Marie Curie Initial Training Network ``Biomineralization: understanding of basic mechanisms for the design of novel strategies in nanobiotechnology (BIOMINTEC)

Venus' Flower Basket (Euplectella aspergillum)

The University of Amsterdam (The Informatics Institute) is one of the partners
in the BIOMINTEC project. The BIOMINTEC project is coordinated by
Prof. Dr. Dr. H.C Schröder (Johannes Gutenberg Universität, Mainz, Germany).

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 also the participation
to workshops and summer schools.

ESR2: Topic of PhD thesis: ``Fractal mechanism of silicatein self-assembly and
biosilicification (Experimental studies and Modelling studies) ''
Research at Johannes Gutenberg Universität (Mainz, Germany) (Month 1-18): 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 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 (Month 19-36): 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.

ESR8: Topic of PhD thesis: ``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 scleraactinian 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
(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.

The Research Team