Desarrollo de una plataforma computacional para el modelado metabólico de microorganismos

[EN] Synthetic biology focuses on the design and construction of artificial genetic systems that are capable of carrying out a specific function after being inserted into a living system. With the development of synthetic biology a new generation of bioengineers has appeared who develop complex, highly integrated genetic biological pathways. Te improvement of this scientific discipline aims to establish a computational and conceptual framework that will support the development of modular artificial biological systems based on an engineering and systematic methodology. To achieve this, it will be necessary to provide new integrated computational tools in a common environment for the analysis of metabolic phenotypes, the design of new complex genetic pathways and the visualisation of metabolic maps to the next generation of designers in synthetic biology and future biotechnologists and biological engineers. A result of this research is the Hydra platform (Hybrid Draw and Routes Analysis) that integrates various tools for the design, analysis, and visualisation of metabolic networks.[ES] La Biología Sintética (BS) se centra en el diseño y la construcción de sistemas genéticos artificiales, capaces de desarrollar una función específica después de haber sido introducidos en un sistema vivo. Con el desarrollo de la BS, se observa una nueva generación de bioingenieros que desarrollan complejos circuitos biológicos genéticos con un alto nivel de integración. La mejora de esta disciplina científica tiene por objeto establecer un marco computacional y conceptual que dé asistencia al desarrollo de sistemas biológicos artificiales modulares basándose en una metodología ingenieril y sistemática, para lo que se necesita proveer a la próxima generación de diseñadores en Biología Sintética y a los futuros biotecnólogos e ingenieros biológicos de nuevas herramientas computacionales integradas en un entorno común para el análisis de fenotipos metabólicos, el diseño de nuevos circuitos genéticos complejos y la visualización de mapas metabólicos. Como resultado de esta investigación se obtiene la plataforma Hydra (Hybrid Draw and Routes Analysis), que integra diversas herramientas para el diseño, análisis y visualización de las redes metabólicas.Los autores desean agradecer el soporte financiero recibido por el Ministerio de Ciencia e Innovación a través de la concesión TIN2009- 12359; la Conselleria de Inmigración y Ciudadanía de la Generalitat Valenciana (concesión 3012/2009) y la Comisión Europea (Proyecto TARPOL FP7 EU KBBE 212894).Reyes, R.; Garrido, J.; Jaime, RA.; Córdova, V.; Triana, J.; Villar, L.; Castro, JC.... (2011). Desarrollo de una plataforma computacional para el modelado metabólico de microorganismos. Nereis. Revista Iberoamericana Interdisciplinar de Métodos, Modelización y Simulación. (3):25-31. http://hdl.handle.net/10251/91952S2531

A hymenopterists' guide to the hymenoptera anatomy ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of ~240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resourc¬es are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, “preferred terms”, and “structural equivalency”. We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the “URI table”) by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the “Analyzer”) to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.Katja C. Seltmann... Andrew D. Austin... John T. Jennings... et al

