N D0-branes and antibranes in the background independent string field theory

In this paper we extend our previous work hep-th/0102063 to the case D0-brane+antibrane system.Comment: 20 page

Upwelling events, coastal offshore exchange, links to biogeochemical processes - Highlights from the Baltic Sea Sciences Congress at Rostock University, Germany, 19-22 March 2007

The Baltic Sea Science Congress was held at Rostock University, Germany, from 19 to 22 March 2007. In the session entitled"Upwelling events, coastal offshore exchange, links to biogeochemical processes" 20 presentations were given,including 7 talks and 13 posters related to the theme of the session.This paper summarises new findings of the upwelling-related studies reported in the session. It deals with investigationsbased on the use of in situ and remote sensing measurements as well as numerical modelling tools. The biogeochemicalimplications of upwelling are also discussed.Our knowledge of the fine structure and dynamic considerations of upwelling has increased in recent decades with the advent ofhigh-resolution modern measurement techniques and modelling studies. The forcing and the overall structure, duration and intensity ofupwelling events are understood quite well. However, the quantification of related transports and the contribution to the overall mixingof upwelling requires further research. Furthermore, our knowledge of the links between upwelling and biogeochemical processes is stillincomplete. Numerical modelling has advanced to the extent that horizontal resolutions of c. 0.5 nautical miles can now be applied,which allows the complete spectrum of meso-scale features to be described. Even the development of filaments can be describedrealistically in comparison with high-resolution satellite data.But the effect of upwelling at a basin scale and possible changes under changing climatic conditions remain open questions

Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks.

<div><p>Genome-scale metabolic networks provide a comprehensive structural framework for modeling genotype-phenotype relationships through flux simulations. The solution space for the metabolic flux state of the cell is typically very large and optimization-based approaches are often necessary for predicting the active metabolic state under specific environmental conditions. The objective function to be used in such optimization algorithms is directly linked with the biological hypothesis underlying the model and therefore it is one of the most relevant parameters for successful modeling. Although linear combination of selected fluxes is widely used for formulating metabolic objective functions, we show that the resulting optimization problem is sensitive towards stoichiometry representation of the metabolic network. This undesirable sensitivity leads to different simulation results when using numerically different but biochemically equivalent stoichiometry representations and thereby makes biological interpretation intrinsically subjective and ambiguous. We hereby propose a new method, Minimization of Metabolites Balance (MiMBl), which decouples the artifacts of stoichiometry representation from the formulation of the desired objective functions, by casting objective functions using metabolite turnovers rather than fluxes. By simulating perturbed metabolic networks, we demonstrate that the use of stoichiometry representation independent algorithms is fundamental for unambiguously linking modeling results with biological interpretation. For example, MiMBl allowed us to expand the scope of metabolic modeling in elucidating the mechanistic basis of several genetic interactions in <em>Saccharomyces cerevisiae</em>.</p> </div

Identification of target genes to reduce acetate yield by Saccharomyces cerevisiae under aerobic conditions

Trabajo presentado en Congreso Nacional de Biotecnología (BIOTEC 2019), celebrado en Vigo (España), del 10 al 13 de junio de 2019Excessive acetic acid production is a key problem in winemaking processes aiming to reduce ethanol content of wine (1). It is related to a boost in acetate yields observed for Saccharomyces cerevisiae and some other yeasts under aerobic fermentation conditions. However, the biochemical mechanisms underlying this problem are unclear. We therefore used a genomic-scale modelling approach, combined with experimentally determined uptake/secretion rates, to gain insights into the metabolic rewiring of S. cerevisiae in response to oxygen under conditions relevant for winemaking. The model was also used to identify gene deletion targets affecting the production of acetic acid under aerobic conditions. Several gene knock-out with expected reduction in acetic acid production were thus identified as targets using MoMa and MiMBl algorithms. The predictions were tested using strains from the prototrophic yeast knockout collection for the fermentation of natural grape must under aerobic conditions. Although many of the prediction did not show any reduction in acetic acid yield, and increased yield was observed in some cases, significant acetate reduction was obtained for three gene deletion strains, ald6¿, mdh3¿ and rip1¿. The involvement of ALD6 on aerobic acetic acid production could be expected from results by other authors. However, the results for MDH3 and RIP1 could not be easily anticipated and thus provide new insights into yeast metabolism concerning acetic acid production, a major concern for the wine industry.We acknowledge funding by MINECO (AGL2015-63629-R and PhD training contract for AJR

A systems and synthetic biology approach for improving wine yeast properties

Póster presentado en el EMBO/EMBL Symposium (Enabling Technologies for Eukaryotic Synthetic Biology), celebrado en Heidelberg (Alemania) del 21 al 23 de junio de 2015.Peer Reviewe