BisoGenet: a new tool for gene network building, visualization and analysis

<p>Abstract</p> <p>Background</p> <p>The increasing availability and diversity of omics data in the post-genomic era offers new perspectives in most areas of biomedical research. Graph-based biological networks models capture the topology of the functional relationships between molecular entities such as gene, protein and small compounds and provide a suitable framework for integrating and analyzing omics-data. The development of software tools capable of integrating data from different sources and to provide flexible methods to reconstruct, represent and analyze topological networks is an active field of research in bioinformatics.</p> <p>Results</p> <p>BisoGenet is a multi-tier application for visualization and analysis of biomolecular relationships. The system consists of three tiers. In the data tier, an in-house database stores genomics information, protein-protein interactions, protein-DNA interactions, gene ontology and metabolic pathways. In the middle tier, a global network is created at server startup, representing the whole data on bioentities and their relationships retrieved from the database. The client tier is a Cytoscape plugin, which manages user input, communication with the Web Service, visualization and analysis of the resulting network.</p> <p>Conclusion</p> <p>BisoGenet is able to build and visualize biological networks in a fast and user-friendly manner. A feature of Bisogenet is the possibility to include coding relations to distinguish between genes and their products. This feature could be instrumental to achieve a finer grain representation of the bioentities and their relationships. The client application includes network analysis tools and interactive network expansion capabilities. In addition, an option is provided to allow other networks to be converted to BisoGenet. This feature facilitates the integration of our software with other tools available in the Cytoscape platform. BisoGenet is available at <url>http://bio.cigb.edu.cu/bisogenet-cytoscape/</url>.</p

El Bovino Criollo Argentino: Principales características de la raza

The Argentine Creole cattle has its origins in the cattle introduced to America by the Spanish during colonization. Phenotypically it is characterized by the great diversity of coat colors and its horns, although there are also animals without it. The breed is also characterized by its relatively small body size and moderate milk aptitude, so that the breeding cows have low energy requirements for maintenance and production. In adverse nutritional environments, the Argentine Creole has a high response capacity. It distinguish for its fertility, calving ease, breeding capacity, longevity and resistance to different environmental factors, considering itself as a breed specialized in the production of calves. Under the same production conditions, the butcher performance of the beef and the quality of meat produced by Creole animals is similar to that of other bovine breeds. This animal genetic resource is considered of great value, and must be preserved due to its genetic variability to face current and future production challenges. The use of genetic resources is the best way to maintain the diversity of domestic animals, and Argentine Creole cattle have excellent qualities to improve cattle breeding in certain environments or through crossbreeding. At the country level, it is important to consider the definition of strategies that favor their diffusion and use.El bovino Criollo Argentino tiene sus orígenes en el ganado introducido a América por los españoles durante la colonización. Fenotípicamente se caracteriza por la gran diversidad de colores de capa y por su cornamenta, aunque existan además animales sin cuernos. La raza se caracteriza también por su tamaño corporal relativamente chico y una aptitud lechera moderada, por lo que los vientres de cría poseen bajos requerimientos energéticos de mantenimiento y producción. En ambientes nutricionales adversos, el Criollo Argentino posee alta capacidad de respuesta. Se destaca por su fertilidad, facilidad de parto, capacidad de cría, longevidad y resistencia a diferentes factores ambientales, considerándose como una raza especializada en la producción de terneros. Bajo iguales condiciones de producción, el rendimiento carnicero de la res y la calidad de carne producida por animales Criollos es similar al de otras razas bovinas. Este recurso zoogenético es considerado de gran valor, debiendo ser preservado por su variabilidad genética para hacer frente a desafíos productivos actuales y futuros. La utilización de los recursos genéticos es el mejor camino para el mantenimiento de la diversidad de los animales domésticos, y el bovino Criollo Argentino posee excelentes cualidades para mejorar la ganadería vacuna en determinados ambientes o a través de cruzamientos. A nivel país, es importante considerar la definición de estrategias que favorezcan su difusión y utilización

Crecimiento predestete de terneros Criollo argentinos

The weaning weight of calves depends mainly on the pre-weaning growth rate, and it is associated with the dairy ability of the cow. Milk is the main food available during the first two months of life of the calf and it is from the third month when the consumption of forage begins to take relevance, being of importance its quality. In the Northwest of Argentina, bovine breeding is based on the use of C4 perennial grasses with summer growth, high levels of fiber, and moderate digestibility. The objective of this work was to evaluate the weight gain of Creole calves in two stages prior to weaning: from birth to 130 days of life and from 131 days to weaning at 205 days. We worked with the offspring born in 2014, 2015, and 2016. For the analysis, we used proc GLM from the statistical package SAS. The model included as fixed effects the mother's age at birth, the sex of the calf, and the year of delivery. The results indicate significant effects for the three variables analyzed (P &lt;0.05). The average weight gain from birth to 130 days of life was 648.0 g/d, being 422.8 g/d higher than in the second period. Male calves presented higher weight gains than females and adult cow calves, 7 to 10 years old at parturition, had the highest values ​​of weight gains in both stages. The daily weight gain, in the second period, represented 68% of the weight gain of the first stage, which reflects a decrease in the milk production of the cow that does not becomes compensated by the available forage.El peso al destete de los terneros depende principalmente de la tasa de crecimiento predestete, y está&nbsp; asociada a la aptitud lechera de la vaca. La leche es el principal alimento disponible durante los dos primeros meses de vida del ternero y es partir del tercer mes cuando el consumo de forraje empieza a tomar relevancia, siendo de importancia su calidad.&nbsp; En el Noroeste Argentino la cría bovina se basa en la utilización de gramíneas perennes C4 de crecimiento estival, niveles elevados de fibra y moderada digestibilidad. El objetivo del presente trabajo fue evaluar la ganancia de peso de terneros Criollos en dos etapas previas al destete: desde el nacimiento hasta los 130 días de vida y desde los 131 días hasta el destete a los 205 días. Se trabajó con las crías nacidas los años 2014, 2015 y 2016. Para el análisis se utilizó proc GLM del paquete estadístico SAS. El modelo incluyó como efectos fijos la edad al parto de la madre, el sexo de la cría y el año de parto. Los resultados indican efectos significativos para las tres variables analizadas (P&lt;0.05). La ganancia de peso promedio desde el nacimiento hasta los 130 días de vida fue de 648,0 g/d, resultando superior a las del segundo período de 422,8 g/d. Los terneros machos presentaron ganancias de peso superiores a las hembras y las crías de vacas adultas, de 7 a 10 años al parto, tuvieron los mayores valores de ganancias de peso en ambas etapas. La ganancia diaria de peso, en el segundo periodo, representó el 68% de la ganancia de peso de la primera etapa, lo que refleja una disminución en la producción de leche de la vaca que no llega a ser compensada por el forraje disponible

