Project description:The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tg(cldn15la:GFP) intestine-specific transgene was used to ease dissections. RNAseq was performed at 5, 7, 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5, 7, 9 dpf on wild type dissected intestines to check the intestinal presence of active (H3K4me3) and repressive (H3K27me3) chromatin marks and to correlate their presence with intestinal gene expression.
Project description:The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA-sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g-/- zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type, hnf4g-/-, and hnf4a-/-;hnf4g-/- zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10-15 pooled gastrointestinal tracts, and 4 biological replicates per treatment group were sequenced.
Project description:We profiled genome-wide accesssible chromatin data and RNA-seq from four species (zebrafish, stickleback, mouse, and human) to identify commonly regulated genes and regulatory metods in intestinal epithelial cells (IECs). We identify a group genes that are commonly expressed in IECs and genes that are commonly expressed along the length of the intestine in fish and mammals. Using accessible chromatin data we identified enriched transcription factor binding site motifs In IECs and sites that are commonly accessible in IECs in all species. Finally, we confirm the ability for these regions from multiple species to drive conserved expression in IECs using a zebrafish reporter assay.
Project description:This study will evaluate longitudinal performance of Epi proColon with respect to test positivity, longitudinal adherence to Epi proColon screening, adherence to follow-up colonoscopy and diagnostic yield, as well as assay failure rates.
Project description:Cyberlindnera jadinii yeast is a potential sustainable novel feed ingredient for aquaculture industries. Yeasts contain bio-active components and proteins such as beta-glucans, mannans, nucleic acids and proteins that can enhance fish immunity against the disease. In our study, we focused on the characterization of intestinal immunoregulatory pathways in zebrafish (Danio rerio) by quantifying the intestine proteins with isobaric tags for relative and absolute quantitation (iTRAQ) and 2D LC-MS/MS approach. Zebrafish were fed either a control diet (C) or a diet supplemented with autolyzed C. jadinii (ACJ). The KEGG pathways analysis revealed that compared with the control diet, the ACJ yeast diet induced an increased abundance of proteins related to arginine and proline metabolism, phagosome, C-lectin receptor signalling pathway, ribosome pathway and PPAR signalling pathway, which can modulate and enhance the innate response of zebrafish. Moreover, fish fed ACJ yeast diet also showed decreased abundance of proteins associated with inflammatory pathways including apoptosis, necroptosis and ferroptosis pathways. These findings support a mobilization of the innate immune response and a control of inflammatory-related pathways in the intestine of zebrafish. Our findings in the well annotated proteome of zebrafish enabled a detailed investigation of intestinal responses and provide insight into the health-beneficial effects of the yeast species C. jadinii relevant for aquaculture species.
Project description:We identified and characterized a rice epigenetic mutant Epi-df which exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We demonstrated that Epi-df participates in Polycomb repressive complex 2 (PRC2) mediated gene silencing. Epigenetic mutations results in ectopic expression of Epi-df and pleiotropic developmental defects in mutant plants. Moreover, ectopic expression of Epi-df leads to mis-regulated H3K27me3 and changed expression of hundreds of genes involved in a wide range of biological processes. We used microarrays to identify differentially expressed genes in Epi-df. For genome-wide expression analysis of Epi-df, three replicates of WT and Epi-df samples (RNA from 3-week-old seedlings) were analyzed on Affymetrix Genechip® Rice Genome arrays by an Affymetrix service facility (CapitalBio Corporation) according to the manufacturer’s protocols. Genes showing a 2-fold change with a q-value ≤ 0.05 were considered to be differentially expressed.