The objective of the BioSapiens Network of Excellence is to provide a large-scale effort to annotate human genome using both informatics tools and input from experimentalists. The Network will create a European Virtual Institute for Genome Annotation, bringing together many of the best laboratories in Europe. This institute will help to improve bioinformatics research in Europe and encourage cooperation between various laboratories.
The BioSapiens network tries also to integrate experimentalists and bioinformaticians, through a directed programme of genome analysis, focused on specific biological problems. The annotations generated by the Institute will be available in the public domain and easily accessible on the web. This will be achieved initially through a distributed annotation system (DAS), which will evolve to take advantage of new developments in the GRID.
The Institute will establish a permanent European School of Bioinformatics, to train bioinformaticians and to encourage best practise in the exploitation of genome annotation data for biologists. The courses and meetings will be open to all scientists throughout Europe, and available at all levels, from basic courses for experimentalists to more advanced training for experts. The BioSapiens NoE will increase European competitiveness, by new discoveries, increased integration, expert training and improved tools and services, and enhance Europe’s role in the academic and industrial exploitation of genomics.
Python Lead Software Engineer Tasks: develop highly scalable p2p and cloud based products in Python create easy-to-read, fast and well architected quality code designing application architecture creating technical documentation providing…
Chirality is a key factor in the efficacy of many drugs and the production of single enantiomers of chiral intermediates has therefore become increasingly important. Biocatalysis offers high enantioselectivity and regioselectivity in chiral synthesis through enzyme-catalyzed reactions and thus has an important advantage over chemical synthesis. Molecular genomic data is an unprecedented resource of enzymes for biocatalysis, but rational and effective methodologies must be established to realize the full potential of these resources. This project will focus on the discovery of novel enzymes, from both public and proprietary eubacterial genomes, in particular novel alcohol dehydrogenases, cytochrome P450 monooxygenases and amino acid modifying enzymes for use in established and innovative processes for chiral synthesis.
The DataGenome project extends from genome analysis, through cloning, expression, enzyme production, screening and protein engineering, to the enzymatic production of chiral biomolecules. The design of the project takes advantage of broad funnel-approach starting with innovative data-mining and processing of a large number of genes to ensure high flow-through in the process and rational selection of best enzyme candidates. The specific combination of expertise and design of the research project is aimed at high success-rate for the development of successful biocatalysts. Emphasis will be put on effective bioinformatics analysis to minimize the requirement for the more laborious “wet chemistry” analysis as well as development of optimized vector-host systems for efficient gene expression and enzyme production. Rational protein engineering or directed molecular evolution will be employed in order to obtain more robust variants, new substrate preferences or enhanced enantiomeric selectivity. Selected enzymes will be tested in existing and/or novel biocatalytic processes for production of chiral pharmaceutical intermediates with applications in therapeutic areas including AIDS, cancer and Alzheimer’s disease.
Genetically Modified Microbes (GMM) are a biotechnological alternative to different environmental problems such as remediation of polluted sites, where microbes with recombinant catabolic pathways are envisaged as the solution for removal of toxic organic compounds. Moreover, the exploration and exploitation of synergistic interactions between plants and microbes for phytoremediation is also a target to solve contamination problems. Critical to the safe application of recombinant microbes in the environment, and re-assurance of public concerns, is adequate information on safety-related properties of the microbes in question. Current whole genome sequencing efforts on relevant microbes provide a unique opportunity to extract completely new safety-related information, to conduct experiments to generate important new data, and to create new tools for increasing the degree of predictability of the behaviour of strains designed for applications in the open environment or in industrial bioreactors.
One of the microorganisms with current applications in Biotechnology is Pseudomonas putida, a paradigm of metabolically versatile microorganism which recycles organic wastes in aerobic compartments of the environment, and thereby plays a key role in the maintenance of environmental quality. The strain KT2440 is the most extensively characterised and best understood strain of P. putida. KT2440 is a nonpathogenic bacterium certified in 1981 by the Recombinant DNA Advisory Committee (RAC) of the United States National Institutes of Health as the host strain of the first Host-Vector Biosafety (HV1) system for gene cloning in Gram negative soil bacteria. Since then, KT2440 has been used world-wide as host of choice for environmental applications involving expression of cloned genes. This strain is one of the few nonpathogenic microbes which are subject to whole genome sequencing by a P. putida genome project currently in progress in Germany. The sequence data generated in the genome project is being made public at appropriate intervals (a 10-fold genome equivalent of raw sequence data is already available) and will constitute an invaluable resource for this project. Therefore, this microorganism, its recombinant derivatives and the body of knowledge accumulated in the last 20 years on its genetics, physiology and biochemistry make it an ideal and friendly microbe for safe biotechnological applications in the environment.
The major aim of this project is to settle the basis to reduce in a rational, environmentally friendly, and safe manner our contamination problems by developing P. putida strains useful to design environmental treatment systems in harmony with the biosphere.
Our particle-based method allows us to synthesise high complexity peptide arrays by combinatorial synthesis and for an unrivalled prize. We plan to further develop this new technology up to the level of robust prototype machines, and mate it to bioinformatics and readout tools. Together, our procedure(s) should boost the field of proteomics in a similar way as the lithographic technologies did with the field of genomics. Central to our novel method are the activated chemical building blocks that are “frozen” within solid amino acid particles. Thereby, we can use a colour laser printer to send them to defined addresses on a 2D support, where the particles are simply melted to induce a spatially defined coupling reaction of now freed amino acid derivatives. By repeated printing and melting cycles this simple trick yields high complexity peptide arrays. Based on existing pre-prototypes, we will develop a user-friendly peptide laser printer that spatially defined addresses our 20 different amino acid toners in high resolution to a support (WP1), and a scanner that especially fast and sensitive reads out the large formats delivered by the peptide laser printer (WP2). The increased production of amino acid toners and array supports are other bottlenecks in the output of peptide arrays that are tackled in WP3. This should allow us to increase the output of individual peptide spots from currently 0,5 Million to >10 Million peptides per month. Finally, to foster a market for high complexity peptide arrays, we will work out paradigmatic application examples in WP4. These aim to directly screen for antibiotic or apoptosis inducing D-peptides, and for the comprehensive readout of the different antibodies that patrol the serum of autoimmune patients. Based on user-friendly prototype machines, on first paradigmatic application examples for high complexity peptide arrays, and shielded by a strong patent, the participating SMEs will commercialise this new technology.