PUMA publications for /user/bvosshttps://puma.ub.uni-stuttgart.de/user/bvossPUMA RSS feed for /user/bvoss2024-03-29T15:42:32+01:00RNAnue: efficient data analysis for RNA–RNA interactomicshttps://puma.ub.uni-stuttgart.de/bibtex/26d54529f088d5fb7b6b2b68b313355c4/bvossbvoss2021-06-08T12:06:57+02:00cobi myown rna <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Richard A Schäfer" itemprop="url" href="/person/16fb0d70720b6c07eb7993416249b4cb8/author/0"><span itemprop="name">R. Schäfer</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/16fb0d70720b6c07eb7993416249b4cb8/author/1"><span itemprop="name">B. Voß</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Nucleic Acids Research</span>, </em> </span>(<em><span>May 2021<meta content="May 2021" itemprop="datePublished"/></span></em>)</span>Tue Jun 08 12:06:57 CEST 2021Nucleic Acids Research5gkab340RNAnue: efficient data analysis for RNA–RNA interactomics2021cobi myown rna RNA–RNA inter- and intramolecular interactions are fundamental for numerous biological processes. While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. Recently, different strategies to detect RNA–RNA duplexes in living cells, so called direct duplex detection (DDD) methods, have been developed. Common to all is the Psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to join the two interacting RNA strands. Sequencing of the RNA via classical RNA-seq and subsequent specialised bioinformatic analyses the result in the prediction of inter- and intramolecular RNA–RNA interactions. Existing approaches adapt standard RNA-seq analysis pipelines, but often neglect inherent features of RNA–RNA interactions that are useful for filtering and statistical assessment. Here we present RNAnue, a general pipeline for the inference of RNA–RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. We applied RNAnue to data from different DDD studies and compared our results to those of the original methods. This showed that RNAnue performs better in terms of quantity and quality of predictions.A small RNA is linking CRISPR-Cas and zinc transporthttps://puma.ub.uni-stuttgart.de/bibtex/2ec48e9e157a9dffd78ef55459b7da978/bvossbvoss2021-03-04T07:57:15+01:00myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Pascal Märkle" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/0"><span itemprop="name">P. Märkle</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Lisa-Katharina Maier" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/1"><span itemprop="name">L. Maier</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Sandra Maaß" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/2"><span itemprop="name">S. Maaß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Claudia Hirschfeld" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/3"><span itemprop="name">C. Hirschfeld</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jürgen Bartel" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/4"><span itemprop="name">J. Bartel</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Dörte Becher" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/5"><span itemprop="name">D. Becher</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/6"><span itemprop="name">B. Voß</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Anita Marchfelder" itemprop="url" href="/person/1a906de3a90841f6051a51dfe7e8dc9ee/author/7"><span itemprop="name">A. Marchfelder</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Frontiers in Molecular Biosciences</span>, </em> </span>(<em><span>2021<meta content="2021" itemprop="datePublished"/></span></em>)</span>Thu Mar 04 07:57:15 CET 2021Frontiers in Molecular BiosciencesA small RNA is linking CRISPR-Cas and zinc transportarticle82021myown The function and mode of action of small regulatory RNAs is currently still understudied in archaea. In the halophilic archaeon H. volcanii a plethora of sRNAs have been identified, however, in-depth functional analysis is missing for most of them. We selected a small RNA (s479) from H. volcanii for detailed characterization. The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. Three of the six up-regulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, ZnuC1) suggesting involvement of s479 in regulation of zinc transport. Upregulation of these genes in the deletion strain was confirmed by northern blot and proteome analyses. Furthermore, electrophoretic mobility shift assays demonstrate a direct interaction of s479 with the target znuC1 mRNA. Proteome comparison of wild type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance. Interestingly, s479 is not only encoded next to CRISPR-cas genes but the mature s479 contains a crRNA-like 5´ handle and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. Together this might suggest that the CRISPR-Cas system is involved in s479 function. Frontiers | A small RNA is linking CRISPR-Cas and zinc transport | Molecular BiosciencesSimulation of Folding Kinetics for Aligned RNAshttps://puma.ub.uni-stuttgart.de/bibtex/2a9d7a14e56d355ade50e306fe823f70d/bvossbvoss2021-03-04T07:47:59+01:00myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jiabin Huang" itemprop="url" href="/person/149952ee00dae33853d21ebb3395eb744/author/0"><span itemprop="name">J. Huang</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/149952ee00dae33853d21ebb3395eb744/author/1"><span itemprop="name">B. Voß</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Genes</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">12 </span></span>(<span itemprop="issueNumber">3</span>):
