Saccharomyces
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA376801 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To characterize the ecological interactions among S. cerevisiae strains coming from the same geographical area, we examined the fitness of two natural isolates from San Giovese grapes, alone or in competition, in synthetic wine must (SWM). We performed genome-wide analyses in order to identify the genes involved in yeast competition and cooperation.
2015-07-07 | GSE49550 | GEO
Project description:To characterize the ecological interactions among S. cerevisiae strains coming from the same geographical area, we examined the fitness of two natural isolates from San Giovese grapes, alone or in competition, in synthetic wine must (SWM). We performed genome-wide analyses in order to identify the genes involved in yeast competition and cooperation.
2015-07-07 | GSE49549 | GEO
Project description:The aim of this study is to phenotype a collection of 27 S. cerevisiae commercial wine strains growing within temperatures (4-45ºC) in both minimal media (SD) and synthetic must (SM) and, taking into account µmax value, to select two strains with divergent phenotype in their capacity to grow at low temperature. To confirm this differential phenotype, we design a competition between both strains during wine fermentations. As expected, at low temperature fermentation, the strain showing a good performance out-competes to the strain growing badly in cold. Finally we aimed to decipher the molecular basis underlying this divergent phenotype by analyzing the genomic, proteomic and transcriptomic differences between both strains at low temperature (15ºC) and optimum temperature (28ºC).
2015-03-31 | GSE60140 | GEO
Project description:We describe design, rapid assembly, and characterization of Sc2.0 chromosome VI, synVI. A mitochondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR055W), encoding an essential proteasome subunit; Sc2.0 coding changes reduced Pre4 protein accumulation by half. Completing Sc2.0 specifies consolidation of sixteen synthetic chromosomes into a single strain. We investigated phenotypic, transcriptional, and proteome-wide consequences of Sc2.0 chromosome consolidation in poly-synthetic strains.
2017-02-28 | MSV000080584 | MassIVE
Project description:We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. Strikingly, in a foreign species, nucleosome-depleted regions occur fortuitously in coding regions, and they often act as promoters that are associated with a positioned nucleosome array linked to the length of the transcription unit. nucleosome mapping for 3 strains bearing yeast artificial chromosomes from Kluyveromyces lactis and 2 strains with Debaryomyces hansenii artificial chromosomes in Saccharomyces cerevisiae
2012-06-30 | E-GEOD-39011 | biostudies-arrayexpress
Project description:Alternative polyadenylation gives rise to a wide variety of mRNA isoforms with distinct 3' ends; an individual gene can yield many 3' mRNA isoforms and has a typical pattern of poly(A) site use. To identify possible determinants of polyadenylation site distribution, we have used CRISPR to create Saccharomyces cerevisiae strains harboring precise ORF deletions in candidate genes encoding various factors involved in gene expression. We have performed 3' READS to determine the genome-wide pattern of 3' mRNA isoform endpoints in these mutant strains.
2024-06-20 | GSE235359 | GEO
Project description:To characterize the ecological interactions among S. cerevisiae strains coming from the same geographical area, we examined the fitness of two natural isolates from San Giovese grapes, alone or in competition, in synthetic wine must (SWM). We performed genome-wide analyses in order to identify the genes involved in yeast competition and cooperation. 2 samples and 2 replicates.
2015-07-07 | E-GEOD-49550 | biostudies-arrayexpress
Project description:To characterize the ecological interactions among S. cerevisiae strains coming from the same geographical area, we examined the fitness of two natural isolates from San Giovese grapes, alone or in competition, in synthetic wine must (SWM). We performed genome-wide analyses in order to identify the genes involved in yeast competition and cooperation. 2 samples and 4 replicates.
2015-07-07 | E-GEOD-49549 | biostudies-arrayexpress
Project description:Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains. We identified both common and strain-specific responses. Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance. Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity. We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins. Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses. RNA-seq and transcriptome analysis of six S. cerevisiae natural isolates having different resistant to lignocellulosic hydrolysate. Two biological replicate cell samples (collected on different days) were harvested for RNAseq analysis. Strains were grown in YPD, synthetic hydrolysate without toxins (SynH -HTs), and synthetic hydrolysate with toxins (SynH). Cells were grown for at least three generations to log phase (OD600 ~0.5) and collected by centrifugation.
2016-04-01 | E-GEOD-77505 | biostudies-arrayexpress