Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A 3D printed plastic frame deeply impacts yeast cell growth

ABSTRACT: Solid State Fermentation (SSF) processes have been explored for yeast growth and protein and metabolites production. However, most of these processes lack standardization. In this work, we present a polylactic acid (PLA) 3D printed matrix that dramatically enhances yeast growth when embedded in liquid media compared to equivalent static cultures, and changes yeast expression patterns at the proteome level. Moreover, differences in sugar assimilation and ethanol production, as the main product of alcoholic fermentation, are observed. Our results suggest that these matrixes may be useful for a vast range of biotechnological applications based on yeast fermentation.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: María Luz Valero

LAB HEAD: Manuel Porcar

PROVIDER: PXD043759 | Pride | 2023-09-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Interactors associated to Sas3-dependent NuA3 histone acetyltransferase complex

Project description:The aim of the study is to improve the knowledge on the functionality and dynamic interactions of Sas3 as related to the presence of Gcn5.

2014-11-10 | PXD001090 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: SWATH quantitation of Seminal Plasma proteins

Project description:Breeding schemes for meat production in rabbits involved a three-way cross of specialized lines in which a paternal line inseminates maternal crossbred females. Paternal line or terminal sire are selected for growth traits, being the males used for the production of fertile dose at the insemination centres and farms. So high growth rate males must produce, in addition, semen in sufficient quantity and quality to meet the demand of insemination and, nevertheless, several studies have been showed that selection for growth have effects on reproduction performance in female and males. In rabbits, negative effects has been observed in ovulation induction, prenatal survival and genetic correlation to fertility. Many factors influence the production and quality of rabbit semen, management as collection frequency, environment (season or photoperiod, nutrition and genetic. Most of the previous studies have been focused in the effects of selection on the seminal and sperm parameters but, little attention has been paid to the protein seminal plasma or sperm composition and if these changes could be affect the fertility of seminal doses obtained from the paternal males. The aim of this study was to evaluate if selection program by daily gain in fattening period has changed seminal traits, plasma and sperm proteoma and, the fertility of semen when it is used in artificial insemination. To do this we uses two re-derived groups of paternal males obtained from vitrified embryos with a difference of 18 generations between both groups.

2020-01-13 | PXD015517 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: SWATH quantitation sperm membrane proteins

2020-01-13 | PXD015516 | Pride

Metaprotemic analysis of groundwaters from a coal tar-contaminated aquifer in South Glens Falls, NY: MW37, Gel Slice

Project description:Deciphering the in situ activities of microorganisms is essential for understanding the biogeochemical processes occurring in complex environments. Here we used environmental metaproteomics to obtain information about the identity and activity of subsurface microbial populations in coal-tar-contaminated groundwater. The present study reports metaproteomic data showing high representation of Candidatus Methylomirabilis oxyfera in our study site’s subsurface microbial community. In addition, eight of the nine proteins of the n-damo pathway were identified—indicating that n-damo is an active process occurring in situ in this habitat.

2022-02-22 | PXD001035 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: spermatozoon membrane proteins Spectral Library

2020-01-13 | PXD015510 | Pride

Evaluation by re-derivation of a paternal line after 18th generations on seminal traits, proteome and fertility: Seminal Plasma Spectral Library

2020-01-13 | PXD015511 | Pride

Quantitative Proteome of enzymatically isolated rumen epithelium in sheep with low or high methane emission.

Project description:Ruminant livestock are one of the major contributors to carbon emission contributing the global warming issue. Methane (CH4) produced from enteric microbial fermentation of feed in the reticulo-rumen are known to differ between sheep with different digestive function and fermentation products such as metabolites. However, the molecular mechanism underpinning differences in methane emission remains to be fully elucidated. We extracted a membrane and cytosolic protein fraction of rumen epithelium proteins from both high (H) and low (L) CH4 emitting sheep. Protein abundance differences between the phenotypes were quantified using SWATH-mass spectrometry. We identified 92 proteins annotated as cell surface transporters, of which only solute carrier family (SLC) 40A1 had a greater fold change of protein expression in the high methane emission phenotype. The main difference in protein abundance we found were related to the metabolism of glucose, lactate and processes of cell defence against microbes in the epithelium of sheep in each group. To best of our knowledge, this represents one of the most comprehensive proteomes of ovine rumen epithelium to date.