<span itemprop="pagination">347</span></em> </span>(<em><span>February 2021<meta content="February 2021" itemprop="datePublished"/></span></em>)</span>Thu Mar 04 07:47:59 CET 2021Genes23347Simulation of Folding Kinetics for Aligned {RNAs}122021myown Genes | Free Full-Text | Simulation of Folding Kinetics for Aligned RNAsGLASSGo in Galaxy: High-Throughput, Reproducible and Easy-to-Integrate Prediction of sRNA Homologshttps://puma.ub.uni-stuttgart.de/bibtex/2a1ff6b23043c4d6b9e4d39f6ab36bf2c/bvossbvoss2020-06-17T13:07:05+02:00cobi myown rna <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Richard A Schäfer" itemprop="url" href="/person/1f71f7d8c89329dad7cfba8ff4610e338/author/0"><span itemprop="name">R. Schäfer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Steffen C Lott" itemprop="url" href="/person/1f71f7d8c89329dad7cfba8ff4610e338/author/1"><span itemprop="name">S. Lott</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jens Georg" itemprop="url" href="/person/1f71f7d8c89329dad7cfba8ff4610e338/author/2"><span itemprop="name">J. Georg</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn A Grüning" itemprop="url" href="/person/1f71f7d8c89329dad7cfba8ff4610e338/author/3"><span itemprop="name">B. Grüning</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Wolfgang R Hess" itemprop="url" href="/person/1f71f7d8c89329dad7cfba8ff4610e338/author/4"><span itemprop="name">W. Hess</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1f71f7d8c89329dad7cfba8ff4610e338/author/5"><span itemprop="name">B. Voß</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Bioinformatics</span>, </em> </span>(<em><span>June 2020<meta content="June 2020" itemprop="datePublished"/></span></em>)</span>Wed Jun 17 13:07:05 CEST 2020Bioinformatics6btaa556{{GLASSGo}} in {{Galaxy}}: High-Throughput, Reproducible and Easy-to-Integrate Prediction of {{sRNA}} Homologs2020cobi myown rna The correct prediction of bacterial sRNA homologs is a prerequisite for many downstream analyses based on comparative genomics, but it is frequently challenging due to the short length and distinct heterogeneity of such homologs. GLASSGo is an efficient tool for the prediction of sRNA homologs from a single input query. To make the algorithm available to a broader community, we offer a Docker container along with a free-access web service. For non-computer scientists, the web service provides a user-friendly interface. However, capabilities were lacking so far for batch processing, version control, and direct interaction with compatible software applications as a workflow management system can provide.Here we present GLASSGo 1.5.2, an updated version that is fully incorporated into the workflow management system Galaxy. The improved version contains a new feature for extracting the upstream regions, allowing the search for conserved promoter elements. Additionally, it supports the use of accession numbers instead of the outdated GI numbers, which widens the applicability of the tool.GLASSGo is available at https://github.com/lotts/GLASSgo/ under the MIT license and is accompanied by instruction and application data. Furthermore, it can be installed into any Galaxy instance using the Galaxy ToolShed.Pseudomonas Putida KT2440 Is Naturally Endowed to Withstand Industrial-Scale Stress Conditionshttps://puma.ub.uni-stuttgart.de/bibtex/21719766e973463b208200349ec7b6340/bvossbvoss2020-04-16T15:13:36+02:00myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Andreas Ankenbauer" itemprop="url" href="/person/1a26368dcdff8794331ac658b59fd1b59/author/0"><span itemprop="name">A. Ankenbauer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Richard A. Schäfer" itemprop="url" href="/person/1a26368dcdff8794331ac658b59fd1b59/author/1"><span itemprop="name">R. Schäfer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Sandra C. Viegas" itemprop="url" href="/person/1a26368dcdff8794331ac658b59fd1b59/author/2"><span itemprop="name">S. Viegas</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Vânia Pobre" itemprop="url" href="/person/1a26368dcdff8794331ac658b59fd1b59/author/3"><span itemprop="name">V. Pobre</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1a26368dcdff8794331ac658b59fd1b59/author/4"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Cecília M. Arraiano" itemprop="url" href="/person/1a26368dcdff8794331ac658b59fd1b59/author/5"><span itemprop="name">C. Arraiano</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Ralf Takors" itemprop="url" href="/person/1a26368dcdff8794331ac658b59fd1b59/author/6"><span itemprop="name">R. Takors</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Microbial Biotechnology</span>, </em> </span>(<em><span>2020<meta content="2020" itemprop="datePublished"/></span></em>)</span>Thu Apr 16 15:13:36 CEST 2020Microbial Biotechnologyn/aPseudomonas Putida KT2440 Is Naturally Endowed to Withstand Industrial-Scale Stress Conditionsn/a2020myown Pseudomonas putida is recognized as a very promising strain for industrial application due to its high redox capacity and frequently observed tolerance towards organic solvents. In this research, we studied the metabolic and transcriptional response of P. putida KT2440 exposed to large-scale heterogeneous mixing conditions in the form of repeated glucose shortage. Cellular responses were mimicked in an experimental setup comprising a stirred tank reactor and a connected plug flow reactor. We deciphered that a stringent response-like transcriptional regulation programme is frequently induced, which seems to be linked to the intracellular pool of 3-hydroxyalkanoates (3-HA) that are known to serve as precursors for polyhydroxyalkanoates (PHA). To be precise, P. putida is endowed with a survival strategy likely to access cellular PHA, amino acids and glycogen in few seconds under glucose starvation to obtain ATP from respiration, thereby replenishing the reduced ATP levels and the adenylate energy charge. Notably, cells only need 0.4\% of glucose uptake to build those 3-HA-based energy buffers. Concomitantly, genes that are related to amino acid catabolism and {$\beta$}-oxidation are upregulated during the transient absence of glucose. Furthermore, we provide a detailed list of transcriptional short- and long-term responses that increase the cellular maintenance by about 17\% under the industrial-like conditions tested.CRISPR-Cas Bioinformaticshttps://puma.ub.uni-stuttgart.de/bibtex/2c3dcf768a5264a3f50c4aa28a3ae9254/bvossbvoss2019-07-25T11:37:04+02:00cobi myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Omer S. Alkhnbashi" itemprop="url" href="/person/18e951d2138b54af9916f894a140c8540/author/0"><span itemprop="name">O. Alkhnbashi</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Tobias Meier" itemprop="url" href="/person/18e951d2138b54af9916f894a140c8540/author/1"><span itemprop="name">T. Meier</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Alexander Mitrofanov" itemprop="url" href="/person/18e951d2138b54af9916f894a140c8540/author/2"><span itemprop="name">A. Mitrofanov</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Rolf Backofen" itemprop="url" href="/person/18e951d2138b54af9916f894a140c8540/author/3"><span itemprop="name">R. Backofen</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/18e951d2138b54af9916f894a140c8540/author/4"><span itemprop="name">B. Voß</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Methods</span>, </em> </span>(<em><span>February 2020<meta content="February 2020" itemprop="datePublished"/></span></em>)</span>Thu Jul 25 11:37:04 CEST 2019Methods23-11CRISPR-Cas Bioinformatics1722020cobi myown Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are essential genetic elements in many archaeal and bacterial genomes, playing a key role in a prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas system has also been engineered to facilitate target gene editing in eukaryotic genomes. Bioinformatics played an essential role in the detection and analysis of CRISPR systems and here we review the bioinformatics-based efforts that pushed the field of CRISPR-Cas research further. We discuss the bioinformatics tools that have been published over the last few years and, finally, present the most popular tools for the design of CRISPR-Cas9 guides.CRISPR-Cas Bioinformatics - ScienceDirectRNA interactomics: recent advances and remaining challengeshttps://puma.ub.uni-stuttgart.de/bibtex/260d4b15bed5bc2ff18d0cb1860fd7de4/bvossbvoss2018-11-21T09:27:46+01:00cobi myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Brigitte Schönberger" itemprop="url" href="/person/18b3d2bf5e4b37a06e1105ae945f03a10/author/0"><span itemprop="name">B. Schönberger</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Christoph Schaal" itemprop="url" href="/person/18b3d2bf5e4b37a06e1105ae945f03a10/author/1"><span itemprop="name">C. Schaal</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Richard Schäfer" itemprop="url" href="/person/18b3d2bf5e4b37a06e1105ae945f03a10/author/2"><span itemprop="name">R. Schäfer</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/18b3d2bf5e4b37a06e1105ae945f03a10/author/3"><span itemprop="name">B. Voß</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">F1000Research</span>, </em> </span>(<em><span>November 2018<meta content="November 2018" itemprop="datePublished"/></span></em>)</span>Wed Nov 21 09:27:46 CET 2018F1000Research111824{RNA} interactomics: recent advances and remaining challenges72018cobi myown RNA interactomics: recent advances and remaining challenges - F1000ResearchGLASSgo - Automated and reliable detection of sRNA homologs from a single input sequencehttps://puma.ub.uni-stuttgart.de/bibtex/2d54d1af2b2c05a80be0732d84d00cd32/bvossbvoss2018-04-13T13:58:00+02:00cobi myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Steffen Christian Lott" itemprop="url" href="/person/1b026d4b1831738923557e550c6d8d685/author/0"><span itemprop="name">S. Lott</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Richard A. Schäfer" itemprop="url" href="/person/1b026d4b1831738923557e550c6d8d685/author/1"><span itemprop="name">R. Schäfer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Martin Mann" itemprop="url" href="/person/1b026d4b1831738923557e550c6d8d685/author/2"><span itemprop="name">M. Mann</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Rolf Backofen" itemprop="url" href="/person/1b026d4b1831738923557e550c6d8d685/author/3"><span itemprop="name">R. Backofen</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Wolfgang R. Hess" itemprop="url" href="/person/1b026d4b1831738923557e550c6d8d685/author/4"><span itemprop="name">W. Hess</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1b026d4b1831738923557e550c6d8d685/author/5"><span itemprop="name">B. Voß</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jens Georg" itemprop="url" href="/person/1b026d4b1831738923557e550c6d8d685/author/6"><span itemprop="name">J. Georg</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Frontiers in Genetics</span>, </em> </span>(<em><span>2018<meta content="2018" itemprop="datePublished"/></span></em>)</span>Fri Apr 13 13:58:00 CEST 2018Frontiers in GeneticsGLASSgo - Automated and reliable detection of sRNA homologs from a single input sequencearticle92018cobi myown Bacterial small RNAs (sRNAs) are