Transcriptome profiling of Listeria monocytogenes during growth on a RTE-meat matrix
Ontology highlight
ABSTRACT:
ORGANISM(S): Listeria monocytogenes
PROVIDER: GSE20274 | GEO | 2010/02/25
SECONDARY ACCESSION(S): PRJNA125257
REPOSITORIES: GEO
Similar Datasets
Project description:The gene expression profiles of L. monocytogenes strain F2365 grown in BHI agar (reference) or on a turkey deli meat (query) was examined. Aminosilane-coated cDNA microarray slide was used. The data from the normalized ratio of query to reference signal for each spot were transformed using a log2 scale. The expression level of genes obtained from the mean of each gene on the twelve slides was considered significantly different over 1.5 fold changes. Thirty nine and forty five genes in L. monocytogenes grown on a turkey meat matrix were upregulated and downregulated, respectively. To examine the gene expression profiles of L. monocytogenes grown in BHI agar or on a turkey deli meat, L. monocytogenes strains 4b F2365 aminosilane-coated cDNA microarray slide was used. Cy3 and Cy5 dyes were used for cDNA labelling. Data were obtained from three biological and four technical replicates (n = 12). Each biological replicate included a flip dye assay. TM4 package developed by TIGR was used to analyze the data.
2010-05-14 | E-GEOD-20274 | biostudies-arrayexpress
Project description:Gene expression profiles of L. monocytogenes strain F2365 to osmotic stress was examined. Based on a log2 scale, four and 24 genes were upregulated and downregulated by the stress, respectively.The expression level of ATP-binding cassette superfamily and ribosomal protein L2 genes were increased, whereas genes associated with PTS system, its metabolic enzymes, pathogenesis, and hypothetical protein were downregulated. To examine the gene expression profiles of L. monocytogenes grown in the medium added with or without 1.2% NaCl , L. monocytogenes strains 4b F2365 aminosilane-coated cDNA microarray slide was used. Cy3 and Cy5 dyes were used for cDNA labelling. Data were obtained from three biological and four technical replicates (n = 12). Each biological replicate included a flip dye assay.
2010-05-15 | E-GEOD-19570 | biostudies-arrayexpress
Project description:The success of turkey breeding for rapid growth rate and larger breast size has coincided with an increasing incidence of a meat quality defect described as pale, soft and exudative (PSE). We hypothesized that this defect, which is associated with an abnormally rapid rate of postmortem metabolism, derives from altered expression of genes involved in metabolic regulation. Our objective was to use deep transcriptome RNA sequence analysis (RNAseq) to identify differentially expressed genes between normal and PSE turkey breasts. Following harvest of turkey breasts (n = 43), the pH at 15 min post-slaughter and percent marinade uptake at 24h post-slaughter were determined. Breast samples were classified as normal or PSE based on marinade uptake (high = normal; low = PSE). Total RNA from samples with the highest (n=4) and lowest (n=4) marinade uptake were isolated and sequenced using the Illumina GAIIX platform. Of 21,340 gene loci discovered by RNAseq, 8480 loci completely matched the turkey reference genome, and 480 genes were differentially expressed (false discovery rate, FDR<0.05) between normal and PSE samples. Two highlights were the genes nephroblastoma overexpressed (NOV), upregulated about 38-fold and pyruvate dehydrogenase kinase isoform 4 (PDK4), downregulated 14-fold in PSE samples. Pathway analysis suggested that several biological functions, including carbohydrate metabolism and energy production, were affected by meat quality. Because PDK4 regulates conversion of pyruvate to acetyl CoA, differences in regulation of oxidative metabolism may exist among turkeys. Accelerated early postmortem metabolism would result in faster pH decline in PSE meat. This hypothesis was supported by the fact that decreased expression of PDK4 was associated with lower pH in PSE samples (pH[PSE] = 5.59±0.09, pH[normal] = 5.77±0.17). The RNAseq results provided a greater molecular mechanistic understanding of development of PSE turkey, which will be a foundation for new intervention strategies to prevent development of this defect.
