Semiautomatic generation of CORBA interfaces for databases in molecular biology

The amount and complexity of genome related data is growing quickly. This highly interrelated data is distributed at many different sites, stored in numerous different formats, and maintained by independent data providers. CORBA, the industry standard for distributed computing, offers the opportunity to make implementation differences and distribution transparent and thereby helps to combine disparate data sources and application programs. In this thesis, the different aspects of CORBA access to molecular biology data are examined in detail. The work is motivated by a concrete application for distributed genome maps. Then, the different design issues relevant to the implementation of CORBA access layers are surveyed and evaluated. The most important of these issues is the question of how to represent data in a CORBA environment using the interface definition language IDL. Different representations have different advantages and disadvantages and the best representation is highly application specific. It is therefore in general impossible to generate a CORBA wrapper automatically for a given database. On the other hand, coding a server for each application manually is tedious and error prone. Therefore, a method is presented for the semiautomatic generation of CORBA wrappers for relational databases. A declarative language is described, which is used to specify the mapping between relations and IDL constructs. Using a set of such mapping rules, a CORBA server can be generated automatically. Additionally, the declarative mapping language allows for the support of ad-hoc queries, which are based on the IDL definitions

The essential JIL-1 kinase regulates histone H3 phosphorylation and maintains chromatin structure in Drosophila

JIL-1 encodes a chromatin-associated tandem serine/threonine kinase in Drosophila melanogaster. JIL-1 predominantly associates with interbands on polytene chromosomes. It appears at higher levels on the X chromosome than on autosomes in males, and distributes about equally on all chromosomes in females. In addition, in males JIL-1 overlaps with the MSL (for male specific lethal) complex that specifically associates with the male X chromosome on which expression of most genes are upregulated.;We isolated JIL-1 mutants by inducing imprecise excision of an EP element inserted in JIL-1. We found that JIL-1 is required for viability of both females and males, but male viability is more sensitive to reduction of JIL-1 levels. Additionally, JIL-1 is required for embryogenesis, oogenesis and segment identity. Polytene chromosomes from JIL-1 mutant third instar larvae are shortened, coiled and lose their banding patterns, suggesting that JIL-1 plays a role in maintaining higher order chromatin structure. JIL-1 mutants show reduced levels of histone H3 serine10 (ser10) phosphorylation. The higher level of histone H3 ser10 phosphorylation on the male X chromosome is dependent upon JIL-1. However, the level of histone H3 ser10 phosphorylation in mitotic cells is similar between JIL-1 mutants and wild type, suggesting that JIL-1 mainly controls histone H3 ser10 phosphorylation in interphase.;JIL-1 kinase domain I (KDI) interacts with Lola ZF5, a splice isoform of the lola locus. Most Lola isoforms belong to the class of BTB (for b&barbelow;ric-a-brac, t&barbelow;ramtrack, and B&barbelow;road-complex) domain containing zinc finger proteins while two of them contain no zinc finger motif. A lola P-element mutation potentially disrupting all isoforms partially suppresses the reduced hatch rate phenotype in JIL-1EP(3)3657/JIL-1 EP(3)3657 embryos. The mode of interaction between lola and JIL-1 is consistent with the general nature of BTB zinc finger proteins as transcription repressors, and suggests possible mechanisms through which other proteins can modify JIL-1 functions or JIL-1 regulates other proteins involved in chromatin organization

IXDB, an X chromosome integrated database (update).

Chromosome specific databases are an important research tool as they integrate data from different directions, such as genetic and physical mapping data, expression data, sequences etc. They supplement the genome-wide repositories in molecular biology, such as GenBank, Swiss-Prot or OMIM, which usually concentrate on one type of information. The Integrated X Chromosome Database (IXDB, http://ixdb.mpimg-berlin-dahlem.mpg.de/) is a repository for physical mapping data of the human X chromosome and aims at providing a global view of genomic data at a chromosomal level. We present here an update of IXDB which includes schema extensions for storing submaps and sequence information, additional links to external databases, and the integration of an increasing number of physical and transcript mapping data. The gene data was completely updated according to the approved gene symbols of the HUGO Nomenclature Committee. IXDB receives over 1000 queries per month, an indication that its content is valuable to researchers seeking mapping data of the human X chromosome