important post-transcriptional regulators of gene expression. The functional and evolutionary characterization of sRNAs requires the identification of homologs, which is frequently challenging due to their heterogeneity, short length and partly, little sequence conservation. We developed the GLobal Automatic Small RNA Search go (GLASSgo) algorithm to identify sRNA homologs in complex genomic databases starting from a single sequence. GLASSgo combines an iterative BLAST strategy with pairwise identity filtering and a graph-based clustering method that utilizes RNA secondary structure information. We tested the specificity, sensitivity and runtime of GLASSgo, BLAST and the combination RNAlien/cmsearch in a typical use case scenario on 40 bacterial sRNA families. The sensitivity of the tested methods was similar, while the specificity of GLASSgo and RNAlien/cmsearch was significantly higher than that of BLAST. GLASSgo was on average ~87 times faster than RNAlien/cmsearch, and only ~7.5 times slower than BLAST, which shows that GLASSgo optimizes the trade-off between speed and accuracy in the task of finding sRNA homologs. GLASSgo is fully automated, whereas BLAST often recovers only parts of homologs and RNAlien/cmsearch requires extensive additional bioinformatic work to get a comprehensive set of homologs. GLASSgo is available as an easy-to-use web server to find homologous sRNAs in large databases.Frontiers | GLASSgo - Automated and reliable detection of sRNA homologs from a single input sequence | GeneticsGenome of a giant bacteriophage from a decaying Trichodesmium bloomhttps://puma.ub.uni-stuttgart.de/bibtex/241cc37ee4359aa6c90b0c29e7548b427/bvossbvoss2018-01-22T15:05:52+01:00myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Ulrike Pfreundt" itemprop="url" href="/person/162d4bd870800e5cd756a25b14d1728d7/author/0"><span itemprop="name">U. Pfreundt</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Dina Spungin" itemprop="url" href="/person/162d4bd870800e5cd756a25b14d1728d7/author/1"><span itemprop="name">D. Spungin</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Shengwei Hou" itemprop="url" href="/person/162d4bd870800e5cd756a25b14d1728d7/author/2"><span itemprop="name">S. Hou</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/162d4bd870800e5cd756a25b14d1728d7/author/3"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Ilana Berman-Frank" itemprop="url" href="/person/162d4bd870800e5cd756a25b14d1728d7/author/4"><span itemprop="name">I. Berman-Frank</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Wolfgang R. Hess" itemprop="url" href="/person/162d4bd870800e5cd756a25b14d1728d7/author/5"><span itemprop="name">W. Hess</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Marine Genomics</span>, </em> </span>(<em><span>2017<meta content="2017" itemprop="datePublished"/></span></em>)</span>Mon Jan 22 15:05:52 CET 2018Marine Genomics21 - 25Genome of a giant bacteriophage from a decaying Trichodesmium bloom332017myown De-novo assembly of a metagenomic dataset obtained from a decaying cyanobacterial Trichodesmium bloom from the New Caledonian lagoon resulted in a complete giant phage genome of 257,908bp, obtained independently with multiple assembly tools. Noteworthy, gammaproteobacteria were an abundant fraction in the sequenced samples. Mapping of the raw reads with 99% accuracy to the giant phage genome resulted in an average coverage of 262X. The closest sequenced relatives, albeit still distant, are the Pseudomonas phages PaBG from Lake Baikal and Lu11 isolated from a soil sample from the Philippines. The phage reported here might belong to the same family within the Myoviridae as PaBG and Lu11 and would thus be its first marine member, indicating a more widespread occurrence of this group. We named this phage NCTB (New Caledonia Trichodesmium Bloom) after its origin.Genome of a giant bacteriophage from a decaying Trichodesmium bloom - ScienceDirect5'UTR-Mediated Translational Control of Splice Variants of Phytoene Synthasehttps://puma.ub.uni-stuttgart.de/bibtex/24d6f03dc90dd121f59f6997e83e27a41/bvossbvoss2016-10-13T13:25:15+02:00myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Daniel Álvarez" itemprop="url" href="/person/18f163f2b160e1450b7f8fd72f149b85f/author/0"><span itemprop="name">D. Álvarez</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/18f163f2b160e1450b7f8fd72f149b85f/author/1"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Dirk Maass" itemprop="url" href="/person/18f163f2b160e1450b7f8fd72f149b85f/author/2"><span itemprop="name">D. Maass</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Florian Wüst" itemprop="url" href="/person/18f163f2b160e1450b7f8fd72f149b85f/author/3"><span itemprop="name">F. Wüst</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Patrick Schaub" itemprop="url" href="/person/18f163f2b160e1450b7f8fd72f149b85f/author/4"><span itemprop="name">P. Schaub</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Peter Beyer" itemprop="url" href="/person/18f163f2b160e1450b7f8fd72f149b85f/author/5"><span itemprop="name">P. Beyer</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Ralf Welsch" itemprop="url" href="/person/18f163f2b160e1450b7f8fd72f149b85f/author/6"><span itemprop="name">R. Welsch</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Plant Physiol.</span>, </em> </span>(<em><span>2016<meta content="2016" itemprop="datePublished"/></span></em>)</span>Thu Oct 13 13:25:15 CEST 2016Plant Physiol.pp.01262.20165'{{UTR}}-Mediated Translational Control of Splice Variants of Phytoene Synthase2016myown Abstract shapes of RNAhttps://puma.ub.uni-stuttgart.de/bibtex/2db36b897810e62b4d959aea9b1805177/bvossbvoss2016-08-23T12:53:21+02:00imported myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Robert Giegerich" itemprop="url" href="/person/1b004ac5611fa78df6fd3b33956a0cbea/author/0"><span itemprop="name">R. Giegerich</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Bjoern Voß" itemprop="url" href="/person/1b004ac5611fa78df6fd3b33956a0cbea/author/1"><span itemprop="name">B. Voß</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Marc Rehmsmeier" itemprop="url" href="/person/1b004ac5611fa78df6fd3b33956a0cbea/author/2"><span itemprop="name">M. Rehmsmeier</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Nucl. Acids Res.</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">32 </span></span>(<span itemprop="issueNumber">16</span>):
