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Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been(More)
Phages are recognized as the most abundant and diverse entities on the planet. Their diversity is determined predominantly by their dynamic adaptation capacities when confronted with different selective pressures in an endless cycle of coevolution with a widespread group of bacterial hosts. At the end of the infection cycle, progeny virions are confronted(More)
One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metabolic phenotype which typically means having a high yield/productivity. This challenge is not only due to the inherent complexity of the metabolic and(More)
(Bacterio)phage PVP-SE1, isolated from a German wastewater plant, presents a high potential value as a biocontrol agent and as a diagnostic tool, even compared to the well-studied typing phage Felix 01, due to its broad lytic spectrum against different Salmonella strains. Sequence analysis of its genome (145,964 bp) shows it to be terminally redundant and(More)
MOTIVATION The description of a metabolic network in terms of elementary (flux) modes (EMs) provides an important framework for metabolic pathway analysis. However, their application to large networks has been hampered by the combinatorial explosion in the number of modes. In this work, we develop a method for generating random samples of EMs without(More)
Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete(More)
— The optimization of biotechnological processes is a complex problem that has been intensively studied in the past few years due to the economic impact of the products obtained from fermentations. In fed-batch processes, the goal is to find the optimal feeding trajectory that maximizes the final productivity. Several methods, including Evolutionary(More)
Activated sludge systems are prone to be affected by changes in operating conditions leading to problems such as pinpoint flocs formation, filamentous bulking, dispersed growth, and viscous bulking. These problems are often related with the floc structure and filamentous bacteria contents. In this work, a lab-scale activated sludge system was operated(More)
Although important contributions have been made in recent years within the field of bioprocess model development and validation , in many cases the utility of even relatively good models for process optimization with current state-of-the-art algorithms (mostly of-fline approaches) is quite low. The main cause for this is that open-loop fermentations do not(More)