Chronological Aging of Yeast in SD medium
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe
PROVIDER: GSE55508 | GEO | 2014/03/04
SECONDARY ACCESSION(S): PRJNA239807
REPOSITORIES: GEO
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Project description:Yeast grown in synthetic complete medium (SD) until glucose depletion is aged chronologically. Cells are stressed by lacking of nutrients and accumulating toxic substances, and thus undergo gene expression changes in response to those. We performed microarray experiments to capture gene expression profiles of yeast cultured at 4 different time points. Saccharomyces cerevisiae CENPK 113-7D strain was grown in SD medium (2% glucose). Yeast cells were harvested at Log phase, 2 days, 6 days and 10 days of cultivation for microarray analysis. Each time point was perfromed in triplicate and prepared according to the manufacturer's instructions.
2014-03-04 | E-GEOD-55508 | biostudies-arrayexpress
Project description:Studies using yeast have advanced our understanding of both replicative and chronological aging, leading to the discovery of longevity genes that have homologues in higher eukaryotes. Chronological lifespan in yeast is conventionally defined as the lifespan of a non-dividing cell. To date, this parameter has only been estimated under calorically restricted (CR) conditions, mimicked by starvation. Since post-mitotic cells in higher eukaryotes are rarely calorically-restricted, we sought to develop an alternative experimental system where non-dividing yeast would age chronologically, in the presence of excess nutrients. We report here on a system wherein alginate-encapsulated yeast are packed in a pH- and temperature-controlled bioreactor, then continuously fed non-limiting substrate for extended periods of time. We present demographic, physiological and genomic evidence indicating that after ~120 hrs, immobilized cells cease dividing, remain metabolically very active and retain >95% viability for periods of 17 days. Over the same time interval, starved planktonic cells, cultured using the same media, and also controlled for temperature and pH, retained < 1 % viability in both aerobic and anaerobic cultures,. Unlike planktonic yeast, continuously-fed immobilized cells hyper-accumulate glycogen. FACS analysis of SYTOX green-stained yeast confirms that immobilized cells completely arrest within 5 days of culture, and unlike starving planktonic cells, remain free thereafter of replicative stress and are non-apoptotic. This unusual state is supported by a global gene expression profile that is stable over time, repeatable across replicate experiments, and altogether distinct from planktonic cells cultured in the presence and absence of limiting nutrients. DNA expression profiling, performed here for the very first time on immobilized cells, reveals that glycolytic genes and their trans-acting regulatory elements are upregulated, as are genes involved in remodeling the cell wall and resisting stress; by contrast, many genes that promote cell cycle progression and carry out oxidative metabolism are repressed. Stress resistance transcription factor MSN4 and its upstream effector RIM15 are conspicuously upregulated in the immobilized state, suggesting that nutrient-sensing pathways may play a role in cell viability and longevity when yeast are immobilized and placed in prolonged culture under calorically-unrestricted conditions. The cell cycle arrest in the immobilized state is mediated by RIM 15. Over the time-course of our experiments, well-fed, non-diving immobilized cells do not appear to age. Keywords: comparison of growth states and a time course of immobilized cells Nine growth conditions or time points with two to four replicates each
2011-03-31 | E-GEOD-21187 | biostudies-arrayexpress
Project description:Studies using yeast have advanced our understanding of both replicative and chronological aging, leading to the discovery of longevity genes that have homologues in higher eukaryotes. Chronological lifespan in yeast is conventionally defined as the lifespan of a non-dividing cell. To date, this parameter has only been estimated under calorically restricted (CR) conditions, mimicked by starvation. Since post-mitotic cells in higher eukaryotes are rarely calorically-restricted, we sought to develop an alternative experimental system where non-dividing yeast would age chronologically, in the presence of excess nutrients. We report here on a system wherein alginate-encapsulated yeast are packed in a pH- and temperature-controlled bioreactor, then continuously fed non-limiting substrate for extended periods of time. We present demographic, physiological and genomic evidence indicating that after ~120 hrs, immobilized cells cease dividing, remain metabolically very active and retain >95% viability for periods of 17 days. Over the same time interval, starved planktonic cells, cultured using the same media, and also controlled for temperature and pH, retained < 1 % viability in both aerobic and anaerobic cultures,. Unlike planktonic yeast, continuously-fed immobilized cells hyper-accumulate glycogen. FACS analysis of SYTOX green-stained yeast confirms that immobilized cells completely arrest within 5 days of culture, and unlike starving planktonic cells, remain free thereafter of replicative stress and are non-apoptotic. This unusual state is supported by a global gene expression profile that is stable over time, repeatable across replicate experiments, and altogether distinct from planktonic cells cultured in the presence and absence of limiting nutrients. DNA expression profiling, performed here for the very first time on immobilized cells, reveals that glycolytic genes and their trans-acting regulatory elements are upregulated, as are genes involved in remodeling the cell wall and resisting stress; by contrast, many genes that promote cell cycle progression and carry out oxidative metabolism are repressed. Stress resistance transcription factor MSN4 and its upstream effector RIM15 are conspicuously upregulated in the immobilized state, suggesting that nutrient-sensing pathways may play a role in cell viability and longevity when yeast are immobilized and placed in prolonged culture under calorically-unrestricted conditions. The cell cycle arrest in the immobilized state is mediated by RIM 15. Over the time-course of our experiments, well-fed, non-diving immobilized cells do not appear to age. Keywords: comparison of growth states and a time course of immobilized cells
2011-03-31 | GSE21187 | GEO
Project description:jaw-D plants grown in SD compared to columbia wt. Keywords: parallel sample
2005-02-01 | GSE2081 | GEO
Project description:Bacteroides xylanisolvens SD CC 2a strain:SD CC 2a Genome sequencing and assembly
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Project description:Paenarthrobacter sp. SD Raw sequence reads
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Project description:Yeast cells were grown up in SD media containing all required amino acids. Each strain set was performed in triplicate. One set had no changes, the second set had 1mM methionine supplenting the media for the duration of growth and the third set was exposed to 0.5mM hydrogen peroxide for 15 minutes prior to harvesting
2007-05-01 | E-MEXP-998 | biostudies-arrayexpress
Project description:The present study aimed to perform an extensive, unbiased RNA sequencing (RNA-seq) analysis to identify biological pathways, as well as related diseases and functions, modified by SD in healthy brains. SDs were induced repetitively (2 hours, 30 min intervals) in healthy, female mice and monitored with intrinsic optical signal (IOS) imaging. SD induction was with either focal application of KCl in C57Bl/6 mice or with optogenetic stimulation in Thy1-ChR2-YFP mice. Two hours after onset of SD, total cortical RNA was extracted and subjected to Illumina paired-end RNA sequencing to identify differentially expressed genes (DEGs; fold change >1.25, p-value <0.05). We identified 101 significantly upregulated genes after KCl-induced SDs and 136 after optogenetic induction; of these 57 (31.7%) genes were in common.
2022-10-05 | GSE214623 | GEO