<span itemprop="pagination">4843--4851</span></em> </span>(<em><span>September 2004<meta content="September 2004" itemprop="datePublished"/></span></em>)<em>00166.</em></span>Tue Aug 23 12:53:21 CEST 2016Nucl. Acids Res.900166164843--4851Abstract shapes of {RNA}322004imported myown The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.Evaluating the predictability of conformational switching in RNAhttps://puma.ub.uni-stuttgart.de/bibtex/2c332aac0fd00454753d652f8ea122969/bvossbvoss2016-08-23T12:53:21+02:00imported myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1965627590fba9aa87aeea758921afde2/author/0"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Carsten Meyer" itemprop="url" href="/person/1965627590fba9aa87aeea758921afde2/author/1"><span itemprop="name">C. Meyer</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Robert Giegerich" itemprop="url" href="/person/1965627590fba9aa87aeea758921afde2/author/2"><span itemprop="name">R. Giegerich</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Bioinformatics</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">20 </span></span>(<span itemprop="issueNumber">10</span>):
<span itemprop="pagination">1573--1582</span></em> </span>(<em><span>July 2004<meta content="July 2004" itemprop="datePublished"/></span></em>)<em>00000.</em></span>Tue Aug 23 12:53:21 CEST 2016Bioinformatics700000101573--1582Evaluating the predictability of conformational switching in {RNA}202004imported myown Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on three hypotheses about the secondary structure space of a switching RNA molecule that can be evaluated by RNA folding and structure comparison. In the positive case, the predicted structural switching must be verified experimentally.
Results: After reviewing the strategy used in paRNAss, we present recent improvements on the algorithmic level of the approach, and the results of an evaluation procedure, comprising 1500 RNA sequences. It could be shown that the paRNAss approach performs well on known examples for conformational switching in RNA. The overall number of positive predictions was small, whereas for human 3′ UTRs, representing regulatory important regions, it was substantially higher than for arbitrary natural and random sequences.
Availability: paRNAss is available as a Web service at http://bibiserv.techfak.uni-bielefeld.de/parnass
Supplementary information: Detailed information on the analyses summarized in Table 1 can be found at http://bibiserv.techfak.uni-bielefeld.de/parnass/examples.htmlAdvanced tools for RNA secondary structure analysishttps://puma.ub.uni-stuttgart.de/bibtex/224e4abc131fcf085a0d877b9f8be8373/bvossbvoss2016-08-23T12:53:21+02:00imported myown <meta content="thesis" itemprop="educationalUse"/><span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Bjoern Voß" itemprop="url" href="/person/15a4359b17b27a2e77b97d2421f682c03/author/0"><span itemprop="name">B. Voß</span></a></span></span>. </span><span class="additional-entrytype-information"><em>Universitätsbibliothek Bielefeld, </em>(<em><span>April 2005<meta content="April 2005" itemprop="datePublished"/></span></em>)<em>00000.</em></span>Tue Aug 23 12:53:21 CEST 2016400000Advanced tools for {RNA} secondary structure analysis2005imported myown The analysis of RNA secondary structure has become more and more important throughout the last decades after it was recognised that RNA does not only serve as a passive messenger (mRNA), but also as a functional compound of the cell. Furthermore, it was elucidated that mainly the structure rather than the sequence determines the function of such non-protein-coding RNA. This means that two RNA molecules which have low sequence similarity but high structure similarity are likely to have a similar function.
The prediction of RNA secondary structure is based on parameters that have been measured in vitro. This results in rather static parameters, that do not incorporate the dynamic change of environment occurring in living organisms. Nevertheless, the use of these parameters, that are summarised in the energy model, gave valuable results, especially for short sequences. Several refinements throughout the years improved the predictions, but still the calculated optimal structure is not guaranteed to correspond to the native one. In this case, and due to the fact that the native structure is feasible under the energy model, it is common practice to additionally calculate suboptimal structures and incorporate these in the study. The set of all suboptimal structures is referred to as the structure space, which actually holds the information needed to answer questions such as: Is the optimal structure also the native one? Are there more than one structure an RNA molecule can adopt? How well-defined is the optimal structure?
