Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA126999 | ENA |
REPOSITORIES: ENA
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Project description:Our approach for the identification and quantification of growth control by the components of yeast cells relies on two complementary screens: In the first, growth rate is changed and the effect on the concentration of cell components is measured (Castrillo et al. 2007, Genome Biology, 6,4). In the second, the concentration of the components is changed (by reducing gene copy number) and the effect on growth rate is measured (Delneri et al., 2008, Nat Gen, 40, 113). The heterozygous deletant (hemizygote) library we use is composed of diploid mutants each lacking one copy of a different gene (Giaever et al., 2002, Nature, 418, 387). When such a pool of mutants is grown in competition, some will grow slower than the others due to their particular mutation. Over time, the proportion of these mutants in the population will decrease a phenotype termed `haploinsufficient. Conversely, some mutants will have a growth-rate advantage and so will increase their proportion in the population; we call these strains `haploproficient. Screening a pool of hemizygotes for their haploinsufficiency (HI)/haploproficiency (HP) phenotypes thus identifies cellular components that have high flux control (HFC) over growth rate. We found that genes that are major controllers of growth rate under nutrient-limitation are not, themselves, subject to growth rate control of their transcription. In this study we have investigated the generality of this rule, first by identifying HFC genes in turbidostat culture, where biomass concentration sets the rate of nutrient addition, growing at the maximum rate (mmax=0.32h-1) permitted by the complex defined medium (FPM) employed. And to study growth-rate effects, competition experiments were performed at higher growth rates (D=0.2h-1 and 0.3h-1) in nitrogen-limited chemostats and, to control for the effect of nitrogen limitation, in FPM using a chemostat at D=0.3h-1 (Pir et al., manuscript in preparation)
2010-12-01 | E-TABM-892 | biostudies-arrayexpress
Project description:Genome expression analysis between the yeast wine strain L-846 (diploid heterozygous) and spore derived from it (diploid homozygous).
2010-06-30 | GSE21214 | GEO
Project description:In order to identify molecular mechanisms associated with PNPLA3 associated non-alcoholic fatty liver disease, we ran RNA sequencing on human induced pluripotent stem cell-derived hepatocyte like cells that were homozygous for the wild type PNPLA3 allele, homozygous for the risk PNPLA3 allele (I148M), or had a complete knock-out of the PNPLA3 gene. The cells were then treated with either oleic acid or palmitic acid to induce a steatotic or a lipotoxic phenotype, respectively. The cells were treated with control medium or medium supplemented with 0.25 mM oleic acid or palmitic acid for 24 hours before samples were collected for RNA sequencing.
2021-09-10 | GSE158182 | GEO
Project description:Cell competition promotes the elimination of weaker cells from a growing population. Here we investigate how cells of Drosophila wing imaginal discs distinguish “winners” from “losers” during cell competition. Using genomic and functional assays we have identified Maxwell`s Demon (Mwd), a cell membrane protein conserved in multicellular animals. Our results suggest that the membrane protein Mwd is a dedicated component of the cell competition response that is required and sufficient to label cells as “winners” or “losers”. In Drosophila, the mwd locus produces three isoforms, mwdubi, mwdLose-A and mwdLose-B. Basal levels of mwdubi are constantly produced. During competition the mwdLose isoforms are upregulated in prospective loser cells. Cell-cell comparison of relative mwdLose and mwdubi levels ultimately determine which cell undergoes apoptosis. This “extracellular code” may constitute an ancient mechanism to terminate competitive conflicts among cells. Two samples have been analysed: tub>dmyc>Gal4 transgene cells (competitor) and tub>cd2>Gal4 control cells (non competitor) at different time points (0, 12, 24 and 48 hours). Each experiment was replicated 6 times, three of them by dye swap.
2011-02-09 | E-GEOD-21230 | biostudies-arrayexpress
Project description:Cell competition promotes the elimination of weaker cells from a growing population. Here we investigate how cells of Drosophila wing imaginal discs distinguish “winners” from “losers” during cell competition. Using genomic and functional assays we have identified Maxwell`s Demon (Mwd), a cell membrane protein conserved in multicellular animals. Our results suggest that the membrane protein Mwd is a dedicated component of the cell competition response that is required and sufficient to label cells as “winners” or “losers”. In Drosophila, the mwd locus produces three isoforms, mwdubi, mwdLose-A and mwdLose-B. Basal levels of mwdubi are constantly produced. During competition the mwdLose isoforms are upregulated in prospective loser cells. Cell-cell comparison of relative mwdLose and mwdubi levels ultimately determine which cell undergoes apoptosis. This “extracellular code” may constitute an ancient mechanism to terminate competitive conflicts among cells.
