Metaheuristics for strain optimization using transcriptional information enriched metabolic models

Publicado em "Evolutionary computation, machine learning and data mining in bioinformatics : 8th European Conference, EvoBIO 2010...", ISBN 978-3-642-12210-1The identification of a set of genetic manipulations that result in a microbial strain with improved production capabilities of a metabolite with industrial interest is a big challenge in Metabolic Engineering. Evolutionary Algorithms and Simulated Annealing have been used in this task to identify sets of reaction deletions, towards the maximization of a desired objective function. To simulate the cell phenotype for each mutant strain, the Flux Balance Analysis approach is used, assuming organisms have maximized their growth along evolution. In this work, transcriptional information is added to the models using gene-reaction rules. The aim is to find the (near-)optimal set of gene knockouts necessary to reach a given productivity goal. The results obtained are compared with the ones reached using the deletion of reactions, showing that we obtain solutions with similar quality levels and number of knockouts, but biologically more feasible. Indeed, we show that several of the previous solutions are not viable using the provided rules.This work was partially funded by Portuguese FCT through the AspectGrid project and also through project MIT-PT/BS-BB/0082/2008

Where is the primary contradiction? Reflections on the intricacies of research predicated on activity theory

This article reflects on the idea that there is an omnipresent primary contradiction lurking at the bottom of every activity in capitalism. In doing so, it articulates the relationship between Marxism and Activity Theory. Whilst Marx’s ideas suggest that a trademark of capitalist social formations is the way surplus is pumped out from living labour, Activity Theory posits that the dual nature of commodities (i.e. their use and exchange-value) is the fundamental contradiction existent among all activities. The article argues that such distinction bears a direct impact on empirical research predicated on Activity Theory and goes on to consider the practical and theoretical implications of the Activity Theory’s departure from Marx’s ideas. The point is illustrated with an example of the challenges faced by the author while conducting an activity theoretical field research attempting to identify the primary contradiction in the activity system of a public organisation in the UK