TY  - JOUR
A1  - Barquist, Lars
A1  - Mayho, Matthew
A1  - Cummins, Carla
A1  - Cain, Amy K.
A1  - Boinett, Christine J.
A1  - Page, Andrew J.
A1  - Langridge, Gemma C.
A1  - Quail, Michael A.
A1  - Keane, Jacqueline A.
A1  - Parkhill, Julian
T1  - The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
JF  - Bioinformatics
N2  - Transposon insertion sequencing is a high-throughput technique for assaying large libraries of otherwise isogenic transposon mutants providing insight into gene essentiality, gene function and genetic interactions. We previously developed the Transposon Directed Insertion Sequencing (TraDIS) protocol for this purpose, which utilizes shearing of genomic DNA followed by specific PCR amplification of transposon-containing fragments and Illumina sequencing. Here we describe an optimized high-yield library preparation and sequencing protocol for TraDIS experiments and a novel software pipeline for analysis of the resulting data. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. This article can serve as a general reference for the application of the TraDIS methodology.
KW  - mechanisms
KW  - Transposon insertion sequencing
KW  - sequencing protocol
KW  - TraDIS
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-189667
VL  - 32
IS  - 7
ER  - 
TY  - JOUR
A1  - Harrison, Odile B.
A1  - Claus, Heike
A1  - Jiang, Ying
A1  - Bennett, Julia S.
A1  - Bratcher, Holly B.
A1  - Jolley, Keith A.
A1  - Corton, Craig
A1  - Care, Rory
A1  - Poolman, Jan T.
A1  - Zollinger, Wendell D.
A1  - Frasch, Carl E.
A1  - Stephens, David S.
A1  - Feavers, Ian
A1  - Frosch, Matthias
A1  - Parkhill, Julian
A1  - Vogel, Ulrich
A1  - Quail, Michael A.
A1  - Bentley, Stephen D.
A1  - Maiden, Martin C. J.
T1  - Description and Nomenclature of Neisseria meningitidis Capsule Locus
JF  - Emerging Infectious Diseases
N2  - Pathogenic Neisseria meningitidis isolates contain a polysaccharide capsule that is the main virulence determinant for this bacterium. Thirteen capsular polysaccharides have been described, and nuclear magnetic resonance spectroscopy has enabled determination of the structure of capsular polysaccharides responsible for serogroup specificity. Molecular mechanisms involved in N. meningitidis capsule biosynthesis have also been identified, and genes involved in this process and in cell surface translocation are clustered at a single chromosomal locus termed cps. The use of multiple names for some of the genes involved in capsule synthesis, combined with the need for rapid diagnosis of serogroups commonly associated with invasive meningococcal disease, prompted a requirement for a consistent approach to the nomenclature of capsule genes. In this report, a comprehensive description of all N. meningitidis serogroups is provided, along with a proposed nomenclature, which was presented at the 2012 XVIIIth International Pathogenic Neisseria Conference.
KW  - genetics
KW  - nuclear magnetic resonance
KW  - structural determination
KW  - meningococcal polysaccharides
KW  - chemical properties
KW  - serogroup-Y
KW  - group-B
KW  - antigen
KW  - biosynthesis
KW  - elucidation
Y1  - 2013
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131703
VL  - 19
IS  - 4
ER  -