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Anaerobic digester metagenome

ABSTRACT: Directional selection reduces propionate accumulation in glycerol and glucose mixed culture fermentations under elevated pCO2

PROVIDER: PRJNA704575 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13781740_1.fastq.gz	Fastqsanger.gz
	SRR13781740_2.fastq.gz	Fastqsanger.gz
	SRR13781741_1.fastq.gz	Fastqsanger.gz
	SRR13781741_2.fastq.gz	Fastqsanger.gz
	SRR13781742_1.fastq.gz	Fastqsanger.gz

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anaerobic digester metagenome

Project description:Glucose Glycerol fed-batch fermentation under elevated pCO2

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Substrate and oxygen dependent citric acid production by Yarrowia lipolytica: Insights through transcriptome and fluxome analysis

Project description:The goal of the study is to use Next generation sequencing (RNA-seq) and 13C based flux analysis to study the underlying regulation of citric acid metabolism in mixed culture fermentation (glucose and glycerl) of Yarrowia lipolytica. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) under oxygen excess and limited conditions with 2 replicates each . Transcriptional profiles showed that under oxygen limited conditions, due to deficient mitochondrial activity, citric acid is being consumed back after glycerol exhaustion eventhough glucose is present in excess. Transcriptome and fluxome profiles showed that glucose is mainly directed towards the Pentose phosphate pathway in the dual substrate fermentations.

2017-05-08 | GSE83109 | GEO

Deletion of glycerol channel aquaporin-9 (Aqp9) impairs long-term blood glucose control in C57BL/6 leptin receptor-deficient (db/db) obese mice

Project description:Deletion of the glycerol channel aquaporin-9 (Aqp9) reduces postprandial blood glucose levels in leptin receptor deficient (db/db) obese mice on a C57BL/6×C57BLKS mixed genetic background. Furthermore, shRNA mediated reduction of Aqp9 expression reduces liver triacylglycerol (TAG) accumulation in a diet induced rat model of obesity. The aim of this study was to investigate metabolic effects of Aqp9 deletion in coisogenic db/db mice of the C57BL/6 background. Aqp9wt db/db and Aqp9-/- db/db mice did not differ in body weight and liver TAG contents. On the C57BL/6 genetic background we observed elevated plasma glucose in Aqp9-/- db/db mice (+ 1.1 mM, life-time average) while plasma insulin concentration was reduced at time of death. Glucose levels changed similarly in pentobarbital anesthetized, glucagon challenged Aqp9wt db/db and Aqp9-/- db/db mice. Liver transcriptional profiling did not detect differential gene expression between genotypes. Metabolite profiling revealed a sex independent increase in plasma glycerol (+55%), glucose (+24%) and reduction in threonate (all at q<0.1) in Aqp9-/- db/db mice compared to controls. Metabolite profiling thus confirms a role of AQP9 in glycerol metabolism of obese C57BL/6 db/db mice. In this animal model of obesity Aqp9 gene deletion elevates plasma glucose and does not alleviate hepatosteatosis.

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Pichia pastoris Glucose/Methanol comparison

2015-08-31 | GSE67690 | GEO

Pichia pastoris Glucose/Methanol comparison

Project description:Comparison of transcription profile of Pichia pastoris cells grown on Glucose medium with Pichia pastoris cells grown on Methanol/Glycerol medium, the fermentations were done in a chemostat. 2 color experiment in reference design. Pichia pastoris reference mix [mixed pool of Pichia pastoris cells sampled from various conditions including cells grown on glycerine, glucose and methanol, on full andminimal medium, in stationary and exponential growth phase, and in different stress states]

2015-08-31 | E-GEOD-67690 | biostudies-arrayexpress

Effects of elevated seawater pCO2 on gene expression patterns in the gills of the green crab, Carcinus maenas

Project description:In order to promote our understanding of the responses of green crab acid-base regulatory epithelia to high pCO2, Baltic Sea green crabs were exposed to a pCO2 of 400 Pa for 3 and 7 days after which posterior gills 7 and 9 were sampled. Gills were then subsequently screened for differentially expressed gene transcripts using a 4,462-feature microarray developed by Towle et al. 2010. For each experimental block (gill7-day3, gill7-day7, gill9-day3, gill9-day7), 6 replicate samples were obtained for control (= 39 Pa) and elevated (= 400 Pa) pCO2 exposed animals. Each microarray slide included 4 technical replicates for each transcript and was hybridized with one control pCO2 (labelled with AlexaFluor555) and one elevated pCO2 cDNA (labelled with AlexaFluor647). Lowess-normalized gene expression was calculated as the log2 of the ratio of the fluorescence intensity of the CO2-treatment cDNA to the fluorescence intensity of the control cDNA (log2 ratio=F635/F532).

2011-10-09 | E-GEOD-28870 | biostudies-arrayexpress

Interactions between Streptococcus thermophilus and Lactobacillus bulgaricus in yoghurt

Project description:Many food fermentations are carried out by mixed cultures of lactic acid bacteria. Interactions between strains are of key importance for the performance of these fermentations. Yoghurt fermentation by Streptoccus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus (L.bulgaricus) is one of the best-described mixed culture fermentations. These species stimulate each other’s growth by the exchange of metabolites such as folic acid and carbon dioxide. Recently, post-genomic studies have been applied to reveal the global physiological response to mixed culture growth in S. thermophilus, but an in-depth molecular analysis of mixed culture growth of both strains remains to be established. Here we report the application of mixed culture transcriptome profiling and a systematic analysis of candidate interaction compounds on growth, which allowed the unraveling of the molecular responses associated with co-culture growth in batch of S. thermophilus CNRZ1066 and L. bulgaricus ATCC BAA-365 in milk.

2010-05-05 | GSE21593 | GEO

Glucose-mediated regulation of glycerol uptake in Rhodosporidium toruloides: Insights through transcriptomic analysis on dual substrate fermentation

Project description:The goal of the study is to use Next generation sequencing (RNA-seq) to study the underlying regulation of glycerol metabolism in mixed culture fermentation (glucose and glycerol) of Rhodosporidium toruloides. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) with 2 replicates each. Transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3–phosphate dehydrogenase (GUT2) enzymes were not down-regulated in the presence of glucose at the transcriptional level. It also showed that this yeast has a different regulation compared to S.cerevisiae. Certain insights into lipid biosynthesis on these mixed cultures are provided at systems level. This analysis provides interesting targets for metabolic engineering in this organism growing on glucose and glycerol.

2016-05-12 | GSE74307 | GEO

Rapid acclimation of juvenile corals to CO2-mediated acidification by up-regulation of HSP and Bcl-2 genes

Project description:We compared the effect of acute (Moya et al 2012) and chronic exposure to elevated pCO2 on gene expression in primary polyps of Acropora millepora

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