Genomic content analysis of Clostridium botulinum type F strains
Ontology highlight
ABSTRACT:
ORGANISM(S): Clostridium botulinum
SUBMITTER: Brian Raphael
PROVIDER: E-GEOD-53456 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The purpose of this study was to compare the gene content of several group II C. botulinum strains to determine the utility of DNA microarrays for subtyping this organism. Group II type B, E, and F C. botulinum strains were compared in a study to examine the gene content of a unique type E strain (CDC66177). One replicate of genomic DNA isolated from 16 type E strains, 4 type B strains, and 2 type F strains were examined.
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Project description:Strains were differentiated on the basis of hybridization to probes representing strain variable regions in C. botulinum strain ATCC 3502. Probes for selected genes (eg. toxin genes) were also featured on the microarray to allow detection of other serotypes/subtypes. 44 strains were evaluated for selected gene detection and/or strain differentiation. DNA from strain ATCC 3502 was used as a control as the featured probes were based on the ATCC 3502 genome sequence.
2010-05-18 | E-GEOD-16101 | biostudies-arrayexpress
Project description:Strains were differentiated on the basis of hybridization to probes representing strain variable regions in C. botulinum strain ATCC 3502. Probes for selected genes (eg. toxin genes) were also featured on the microarray to allow detection of other serotypes/subtypes. 27 strains were evaluated for selected gene detection and/or strain differentiation. DNA from strain ATCC 3502 was used as a control as the featured probes were based on the ATCC 3502 genome sequence.
2010-05-05 | E-GEOD-18086 | biostudies-arrayexpress
Project description:Comparative genomic hybridizations were performed to compare bont/A1 strains with an A2-like toxin gene cluster organization to the genome sequenced strain, C. botulinum ATCC 3502. Keywords: comparative genomic hybridization For each hybridization, the reference strain (C. botulinum ATCC 3502) was labeled with Cy5 and each test strain was labeled with Cy3.
2010-05-26 | E-GEOD-10223 | biostudies-arrayexpress
Project description:The PFGRC has developed a cost effective alternative to complete genome sequencing in order to study the genetic differences between closely related species and/or strains. The comparative genomics approach combines Gene Discovery (GD) and Comparative Genomic Hybridization (CGH) techniques, resulting in the design and production of species microarrays that represent the diversity of a species beyond just the sequenced reference strain(s) used in the initial microarray design. These species arrays may then be used to interrogate hundreds of closely related strains in order to further unravel their evolutionary relationships. Clostridium botulinum produces botulinum neurotoxin (BoNT)and is classified as a “Category A” select agent. BoNT can be classified into seven serotypes designated A-G. There is considerable genetic variation within these serotypes, as demonstrated by the recognition of at least 47 subtypes. The most studied serotype, BoNT/A, has been found in a large and diverse group of clostridia, most of which express the subtype BoNT/A1. The BoNT/A1 producing C. botulinum strain ATCC 3502, used to obtain an initial annotated genome sequence, is not representative of the diverse clostridia group producing BoNT. Nearly 50% of C. botulinum strains producing BoNT/A1 have been shown to also encode unexpressed variants of BoNT/B with a distinct cluster arrangement. This nucleotide cluster is completely absent from the published genome sequence. In addition, a recently identified novel BoNT/A1 strain lacks the gene cluster seen in the genome sequence of ATCC 3502. Furthermore, a strain designated Hall A Hyper differs greatly from the sequenced strain as indicated by its ability to produce higher quantities of BoNT/A1. The genetic and phenotypic basis for this difference in BoNT expression is currently unknown, and the sequences of the BoNT gene and the cluster are identical in both strains. This observation supports the hypothesis that genes outside the toxin cluster are involved in the regulation and maturation of BoNT. The flow of genetic information within this group motivated us to identify novel genes for the purpose of creating a “species” DNA microarray to better understand the ancestral relationships among its members. Based on preliminary genotyping (MLST, and CGH using a single-genome-based array), 20 diverse C. botulinum strains were selected for sequencing. Sequence information obtained from this project, and from other publicly available sources, led to the development of a comprehensive species microarray for C. botulinum group members. The availability of the C. botulinum species DNA microarray has allowed us to carry out a collaborative CGH genotyping project to validate this microarray as well as understand the phylogenomic relationships among members of C. botulinum group.
