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RF T3SPs specifications

Information


Unique identifier OMICS_19754
Name RF T3SPs
Alternative names Random Forest algorithm for Type III Secreted Proteins, T3SPs, RF
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Menglong Li
  • person_outline Yanzhi Guo

Publication for Random Forest algorithm for Type III Secreted Proteins

RF T3SPs citations

 (6)
library_books

Pan Genomic Analysis Permits Differentiation of Virulent and Non virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors

2017
Front Microbiol
PMCID: 5389983
PMID: 28450852
DOI: 10.3389/fmicb.2017.00573

[…] e Prunus-non-virulent strain CITA 44, none of the genes that composed the macromolecular structure of the T3SS were found (Table ). Regarding to the T3SS related effectors, from the 61 T3Es and other T3SPs described in Xanthomonas, the genome sequence of CITA 14 presented a total of six orthologs to the genes avrBs2, hpaA, hrpW, xopA, xopF1 and xopR, while genome sequence of CITA 124 did not prese […]

library_books

Identification of epitopes recognised by mucosal CD4+ T cell populations from cattle experimentally colonised with Escherichia coli O157:H7

2016
PMCID: 5010706
PMID: 27590451
DOI: 10.1186/s13567-016-0374-5

[…] N-γ release was used as a readout as this study also demonstrated the presence of TH1 responses in colonised cattle, and rectal lymph node cells released IFN-γ following re-stimulation with EHEC O157 T3SPs.The CD4+ T-cell line from animal 101 053 exhibited high background IFN-γ release (mean of 30 439 pg/mL in the negative control wells compared to 120 326 pg/mL in PHA controls; ~25% of the PHA po […]

library_books

Antibodies Directed against Shiga Toxin Producing Escherichia coli Serotype O103 Type III Secreted Proteins Block Adherence of Heterologous STEC Serotypes to HEp 2 Cells

2015
PLoS One
PMCID: 4599963
PMID: 26451946
DOI: 10.1371/journal.pone.0139803

[…] To test the effect of rabbit polyclonal sera against recombinant STECO103 T3SPs on adherence, we used a functional assay where we measured the level of STECO103 adherence to HEp-2 cells. Our results demonstrate that pooled sera against STECO103 recombinant proteins signific […]

library_books

Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834 R reveals that flagellar motility is not a general feature of xanthomonads

2013
BMC Genomics
PMCID: 3826837
PMID: 24195767
DOI: 10.1186/1471-2164-14-761

[…] To mine for the presence of genes coding candidate T3Es (including T3 secreted proteins, T3SPs), we first blasted on the genome of Xff 4834-R the sequence of all known T3Es genes listed on the Xanthomonas.org website. Such a mining of the genome of Xff 4834-R predicts 29 genes encoding T3 […]

library_books

Natural Genetic Variation of Xanthomonas campestris pv. campestris Pathogenicity on Arabidopsis Revealed by Association and Reverse Genetics

2013
MBio
PMCID: 3685212
PMID: 23736288
DOI: 10.1128/mBio.00538-12

[…] ype III secretome size and aggressivity on Kas plants (P = 0.007, ρ = −0.39). Genetic diversity observed among X. campestris pv. campestris strains suggests that genome sequencing might unravel other T3SPs that are absent from the genomes of the 3 X. campestris pv. campestris reference strains or other Xanthomonas pathovars (). Furthermore, no systematic experimental T3SP mining has been reported […]

library_books

Treatment of enterohemorrhagic Escherichia coli (EHEC) infection and hemolytic uremic syndrome (HUS)

2012
PMCID: 3286370
PMID: 22300510
DOI: 10.1186/1741-7015-10-12

[…] mucosal pathogens including EHEC have obvious advantages []. Other approaches are listed in Table [-].Antibodies produced in humans with HUS and in rabbits immunized with type III secreted proteins (T3SPs) from four STEC serotypes, and experimentally infected cattle revealed proteins common to several HUS serotypes [] (Table ). These were highly immunogenic in vaccinated and naturally infected su […]

Citations

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RF T3SPs institution(s)
College of Chemistry, Sichuan University, Chengdu, China
RF T3SPs funding source(s)
Supported by the National Natural Science Foundation of China (Nos. 20905054, 20972103, 20973115) and the Specialized Research Fund for the Doctoral Program of Higher Education (No. 20090181120058).

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