Major problems in the analysis of the structure space are its size and its shape. The number of suboptimal structures is exponential in the sequence length, which means that for sequences of moderate length the size quickly exceeds several billion. Besides the size, the appearance of the structure space complicates its study. The structure space can be imagined as a rough landscape with valleys, holding local optimal structures, separated by mountains and saddles. This landscape is not smooth but cliffy and complex, which prevents the development of a practical and still intuitive visualisation.
In general, the intention of structure space analysis is not its visualisation, but its complexity also hampers approaches to derive specific features hidden in the structure space. Despite these problems, several tools exist that analyse the complete structure space or at least a part of it to answer the aforementioned questions. Among these are MFOLD which produces a subset of all possible structures according to a threshold of structural similarity, SFOLD which samples the structures in a probabilistic fashion and provides a method to identify alternating structures, RNAsubopt to produce all suboptimal structures within a given energy threshold, barriers to identify valleys, mountains and saddles of the structure landscape, and others.
My contribution to this area of research is twofold: First, I present paRNAss (prediction of alternating RNA secondary structures) which focuses on the detection of conformational switches and analyses the structure space based on pairwise comparisons. paRNAss has been available since 1997 and I could improve its predictive power as well as its speed which made possible a systematic evaluation. During this evaluation it turned out that paRNAss can even be used to identify more than two competing structures and hence get a deeper insight into the structure space. The second tool I introduce is RNAshapes which facilitates different kinds of analyses. The algorithm makes use of abstract representations of the secondary structure to compute only those that are morphologically dissimilar, i.e. are composed of different structural elements. Structures being morphologically similar are pooled in a class of structures and each class is represented by its best member. The list of these representatives gives a general overview of what is there in the structure space. In addition to this, I introduce an algorithm to compute probabilities of the aforementioned classes of structures. This gives hints to properties such as alternating secondary structures (two classes with similar probabilities) and structural well-definedness (one class with very high probability).Structural analysis of aligned RNAshttps://puma.ub.uni-stuttgart.de/bibtex/2fcb64a5b6dc3488195f4d6a7ab4921b9/bvossbvoss2016-08-23T12:53:21+02:00imported myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Bjoern Voß" itemprop="url" href="/person/1ac5bf5cf59b1d0c3e6657a0950fc0a9d/author/0"><span itemprop="name">B. Voß</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Nucl. Acids Res.</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">34 </span></span>(<span itemprop="issueNumber">19</span>):
<span itemprop="pagination">5471--5481</span></em> </span>(<em><span>November 2006<meta content="November 2006" itemprop="datePublished"/></span></em>)<em>00020 bibtex: Voss:2006a.</em></span>Tue Aug 23 12:53:21 CEST 2016Nucl. Acids Res.1100020 bibtex: Voss:2006a195471--5481Structural analysis of aligned {RNAs}342006imported myown The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de.Small RNAs of the halophilic archaeon Haloferax volcaniihttps://puma.ub.uni-stuttgart.de/bibtex/2db7687e4adca3a47092f39cc8d12ba9d/bvossbvoss2016-08-23T12:53:21+02:00myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jörg Soppa" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/0"><span itemprop="name">J. Soppa</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Julia Straub" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/1"><span itemprop="name">J. Straub</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Mariam Brenneis" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/2"><span itemprop="name">M. Brenneis</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Angelika Jellen-Ritter" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/3"><span itemprop="name">A. Jellen-Ritter</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Ruth Heyer" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/4"><span itemprop="name">R. Heyer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Susan Fischer" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/5"><span itemprop="name">S. Fischer</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Michaela Granzow" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/6"><span itemprop="name">M. Granzow</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/7"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Wolfgang R Hess" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/8"><span itemprop="name">W. Hess</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Brian Tjaden" itemprop="url" href="/person/1cd17a2211d5150135c6d6f848fe72744/author/9"><span itemprop="name">B. Tjaden</span></a></span></span> and 1 other author(s). </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Biochemical Society Transactions</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">37 </span></span>(<span itemprop="issueNumber">Pt 1</span>):
