TY  - JOUR
A1  - Brehony, Carina
A1  - Trotter, Caronline L.
A1  - Ramsay, Mary E.
A1  - Chandra, Manosree
A1  - Jolley, Keith A.
A1  - van der Ende, Arie
A1  - Carion, Françoise
A1  - Berthelsen, Lene
A1  - Hoffmann, Steen
A1  - Harðardóttir, Hjördís
A1  - Vazques, Julio A.
A1  - Murphy, Karen
A1  - Toropainen, Maija
A1  - Caniça, Manuela
A1  - Ferreira, Eugenia
A1  - Diggle, Mathew
A1  - Edwards, Giles F.
A1  - Taha, Muhamed-Kheir
A1  - Stefanelli, Paola
A1  - Kriz, Paula
A1  - Gray, Steve J.
A1  - Fox, Andrew J.
A1  - Jacobsson, Susanne
A1  - Claus, Heike
A1  - Vogel, Ulrich
A1  - Tzanakaki, Georgina
A1  - Heuberger, Sigrid
A1  - Caugant, Dominique A.
A1  - Frosch, Matthias
A1  - Maiden, Martin C. J.
T1  - Implications of Differential Age Distribution of Disease-Associated Meningococcal Lineages for Vaccine Development
JF  - Clinical and Vaccine Immunology : CVI
N2  - New vaccines targeting meningococci expressing serogroup B polysaccharide have been developed, with some being licensed in Europe. Coverage depends on the distribution of disease-associated genotypes, which may vary by age. It is well established that a small number of hyperinvasive lineages account for most disease, and these lineages are associated with particular antigens, including vaccine candidates. A collection of 4,048 representative meningococcal disease isolates from 18 European countries, collected over a 3-year period, were characterized by multilocus sequence typing (MLST). Age data were available for 3,147 isolates. The proportions of hyperinvasive lineages, identified as particular clonal complexes (ccs) by MLST, differed among age groups. Subjects <1 year of age experienced lower risk of sequence type 11 (ST-11) cc, ST-32 cc, and ST-269 cc disease and higher risk of disease due to unassigned STs, 1- to 4-year-olds experienced lower risk of ST-11 cc and ST-32 cc disease, 5- to 14-year-olds were less likely to experience ST-11 cc and ST-269 cc disease, and ≥25-year-olds were more likely to experience disease due to less common ccs and unassigned STs. Younger and older subjects were vulnerable to a more diverse set of genotypes, indicating the more clonal nature of genotypes affecting adolescents and young adults. Knowledge of temporal and spatial diversity and the dynamics of meningococcal populations is essential for disease control by vaccines, as coverage is lineage specific. The nonrandom age distribution of hyperinvasive lineages has consequences for the design and implementation of vaccines, as different variants, or perhaps targets, may be required for different age groups.
KW  - differential age distribution
KW  - disease-associated
KW  - meningococcal lineages
KW  - vaccine development
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-120808
VL  - 21
IS  - 6
ER  - 
TY  - JOUR
A1  - Schmidtke, Cornelius
A1  - Findeiß, Sven
A1  - Sharma, Cynthia M.
A1  - Kuhfuss, Juliane
A1  - Hoffmann, Steve
A1  - Vogel, Jörg
A1  - Stadler, Peter F.
A1  - Bonas, Ulla
T1  - Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
JF  - Nucleic Acids Research
N2  - The Gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) is an important model to elucidate the mechanisms involved in the interaction with the host. To gain insight into the transcriptome of the Xcv strain 85-10, we took a differential RNA sequencing (dRNA-seq) approach. Using a novel method to automatically generate comprehensive transcription start site (TSS) maps we report 1421 putative TSSs in the Xcv genome. Genes in Xcv exhibit a poorly conserved -10 promoter element and no consensus Shine-Dalgarno sequence. Moreover, 14% of all mRNAs are leaderless and 13% of them have unusually long 5'-UTRs. Northern blot analyses confirmed 16 intergenic small RNAs and seven cis-encoded antisense RNAs in Xcv. Expression of eight intergenic transcripts was controlled by HrpG and HrpX, key regulators of the Xcv type III secretion system. More detailed characterization identified sX12 as a small RNA that controls virulence of Xcv by affecting the interaction of the pathogen and its host plants. The transcriptional landscape of Xcv is unexpectedly complex, featuring abundant antisense transcripts, alternative TSSs and clade-specific small RNAs.
