@article{SassVanAckerFoerstneretal.2015,
  author    = {Sass, Andrea M. and Van Acker, Heleen and F{\"o}rstner, Konrad U. and Van Nieuwerburgh, Filip and Deforce, Dieter and Vogel, J{\"o}rg and Coenye, Tom},
  title     = {Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315},
  series = {BMC Genomics},
  volume    = {16},
  journal   = {BMC Genomics},
  number    = {775},
  doi       = {10.1186/s12864-015-1993-3},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-139748},
  year      = {2015},
  abstract  = {Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. Methods: RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Results: Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Conclusions: Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.},
  language  = {en}
}
@article{EspinaPaganLopezetal.2015,
  author    = {Espina, Laura and Pag{\´a}n, Rafael and L{\´o}pez, Daniel and Garc{\´i}a-Gonzalo, Diego},
  title     = {Individual Constituents from Essential Oils Inhibit Biofilm Mass Production by Multi-Drug Resistant Staphylococcus aureus},
  series = {Molecules},
  volume    = {20},
  journal   = {Molecules},
  doi       = {10.3390/molecules200611357},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151845},
  pages     = {11357 -- 11372},
  year      = {2015},
  abstract  = {Biofilm formation by Staphylococcus aureus represents a problem in both the medical field and the food industry, because the biofilm structure provides protection to embedded cells and it strongly attaches to surfaces. This circumstance is leading to many research programs seeking new alternatives to control biofilm formation by this pathogen. In this study we show that a potent inhibition of biofilm mass production can be achieved in community-associated methicillin-resistant S. aureus (CA-MRSA) and methicillin-sensitive strains using plant compounds, such as individual constituents (ICs) of essential oils (carvacrol, citral, and (+)-limonene). The Crystal Violet staining technique was used to evaluate biofilm mass formation during 40 h of incubation. Carvacrol is the most effective IC, abrogating biofilm formation in all strains tested, while CA-MRSA was the most sensitive phenotype to any of the ICs tested. Inhibition of planktonic cells by ICs during initial growth stages could partially explain the inhibition of biofilm formation. Overall, our results show the potential of EOs to prevent biofilm formation, especially in strains that exhibit resistance to other antimicrobials. As these compounds are food additives generally recognized as safe, their anti-biofilm properties may lead to important new applications, such as sanitizers, in the food industry or in clinical settings.},
  language  = {en}
}