Data points are clickable and lead to the corresponding metabolite of the database (Figure 2). Therefore, we searched for all deduced proteins of the SYSTOMONAS database for orthologous proteins in other Pseudomonas species to obtain orthologous protein clusters. Tel. Angestellt, Werkstudentin am Institut für Marketing, Technische Universität Braunschweig. Corresponding Author. Most enzyme information was provided by KEGG. Forscher der Technischen Universität (TU) Braunschweig sind den schwarzen Flecken in Kartoffeln auf der Spur. In order to improve the metabolic network reconstruction by applying another method, we also used the tool metaSHARK (1). Dear students and all interested parties, we are re-designing our website and want to include you in the process. Medizinische Hochschule Hannover. Claudia Choi, Richard Münch, Stefan Leupold, Johannes Klein, Inga Siegel, Bernhard Thielen, Beatrice Benkert, Martin Kucklick, Max Schobert, Jens Barthelmes, Christian Ebeling, Isam Haddad, Maurice Scheer, Andreas Grote, Karsten Hiller, Boyke Bunk, Kerstin Schreiber, Ida Retter, Dietmar Schomburg, Dieter Jahn, SYSTOMONAS — an integrated database for systems biology analysis of Pseudomonas, Nucleic Acids Research, Volume 35, Issue suppl_1, 1 January 2007, Pages D533–D537, https://doi.org/10.1093/nar/gkl823. Dr. Chris Carrie, Ludwig-Maximilians-Universität München Plant inner mitochondrial membrane insertion pathways 13.01.2016 Prof. Ludger Beerhues, Institut für Pharmazeutische Biologie, Technische Universität Braunschweig Biotechnology of active plant polyketide derivatives 2015. Our database comprises information on eight different Pseudomonas species and strains, which genomes have been completely sequenced and functionally annotated. E-mail address: h.waetzig@tu‐braunschweig.de Technische Universität Braunschweig, Institut für Pharmazeutische Chemie, Braunschweig, Germany. Institut für Mikrobiologie, Technische Universität Braunschweig Spielmannstraße 7, 38106 Braunschweig, Germany. This tool is able to identify potential enzyme-encoding genes in raw DNA sequences, which are not annotated yet. Region: Global Subject/journal group: All. Several tools for the analysis of stored data and for the visualization of the corresponding results are provided, enabling a quick understanding of metabolic pathways, genomic arrangements or promoter structures of interest. Please check for further notifications by email. Deutschland. Several other databases, such as Atlas (26) are organized as data warehouses. Different colours for rectangles specify distinct Pseudomonas species, which catalyse the corresponding reaction. Technische Universität Braunschweig, Helmholtz-Zentrum für Infektionsforschung. Prof. Dr. rer. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Logg Dich jetzt ein, um das ganze Profil zu sehen. Josef-Schneider-Straße 2 / E1 97080 Würzburg . Technische Universität Braunschweig Fakultäten Fakultät 2: Fakultät für Lebenswissenschaften Institute der Fachrichtung Biologie Institut für Mikrobiologie - - - 1. * strain absent in KEGG (version 13th April 2006). Ovarian cancer risk score predicts chemo-response and outcome in epithelial ovarian carcinoma patients. Search for more papers by this author. Recombinant human antibodies are proven potent neutralizers of viruses and can block the interaction of viral surface proteins with their host receptors. International business. Institut für Konstruktionstechnik - - - 1 Server: LSF19 Imprint and privacy Accessibility Statement QIS and LSF are products of eG The Institute for Information Systems at Technische Universität Braunschweig, Germany, focuses on research and teaching in the area of databases and information systems.. We have chosen the open source object-relational database management system PostgreSQL 8.0.3 (Author Webpage) for our database. Institut für Medizinische Mikrobiologie und Krankenhaushygiene. Institut für Mikrobiologie, TU Braunschweig Germany . The database is accessible at Author Webpage. Traditionally, metabolic and gene-regulatory networks were analysed separately. However, all current information coming from genomics, transcriptomics and proteomics (13) is also stored in our database as data warehouse (14) or dynamically accessible via web services using SOAP interfaces (15), a platform-independent data transfer