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 Gene expression and proteomics Structural genomics Comparative & population bioinformatics Basic biological processes

Integrated Projects

Integrated Projects are designed to create the knowledge required to implement the priority thematic areas in the Sixth Framework Programme (FP6), by integrating a critical mass of activities (research, demonstration, training, innovation, management) and resources (staff, skills, competences, finances, infrastructure, equipment). 

Nine Integrated Projects have been funded in fundamental genomics from the first call for proposals in FP6, covering a wide spectrum of topics under the five key research areas in this sector:

Gene expression and proteomics

Structural genomics

Comparative genomics and population genetics

Multidisciplinary functional genomics approaches to basic biological processes

Gene expression and proteomics 

  • Moltools: advanced molecular tools for array-based analyses of genomes, transcriptomes, proteomes, and cells
    EU contribution: €9 million
    Duration: 3 years

The Moltools project addresses the next big challenge in molecular technology development: the need for analyses of individual genomes and proteomes. Current microarray technology enables entire genomes to be sequenced successfully, and many protein products to be identified and the protein functions analysed. However, these techniques can only capture a small fraction of the information embodied in the molecules, making it difficult to apply this technology to analysing genome variation between humans or between different somatic cells within one individual – factors that are vital in establishing the link between genetic make-up and disease.

Leading European groups, in collaboration with one US team, working in the area of molecular biological technology, will develop a next-generation toolbox, combining microarray technologies with improved sensitivity and specificity to allow analysis of the genome and proteome of individuals and the study of protein interactions in the cell.

http://www.moltools.org/

Project coordinator:
Ulf Landegren
Uppsala University
Sweden
ulf.landegren@genpat.uu.se 

  • Interaction Proteome: functional proteomics – towards defining the interaction
    EU contribution: €12 million
    Duration: 5 years 

The Interaction Proteome project aims to establish Europe as the front runner in functional proteomics – the large-scale study of protein structure, function and interactions.

Using a multi-disciplinary approach, 11 leading EU research institutions and companies, including the largest European manufacturers of mass spectrometers and electron microscopes, will develop new technologies in mass spectrometry and peptide arrays and improved visualisation technology for light and electron microscopy. The aim is to study different aspects of a large set of protein interactions within the cellular environment. The data from the experiments will be collected in a new public proteins interaction database and, in conjunction with new bioinformatics tools, used to generate computer-based predictions and models of protein interaction. These will then be validated using cell biological, biochemical and biophysical methods.

The project will ensure that state-of-the-art technology is available to researchers to study the molecular basis for important biological processes in health and disease. 

http://www.biochem.mpg.de/eu/ 

Project coordinator:
F.-Ulrich Hartl
Max Planck Institute of Biochemistry
Germany
uhartl@biochem.mpg.de

Structural genomics

  • Bioxhit: biocrystallography (X) on a highly integrated technology platform for European structural genomics
    EU contribution: €10.5 million
    Duration: 4 years

The Bioxhit project aims to develop an integrated technology platform to increase the capacity of X-ray crystallography to determine the 3-D structure of the macromolecules involved in fundamental biological processes – which constitute the majority of new drug targets.

The most common method for determining 3-D structure is to bombard crystallised proteins with the high-powered X-rays generated at huge synchrotron radiation facilities. However, current facilities were not originally designed for the high throughput necessary to analyse the tens of thousands of new molecules discovered in genome sequencing projects.

The project will coordinate scientists at all European synchrotrons and leading software developers to develop new approaches to crystallisation and to automate the X-ray diffraction data collection process completely using robots to perform time-consuming manual steps. This increasing level of automation will enable highly accurate results to be obtained by non-experts, thus opening the technology up to a wider community of users. The project should ultimately lead to the provision of remote access to the high-throughput facilities from users’ own laboratories or companies.

http://www.embl-hamburg.de/BIOXHIT/ 

Project coordinator:
Victor Lamzin
European Molecular Biology Laboratory - Hamburg Outstation
Germany
victor@embl-hamburg.de

  • E-MeP: European membrane protein consortium
    EU contribution: €10 million
    Duration: 5 years 

The E-MeP consortium of European laboratories will develop new high throughput technologies to solve the current bottlenecks hampering the successful determination of the structures of membrane proteins and membrane protein complexes. 

Membrane proteins are essential for cellular life and have a particularly important role to play in the many processes in which cells interact with their environment. However, because of the specificity of the cell membrane environment, and its water, lipid and protein components, certain structural features are imposed on membrane proteins which make them much more difficult to study than the soluble proteins found elsewhere in the cell. Even though they make up around 30% of the proteins encoded by most genomes, very few membrane protein structures have so far been solved because of the difficulty in obtaining the large quantities of pure crystals necessary for classic methods of 3-D structure determination.

The E-MeP project will study the different stages of membrane protein crystallisation to see which factors are responsible for success and failure so that new ways of determining their structure can be developed.

