@article{LuDreyerDickinsonetal.2023,
  author    = {Lu, Jinping and Dreyer, Ingo and Dickinson, Miles Sasha and Panzer, Sabine and Jaślan, Dawid and Navarro-Retamal, Carlos and Geiger, Dietmar and Terpitz, Ulrich and Becker, Dirk and Stroud, Robert M. and Marten, Irene and Hedrich, Rainer},
  title     = {Vicia faba SV channel VfTPC1 is a hyperexcitable variant of plant vacuole two pore channels},
  series = {eLife},
  volume    = {12},
  journal   = {eLife},
  doi       = {10.7554/eLife.86384},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-350264},
  year      = {2023},
  abstract  = {To fire action-potential-like electrical signals, the vacuole membrane requires the two-pore channel TPC1, formerly called SV channel. The TPC1/SV channel functions as a depolarization-stimulated, non-selective cation channel that is inhibited by luminal Ca\(^{2+}\). In our search for species-dependent functional TPC1 channel variants with different luminal Ca\(^{2+}\) sensitivity, we found in total three acidic residues present in Ca\(^{2+}\) sensor sites 2 and 3 of the Ca\(^{2+}\)-sensitive AtTPC1 channel from Arabidopsis thaliana that were neutral in its Vicia faba ortholog and also in those of many other Fabaceae. When expressed in the Arabidopsis AtTPC1-loss-of-function background, wild-type VfTPC1 was hypersensitive to vacuole depolarization and only weakly sensitive to blocking luminal Ca\(^{2+}\). When AtTPC1 was mutated for these VfTPC1-homologous polymorphic residues, two neutral substitutions in Ca\(^{2+}\) sensor site 3 alone were already sufficient for the Arabidopsis At-VfTPC1 channel mutant to gain VfTPC1-like voltage and luminal Ca\(^{2+}\) sensitivity that together rendered vacuoles hyperexcitable. Thus, natural TPC1 channel variants exist in plant families which may fine-tune vacuole excitability and adapt it to environmental settings of the particular ecological niche.},
  language  = {en}
}
@article{BemmBeckerLarischetal.2016,
  author    = {Bemm, Felix and Becker, Dirk and Larisch, Christina and Kreuzer, Ines and Escalante-Perez, Maria and Schulze, Waltraud X. and Ankenbrand, Markus and Van de Weyer, Anna-Lena and Krol, Elzbieta and Al-Rasheid, Khaled A. and Mith{\"o}fer, Axel and Weber, Andreas P. and Schultz, J{\"o}rg and Hedrich, Rainer},
  title     = {Venus flytrap carnivorous lifestyle builds on herbivore defense strategies},
  series = {Genome Research},
  volume    = {26},
  journal   = {Genome Research},
  number    = {6},
  doi       = {10.1101/gr.202200.115},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-188799},
  pages     = {812-825},
  year      = {2016},
  abstract  = {Although the concept of botanical carnivory has been known since Darwin's time, the molecular mechanisms that allow animal feeding remain unknown, primarily due to a complete lack of genomic information. Here, we show that the transcriptomic landscape of the Dionaea trap is dramatically shifted toward signal transduction and nutrient transport upon insect feeding, with touch hormone signaling and protein secretion prevailing. At the same time, a massive induction of general defense responses is accompanied by the repression of cell death-related genes/processes. We hypothesize that the carnivory syndrome of Dionaea evolved by exaptation of ancient defense pathways, replacing cell death with nutrient acquisition.},
  language  = {en}
}
@article{AnkenbrandWeberBeckeretal.2016,
  author    = {Ankenbrand, Markus J. and Weber, Lorenz and Becker, Dirk and F{\"o}rster, Frank and Bemm, Felix},
  title     = {TBro: visualization and management of de novo transcriptomes},
  series = {Database},
  volume    = {2016},
  journal   = {Database},
  doi       = {10.1093/database/baw146},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-147954},
  pages     = {baw146},
  year      = {2016},
  abstract  = {RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro's modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers.},
  language  = {en}
}