Brachyspira
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA513011 | ENA |
REPOSITORIES: ENA
Similar Datasets
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).
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2017-08-04 | MSV000081410 | MassIVE
Project description:Whole genome sequencing of Brachyspira pilosicoli, an opportunistic pathogen
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Project description:The whole-genome oligonucleotide microarray analysis of laser microdissected human colonic epithelial cells can contribute to determination of disease-specific expression alterations in colonic epithelial cells and to localize the origin the expression changes measured in whole biopsy samples. Keywords: whole genomic expression
2010-03-03 | GSE15960 | GEO
Project description:Despite high vaccination coverage, pertussis is on the rise in many countries including Czech Republic. To better understand B. pertussis resurgence we compared the changes in genome structures between Czech vaccine and circulating strains and subsequently, we determined how these changes translated into global transcriptomic and proteomic profiles. The whole-genome sequencing revealed that both historical and recent isolates of B. pertussis display substantial variation in genome organization and cluster separately. The RNA-seq and LC-MS/MS analyses indicate that these variations translated into discretely separated transcriptomic and proteomic profiles. Compared to vaccine strains, recent isolates displayed increased expression of flagellar genes and decreased expression of polysaccharide capsule operon. Czech strains (Bp46, K10, Bp155, Bp318 and Bp6242)exhibited increased expression of T3SS and sulphate metabolism genes when compared to Tohama I. In spite of 50 years of vaccination the Czech vaccine strains (VS67, VS393 and VS401) differ from recent isolates to a lesser extent than from another vaccine strain Tohama I.
2021-09-08 | PXD015184 | Pride
Project description:The opportunistic pathogen Staphylococcus aureus is carried asymptomatically by about one-third of the human population. Body sites known to be colonized by S. aureus are the skin, nasopharynx and gut. In particular, the mechanisms that allow S. aureus to pass the gut epithelial barrier and to invade the bloodstream are poorly understood. Therefore, our present study was aimed at investigating possible differences between gut-colonizing and bacteremia isolates of S. aureus. To this end, 74 gut-colonizing isolates from healthy individuals and 144 blood-culture isolates were characterized by whole-genome sequencing. Subsequently, the cellular and extracellular proteomes of six representative isolates were examined by mass spectrometry. Lastly, the virulence potential of these isolates was evaluated using infection models based on human gut epithelial cells, blood cells, and a small animal infection model. Intriguingly, our results show that gut-colonizing and bacteremia isolates with the same sequence type (ST1 or ST5) are very similar at the genomic and proteomic levels. Nonetheless, they display differences in virulence, but gut-colonizing isolates may be more virulent than bacteremia isolates and vice versa. Importantly, we show that the main decisive factor preventing infection of gut epithelial cells in vitro is the presence of a tight barrier. Based on our present observations, we propose that the integrity of the gut epithelial layer, rather than the pathogenic potential of a gut-colonizing S. aureus strain, is the main decisive factor that determines whether this colonizer will become an invasive pathogen.
2023-03-11 | PXD030971 | Pride
Project description:Whole-genome sequencing of Brachyspira hyodysenteriae isolates from England and Wales reveals similarities to European isolates and mutations associated with reduced sensitivity to antimicrobials.
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Project description:The whole-genome oligonucleotide microarray analysis of laser microdissected human colonic epithelial cells can contribute to determination of disease-specific expression alterations in colonic epithelial cells and to localize the origin the expression changes measured in whole biopsy samples. Keywords: whole genomic expression Total RNA was extracted from laser microdissected human colon epithelial cells and hybridized on Affymetrix HGU133 Plus 2.0 microarrays
2010-03-15 | E-GEOD-15960 | biostudies-arrayexpress
Project description:The anaerobic spirochete Brachyspira causes intestinal spirochetosis, characterized by the intimate attachment of bacterial cells to the colonic mucosa, potentially leading to symptoms such as diarrhea, abdominal pain, and weight loss. Despite the clinical significance of Brachyspira infections, the mechanism of the interaction between Brachyspira and the colon epithelium is not known. We characterized the molecular mechanism of the B. pilosicoli-epithelium interaction and its impact on the epithelial barrier during infection. Through a proteomics approach, we identified BPP43_05035 as a candidate B. pilosicoli surface protein that mediates bacterial attachment to cultured human colonic epithelial cells. The crystal structure of BPP43_05035 revealed a globular lipoprotein with a six-bladed beta-propeller domain. Blocking the native BPP43_05035 on B. pilosicoli, either with a specific antibody or via competitive inhibition, abrogated its binding to epithelial cells, which required cell surface-exposed N-glycans. Proximity labeling and interaction assays revealed that BPP43_05035 bound to tight junctions, thereby increasing the permeability of the epithelial monolayer. Extending our investigation to humans, we discovered a downregulation of tight junction and brush border genes in B. pilosicoli-infected patients carrying detectable levels of epithelium-bound BPP43_05035. Collectively, our findings identify BPP43_05035 as a B. pilosicoli adhesin that weakens the colonic epithelial barrier during infection.
2024-10-18 | PXD056942 | Pride
Project description:Using RNA-seq, we investigated for the first time the in vivo transcriptome of colonic mucosa in 16 control pigs and 16 pigs experimentally infected with Brachyspira hyodysenteriae, which were euthanized at different stages of the disease: 8 during a preclinical stage characterized by bacterial shedding without clinical signs (early infection group), and 8 during an acute stage presenting with dysentery (acute infection group). No significant differences in gene expression were observed between the control and early infection groups, except for an overexpression of matrix metalloproteinases (MMPs), which may be associated with early ulceration of the colonic epithelium. The acute infection group showed a significant upregulation of the S100A8, S100A9 and S100A12 proteins, but most of the host biological processes were downregulated, particularly those related to the immune response, such as chemokines and cytokines signalling or immune cells chemotaxis and migration. Accordingly, the prediction of cell types associated with the detected transcripts revealed a depletion of immune cells, except neutrophils, and an enrichment of stromal cells in the acute infection group. Marked alterations in mucin gene expression were observed in this group, including overexpression of MUC5AC, MUC20, and GCNT3, a trend toward increased MUC2, and downregulation of MUC1 and MUC3. Although no significant changes were detected in the early infection group, a similar trend was observed. These findings suggest that B. hyodysenteriae may suppress host immune responses, particularly through inhibition of the IFNγ signalling pathway, accompanied by a depletion of cellular responses, except for neutrophils, and promotion of tissue damage via overexpression of multiple MMPs, even at early stages of the disease. Significant alterations in mucin composition were observed during the acute stage, likely driven by the overexpression of S100 proteins and activation of the SPDEF pathway. This study proposes several mechanisms associated with the pathophysiology of swine dysentery, revealing key aspects of host–pathogen interactions, particularly the host response to B. hyodysenteriae infection.
2025-07-28 | GSE302242 | GEO