Microarray gene expression profiles from temperature acclimated atrial, ventricular compact and spongy tissues of Pacific bluefin tuna Thunnus orientalis
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ABSTRACT:
ORGANISM(S): Thunnus thynnus Thunnus orientalis
PROVIDER: GSE36886 | GEO | 2012/04/01
SECONDARY ACCESSION(S): PRJNA157011
REPOSITORIES: GEO
Similar Datasets
Project description:In this study, we examined the transcriptomic responses to temperature acclimation (14oC, 20oC, and 25oC) in atrial and ventricular tissues of Pacific bluefin tuna (PBFT). A global gene expression analysis using a bluefin tuna-specific microarray indicated profound changes in expression of genes associated with energy metabolism, protein turnover, cellular stress response, oxidative stress and apoptosis. A principal component analysis revealed tissue-specific transcriptomic responses to temperature, with atrium at 25oC showing the greatest variation. Overall transcriptomic data suggests that PBFT can optimize cardiac function in the cold by acclimating to 14oC. Capacity to acclimate to colder temperatures potentially underlies this species ability to expand its vertical and horizontal thermal niche and migrate to colder oceans at high latitudes. In contrast, the cardiac phenotype of 25oC acclimated fish infers that PBFT hearts struggle to maintain cellular homeostasis and are subjected to programmed cell death. The goal of this study was to compare transcriptomic response to cold and warm temperature acclimations across cardiac tissues in Pacific bluefin tuna. Fish (n=4) were acclimated to 14C, 20C and 25C, and RNA was extracted from atrial, ventricular compact and spongy tissues. Experimental samples were hybridyzed against a reference pool that contained a mix of RNA from every sample.
2012-03-31 | E-GEOD-36886 | biostudies-arrayexpress
Project description:The transcriptomes of model organisms have been defined under specific laboratory growth conditions. The standard protocol for Caenorhabditis elegans growth and maintenance is 20ºC on an Escherichia coli diet. Temperatures ranging from 15ºC to 25ºC or feeding with other species of bacteria are considered physiological lab conditions, but the effect of these conditions on the worm transcriptome have not been well characterized. Here, we compare the global patterns of gene expression for the reference Caenorhabditis elegans strain (N2) grown at 15oC, 20oC, and 25oC on two different diets, Escherichia coli and Bacillus subtilis. When C. elegans were fed E. coli and the growth temperature was increased, we observed an enhancement of defense response pathways and down-regulation of genes associated with metabolic functions. However, when C. elegans were fed B. subtilis and the growth temperature was increased, the nematodes exhibited a decrease in defense response pathways and an enhancement of expression of genes associated with metabolic functions. Our results show that C. elegans undergo significant metabolic and defense response changes when the maintenance temperature fluctuates within the physiologically accepted experimental range and that the degree of pathogenicity of the bacterial diet can further alter the worm transcriptome.
2017-11-02 | GSE101524 | GEO
Project description:Background: Ocean temperatures are projected to increase over the coming century, with dramatic consequences for the marine biosphere. Diatoms are important contributors to marine primary production and the ocean carbon cycle, yet the molecular mechanisms that regulate their acclimation and adaptation to temperature are poorly understood. Method: Here we use a transcriptomic approach to identify the molecular mechanisms associated with temperature acclimation and adaptation in closely related colder- and warmer-adapted diatom species. Results: We find contrasting patterns of differential expression at sub- and supra-optimal temperatures across the two species, which may be due to adaptive changes in baseline expression. Frontloaded and divested pathways indicate protein processing machinery, membrane structure, and the balance between temperature-independent photosynthesis and temperature-dependent metabolism are key elements of adaptation to temperature changes. Conclusions: Our findings suggest that transcriptional frontloading and divestment may provide a framework to interpret diatom acclimation and adaptation to temperature and success under future warming.
