Saccharomyces cerevisiae BY4741
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA385168 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here, we investigate the genetic mechanisms that underlie thermal specialization of closely-related vibrios isolated from coastal water at the Beaufort Inlet (Beaufort, NC, USA). This location experiences large seasonal temperature fluctuations (annual range of ~20°C), and a clear seasonal shift in vibrio diversity has been observed (Yung et al. 2015). This previous study suggested that the mechanisms of thermal adaptation apparently differ based on evolutionary timescale: shifts in the temperature of maximal growth occur between deeply branching clades but the shape of the thermal performance curve changes on shorter time scales (Yung et al. 2015). The observed thermal specialization in vibrio populations over relatively short evolutionary time scales indicates that few genes or cellular processes may contribute to the differences in thermal performance between populations. In order to understand the molecular mechanisms that underlie adaptation to local thermal regimes in environmental vibrio populations, we employ genomic and transcriptomic approaches to examine transcriptomic changes that occur within strains grown at their thermal optima and under heat and cold stress. Moreover, we compare two closely-related strains with different laboratory thermal preferences to identify in situ evolutionary responses to different thermal environments in genome content and alleles as well as gene expression.
2018-07-31 | GSE83396 | GEO
Project description:This experiment examines gene expression profiles in the brains of adult honey bee workers (Apis mellifera) performing different behavioral tasks in the hive. The different behavioral groups examined were nurse, comb builder, guard, undertaker, and forager. The comb builder, guard, and undertaker behavioral groups perform their respective tasks over a relatively short time scale (typically 1 day), while nursing and foraging are longer duration (lasting > 1 week). The purpose of this study was to examine whether behaviors that persist over different time scales are associated with differences in the extent of gene expression changes in the brain.
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Project description:Mammalian genomes are folded into tens of thousands of long-range looping interactions1,2. The cause and effect relationship between looping and genome function is poorly understood, and the extent to which chromatin loops are dynamic on short time scales remains a fundamental unanswered question. Currently available strategies for loop engineering involve synthetic transcription factors tethered to dCas93,4or zinc fingers5,6, which are constitutively expressed5,6or induced on long time scales by the presence of a small molecule3.Here we report a new class of 3D optoepigenetic toolsfor the directed rearrangement of 3D chromatin looping on short time scales using blue light. We create synthetic architectural proteins by fusing the CIBN protein subunit from Arabidopsis thaliana with enzymatically dead Cas9 (dCas9). We target our light-activated dynamic looping system (LADL) to two genomic anchors with CRISPR guide RNAs and engineer their spatial co-localization via light-induced heterodimerization of the cryptochrome 2 (CRY2) protein with dCas9-CIBN. We apply LADL to redirect a stretch enhancer(SE)away from its endogenous Klf4target gene and to the Zfp462promoter. Looping changes occur as early as four hours after light induction. Using single molecule RNA FISH, we observe a LADL-induced increase in the total nascent Zfp462transcripts and the number of Zfp462 alleles expressing simultaneously per cell.Moreover, LADL also increased synchronous Sox2 expression after reinforcement of a known Sox2-SElooping interaction. LADL facilitates loop synchronization across a large population of cells without exogenous chemical cofactors and can enable future efforts to engineer reversible and oscillatory looping on short time scales.
2019-06-24 | GSE115963 | GEO
Project description:Transcripitonal profiling of Saccharomyces cerevisiae treated with 2% n-alkanes vs untreatment
2015-04-07 | GSE38653 | GEO
Project description:RPA12 is a subunit of RNA polymerase I. We used microarrays to know the effect RPA12 deltion in lipid metabolism and identified distinct classes of up-regulated genes during this process.
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Project description:Birds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.
2019-05-01 | GSE120493 | GEO