Functional Genomics Workshop at the European Congress of Biotechnology
16-19 September, 2007
Barcelona, Spain

Organisers:

Mike Taussig: Babraham Institute, Cambridge, UK

Draft Report

The 13th European Congress of Biotechnology was held in Barcelona from 16-19 th September 2007, under the theme of Symbiosis (Science, Industry and Society) and organised by the European Federation of Biotechnology. The conference was well attended and was regarded as a considerable success at all levels. The scientific content was divided into plenary sessions and workshops, which were organised as 5 streams, namely Symbiosis, Industrial Biotechnology, Health and Medicine, Green Biotechnology, and Functional Genomics and Systems Biology. The latter were organised by members of the ESF Programme Frontiers in Functional Genomics, with the overall chairmanship of Dr Mike Taussig, and speaker travel and subsistence were supported by this award from the ESF. All the sessions in this stream were very well attended, with over 150 people per session (i.e. a full meeting room).

The aim of the stream was to connect the most promising developments in functional studies of genes and their protein products with the expanding concept of systems biology. The focus was on technologies and their applications in biomedicine, industry and the environment, together with data integration into systems level understanding. The chosen topics supported by the ESF funds were:

•  Alternatives to Antibodies

•  Genome Technologies

•  Human Atlas Projects

•  Comparative Genomcs

•  Systems and Synthetic Biology

The Alternatives to Antibodies session (joint with EU ProteomeBinders consortium) provided an overview of the major molecular alternatives to conventional antibodies in the bid to develop novel binding reagents to characterise and isolate human proteins. Such ‘alternative binders' include engineered scaffolds, such as affibodies and ankyrin repeat proteins, and single stranded nucleic acids with a similar binding affinity to proteins. The talks were given by Professor Per-Ake Nygren (KTH Royal Institute for Technology, Stockholm), on the Affibody molecules, which are based on the Staph. aureus protein A scaffold; Professor Andreas Plückthun, Zurich University, who described progress with Designer Ankyrin Repeat Proteins, another scaffold with great potential as a general binding entity; and Professor Larry Gold, of SomaLogic, Boulder, USA, a pioneer of nucleic acid protein-binders known as aptamers. The speakers described the potential applications of these molecules, including as potential discovery tools for biomarkers and for clinical diagnostics or intervention. The session concluded with a description of the activities of the EU ProteomeBinders initiative by Mike Taussig.

The Genome Technologies speakers reflected the great developments in the field which have taken place recently. In particular, there has been a quantum leap in the ability to carry out ultra-high throughput sequencing, as reported by Dr Michael Egholm, VP Research and Development at 454 Life Sciences. The company's revolutionary technology, producing tens of millions of high-quality bases per hour on a single instrument, means that many biologically meaningful and complex regions of genomes can be analysed without the time or cost constraints of hitherto current DNA sequencing methods. Through this technology 454 provides an enabling solution for ultra-high-throughput DNA sequencing. Professor Ulf Landegren (Uppsala University) concentrated on the ability of highly sensitive and specific technologies developed in his group to improve dramatically on ELISA for detection of proteins in fluids and to detect even single molecules and their complexes in fixed cells. The proximity ligation method has also been commercialised through the start-up company Olink based in Uppsala . Dr Jörg Hoheisel of the German Cancer Research Centre (DKFZ) in Heidelberg focused on microarray technologies of which his group has been in the forefront of innovation, and their applications in analysis of gene expression in diseases such as pancreatic cancer. Finally, Professor Wilhelm Ansorge of Lausanne University brought together all the high throughput systems in a grand technology overview.

The Human Atlas Projects, the topic of the third workshop session, aim to define the location of all human proteins in cells and tissues, using approaches such as antibodies, cellular knockdown by RNAi, and mass spectrometry. Professor Mathias Uhlen (KTH, Stockholm) introduced the session and Dr Sophia Hober from his group described the Human Proteome Resource atlas project, in which polyclonal antibodies are being raised systematically against every human gene product and screened on tissue arrays of normal and caner tissues to generate high resolution images of protein localisation, which are available on the web. Professor Olli Kallioniemi (University of Turku, Finland) described a complementary approach of knocking down individual genes using RNAi on cell arrays which can now be employed in high throughput. Dr. Bernhard Küster, formerly of CellZome and now at Technical University of Munich, described the isolation of protein-protein complexes and their analysis by mass spectrometry, which has been extremely central in defining protein networks.

The session on Comparative Genomics covered a wide spectrum of genome projects, from the human and neanderthal (Professor Svante Paabo, Max Planck Institute, Leipzig), to high throughput sequencing of plant and animal genomes carried out in China by Professor Huanming Yang 's group at the Beijing Genomics Institute. Dr Siv Andersson (Dept of Evolution, Uppsala University) described the molecular evolutionary analysis of microbial genomes as a result of sequencing several microbial genomes, revealing insights into the influence of selection on proteins involved in host-pathogen interactions. The genomes of Rickettsiae in particular have provided exciting insights into reductive genome evolution, antigenic variation and host cell manipulation. Finally, Professor Leif Andersson, also of University of Uppsala, described how a genomics approach to the analysis of genetic traits of domestic animals provides a unique opportunity to unravel the genes underlying phenotypic variation. The research includes genetic studies of both monogenic traits, like inherited disorders and coat colour, and multifactorial traits, like muscle development, fat deposition, autoimmune disorders and general disease resistance.