Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1129516 | 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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2007-11-28 | GSE7780 | GEO
Project description:We performed whole genome sequencing on four isolates of C. jejuni, two of which were closely related phylogenetically while the remaining two were phylogenetically divergent. Genomes were closed and finished. 4-plex iTRAQ experiments were performed on the four isolates after growth on solid medium for a standard time. The research questions were: 1) how closely do the protein profiles match among the four isolates, and 2) were there any results consistent with differences in regulation among isolates.
2017-08-04 | MSV000081410 | MassIVE
Project description:Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host?pathogen relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
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Project description:Hypermutable P. aeruginosa isolates are prevalent in cystic fibrosis and associated with acute exacerbations of chronic lung infections leading to early death and increased resistance emergence. Achievable epithelial lining fluid concentration-time profiles of meropenem and tobramycin in monotherapy and combination regimens were simulated against two clinical hypermutable P. aeruginosa isolates; CW8 (MICmeropenem=8mg/L, MICtobramycin=8mg/L) and CW44 (MICmeropenem=4mg/L, MICtobramycin=2mg/L) in an 8-day hollow fiber infection model (HFIM). Both isolates were previously characterised with genotypes resembling those of carbapenem- and aminoglycoside-resistant strains. Meropenem at 1 or 2g every 8h (3h infusion) and tobramycin at 5 or 10mg/kg body weight every 24h (0.5h infusion) were studied. Total and resistant bacterial counts were determined. Whole genome sequencing was performed on mutants and whole population samples at 191h, and transcriptomics at 1 and 191h. Mechanism-based modelling of total and resistant populations was informed by the multi-omics analysis. While all regimens against both isolates produced regrowth, the high dose combination synergistically suppressed resistant regrowth against CW8 up to ~96h. The high dose combination provided some killing against CW44, however failed to prevent resistant regrowth. In CW8, mutations emerged during treatment in pmrB, ampR, and multiple efflux pump regulators; in CW44, mutations in pmrB and PBP2 were observed. In CW8, resistance genes mexB and oprM were downregulated by the combination at 1h and coincided with synergistic killing, with differential expression of outer membrane norspermidine and lipopolysaccharide genes at 191h. Mechanism-based modelling incorporating subpopulation and mechanistic synergy successfully characterized the bacterial response of CW8, while mechanistic synergy was not required for CW44. Incorporating information from the multi-omics analyses was instrumental in building the mechanism-based model to describe the bacterial response of the hypermutable isolates, whereas MICs and traditional PK/PD indices could not predict the outcomes of the HFIM.
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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:Following a pacemaker implantation, a 75-years-old patient suffered from five successive bacteremia episodes between in 1999 and 2013, during which five bacterial strains were isolated. Phenotypic and whole-genome sequencing analysis of four isolates identified the strains as Yersinia enterocolitica bioserotype 4/O:3. Phylogenetic reconstruction showed that the patient was chronically infected by the same strain, which evolved within the host during 14 years. Single-nucleotide polymorphhism (SNP) analysis indicates that the last two isolates which displayed severe growth defects in vitro and acquired resistance to quinolones, evolved in parallel and formed two independent lineages within the host. Pan-genome analysis and genome comparison showed that their common evolution was characterized by 41 small insertion/deletion events and loss of three large DNA fragments. These mutations, which may account for the observed growth defect and also for the appearance of vegetations on the pacemaker, support antibiotics tolerance. Quinolone resistance was acquired through a so far undescribed deletion in the gyrA gene. 140 genes containing mutations vertically acquired from a common ancestor were also identified in the two lineages. A phylogenetic analysis by maximum likelihood identified two genes presenting a positive selection signal, suggesting that these mutations provided a survival advantage to bacteria during chronic infection. This is the first report allowing identification of genetic changes associated to within-host adaptation of a pathogenic Yersinia species.
2025-05-26 | PXD043567 | Pride
Project description:In a comprehensive study using comparative whole genome sequencing, 100 African isolates were examined, revealing the pilin glycosylation (pgl) locus as a prominent site for recombination events. Notably, the transfer of pgl genes through lateral gene transfer occurs frequently within N. meningitidis serogroup A, leading to variations in the glycosylation patterns of pilin and other glycoproteins on the cell surface. To elucidate these differences, mass spectrometry was employed to analyze the glycan structure associated with different pgl allele types.
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Project description:Acinetobacter baumannii is often highly resistant to multiple antimicrobials, posing a risk of treatment failure, and colistin is a "last resort" for treatment of the bacterial infection. However, colistin resistance is easily developed when the bacteria are exposed to the drug, and a comprehensive analysis of colistin-mediated changes in colistin-susceptible and -resistant A. baumannii is needed. In this study, using an isogenic pair of colistin-susceptible and -resistant A. baumannii isolates, alterations in morphologic and transcriptomic characteristics associated with colistin resistance were revealed. Whole-genome sequencing showed that the resistant isolate harbored a PmrBL208F mutation conferring colistin resistance, and all other single-nucleotide alterations were located in intergenic regions. Using scanning electron microscopy, it was determined that the colistin-resistant mutant had a shorter cell length than the parental isolate, and filamented cells were found when both isolates were exposed to the inhibitory concentration of colistin. When the isolates were treated with inhibitory concentrations of colistin, more than 80% of the genes were upregulated, including genes associated with antioxidative stress response pathways. The results elucidate the morphological difference between the colistin-susceptible and -resistant isolates and different colistin-mediated responses in A. baumannii isolates depending on their susceptibility to this drug.
2025-05-02 | GSE267612 | GEO
Project description:Sexual reproduction and recombination are essential for the survival of most eukaryotic populations. Until recently, the impact of these processes on the structure of bacterial populations has been largely overlooked. The advent of large-scale whole-genome sequencing and the concomitant development of molecular tools, such as microarray technology, facilitate the sensitive detection of recombination events in bacteria. These techniques are revealing that bacterial populations are comprised of isolates that show a surprisingly wide spectrum of genetic diversity at the DNA level. Our new awareness of this genetic diversity is increasing our understanding of population structures and of how these affect host?pathogen relationships. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-10-20 | E-GEOD-3479 | biostudies-arrayexpress