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

Search for endotherm genes involved in early patterning of vertebrates.

In addition to giving rise to the gut, the endoderm plays a crucial role in embryonic axis determination. The murine extra-embryonic endoderm is thought to provide an early positional cue defining the antero-posterior axis of the embryo. The axial mesendoderm, which emanates from the gastrula organizer, populates the midline of the embryo and patterns it in all three axes. Later, maintenance and refinement of the antero-posterior axis of the brain requires the embryonic endoderm (reviewed in Martinez-Barbera and Beddington, 2001). Genes expressed in the endoderm are responsible for imparting it with its patterning properties. It is therefore useful to identify the expression profile of the endoderm. To this end, a cDNA library was made from 7.5 days post-coitum mouse endoderm (Harrison et al., 1995). Many clones from this library were sequenced and constitute a set of expression sequence tags (ESTs). I screened these ESTs in silico for non- essential molecules whose role in embryonic patterning had not been determined. I then screened clones obeying these criteria by whole-mount in situ hybridisation on 6.5 - 9.5 dpc mouse embryos. Restricted expression was displayed by 18% of the clones (from the total of my work and that of two other students). The restricted expression patterns encountered are presented. One of the restricted genes I encountered in the mouse in situ hybridisation screen was that encoding the serum and glucocorticoid-regulated kinase (Sgk). I was very interested in the expression pattern of Sgk since it was asymmetric in the visceral endoderm at the onset of gastrulation. Sgk expression presented other interesting features, such as being exclusively expressed in angioblasts at 9.5 dpc. I constructed a targeting vector in order to analyse Sgk function in mouse by a loss-of-function approach. I targeted embryonic stem (ES) cells with this construct and recovered neomycin-resistant clones. One of these is possibly a clone where homologous recombination took place at the Sgk locus. I cloned zebrafish orthologues of some of the restrictedly expressed endoderm genes. I functionally screened these genes in zebrafish by a loss-of-function approach, using antisense morpholino oligonucleotides (MOs). I uncovered several molecules required for proper early embryonic development, one of which I studied in more detail. This was Nop seven-associated protein 2 (Nsa2), a eukaryotic protein involved in ribosome biogenesis (Harnpicharnchai et al., 2001). Zebrafish nsa2 morphants have slowed epiboly and early patterning defects. Furthermore, nsa2 morphant cells gradually die by apoptosis. A smaller embryo develops from surviving nsa2 morphant cells during the first day of development, after which presumably all cells die. The phenotype of nsa2 zebrafish morphants is analogous to that of morphants for the ribosomal proteins RpL19 and RpS5, which when mutated in fly cause the Minute phenotype. I describe the zebrafish Minute phenotype and hypothesize that nsa2 is likely to be a Minute

The Radiation Hybrid Database

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/ RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is anOutstation of the European Molecular Biology Laboratory (EMBL). INTRODUCTION The radiation hybrid mapping technique (1,2) is a method for ordering markers along a chromosome, and gives estimates of physical distances between them. Radiation hybrids are produced by fusing irradiated donor cells with recipient rodent cells. These hybrid cell lines are grouped in so-called panels of clones, each containing different sets of chromosome fragments produced by radiation-induced breakage. The clones are screened by PCR amplification (producing `scoring data') to establish the presence or absence of a given marker. Nearby loci will tend to show similar retention patterns, the so-call..