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

Changes in the marine carbonate system of the western Arctic: patterns in a rescued data set

A recently recovered and compiled set of inorganic carbon data collected in the Canadian Arctic since the 1970s has revealed substantial change, as well as variability, in the carbonate system of the Beaufort Sea and Canada Basin. Whereas the role of this area as a net atmospheric carbon sink has been confirmed, high pCO2 values in the upper halocline underscore the potential for CO2 outgassing as sea ice retreats and upwelling increases. In addition, increasing total inorganic carbon and decreasing alkalinity are increasing pCO2 and decreasing CaCO3 saturation states, such that undersaturation with respect to aragonite now occurs regularly in both deep waters and the upper halocline