Functional dissection of QTL-region affecting fat-deposition
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: leila leila farajzadeh
PROVIDER: E-MTAB-1434 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride
Project description:In this study we have employed RNA seq on ten different tissues including four brain tissues from two boars to gain a understanding of the differential variations in transcriptional profiles for these tissues consisting of occipital cortex, frontal cortex, hypothalamus and cerebellum along with such diverse tissues as heart, spleen, liver, kidney, lung and musculus longissimus dorsi. This has enabled us to perform comparative gene expression analysis of brain regions versus non-brain tissues along with inter-brain tissue comparisons. Hence, we have tested for differentially expressed genes and isoforms, differential splicing, transcription start sites (TSS), and differential promoter usage between all ten porcine tissues.
2013-07-22 | E-MTAB-1405 | biostudies-arrayexpress
Project description:The two subunits of IL-35, EBI3 and P35, were fused together and transfected into Panc-1 cell via lentivirus. The sequence of the fused gene is identical to that of a commercial IL-35-overexpessed plasmid (InvivoGEN, pORF9-hIL35elasti). An empty vector was used as the control. The two cell lines were subjected to a genome-wide RNA sequencing.
2016-01-15 | E-MTAB-3710 | biostudies-arrayexpress
Project description:In a previous study, we found that H2S alleviates salinity stress in cucumber by maintaining the Na+/K+ balance and by regulating H2S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H2S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H2S-regulated salt-stress tolerance. In total, 11 761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H2S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase and Peroxidase 2. We present the first global analysis of the mechanism underlying H2S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.
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Project description:Background and Objectives: Brain age is a global measure that compares structural brain MRI with large reference datasets. Predicted age deviation (PAD) is the deviation between predicted brain age and chronological age, with positive values indicating advanced aging. Identifying blood-based biomarkers that approximate brain PAD could provide an accessible and cost-effective measure of brain health as an alternative to MRI, but no blood-based biomarkers have yet been identified. This study aimed to investigate novel blood-based biomarkers associated with accelerated PAD using an unbiased proteomics approach to discover new biomarkers. Methods: This study is a secondary analysis with a cross-sectional case-control design using the LIMBIC-CENC dataset as a discovery approach to understand novel biomarker patterns. Brain age was estimated using brainageR in 137 participants aged ≤40 years with no substantial cognitive deficits or neurological disorders. Cases (n=76) included individuals with brain age ≥5 years older than chronological age, whereas controls (n=61) had brain age equal to or younger than chronological age (PAD range: -1.3 to 0; mean=-0.9) and were otherwise matched on demographics and clinical features. Unbiased proteomic profiling of ~5,400 proteins was performed using the Olink Explore platform. Differential protein expression between groups was assessed using Wilcoxon tests with Benjamini-Hochberg correction. Receiver operating characteristic (ROC) analysis was performed on probabilities derived from generalized linear models (GLMs) to identify optimal protein combinations, prioritizing maximizing both sensitivity and negative predictive value. Results: Olink analyses identified 418 proteins that were significantly different between groups after multiple-comparison correction. Up-regulated proteins in participants with PAD≥5 years included: component inhibitor-nuclear factor kappa-b kinase (CHUK), methenyltetrahydrofolate synthetase domain containing (MTHFSD), and epidermal growth factor (EGF), with log2 fold changes of 1.70-1.80. Insulin-like peptide 3 (INSL3) was the most downregulated protein (log2 fold change -2.27). Enriched pathways involved nuclear factor kappa-b (NF-κB), heat-shock protein, and Wingless/Integrated (Wnt) signaling. Models including 6-7 dysregulated proteins (e.g., CHUK and INSL3) achieved AUCs>0.9, with sensitivities >0.90 and specificities >0.70. Discussion: These discovery-based findings warrant validation in larger cohorts and suggest potential for blood-based protein panel detection of early, clinically silent, pre-pathological accelerated brain aging changes when interventions may be most effective.
2026-09-07 | PAD000050 | Pride
Project description:Objective: This study examined the ability of established brain biomarkers, glial fibrillary acid protein (GFAP), neuro-filament light chain (NFL), ubiquitin carboxy hydrolase-L1(UCH-L1), tau, and phosphorylated tau (p-tau), and novel biomark- ers from blood collected sub-acutely after concussion to determine prediction of persisting post-concussion symptoms (PPCS) beyond 3 months. We hypoth- esized that a combination of established and novel proteins would predict high PPCS burden. Participants: Adolescents 11 to 17.99 years with a concussion based on Concussion In Sport Group (CISG) criteria were eligible. Participants were assessed 7–35 days post-injury (baseline) and then reassessed at 3 months (follow-up) for persistent post-concussion symptoms (PPCS) using the Post- Concussion Symptom Inventory, 2nd Edition (PCSI-2). A total of 155 participants (78 females, 77 males) with both blood biomarkers and 3-month symptom data were analyzed. Design: Plasma proteins collected sub-acutely (7–35 days post concussion) were quantified by both Quanterix and the Olink Explore platform, and compared between participants with the highest and lowest quartiles of PPCS severity at follow-up (85–95 days post concussion) using the PCSI-2. An exhaustive best- subsets logistic regression strategy was executed following clinical and biologi- cal pre-filtering to identify parsimonious multivariable configurations of protein biomarkers distinguishing individuals with high and low PPCS at follow-up. A stratified 10-fold cross-validation framework was implemented to evaluate model generalizability and safeguard against overfitting, while bootstrapping was used to calculate confidence intervals. Ingenuity Pathway Analysis (IPA) was performed to generate hypotheses of molecular pathways implicated in PPCS pathogenesis. Results: None of the brain biomarkers collected sub-acutley were signifi- cantly different in PPCS-high and PPCS-low groups at 90-day follow-up. No Olink proteins survived multiple testing correction, but a cross-validated mul- tivariable model, including Tripartite Motif Containing 39 (TRIM39) + Sclerostin (SOST) + Transcription factor Dp family member 3 (TFDP3) + TNF receptor superfamily member 9 (TNFRSF9) + Leptin (LEP) + Prune Homolog 2 With BCH Domain (PRUNE2) + Trimethylguanosine Synthase 1 (TGS1) + EPCAM (Epithelial Cell Adhesion Molecule) distinguished high PPCS at follow-up with an area under the curve (AUC) of 0.86 (95% CI 0.80–0.92). IPA identified three significant net- works associated with PPCS: (a) cardiovascular and neurological disease, organ- ismal injury, and abnormalities (score = 45; 28 focus molecules); (b) connective tissue disorders, inflammatory disease, and organismal injury and abnormalities (score = 41; 26 focus molecules); and (c) connective tissue development and function, embryonic development, and organismal development (score = 41; 26 focus molecules). Conclusion: This study suggests the possibility to utilize novel biomarkers discov- ered by high throughput proteomic analysis to predict high PPCS. Future research should further develop precision of unique biomarker profiles and prolonged symptomatology in adolescents’ post-concussion.
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