2019-07-31 | GSE125205 | GEO
Project description:Healthy five-weeks old S. tuberosum (Red Pontiac) and S. commersonii (Oka 5040) were subjected to cold-acclimating temperature (2oC) in the growth chamber. Control plants at identical developmental stage were also grown in growth chamber at optimum conditions for growth (28oC, 14/10, light/dark, 65% RH). Leaf tissues were collected from the control (reference) and cold-acclimating (experimental treatment, 2oC) plants for each species at 2, 4, 7, 10 and 14 days after the initiation of the control and low temperature treatments. A total of two plants for each species were used for both the control and treatment experiments and tissue samples from each plant (within replicate) were pooled for RNA isolation. These experiments were performed twice in order to produce two sets of biological replicates for each species for all sampling time-points. Keywords: Reference design 17 hybs total
2007-08-31 | E-GEOD-8281 | biostudies-arrayexpress
Project description:Healthy five-weeks old S. tuberosum (Red Pontiac) and S. commersonii (Oka 5040) were subjected to cold-acclimating temperature (2oC) in the growth chamber. Control plants at identical developmental stage were also grown in growth chamber at optimum conditions for growth (28oC, 14/10, light/dark, 65% RH). Leaf tissues were collected from the control (reference) and cold-acclimating (experimental treatment, 2oC) plants for each species at 2, 4, 7, 10 and 14 days after the initiation of the control and low temperature treatments. A total of two plants for each species were used for both the control and treatment experiments and tissue samples from each plant (within replicate) were pooled for RNA isolation. These experiments were performed twice in order to produce two sets of biological replicates for each species for all sampling time-points. Keywords: Reference design
2007-09-01 | GSE8281 | GEO
Project description:Cyanidioschyzon merolae is a thermophilic red alga with an optimum growth temperature of 42°C. In this study we investigated the acclimation process of the alga to a colder temperature (25°C). To this aim we performed quantitative proteomic analyses of whole cells as well as solubilized thylakoid protein complexes.
2017-04-03 | PXD005615 | Pride
Project description:Purpose: House fly has a stable polygenic sex determination system. The male determining factor (Mdmd) is commonly found on the Y chromosome (Y^M) or the third chromosome (III^M). These proto-Y chromosomes are clinally distributed, with Y^M found most commonly in northern latitudes and III^M most commonly found at southern latitudes, hinting at possible genotype-by-temperature interactions that maintain the polymorphism. If this distribution is maintained by temperature-dependent selection pressures, we expect the fitness of III^M and Y^M flies to vary across developmental temperatures. These temperature-dependent effects could be driven by differential gene expression in III^M and Y^M males at different temperatures. Here, we performed RNA-seq experiments to study how genotype-by-temperature interactions affect gene expression in male houseflies carrying different proto-Y chromosomes. Methods: We raised a Y^M strain known as IsoCS and a III^M strain known as CSrab at 18°C and 29°C for two generations. We dissected 5 heads and 15-20 pairs of testes for each of three replicates of each genotype-by-temperature combination. We carried out RNA-seq on these tissues. Results: We identified 247 genes whose expression in testis and 50 genes whose expression in head depends on genotype-by-temperature interactions.
2020-09-01 | GSE136188 | GEO
Project description:Yeast cells were blocked in telophase using a cdc15-2 temperature senstive mutant at restrictive temperature. The culture was then shifted to permissive temperature (25oC), and released into the cell cycle. Samples were then taken during the course of almost three full cell cycles. This study is described in more detail in Spellman PT et al.(1998) Mol Biol Cell 9:3273-97
2002-02-11 | E-GEOD-23 | biostudies-arrayexpress
Project description:Functions of Arabidopsis REI1-LIKE (REIL) proteins, two homologs of a yeast ribosome biogenesis protein (RBP) that takes part in the late cytoplasmic steps of 60S ribosomal subunit maturation, were characterized by systems analyses of the 10°C cold acclimating reil1-1 reil2-1 double mutant compared to Col-0 wildtype. The mutant lacked both REIL proteins, was strongly growth inhibited in the cold and complemented by constitutive expression of N-terminal FLUORESCENT PROTEIN (FP)-REIL1 and FP-REIL2 fusion proteins under control of the UBIQUITIN 10 promoter. Wildtype acclimation to 10°C causes relative accumulation of cytosolic ribosome subunits and rRNA. Expression of cytosolic ribosomal genes, known cytosolic RBPs, translation initiation- and elongation-factors was activated. Conserved function of Arabidopsis