@article{SchneiderDobrindtMiddendorfetal.2011,
  author    = {Schneider, Gy{\"o}rgy and Dobrindt, Ulrich and Middendorf, Barbara and Hochhut, Bianca and Szij{\´a}rt{\´o}, Valeria and Em{\´o}dy, Levente and Hacker, J{\"o}rg},
  title     = {Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic \(Escherichia\) \(coli\) \(in\) \(vitro\) support the role of conjugation for horizontal transfer of genomic islands},
  series = {BMC Microbiology},
  volume    = {11},
  journal   = {BMC Microbiology},
  doi       = {10.1186/1471-2180-11-210},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-140975},
  pages     = {210},
  year      = {2011},
  abstract  = {Background: A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results: To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II(536) was supplemented with the mob(RP4) region, an origin of replication (oriV(R6K)), an origin of transfer (oriT(RP4)) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II(536) construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II(536) existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II(536) in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II(536) construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II(536) deletion mutant of E. coli 536. Conclusions: Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.},
  language  = {en}
}
@article{ArhondakisFrousiosIliopoulosetal.2011,
  author    = {Arhondakis, Stilianos and Frousios, Kimon and Iliopoulos, Costas S. and Pissis, Solon P. and Tischler, German and Kossida, Sophia},
  title     = {Transcriptome map of mouse isochores},
  series = {BMC Genomics},
  volume    = {12},
  journal   = {BMC Genomics},
  number    = {511},
  doi       = {10.1186/1471-2164-12-511},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142773},
  pages     = {1-9},
  year      = {2011},
  abstract  = {Background: The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest. Results: We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families. Conclusions: This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.},
  language  = {en}
}