In the Hepatosys project, as part of the German Systems Biology initiative on the Liver Cell, we are collaborating with a team of German researchers from several institutions coordinated by Marino Zerial to develop a high throughput imaging approach to understanding endocytosis in hepatocytes. BioMIP's role is to develop an integrated mesoscale simulation platform for addressing the complex reactive transport and morphpological changes occuring in intracellular compartments such as endosomes, in concert with experimental fluorescence image data.
To this end we have introduced a physical self-assembly extension to spatially resolved stochastic reaction kinetics, mprDPD, alllowing the simulation of key endocytotic subprocesses, and a link up via SBML with standard reaction kinetic systems biology databases. Protein sorting is a key combinatorial phenomena in hepatocytes that we can address using this methodology.
In addition we are investigating the potential of optically optimized microfluidic systems for managing high throughput imaging endocytotic analysis on polarized hepatocytes using a parallel confocal microscope, in collaboration with our experimental partners.