2014-01-27 | GSE37176 | GEO
Project description:The success of turkey breeding for rapid growth rate and larger breast size has coincided with an increasing incidence of a meat quality defect described as pale, soft and exudative (PSE). We hypothesized that this defect, which is associated with an abnormally rapid rate of postmortem metabolism, derives from altered expression of genes involved in metabolic regulation. Our objective was to use deep transcriptome RNA sequence analysis (RNAseq) to identify differentially expressed genes between normal and PSE turkey breasts. Following harvest of turkey breasts (n = 43), the pH at 15 min post-slaughter and percent marinade uptake at 24h post-slaughter were determined. Breast samples were classified as normal or PSE based on marinade uptake (high = normal; low = PSE). Total RNA from samples with the highest (n=4) and lowest (n=4) marinade uptake were isolated and sequenced using the Illumina GAIIX platform. Of 21,340 gene loci discovered by RNAseq, 8480 loci completely matched the turkey reference genome, and 480 genes were differentially expressed (false discovery rate, FDR<0.05) between normal and PSE samples. Two highlights were the genes nephroblastoma overexpressed (NOV), upregulated about 38-fold and pyruvate dehydrogenase kinase isoform 4 (PDK4), downregulated 14-fold in PSE samples. Pathway analysis suggested that several biological functions, including carbohydrate metabolism and energy production, were affected by meat quality. Because PDK4 regulates conversion of pyruvate to acetyl CoA, differences in regulation of oxidative metabolism may exist among turkeys. Accelerated early postmortem metabolism would result in faster pH decline in PSE meat. This hypothesis was supported by the fact that decreased expression of PDK4 was associated with lower pH in PSE samples (pH[PSE] = 5.59M-BM-10.09, pH[normal] = 5.77M-BM-10.17). The RNAseq results provided a greater molecular mechanistic understanding of development of PSE turkey, which will be a foundation for new intervention strategies to prevent development of this defect. The mRNA profiles of normal and PSE turkey breast muscle were generated by deep sequencing using Illumina GAIIx platform. Multiplexing was performed (2 samples/lane). Afterwards, difference in gene expression between normal and PSE samples were tested.
2014-01-27 | E-GEOD-37176 | biostudies-arrayexpress
Project description:The proteomes of breast, leg, and thigh meat from turkey were compared using label-free methods.
2017-11-27 | PXD008207 | Pride
Project description:The objective of this study was to determine differential gene expression of turkey breast muscle regarding development of PSE meat defect. Genetically unimproved, random-bred (RBC2) turkeys representing turkeys from 1966, which are smaller and grow slower than modern turkeys, were raised at the Michigan State University (MSU) Poultry farm and harvested at 22 week of age. Breast meat was collected and snap frozen in liquid nitrogen. Percent marinade uptake at 24h post-slaughter of each sample was determined. The highest (n=6) and the lowest (n=6) marinade uptake were classified as normal and PSE, respectively. Differentially expressed genes between normal and PSE was identified using TSMLO microarray and confirmed by qRT-PCR. Forty-one oligos were differentially expressed (false discovery rate, FDR<0.1). Candidate genes and pathways associated with development of PSE in turkey were suggested for further experiment to gain greater comprehension about this meat quality defect.
2013-03-20 | GSE36660 | GEO
Project description:The objective of this study was to determine differential gene expression of turkey breast muscle regarding development of PSE meat defect. Genetically unimproved, random-bred (RBC2) turkeys representing turkeys from 1966, which are smaller and grow slower than modern turkeys, were raised at the Michigan State University (MSU) Poultry farm and harvested at 22 week of age. Breast meat was collected and snap frozen in liquid nitrogen. Percent marinade uptake at 24h post-slaughter of each sample was determined. The highest (n=6) and the lowest (n=6) marinade uptake were classified as normal and PSE, respectively. Differentially expressed genes between normal and PSE was identified using TSMLO microarray and confirmed by qRT-PCR. Forty-one oligos were differentially expressed (false discovery rate, FDR<0.1). Candidate genes and pathways associated with development of PSE in turkey were suggested for further experiment to gain greater comprehension about this meat quality defect. Two-condition experiment: normal vs PSE; Biological replicate: n=6 for each condition; Birds were randomly assigned to an array and hybridizations were performed in random order.