Project coordinator:
Roslyn Bill
Aston University
UK
r.m.bill@aston.ac.uk

Comparative genomics and population genetics

  • ZF-models: zebrafish models for human development and disease
    EU contribution: €12 million
    Duration: 5 years

The ZF-models project will produce models of disease, drug targets and insight into pathways of gene regulation applicable to human development and disease.

Due to its small size, short generation time and the transparency of its embryos – making it possible to observe developing embryos in their natural environment – the zebrafish has become a favourite model organism for biologists studying the development of vertebrates by using a genetic approach.

A consortium of 15 European institutions will use several newly developed genomic tools, such as high-throughput screening techniques, on a massive scale to harvest large data sets on gene functions from the zebrafish genome sequence, including the identification of novel genes of medical interest.

They will also establish a European Working Group on Vertebrate Models to ensure a wider impact of the project beyond the community of researchers working on zebrafish.

http://www.zf-models.org/

Project coordinator:
Robert Geisler
Max Planck Institute for Developmental Biology
Germany
robert.geisler@tuebingen.mpg.de
 

  • MolecularImaging: integrated technologies for in-vivo molecular imaging
    EU contribution: €11 million
    Duration: 5 years

The Molecular Imaging project brings together a multi-disciplinary team, including engineers, physicists, biochemists and biologists, to develop and apply high-resolution methods for non-invasive imaging in living systems.

By developing new generation biosensors, which convert biological responses into electrical signals, improving the resolution of microscopes and tomographic imaging systems, and developing multimodal imaging platforms, the consortium hopes to provide new opportunities to examine biomolecular function in single cells right through to the level of the whole animal.

The driver for technological innovation in this project will come from close collaboration with biologists asking fundamental questions about the functioning of living systems.

Project coordinator:
Eleftherios Economou
Foundation for Research and Technology
Greece
economou@admin.forth.gr 

Multidisciplinary functional genomics approaches to basic biological processes

  • Mitocheck: regulation of mitosis by phosphorylation – a combined functional genomics, proteomics and chemical biology approach
    EU contribution: €8.5 million
    Duration: 4 years

The Mitocheck project focuses on the regulation of mitosis – a highly complex process which enables cells to proliferate through duplication then segregation of their genomes.

In mitosis, duplicated chromosomes are segregated to opposite poles of a dividing cell which  then splits into two new cells. Many of the events that occur during mitosis require that the  chromosomes are compacted. This packaging of the chromosomes is regulated by a process called phosphorylation and catalysed by enzymes called protein kinases.

The project will use innovative techniques, such as RNA interference, to identify which proteins associated with the chromosomes are targeted by the kinases, what their function is, and how phosphorylation changes their activity.

Uncontrollable cell proliferation is a key factor in cancer so a better understanding of how mitosis is regulated will lead to important advances in understanding the molecular basis of cancer and other diseases.

Project coordinator:
Jan-Michael Peters
Research Institute of Molecular Pathology
Austria
peters@imp.univie.ac.at 

  • FunGenES: functional genomics in engineered ES cells
    EU contribution: €8.5 million
    Duration: 3 years

The goal of the FunGenES project, which involves 18 academic and industrial partners, is to create an atlas mapping out which genes are important to the development of different types of cell. It aims to improve the understanding of how the information contained in the sequence of a mammalian genome directs development from a single-celled fertilised egg to a complex adult organism.

The study of mouse embryonic stem cells is key to the project. These cells are pluripotent which means that they have the ability to differentiate into any type of cell in the body (blood, bone or muscle, for example). They can also be easily manipulated genetically to enable researchers to track changes resulting from single gene mutations. Stemcells have a potentially important role to play in the development of cell-based therapies to treat a variety of diseases.

The consortium’s researchers will study gene expression, regulatory pathways, and the fundamental molecular processes involved in the transition from cells with undefined fates to differentiated cell types.

Project coordinator:
Jürgen Hescheler
University of Cologne
Germany
j.hescheler@uni-koeln.de 

  • Lymphangiogenomics: genome-wide discovery and functional analysis of novel genes in lymphangiogenesis
    EU contribution: €9 million
    Duration: 5 years 

The aim of the Lymphangiogenomics project is to discover novel genes important for the development of the lymphatic vascular system.

Lymph vessels are essential for the maintenance of fluid balance in the body, for immune defence, and for the uptake of dietary fat. However, they are also responsible for the metastatic spread of cancer cells to distant organs, one of the major causes of death in cancer patients and, when damaged, can cause a disfiguring swelling of the extremities, known as lymph oedema.

The consortium of researchers will use mouse and zebrafish model organisms and embryonic stem cell technology to study the genes involved in lymph vessel development and the therapeutic potential of their gene products. They hope ultimately to develop therapies to suppress the growth of lymphatic vessels (e.g. for cancer treatment) or to stimulate their growth (e.g. for the treatment of lymph oedema).

Project coordinator:
Kari Alitalo
University of Helsinki
Finland
kari.alitalo@helsinki.fi

 

 
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