarrhalis strain O35E.rpsl was inoculated into the nasopharynx of healthy, male adult chinchillas. 24 hours later the nasopharyngeal tissues were extracted and homogenized. Total RNA was extracted from these tissue samples. Subsequently, M. catarrhalis genome directed primers were utilized to synthesize cDNA from the total RNA sample. As a control, M.catarrhalis strain O35E.rpsl was grown in BHI broth to a Klett density of 200 units and underwent RNA extraction per standard protocols. The genome directed primers mentioned above were utilized to synthesize cDNA. Both cDNA samples were subsequently labelled with either Cy3 or Cy5 and hybridized to a custom Microarrays, Inc. gene chip and scanned after 16 hours. Differential gene expression was measured utilizing the broth grown cells as the baseline and the chinchilla isolated cells as the experimental variable. There are 5 individual sample results included in this series. These represent the data from four individual biological replicates (i.e. 4 different sets of inoculated animals). For each replicate the control samples are simultaneously grown broth samples. Three dye swap experiments were performed.
2012-04-03 | E-GEOD-13559 | biostudies-arrayexpress
Project description:This series of microarrays explores the genes regulated by the Zur gene of Moraxella catarrhalis. The gene expression profile of O35E Wild-type cells was utilized as the baseline and compared with the gene expression profile of a non-polar mutant of the Zur gene constructed in the O35E background. There were two biologic replicates and two internal dye swaps performed.
2014-03-23 | E-GEOD-28151 | biostudies-arrayexpress
Project description:Comparison of the gene expression profile of Moraxella catarrhalis grown in the presence of 20% pooled human sputum in chemically-defined medium relative to Moraxella catarrhalis grown in chemically-defined medium alone. Moraxella catarrhalis ATCC43617 was grown to mid-logarithmic phase either in the presence of 20% pooled human sputum in chemically-defined medium or in chemically-defined medium alone. Total RNA was extracted from bacterial cells exposed to each of these conditions and cDNA was generated for CyDye labelling. 3 biologic replicates were generated and each replicate underwent a dye swap (total of 6 experimental data collections). The gene expression profile reported is that of Moraxella catarrhalis grown in the presence of pooled human sputum in a chemically-defined medium relative to Moraxella catarrhalis grown only in the presence of the chemically-defined medium.
2014-02-02 | E-GEOD-27059 | biostudies-arrayexpress
Project description:The yeast M-NM-6-crystallin Zta1p interacts specifically with RNA sequences rich in adenine and uracil (AU-rich element). We have looked for possible targets of Zta1p through a comparative transcriptional analysis of the yeast defective in ZTA1 (M-NM-^Tzta1) versus the wild-type by microarray. This revealed that a group of genes implicated on amino acid biosynthesis are affected by the lack of ZTA1. The effect on one of the targets ARG4 was studied in more detail, revealing a clear positive correlation between ZTA1 and ARG4 expression at the mRNA level. We demonstrate that Zta1p is able to bind specifically to the 3M-bM-^@M-^YUTR AU-rich elements of ARG4 mRNA in vitro, suggesting that the mechanism by which ZTA1 modulates the expression of ARG4 is probably mediated by this mRNA binding ability. Moreover, the expression of ZTA1 is also under the control of the TOR pathway, and under Gcn4p, which regulates genes implicated in the response to nutrient availability and the general amino acid control (GAAC). In summary, our results shed light on the functional role of the M-NM-6-crystallin family as stress response proteins, with a conserved functional role, from yeast to humans, in the post-transcriptional regulation of genes that need to be rapidly activated for cell defense. Triplicate biological replicate experiments were performed, where the two strains, M-bM-^HM-^Fzta1 and wild-type, were grown in the presence or absence of hydrogen peroxide. The experimental design was defined to directly compare the M-bM-^HM-^Fzta1 versus the wild-type strain in either of the two hydrogen peroxide treatment conditions (i.e. treated M-bM-^HM-^Fzta1 versus treated wt, or untreated M-bM-^HM-^Fzta1 versus untreated wt). A duplicate hybridization on a separate array with dye swapping was performed in each case to correct for dye bias effects. Thus, a total of 12 array data sets were produced as a result of processing three experimental pairs of samples, for each of two treatment conditions, with dye swap duplicates.
2015-02-27 | E-GEOD-45297 | biostudies-arrayexpress
Project description:Study Objectives: Sleep deprivation is highly prevalent and caused by conditions such as night shift work or illnesses like obstructive sleep apnea. Compromised sleep is proposed to play a role in several cardiovascular, immune related and neurodegenerative disorders. We recently published human serum proteome changes after a simulated night shift. This study aimed to further explore changes in the human blood serum after 6h of sleep deprivation at night by proteomics and systems biological databases. Methods: Human blood serum samples from 8 self-declared healthy females were analyzed using mass spectrometry and high-pressure liquid chromatography. Each subject was their own control, and two samples were taken from each subject, the first one after 6h of sleep at night and the second one after 6h of sleep deprivation the following night. Biological databases and bioinformatic software were used for systems biological analyzes and comparative analysis with other published sleep-related datasets. Results: Of 494 proteins, 66 were found to be differentially expressed after 6h of sleep deprivation at night. Functional enrichment analysis revealed associations of these proteins with several biological functions related to the regulation of cellular processes like protein- and ion-binding connected to platelet degranulation and blood coagulation, as well as associations with different curated gene sets. Conclusions: This study presents serum proteomic changes after 6h of sleep deprivation, supports previous findings that only 6h of sleep deprivation affects several biological processes and revealed a molecular signature of protein changes related to pathological conditions like altered coagulation and platelet function, impaired lipid and immune function and cancer. Keywords: Human blood serum, proteomics, sleep deprivation, cellular stress, functional enrichment analysis
2024-06-27 | PXD045729 | Pride
Project description:To identify genes differentially expressed during L3 lethargus, we collected RNA during the third larval stage (L3) lethargus period, 37 hours after feeding developmentally-arrested L1 animals. Animals in lethargus were identified based on quiescence of locomotion and feeding. Additional time point for RNA collection was in the mid-L3 stage, 32 hours after feeding developmentally-arrested L1 animals. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 153 gene transcripts were up regulated, and 48 gene transcripts were down regulated, during the L3 lethargus period compared to the L3 stage (false discovery rate (FDR) < 0.05). There were 2 groups and 3x replication for each group, for 6 total samples. The groups were (1) L3 and (2) L3-lethargus. We compared L3-lethargus vs L3 using R/maanova. The permutation based p-values for each test were significant for FDRM-bM-^IM-$5%.