KW  - SUBSP carotovora
KW  - regulatory RNA
KW  - gene-cluster
KW  - campestris PV vesicatoria
KW  - escherichia coli
KW  - determines pathgenicity
KW  - hypersensitive response
KW  - ralstonia solanacearum
KW  - extracellular enzymes
KW  - secretion systems
KW  - transcription initiation site
KW  - RNA sequence analyses
KW  - messanger RNA
KW  - plants
KW  - libraries
KW  - genome
KW  - genes
KW  - gene expression profiling
KW  - genetic transcription
KW  - northern blotting
KW  - untranslated regions
KW  - xanthomonas
KW  - xanthomonas campestris
KW  - bacteria
KW  - virulence
KW  - pathogenetic organism
KW  - RNA
KW  - small RNA
KW  - pathogenicity
KW  - type III secretion system pathways
KW  - maps
KW  - consesus
KW  - host (organism)
KW  - type III protein secretion system complex
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-131781
VL  - 40
IS  - 5
SP  - 2020
EP  - 2031
ER  - 
TY  - JOUR
A1  - López, Cristina
A1  - Kleinheinz, Kortine
A1  - Aukema, Sietse M.
A1  - Rohde, Marius
A1  - Bernhart, Stephan H.
A1  - Hübschmann, Daniel
A1  - Wagener, Rabea
A1  - Toprak, Umut H.
A1  - Raimondi, Francesco
A1  - Kreuz, Markus
A1  - Waszak, Sebastian M.
A1  - Huang, Zhiqin
A1  - Sieverling, Lina
A1  - Paramasivam, Nagarajan
A1  - Seufert, Julian
A1  - Sungalee, Stephanie
A1  - Russell, Robert B.
A1  - Bausinger, Julia
A1  - Kretzmer, Helene
A1  - Ammerpohl, Ole
A1  - Bergmann, Anke K.
A1  - Binder, Hans
A1  - Borkhardt, Arndt
A1  - Brors, Benedikt
A1  - Claviez, Alexander
A1  - Doose, Gero
A1  - Feuerbach, Lars
A1  - Haake, Andrea
A1  - Hansmann, Martin-Leo
A1  - Hoell, Jessica
A1  - Hummel, Michael
A1  - Korbel, Jan O.
A1  - Lawerenz, Chris
A1  - Lenze, Dido
A1  - Radlwimmer, Bernhard
A1  - Richter, Julia
A1  - Rosenstiel, Philip
A1  - Rosenwald, Andreas
A1  - Schilhabel, Markus B.
A1  - Stein, Harald
A1  - Stilgenbauer, Stephan
A1  - Stadler, Peter F.
A1  - Szczepanowski, Monika
A1  - Weniger, Marc A.
A1  - Zapatka, Marc
A1  - Eils, Roland
A1  - Lichter, Peter
A1  - Loeffler, Markus
A1  - Möller, Peter
A1  - Trümper, Lorenz
A1  - Klapper, Wolfram
A1  - Hoffmann, Steve
A1  - Küppers, Ralf
A1  - Burkhardt, Birgit
A1  - Schlesner, Matthias
A1  - Siebert, Reiner
T1  - Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma
JF  - Nature Communications
N2  - Burkitt lymphoma (BL) is the most common B-cell lymphoma in children. Within the International Cancer Genome Consortium (ICGC), we performed whole genome and transcriptome sequencing of 39 sporadic BL. Here, we unravel interaction of structural, mutational, and transcriptional changes, which contribute to MYC oncogene dysregulation together with the pathognomonic IG-MYC translocation. Moreover, by mapping IGH translocation breakpoints, we provide evidence that the precursor of at least a subset of BL is a B-cell poised to express IGHA. We describe the landscape of mutations, structural variants, and mutational processes, and identified a series of driver genes in the pathogenesis of BL, which can be targeted by various mechanisms, including IG-non MYC translocations, germline and somatic mutations, fusion transcripts, and alternative splicing.
KW  - cancer genomics
KW  - lymphocytes
KW  - lymphoid tissues
KW  - oncology
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-237281
VL  - 10
ER  -