Generation of a dynamic germ-line V gene database and in-silico characterisation of the immunoglobulin heavy chain locus of the mouse

Die vorliegende Arbeit beschäftigt sich mit der in-silico-Analyse von antikörper- kodierenden DNA- Sequenzen. Zum einen wurde ein automatischer V-Gen-Analyse- Prozess entwickelt, mit dem die Datenbank VBASE2 erzeugt wird. Zum anderen wurde mit Unterstützung der automatischen V-Gen-Analyse und weiteren bioinformatischen Methoden die genomische Sequenz des Immunglobulin-Schwerekettenlocus (IgH- Locus) des Mausstammes 129/Sv untersucht und annotiert. Der Prozess zur automatischen V-Gen-Analyse führt eine systematische Sortierung und Klassifizierung der V-Gen-Sequenzen der EMBL-Bank durch. Die durch den Prozess generierte Datenbank VBASE2 ist eine integrative Keimbahn-V-Gen-Datenbank, deren Einträge Verweise auf die EMBL-Bank, andere immunologische Datenbanken und auf Ensembl enthalten. Über den Ensembl DAS Server können VBASE2-V-Gene im Ensem- bl Genombrowser dargestellt werden. Die V-Gen-Einträge von VBASE2 sind in Klassen unterschiedlicher Qualität eingeteilt, die die Zuverlässigkeit der jeweiligen Sequenz widerspiegeln. Der aktuelle Datensatz von VBASE2 beinhaltet 1129 Keimbahn-V-Gene, -Pseudogene, V-Gen-Relikte und Orphans der Immunglobulinloci von Mensch und Maus. Auf der Grundlage des VBASE2-Generierungsprozesses wurde ein Modul für die Proteindatenbank UniProtKB/TrEMBL entwickelt, das den Eingang von Immunglobu- linsequenzen in diese automatisch erzeugte Datenbank kontrolliert. Weiterhin wurde der Prozess für die Annotation der V-Segmente des IgH-Locus des Mausstammes 129/Sv genutzt. Der in der vorliegenden Arbeit untersuchte Teil des IgH-Locus umfasst mit 1,4 Mb die konstante Region, D-Region, J-Region und etwa ein Drittel der variablen Region. Durch die Annotation dieser Sequenz konnten neue V- und D-Segmente be- schrieben werden. Vier V-Gen-Relikte und ein funktionelles V-Gen der Vh7183- und der VhQ52-Familie liegen jeweils als exakte Duplikationen vor. Sequenzvergleiche der D- Region von 129/Sv zeigen deutliche Unterschiede sowohl zum Igha- (Stamm BALB/c) als auch zum Ighb- (Stamm C57BL/6) Haplotyp. Eine Untersuchung der repetitiven Elemente im IgH-Locus von 129/Sv ergab unter anderem einen ungewöhnlich hohen Anteil an LINE1-Elementen. Die hier beschriebene Charakterisierung des IgH-Locus der 129/Sv-Maus setzt die am Mausstamm C57BL/6 begonnene Arbeit fort und trägt zur Aufklärung dieses komplexen Locus im Modellorganismus Maus bei.Generation of a dynamic germ-line V gene database and in-silico characterisation of the immunoglobulin heavy chain locus of the mouse Focus of this thesis is on the in-silico analysis of antibody coding DNA sequences. Firstly, an automatic V gene analysis procedure has been developed which generates the database VBASE2. Secondly, this prodedure and other bioinformatic applications have been used to analyse and annotate the genomic sequence of the immunoglobulin heavy chain locus (IgH locus) of the mouse strain 129/Sv. The automatic V gene analysis procedure performs a systematical sorting and classification of all V genes in the EMBL-Bank. The resulting database VBASE2 is an integrative germ-line V gene database, where each entry links to the EMBL-Bank, Ensembl and immunological databases. The implementation of an Ensembl DAS server allows the display of VBASE2 V genes within the Ensembl genome browser. V gene entries are assigned into different classes, reflecting differences in the reliability of a sequence. The dataset comprises functional and pseudo V genes, relics and orphans from the immunoglobulin loci of human and mouse. The V gene analysis procedure has further been used to annotate the V genes in the IgH locus of the mouse strain 129/Sv. The available elucidated genomic sequence covers the constant region and approximately one third of the variable region. The analysis of this sequence revealed new V and D genes. The comparison of the 129/Sv D region with the homologous regions in C57BL/6 and BALB/c exhibited considerable differences between these inbred mouse strains. The portion of interspersed repeats within the variable region is exeptionally high compared to the average of the genome. The characterisation of the IgH locus of 129/Sv complements the knowledge of this locus in C57BL/6 and contributes to a profound comprehension of this complex locus

