@article{HollenhorstJurastowNandigamaetal.2020,
  author    = {Hollenhorst, Monika I. and Jurastow, Innokentij and Nandigama, Rajender and Appenzeller, Silke and Li, Lei and Vogel, J{\"o}rg and Wiederhold, Stephanie and Althaus, Mike and Empting, Martin and Altm{\"u}ller, Janine and Hirsch, Anna K. H. and Flockerzi, Veit and Canning, Brendan J. and Saliba, Antoine-Emmanuel and Krasteva-Christ, Gabriela},
  title     = {Tracheal brush cells release acetylcholine in response to bitter tastants for paracrine and autocrine signaling},
  series = {The FASEB Journal},
  volume    = {34},
  journal   = {The FASEB Journal},
  number    = {1},
  doi       = {10.1096/fj.201901314RR},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-213516},
  pages     = {316 -- 332},
  year      = {2020},
  abstract  = {For protection from inhaled pathogens many strategies have evolved in the airways such as mucociliary clearance and cough. We have previously shown that protective respiratory reflexes to locally released bacterial bitter "taste" substances are most probably initiated by tracheal brush cells (BC). Our single-cell RNA-seq analysis of murine BC revealed high expression levels of cholinergic and bitter taste signaling transcripts (Tas2r108, Gnat3, Trpm5). We directly demonstrate the secretion of acetylcholine (ACh) from BC upon stimulation with the Tas2R agonist denatonium. Inhibition of the taste transduction cascade abolished the increase in [Ca\(^{2+}\)]\(_{i}\) in BC and subsequent ACh-release. ACh-release is regulated in an autocrine manner. While the muscarinic ACh-receptors M3R and M1R are activating, M2R is inhibitory. Paracrine effects of ACh released in response to denatonium included increased [Ca\(^{2+}\)]\(_{i}\) in ciliated cells. Stimulation by denatonium or with Pseudomonas quinolone signaling molecules led to an increase in mucociliary clearance in explanted tracheae that was Trpm5- and M3R-mediated. We show that ACh-release from BC via the bitter taste cascade leads to immediate paracrine protective responses that can be boosted in an autocrine manner. This mechanism represents the initial step for the activation of innate immune responses against pathogens in the airways.},
  language  = {en}
}
@article{HeidrichBauriedlBarquistetal.2017,
  author    = {Heidrich, Nadja and Bauriedl, Saskia and Barquist, Lars and Li, Lei and Schoen, Christoph and Vogel, J{\"o}rg},
  title     = {The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq},
  series = {Nucleic Acids Research},
  volume    = {45},
  journal   = {Nucleic Acids Research},
  number    = {10},
  doi       = {10.1093/nar/gkx168},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-170828},
  pages     = {6147-6167},
  year      = {2017},
  abstract  = {Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of -35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.},
  language  = {en}
}
@article{FanLiChaoetal.2015,
  author    = {Fan, Ben and Li, Lei and Chao, Yanjie and F{\"o}rstner, Konrad and Vogel, J{\"o}rg and Borriss, Rainer and Wu, Xiao-Qin},
  title     = {dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42},
  series = {PLoS One},
  volume    = {10},
  journal   = {PLoS One},
  number    = {11},
  doi       = {10.1371/journal.pone.0142002},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-138369},
  pages     = {e0142002},
  year      = {2015},
  abstract  = {Bacillus amyloliquefaciens subsp. plantarum FZB42 is a representative of Gram-positive plant-growth-promoting rhizobacteria (PGPR) that inhabit plant root environments. In order to better understand the molecular mechanisms of bacteria-plant symbiosis, we have systematically analyzed the primary transcriptome of strain FZB42 grown under rhizospheremimicking conditions using differential RNA sequencing (dRNA-seq). Our analysis revealed 4,877 transcription start sites for protein-coding genes, identified genes differentially expressed under different growth conditions, and corrected many previously mis-annotated genes. We also identified a large number of riboswitches and cis-encoded antisense RNAs, as well as trans-encoded small noncoding RNAs that may play important roles in the gene regulation of Bacillus. Overall, our analyses provided a landscape of Bacillus primary transcriptome and improved the knowledge of rhizobacteria-host interactions.},
  language  = {en}
}
@article{LiWongNongetal.2014,
  author    = {Li, Lei and Wong, Hin-chung and Nong, Wenyan and Cheung, Man Kit and Law, Patrick Tik Wan and Kam, Kai Man and Kwan, Hoi Shan},
  title     = {Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus},
  series = {BMC Genomics},
  volume    = {15},
  journal   = {BMC Genomics},
  number    = {1135},
  issn      = {1471-2164},
  doi       = {10.1186/1471-2164-15-1135},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-118080},
  year      = {2014},
  abstract  = {Background: Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinical isolates of V. parahaemolyticus are currently available, but the genome dynamics across the species and virulence potential of environmental strains on a genome-scale have not been described before. Results: Here we present genome sequences of four V. parahaemolyticus clinical strains from stool samples of patients and five environmental strains in Hong Kong. Phylogenomics analysis based on single nucleotide polymorphisms revealed a clear distinction between the clinical and environmental isolates. A new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus was found in clincial strains. In addition, a novel small genomic island frequently found among clinical isolates was reported. A few environmental strains were found harboring virulence genes and prophage elements, indicating their virulence potential. A unique biphenyl degradation pathway was also reported. A database for V. parahaemolyticus (http://kwanlab.bio.cuhk.edu.hk/vp webcite) was constructed here as a platform to access and analyze genome sequences and annotations of the bacterium. Conclusions: We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium. "},
  language  = {en}
}