2013-03-20 | E-GEOD-36660 | biostudies-arrayexpress
Project description:Listeria monocytogenes strain F2365 was the first strain representative of serotype 4b (lineage I) to be sequenced in 2004, suggesting it could become the model organism for this serotype, which is associated with most human outbreaks of listeriosis worldwide to date. F2365 itself is an outbreak strain involved in the Mexican-style soft cheese outbreak in California in 1985. In this study we show through phenotypic and transcriptomic analysis that L. monocytogenes strain F2365 has reduced ability to respond to stress due to the absence of a functional M-OM-^CB-dependent stress response system. F2365 shows no M-oM-^AM-3B-dependent ability to survive acid or oxidative stress nor M-oM-^AM-3B-dependent ability to infect Caco-2 epithelial cell in vitro or guinea pigs in vivo. Therefore, there is substantial evidence that F2365 is an atypical strain and is not a suitable representative of outbreak-associated serotype 4b strains. Independent RNA isolations were performed for F2365 and M-NM-^TsigB strains from cells grown to early stationary phase. Three biological replicates were used in competitive whole-genome microarray experiments. For each set of hybridizations, RNA from a L. monocytogenes wildtype strain was hybridized with RNA from its isogenic M-NM-^TsigB null mutant.
2013-06-01 | E-GEOD-42730 | biostudies-arrayexpress
Project description:Listeria monocytogenes strain F2365 was the first strain representative of serotype 4b (lineage I) to be sequenced in 2004, suggesting it could become the model organism for this serotype, which is associated with most human outbreaks of listeriosis worldwide to date. F2365 itself is an outbreak strain involved in the Mexican-style soft cheese outbreak in California in 1985. In this study we show through phenotypic and transcriptomic analysis that L. monocytogenes strain F2365 has reduced ability to respond to stress due to the absence of a functional σB-dependent stress response system. F2365 shows no B-dependent ability to survive acid or oxidative stress nor B-dependent ability to infect Caco-2 epithelial cell in vitro or guinea pigs in vivo. Therefore, there is substantial evidence that F2365 is an atypical strain and is not a suitable representative of outbreak-associated serotype 4b strains.
2013-06-01 | GSE42730 | GEO
Project description:The formation of Listeria monocytogenes biofilms contributes to persistent contamination in food processing facilities. A microarray comparison of L. monocytogenes between the transcriptome of the strong biofilm forming strain (Bfms) Scott A and the weak biofilm forming (Bfmw) strain F2365 was conducted to identify genes potentially involved in biofilm formation. Among 951 genes with significant difference in expression between the two strains, a GntR-family response regulator encoding gene (LMOf2365_0414), designated lbrA, was found to be highly expressed in Scott A relative to F2365. A Scott A lbrA-deletion mutant, designated AW3, formed biofilm to a much lesser extent as compared to the parent strain by a rapid attachment assay and scanning electron microscopy. Complementation with lbrA from Scott A restored the Bfms phenotype in the AW3 derivative. A second microarray assessment using the lbrA deletion mutant AW3 and the wild type Scott A revealed a total of 304 genes with expression significantly different between the two strains, indicating the potential regulatory role of LbrA in L. monocytogenes. A cloned copy of Scott A lbrA was unable to confer enhanced biofilm forming potential in F2365, suggesting that additional factors contributed to weak biofilm formation by F2365. Findings from the study may lead to new strategies to modulate biofilm formation. Two comparisons were performed between 1) strong biofilm former Listeria monocytogenes strain ScottA versus weak biofilm former Listeria monocytogenes strain F2365; 2) Listeria monocytogenes ScottA LbrA deletion mutant strain versus Listeria monocytogenes ScottA. Four replicates were loaded for the first comparison and two replicates were loaded for the second comparison.
2012-09-06 | E-GEOD-40598 | biostudies-arrayexpress