Metabolomics Workbench ST000328 - GNPS - Primary metabolites at different points along dog gastrointestinal tract (CSH chromatography)
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ABSTRACT: This experiment tests the primary metabolites at four different points along the gastrointestinal tract of a dog. The four points being tested were the duodenum, ileum, colon, and rectum.
Project description:This experiment tests the primary metabolites at four different points along the gastrointestinal tract of a dog. The four points being tested were the duodenum, ileum, colon, and rectum.
Project description:The aim of the project is to generate a peptidomics map of gut hormone peptides along the gastrointestinal tract, starting with the stomach and including the duodenum, jejunum, ileum, ascending colon, sigmoid colon and rectum. The tissues would be collected after surgery and the peptide fraction extracted and anlysed by nano LC-MS to identify what peptide hormones are present. These data will then be used to compare against the human transcriptome, and also for comparison against equivent peptides from murine intestinal extracts.
Project description:The aim of the project is to generate a peptidomics map of gut hormone peptides along the gastrointestinal tract, starting with the stomach and including the duodenum, jejunum, ileum, colon and rectum. The tissues would be collected after surgery and the peptide fraction extracted and anlysed by nano LC-MS to identify what peptide hormones are present. These data will then be used to compare against the murine transcriptome, and also for comparison against equivent peptides from human intestinal extracts.
Project description:Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to study the pre-weaned lamb proteome and metaproteome in ten different gastrointestinal tracts: rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum.
Project description:Long non-coding RNA (lncRNA) mechanisms in gut inflammation are poorly understood. Tissue-specificity of lncRNAs linked to patient outcomes may direct interventions with fewer off-target effects. Using 693 mucosal samples, we prioritize lncRNAs linked with ulcerative colitis (UC) course and define an atlas of lncRNAs expressed along the gastrointestinal tract dysregulated in celiac duodenum, Crohn Disease ileum, and UC rectum using independent test and validation cohorts.
Project description:High fat diets (HFDs) are linked to several diseases including obesity, diabetes, insulin resistance, fatty liver, and susceptibility to inflammatory bowel disease (IBD) in both mouse and humans. RNA-seq from male mice (C57BL/6N) fed Vivarium Chow (VIV) or any one of three high fat diets (40% kcal fat) (SO+CO, PL+CO, CO) for 24 weeks was performed on four segments of the intestinal tract (Duodenum, Jejunum, Terminal Ileum and Proximal Colon).
Project description:Background and aims: Dysregulation of intestinal epithelial cells performance associates with an array of pathologies whose onset mechanisms are incompletely understood. The aim of the present study was to provide a map of gene expresssion patterns along the human healthy adult gastro-intestinal tract and to implement a new procedure for microarray data noise filtering that would allow their use as a reference when screening for pathological deviations, such as inflammatory bowel disease (IBD). Methods: Gene expression profiles in antrum, duodenum, jejunum, ileum and transverse colon biopsies were measured with the Affymetrix U133A array and principal component analysis was used to identify region-selective biomarkers. These data were intersected with highly variable genes from a public dataset of gene expression in the ileal and colonic healthy regions of UC and Crohn’s disease patients. Moreover, gene sets covering gut functions not entirely accounted for by the available public tools were constructed to monitor their expression along the GI tract. Results: 166 genes were found to be responsible for distinguishing the five regions considered. Fourteen had never been described in the GI tract, including a semaphorin probably implicated in pathogen invasion, and six other novel genes. Similar analysis of the IBD datasets revealed that samples stratify based on disease rather than on the intestinal region. This withstanding, eleven genes were identified as possible early predictors of Crohn’s and/or UC in ileum and/or colon. These include CLCA4 and SLC26A2, both implicated in ion transport. Conclusions: This novel approach, validated by retrieving known gene profiles, allowed the identification of promising new leads both in health and IBD state. Keywords: gastro-intestinal tract comparison
Project description:We report here the transcriptome of sorted cells from a Guca2a promoter GFP mouse model, positve and negative cells for GFP from 4 different regions of the GI tract, duodenum (top 3cm), jejunum (intermediate small intestine), ileum (bottom 10 cm) and colon +rectum from 3 different mice. This data allows the characterization of the cells expressing Guca2a at the trancriptome level, revealling expression of different cell markers and showing diversity of Guca2a producing cells along the GI tract.
Project description:The gastrointestinal mucus is a hydrogel that lines the luminal side of the gastrointestinal epithelium, offering barrier protection from pathogens and lubrication of the intraluminal contents. These barrier properties likewise affect nutrients and drugs that need to penetrate the mucus to reach the epithelium prior to absorption. In order to assess the potential impact of the mucus on drug absorption, we need information about the nature of the gastrointestinal mucus. Today, most of the relevant available literature is mainly derived from rodent studies. In this work, we used a larger animal species; the pig model to characterize the mucus throughout the length of the gastrointestinal tract. This is the first report of the physiological properties (physical appearance, pH and water content), composition and structural profiling of the porcine gastrointestinal mucus. Gastrointestinal mucus was collected from the stomach, small intestine (duodenum, jejunum, ileum) and large intestine (cecum, proximal and distal colon) from slaughtered pigs. The composition of the mucus was characterized both with labelfree and TMT proteomics, with lipidomics and metabolomics. The structural profiling was determined with rheological measurements and cryo-Scanning Electron Microscopy. These findings allow for direct comparisons between the characteristics of mucus from various segments and can be further utilized to improve our understanding of the role of the mucus on region dependent drug absorption. Additionally, the present work is expected to contribute to the assessment of the porcine model as a preclinical species in the drug development process.
Project description:Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum, and proximal colon under three colonization states: germ-free, monocolonized with Bacteroides thetaiotaomicron, and conventionally raised. Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal tract. Unsupervised clustering showed that host protein abundance primarily depended on gastrointestinal location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between conventionally raised mice relative to germ-free and monocolonized mice. Finally, comparison to fecal proteomic datasets suggested that the identities of stool proteins are not biased to any region of the gastrointestinal tract, but are substantially impacted by the microbiota in the distal colon.