Ontology highlight
ABSTRACT:
PROVIDER: PRJNA972270 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24579057_1.fastq.gz | Fastqsanger.gz | |||
| SRR24579057_2.fastq.gz | Fastqsanger.gz | |||
| SRR24579058_1.fastq.gz | Fastqsanger.gz | |||
| SRR24579058_2.fastq.gz | Fastqsanger.gz | |||
| SRR24579059_1.fastq.gz | Fastqsanger.gz |
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Project description:Exploring the metabolic effects of fish protein is important, as by-products from fish contain large amounts of proteins that could be used for human consumption. The aim of this study was to investigate the postprandial effects of intake of protein from salmon by-products, compared to whey. As part of this effort, the effects on gene expression in liver cells were studied in vitro. This was done by incubating HepG2 cells with human serum taken before (fasting) or 30 and 60 min after intake of salmon protein or whey and comparing that with HepG2 cells incubated in serum-free medium. Transcriptomic profiling of the cells was done with RNA sequencing.
2022-04-12 | GSE178584 | GEO
Project description:Over the past decades, stress incidence has dramatically increased in occidental societies. The use of natural resources, like fish hydrolysates, appeared as an interesting strategy to improve stress management. Our previous study demonstrated the anxiolytic effects of a fish hydrolysate supplementation in mice exposed to an acute mild stress, by limiting the stress-induced corticosterone release and modulating expression of some stress-responsive genes. Our work now explores hippocampal protein modulation induced by fish hydrolysate supplementation, in mice submitted to an acute mild stress, with the aim to better elucidate the underlying mechanisms. Hippocampi from the same cohort, Balb/c mice supplemented with fish hydrolysate (300 mg/kg body weight) or vehicle daily for 7 days before being submitted or not to an acute mild stress protocol (4 groups, n=8/group), were subjected to a label-free quantitative proteomics analysis conjugated with gene ontology data mining. Our results demonstrated that an acute mild stress modulated the expression of proteins involved in dopamine metabolism, neuron projection and metabolic process. Moreover, fish hydrolysate supplementation prevented stress-induced dysregulation of proteins relative to mitochondrial pathways and neuronal network. These findings suggest that fish hydrolysate represents an innovative strategy to prevent stress-induced aversive effects and participates in stress management.
2022-05-30 | PXD033053 | Pride
Project description:Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains. We identified both common and strain-specific responses. Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance. Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity. We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins. Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses. RNA-seq and transcriptome analysis of six S. cerevisiae natural isolates having different resistant to lignocellulosic hydrolysate. Two biological replicate cell samples (collected on different days) were harvested for RNAseq analysis. Strains were grown in YPD, synthetic hydrolysate without toxins (SynH -HTs), and synthetic hydrolysate with toxins (SynH). Cells were grown for at least three generations to log phase (OD600 ~0.5) and collected by centrifugation.
2016-04-01 | E-GEOD-77505 | biostudies-arrayexpress
Project description:CRISPR interference screening of 129 protein kinases and 161 transcription factors in S. cerevisiae. Repression effects on yeast growth in oxygen-limited conditions were quantified in synthetic complete media (SCM), SCM supplemented with 10% lignocellulose hydrolysate and SCM supplemented with 45% of a mixture of growth-inhibiting lignocellulosic compounds. The aim of this project was to determine the reproducibility of CRISPRi effects across studies and to characterize CRISPRi for screening of phenotypes relevant for industrial biotechnology. We identify gene functions in general growth in oxygen-limited conditions, and specific for cellular fitness in lignocellulose hydrolysate. A further screen with a cocktail of lignocellulosic compounds enables us to explain hydrolysate-specific gene functions with roles in toxicity.
2021-02-15 | GSE155590 | GEO
Project description:Here, we explored natural variation in stress tolerance and in transcriptomic responses to synthetic hydrolysate, mimicking chemically pretreated plant material, to dissect the physiological effects hydrolysate components. Using six different Saccharomyces cerevisiae strains that together maximized phenotypic and genetic diversity, we explored transcriptomic differences between resistant and sensitive strains. We identified both common and strain-specific responses. Comparing responses of resistant and sensitive strains provided insights about primary cellular targets of hydrolysate toxins, implicating cell wall structure, protein and DNA stability, energy stores and redox balance. Importantly, we uncovered lower expression of thiamine genes while in the presence of toxins, which we argue are most likely an indirect effect that increases sensitivity. We also demonstrate synergistic interactions between the nutrient composition, osmolarity, pH, and classes of hydrolysate toxins. Together, this work provides a platform for further dissecting hydrolysate toxins and strain responses.
2016-04-01 | GSE77505 | GEO
Project description:Interventions: Whey protein
Placebo
Primary outcome(s): After taking whey protein for 1 year, the prevention of colorectal neoplasia will be examined with colonoscopy.
Study Design: Parallel Randomized
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Project description:The effect of dietary calcium and dairy proteins on adipose tissue gene expression profile in diet induced obesity Experiment Overall Design: 9-week-old C57Bl/6J-mice were divided into two groups (n=10/group). The control diet was a standard high-fat diet (60% of energy) low in calcium (0.4%). The whey protein diet was a high-calcium (1.8%) high-fat diet with whey protein isolate. After the 21-week treatment, the adipose tissue transcript profiling (2 mice/group) was carried out using Affymetrix Mouse Genome 430 2.0 array.
2008-04-07 | E-GEOD-9280 | biostudies-arrayexpress
Project description:We previously reported that lifetime consumption of soy proteins or whey proteins reduced the incidence of azoxymethane (AOM)-induced colon tumors in rats. To obtain insights into these effects, global gene expression profiles of colons from rats with lifetime ingestion of casein (CAS, control diet), soy protein isolate (SPI), and whey protein hydrolysate (WPH) diets were determined. We identified 31 induced and 49 repressed genes in the proximal colons of the SPI-fed group and 44 induced and 119 repressed genes in the proximal colons of the WPH-fed group, relative to CAS. Hierarchical clustering identified the co-induction or co-repression of multiple genes by SPI and WPH. The differential expression of I-FABP (2.92-, 3.97-fold down-regulated in SPI and WPH fed rats; P = 0.023, P = 0.01, respectively), cyclin D1 (1.61-, 2.42-fold down-regulated in SPI and WPH fed rats; P = 0.033, P = 0.001, respectively), and the c-neu proto-oncogene (2.46-, 4.10-fold down-regulated in SPI and WPH fed rats; P < 0.001, P < 0.001, respectively) mRNAs were confirmed by real-time quantitative RT-PCR. SPI and WPH affected colonic neuro-endocrine gene expression: peptide YY (PYY) and glucagon mRNAs were down-regulated in WPH fed rats, whereas somatostatin mRNA and corresponding circulating protein levels, were enhanced by SPI and WPH. The identification of transcripts co- or differentially-regulated by SPI and WPH diets suggests common as well as unique anti-tumorigenesis mechanisms of action which may involve growth factor, neuroendocrine and immune system genes. SPI and WPH induction of somatostatin, a known anti-proliferative agent for colon cancer cells, would inhibit tumorigenesis Experiment Overall Design: Male Sprague Dawley rats, fed one of the three purified diets, were studied at 40 weeks after AOM injection and when tumors had developed in some animals of each group. Total RNA, purified from non-tumor tissue within the proximal half of each colon, was used to prepare biotinylated probes, which were hybridized to Affymetrix RG_U34A rat microarrays.
2009-04-30 | E-GEOD-6102 | biostudies-arrayexpress