Null
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB71735 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12658700_1.fastq.gz | Fastqsanger.gz | |||
| ERR12658700_2.fastq.gz | Fastqsanger.gz | |||
| ERR12658701_1.fastq.gz | Fastqsanger.gz | |||
| ERR12658701_2.fastq.gz | Fastqsanger.gz | |||
| ERR12658702_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 212 |
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Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH
2014-02-11 | GSE54859 | GEO
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH
2014-02-11 | GSE54858 | GEO
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH Each isolate was compared to IA3902, a dye-swap replicate was applied for each isolate
2014-02-11 | E-GEOD-54859 | biostudies-arrayexpress
Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH Each isolate was compared to IA3902, a dye-swap replicate was applied for each isolate
2014-02-11 | E-GEOD-54858 | biostudies-arrayexpress
Project description:Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions, and allows assessment of the generalizability of laboratory findings. One notable discovery made in Saccharomyces cerevisiae natural isolates is frequent (~20%) aneuploidy – an imbalance in chromosome copy numbers – that appears to contradict the significant fitness costs and transient nature reported for lab-engineered aneuploids. Here, we generated a proteomic resource and merged it with genomic and transcriptomic data for 796 euploid and aneuploid natural isolates. We found that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins, especially protein complex subunits, show reduced expression, yet the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage-compensated, with average protein levels being shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and demonstrates the utility of exploiting the natural diversity of species to reach generalizable molecular insights into complex biological processes. This resource provides the SILAC dataset from this work.
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Project description:Isolates of the gastric pathogen Helicobacter pylori harvested from different individuals are highly polymorphic. Strain variation also has been observed within a single host. To more fully ascertain the extent of H. pylori genetic diversity within the ecological niche of its natural host, we harvested additional isolates of the sequenced H. pylori strain J99 from its human source patient after a 6-year interval. Randomly amplified polymorphic DNA PCR and DNA sequencing of four unlinked loci indicated that these isolates were closely related to the original strain. In contrast, microarray analysis revealed differences in genetic content among all of the isolates that were not detected by randomly amplified polymorphic DNA PCR or sequence analysis. Several ORFs from loci scattered throughout the chromosome in the archival strain did not hybridize with DNA from the recent strains, including multiple ORFs within the J99 plasticity zone. In addition, DNA from the recent isolates hybridized with probes for ORFs specific for the other fully sequenced H. pylori strain 26695, including a putative traG homolog. Among the additional J99 isolates, patterns of genetic diversity were distinct both when compared with each other and to the original prototype isolate. These results indicate that within an apparently homogeneous population, as determined by macroscale comparison and nucleotide sequence analysis, remarkable genetic differences exist among single-colony isolates of H. pylori. Direct evidence that H. pylori has the capacity to lose and possibly acquire exogenous DNA is consistent with a model of continuous microevolution within its cognate host.
2005-06-29 | E-SMDB-1588 | biostudies-arrayexpress
Project description:Exploring the diversity of Erysipelothrix rhusiopathiae isolates from the Canadian Arctic
| PRJEB73478 | ENA
Project description:Analysis of genetic diversity of 25 Coxiella burnetii isolates with relative to the Nine Mile (RSA493) reference isolate.
2006-10-30 | E-TABM-35 | biostudies-arrayexpress
Project description:Isolates of the gastric pathogen Helicobacter pylori harvested from different individuals are highly polymorphic. Strain variation also has been observed within a single host. To more fully ascertain the extent of H. pylori genetic diversity within the ecological niche of its natural host, we harvested additional isolates of the sequenced H. pylori strain J99 from its human source patient after a 6-year interval. Randomly amplified polymorphic DNA PCR and DNA sequencing of four unlinked loci indicated that these isolates were closely related to the original strain. In contrast, microarray analysis revealed differences in genetic content among all of the isolates that were not detected by randomly amplified polymorphic DNA PCR or sequence analysis. Several ORFs from loci scattered throughout the chromosome in the archival strain did not hybridize with DNA from the recent strains, including multiple ORFs within the J99 plasticity zone. In addition, DNA from the recent isolates hybridized with probes for ORFs specific for the other fully sequenced H. pylori strain 26695, including a putative traG homolog. Among the additional J99 isolates, patterns of genetic diversity were distinct both when compared with each other and to the original prototype isolate. These results indicate that within an apparently homogeneous population, as determined by macroscale comparison and nucleotide sequence analysis, remarkable genetic differences exist among single-colony isolates of H. pylori. Direct evidence that H. pylori has the capacity to lose and possibly acquire exogenous DNA is consistent with a model of continuous microevolution within its cognate host. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set Computed
2005-08-16 | E-GEOD-3137 | biostudies-arrayexpress
Project description:Although the major food-borne pathogen Campylobacter jejuni has been isolated from diverse animal, human and environmental sources, our knowledge of genomic diversity in C. jejuni is based exclusively on human or human food-chain-associated isolates. Studies employing multilocus sequence typing have indicated that some clonal complexes are more commonly associated with particular sources. Using comparative genomic hybridization on a collection of 80 isolates representing diverse sources and clonal complexes, we identified a separate clade comprising a group of water/wildlife isolates of C. jejuni with multilocus sequence types uncharacteristic of human food-chain-associated isolates. By genome sequencing one representative of this diverse group (C. jejuni 1336), and a representative of the bank-vole niche specialist ST-3704 (C. jejuni 414), we identified deletions of genomic regions normally carried by human food-chain-associated C. jejuni. Several of the deleted regions included genes implicated in chicken colonization or in virulence. Novel genomic insertions contributing to the accessory genomes of strains 1336 and 414 were identified. Comparative analysis using PCR assays indicated that novel regions were common but not ubiquitous among the water/wildlife group of isolates, indicating further genomic diversity among this group, whereas all ST-3704 isolates carried the same novel accessory regions. While strain 1336 was able to colonize chicks, strain 414 was not, suggesting that regions specifically absent from the genome of strain 414 may play an important role in this common route of Campylobacter infection of humans. We suggest that the genomic divergence observed constitutes evidence of adaptation leading to niche specialization. Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-95 target=_blank>BuG@Sbase</a>
2011-04-15 | E-BUGS-95 | biostudies-arrayexpress