Taxonomy based on science is necessary for global conservation

Peer reviewe

Canagliflozin and renal outcomes in type 2 diabetes and nephropathy

BACKGROUND Type 2 diabetes mellitus is the leading cause of kidney failure worldwide, but few effective long-term treatments are available. In cardiovascular trials of inhibitors of sodium–glucose cotransporter 2 (SGLT2), exploratory results have suggested that such drugs may improve renal outcomes in patients with type 2 diabetes. METHODS In this double-blind, randomized trial, we assigned patients with type 2 diabetes and albuminuric chronic kidney disease to receive canagliflozin, an oral SGLT2 inhibitor, at a dose of 100 mg daily or placebo. All the patients had an estimated glomerular filtration rate (GFR) of 30 to <90 ml per minute per 1.73 m2 of body-surface area and albuminuria (ratio of albumin [mg] to creatinine [g], >300 to 5000) and were treated with renin–angiotensin system blockade. The primary outcome was a composite of end-stage kidney disease (dialysis, transplantation, or a sustained estimated GFR of <15 ml per minute per 1.73 m2), a doubling of the serum creatinine level, or death from renal or cardiovascular causes. Prespecified secondary outcomes were tested hierarchically. RESULTS The trial was stopped early after a planned interim analysis on the recommendation of the data and safety monitoring committee. At that time, 4401 patients had undergone randomization, with a median follow-up of 2.62 years. The relative risk of the primary outcome was 30% lower in the canagliflozin group than in the placebo group, with event rates of 43.2 and 61.2 per 1000 patient-years, respectively (hazard ratio, 0.70; 95% confidence interval [CI], 0.59 to 0.82; P=0.00001). The relative risk of the renal-specific composite of end-stage kidney disease, a doubling of the creatinine level, or death from renal causes was lower by 34% (hazard ratio, 0.66; 95% CI, 0.53 to 0.81; P<0.001), and the relative risk of end-stage kidney disease was lower by 32% (hazard ratio, 0.68; 95% CI, 0.54 to 0.86; P=0.002). The canagliflozin group also had a lower risk of cardiovascular death, myocardial infarction, or stroke (hazard ratio, 0.80; 95% CI, 0.67 to 0.95; P=0.01) and hospitalization for heart failure (hazard ratio, 0.61; 95% CI, 0.47 to 0.80; P<0.001). There were no significant differences in rates of amputation or fracture. CONCLUSIONS In patients with type 2 diabetes and kidney disease, the risk of kidney failure and cardiovascular events was lower in the canagliflozin group than in the placebo group at a median follow-up of 2.62 years

Figure 35 from: Höcherl A, Shaw MR, Boudreault C, Rabl D, Haszprunar G, Raupach MJ, Schmidt S, Baranov V, Fernández-Triana J (2024) Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions. ZooKeys 1188: 305-386. https://doi.org/10.3897/zookeys.1188.112516

Figure 35 Microgaster nixalebion Shaw, 2004, female (ZSM-HYM-42380-A06) A lateral and B dorsal views. Length of the specimen: 4.25 mm

Supplementary material 4 from: Höcherl A, Shaw MR, Boudreault C, Rabl D, Haszprunar G, Raupach MJ, Schmidt S, Baranov V, Fernández-Triana J (2024) Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions. ZooKeys 1188: 305-386. https://doi.org/10.3897/zookeys.1188.112516

NJ-topology of DS-MCGNREC

Supplementary material 11 from: Höcherl A, Shaw MR, Boudreault C, Rabl D, Haszprunar G, Raupach MJ, Schmidt S, Baranov V, Fernández-Triana J (2024) Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions. ZooKeys 1188: 305-386. https://doi.org/10.3897/zookeys.1188.112516

BOLD:ABY6385 trait

Supplementary material 3 from: Höcherl A, Shaw MR, Boudreault C, Rabl D, Haszprunar G, Raupach MJ, Schmidt S, Baranov V, Fernández-Triana J (2024) Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions. ZooKeys 1188: 305-386. https://doi.org/10.3897/zookeys.1188.112516

Alignment used for NJ-topology of DS-MCGNREC

Supplementary material 10 from: Höcherl A, Shaw MR, Boudreault C, Rabl D, Haszprunar G, Raupach MJ, Schmidt S, Baranov V, Fernández-Triana J (2024) Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions. ZooKeys 1188: 305-386. https://doi.org/10.3897/zookeys.1188.112516

BOLD:ABY6385 sequence

Supplementary material 2 from: Höcherl A, Shaw MR, Boudreault C, Rabl D, Haszprunar G, Raupach MJ, Schmidt S, Baranov V, Fernández-Triana J (2024) Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions. ZooKeys 1188: 305-386. https://doi.org/10.3897/zookeys.1188.112516

COI-Sequences for DS-MCGNREC