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947 results for “S. cerevisiae”
Transient acetaldehyde production by SO2 producing S. cerevisiae promotes survival of Oenococcus oeni during co-fermentation
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Historical effects during experimental evolution of multicellularity in <em>Saccharomyces cerevisiae</em>
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Dataset for genome-wide profiling of autophagy dynamics under nutrient availability in <em>Saccharomyces cerevisiae</em>
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Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae
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A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae
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Saccharomyces cerevisiae protein phosphorylation and translation accuracy
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Infection by dsRNA viruses is associated with enhanced sporulation efficiency in Saccharoymces cerevisiae
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Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes
<p>Data and code supporting the manuscript "Evidence for two main domestication trajectories in <em>Saccharomyces cerevisiae</em> linked to distinct bread-making processes" by Bigey et al. (2020)</p>
Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change
<p>"Evolve and resequence" (E&R) studies combine experimental evolution and whole-genome sequencing to interrogate the genetics underlying adaptation. Due to ease of handling, E&R work with asexual organisms like bacteria can employ optimized experimental design, with large experiments and many generations of selection. By contrast, E&R experiments with sexually reproducing organisms are more difficult to implement, and design parameters vary dramatically among studies. Thus, efforts have been made to assess how these differences, such as number of independent replicates, or size of experimental populations, impact inference. We add to this work by investigating the role of time sampling – the number of discrete timepoints sequence data is collected from evolving populations. Using data from an E&R experiment with outcrossing <i>Saccharomyces cerevisiae </i>in which populations were sequenced 17 times over ~540 generations, we address the following questions: (i) do more timepoints improve the ability to identify candidate regions underlying selection? And (ii) does high-resolution sampling provide unique insight into evolutionary processes driving adaptation? We find that while time sampling does not improve the ability to identify candidate regions, high-resolution sampling does provide valuable opportunities to characterize evolutionary dynamics. Increased time sampling reveals three distinct trajectories for adaptive alleles: one consistent with classic population genetic theory (i.e. models assuming constant selection coefficients), and two where trajectories suggest more context-dependent responses (i.e. models involving dynamic selection coefficients). We conclude that while time sampling has limited impact on candidate region identification, sampling 8 or more timepoints has clear benefits for studying complex evolutionary dynamics.</p>
Variation at an adhesin locus suggests sociality in natural populations of the yeast Saccharomyces cerevisiae
<p>Microbes engage in numerous social behaviors that are critical for survival and reproduction, and that require individuals to act as a collective. Various mechanisms ensure that collectives are composed of related, cooperating cells, thus allowing for the evolution and stability of these traits, and for selection to favor traits beneficial to the collective. Since microbes are difficult to observe directly, sociality in natural populations can instead be investigated using evolutionary genetic signatures, as social loci can be evolutionary hotspots. The budding yeast has been studied for over a century, yet little is known about its social behavior in nature. Flo11 is a highly regulated cell adhesin required for most lab social phenotypes; studies suggest it may function in cell recognition and its heterogenous expression may be adaptive for collectives such as biofilms. We investigated this locus and found positive selection in the areas implicated in cell-cell interaction, suggesting selection for kin discrimination. We also found balancing selection at an upstream activation site, suggesting selection on the level of variegated gene expression. Our results suggest this model yeast is surprisingly social in natural environments and is likely engaging in various forms of sociality. By utilizing genomic data, this research provides a glimpse of otherwise unobservable interactions.</p>
Figs 22–24 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 22–24. Orthogonius pseudocheni Tian & Deuve, 2006. 22. habitus, male; 23–24. aedeagus, lateral view and apical lamella, dorsal view.
Figs 19–21 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 19–21. Orthogonius macrophthalmus Tian & Deuve, 2013. 19. habitus, male; 20–21. aedeagus, lateral view and apical lamella, dorsal view.
Figs 16–18. Orthogonius angustus Chaudoir, 1871. 16 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 16–18. Orthogonius angustus Chaudoir, 1871. 16. habitus, male; 17–18. aedeagus, lateral view and apical lamella, dorsal view.
Figs 10–12. Orthogonius picipennis Chaudoir, 1871. 10 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 10–12. Orthogonius picipennis Chaudoir, 1871. 10. habitus, holotype, male; 11–12. aedeagus, lateral view and apical lamella, dorsal view.
Figs 6–9 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 6–9. Adeagus of Orthogonius punctum sp. nov., lateral view and dorsal view for apical lamella. 6–7. paratype, from NongNai, S. Vietnam; 8–9. paratype, male, from Khao Lak, S. Thailand.
Figs 4–5 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 4–5. Habitus of Orthogonius punctum sp. nov. 4. paratype, male, from NongNai, S. Vietnam; 5. paratype, male, from Khao Lak, S. Thailand.
Figs 1–3 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 1–3. Orthogonius pectinatus sp. nov. 1. habitus, holotype, male; 2–3. aedeagus, lateral view and apical lamella, dorsal view.
Figs 13–15 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 13–15. Orthogonius nigripes Tian & Deuve, 2000. 13. habitus, male; 14–15. aedeagus, lateral view and apical lamella, dorsal view.
Photo-activatable Ub-PCNA probes reveal new structural features of the S. cerevisiae Polη/PCNA complex
<p><span><span><span><span><span><span><span><span><span><span><span>The Y-family DNA polymerase η (Polη) is critical for the synthesis past damaged DNA nucleotides in yeast through translesion DNA synthesis (TLS). TLS is initiated by monoubiquitination of proliferating cell nuclear antigen (PCNA) and the subsequent recruitment of TLS polymerases. Although individual structures of the Polη catalytic core and PCNA have been solved, a high-resolution structure of the complex of Polη/PCNA or Polη/monoubiquitinated PCNA (Ub-PCNA) still remains elusive, partly due to the disordered Polη C-terminal region and the flexibility of ubiquitin on PCNA. To circumvent these obstacles and obtain structural insights into this important TLS polymerase complex, we developed photo-activatable PCNA and Ub-PCNA probes containing a <i>p</i>-benzoyl-L-phenylalanine (<i>p</i>Bpa) crosslinker at selected positions on PCNA. By photo-crosslinking the probes with full-length Polη, specific crosslinking sites were identified following tryptic digestion and tandem mass spectrometry analysis. We discovered direct interactions of the Polη catalytic core and its C-terminal region with both sides of the PCNA ring. Model building using the crosslinking site information as a restraint revealed multiple conformations of Polη in the polymerase complex. Availability of the photo-activatable PCNA and Ub-PCNA probes will also facilitate investigations into other PCNA-containing complexes important for DNA replication, repair and damage tolerance. </span></span></span></span></span></span></span></span></span></span></span></p>
Supporting Information: High-throughput Saccharomyces cerevisiae cultivation method for credentialing-based untargeted metabolomics
<p>F1: Physiological Constraints: Growth rate, glucose uptake, and intracellular 13C succinate concentration</p> <p>F2: PAVE input and adduct list</p> <p>F3: Credentialing results, HILIC data</p> <p>F4: Credentialing results, RP lipids data</p> <p>F5: HILIC Level 2A annotation with MS-DIAL and manual mass shift quality control</p> <p>F6: R script for the MetFrag/PCLite-based annotation</p> <p>F7: HILIC annotation with MetFrag/PCLite</p> <p>F8: RP-lipids annotation with MS-DIAL</p> <p>F9: Level 1 compounds identification</p> <p>F10: InChKey-based YMDB and HMDB recovery analysis </p> <p>F11: InChKey-based comparison with PAVE publication</p> <p>F12: Statistic Results</p> <p>F13: Supernatant measurements</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.