Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

International audienceIncreasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system

Supernormal functional reserve of apical segments in elite soccer players: an ultrasound speckle tracking handgrip stress study

<p>Abstract</p> <p>Background</p> <p>Ultrasound speckle tracking from grey scale images allows the assessment of regional strain derived from 2D regardless of angle intonation, and it is highly reproducible. The study aimed to evaluate regional left ventricular functional reserve in elite soccer players.</p> <p>Methods</p> <p>50 subjects (25 elite athletes and 25 sedentary controls), aged 26 ± 3.5, were submitted to an echo exam, at rest and after the Hand Grip (HG) test. Both standard echo parameters and strain were evaluated.</p> <p>Results</p> <p>Ejection fraction was similar in athletes and controls both at rest (athletes 58 ± 2 vs controls 57 ± 4 p ns) and after HG (athletes 60 ± 2 vs controls 58 ± 3 p ns). Basal (septal and anterior) segments showed similar strain values in athletes and controls both at rest (athletes S% -19.9 ± 4.2; controls S% -18.8 ± 4.9 p = ns) and after HG (athletes S% -20.99 ± 2.8; controls S% -19.46 ± 4.4 p = ns). Medium-apical segments showed similar strain values at rest (athletes S% -17.31 ± 2.3; controls S% -20.00 ± 5.3 p = ns), but higher values in athletes after HG (athletes S% -24.47 ± 2.8; controls S% -20.47 ± 5.4 p < 0.05)</p> <p>Conclusion</p> <p>In athletes with physiological myocardial hypertrophy, a brief isometric effort produces enhancement of the strain in medium-apical left ventricular segments, suggesting the presence of a higher regional function reserve which can be elicited with an inotropic challenge and suitable methods of radial function quantification such as 2D-derived strain.</p

Biotechnological production of γ-decalactone, a peach like aroma, by Yarrowia lipolytica

The request for new flavourings increases every year. Consumer perception that everything natural is better is causing an increase demand for natural aroma additives. Biotechnology has become a way to get natural products. γ-Decalactone is a peach-like aroma widely used in dairy products, beverages and others food industries. In more recent years, more and more studies and industrial processes were endorsed to cost-effect this compound production. One of the best-known methods to produce -decalactone is from ricinoleic acid catalyzed by Yarrowia lipolytica, a generally regarded as safe status yeast. As yet, several factors affecting -decalactone production remain to be fully understood and optimized. In this review, we focus on the aromatic compound -decalactone and its production by Y. lipolytica. The metabolic pathway of lactone production and degradation are addressed. Critical analysis of novel strategies of bioprocess engineering, metabolic and genetic engineering and other strategies for the enhancement of the aroma productivity are presented.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684)

Doing synthetic biology with photosynthetic microorganisms

The use of photosynthetic microbes as synthetic biology hosts for the sustainable production of commodity chemicals and even fuels has received increasing attention over the last decade. The number of studies published, tools implemented, and resources made available for microalgae have increased beyond expectations during the last few years. However, the tools available for genetic engineering in these organisms still lag those available for the more commonly used heterotrophic host organisms. In this mini-review, we provide an overview of the photosynthetic microbes most commonly used in synthetic biology studies, namely cyanobacteria, chlorophytes, eustigmatophytes and diatoms. We provide basic information on the techniques and tools available for each model group of organisms, we outline the state-of-the-art, and we list the synthetic biology tools that have been successfully used. We specifically focus on the latest CRISPR developments, as we believe that precision editing and advanced genetic engineering tools will be pivotal to the advancement of the field. Finally, we discuss the relative strengths and weaknesses of each group of organisms and examine the challenges that need to be overcome to achieve their synthetic biology potential.Peer reviewe

Synthesis and in vitro release study of ibuprofen-loaded gelatin graft copolymer nanoparticles.

This work deals with the preparation, characterization and in vitro release study of IBU-loaded gel graft copolymer nanoparticles

Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming

International audienceMetabolic network reconstruction is of great biological relevance be- cause it offers a way to investigate the metabolic behavior of organisms. However, such a reconstruction remains a difficult task at both the biological and compu- tational level. Building on previous work establishing an ASP-based approach to this problem, we present a report from the field resulting in the discovery of new biological knowledge. In fact, for the first time ever, we automatically reconstructed a metabolic network for a macroalgea. We accomplished this by taking advantage of ASP's integrated optimization and enumeration capacities. Both tasks have been modeled in an improved ASP problem representation, in- corporating the concept of reversible reactions. Interestingly, it turned out that optimization highly benefits from the usage of unsatisfiable cores available in the ASP solver unclasp. Finally, applied to Ectocarpus siliculosus, only the combi- nation of unclasp and clasp allowed us to obtain a metabolic network able to produce all recoverable metabolites among the experimentally measured ones. Moreover, 70% of the identified reactions are supported by the existence of an homologous enzyme in Ectocarpus siliculosus, confirming the quality of the re- constructed network from a biological point of view

Non-Saccharomyces yeasts in ternary culture fermentations as a biotechnology to improve quality in warm climate wines = Fermentaciones ternarias con levaduras no-saccharomyces como estrategia biotecnológica para mejorar la calidad organoléptica de vinos de zonas cálidas

Changes in climate patterns have produced modifications in Vitis vinifera grapes maturation processes, especially in recent years, with an impact on the winemaking technology. Microbiological strategies may represent alternatives to mitigate the negative effects that climate change can produce on vines and grapes. Yeast species like Torulaspora delbrueckii and Metschnikowia pulcherrima with important enzymatic activity and, strains of the species Lachancea thermotolerans with the potential to produce large amounts of lactic acid during fermentation may be used in mixed cultures as starters in winemaking to modify the whole sensory perception after an increase in lactic acid production. The final alcoholic volume is achieved by the use of highfermentative power yeasts strains from the species Saccharomyces cerevisiae. The overall perception of these ongoing experimental wines is expected to be translated into less astringent and slightly more acidic wines with floral and fruity notes often not associated to these types of wine. Such sensory profile may be perceived as freshness by consumers. Important to mention is the fact that having wines with lower pH values may also imply the use of less dosages of SO2 as antimicrobial adjuvant also translated into the production of red wines with interesting color profiles

Non-Saccharomyces yeasts in ternary culture fermentations as a biotechnology to improve quality in warm climate wines = Fermentaciones ternarias con levaduras no-saccharomyces como estrategia biotecnológica para mejorar la calidad organoléptica de vinos de zonas cálidas

Changes in climate patterns have produced modifications in Vitis vinifera grapes maturation processes, especially in recent years, with an impact on the winemaking technology. Microbiological strategies may represent alternatives to mitigate the negative effects that climate change can produce on vines and grapes. Yeast species like Torulaspora delbrueckii and Metschnikowia pulcherrima with important enzymatic activity and, strains of the species Lachancea thermotolerans with the potential to produce large amounts of lactic acid during fermentation may be used in mixed cultures as starters in winemaking to modify the whole sensory perception after an increase in lactic acid production. The final alcoholic volume is achieved by the use of highfermentative power yeasts strains from the species Saccharomyces cerevisiae. The overall perception of these ongoing experimental wines is expected to be translated into less astringent and slightly more acidic wines with floral and fruity notes often not associated to these types of wine. Such sensory profile may be perceived as freshness by consumers. Important to mention is the fact that having wines with lower pH values may also imply the use of less dosages of SO2 as antimicrobial adjuvant also translated into the production of red wines with interesting color profiles