GNPS CF Strains Todd Hewitt Agar
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: Dorrestein
PROVIDER: MSV000080251 | GNPS | Tue Oct 18 09:56:00 BST 2016
REPOSITORIES: GNPS
Similar Datasets
Project description:A collection of cystic fibrosis bacterial isolates from the clinical laboratory. .d files
2016-10-20 | MSV000080253 | GNPS
Project description:This SuperSeries is composed of the following subset Series: GSE28306: Expression data from Burkholderia multivorans cystic fibrosis clinical isolates GSE30402: Hybridization of Burkholderia multivorans D2095 and D2214 genomic DNA Refer to individual Series
2011-08-21 | E-GEOD-30568 | biostudies-arrayexpress
Project description:To provide a more detailed survey of adaptive changes in the physiology of P. aeruginosa (PA) during long-term infection of the cystic fibrosis (CF) lung, we performed a comparative proteome and transcriptome analysis of a set of isogenic sequential non-mutator and mutator isolates from three selected CF patients. Recently, we showed that during CF lung persistence PA mutators converge to a virulence-attenuated phenotype. In this study, we demonstrate that besides virulence-associated traits (VATs) the adaptation process of PA predominantly comprises metabolic pathways. In end-stage mutator strains, transcripts of genes encoding VATs, chemotaxis, degradation of aromatic compounds and several two-component regulatory systems were decreased. In contrast, several transcripts of genes or proteins involved in metabolism of fatty acids, nucleotides, amino acids and the generation of energy were increased. Of particular interest is the increased expression level of genes involved in (i) the anaerobic arginine-deiminase pathway, (ii) the anaerobic respiration such as nitrate-uptake protein OprF, redox-active azurin and cytchrome c551 peroxidase, (iii) the micro-aerobic respiration such as high oxygen-affinity cytochrome oxidase cbb3 (iv) the tricarboxylic acid cycle (TCA), glyoxylate shunt and anaplerotic carboxylation reactions to oxaloacetate. Strikingly, an increased transcription of the anaerobic regulator gene anr correlates with the up-regulation of ANR-dependent genes. In conclusion, these changes in transcriptome and proteome indicate an adaptive shift towards constitutive expression of genes of metabolic pathways obviously required for growth under micro-aerobic and nutritional conditions of suppurative CF lung tissue. Finally, these results provide us with new targets for antimicrobial agents and biomarkers reflecting adaptation of PA towards progressive CF lung disease. Experiment Overall Design: P. aeruginosa isolates recovered from different time points of chronic cystic fibrosis lung disease were cultered in vitro, harvested for RNA extraction and hybridization on Affymetrix microarrays. We compared the transcriptome (triplicate microarrays) of early non-mutator P. aeruginosa isolates with late mutator isolates with high mutation frequency probably the driving force of an efficient adaptation to changing environements to conclude from differences in gene expression to the requirements of CF lung environment. Experiment Overall Design: Second publication of array data to be added later
2009-06-08 | E-GEOD-10362 | biostudies-arrayexpress
Project description:To provide a more detailed survey of adaptive changes in the physiology of P. aeruginosa (PA) during long-term infection of the cystic fibrosis (CF) lung, we performed a comparative proteome and transcriptome analysis of a set of isogenic sequential non-mutator and mutator isolates from three selected CF patients. Recently, we showed that during CF lung persistence PA mutators converge to a virulence-attenuated phenotype. In this study, we demonstrate that besides virulence-associated traits (VATs) the adaptation process of PA predominantly comprises metabolic pathways. In end-stage mutator strains, transcripts of genes encoding VATs, chemotaxis, degradation of aromatic compounds and several two-component regulatory systems were decreased. In contrast, several transcripts of genes or proteins involved in metabolism of fatty acids, nucleotides, amino acids and the generation of energy were increased. Of particular interest is the increased expression level of genes involved in (i) the anaerobic arginine-deiminase pathway, (ii) the anaerobic respiration such as nitrate-uptake protein OprF, redox-active azurin and cytchrome c551 peroxidase, (iii) the micro-aerobic respiration such as high oxygen-affinity cytochrome oxidase cbb3 (iv) the tricarboxylic acid cycle (TCA), glyoxylate shunt and anaplerotic carboxylation reactions to oxaloacetate. Strikingly, an increased transcription of the anaerobic regulator gene anr correlates with the up-regulation of ANR-dependent genes. In conclusion, these changes in transcriptome and proteome indicate an adaptive shift towards constitutive expression of genes of metabolic pathways obviously required for growth under micro-aerobic and nutritional conditions of suppurative CF lung tissue. Finally, these results provide us with new targets for antimicrobial agents and biomarkers reflecting adaptation of PA towards progressive CF lung disease. Keywords: in vitro study/interstrain comparison/clinical isolates/early nonmutator vs. late mutator; variable time point of isolation from cf respiratory secretions