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Project description:The purpose of this study was to evaluate differences in gene content between tests samples isolated from separate food sources. A single biological sample was used for each test strain examined
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Project description:Comparative genomic hybridization microarrays featuring overlapping probes spanning the entire C. botulinum type A1 strain ATCC 3502 genome were used to identify regions whose presence are variable among a diverse panel of type A C. botulinum strains. For each hybridization, the reference strain (C. botulinum ATCC 3502) was labeled with Cy5 and test strains were labeled with Cy3.
2010-05-19 | E-GEOD-16010 | biostudies-arrayexpress
Project description:Transcriptome analysis of RNA extracted from human induced pluripotent stem cell (hipsc)-derived neurons exposed to botulinum neurotoxin type A1 (BoNT/A1) and an atoxic derivative, BoNT/A ad. Botulinum neurotoxin type A1 (BoNT/A1) is a potent protein toxin responsible for the potentially fatal human illness botulism. Despite this, the long-lasting flaccid muscle paralysis caused by BoNT/A has led to its rise as a powerful and versatile bio-pharmaceutical. The flaccid paralysis is due to specific cleavage of SNAREs by BoNTs inside neurons. However, potential effects of BoNTs on intoxicated neurons besides the cleavage of SNAREs have not been studied in detail. In this study we investigated by microarray analysis the effects of BoNT/A and a catalytically inactive derivative (BoNT/A ad) on the transcriptome of human induced pluripotent stem cell (hiPSC)-derived neurons at 2 days and 2 weeks after exposure. While there were only minor changes in expression levels at 2 days post exposure, at 2 weeks post exposure 492 genes were differentially expressed more than 2-fold in BoNT/A1-exposed cells when compared to non-exposed populations, and 682 genes were differentially expressed in BoNT/A ad-exposed cells. The vast majority of genes were similarly regulated in BoNT/A1 and BoNT/A ad-exposed neurons, and the few genes differentially regulated between BoNT/A1 and BoNT/A ad-exposed neurons were regulated less than 3.5 fold. These data indicate a similar response of neurons to BoNT/A1 and BoNT/A ad exposure. The most highly regulated genes in cells exposed to either BoNT/A1 or BoNT/A ad are involved in neurite outgrowth and calcium channel sensitization.
2014-09-15 | GSE58149 | GEO
Project description:Transcriptome analysis of RNA extracted from human induced pluripotent stem cell (hipsc)-derived neurons exposed to botulinum neurotoxin type A1 (BoNT/A1) and an atoxic derivative, BoNT/A ad. Botulinum neurotoxin type A1 (BoNT/A1) is a potent protein toxin responsible for the potentially fatal human illness botulism. Despite this, the long-lasting flaccid muscle paralysis caused by BoNT/A has led to its rise as a powerful and versatile bio-pharmaceutical. The flaccid paralysis is due to specific cleavage of SNAREs by BoNTs inside neurons. However, potential effects of BoNTs on intoxicated neurons besides the cleavage of SNAREs have not been studied in detail. In this study we investigated by microarray analysis the effects of BoNT/A and a catalytically inactive derivative (BoNT/A ad) on the transcriptome of human induced pluripotent stem cell (hiPSC)-derived neurons at 2 days and 2 weeks after exposure. While there were only minor changes in expression levels at 2 days post exposure, at 2 weeks post exposure 492 genes were differentially expressed more than 2-fold in BoNT/A1-exposed cells when compared to non-exposed populations, and 682 genes were differentially expressed in BoNT/A ad-exposed cells. The vast majority of genes were similarly regulated in BoNT/A1 and BoNT/A ad-exposed neurons, and the few genes differentially regulated between BoNT/A1 and BoNT/A ad-exposed neurons were regulated less than 3.5 fold. These data indicate a similar response of neurons to BoNT/A1 and BoNT/A ad exposure. The most highly regulated genes in cells exposed to either BoNT/A1 or BoNT/A ad are involved in neurite outgrowth and calcium channel sensitization. 18 samples were used for this project: 6 populations were exposed to BoNT/A1, 6 to BoNT/A ad, and 6 were non-exposed. All exposures lasted for 48h, at which point 3 samples of each exposure group were harvested (2d condition), and the remaining 3 samples were grown for an additional 12d (2wk condition). Analysis was performed using the Affymetrix HG U133 Plus 2.0 array, and data was extracted using the Affymetrix Expression Console v 1.2.0.20 software
2014-09-15 | E-GEOD-58149 | biostudies-arrayexpress