VBASE2, an integrative V gene database

The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. It acts as an interconnecting platform between several existing self-contained data systems: VBASE2 integrates genome sequence data and links to the V genes in the Ensembl Genome Browser. For a single V gene sequence, all references to the EMBL nucleotide sequence database are provided, including references for V(D)J rearrangements. Furthermore, cross-references to the VBASE database, the IMGT database and the Kabat database are available. A DAS server allows the display of VBASE2 V genes within the Ensembl Genome Browser. VBASE2 can be accessed either by a web-based text query or by a sequence similarity search with the DNAPLOT software. VBASE2 is available at http://www.vbase2.org, and the DAS server is located at http://www.dnaplot.com/das

SYSTOMONAS — an integrated database for systems biology analysis of Pseudomonas

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. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as gene-regulatory networks were stored. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration is realized using SOAP interfaces for the well established databases BRENDA, KEGG and PRODORIC. 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. The focus of SYSTOMONAS is on pseudomonads and in particular Pseudomonas aeruginosa, an opportunistic human pathogen. With this database we would like to encourage the Pseudomonas community to elucidate cellular processes of interest using an integrated systems biology strategy. The database is accessible at

Optical and X-ray Transients from Planet-Star Mergers

We evaluate the prompt observational signatures of the merger between a massive close-in planet (a `hot Jupiter') and its host star, events with an estimated Galactic rate of ~0.1-1/yr. Depending on the ratio of the mean density of the planet rho_p to that of the star rho_star, a merger results in three possible outcomes. If rho_p/rho_star > 5, then the planet directly plunges below the stellar atmosphere before being disrupted by tidal forces. Dissipation of orbital energy creates a hot wake behind the planet, producing a EUV/soft X-ray transient as the planet sinks below the stellar surface. The peak luminosity L_X ~ 1e36 erg/s is achieved weeks-months prior to merger, after which the stellar surface is enshrouded by an outflow. The final inspiral is accompanied by an optical transient powered by the recombination of hydrogen in the outflow, which peaks at L~1e37-38 erg/s on a timescale ~days. If instead rho_planet/rho_star < 5, then Roche Lobe overflow occurs above the stellar surface. For rho_p/rho_star < 1, mass transfer is stable, resulting the planet being accreted on a relatively slow timescale. However, for 1 < rho_p/rho_star < 5, mass transfer may instead be unstable, resulting in the planet being dynamically disrupted into an accretion disk around the star. Super-Eddington outflows from the disk power an optical transient with L~1e37-38 erg/s and characteristic duration ~week-months. The disk itself becomes visible once the accretion rate become sub-Eddington, resulting in a bolometric brightening and spectral shift to the UV. Optical transients from planet merger events may resemble classical novae, but are distinguished by lower ejecta mass and velocity ~100s km/s, and by hard pre- and post-cursor emission, respectively. Promising search strategies include combined optical, UV, and X-ray surveys of nearby massive galaxies with cadences from days to months.Comment: 20 pages, 11 figures, 2 tables, submitted to MNRA

ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks

ProdoNet is a web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. For a given list of genes, the system detects shared operons, identifies co-expressed genes and deduces joint regulators. In addition, the contribution to shared metabolic pathways becomes visible on KEGG maps. Furthermore, the co-occurrence of genes of interest in gene expression profiles can be added to the visualization of the global network. In this way, ProdoNet provides the basis for functional genomics approaches and for the interpretation of transcriptomics and proteomics data. As an example, we present an investigation of an experimental membrane subproteome analysis of Pseudomonas aeruginosa with ProdoNet. The ProdoNet dataset on transcriptional regulation is based on the PRODORIC Prokaryotic Database of Gene Regulation and the Virtual Footprint tool. ProdoNet is accessible at http://www.prodonet.tu-bs.de

VBASE2, an integrative V gene database

The database VBASE2 provides germ-line sequences of human and mouse immunoglobulin variable (V) genes. It acts as an interconnecting platform between several existing self-contained data systems: VBASE2 integrates genome sequence data and links to the V genes in the Ensembl Genome Browser. For a single V gene sequence, all references to the EMBL nucleotide sequence database are provided, including references for V(D)J rearrangements. Furthermore, cross-references to the VBASE database, the IMGT database and the Kabat database are available. A DAS server allows the display of VBASE2 V genes within the Ensembl Genome Browser. VBASE2 can be accessed either by a webbased text query or by a sequence similarity search with the DNAPLOT software. VBASE2 is available a

GeneReporter--sequence-based document retrieval and annotation.

GeneReporter is a web tool that reports functional information and relevant literature on a protein-coding sequence of interest. Its purpose is to support both manual genome annotation and document retrieval. PubMed references corresponding to a sequence are detected by the extraction of query words from UniProt entries of homologous sequences. Data on protein families, domains, potential cofactors, structure, function, cellular localization, metabolic contribution and corresponding DNA binding sites complement the information on a given gene product of interest