<span itemprop="pagination">133--136</span></em> </span>(<em><span>February 2009<meta content="February 2009" itemprop="datePublished"/></span></em>)<em>00017.</em></span>Tue Aug 23 12:53:21 CEST 2016Biochemical Society Transactions200017Pt 1133--136Small {RNAs} of the halophilic archaeon {Haloferax} volcanii372009myown In recent years, sRNAs (small non-coding RNAs) have been found to be abundant in eukaryotes and bacteria and have been recognized as a novel class of gene expression regulators. In contrast, much less is known about sRNAs in archaea, except for snoRNAs (small nucleolar RNAs) that are involved in the modification of bases in stable RNAs. Therefore bioinformatic and experimental RNomics approaches were undertaken to search for the presence of sRNAs in the model archaeon Haloferax volcanii, resulting in more than 150 putative sRNA genes being identified. Northern blot analyses were used to study (differential) expression of sRNA genes. Several chromosomal deletion mutants of sRNA genes were generated and compared with the wild-type. It turned out that two sRNAs are essential for growth at low salt concentrations and high temperatures respectively, and one is involved in the regulation of carbon metabolism. Taken together, it could be shown that sRNAs are as abundant in H. volcanii as they are in well-studied bacterial species and that they fulfil important biological roles under specific conditions.The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteriahttps://puma.ub.uni-stuttgart.de/bibtex/2955bf00b0caa4e4dc6925aa6ebd294b3/bvossbvoss2016-08-23T12:53:21+02:00imported myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Gregor Gierga" itemprop="url" href="/person/1af18a3824771ca60d4467a2700443dfb/author/0"><span itemprop="name">G. Gierga</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1af18a3824771ca60d4467a2700443dfb/author/1"><span itemprop="name">B. Voß</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Wolfgang R. Hess" itemprop="url" href="/person/1af18a3824771ca60d4467a2700443dfb/author/2"><span itemprop="name">W. Hess</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">RNA Biology</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">6 </span></span>(<span itemprop="issueNumber">3</span>):
<span itemprop="pagination">222--227</span></em> </span>(<em><span>July 2009<meta content="July 2009" itemprop="datePublished"/></span></em>)<em>00011.</em></span>Tue Aug 23 12:53:21 CEST 2016RNA Biology7000113222--227The {Yfr}2 {ncRNA} family, a group of abundant {RNA} molecules widely conserved in cyanobacteria62009imported myown Heterocyst-Specific Transcription of NsiR1, a Non-Coding RNA Encoded in a Tandem Array of Direct Repeats in Cyanobacteriahttps://puma.ub.uni-stuttgart.de/bibtex/28c83488d041e876622ed0c4488fa8619/bvossbvoss2016-08-23T12:53:21+02:00myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Danny Ionescu" itemprop="url" href="/person/1d076c28b04c9b25c652e2c71e061f046/author/0"><span itemprop="name">D. Ionescu</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1d076c28b04c9b25c652e2c71e061f046/author/1"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Aharon Oren" itemprop="url" href="/person/1d076c28b04c9b25c652e2c71e061f046/author/2"><span itemprop="name">A. Oren</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Wolfgang R. Hess" itemprop="url" href="/person/1d076c28b04c9b25c652e2c71e061f046/author/3"><span itemprop="name">W. Hess</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Alicia M. Muro-Pastor" itemprop="url" href="/person/1d076c28b04c9b25c652e2c71e061f046/author/4"><span itemprop="name">A. Muro-Pastor</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Journal of Molecular Biology</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">398 </span></span>(<span itemprop="issueNumber">2</span>):
<span itemprop="pagination">177--188</span></em> </span>(<em><span>April 2010<meta content="April 2010" itemprop="datePublished"/></span></em>)<em>00016.</em></span>Tue Aug 23 12:53:21 CEST 2016Journal of Molecular Biology4000162177--188Heterocyst-{Specific} {Transcription} of {NsiR}1, a {Non}-{Coding} {RNA} {Encoded} in a {Tandem} {Array} of {Direct} {Repeats} in {Cyanobacteria}3982010myown In response to nitrogen deficiency, some cyanobacteria develop heterocysts, a terminally differentiated cell type, specialized for the fixation of atmospheric nitrogen. In Nostocales, this differentiation process is controlled by two major regulators, NtcA and HetR, but additional unknown factors are likely to be involved as well. In the context of a genome-wide search for potential non-coding RNAs, we identified an array of 12 tandem repeats that is transcribed in large amounts when cells enter conditions that trigger cell differentiation and switch to nitrogen fixation. The main accumulating transcript, which we suggest designating nitrogen stress-induced RNA 1 (NsiR1), has properties similar to regulatory non-coding RNAs. In Anabaena sp. PCC 7120, it is about 60 nt in length, has a very distinct predicted secondary structure, and is expressed very early and transiently after nitrogen step-down. Moreover, its expression requires HetR and NtcA and is restricted to cells that are differentiating into heterocysts, clearly placing NsiR1 within the regulon that controls the switch to nitrogen fixation and heterocyst formation. The genomic arrangement of NsiR1, located upstream of hetF, a gene whose product is involved in heterocyst formation, is conserved in all five Nostocales whose genomes are completely sequenced. Additionally, we detected NsiR1 expression in 19 different heterocyst-forming cyanobacteria. Our data suggest that every repeat is a complete transcriptional unit furnished with a cell-type-specific promoter and a Rho-independent terminator, which gives rise to a very high NsiR1 transcript level. NsiR1 is the first known bacterial non-coding RNA that is specifically upregulated in response to nitrogen step-down.A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochlorishttps://puma.ub.uni-stuttgart.de/bibtex/2394e64549ff5ceb6670af662511143fb/bvossbvoss2016-08-23T12:53:21+02:00imported myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Remus Mohr" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/0"><span itemprop="name">R. Mohr</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Bjorn Voß" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/1"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Martin Schliep" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/2"><span itemprop="name">M. Schliep</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Thorsten Kurz" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/3"><span itemprop="name">T. Kurz</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Iris Maldener" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/4"><span itemprop="name">I. Maldener</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="David G Adams" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/5"><span itemprop="name">D. Adams</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Anthony D W Larkum" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/6"><span itemprop="name">A. Larkum</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Min Chen" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/7"><span itemprop="name">M. Chen</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Wolfgang R Hess" itemprop="url" href="/person/16966e009dfa31049ee277b4ff57747f8/author/8"><span itemprop="name">W. Hess</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">ISME J</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">4 </span></span>(<span itemprop="issueNumber">11</span>):
