Transcription profiling of heat shocked Methanococcus jannaschii]
Ontology highlight
ABSTRACT:
ORGANISM(S): Methanococcus jannaschii
SUBMITTER: Douglas Clark
PROVIDER: E-TIGR-18 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Experimental factor: Time after the temperature shift from 30C to 37C or 30C to 48C. Conidia (5x106 /ml) from Aspergillus fumigatus Af293 were incubated in the CM medium for germination (~ 17 hrs) at 30C. The culture was transferred to a water bath of 37C or 48C for continued growth. Samples were taken after the defined time (i.e. 0, 15, 30, 60, 120, and 180 min.).
2005-05-15 | E-MEXP-332 | biostudies-arrayexpress
Project description:Legionella pneumophila Philadelphia-1 strain was grown to stationary phase in AYE broth and starved in freshwater for 2 hours and RNA was harvested with or without sublethal heat shock via immersion in a 55 degree C hot water bath for 5 minutes
2022-02-15 | GSE196713 | GEO
Project description:We have performed quantitative phosphoproteomic analysis on jurkat cells. Phosphorylation change was compared between jurkat cells incubated on ice and those incubated in 37 degree water bath. And the combination of cold induced and OKT3/4 antibody induced signaling was compared.
2022-02-28 | PXD001105 | Pride
Project description:shock treatment<br>Differential gene expression between the alternate 2La arrangements was examined for heat shock treated and control fourth instar larvae at three discrete time points to examine temporal variation in thermal stress response. One week after egg hatching, 72 fourth instar larvae of each 2La inversion polmorphism were randomly selected from multiple pans and placed into individual 13x100 mm glass culture tubes containing 2 mL of water. Heat shock treatment was carried out by placing tube racks containing larvae into a 38?C water bath for 60 min. After heat shock, larvae were placed back into 27?C water until collection, which took place 0.25 h, 2 h, and 8 h later by pooling 24 individuals into a 1.5 mL microcentrifuge tube and snap-freezing them in liquid nitrogen. Samples were stored at -80 ?C until RNA isolation. Control groups were treated identically for each time point with the only difference being that they were not exposed to the 60 min heat shock but rather placed into 27?C water<br>
2011-12-02 | E-MEXP-3078 | biostudies-arrayexpress
Project description:Transcriptional profiling of Bacillus subtilis to lethal heat stress by systematic sampling of bacterial cell suspensions exposed to gradually increasing temperatures. Keywords: Stress response Bacterial cell suspensions exposed to increasing temperatures ranging from 30-62ºC (Cy5 channel) versus 30 degrees C reference (Cy 3 channel), by transfer of the bacterial cell suspension from a 30ºC to a 65ºC water bath; sampling and quenching at 30, 40, 50, 57, 58, 59, 60 and 62ºC; total time to reach 62ºC is ~12 minutes . Biological replicates: 2, independently grown cultures. One replicate per array. Strains B subtilis 168 1A1; B subtilis A163 (food product isolate); B. subtilis MC85 (food product isolate).
2008-12-07 | E-GEOD-12372 | biostudies-arrayexpress
Project description:Transcriptional profiling of Coxiella burnetii phase I (RSA 493) submitting either to Cold and Heat shock comparing to control untreated Coxiella burnetii phase I (RSA 493) grown at 35°C. Four experiments : Cold shock 30 min Vs 35°C; Cold shock 60 min Vs 35°C; Heat shock 30 min Vs 35°C; Heat shock 60 min Vs 35°C 3 biological replicates, independently grown and harvested. Four replicate per array.
