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BioSCENTer @ iGEM 2013BioSCENTer @ iGEM 2013

Sponsoring 2013

BioSCENTer Summerschool 2013

Cluster composition

BioSCENTer - Virtual Life

Contact person

Prof. Bart Nicolaï

MeBioS division
BIOSYST Department
Katholieke Universiteit Leuven
Box 2428, de Croylaan 42, B-3001 Leuven (Heverlee), Belgium

T +32 16 322375
F: +32 16 322955
E: bart.nicolai@biw.kuleuven.be
W: www.virtual-life.be

Partners

Background and goal

Living systems are characterised by a plethora of processes at multiple levels of organisation and spatial scales. Advances in high-throughput experimental techniques and the advent of emerging disciplines in biology such as genomics, proteomics and metabolomics, however, have led to large numbers of increasingly complex data which can only be analysed by means of computers. While indispensable for understanding life, knowledge of the genome, transcriptome, proteome, metabolome and their interaction is not sufficient, like knowledge of the materials used to construct a diesel engine is insufficient to fully explain its operation. Insight in biophysical processes including transport of water, nutrients and metabolic gasses, muscle motion, tissue growth, adaptation and regeneration is also essential. Mathematical models are increasingly being used to explore these processes.

Strategic mission

The cluster Virtual Life aims at developing and applying data-analytical and theoretical methods, mathematical modelling and computational simulation techniques to understand, predict and ultimately optimise and control dynamic processes that take place in living systems at multiple spatial scales and levels of organisation. The long term objective is to construct in silico models of complete living systems. In this cluster we will address living systems of all levels of complexity, from micro-organism to plant, animal and human.

Research lines

The Virtual Life cluster has the following research lines:

  • Mechanistic modelling: biological systems involve a multitude of factors that interact with each other in highly complex signalling cascades. Mechanistic models are based on a priori biochemical knowledge rather than on available high-throughput data, such as stoechiometric network models, carbon flux models, stationary and nonstationary enzyme kinetics based models. While for micro-organisms much progress has been achieved during the last years, this is certainly not the case for higher organisms.
  • Multiscale aspects: organisms are hierarchically structured into tissues and cells, and the biophysics at the macroscopic scale is determined by processes and mechanisms which operate at the cellular level or beyond. Likewise, the biochemistry of the cell is organised in different hierarchical but interacting levels, from genomics to metabolomics. Multiscale models are basically a hierarchy of submodels which describe the physical behaviour at different spatial scales or organisational levels in such a way that the submodels are interconnected. A particular challenge is the measurement of material properties and topology at small scales.
  • Multiphysics: biological processes involve several physical processes; mechanical deformation of vegetative tissue is, for example, coupled to intercellular transport of water. Another example is related to human (animal) tissues, where adaptive and regenerative processes are mediated by mechanical deformation. A major challenge is to combine biophysical processes such as transport of biological fluids with cell metabolism in a multiphysics framework and integrating them into an organism-wide mathematical model
  • Scientific computing: due to the complexity and size of the mathematical models a major challenge lies in the development of computationally efficient algorithms to discretise and solve these models.
More specifically, we will focus on the following life science areas:
  • Plant systems (contact person: Bart Nicolai)
    • Gas exchange in plants; insight in oxygen and carbon dioxide transport processes is essential in understanding metabolic processes such as respiration and photosynthesis in plants and plant organs. Such knowledge can be used for breeding new cultivars for enhanced quality or nutritional value, reducing fertiliser and pesticide application, and optimising postharvest storage procedures
    • Mechanical deformation of fruit tissue for designing novel methods to measure fruit texture
    • Organogenesis in plants
  • Animal systems (contact person: Herman Ramon)
    • Tissue development, regeneration and engineering, with an emphasis on skeletal tissues such as incopororation of angiogenesis, cell metabolism and mechanobiological regulation
    • Physiological and immunological responses/interactions/influences of gastro-intestinal cells (enterocytes, immune and neuronal cells) on the general health status of the organism
    • Angiogenesis and vasculogenesis in incubating eggs: insight in mechanisms of physical factors influencing ontogenetic processes
    • Pleiotropic effect of selection for production characteristics in farm animals (e. g. growth – reproduction antithesis)
    • Comparative aspects of embryogenesis in avian, reptiles and mammals
  • Micro-organisms (contact person: Jan Van Impe)
    • Modelling and control of industrial fermentations with the aim of improving yield, reducing energy costs and substrate use
    • Predictive food microbiology and microbial risk assessment to improve the microbial safety of foods
    • Biological wastewater treatment

