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174 results for “S. pombe”
Data for integrative modeling of the Nuclear Pore Complex from Schizosaccharomyces pombe
<p>Repository with input and output files utilized for integrative modeling of the Nuclear Pore Complex from Schizosaccharomyces pombe.</p>
Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities
<p>Experimental evolution studies with microorganisms such as bacteria and yeast have been an increasingly important and powerful tool to draw long-term inferences of how microbes interact. However, while several strains of the same species often exist in natural environments, many ecology and evolution studies in microbes are typically performed with isogenic populations of bacteria or yeast. In the present study, we firstly perform a genotypic and phenotypic characterization of two lab and eight natural strains of the yeast <i>Schizosaccharomyces pombe</i>. We then propagated, in a rich resource environment, yeast communities of 2-, 3-, 4- and 5-strains for hundreds of generations and asked which fitness related phenotypes – maximum growth rate or relative competitive fitness – would better predict the outcome of a focal strain during the propagations. While the strain's growth rates would wrongly predict long-term co-existence, pairwise competitive fitness with a focal strain qualitatively predicted the success or extinction of the focal strain by a simple multi-genotype population genetics model, given the initial community composition. Interestingly, we have also measured the competitive fitness of the ancestral and evolved communities by the end of the experiment (≈370 generations) and observed frequent maladaptation to the abiotic environment in communities with more than three members. Overall, our results aid establishing pairwise competitive fitness as good qualitative measurement of long-term community composition but also reveal a complex adaptive scenario when trying to predict the evolutionary outcome of those communities.</p>
Competition dynamics in long-term propagations of Schizosaccharomyces pombe strain communities
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Data from: Aging, mortality, and the fast growth trade-off of Schizosaccharomyces pombe
Replicative aging has been demonstrated in asymmetrically dividing unicellular organisms, seemingly caused by unequal damage partitioning. Although asymmetric segregation and inheritance of potential aging factors also occurs in symmetrically dividing species, it nevertheless remains controversial whether this results in aging. Based on large-scale single-cell lineage data obtained by time-lapse microscopy with a microfluidic device, in this report, we demonstrate the absence of replicative aging in old-pole cell lineages of Schizosaccharomyces pombe cultured under constant favorable conditions. By monitoring more than 1,500 cell lineages in seven different culture conditions, we showed that both cell division and death rates are remarkably constant for at least 50–80 generations. Our measurements revealed that the death rate per cellular generation increases with division rate, pointing to a physiological trade-off with fast growth under balanced growth conditions. We also observed the formation and inheritance of Hsp104-associated protein aggregates, which are a potential aging factor in old-pole cell lineages, and found that these aggregates exhibited a tendency to preferentially remain at the old-poles for several generations. However, the aggregates were eventually segregated from old-pole cells upon cell division and probabilistically allocated to new-pole cells. We found that cell deaths were typically preceded by sudden acceleration of protein aggregation, thus relatively large amount of protein aggregates existed at the very ends of the dead cell lineages. Our lineage tracking analyses, however, revealed that the quantity and inheritance of protein aggregates increased neither cellular generation time nor cell death initiation rates. Furthermore, our results demonstrated that unusually large amounts of protein aggregates induced by oxidative stress exposure did not result in aging; old-pole cells resumed normal growth upon stress removal, despite the fact that most of them inherited significant quantities of aggregates. These results collectively indicate that protein aggregates are not a major determinant of triggering cell death in S. pombe, and thus cannot be an appropriate molecular marker or index for replicative aging under both favorable and stressful environmental conditions.
Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array
<p>Although <em>Schyzosaccharomyces pombe</em> is one of the principal model organisms for studying the cell cycle, surprisingly few methods have characterized <em>S. pombe</em> growth on the single cell level, and no methods exist capable of analyzing thousands of cells and tens of thousands of cell division events. We developed an automated microfluidic platform permitting <em>S. pombe</em> to be grown on-chip for several days under defined and changeable conditions. We developed an image processing pipeline to extract and quantitate several physiological parameters including cell length, time to division, and elongation rate without requiring synchronization of the culture. Over a period of 50 hours our platform analyzed over 100000 cell division events and reconstructed single cell lineages up to 10 generations in length. We characterized cell lengths and division times in a temperature shift experiment in which cells were initially grown at 30°C and transitioned to 25°C. Although cell length was identical at both temperatures at steady-state, we observed transient changes in cell length if the temperature shift took place during a critical phase of the cell cycle. We further show that cells born with normal length do divide over a wide range of cell lengths and that cell length appears to be controlled in the second generation, were large newly born cells have a tendency to divide more rapidly and thus at a normalized cell size. The platform is thus applicable to measure fine-details in cell cycle dynamics, should be a useful tool to decipher the molecular mechanism underlying size homeostasis, and will be generally applicable to study processes on the single cell level that require large numbers of precision measurements and single cell lineages.</p>
Data from: Aging, mortality, and the fast growth trade-off of Schizosaccharomyces pombe
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CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5’ ends of genes in S. Pombe
GEO Series GSE41024. Schizosaccharomyces pombe. 40 samples. Type: Expression profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array.
H3K14 and H4 acetylation in wild-type cells of S. pombe
GEO Series GSE72479. Schizosaccharomyces pombe. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A new transcription factor for mitosis: In S. pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression (array)
GEO Series GSE60718. Schizosaccharomyces pombe. 24 samples. Type: Expression profiling by array.
Expression profiling and ChIP-chip of Schizosaccharomyces pombe strains wildtype, erh1∆, and ccr4∆
GEO Series GSE76114. Schizosaccharomyces pombe. 21 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array.
ChIP-chip of histone variants and modifications in S. pombe WT and various mutants
GEO Series GSE31071. Schizosaccharomyces pombe. 26 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ppr10 deletion Schizosaccharomyces pombe cell Transcriptomes
GEO Series GSE90144. Schizosaccharomyces pombe. 2 samples. Type: Expression profiling by high throughput sequencing.
A new transcription factor for mitosis: In S. pombe, the RFX transcription factor Sak1 works with forkhead factors to regulate mitotic expression (ChIP-Seq)
GEO Series GSE60712. Schizosaccharomyces pombe. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Replication origin mapping in cdc25-22 rif1∆ and cdc25-22 rif1∆rad3∆ in S. pombe
GEO Series GSE98446. Schizosaccharomyces pombe. 12 samples. Type: Other.
Genome wide map of heterochromatin state in fission yeast Schizosaccharomcyces pombe (S. pombe)
GEO Series GSE61136. Schizosaccharomyces pombe. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
ChIP-on-chip of RPA (Ssb1) in cdc25-22 and cdc25-22 rad3∆ in Schizosaccharomyces pombe
GEO Series GSE107097. Schizosaccharomyces pombe. 6 samples. Type: Other.
The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage
GEO Series GSE59178. Schizosaccharomyces pombe. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Quantitative mRNA profile of eif3e (yin6, int6) deleted S. pombe cells
GEO Series GSE80349. Schizosaccharomyces pombe. 4 samples. Type: Expression profiling by high throughput sequencing.
Expression profiling in alp13 deletion, clr6-1 mutant and pst1-1 mutant, versus WT S. pombe cells.
GEO Series GSE7252. Schizosaccharomyces pombe. 12 samples. Type: Expression profiling by array.
Structural and functional characterization of the N-terminus of Schizosaccharomyces pombe Cwf10
GEO Series GSE47573. Schizosaccharomyces pombe. 8 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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