Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative genomic hybridization in traditional fermentative Saccharomyces cerevisiae yeasts

ABSTRACT: We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media. Seven S. cerevisiae strains were obtained from natural environments and different fermentation processes. The S. cerevisiae strain S288C was used as a control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Clara IbÃ¡Ã±ez

PROVIDER: E-GEOD-46165 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Molecular Analysis of the Genes Involved in Aroma Synthesis in the Species S. cerevisiae, S. kudriavzevii and S. bayanus var. uvarum in Winemaking

Project description:This research work investigates the hybridization of the genes of Saccharomyces bayanus var. uvarum CECT 12600 and S. kudriavzevii IFO1802 employing S. cerevisiae microarrays. Two strains,one S. kudriavzevii and one S. bayanus var. uvarum were employed for the study. The S. cerevisiae strain S288C was used as control for microarray hybridizations. All experiments were performed using duplicate arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

2014-06-23 | E-GEOD-52446 | biostudies-arrayexpress

Comparative genomic hybridization of wild type yeast isolated from clinical samples and wine fermentations to investigate genetic variability in yeast from different ecological niches

Project description:Using microarrays targeting the complete ORFeome of Saccharomyces cerevisiae S288c, this study investigates the genetic variability present in wild type yeast from different ecological niches by comparative genome hybridization on array (aCGH). Genomic DNA of Saccharomyces strains isolated from clinical samples and strains from wine fermentations, either commercially available or isolated form spontaneous wine fermentations, was compared to genomic DNA of the sequenced laboratory strain S288c, using a common reference experimental design, with two dye-swap replicate hybridizations for each strain and six S288c self-self hybridizations for background noise estimation, in a total of 38 hybridizations.

2008-10-01 | E-MTAB-29 | biostudies-arrayexpress

Comparative genomic hybridization in traditional fermentative Saccharomyces cerevisiae yeasts

Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization, to explore global changes in the genomic DNA of seven S. cerevisiae strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNVs) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.

2013-12-15 | GSE46165 | GEO

Comparative Genomic Hybridization in traditional fermentative Saccharomyces cerevisiae yeasts

Project description:We study the genetics, including microarray karyotyping using comparative genomic hybridization to explore global changes in the genomic DNA, of four S. bayanus var uvarum strains related to traditional fermentations of very different sources comparing to the sequenced S. cerevisiae laboratory strain (S288C). Our final goal is to determine the adaptive evolution of properties of biotechnological interest in Saccharomyces yeasts. Many copy number variations (CNV) were observed, especially in genes associated to subtelomeric regions and transposon elements. Among the fermentation strains, differential CNV was observed in genes related to sugar transport and metabolism. An outstanding example of diverse CNV is the gen PUT1, involved in proline assimilation, which correlated with the adaptation of the strains to the presence of this nitrogen source in the media.

2016-04-15 | GSE67917 | GEO

Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains

Project description:The aim of this study is to phenotype a collection of 27 S. cerevisiae commercial wine strains growing within temperatures (4-45ºC) in both minimal media (SD) and synthetic must (SM) and, taking into account µmax value, to select two strains with divergent phenotype in their capacity to grow at low temperature. To confirm this differential phenotype, we design a competition between both strains during wine fermentations. As expected, at low temperature fermentation, the strain showing a good performance out-competes to the strain growing badly in cold. Finally we aimed to decipher the molecular basis underlying this divergent phenotype by analyzing the genomic, proteomic and transcriptomic differences between both strains at low temperature (15ºC) and optimum temperature (28ºC). Two Saccharomyces cerevisiae strains with divergent phenotype in their capacity to grow and ferment at low temperature were analyzed (P5 strain as a candidate with a good performance in fermentations at low temperature (15ºC) and P24 as a candidate with a worse behavior at low temperature). All experiments were performed using triplicates arrays, and Cy5-dCTP and Cy3-dCTP dye-swap assays were performed to reduce dye-specific bias.

2015-03-31 | E-GEOD-60140 | biostudies-arrayexpress

Identification of multiple transferrin species in spleen from mice with collagen-induced arthritis which may reflect changes in transferrin glycosylation associated with the disease activity. Role of CD38. Set 2 of identified proteins (MALDI TOF/TOF UltrafleXtreme, Bruker).