2009-05-26 | GSE10362 | GEO
Project description:THE RESPIRATORY MICROBIOME IN CYSTIC FIBROSIS: COMPARTMENT PATTERNS AND CLINICAL RELATIONSHIPS
| PRJEB31332 | ENA
Project description:We have compared gene expression in human nasal brushing cells from 19 cystic fibrosis (CF) patients and 19 healthy controls using a 5.2K cDNA microarray. Our aim is to identify new disease biomarkers for the Cystic Fibrosis Gene Therapy Consortium. These markers will be used to report more effectively on the response to the administration of gene therapy in vivo. Cystic Fibrosis is a recessive genetic disease caused by mutations in the cystic fibrosis conductance regulator (CFTR) gene which encodes a chloride ion channel. The most common mutation is the ∆F508 mutation, present on 70% of CF chromosomes in Caucasian populations. The disease affects many organs in the body such as the pancreas, liver, sweat glands, small intestine and reproductive tracts but is most commonly associated with progressive, inflammatory lung disease. The current average life expectancy of CF patients is 35 years. Gene therapy is being developed as a treatment for CF airway disease, however, means of measuring the efficiency and efficacy of gene therapy in vivo are lacking. This is mainly due to the difficulty in measuring the chloride conductance of CFTR in cells and tissues. Furthermore, clinical assays for measuring improvements in lung function are insensitive. Surrogate markers of inflammation and CFTR function will therefore be important for the effective assessment of gene therapy in vivo. We have analysed gene expression in human nasal epithelium as this is considered an accessible surrogate for the conducting airways where disease manifests in the majority of patients. Additionally, this tissue will be sampled in clinical trials.
2011-04-30 | E-MEXP-436 | biostudies-arrayexpress
Project description:Bacteria of the genus Achromobacter are environmental germs, with an unknown reservoir, which can become opportunistic pathogens in immunocompromised patients, and be responsible for bacteremia, meningitis, pneumonia and peritonitis. Achromobacter xylosoxidans is an emerging pathogenic bacterium frequently isolated in the context of cystic fibrosis (CF). Recent studies show that A. xylosoxidans is involved in the degradation of the respiratory function of CF patients. The respiratory ecosystem of CF patients is colonized by bacterial species that constantly fight for space and access to nutrients. In particular, these bacteria use an antagonism system, a type VI secretion nanomachine (T6SS), which represents a virulence factor in many pathogenic bacteria. This study aimed to investigate the prevalence of the T6SS genes in Achromobacter xylosoxidans isolated in cystic fibrosis patient. We also evaluated clinical and molecular characteristics of T6SS-positive A. xylosoxidans strains. We have shown that A. xylosoxidans possesses a T6SS-encoded gene cluster and that some environmental and clinical isolates assemble a functional T6SS nanomachine. The A. xylosoxidans T6SS is used to target competitor bacteria, including other CF-specific pathogens. We gathered some evidences pointing toward a role of T6SS in CF-lung colonization: i, CF mimicking conditions trigger the activation of A. xylosoxidans T6SS; ii, we detected Hcp in the sputum of CF patient and iii, the T6SS helps internalization of A. xylosoxidans in lung epithelial cells. Our study highlights a new clinical determinant of the virulence of A. xylosoxidans as well as new diagnostic and therapeutic options in cystic fibrosis.
2024-02-01 | PXD031682 | Pride
Project description:The opportunistic pathogen Pseudomonas aeruginosa is among the main colonizers of the lungs of cystic fibrosis (CF) patients. We have isolated and sequenced several P. aeruginosa isolates from the sputum of CF patients and used phenotypic, genomic and proteomic analyses to compare these CF derived strains with each other and with the model strain PAO1.
2015-10-14 | PXD002865 | Pride
Project description:Whole-genome sequencing of sequential clinical mucoid/nonmucoid isolates of Burkholderia cenocepacia from a decade of cystic fibrosis lung infection
| PRJEB9630 | ENA
Project description:A collection of Cystic Fibrosis bacterial and fungal strains grown in artificial sputum media.
2016-11-14 | MSV000080337 | GNPS