<span itemprop="pagination">1456--1469</span></em> </span>(<em><span>November 2010<meta content="November 2010" itemprop="datePublished"/></span></em>)<em>00022.</em></span>Tue Aug 23 12:53:21 CEST 2016ISME J1100022111456--1469A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus {Acaryochloris}42010imported myown Shape-based barrier estimation for RNAshttps://puma.ub.uni-stuttgart.de/bibtex/2c17846c6b7f66f118ffea595b75a6973/bvossbvoss2016-08-23T12:53:21+02:00imported myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Sergiy Bogomolov" itemprop="url" href="/person/1cee766a1ea3f4be3b979cee43c46bcee/author/0"><span itemprop="name">S. Bogomolov</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Martin Mann" itemprop="url" href="/person/1cee766a1ea3f4be3b979cee43c46bcee/author/1"><span itemprop="name">M. Mann</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/1cee766a1ea3f4be3b979cee43c46bcee/author/2"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Andreas Podelski" itemprop="url" href="/person/1cee766a1ea3f4be3b979cee43c46bcee/author/3"><span itemprop="name">A. Podelski</span></a></span>, </span> and <span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Rolf Backofen" itemprop="url" href="/person/1cee766a1ea3f4be3b979cee43c46bcee/author/4"><span itemprop="name">R. Backofen</span></a></span></span>. </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/Book" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="name">In Proceedings of German Conference on Bioinformatics GCB'10</span>, </em></span><em>volume 173 of LNI, </em><em>page <span itemprop="pagination">42--51</span>. </em><em><span itemprop="publisher">GI</span>, </em>(<em><span>2010<meta content="2010" itemprop="datePublished"/></span></em>)<em>00004.</em></span>Tue Aug 23 12:53:21 CEST 2016In {Proceedings} of {German} {Conference} on {Bioinformatics} {GCB}'100000442--51{LNI}Shape-based barrier estimation for {RNAs}1732010imported myown The ability of some RNA molecules to switch between different metastable conformations plays an important role in cellular processes. In order to identify such molecules and to predict their conformational changes one has to investigate the refolding pathways. As a qualitative measure of these transitions, the barrier height marks the energy peak along such refolding paths. We introduce a meta-heuristic to estimate such barriers, which is an NP-complete problem. To guide an arbitrary path heuristic, the method uses RNA shape representative structures as intermediate checkpoints for detours. This enables a broad but estimationcient search for refolding pathways. The resulting Shape Triples meta-heuristic enables a close to optimal estimation of the barrier height that outperforms the precision of the employed path heuristic.An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803https://puma.ub.uni-stuttgart.de/bibtex/2043f28b5f8eafbead52d8da3eae12bff/bvossbvoss2016-08-23T12:53:21+02:00imported myown <span data-person-type="author" class="authorEditorList "><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jan Mitschke" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/0"><span itemprop="name">J. Mitschke</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jens Georg" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/1"><span itemprop="name">J. Georg</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Ingeborg Scholz" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/2"><span itemprop="name">I. Scholz</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Cynthia M. Sharma" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/3"><span itemprop="name">C. Sharma</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Dennis Dienst" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/4"><span itemprop="name">D. Dienst</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jens Bantscheff" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/5"><span itemprop="name">J. Bantscheff</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Björn Voß" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/6"><span itemprop="name">B. Voß</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Claudia Steglich" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/7"><span itemprop="name">C. Steglich</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Annegret Wilde" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/8"><span itemprop="name">A. Wilde</span></a></span>, </span><span><span itemtype="http://schema.org/Person" itemscope="itemscope" itemprop="author"><a title="Jörg Vogel" itemprop="url" href="/person/12b9186b518850fc2aac4262dd4c99b2d/author/9"><span itemprop="name">J. Vogel</span></a></span></span> and 1 other author(s). </span><span class="additional-entrytype-information"><span itemtype="http://schema.org/PublicationIssue" itemscope="itemscope" itemprop="isPartOf"><em><span itemprop="journal">Proceedings of the National Academy of Sciences</span>, </em> <em><span itemtype="http://schema.org/PublicationVolume" itemscope="itemscope" itemprop="isPartOf"><span itemprop="volumeNumber">108 </span></span>(<span itemprop="issueNumber">5</span>):
<span itemprop="pagination">2124 --2129</span></em> </span>(<em><span>February 2011<meta content="February 2011" itemprop="datePublished"/></span></em>)<em>00150.</em></span>Tue Aug 23 12:53:21 CEST 2016Proceedings of the National Academy of Sciences20015052124 --2129An experimentally anchored map of transcriptional start sites in the model cyanobacterium {Synechocystis} sp. {PCC}68031082011imported myown There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64\% of all TSS give rise to antisense or ncRNAs in a genome that is to 87\% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5′ annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.