protocol (see section ‘Database Techniques’). Herzlich mit vielen Willkommens-Mails wurde Professor Dan Schürch im Department Architektur Technische Universität Braunschweig empfangen. Universität Regensburg, Institut für Biochemie, Genetik und Mikrobiologie … These pathways can be obtained from metabolic pathway entries. (3)Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, Braunschweig 38106, Germany Helmholtz Centre for Infection Research, Braunschweig 38124, Germany. Phone: +49 (0) 531 391-0 Institut für Volkswirtschaftslehre, Technische Universität Braunschweig Collections in this community. University of California, Janin Heuer. Die Daten dienen dazu, das Webangebot zu optimieren.Weitere Informationen finden Sie in unserer Datenschutzerklärung. Comparing a Pseudomonas protein of interest with other well-characterized proteins may deliver useful insights into the evolution, distribution and species specific function. Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstraße 7, D-38106 Braunschweig, Germany. We need your help to improve our website! Contact. For this purpose, the engineering and science expertise of 9 institutes of the TU Braunschweig as well as Technische Universität Clausthal, Leibniz Universität Hannover, Fraunhofer Institute for Surface Engineering and Thin Films IST and Physikalisch-Technische Bundesanstalt (PTB) is bundled in this joined LabFactory. All newly detected EC numbers by metaSHARK are also indicated as ‘predicted’ in SYSTOMONAS. This organism is a versatile soil bacterium and an important opportunistic pathogen causing persistent infection in immunocompromised patients (12). The novel betacoranavirus SARS-CoV-2 causes a form of severe pneumonia disease, termed COVID-19 (coronavirus disease 2019). Further enzymes were annotated by comparative genomics (column ‘Predicted’), which were missing in the databases mentioned afore. : ++49 931-31-46168 We provide SBML (27) formatted files for downloading our metabolic and gene-regulatory networks along with a database copy at the SYSTOMONAS website. Hartmut Fricke: Technische … Susanne ERNST of Technische Universität Braunschweig, Braunschweig | Read 10 publications | Contact Susanne ERNST The web services via SOAP, which are used on the websites of SYSTOMONAS, are listed in Table 2. The basis of our approach is SYSTOMONAS, a comprehensive database that includes data from all levels of analysis as microarray and proteomics data, metabolite measurements, sequence data, gene-regulatory networks and corresponding enzyme data. Semi-quantitative scatter plot for the comparison of metabolic profiles measured for P.aeruginosa PAO1 grown under aerobic conditions. Institut für Finanzwirtschaft, Technische Universität Braunschweig Collections in this community. Welcome to the Institute of Applied Biosciences (IAB) The Institute of Applied Biosciences was founded in 2005 and consists of seven different departments. Institut für Organische Chemie. Oxford University Press is a department of the University of Oxford. In particular, the step of plasma membrane merger and the contributing proteins and physicochemical factors remain mostly unknown. Conflict of interest statement. Leibniz Universität Hannover. OK Abbrechen. Metabolites were analysed by GC/MS. A metabolic network including all involved enzymes, metabolic reactions and metabolites of all pseudomonads is delivered by our own adapted tool, which is based on GraphViz (22) and creates clickable image maps (Figure 1). Effect of Cryptotanshinone on Measures of Rat Cardiomyocyte Oxidative Stress and Gene Activation Associated with Apoptosis. However, there still exist only a few tools combining both networks such as the Pathway Tools Omics Viewer (5). Currently, the data of SYSTOMONAS along with its visualization tools and web services can be accessed freely via a web-based user interface (Author Webpage). Braunschweig und Umgebung, Deutschland Research assistant - implementation of driving tests with measuring instruments with vehicles of various categories . Genes and proteins of eight Pseudomonas species and strains are carefully annotated by the Pseudomonas community and involved genome projects (16). Social Media Facebook; Twitter; YouTube; Instagram; Kontakt. Es werden keine Bewerbungen mehr angenommen. Research; Relationships; 1 August 2019 - 31 July 2020. Despite this importance, the molecular mechanisms mediating this process are only poorly understood in biological systems. To develop neutralizing anti-SARS-CoV-2 antibodies, antibody gene libraries from convalescent COVID-19 … 38106 Braunschweig Professorin Dr. Christine Falk: Medizinische Hochschule Hannover (MHH) Institut für Transplantationsimmunologie Carl-Neuberg-Straße 1 30625 Hannover Professorin Dr. Nicole Frankenberg-Dinkel: Technische Universität Kaiserslautern Fachbereich Biologie Fachgebiet Mikrobiologie Paul-Ehrlich-Straße 23 67663 Kaiserslautern Professor Dr.