Modelling the Human Immune System by Combining Bioinformatics and Systems Biology Approaches

Over the past decade a number of bioinformatics tools have been developed that use genomic sequences as input to predict to which parts of a microbe the immune system will react, the so-called epitopes. Many predicted epitopes have later been verified experimentally, demonstrating the usefulness of such predictions. At the same time, simulation models have been developed that describe the dynamics of different immune cell populations and their interactions with microbes. These models have been used to explain experimental findings where timing is of importance, such as the time between administration of a vaccine and infection with the microbe that the vaccine is intended to protect against. In this paper, we outline a framework for integration of these two approaches. As an example, we develop a model in which HIV dynamics are correlated with genomics data. For the first time, the fitness of wild type and mutated virus are assessed by means of a sequence-dependent scoring matrix, derived from a BLOSUM matrix, that links protein sequences to growth rates of the virus in the mathematical model. A combined bioinformatics and systems biology approach can lead to a better understanding of immune system-related diseases where both timing and genomic information are of importance

A Europe-South America network for climate change assessment and impact studies

International audienceThe goal of the CLARIS project was to build an integrated European-South American network dedicated to promote common research strategies to observe and predict climate changes and their consequent socio-economic impacts taking into account the climate and societal peculiarities of South America. Reaching that goal placed the present network as a privileged advisor to contribute to the design of adaptation strategies in a region strongly affected by and dependent on climate variability (e. g. agriculture, health, hydro-electricity). Building the CLARIS network required fulfilling the following three objectives: (1) The first objective of CLARIS was to set up and favour the technical transfer and expertise in earth system and regional climate modelling between Europe and South America together with the providing of a list of climate data (observed and simulated) required for model validations; (2) The second objective of CLARIS was to facilitate the exchange of observed and simulated climate data between the climate research groups and to create a South American high-quality climate database for studies in extreme events and long-term climate trends; (3) Finally, the third objective of CLARIS was to strengthen the communication between climate researchers and stakeholders, and to demonstrate the feasibility of using climate information in the decision-making process. © Springer Science + Business Media B.V. 2009