Project description:The degradation of glycosaminoglycans (GAGs) by intestinal bacteria is critical for their colonization in the human gut and the health of the host. Both Bacteroides and Firmicutes have been reported to degrade GAGs, while the enzymatic details of the latter remain largely unknown. In this study, we isolated a Firmicutes strain, Hungatella hathewayi N2-326, that can catabolize various GAGs. While H. hathewayi N2-326 was less efficient in utilizing chondroitin sulfate A (CSA) and dermatan sulfate (DS) than Bacteroides thetaiotaomicron, a characterized GAG degrader, it outperformed B. thetaiotaomicron in assimilating hyaluronic acid. Unlike B. thetaiotaomicron, H. hathewayi N2-326 could not utilize heparin. The chondroitin lyase activity of H. hathewayi N2-326 was found to be induced by CSA and displayed both cell-associated and extracellular distributions. We further identified and characterized the first chondroitin ABC lyase from Firmicutes. The recombinant H. hathewayi chondroitin ABC lyase was found to be a predominantly exolyase and exhibited higher specific activity than any other characterized chondroitin ABC lyase. Thus, the HH-chondroitin ABC lyase offers a viable commercial option for the production of chondroitin, dermatan, and hyaluronan oligosaccharides and potential medical applications.

2022-08-14 | GSE211011 | GEO

Proteome of standard WHO L. donovani DD8 strain and Leptomonas clinical isolates from India

Project description:Leishmania donovani WHO reference strain MHOM/IN/80/DD8 and Leptomonas seymouri isolates Ld 2001 and Ld39 were used for proteome analysis which were originally isolated from clinical cases of kala azar patients with different inherent antimonial sensitivities. Ld 2001 was Sb-S and Ld 39 was Sb-R. The genome sequencing of these isolates had confirmed co-infection with Leptomonas.

2016-03-16 | MSV000079588 | MassIVE

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

2023-06-08 | GSE209815 | GEO

Proteomic analysis of the dpp3 knockout mutant, the reconstituted strain and the wild-type strain of Candida lusitaniae

Project description:Candida lusitaniae is an emerging human opportunistic yeast, which can switch from yeast to pseudohyphae, and one of the rare Candida species capable of sexual reproduction. Its haploid genome and the genetic tools available make it a model of interest to study gene function. This study describes the consequences of DPP3 inactivation on cell morphology and mating, both altered in the dpp3Δ knock-out. Interestingly, reintroducing a wild-type copy of the DPP3 gene in the dpp3Δ mutant failed to restore the wild-type phenotypes. Proteomic analyses showed that about 150 proteins were statistically deregulated in the dpp3Δ mutant, and that most of them did not return to their wild-type level in the reconstituted DPP3 strain. The analysis of the segregation of the dpp3Δ mutation and the phenotypes in the progeny of a cross (between the dpp3Δ knock-out and a wild-type strain) showed that the phenotypes are not linked to dpp3Δ, but to a secondary mutation. Genome sequencing of the dpp3Δ mutant allowed us to identify this secondary mutation.

2023-05-02 | PXD020220 | Pride

Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [ATAC-seq]

Project description:Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability

2023-06-08 | GSE209810 | GEO

H. pylori strain comparisons

Project description:Helicobacter pylori enhances the risk for ulcer disease and gastric cancer, yet only a minority of H. pylori-colonized individuals develop disease. We examined the ability of two H. pylori isolates to induce differential host responses in vivo or in vitro, and then used an H. pylori whole genome microarray to identify bacterial determinants related to pathogenesis. Gastric ulcer strain B128 induced more severe gastritis, proliferation, and apoptosis in gerbil mucosa than did duodenal ulcer strain G1.1, and gastric ulceration and atrophy occurred only in B128+ gerbils. In vitro, gerbil-passaged B128 derivatives significantly increased IL-8 secretion and apoptosis compared with G1.1 strains. DNA hybridization to the microarray identified several strain-specific differences in gene composition including a large deletion of the cag pathogenicity island in strain G1.1. Partial and complete disruption of the cag island in strain B128 attenuated induction of IL-8 in vitro and significantly decreased gastric inflammation in vivo. These results indicate that the ability of H. pylori to regulate epithelial cell responses related to inflammation depends on the presence of an intact cag pathogenicity island. Use of an H pylori whole genome microarray is an effective method to identify differences in gene content between H. pylori strains that induce distinct pathological outcomes in a rodent model of H. pylori infection. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-08-16 | GSE3135 | GEO

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

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