2011-01-01 | E-GEOD-21778 | biostudies-arrayexpress
Project description:A screening process was used to determine hyperosmotic as well as cold stress tolerance of a diverse set of Listeria monocytogenes strains and was based on the capacity to grow at sub lethal levels of NaCl and 4M-BM-0C. Analysis of gene expression in cells adapted to cold and hyperosmotic stress revealed significant strain specificity in terms of individual gene expression profiles though general patterns of expression within functional gene subsets were largely similar. . Strain ATCC19115 revealed 150 significantly up- and 146 down-regulated genes in cells adapted to both hyperosmotic and cold stress, 82 up- and 56 down-regulated genes were matching in response to both stresses in strain 70-1700, whereas ScottA, a relatively stress-tolerant strain, showed up-regulation of 77 genes whilst 106 genes were significantly down-regulated. Among these homologously expressed genes only 22 were found to be significantly up-regulated and only 7 were down-regulated in all three strains adapted to hyperosmotic stress and cold temperature, suggesting a dominating strain specific response. Overall adaptation to hyperosmotic and low temperature growth conditions in three L. monocytogenes strains were found to have many parallels, especially when examined using a statistically-based ontological approach. Evidence was presented for strong activation of genes associated with protein synthesis, in particular those coding proteins of the ribosome and involved directly in transcription. Genes associated with DNA maintenance; modification to cell envelope, and cell division were also up-regulated. On the other hand strong suppression of genes associated with carbohydrate metabolism and transport as well as flagella assembly was evident in stress adapted cells most likely due to energy preservation via CodY regulon. This suggests that adaptation to these adverse conditions engages similar mechanisms to cope with the induced stressful environments. The microarray component of the experiments had the aim of determining: i) To examine the gene expression responses of three L. monocytogenes strains that had different intrinsic salt resistances following adaptation to hyperosmotic stress. ii) To examine the gene expression responses of three L. monocytogenes strains that had different intrinsic cold tolerances following adaptation to cold stress. iii) To evaluate common pathways of adaptation to hyperosmotic and cold stresses Control cultures (four biological replicates; exception strain ATCC19115 for the 10%NaCl stress which had three biological replicates) were labeled with Cy3 (exception strain ATCC19115 for the 10%NaCl-3 dyeswapped, where the control was labeled with Cy5 and sample with Cy3) for each treatment sample for three different L. monocytogenes strains. Sample cultures (four biological replicates; exception strain ATCC19115 for the 10%NaCl which had three biological replicates) were labeled with Cy5 (exception strain ATCC19115 for the 10%NaCl-3 dyeswapped, where the control was labeled with Cy5 and sample with Cy3) for each treatment sample for three different L. monocytogenes strains. Condition one M-bM-^@M-^Ssub-lethal hyperosmotic stress: Control culture (Cy3-labelled RNA, except ATCC19115 for the 10%NaCl-3 dyeswapped , where the control was labeled with Cy5 and sample with Cy3) - strains were grown to mid exponential growth phase at 25M-BM-0C (in a shaking water bath) in brain-heart infusion broth. Test cultures (Cy5-labelled RNA, except ATCC19115 for the 10%NaCl-3 dyeswapped , where the control was labeled with Cy5 and sample with Cy3) M-bM-^@M-^S strains grown to mid exponential growth at 25M-BM-0C phase (in a shaking water bath) in BHI broth supplemented with 8% additional NaCl (strain 701700), 10% additional NaCl (strain ATCC19115) or 12% additional NaCl (ScottA). Condition two M-bM-^@M-^S cold stress: Control culture (Cy3-labelled RNA) - strains were grown to mid exponential growth phase at 25M-BM-0C (in a shaking water bath) in brain-heart infusion broth. Test cultures (Cy5-labelled RNA) M-bM-^@M-^S strains grown to exponential growth phase at 4M-BM-0C in BHI broth.
