Microbial community at low temperature
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PROVIDER: PRJEB81546 | ENA |
REPOSITORIES: ENA
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Project description:Adult male fish were exposed to the various temperature acclimation conditions as outlined in the published manuscript and RNA was extracted from fish at each time point as listed in the experiment set description. Abstract: Eurythermal ectotherms commonly thrive in environments that expose them to large variations in temperature on daily and seasonal bases. The roles played by alterations in gene expression in enabling eurytherms to adjust to these two temporally distinct patterns of thermal stress are poorly understood. We used cDNA microarray analysis to examine changes in gene expression in a eurythermal fish, Austrofundulus limnaeus, subjected to long-term acclimation to constant temperatures of 20, 26 and 37 degrees C and to environmentally realistic daily fluctuations in temperature between 20 degrees C and 37 degrees C. Our data reveal major differences between the transcriptional responses in the liver made during acclimation to constant temperatures and in response to daily temperature fluctuations. Control of cell growth and proliferation appears to be an important part of the response to change in temperature, based on large-scale changes in mRNA transcript levels for several key regulators of these pathways. However, cell growth and proliferation appear to be regulated by different genes in constant versus fluctuating temperature regimes. The gene expression response of molecular chaperones is also different between constant and fluctuating temperatures. Small heat shock proteins appear to play an important role in response to fluctuating temperatures whereas larger molecular mass chaperones such as Hsp70 and Hsp90 respond more strongly to chronic high temperatures. A number of transcripts that encode for enzymes involved in the biosynthesis of nitrogen-containing organic osmolytes have gene expression patterns that indicate a possible role for these 'chemical chaperones' during acclimation to chronic high temperatures and daily temperature cycling. Genes important for the maintenance of membrane integrity are highly responsive to temperature change. Changes in fatty acid saturation may be important in long-term acclimation and in response to fluctuating temperatures; however cholesterol metabolism may be most critical for short-term acclimation to fluctuating temperatures. The variable effect of temperature on the expression of genes with daily rhythms of expression indicates that there is a complex interaction between the temperature cycle and daily rhythmicity in gene expression. A number of new hypotheses concerning temperature acclimation in fish have been generated as a result of this study. The most notable of these hypotheses is the possibility that the high mobility group b1 (HMGB1) protein, which plays key roles in the assembly of transcription initiation and enhanceosome complexes, may act as a compensatory modulator of transcription in response to temperature, and thus as a global gene expression temperature sensor. This study illustrates the utility of cDNA microarray approaches in both hypothesis-driven and 'discovery-based' investigations of environmental effects on organisms. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs
2006-01-06 | GSE3981 | GEO
Project description:Bacterial community dynamics in horizontal subsurface flow constructed wetland units treating municipal wastewater
| PRJEB8946 | ENA
Project description:Atlantic cod (~70 g) were exposed to water temperatures of 12 and 17 degrees Celsius (flow-through system), then half the fish in each temperature group were infected with Francisella noatunensis (injection). Fish were sampled prior to temperature challenge, when water temp reached 17 degrees, and five weeks after infection. The left section of the olfactory organ was collected on RNAlater for RNA isolation and sequencing.
2023-08-30 | E-MTAB-12870 | biostudies-arrayexpress
Project description:Continuous airlift operation treating saline oilfield PW
| PRJEB46531 | ENA
Project description:Permafrost soils are extreme environments that exert low-temperature, desiccation and starvation stress on bacteria over thousands to millions of years. To understand how Psychrobacter arcticus 273-4 survived for > 20,000 years in permafrost, transcriptome analysis was performed during growth at 22°C, 17°C, 0°C, and -6°C using a mixed effects ANOVA model. Genes for transcription, translation, energy production and most biosynthetic pathways were down-regulated at low temperatures. Evidence of isozyme exchange was detected over temperature for D-alanyl-D-alanine carboxypeptidases (dac1 and dac2), DEAD-box RNA helicases (csdA and Psyc_0943) and energy efficient substrate incorporation pathways for ammonium and acetate. Specific functions were compensated by up-regulation at low temperature including genes for the biosynthesis of proline, tryptophan, methionine, and histidine. RNases and peptidases were generally up-regulated at low temperatures. Changes in energy metabolism, amino acid metabolism, and RNase gene expression were consistent with induction of the stringent response by relA activity. In contrast to results observed in other psychrophiles and mesophiles, only clpB and hsp33 were up-regulated at low temperature with no up-regulation of other chaperones and peptidyl-prolyl isomerases. Knockout mutants of relA, csdA, and dac2 were all deficient in low temperature growth, but a mutant in dac1 was deficient in growth at 17°C. The combined data suggest that the basal biological machinery including translation, transcription and energy metabolism are well adapted to function across the -6°C to 22°C growth range of P. arcticus and temperature compensation by gene expression was employed to address specific challenges to low-temperature growth.
2008-12-10 | GSE12871 | GEO
Project description:These samples are from RNA collected from specimens held at 4 temperatures (15.5, 20.0, 25.0 and 28.6degC). Specimens were ramped to one of those temperatures over 4 days following a common garden at 11degC for two weeks. RNA was extracted from thorax tissue and used for RNA-seq. Genes with statistically different expression levels among temperatures were identified.
2022-06-20 | GSE206349 | GEO
Project description:Stress resistance induced by mild environmental stress protects animals against aging-associated cellular damages and promotes longevity. Here, we reveal that mild heat triggers innate immune and detoxification responses that confers longevity at warm temperatures. We compared the transcriptome of 25°C-cultivated animals to that of 15°C controls through RNA-seq analysis. A total of 1958 transcripts were differentially regulated, with 1143 up-regulations and 815 down-regulations.
2019-04-18 | GSE115095 | GEO