2011-02-09 | GSE21230 | GEO
Project description:Reciprocal crosses of a diploid Arabidopsis with different ploidies results in different endosperm development patterns and phenotype. Typically if the ploidy is higher on the maternal side, there are fewer endosperm cells which cellularize early, and conversely, if the paternal ploidy is higher, there is more number of endosperm cells which cellularize late. Crosses involving diploid and tetraploid Arabidopsis (C24) are viable, whereas crosses involving the diploid and hexaploid, even though exhibit the above mentioned directional trend in endosperm development, abort (Scott et al 1998). The 'maternalised' and 'paternalised' development of endosperm is also observed in crosses involving some Arabidopsis mutants. Mutants in the fis class of genes, e.g. fis1-medea, when crossed with a diploid Arabidopsis (pollen parent) show endosperm development-seed development similar to a diploid (seed parent) crossed with hexaploid pollen parent. Reciprocal crosses of homozygous met1 and diploid Arabidopsis also exhibit reciprocal trends in endosperm development, where a homozygous met1 mutant (seed parent) crossed with diploid is similar in phenotype to a diploid (seed parent) - tetraploid cross. Endosperm development in the reciprocal cross has phenotypic similarity to the tetraploid (seed parent)-diploid cross (Adams et al 2000). We are interested in understanding gene profiles and trends in expression underlying the endosperm development in the interploidy crosses as well as the fis and met1 mutant.
2010-01-09 | GSE19259 | GEO
Project description:Root and leaf transcriptomes of Arabidopsis plants growing alone or subjected to intraspecific competition
2012-12-06 | E-MEXP-3735 | biostudies-arrayexpress
Project description:The combination of genetic analysis and genome-wide expression profiles make Saccharomyces cerevisiae the cradle of Systems Biology. The way S. cerevisiae uses carbon sources has long been a landmark for studies concerning cellular responses to environmental conditions. S. cerevisiae conserves the entire machinery for utilization of fatty acids, yet with a different compartmentalization compared to higher eukaryotes. We propose S. cerevisiae as a model to understand how perixosomal compartmentalization of oleate metabolism co-evolved with the transcriptional regulatory networks of FA metabolism. With this aim, we performed growth competition experiments in oleate on the pooled collection of all viable yeast null mutants. We integrated results of competitive fitness with transcriptional profiles in oleate, identifying two genes previously not directly associated to FA metabolism: OAR1 and FET3. For the first time we show the importance of iron metabolism not only in maintaining functional mitochondria, but also in influencing peroxisome wellness. An aliquot of the Yeast Homozygous Diploid Deletion Pool (95401.H1Pool, Invitrogen), containing equal amounts of each barcoded viable knock-out mutant from the Saccharomyces Genome Deletion project, was grown in the presence of G418 in YPD medium for 24h, then aliquots of 5x10^7 cells were harvested and stored at -80M-BM-0C. From the same pooled culture, equal amounts of cells were washed and transferred to YP medium added with oleic acid 0.1% and 5%. We collected samples of cells 24h and 72h after carbon source metabolic shift, and genomic DNA was extracted. Each experiment was performed in biological duplicate. The upTAG and downTAG regions were amplified separately in PCR reactions, one for each experimental condition, using specific primers. Amplified upTAG and downTAG sequences were combined in equal amounts and used to probe high-density oligonucleotide arrays (Affymetrix GeneChip_DNA_Tag3). Data analysis was performed as previously described (Pierce et al., 2007). In order to adapt this data analysis protocol to our experimental design, and to the use of GeneChip_DNA_Tag3 arrays, some changes to the procedure have been improved.
2012-04-25 | E-GEOD-21620 | biostudies-arrayexpress
Project description:This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.
| EGAD00001011193 | EGA
Project description:This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.
| EGAD00001011192 | EGA