Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression Data from the Riesling grape must fermentation by industrial M2 and M2 nsf1M-bM-^HM-^F S. cerevisiae strains for functional characterization of the NSF1 (YPL230W) gene via Correlation Clustering-based method

ABSTRACT: The main objectives of this study were to expand our understanding of NSF1 gene function in industrial S. cerevisiae M2 strain during fermentation by finding the largest maximal clique of co-expressed genes (i.e. Interdependent Correlation Cluster), and to establish the impact of Nsf1p on genome-wide gene expression during the fermentation process with possible implications related to wine quality and S. cerevisiae adapation to stressful fermentation conditions The Affymetrix Yeast 2.0 microarrays were used to capture the global gene expression profile of M2 and M2 nsf1M-bM-^HM-^F grown under fermentation conditions in Riesling grape must at 18M-BM-0C with no shaking at various time points. The analysis of this microarray dataset expanded our understanding of the mechanism of action and the roles of NSF1 under fermentation stress conditions. The overall experimental setup consisted of 2 stains (M2 and M2 nsf1M-bM-^HM-^F) and 3 sample time points (24h post-innoculation, 20% and 85% of total glucose fermented) .

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Kyrylo Bessonov

PROVIDER: E-GEOD-34117 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Functional analyses of NSF1 in wine yeast using interconnected correlation clustering and molecular analyses.

Bessonov Kyrylo K Walkey Christopher J CJ Shelp Barry J BJ van Vuuren Hennie J J HJ Chiu David D van der Merwe George G

PloS one 20131009 10

Analyzing time-course expression data captured in microarray datasets is a complex undertaking as the vast and complex data space is represented by a relatively low number of samples as compared to thousands of available genes. Here, we developed the Interdependent Correlation Clustering (ICC) method to analyze relationships that exist among genes conditioned on the expression of a specific target gene in microarray data. Based on Correlation Clustering, the ICC method analyzes a large set of co ...[more]

PMID: 24130853

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Project description:BACKGROUND: Food-borne allergens in human milk (HM) may cause allergic responses in HM-fed infants, but variability of allergen transfer complicates recommendations for individuals nursing food-allergic infants. OBJECTIVE: We aimed to identify bovine- and soy-derived peptides in HM after maternal elimination and reintroduction of bovine milk (BM) and soy beverage (SB). METHODS: In this randomized, cross-over, dietary intervention trial, 38 lactating participants underwent 2 study phases, each including a 5-day diet elimination, 3-day diet intervention, and 2-day washout. Each diet intervention required daily consumption of increasing amounts of BM or SB (175, 295, and 415 mL). Peptidomics analysis was performed on a subset of HM samples (24 participants) collected after dietary elimination, and 2 and 4 h after BM/SB consumption (415 mL). Peptides were isolated via ethanol precipitation and C18 solid-phase extraction, analyzed by LC-MS/MS, and identified with Proteome Discoverer. RESULTS: We identified 121 bovine-derived peptides (associated with 6 proteins) in HM collected during the BM phase. From most to least abundant, these proteins were β-lactoglobulin, κ-casein, αs1-casein, β-casein, α-lactalbumin protein variant D, and glycosylation-dependent cell adhesion molecule 1. Generalized linear mixed models demonstrated differences in relative abundance for 14 peptides when comparing before, and 2 and 4 h after BM consumption. We identified 8 peptides of possible soy origin in HM collected during the SB phase, but they were not matched to parent proteins with adequate confidence. CONCLUSIONS: The relative abundance of some BM-derived peptides, while low overall, may differ in human milk collected after maternal BM dietary elimination compared to 2 and 4 h after BM consumption. Five days of dietary elimination may not be adequate for the elimination of BM-derived peptides or low levels of these non-human peptides may be present in HM from other sources. Soy-derived peptides

Project description:Ubiquitination is a reversible protein modification involved in various cellular processes in eukaryotic cells. Deubiquitinating enzymes, the proteins responsible for the removal of ubiquitin, act as essential regulators to maintain ubiquitin homeostasis and to exquisitely regulate protein degradation via the ubiquitination pathway. Cryptococcus neoformans is an important basidiomycete pathogen that causes life-threatening meningoencephalitis primarily within the immunocompromised population. In order to understand the possible influence deubiquitinating enzymes have on growth and virulence of the model pathogenic yeast Cryptococcus neoformans, we generated deletion mutants of 7 putative deubiquitinase genes. Compared to other deubiquitinating enzyme mutants, a ubp5M-bM-^HM-^F mutant exhibited severely attenuated virulence and many distinct phenotypes, including decreased capsule formation, hypomelanization, defective sporulation, and elevated sensitivity to several external stressors (such as high temperature, oxidative and nitrosative stresses, high salts, and antifungal agents). Ubp5 appears to be the major deubiquitinating enzyme in C. neoformans for maintaining a pool of free ubiquitin for stress responses, supports the evolutionary divergence of Cryptococcus sp. from the model yeast S. cerevisiae, and provides an important paradigm for understanding the potential role of deubiquitination in virulence by other pathogenic fungi. In addition, other putative deubiquitinase mutants (doa4M-bM-^HM-^F and ubp13M-bM-^HM-^F) exhibit similar phenotypes to the ubp5M-bM-^HM-^F mutant, illustrating possible functional overlap among deubiquitinating enzymes in C. neoformans. Certain functioning deubiquitinating enzymes are essential for the virulence composite of C. neoformans and provide an additional yeast survival and propagation advantage in the host. WT strain H99, mutant strains 1A10 (ena1M-bM-^HM-^F, CNAG_00531), and 14A4 (pik1M-bM-^HM-^F, CNAG_07744) were incubated in filter-sterilized human CSF or serum from anonymous human donors at 37M-BM-0C with shaking, and harvested at either 1 or 24 hours post-resuspension in each biological fluid for RNA extraction.

Dataset Information

Expression Data from the Riesling grape must fermentation by industrial M2 and M2 nsf1M-bM-^HM-^F S. cerevisiae strains for functional characterization of the NSF1 (YPL230W) gene via Correlation Clustering-based method

Publications

Functional analyses of NSF1 in wine yeast using interconnected correlation clustering and molecular analyses.

Similar Datasets

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