The substitution of the synthetic bases of fossil origin used in the lubricant by environment-respecting compounds has become a central question. In such respect, it has been recently shown that one of the many of unusual fatty acids that are known to occur in nature, namely the branched-chain fatty acids, BcFAs, could advantageously replace these synthetic bases. Contrasting to other vegetable oils used as lubricant bases, BcFA-containg oil has both excellent oxidative resistance and thermal stability, thereby making them potent substitutes for high-temperature applications such as motor lubricants. Coupled with the improvements in plant transformation, the increasing needs for cost-effective bioproduction of unusual fatty acids has made oilseeds ideal production systems. The project REFLAX (for Rational Engineering of FLAX) aims at the integration of metabolic, physiological, molecular biological, genetical, structural biological, proteomics and bioinformatics studies to provide a basis for the rational engineering of oilseeds – rapeseed but more specifically flax – towards the production of BcFAs. REFLAX is a feasibility program consisting is an innovative strategy for modulating the spectrum of fatty acids by enlarging the spectrum of de novo precursors.
Enzymes are extremely powerful natural catalysts able to perform almost any type of chemical reaction while being mild by nature and highly specific. In fact, the delicate functioning of enzymes forms the basis of every living creature. The catalytic potential of enzymes is more and more appreciated by the industry as many industrial processes rely on these sophisticated catalysts. However, the number of reactions catalyzed by enzymes is restricted as enzymes only have evolved to catalyze reactions that are physiologically relevant. Furthermore, enzymes have adapted to the direct (cellular) environment in which they have to function (e.g. operative at ambient temperature, resilient towards proteolysis, catalytic turnover rate should fit with metabolic enzyme partners). This excludes the existence of enzymes that do not fit within boundaries set by nature. It is a great challenge to go beyond these natural boundaries and develop methodologies to design ‘unnatural’ tailor-made enzymes. Ideally it should become possible to (re)design enzymes to convert pre-defined substrates. Such designer enzymes could theoretically exhibit unsurpassed catalytic properties and, obviously, will be of significant interest for industrial biotechnology. The OXYGREEN project aims at the design and construction of novel oxygenating enzymes (designer oxygenases) for the production of compounds that can be used in medicine, food and agriculture and the development of novel powerful and generic enzyme redesign tools for this purpose. The enzymes and whole-cell biocatalysts that will be developed should catalyze the specific incorporation of oxygen to afford synthesis of bioactive compounds in a selective and clean way, with minimal side products and with no use of toxic materials. For this, generic platform technologies (novel high-throughput methodology and methods for engineering dedicated host cells) will be developed that allow effective structure-inspired directed evolution of enzyme.
Genome scale analysis of the immune response against pathogenic micro-organisms; identification of diagnostic markers, vaccine candidates and development of an integrated micro array platform for clinical investigations.
The genome sequences of microbial organisms responsible for diseases of world-wide medical importance have been sequenced or will be available in the near future. Technologies for producing large numbers of proteins have been developed and high-throughput assays such as protein micro arrays have been clinically validated for detecting the presence of antibodies, in serum, directed against microbial antigens. These achievements offer the opportunity of investigating the natural immune response against the whole proteome of a variety of micro-organisms. Powerful combinations of genomic information, molecular tools and immunological assays are becoming available to help identify the antigens that function as targets of protective immunity or could be used as markers for serodiagnosis. We propose here to identify in micro-organisms of great medical relevance (M. pneumoniae, C. pneumoniae, L. pneumophila, coronavirus spp and P. falciparum), a large collection of surface and secreted proteins as well as putative endotoxins. This protein repertoire will be produced as recombinant molecules or as sets of overlapping synthetic peptides and printed on array slides. The serum reactivity of groups of individuals with proven history of exposure to the selected micro-organisms will be analysed against the arrayed proteins to identify diagnostic markers and correlates of protection.
This project will significantly expand the SMEs bank of Intellectual Property and contribute to expertise within the RTDs. It is anticipated that the proposed work in high throughput protein expression, software analysis, surface peptides synthesis, protein and peptide surface capture, and array reader instrumentation will create an integrated platform of great commercial and research value. Finally it will contribute to unravelling how the humoral immune response interacts with the microbial proteomes thus filling the gap between genomic data and development of novel vaccines and diagnostic tools.
Deciphering the information on genome sequences in terms of the biological function of the genes and proteins is a major challenge of the post-genomic era. Currently, the bulk of function assignments for newly sequenced genomes is performed using bioinformatics tools that infer the function of a gene on the basis of sequence similarity with other genes of known function. It is now well recognised that these primary, sequence similarity-based function annotation procedures are frequently inaccurate and error prone. Continuing to use them without clearly defining the limits of their applicability would lead to an unmanageable propagation of errors that could jeopardise progress in Biology. On the other hand, various novel bodies of data and resources are becoming available. These provide information on context-based aspects of the biological function of genes, namely on physical and functional interactions between genes and proteins, and on whole networks and processes. In parallel structural genomics efforts world wide are providing a much better coverage of the structural motifs adopted by proteins and on their interactions. The availability of these additional and novel data offers an unprecedented opportunity for the development of methods for incorporating higher-level functional features into the annotation pipeline.
The GeneFun project aims at addressing these two important issues. The issue of annotation errors will de addressed by developing criteria for evaluating the reliability of the annotations currently available in databases. These criteria will be used to assign reliability scores to these annotations and will be incorporated into standard annotation pipelines, for future use. The issue of incorporating higher-level features into functional annotations will be addressed by combining sequence and structure information in order to identify non-linear functional features (e.g. interaction sites), and by integrating available and newly developed methods for inferring function from higher-level and context-based information (protein domain architecture, protein-protein interaction, genomic context such as gene order etc.).
To achieve these aims several European groups with strong track record in developing novel methods and analyses in comparative genomics, structural- and systems- oriented bioinformatics, and in information technology, have teamed up with an experimental group from Canada, which is well known for its outstanding achievements in the field of structural and functional proteomics. The expected output of the GeneFun project is: improved procedures for inferring function on the basis of sequence similarity, a set of procedures for predicting non-linear functional features from sequence and 3D structure in a more automated way, and benchmarked procedures for predicting context-based functional features. Major efforts will be devoted to devising protocols that optimally combine the results from several methods. In particular Web-based servers to the individual and combined procedures will be developed, and made available to the scientific community. The community will be introduced to these new tools through open workshops and training sessions.
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.
Within this project we will test the applicability of crypto currencies as a facilitator of political movements. The currency will be used to motivate people to (1) select members of parliament based on fitness of personal opinions on major political issues and (2) monitor the correlation between verbally expressed statements and actually passed acts. The currency will be also tested as an alternative means to finance political activities and assess the trust towards political organizations. The currency will be designed to offer advantages over other currently most popular currencies and remain competitive also after the experiment.