BIOMINTEC

Research in the BIOMINTEC project is in the field of biomineralization and applications in nano-biotechnologies. Biomineralization is the formation of minerals by living cells and organisms. To understand the processes involved in biomineralization, at the cutting edge between inorganic and organic world, the cooperation between molecular and cell biologists, inorganic chemists, and physical chemists, but also computational scientists is required. The products formed by bio-mineralization are often composite materials. The ability of organisms to form nanostructured biominerals with high precision and in large copy number under biological, environmentally benign conditions makes the mechanisms underlying biomineral formation extremely interesting for nano(bio)-technology, a key technology of the 21st century. During the project, training will be provided on the following topics: Molecular and chemical principles of biomineralization; Molecular biology techniques; Cell and embryo cultures, cell biology techniques; Advanced methods in analytical inorganic chemistry; Functionalization of surfaces; Macromolecular crystallography; Computational biology, Gene regulatory networks; and Training in intellectual property, Writing business and marketing plans. The project includes participation in workshops and summer schools. The Section Computational Science is involved in two sub-projects within BIOMINTEC

project 1: Fractal mechanism of silicatein self-assembly and biosilicification (Experimental studies and Modelling studies Research at Johannes Gutenberg Universität (Mainz, Germany): The fellow will investigate the mechanism of self-assembly of sponge silicatein and the intermediary formation of fractal aggregates. The effect of the molar ratio of the silicatein isoforms (α and β) on the kinetics of this process as well as on the size and shape of the formed aggregates/ fibres will be determined. Research at the University of Amsterdam: A model will developed for the regulatory network controlling biosilicification in sponges. The processes in the regulatory network will be modelled at different levels of detail. Stochastic effects because of low molecule numbers and spatial inhomogeneties can be very relevant here. To incorporate this type of effects it is required to use different modelling paradigms (Monte Carlo simulations, particle - (individual-based) modelling, Ordinary Differential Equations and Partial Differential Equations) in combination. Modelling the biochemical reactions in a complex-shaped interface will require the application of particle-based methods.

project 2: Biocalcification: Characterization of crystal-shaping proteins of the molluscan shell and modelling gene regulation. Research at the University of Amsterdam (Month 1-18): From ongoing research it is known that there is close link between Ca signalling and Ca homeostasis in yeast and calcification, e.g., in scleractinian corals and molluscs. We will investigate this hypothesis by developing a coupled model of gene regulation, Ca-homeostasis and calcification. Modelling gene expression in tissues will require individual-based modelling of cells and tissues. We want to develop a physically-based model of cells suitable to represent cell-cell contacts, cell migration and adhesion. Research at the Université de Bourgogne (Dr. F. Marin, Dijon France): From all non vertebrate calcifying metazoans, molluscs are usually considered as the master biomineralizers. Their shell secretion implies that they control the shapes of the crystals and the spatial organization of the crystallites (shell microstructures) as well as the mineralogy (calcite versus aragonite). The fellow will characterize new proteins in relation with different shell microstructures. The emphasis will be put on non nacro-prismatic molluscs for which hardly any data are available. Shell proteins will be investigated at the protein and transcript levels.