AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license

AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system

We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be orchestrated in terms of a global annotation strategy; this facilitates coordination between a team of annotators and automatic data analysis. Third, the annotation strategy should allow progressive and incremental annotation from a time when only a few draft contigs are available, to when a final finished assembly is produced. The overall architecture employed is modular and extensible, being based on the W3 standard Web services framework. Specialized modules interact with two independent core modules that are used to annotate, respectively, genomic and protein sequences. AGMIAL is currently being used by several INRA laboratories to analyze genomes of bacteria relevant to the food-processing industry, and is distributed under an open source license

Coeficientes de difusión durante la deshidratación osmótica de anco (<i>Cucurbita moschata</i>) : Efecto del tamaño

La deshidratación osmótica del anco surge como un tratamiento mínimo que permite prolongar su vida útil. Esta hortaliza se consume en el Noroeste argentino por su sabor suave, bajo costo y disponibilidad; es rica en fibra, vitaminas y potasio. El objetivo del presente trabajo fue evaluar el ajuste al modelo de Azuara de la cinética de la deshidratación osmótica de cubos de anco de 0,5; 1 y 1,5 cm de espesor y analizar el efecto de la dimensión característica en las difusividades que determinan las transferencias de masa. Se determinaron gravimétricamente la pérdida de peso y la ganancia de sólidos; la pérdida de agua se obtuvo a partir de las variables anteriores. Las mayores pérdidas de agua y ganancias de sólidos se obtuvieron para cubos de menor espesor. Se calcularon los parámetros cinéticos mediante el modelo matemático, lográndose muy buenos ajustes y se determinaron las difusividades para la pérdida de agua y la ganancia de sólidos, obteniéndose coeficientes menores para la ganancia de sólidos. Los valores de difusividad másica calculados aumentaron linealmente con el cuadrado de la dimensión característica de los cubos.Centro de Investigación y Desarrollo en Criotecnología de Alimento

Modelling concentration heterogeneities in streets using the street-network model MUNICH

Populations in urban areas are exposed to high local concentrations of pollutants, such as nitrogen dioxide and particulate matter, because of unfavourable dispersion conditions and the proximity to traffic. To simulate these concentrations over cities, models like the street-network model MUNICH (Model of Urban Network of Intersecting Canyons and Highways) rely on parameterizations to represent the air flow and the concentrations of pollutants in streets. In the current version, MUNICH v2.0, concentrations are assumed to be homogeneous in each street segment. A new version of MUNICH, where the street volume is discretized, is developed to represent the street gradients and to better estimate peoples' exposure. Three vertical levels are defined in each street segment. A horizontal discretization is also introduced under specific conditions by considering two zones with a parameterization taken from the Operational Street Pollution Model (OSPM). Simulations are performed over two districts of Copenhagen, Denmark, and one district of greater Paris, France. Results show an improvement in the comparison to observations, with higher concentrations at the bottom of the street, closer to traffic, of pollutants emitted by traffic (NOx, black carbon, organic matter). These increases reach up to 60 % for NO2 and 30 % for PM10 in comparison to MUNICH v2.0. The aspect ratio (ratio between building height and street width) influences the extent of the increase of the first-level concentrations compared to the average of the street. The increase is higher for wide streets (low aspect ratio and often higher traffic) by up to 53 % for NOx and 18 % for PM10. Finally, a sensitivity analysis with regard to the influence of the street network highlights the importance of using the model MUNICH with a network rather than with a single street.</p

Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass

Lignocellulosic biomass is an attractive carbon source for bio-based fuel and chemical production; however, its compositional heterogeneity hinders its commercial use. Since most microbes possess carbon catabolite repression (CCR), mixed sugars derived from the lignocellulose are consumed sequentially, reducing the efficacy of the overall process. To overcome this barrier, microbes that exhibit the simultaneous consumption of mixed sugars have been isolated and/or developed and evaluated for the lignocellulosic biomass utilization. Specific strains of Escherichia coli, Saccharomyces cerevisiae, and Zymomonas mobilis have been engineered for simultaneous glucose and xylose utilization via mutagenesis or introduction of a xylose metabolic pathway. Other microbes, such as Lactobacillus brevis, Lactobacillus buchneri, and Candida shehatae possess a relaxed CCR mechanism, showing simultaneous consumption of glucose and xylose. By exploiting CCR-negative phenotypes, various integrated processes have been developed that incorporate both enzyme hydrolysis of lignocellulosic material and mixed sugar fermentation, thereby enabling greater productivity and fermentation efficacy

Conversion of rice straw to bio-based chemicals: an integrated process using Lactobacillus brevis

Commercialization of lignocellulosic biomass as a feedstock for bio-based chemical production is problematic due to the high processing costs of pretreatment and saccharifying enzymes combined with low product yields. Such low product yield can be attributed, in large part, to the incomplete utilization of the various carbohydrate sugars found in the lignocellulosic biomass. In this study, we demonstrate that Lactobacillus brevis is able to simultaneously metabolize all fermentable carbohydrates in acid pre-processed rice straw hydrolysate, thereby allowing complete utilization of all released sugars. Inhibitors present in rice straw hydrolysate did not affect lactic acid production. Moreover, the activity of exogenously added cellulases was not reduced in the presence of growing cultures of L. brevis. These factors enabled the use of L. brevis in a process termed simultaneous saccharification and mixed sugar fermentation (SSMSF). In SSMSF with L. brevis, sugars present in rice straw hydrolysate were completely utilized while the cellulase maintained its maximum activity due to the lack of feedback inhibition from glucose and/or cellobiose. By comparison to a sequential hydrolysis and fermentation process, SSMSF reduced operation time and the amount of cellulase enzyme necessary to produce the same amount of lactic acid

Comparative Genome Analysis of Lactobacillus reuteri and Lactobacillus fermentum Reveal a Genomic Island for Reuterin and Cobalamin Production

Lactobacillus reuteri is a heterofermentative lactic acid bacterium that naturally inhabits the gut of humans and other animals. The probiotic effects of L. reuteri have been proposed to be largely associated with the production of the broad-spectrum antimicrobial compound reuterin during anaerobic metabolism of glycerol. We determined the complete genome sequences of the reuterin-producing L. reuteri JCM 1112T and its closely related species Lactobacillus fermentum IFO 3956. Both are in the same phylogenetic group within the genus Lactobacillus. Comparative genome analysis revealed that L. reuteri JCM 1112T has a unique cluster of 58 genes for the biosynthesis of reuterin and cobalamin (vitamin B12). The 58-gene cluster has a lower GC content and is apparently inserted into the conserved region, suggesting that the cluster represents a genomic island acquired from an anomalous source. Two-dimensional nuclear magnetic resonance (2D-NMR) with 13C3-glycerol demonstrated that L. reuteri JCM 1112T could convert glycerol to reuterin in vivo, substantiating the potential of L. reuteri JCM 1112T to produce reuterin in the intestine. Given that glycerol is shown to be naturally present in feces, the acquired ability to produce reuterin and cobalamin is an adaptive evolutionary response that likely contributes to the probiotic properties of L. reuteri