2013-05-04 | E-GEOD-46612 | biostudies-arrayexpress
Project description:Yeast cells were incubated at 25˚C, unless otherwise stated. For SILAC, cells were grown in light labeled (0.03mg/ml Lys0, 0.02mg/ml Arg0) or heavy labeled (0.03mg/ml Lys4, 0.02mg/ml Arg6) amino acid in synthetic defined medium with 2% dextrose for at least 7 generations. heat shock was performed in a shaking water bath at 45˚C for 20 minutes before harvest. Equal OD600 of cells from both labels were collected at mid log phase (OD¬600=0.8-1) by centrifugation at 3,220xg for 5 minutes at 4˚C, washed twice with cold 1×TBS (50mM Tris pH 7.5, 150mM NaCl), mixed, and re-suspended in equal volume of 2×Native lysis buffer (200mM Tris pH 7.5, 150mM NaCl, 2mM PMSF, 2×Protease Inhibitor Cocktails (Sigma-Aldrich), 2mM 1,10-Phenanthroline). Re-suspended cells were snap-frozen drop by drop in liquid nitrogen. The resulting cells pellets were lysed by cyro-grinding in liquid nitrogen with a mortar and pestle mounted on an electric driver (OPS Diagnostics). The lysate was thawed on ice and further diluted 3 times by adding ice-cold 1×Native lysis buffer and 1% NP40 (final concentration). Total cell lysate was pre-cleared twice by centrifugation at 1,000×g at 4˚C for 15min. Pellet fraction was separated by centrifugation at 16,100×g at 4˚C for 15min. The insoluble protein pellet was washed twice with ice-cold 1×Native lysis buffer containing 1% NP40 and re-solubilized in 1×Laemmli Sample Buffer (62.5mM Tris-HCl pH6.8, 2% SDS, 10% Glycerol). Protein concentrations were determined by using BioRad DC™ Protein Assay.
2020-06-12 | PXD012631 | Pride
Project description:Cold hardening treatment, a brief exposure to low temperatures (e.g. 0°C for 2 h), can protect certain insects against subsequent exposure to temperatures sufficiently low to cause damage or lethality. Microarray analysis to examine the changes in transcript abundance associated with cold hardening has been undertaken in Drosophila melanogaster in order to gain insight into this phenomenon. Transcripts associated with 36 genes were identified, a subset of which appeared to be also differentially expressed after heat shock treatment. Quantitative RT-PCR was used to independently determine transcript abundance of a subset of these sequences. Taken together, these assays suggest that stress proteins, including Hsp23, Hsp26, Hsp83 and Frost as well as membrane-associated proteins may contribute to the cold hardening response. Co-reared flies were separated into a control group and a treatment group at random. RNA was isolated from the cold-shocked flies and the respective controls and was used for direct comparisons on cDNA microarrays. Treatments were not varied as they had been optimized in previous studies. A pilot experiment was performed using the Drosophila 7k2 array (GPL311) and subsequently three pairs of independent biological samples were evaluated with the Drosophila 12k1 array (GPL1467).
2005-11-30 | E-GEOD-2989 | biostudies-arrayexpress
Project description:Profound understanding of the mechanisms foodborne pathogenic bacteria utilize in adaptation to the environmental stress they encounter during food processing and storage is of paramount importance in design of control measures. Chill temperature is a central control measure applied in minimally processed foods; however, data on the mechanisms the foodborne pathogen Clostridium botulinum activates upon cold stress are scarce. Global gene expression analysis on the C.M-BM- botulinum ATCC 3502 strain upon temperature downshift from 37 M-BM-0C to 15M-BM- M-BM-0C was performed to identify the cold-responsive gene set of this organism. Significant up- or down-regulation of 16 and 11 genes, respectively, was observed already 1 h after the cold shock. At 5 h after the temperature downshift, 199 and 210 genes were up- and down-regulated, respectively. Thus, the cold shock rapidly affected the expression of a gene set of a relatively small size, indicating a targeted acute response to cold shock, whereas extensive metabolic remodeling took place after prolonged exposure to cold. Induction of genes related to fatty acid biosynthesis, oxidative stress response, and iron uptake and storage was observed, in addition to mechanisms previously characterized as cold-tolerance related in bacteria. Furthermore, induction of several uncharacterized DNA-binding transcriptional regulator-encoding genes was observed, suggesting involvement of novel regulatory mechanisms in the cold shock response of C.M-BM- botulinum. The role of such regulatory proteins, CBO0477 and CBO0558A, in cold tolerance of C.M-BM- botulinum ATCC 3502 was demonstrated by the deteriorated growth of mutants of the respective genes at 17M-BM- M-BM-0C. C. botulinum ATCC 3502 wild type cold-shocked vs. pre-cold-shock; 3 replicates; growth at 37C in TPGY broth batch culture and subjected to cold shock to 15C; sampling at mid-log growth phase before cold shock, and 1 h and 5 h after temperature downshift to 15C (= 3 time points). Dye-swapped hybridization.
2014-02-24 | E-GEOD-51465 | biostudies-arrayexpress