REIL proteins was indicated by delay of these processes in reil1-1 reil2-1, cytosolic localization of FP-REIL proteins and native REIL protein interactions with 60S containing ribosome fractions. Non-acclimated reil1-1 reil2-1 triggered plant specific metabolic and transcriptomic cold acclimation responses that included activation of the DREB/CBF-regulon with a preference for the cold acclimation factors, CBF1/DREB1B, CBF2/DREB1C, and CBF3/DREB1A. Cold-acclimating reil1-1 reil2-1 maintained cellular integrity and acquired freezing tolerance but did not activate FLOWERING LOCUS T expression in mature leaves. This block was independent of FLOWERING LOCUS C and AGAMOUS-LIKE 19 mediated vernalization. We conclude that Arabidopsis REIL proteins enhance accumulation of cytosolic ribosome subunits after cold shift and either directly or indirectly feedback on temperature perception by suppression of premature cold acclimation at optimized temperature and by triggering growth and the vegetative to generative phase transition in the cold. Transcriptomic profiling demonstrated a hidden acclimation phenotype of the morphologically inconspicuous reil1-1reil2-1 mutant under optimized temperature conditions. Premature triggering of cold acclimation, a severe growth defect at 10°C and compensation responses indicate that REIL function may extend beyond cytosolic ribosome biogenesis towards translation initiation.
2018-02-01 | GSE101111 | GEO
Project description:In this project, effects of chronic temperature changes on the transcriptome of the rainbow trout heart (Oncorhynchus mykiss) were examined. Ectothermic animals of north-temperate latitudes experience large seasonal changes in temperature which strongly affect the rate of body functions. To compensate for the effects of temperature changes ectotherms can respond to chronic temperature changes by increasing the quantity of tissue or enzyme needed for different physiological tasks, or by expressing proteins isoforms which are more appropriate for the new thermal conditions. On the other hand, proteins which are needed in lesser amounts in the new thermal regime could be depressed or down-regulated. Although expression of proteins can be changed by multiple mechanisms during synthesis and degradation, temperature dependent changes in transcription of genes is probably the most important factor in modifying the proteome of the tissues. Rainbow trout are active throughout their thermal tolerance range (0-25°C). Maintenance of adequate cardiac function at different thermal conditions requires a thorough change of the cardiac phenotype which appears as compensatory changes in relative heart mass, energy metabolism, nervous and humoral control of cardiac contractility and in electrical and mechanical properties of the trout heart. Such an extensive structural and functional remodeling of the heart probably necessitates both qualitative and quantitative changes among the numerous macromolecules which constitute the cardiac phenotype and cannot, therefore, be solely based on posttranslational modification of proteins but is expected to require differential gene expression. As a power supply of the circulatory system, the heart is in the focal point of physiological plasticity and sets limits for the activity level of the animal in different thermal conditions. Although several aspects of heart function have been studied in thermally acclimated fish and a number of structural changes have been noticed on exposure to different temperatures, the cellular and molecular mechanisms involved in chronic thermal stress of the fish heart are only partially elucidated. An interesting and poorly examined feature of the cold-acclimated phenotype of the trout heart is the increased heart mass which attenuates the depressive effect of low temperature on cardiac pump function. The heart is a complex organ composed of multiple tissues which together provide the system all necessary qualifications for cardiac pump function. In addition to the contractile and metabolic machinery of the cardiac myocytes, the amount and quality of the extracellular matrix also contribute to the properties of the heart as a muscular pump. Due to the complexity of the heart an enormous amounts of research efforts are needed to find out and examine all crucial aspects of cardiac plasticity required for thermal acclimation. In this regard the screening of gene expression by cDNA micro arrays might provide a broader view to genomic basis of cardiac remodeling under changing temperatures and aid to reveal the candidate genes which are important for thermal acclimation and which might remain unnoticed by traditional biochemical and physiological methods. In the present study we the steady-state effects of temperature acclimation on gene expression of the rainbow trout heart were screened by micro array analysis.
2010-06-10 | E-GEOD-2277 | biostudies-arrayexpress