2014-04-18 | E-GEOD-46288 | biostudies-arrayexpress
Project description:Background In broilers, heat stress can result in reduced feed consumption, digestive inefficiency, impaired metabolism, and even death. The broiler sector of the U.S. poultry industry incurs approximately $52 million in heat stress-related losses annually. The objective of this study is to characterize the effects of chronic, cyclic heat stress on the transcriptome of a metabolically active organ, the liver. Characterizing the liver transcriptome of heat-stressed broilers will help clarify the effects of heat stress on metabolism. This information will provide a platform for future investigations that further elucidate physiologic responses to heat stress and seek methods to ameliorate the negative impacts of heat. Results Transcriptome sequencing of the livers of 8 broiler males using Illumina HiSeq 2000 technology, resulted in a total of 138 million, 100 base pair single end reads, yielding 13.8 gigabases of sequence. Forty genes were differentially expressed at a significance level of P-value < 0.05 and a fold change ≥ 2 in response to chronic, cyclic heat stress (mid-point of the last day of a 7-day cyclic heat stress of 7 hours per day), with 27 down-regulated and 13 up-regulated. Two gene networks were created from the function-based Ingenuity Pathway Analysis (IPA) of the differentially expressed genes; “Cell Signaling, Molecular Transport, Small Molecule Biochemistry” and “Endocrine System Development and Function, Small Molecule Biochemistry Cell Signaling”. Members of the MAPK signaling pathway and differentially expressed genes that are associated with MAPK-related functions were prominent in the networks. Cellular proliferation and differentiation, inflammationand stress-related signaling, and apoptosis-associated genes were down-regulated in response to heat stress. Genes responsible for inhibiting feed intake and sphingolipidrelated signaling were up-regulated. Genes involved with the regulation of inflammation, stress, thyroid hormone level, and body temperature were both up- and down-regulated. Conclusions Chronic, cyclic heat stress of broilers results in metabolic changes that can be characterized through RNA-seq analysis of the liver transcriptome. The primary affected pathways included cell signaling, molecular transport, endocrine system development and signaling, and small molecule biochemistry. Examination of 2 heat treatments. Four heat stressed liver samples and 4 control liver samples analyzed.
2013-09-20 | E-GEOD-51035 | biostudies-arrayexpress
Project description:This study integrates global transcriptional profiling and the metabolic perturbation induced by fasting and re-feeding. Genetic control of growth and development should be revealed by systematic modeling of metabolic and regulatory pathways. Chicken oligo arrays were used for transcriptional profiling in two time-course experiments. Two critical developmental stages were chosen: immediately after hatchling (Wk1) and prior to marketing of broiler chickens (Wk6). Only male chickens were used to simplify the experimental design. A RNA reference design was employed for microarray hybridization using two reference RNA pools derived from all individuals sampled at either Wk1 or Wk6. Microarray data was acquired using GenePix Pro software. Loess normalization and a linear mixed model were applied in data processing using the R statistical package with LIMMA software [Smyth, G. K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3]. The results show hundreds of differentially expressed genes, which are regulated by age and the metabolic perturbation of fasting and re-feeding. Numerous common genes were found at both developmental stages (Wk1 and Wk6) that could be candidates for controlling growth and development of chickens. Differential expression revealed by either microarray or qRT-PCR analyses of selected genes was highly consistent. QRT-PCR verification of genes acutely depressed by fasting includes AGO1, ANGTPL3, ATPCL, FASN, FAT, ME1, PPARG, SCD1, SREBP1 and THRSPA. Genes up-regulated by fasting were ALDOB, IL-15, LDHB, LIPIN2, PANK1, PPARA and UPP2. These genes are functionally assigned to metabolic enzymes, transcription factors, acute phase proteins, immune factors and involved in various pathways (i.e., fatty acid and amino acid metabolism, glycolysis, growth factor signaling and immune defense). A reference RNA design was used for microarray hybridizations, where the same reference RNA pool was co-hybridized to each target sample on an microarray. The reference RNA pool was made from an equal amount of high-quality amplified RNA (aRNA), derived from all liver samples within each experiment (Wk1 = 50 samples and Wk6 = 30 samples). The reference RNA pool was labeled with Alexa 647 while each target sample was labeled with Alexa 555.
2008-04-01 | E-GEOD-9745 | biostudies-arrayexpress