Undefined
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB56193 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was applied to define the occurrence, diversity and origin of glycosyl-hydrolases along the digestive tract of P. canaliculata. Cellulases, hemicellulases, amylases, maltases, fucosidases and galactosidases were identified across the digestive tract. The digestive gland and the contents of the crop and style sac yield a higher diversity of glycosidase-derived peptides.
2019-07-25 | PXD013550 | Pride
Project description:Bile and its individual components, mainly bile acids, are important for digestion and drive bacteria community dynamics in the upper gastrointestinal tract of chickens. However, specific responses to bile acids have been characterized in only a few commensal bacteria, and it is unclear how other members of the microbiota respond to biliary stress. Here, we used label-free LC-MS/MS to assess the proteomic response of a common inhabitant of the chicken upper intestinal tract, Turicibacter spp. MMM721, to 24 hours of growth in anaerobic growth media supplemented with 0.1% whole chicken bile, 0.1% taurochenodeoxycholic acid, or 0.1% taurocholic acid. 70, 46, and 8 differentially expressed proteins were identified in Turicibacter spp. MMM721 cultured with supplements of whole chicken bile, TCDCA, and TCA, respectively, when compared to unsupplemented controls. Many of the differentially expressed proteins were involved in ribosomal processes, post-translational modifications and chaperones, and modifications to the cell surface. To our knowledge, this work represents the first description of the Turicibacter spp. MMM721 proteomic response to bile and bile acid exposure. Ultimately, the T. bilis MMM721 response to whole bile and bile acids is highly complex, with numerous proteins from a variety of functional categories being induced.
2021-11-21 | MSV000088421 | MassIVE
Project description:Protein-based targeting reagents, such as antibodies and non-antibody scaffold proteins, are rapidly inactivated in the upper gastrointestinal (GI) tract. Hydrochloric acid in gastric juice denatures proteins and activates pepsin, concentrations of which reach 1 mg/mL in the mammalian stomach. Here we present gastrobodies, a protein scaffold derived from Kunitz soybean trypsin inhibitor (SBTI). SBTI is highly resistant to the challenges of the upper GI tract, including digestive proteases, pH 2 and bile acids. Computational prediction of SBTI’s evolvability identified two nearby loops for randomization, to create a potential recognition surface which was experimentally validated by alanine scanning. We established display of SBTI on full-length pIII of M13 phage. Phage selection of gastrobody libraries against the glucosyltransferase domain of Clostridium difficile toxin B (GTD) identified hits with nanomolar affinity and enzyme inhibitory activity. Anti-GTD binders retained high stability to acid, digestive proteases and heat. We use mass spectrometry to identify cut sites outside of the gastrobody.
2021-08-13 | PXD027071 | Pride
Project description:Glomus tumors (GT) are perivascular tumors mostly occurring in the distal extremities. Rare cases occur in the digestive tract and may be misdiagnosed with neuroendocrine or gastrointestinal stromal tumors. We aimed to specify the features of GT of the upper digestive tract. We investigated two cases using whole exome sequencing (WES) and RNA-sequencing, and present clinical, histological, phenotypic and molecular features of 16 cases. WES did not reveal any commonly involved cellular pathway. By contrast, RNA-sequencing disclosed a t(1:5)(p13;q32) translocation between MIR143HG and NOTCH2 in both cases. The deducted fusion protein sequence corresponded to the NOTCH2 intracellular domain known as NICD2, which acts as transcription factor. These data were confirmed by high expression of the transcripts of genes targeted by NOTCH cellular pathway (HES and HEY gene families). In our retrospective multicentric series of 16 GT of upper digestive tract MIR143HG-NOTCH2 translocation was detected in 14 (88%) cases. By contrast, it was present in only 2/6 (33%) GT of the distal extremities. Most digestive GT raised from the stomach (n=13), and the others from duodenal (2) or oesophagous (1). All digestive GT were positive for α-smooth muscle actin and transgelin, and negative for cytokeratin AE1/AE3, chromogranine, DOG1, KIT and S100. Most cases were positive for H-caldesmon (n=14) and/or for synaptophysin (n=10). Desmin, CD34 or CD56 were positive in only one case each. Nuclear expression of NOTCH2 was detected in the 14 cases containing the fusion transcripts. The present study shows that MIR143HG-NOTCH2 translocation is present in most digestive GT. This fusion transcript is associated with activation of the NOTCH2 pathway and may drive tumor development. Detection of nuclear NOTCH2 expression may be helpful for diagnosis.
2019-08-31 | GSE118896 | GEO
Project description:Using H3K27ac HiChIP assays to link genetic variants to target genes in upper digestive cancers
2024-02-25 | GSE235431 | GEO
Project description:Using H3K27ac ChIP-seq assays followed by sequencing to identify regulatory elements in upper digestive cancers
2024-02-25 | GSE240213 | GEO
Project description:Infectious bronchitis virus (IBV), is a coronavirus which infects chickens (Gallus gallus), and is one of the foremost causes of economic loss within the poultry industry, affecting the performance of both meat-type and egg-laying birds. The virus replicates not only in the epithelium of upper and lower respiratory tract tissues, but also in many tissues along the alimentary tract and elsewhere e.g. kidney, oviduct and testes. It can be detected in both respiratory and faecal material. There is increasing evidence that IBV can infect species of bird other than the chicken. Interestingly breeds of chicken vary with respect to the severity of infection with IBV, which may be related to the immune response (Cavanagh, 2006). Here we examine differential expression of genes in the trachea of susceptible and resistant birds, in order to identify genes which may be involved in resistance to IBV.
2015-07-31 | E-TABM-1128 | biostudies-arrayexpress
Project description:Functional characterization of genetic variants associated with upper digestive cancers
| PRJNA1002976 | ENA
Project description:Cdx2 has been suggested to play an important role in Barrett's esophagus (BE), or intestinal metaplasia (IM) in the esophagus. However, in vivo data have been lacking. The aim of the present study was to investigate whether transgenic overexpression of zCdx1b, the functional equivalent of mammalian Cdx2 in zebrafish, may lead to IM of squamous epithelium in zebrafish A transgenic zebrafish system was developed by expressing zCdx1b gene under the control of zebrafish keratin 5 promoter (zK5p). zCdx1b expression in the esophageal squamous epithelium of transgenic zebrafish was analyzed by in situ hybridization, immunohistochemical staining and RT-PCR. Gene expression in the esophageal squamous epithelium of wild-type and transgenic zebrafish was analyzed by Affymetrix microarray and confirmed by in situ hybridization. The upper digestive tract tissue from 3 adult zebrafish (3 months old) was pooled as one sample. Three zCdx1b transgenic samples were used for microarray, and 2 wild type samples were used for control.
2012-02-18 | E-GEOD-35889 | biostudies-arrayexpress