2023-03-11 | PXD026538 | Pride

Bull sperm SWATH-MS-based proteomics reveals link between high fertility and energy production, motility structures, and sperm-oocyte interaction. Quantitation

Project description:Prediction of male or semen fertility potential remains a persistent challenge that has yet to be fully resolved. This work analyzed several in vitro parameters and proteome of spermatozoa in bulls cataloged as high (HF; n=5) and low field (LF; n=5) fertility after more than a thousand artificial inseminations. Sperm motility was evaluated by Computer-Assisted Sperm Analysis. Sperm viability, mitochondrial membrane potential (MMP), and reactive oxygen species (mROS) of spermatozoa were assessed by flow cytometry. Proteome was evaluated by SWATH-MS procedure. Spermatozoa of HF bulls showed significantly higher total motility than the LF group (41.4% vs. 29.7%). Rates of healthy sperm (live, high MMP, and low mROS) for HF and LF bull groups were 49% and 43%, respectively (p > 0.05). Spermatozoa of HF bulls showed higher presence of differentially abundant proteins (DAPs) related to both energy production (COX7C), mainly OXPHOS pathway, and to the development of structures linked with the motility process (TPPP2, SSMEM1 and SPAG16). Furthermore, we observed that EQTN, together with other DAPs related to the interaction with the oocyte, were overrepresented in HF bull spermatozoa. The biological processes related to protein processing, catabolism, and protein folding were found to be overrepresented in LF bull sperm in which the HSP90AA1 chaperone was identified as the most DAP

2023-10-18 | PXD042286 | Pride

Characterization of plasma proteins of HIV/AIDS patients underfirst line anti-retroviral therapy

Project description:The retrospective cohort study was focused on the first line ART patients who were enrolled in the antiretroviral therapy center, Sarojini Naidu Medical College, Agra, India from December 2009 to November 2016. The main criteria for inclusion was based on the immunological marker, i.e. CD4+ count (<350). The all age group adults and adolescents were included in this study. The informed consents were obtained from all patients. A patient information leaflet was used for collection of sociodemographic and clinical profile data. This study protocol was approved by Institute human ethics committee. The Institute ethics committee is constituted as per the guidelines directed by Indian Council of MedicalResearch. Ten ml of blood samples were collected from a total of six AIDS patients after counselling whose CD4+ count was <350 cells/µl. Then plasma was separated by centrifugation at 2000g for 10 minutes. Then plasma was stored at -800C for estimation of viral load and genotyping was carried out at NIRT, ICMR, Chennai, Tamilnadu, India.The viral load was estimated using Abbott automated m2000rt instrument. Those who were having>1000 copies/ml called as a drug resistant and < 1000 copies/ml called as drug responder. Among them, 3 patients were having high viral load >1000 copies/ml (drug resistant and 3 patients were with <1000 copies/ml (drug responder). The 3 treatment failure (>1000 copies/ml) samples were further considered for genotype analysis. Highly abundant proteins (Albumin and IgG) were depleted using the Aurum–Serum protein mini kit (Biorad, USA). The depleted plasma samples were analyzed in SWATH-MS. Then, the proteins were identified and characterized using the SWATH analysis.

2023-10-24 | PXD016843 | Pride

Global impact of diet and temperature over aquaculture of Octopus vulgaris paralarvae from a transcriptomic approach

Project description:Common octopus, Octopus vulgaris, is an economically important cephalopod species. However, its rearing under captivity is currently challenged by massive mortalities previous to their juvenile stage due to nutritional and environmental factors. Dissecting the genetic basis and regulatory mechanism behind this mortality requires genomic background knowledge. A transcriptomic sequencing of 10 dph octopus paralarvae from different experimental conditions was constructed via RNA-seq. A total of 613,767,530 raw reads were filtered and de novo assembled into 363,527 contigs of which 82,513 were annotated in UniProt carrying also their GO and KEGG information. Differential gene expression analysis was carried out on paralarvae reared under different diet regimes and temperatures, also including wild paralarvae. Genes related to lipid metabolism exhibited higher transcriptional levels in individuals whose diet includes crustacean zoeas, which had an impact over their development and immune response capability. High temperature induces acclimation processes at the time that increase metabolic demands and oxidative stress. Wild individuals show an expression profile unexpectedly similar to Artemia fed individuals. Proteomic results support the hypothesis revealed by transcriptional analysis. The comparative study of the O. vulgaris transcriptomic profiles allowed the identification of genes that deserve to be further studied as candidates for biomarkers of development and health. The results obtained here on the transcriptional variations of genes caused by diet and temperature will provide new perspectives in understanding the molecular mechanisms behind nutritional and temperature requirements of common octopus that will open new opportunities to deepen in paralarvae rearing requirements.

2019-11-12 | PXD014141 | 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