EU Framework 6 projects

Scientific Volume Imaging not only develops software applications but also participates in research of scientific projects. SVI is currently involved in these FP6 research projects:

AUTOMATION

Three-dimensional (3D) fluorescence imaging microscopy of individual living cells is an essential tool for cellular biology, pathology and the study of infection and virulence therein. However, today, one critical constraint of established techniques is that samples must be stabilised by attachment to an optically transparent surface, thereby completely precluding their use for non-adherent cell types.

The severity of this limitation becomes clear when one considers that for basic- and biomedical-research, cell-based assay and cell-diagnostic applications some of the most important targets are non-adherent cells, for example, stem cells, systemic cancer cells and lymphocytes. We therefore propose a completely new 3D imaging strategy targeted specifically at live, non-adherent cells.

The core technology combines proprietary state of the art hardware for suspended cell manipulation with super high-speed dynamic imaging methods. Around this, our consortium draws together unique expertise from four SME and three academic teams providing the necessary critical-mass to industrialize this methodology as 1) a routine research-bench tool, and 2) a high-throughput, high-content imaging device AUTOMATION (automated tomographic analysis station).

Towards these goals completed pilot studies already demonstrate the feasibility for hardware and mathematical development, which will pave the way towards prototype design, and construction. As such, AUTOMATION envisages an altogether new micro-imaging technology; enabling hands-off, rapid, quantitative 3D reconstruction, as never before realised. While offering the promise of benefits across multiple areas of FP6 biomedical research, the primarily technological aims of AUTOMATION place it outside the FP6 thematic priority. However, combining ambitious goals with new and exclusive technologies the NEST-Adventure programme wholly embraces the essence of our initiative.

Read more at Automation Project.

3DGENOME

Our knowledge about gene regulation at the single gene and the epigenetic level is rapidly expanding. However, our understanding of the role in gene control of the three-dimensional folding of the genome in the cell nucleus, is still poorly understood; this despite the fact that considerable evidence is available showing that large-scale chromatin organization plays an important role in gene control in higher eukaryotes.

The EU Sixth Framework Programme (FP6) for Research and Development (2002-2006) is one of the world's largest research programmes, with a budget of 17.5 billion Euros, of which around 3 billion Euros is available for life sciences research. Under the FP6, 2.2 million Euros have been awarded to the 3DGENOME-research program.

The 3Dgenome consortium members will develop state-of-the-art 3D light microscopy techniques, along with image processing and analysis tools to visualise DNA inside the cell. They will correlate the genome's 3D structure with the expression of specific genes in human, mice and drosophila cells. Using this range of model systems will help establish which aspects of the 3D genome structure have been conserved through evolution and which are most likely to play an important role in gene regulation.

The research program is conducted by a consortium of seven European partners and is coordinated by Roel van Driel of the Swammerdam Institute for Life Sciences of the University of Amsterdam in The Netherlands.

Results will give new and important insight into how the eukaryotic genome in general, and the human genome in particular, operates inside the living cell. This program will lay the groundwork for understanding how, beyond the regulation at the individual gene level, large-scale chromatin structure affects the complex gene regulation networks in normal and deceased cells. Understanding molecular mechanisms that underlie regulation of this large set of genes is a key target in modern medical sciences and biotechnology. Our knowledge about gene regulation at the single gene and the epigenetic level is rapidly expanding. However, our understanding of the role in gene control of the three-dimensional folding of the genome in the cell nucleus, is still poorly understood; this despite the fact that considerable evidence is available showing that large-scale chromatin organization plays an important role in gene control in higher eukaryotes. 3DGENOME has the ambition to force a breakthrough in our understanding of the relationship between the function of the genome and its dynamic 3D structure in the cell.

To this end we will analyse the 3D structure of the human genome in the cell nucleus and relate this to its transcriptional activity. Structural analysis is carried out by fluorescent in situ hybridization (FISH) in combination with advanced 3D light microscopy. Large-scale chromatin structure of four selected chromosomes (11, 17, 18 and X) will be determined in three different cell types, differing in gene expression. Gene activity along the chromosomal fibre will be read from the human transcriptome map and correlated with structure. Work on human cells will be expanded to mouse and Drosophila, aiming at establishing causal and evolutionary conserved relationships between 3D genome structure and genome

Read more at Three Dee Genome Project.

Proposals

Proposed Projects