Spis CSM longterm warming CBASS thermal tolerance
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ABSTRACT:
PROVIDER: PRJNA1026800 | ENA |
REPOSITORIES: ENA
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Project description:Global warming is causing plastic and evolutionary changes in the phenotypes of ectotherms. Yet, we have limited knowledge on how the interplay between plasticity and evolution shapes thermal responses and underlying gene expression patterns. We assessed thermal reaction norm patterns across the transcriptome and identified associated molecular pathways in northern and southern populations of the damselfly Ischnura elegans. Larvae were reared in a common garden experiment at the mean summer water temperatures experienced at the northern (20 °C) and southern (24 °C) latitudes. This allowed a space-for-time substitution where the current gene expression levels at 24 °C in southern larvae are a proxy for the expected responses of northern larvae under gradual thermal evolution to the predicted 4 °C warming. Most differentially expressed genes showed fixed differences across temperatures between latitudes, suggesting that thermal genetic adaptation will mainly evolve through changes in constitutive gene expression. Northern populations also frequently showed plastic responses in gene expression to mild warming, while southern populations were much less responsive to temperature. Thermal responsive genes in northern populations showed to a large extent a pattern of genetic compensation, i.e. gene expression that was induced at 24 °C in northern populations remained at a lower constant level in southern populations, and were associated with metabolic and translation pathways. There was instead little evidence for genetic assimilation of an initial plastic response to mild warming. Our data therefore suggest that genetic compensation rather than genetic assimilation may drive the evolution of plasticity in response to mild warming in this damselfly species.
2020-09-18 | GSE158138 | GEO
Project description:We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. Using SPIs we identified Spt5 target genes that responded with profoundly diverse kinetics and a novel regulatory element of proximal-promoter-pausing. To obtain a genome-wide view of the impact of SPIs on transcription, we performed Global run-on sequencing (GRO-seq) using nuclei of HeLa cells treated with either DMSO (control) or SPI-21.
2019-10-01 | GSE136024 | GEO
Project description:To investigate the efficacy of CRISPR-Csm complexes for RNA- knockdown in eukaryotes, we quantified transcript abundance in HEK293T cells after targeting several nuclear or cytoplasmic RNAs. RNA-seq demonstrates efficient and specific knockdown of CRISPR-Csm compared to Cas13 and shRNA knockdown.
2022-12-12 | GSE220741 | GEO
Project description:We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. Using SPIs we identified Spt5 target genes that responded with profoundly diverse kinetics and a novel regulatory element of proximal-promoter-pausing. To validate that the effects of SPIs are at the transcriptional level, cellular RNA was metabolically labeled with 4-thio-uridine (4sU) for 2 hours in the presence of DMSO or SPI-21 in the presence or absence of TNFα. Newly synthesized labeled RNA was then purified and subjected to RNA-seq.
2019-10-01 | GSE136025 | GEO
Project description:We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. We determined the global effect of short and long-term SPI-21 treatment by RNA-seq and compared the affected genes between the two treatments. The results revealed that temporary and constitutive Spt5-regulated genes can be distinguished by SPIs.
2019-10-01 | GSE136023 | GEO
Project description:We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown effects on proximal-promoter-pausing, NF-κB activation and the expanded-repeat huntingtin gene in neuronal cells. We determined the global effect of short and long-term SPI-21 treatment by RNA-seq and compared the affected genes between the two treatments. The results revealed that temporary and constitutive Spt5-regulated genes can be distinguished by SPIs.
2019-10-01 | GSE136022 | GEO
Project description:Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mecha-nisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year- old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in sum-mer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils. Citation: Domeignoz-Horta LA, Pold G, Erb H, Sebag D, Verrecchia E, Northen T, Louie K, Eloe-Fadrosh E, Pennacchio C, Knorr MA, Frey SD, Melillo JM, DeAngelis KM. Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long-term warming. Glob Chang Biol. 2023 Mar;29(6):1574-1590. doi: 10.1111/gcb.16544.
The work (proposal:https://doi.org/10.46936/10.25585/60001340) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2023-08-04 | MSV000092599 | MassIVE
Project description:Halorubrum sp. CSM-61 Genome sequencing and assembly
| PRJNA501846 | ENA
Project description:Halomonas sp. CSM-2 Genome sequencing and assembly
| PRJNA381545 | ENA
Project description:In a rapidly warming world, exposure to high temperatures may impact fitness, but the gene regulatory mechanisms that link sublethal heat to sexually selected traits are not well understood, particularly in endothermic animals. Our experiment used zebra finches (Taeniopygia guttata), songbirds that experience extreme temperature fluctuations in their native Australia. We exposed captive males to an acute thermal challenge (43°C) compared with thermoneutral (35°C) and lower (27°C) temperatures. We found significantly more heat dissipation behaviors at 43°C and heat retention behaviors at 27°C, temperatures previously shown to reduce song production and fertility. Next, we characterized gene expression in tissues important for mating effort – the posterior telencephalon, for its role in song production, and the testis, for its role in fertility and hormone production. Differential expression of hundreds of genes in the testes, but few in the brain, suggest the brain is more buffered from extreme temperatures. Nevertheless, dopaminergic signaling in the brain co-varied with heat dissipation behaviors, providing a mechanism by which temporary thermal challenges may alter motivational circuits for song production. In both brain and testis, we also observed quantitative continuous variation between thermally sensitive gene networks and individual differences in thermoregulatory behavior, indicating that mechanisms of thermal-behavioral tolerance have microevolutionary potential. Taken together, these results suggest that selection for thermal tolerance could impact performance of sexually selected traits, and in turn, sexual selection in a warming world could influence how thermal tolerance evolves.
2022-10-01 | GSE185196 | GEO