About: Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays
Creator	Palzkill, Timothy Singh, Jaz Sodergren, Erica Strouhal, Michal Weinstock, George Albert, Thomas Matеjková, Petra Molla, Michael Norris, Steven Norton, Jason Petrosino, Joseph Richmond, Todd
topic	covid:0132b8c2721692d9f53bd33a738fa94618bb4e91#this
Source	Medline; PMC
abstract	BACKGROUND: Syphilis spirochete Treponema pallidum ssp. pallidum remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly understood. Increasing rates of new syphilis cases per year have been observed recently. RESULTS: The genome of the SS14 strain was sequenced to high accuracy by an oligonucleotide array strategy requiring hybridization to only three arrays (Comparative Genome Sequencing, CGS). Gaps in the resulting sequence were filled with targeted dideoxy-terminators (DDT) sequencing and the sequence was confirmed by whole genome fingerprinting (WGF). When compared to the Nichols strain, 327 single nucleotide substitutions (224 transitions, 103 transversions), 14 deletions, and 18 insertions were found. On the proteome level, the highest frequency of amino acid-altering substitution polymorphisms was in novel genes, while the lowest was in housekeeping genes, as expected by their evolutionary conservation. Evidence was also found for hypervariable regions and multiple regions showing intrastrain heterogeneity in the T. pallidum chromosome. CONCLUSION: The observed genetic changes do not have influence on the ability of Treponema pallidum to cause syphilitic infection, since both SS14 and Nichols are virulent in rabbit. However, this is the first assessment of the degree of variation between the two syphilis pathogens and paves the way for phylogenetic studies of this fascinating organism.
has issue date	2008-05-15(xsd:dateTime)
bibo:doi	10.1186/1471-2180-8-76
bibo:pmid	18482458
has license	cc-by
sha1sum (hex)	0132b8c2721692d9f53bd33a738fa94618bb4e91
schema:url	https://doi.org/10.1186/1471-2180-8-76
resource representing a document's title	Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays
has PubMed Central identifier	PMC2408589
has PubMed identifier	18482458
schema:publication	BMC Microbiol
resource representing a document's body	covid:0132b8c2721692d9f53bd33a738fa94618bb4e91#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/0132b8c2721692d9f53bd33a738fa94618bb4e91
is schema:about of	named entity 'Background' named entity 'pallidum' named entity 'sequence' named entity 'GENOME SEQUENCE' named entity 'OLIGONUCLEOTIDE ARRAYS' named entity 'SYPHILIS' named entity 'NEW' named entity 'POORLY' named entity 'DISEASE' named entity 'BACKGROUND' named entity 'STRAIN' named entity 'SSP' named entity 'COMPLETE' named entity 'TREPONEMA PALLIDUM' named entity 'MICROBIOLOGY' named entity 'PALLIDUM' named entity 'PER YEAR' named entity 'CASES' named entity 'SPIROCHETE' named entity 'PATHOGEN' named entity 'OBSERVED' named entity 'PALLIDUM' named entity 'RATES' named entity 'IDENTIFIED' named entity 'RECENTLY' named entity 'BMC' named entity 'INCREASING' named entity 'SSP' named entity 'DETERMINED' named entity 'PATHOGENESIS' named entity 'HAVE' named entity 'TREPONEMA PALLIDUM' named entity 'VIRULENCE FACTORS' named entity 'UNDERSTOOD' covid:arg/0132b8c2721692d9f53bd33a738fa94618bb4e91 named entity 'cases' named entity 'arrays' named entity 'pathogen' named entity 'virulence factors' named entity 'spirochete' named entity 'syphilis' named entity 'genome sequence' named entity 'EtOH' named entity 'SNP' named entity 'Foster City' named entity 'protein' named entity 'haploid' named entity 'gene' named entity 'genome' named entity 'genome' named entity 'homopolymeric' named entity 'microarray' named entity 'staining' named entity 'fibronectin' named entity 'gene' named entity 'tiling array' named entity 'false positives' named entity 'sequence similarity' named entity 'Treponema denticola' named entity 'reproducibility' named entity 'housekeeping genes' named entity 'repeated sequences' named entity 'multiple alleles' named entity 'neuroinvasion' named entity 'SNPs' named entity 'oligonucleotide' named entity 'GenBank' named entity 'SNPs'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software