Effect of Clostridium Group IV Species on mixed culture fermentations
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PROVIDER: PRJEB19351 | ENA |
REPOSITORIES: ENA
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Project description:The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic acid bacteria (LAB) are also an integral part of the microflora of any fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni. Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner. Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control.
2011-06-02 | GSE27085 | GEO
Project description:The yeast Saccharomyces cerevisiae is an important component of the wine fermentation process and determines various attributes of the final product. However, lactic acid bacteria (LAB) are also an integral part of the microflora of any fermenting must. Various wine microorganism engineering projects have been endeavoured in the past in order to change certain wine characteristics, namely aroma compound composition, ethanol concentration, levels of toxic/ allergenic compounds etc. Most of these projects focus on a specific gene or pathway, whereas our approach aims to understand the genetically complex traits responsible for these phenotypes in a systematic manner by implementing a transcriptomic analysis of yeast in mixed fermentations with the LAB O. oeni. Our aim is to investigate interactions between yeast and LAB on a gene expression level to identify targets for modification of yeast and O. oeni in a directed manner. Our goal was to identify the impact that the common wine microorganism O. oeni (malolactic bacteria) has on fermenting yeast cells on a gene expression level. To this end we co-inoculated the yeast and bacteria at the start of fermentation in a synthetic wine must, using yeast-only fermentations witout O. oeni as a control. Fermentations were carried out in synthetic wine must in triplicate for both the control S. cerevisiae VIN13 strain and the mixed fermentation of VIN13 and O. oeni (strain S5). Sampling of yeast for RNA extractions were performed at day 3 of fermentation, during the exponential growth phase of the yeast cells, and again at day 7 of fermentation, during the early stationary growth phase.
2011-06-02 | E-GEOD-27085 | biostudies-arrayexpress
Project description:It is well known that rennin-angiotensin-aldosterone system (RAAS) plays a critical role in the development of diabetic cardiomyopathy. The present study was aimed to clarify the role of a novel member of RAAS, angiotensin IV (Ang IV) and its downstream mediator forkhead box protein O1 (FoxO1), in the pathogenesis of diabetic cardiomyopathy. In vivo, diabetic mice were treated with low-, medium- and high-dose Ang IV, AT4R antagonist divalinal, FoxO1 inhibitor AS1842856 (AS), or their combinations. In vitro, cardiomyocytes and cardiofibroblasts were treated with different concentrations of glucose, low-, medium- and high-dose Ang IV, divalinal, FoxO1-overexpression plasmid (FoxO1-OE), AS or their combinations. The results showed that Ang IV treatment dose-dependently attenuated left ventricular dysfunction, fibrosis, and myocyte apoptosis in diabetic mice. Besides, enhanced autophagy and FoxO1 protein expression by diabetes were dose-dependently suppressed by Ang IV treatment. However, these cardioprotective effects of Ang IV were completely abolished by divalinal administration. Bioinformatics analysis revealed that the differentially expressed genes were enriched in autophagy, apoptosis, and FoxO signaling pathways among control, diabetes, and diabetes+high-dose Ang IV groups. Similar to Ang IV, AS treatment ameliorated diabetic cardiomyopathy in mice. In vitro, high glucose stimulation increased collagen expression, apoptosis, overactive autophagy flux and FoxO1 nuclear translocation in cardiomyocytes, and upregulated collagen and FoxO1 expression in cardiofibroblasts, which were substantially attenuated by Ang IV treatment. However, these protective effects of Ang IV were completely blocked by the use of divalinal or FoxO1-OE, and these detrimental effects were reversed by the additional administration of AS. In summary, Ang IV treatment dose-dependently attenuated left ventricular dysfunction and remodeling in a mouse model of diabetic cardiomyopathy, and the mechanisms involved stimulation of AT4R and suppression of FoxO1-mediated fibrosis, apoptosis, and overactive autophagy.
2020-09-03 | GSE157331 | GEO
Project description:Assembly factors play a critical role in the biogenesis of mitochondrial respiratory chain complexes I-IV where they assist in the membrane insertion of subunits, attachment of co-factors, and stabilization of assembly intermediates. The major fraction of complexes I, III and IV are present together in large molecular structures known as respiratory chain supercomplexes. A number of assembly factors have been proposed as required for supercomplex assembly, including the hypoxia inducible gene 1 domain family member HIGD2A. Using gene-edited human cell lines and extensive steady state, translation and affinity enrichment proteomics techniques we show that loss of HIGD2A leads to defects in the de novo biogenesis of mtDNA-encoded COX3, subsequent accumulation of complex IV intermediates and turnover of COX3 partner proteins. Deletion of HIGD2A also leads to defective complex IV activity. The impact of HIGD2A loss on complex IV was not altered by growth under hypoxic conditions, consistent with its role being in basal complex IV assembly. While in the absence of HIGD2A we show that mitochondria do contain an altered supercomplex assembly, we demonstrate it to harbor a crippled complex IV lacking COX3. Our results redefine HIGD2A as a classical assembly factor required for building the COX3 module of complex IV.
2020-04-22 | PXD016864 | Pride
Project description:Monocot grass species (Poaceae) express a diverse set of multisubunit RNA polymerase enzymes, including Pol II, Pol IV and Pol V. To better understand this functional diversity, we have charted Pol IV function in the model Brachypodium distachyon. Intriguingly, pol IV null mutations in Poaceae crops disrupt growth, reproductive development and seed set. In order to investigate how Pol IV controls vegetative growth and TE activity in these grasses, we have isolated B. distachyon mutant alleles for Pol IV’s largest subunit, NRPD1. We obtained the germplasm in which to screen for these pol IV mutations from the B. distachyon community's sodium azide (NaN) and T-DNA insertion collections.
2024-03-04 | GSE243693 | GEO
Project description:Nudix hydrolase 7 (NUDT7) is a peroxisomal (acyl-)CoA-degrading enzyme that is highly expressed in the liver. We previously showed that liver-specific NUDT7 overexpression affects peroxisomal lipid metabolism, but does not prevent the increase in total liver CoA levels that occurs with fasting. Herein, we show that deletion of Nudt7 alters the composition of the hepatic acyl-CoA pool in mice fed a low fat diet, but only in males fed a western diet does the lack of NUDT7 increase total liver CoA levels. This effect is driven by the accumulation of medium-chain dicarboxylic acyl-CoAs, which are products of the oxidation of dicarboxylic fatty acids in the peroxisomes. We also show that, under conditions of increased cholesterol intake and elevated bile acid synthesis, Nudt7 deletion increases the production of tauro-muricholic acids, decreasing the hydrophobicity index of the intestinal bile acid pool and increasing fecal cholesterol excretion. Collectively, our findings reveal a key role for NUDT7 in the regulation of the final products of bile acid synthesis and dicarboxylic fatty acid oxidation
2022-11-25 | GSE207914 | GEO
Project description:The Mixed Meal Model is a physiology based mathematical model describing the post-meal interplay between glucose, insulin, triglycerides and non-esterified fatty acids (NEFA).The Mixed Meal Model can be fit to meal response data by estimating nine model parameters from measured plasma glucose, insulin, triglyceride, and NEFA trajectories. These estimated model parameters have been shown to capture features of insulin resistance, beta-cell functionality, and liver fat accumulation from the meal response data.
2022-12-31 | MODEL2212300001 | BioModels