Project description:Collagen type II-induced arthritis (CIA) is an autoimmune disease that is accompanied by a complex host systemic response, which includes inflammatory and autoimmune reactions. Since to develop CIA is required the injection of antigen in complete Freund’s adjuvant (CFA), which is a water-in-mineral-oil emulsion containing killed Mycobacteria, systemic response proteins related with inflammation can confound the detection or diagnosis of arthritis. CIA in CD38 deficient mice (CD38 KO) is milder than that in C57BL/6 (B6 WT) mice. Protein extracts from spleen were subjected to 2D-DiGE and MS-MALDI-TOF/TOF analysis to identify proteins that were differentially expressed in CD38 KO and B6 WT mice with arthritis, with inflammation, or non-immunized. Differential protein expression was validated by ELISA, or Western-blotting.

2015-12-10 | PXD002643 | Pride

2015-12-11 | PXD003183 | Pride

Distinct Serum Proteome Profiles Associated with Collagen-induced Arthritis, and Complete Freund’s Adjuvant-induced Inflammation in CD38-/- mice: the Discriminative Power of Protein Species or Proteoforms. Spot 269_Spot 500

Project description:Collagen-type-II-induced arthritis (CIA) is an autoimmune disease, which involves a complex host systemic response including inflammatory and autoimmune reactions. CIA in C57BL/6 mice resembles human rheumatoid arthritis (RA) in terms of its disease course, histological findings, and in its response to commonly used anti-arthritic drugs. In this study, the goal has been to identify proteins from serum that change in their abundance in CD38-KO versus WT mice which may reflect their distinct response to an antigen-challenge that induces the development of an autoimmune disease.CIA is milder in CD38-/- than in Wild-type (WT) mice. We analyzed the sera from CD38-/- versus WT mice either with arthritis (CIA+), with no arthritis (CIA-), or with inflammation (Complete Freund’s adjuvant (CFA)-treated mice). To decrease the dynamic concentration range of serum a combinatorial ligand library composed of hexapeptides was used (called ProteoMiner). ProteoMiner-equalized serum samples were then subjected to 2D-DiGE and MS-MALDI-TOF/TOF analyses to identify proteins that changed in their relative abundances. Multivariate analyses revealed that a multi-protein signature (n = 28) was able to discriminate CIA+ from CIA- mice, and WT from CD38-/- mice within each condition. Likewise, a distinct multi-protein signature (n = 16) was identified which differentiated CIA+CD38-/- mice from CIA+ WT mice, and lastly, a third multi-protein signature (n = 18) indicated that CD38-/- and WT mice could be segregated in response to CFA treatment This approach allows the identification of multiple protein species, or proteoforms of a given protein in a single analysis, and therefore, to focus the interest in fully characterize just the protein species that differ in abundance.

2015-07-17 | PXD002071 | Pride

Distinct Serum Proteome Profiles Associated with Collageninduced Arthritis, and Complete Freund’s Adjuvant-induced Inflammation in CD38-/- mice: the Discriminative Power of Protein Species or Proteoforms

Project description:Collagen-type-II-induced arthritis (CIA) is an autoimmune disease, which involves a complex host systemic response including inflammatory and autoimmune reactions. CIA in C57BL/6 mice resembles human rheumatoid arthritis (RA) in terms of its disease course, histological findings, and in its response to commonly used anti-arthritic drugs. In this study, the goal has been to identify proteins from serum that change in their abundance in CD38-KO versus WT mice which may reflect their distinct response to an antigen-challenge that induces the development of an autoimmune disease. CIA is milder in CD38-/- than in Wild-type (WT) mice. We analyzed the sera from CD38-/- versus WT mice either with arthritis (CIA+), with no arthritis (CIA-), or with inflammation (Complete Freund’s adjuvant (CFA)-treated mice). To decrease the dynamic concentration range of serum a combinatorial ligand library composed of hexapeptides was used (called ProteoMiner). ProteoMiner-equalized serum samples were then subjected to 2D-DiGE and MS-MALDI-TOF/TOF analyses to identify proteins that changed in their relative abundances. Multivariate analyses revealed that a multi-protein signature (n = 28) was able to discriminate CIA+ from CIA- mice, and WT from CD38-/- mice within each condition. Likewise, a distinct multi-protein signature (n = 16) was identified which differentiated CIA+ CD38-/- mice from CIA+ WT mice, and lastly, a third multi-protein signature (n = 18) indicated that CD38-/- and WT mice could be segregated in response to CFA treatment This approach allows the identification of multiple protein species, or proteoforms of a given protein in a single analysis, and therefore, to focus the interest in fully characterize just the protein species that differ in abundance.

2015-07-17 | PXD001788 | Pride

2015-12-10 | PXD002644 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data