-Ing. Important Links . Institut für Gebäude- und Solartechnik, Technische Universität Braunschweig - Intelligent Energy Europe Leibniz Universität Hannover . Institut für Mikrobiologie, Molekulare Infektionsbiologie; null, Germany; Position. Search for more papers by this author. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as gene-regulatory networks were stored. Transcriptome data are provided by PRODORIC via SOAP (see section ‘Database Techniques’). To provide an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology the database SYSTOMONAS (SYSTems biology of pseudOMONAS) was established. Technische Universität Braunschweig Hans-Sommer-Straße 4 38106 Braunschweig Veröffentlichungen und Institutsberichte Prof. Dr.-Ing. Interaction of Streptococcus pneumoniae with the surface of endothelial cells is mediated in blood flow via mechanosensitive proteins such as the Von Willebrand Factor (VWF). Telefon (Sekretariat) +49 40 42878-32 08 | Fax +49 40 42878-23 15 | E-Mail verfahrenstechnik@tuhh.deverfahrenstechnik@tuhh.de Cell-to-cell fusion is crucial for the development and propagation of most eukaryotic organisms. Matthias Luttmann Masterand bei Institut für Raumfahrtsysteme, Technische Universität Braunschweig Braunschweig, Niedersachsen, Deutschland 33 Kontakte ENZYME (17) and BioCyc (5) provide further functional characterization of proteins. 031U110A/031U210A) and the Volkswagen Foundation. Information on transcription factor binding sites can be found for example in RegulonDB (6) or PRODORIC (7), while metabolic reactions or pathways need to be retrieved from other database, such as BRENDA (8), BioCyc (5), KEGG (9), PseudoCyc (10), and UM-BDD (11). The complexity of a systems biology approach requires the focus on a certain well investigated organism. Unsere Abteilungen; Unsere Lehrveranstaltungen; Braunschweiger Zentrum für Systembiologie (BRICS) Forschungsförderung; Unsere Kooperationspartner ; Stellenausschreibung; Bildnachweis: Dr. Hilger Jagau/Alle Rechte bei der TU Braunschweig Biozentrum Spielmannstraße 7 38106 Braunschweig . Your comment will be reviewed and published at the journal's discretion. (4)Zentrum für Biochemie, Medizinische Fakultät, Universität zu Köln, Joseph-Stelzmann-Strasse 52, Köln 50931, Germany ludwig.eichinger@uni-koeln.de. Rectangles depict metabolic reactions, ellipses represent metabolites whose names are abbreviated with an asterisk * when the length exceeds 10 letters. suchen. 2Zentrum für Pharmaverfahrenstechnik (PVZ), Technische Universität Braunschweig, Franz-Liszt-Straße 35A, 38106 Braunschweig, Germany. Our long term goal is the development of a dynamic model simulating the behaviour of P.aeruginosa during infection. With 20,000 students and 3,700 employees, we are the largest technical university in Northern Germany. Gerhard Bringmann. External web services implemented on the SYSTOMONAS (S.) websites via SOAP. TECHNISCHE UNIVERSITÄT MÜNCHEN Institut für Medizinische Mikrobiologie, Immunologie und Hygiene Control of immune responses towards self and non-self by Foxp3 + regulatory T cells Katharina Lahl Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen … Medizinische Hochschule Hannover. Technische Universität Braunschweig, Institut für Physikalische und Theoretische Chemie - NanoBioSciences, and Braunschweig Integrated Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology (LENA), Braunschweig University of Technology, Hans-Sommer-Straße 10, 38106 Braunschweig, Germany. The homologous protein pairs can be obtained from the SYSTOMONAS protein table and visualized as multiple alignments, which are produced by MUSCLE [MUltiple Sequence Comparison by Log-Expectation (20)]. Search for other works by this author on: Institut für Biochemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany, Fachbereich Informatik, Fachhochschule Wolfenbüttel, Institut für Bioverfahrenstechnik, Technische Universität Braunschweig, Gaußstraße 17, D-38106 Braunschweig, Germany, metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of, PathFinder: reconstruction and dynamic visualization of metabolic pathways, Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes, Expansion of the BioCyc collection of pathway/genome databases to 160 genomes, PRODORIC: prokaryotic database of gene regulation, BRENDA, the enzyme database: updates and major new developments, From genomics to chemical genomics: new developments in KEGG, The University of Minnesota Biocatalysis/Biodegradation Database: the first decade, BLAST: at the core of a powerful and diverse set of sequence analysis tools, EMBOSS: the European Molecular Biology Open Software Suite, MUSCLE: multiple sequence alignment with high accuracy and high throughput, An open graph visualization system and its applications to software engineering, DDBJ in preparation for overview of research activities behind data submissions, EMBL Nucleotide Sequence Database: developments in 2005, Atlas–a data warehouse for integrative bioinformatics, Systems biology markup language: level 2 and beyond. All necessary information concerning this reaction is provided by mouse click. Next, we imported KEGG-pathway data and enabled links to pathway maps via the SOAP interface provided by KEGG (9), in which P.aeruginosa enzymes are highlighted. If the metabolic profile during one experimental condition is similar to the condition compared, data points will arrange closely to the diagonal line. Institut für Klinische Radiologie, Klinikum der Universität München, Munich, Germany München Vor 3 Tagen Gehören Sie zu den ersten 25 Bewerbern. To develop neutralizing anti-SARS-CoV-2 antibodies, antibody gene libraries from convalescent COVID-19 … This poor connectivity between the two outlined approaches might be due to the fact that the required information is stored in different databases. Many thanks go to Mathias Krull and Barbara Schulz, who proof-read this paper. We offer teaching, research and transfer with excellent facilities and a personal atmosphere at the same time. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. The visualization of metabolic pathways from KEGG in SYSTOMONAS is based on GraphViz using the dot layout. First, the external databases KEGG (9), PGDv2 (16), ENZYME (17), BioCyc (5) provide EC numbers for the proteins. Zur anonymisierten Webanalyse nutzt die TU Braunschweig die Software Matomo. We are planning to make up for the Technical Seminar which had to be canceled in March due to the coronavirus outbreak. Institut für Mikrobiologie. Recombinant human antibodies are proven potent neutralizers of viruses and can block the interaction of viral surface proteins with their host receptors. Our initial focus was on metabolomics. Fähigkeiten und Kenntnisse. If your group is not listed here, please send us an email : spc@embl-hamburg.de Register. 24.06.2010 Thomas Schirrmann, Technische Universität Braunschweig Generation of human antibodies and antibody fusion proteins for research, diagnostics and therapy 17.06.2010 Volker Wissemann; Institut für Botanik, Universität Gießen Host-parasite interaction in a case study of hybridogenic polyploids. For P.aeruginosa PAO1 1509 unique proteins were annotated in SYSTOMONAS as enzymes. The EC number source on the website is indicated accordingly. 2. Graphical maps of corresponding gene regions can be retrieved via a hyperlink to the BRENDA Genome Explorer, a tool within the BRENDA package (8). We adapted this tool to SYSTOMONAS by limiting the analysis on Pseudomonas species. First, a restricted BLAST analysis (18) was performed on the protein sequences followed by a pairwise global alignment using the tool stretcher of the EMBOSS package (19). It also refers to genome annotation web sites of other Pseudomonas genome projects for the most up-to-date information. An abbreviation code for the species is provided with the visualization output (AO1 = P.aeruginosa PAO1, A14 = P.aeruginosa PA14, P = P.putida KT2440, Pf-5 = P.fluorescens F5, F01 = P.fluorescens PfO-1, ST = P.syringae pv tomato, SP = P.syringae pv phaseolicola, SS = P.syringae pv syringae).