Track record

Key publications

  • Pedreschi, R., Vanstreels, E., Carpentier, S., Hertog, M., Lammertyn, J., Robben, J., Noben, J.P., Swennen, R., Vanderleyden, J., Nicolaï, B.M. 2007. Proteomic analysis of core breakdown disorder in Conference pears (Pyrus communis L.), Proteomics, 7, 2083-2099.
  • Ho QT, Verlinden BE, Verboven P, Vandewalle S, Nicolaï BM (2006) A continuum model for metabolic gas exchange in pear fruit. PLOS Computational Biology, accepted.
  • Valdramidis V.P., Geeraerd A.H. and Van Impe J.F. (2007) Stress-adaptive responses by heat under the microscope of predictive microbiology. Journal of Applied Microbiology, 103, 1922-1930,
  • Janssen M., Geeraerd A.H., Cappuyns A., Garcia-Gonzalez L., Schockaert G., Van Houteghem N., Vereecken K.M., Debevere J., Devlieghere F. and Van Impe J.F. (2007). Individual and combined effects of pH and lactic acid concentration on Listeria innocua inactivation: development of a predictive model and assessment of experimental variability. Applied and Environmental Microbiology, 73(5):1601-1611.
  • Geris, L., A. Gerisch, J. Vander Sloten, R. Weiner, H. Van Oosterwyck, Angiogenesis in bone fracture healing: a bioregulatory model, Journal of Theoretical Biology (accepted)
  • Geris, L., K. Vandamme, I. Naert, J. Vander Sloten, J. Duyck, H. Van Oosterwyck (2008). Application of mechanoregulatory models to simulate peri-implant tissue formation in an in vivo bone chamber, Journal of Biomechanics, 41: 145-154)

Large projects

  • Interuniversity Attraction Poles (IAP). Interuniversity Attraction Poles Phase VI/4 2007 - 2011. "Dynamical systems, control and optimization" DYSCO
  • OPTEC: Optimisation in Engineering Centre (K.U.Leuven Centre of Excellence)
  • IDO/06/008 "Remediatie, karakterisatie en modellering van membraan-vervuiling"
  • SBO-project "Fuzzy finite element method"
  • Many IWT and bilateral projects with industrial companies

Achievement and awards

  • BIOSYST-MeBioS has established together with the Belgian Fruit and Vegetable Auctions the “Flanders Centre of Postharvest Technology (VCBT)”, a non profit organization which provides consultancy and extension services to fruit and vegetable producers in Belgian (yearly turn-over: 900 000 Euro). The VCBT is the only postharvest lab in Europe to run an ISO-17025 accredited laboratory.
  • 3 IOF fellowships for collaborative research with industry
  • Several best paper awards at large international conferences
  • Organisation of international conferences (PMF3 (Leuven), PMF4 (Quimper, FR), PMF5 (Athens, GR), Model-IT 1999 (Wageningen, NL), Model-IT 2001 (Palmerston North, NZ), Model-IT 2005 (Leuven, BE), Postharvest Unlimited 2002 (Leuven), IFAC/CAB (Nancy, FR), ESB Summer Workshop on Mechanobiology of Bone Regeneration and Engineering 2005 (Leuven, BE)