Reseñas de libros

Granero Martín, Francisco. Agua y ciudad, Análisis de estratégias y procesos de planificación. Quince a diecinueve (Por José Mª Gentil Baldrich), pp. 4-5.-- Parra Bañón, José Joaquín. Pensamiento arquitectónico na obra de José Saramago. Acerca da arquitectura da casa (Por José Mª Gentil Baldrich) pp. 5-6.-- Gentil Baldrich, ]osep María, Yanguas Álvarez de Toledo, Ana. Rito V Fiesta: Una aproximación a la arquitectura efímera sevillana (Por Javier García-Gutiérrez Mosteiro) pp. 7-8.-- Puebla Pons, Juan. La plástica del espacio (Por Josep Maria Montaner y Joan Fontbernat) pp. 8.-- Gómez-Blanco Pontes, Antonio J. Dibujar Granada. La Gran Vía de Colón Por Joaquín Casado de Amezúa) pp.9.-- Almagro Gorbea, Antonio. Levantamiento arquitectónico (Por Joaquín Casado de Amezúa) pp.9-10.-- Villalobos Alonso, Daniel. Hasta los pies del Himalaya. Cuaderno de dibujos de Viaje (Por Fernando Linares García) pp. 10-11.-- Fernández Martín,J.J., et. al. Las ruinas de Dios. Arquitectura olvidada en la provincia de Valladolid (Por Fernando Linares García) pp.11.12.-- Delgado Yanes, Magali y Redondo Domínguez, Ernest, Dibujo a mano alzada para arquitectos (Por Lluís Villanueva Bartrina) pp.13-14.-- Edición digital del libro de actas del IX Congreso EGA pp.14.-- Costa Buján, Pablo y Franco Taboada, José Antonio. Análisis gráfico y propuestas de intervención en puertos de Galicia pp.15.-- Franco Taboada, José Antonio, Tarrío Carrodeguas, Santiago. El conjunto catedralicio de Tuy.Documentación Gráfica pp.16.-- Solana Suárez, Enrique, et. al. Crisis del barrio tradicional: ruptura, mutación o continuidad (Por Luis Doreste Chirino) pp.17.-- Bellido Blanco, D. Santiago. El río Duero. Influencia del entorno natural en la conformación del paisaje humanizado pp.18-19.-- Higón Calvet, José Luis. Contribuciones al estudio del asoleo geométrico. Procedimientos para el cálculo del factor de obstrucción solar. Aplicaciones p.19-20.-- Linares Garcia, Fernando. La arquitectura de las Brañas de Somiedo -Asturias- pp.20-21.-- Martínez Ivars, Carlos Salvador. El dibujo arquitectónico en la construcción de la ciudad de Alicante: Del derribo de las murallas a los años treinta pp.21-22.-- Gutiérrez Labory, Eisa Ma. Le Corbusier, el control geométrico matemático de la forma pp22.-- Martín-González Armingol, Manuel. Mies van Der Rohe: Recursos expresivos y elementos arquitectónicos, a través de los archivos depositados en el Museo de Arte Moderno de New York pp.23-24.-- Mata Botella, Elena. El análisis gráfico de la casa pp.24-27.-- Los pabellones españoles en las exposiciones universales e internacionales a partir de 1937 pp.27.-- El ininterrumpido dibujar de Javier Seguí (Por Javier García-Gutiérrez Mosteiro) pp.28.29.-- X Congreso Internacional de Expresión Gráfica Arquitectónica (por Joaquín Casado de Amezúa, Antonio Gómez-Blanco Pontes) pp.29.-- IV Jornadas de Fotogrametría Arquitectónica (Por Jesús San José Alonso) pp.30.-- Dibujos del Alcázar de Sevilla (Por José A. Ruiz de la Rosa) pp.30-31.-- Miguel García Lisón (Por Juan Puebla Pons) pp.32.-- Cándido Orts Bayarri (Por Rafael Contel Comenge) pp.32.-- José Ignacio González Moreno (Por Carmen García Reig) pp.33.-- Julio Vidaurre Jofre (Por Enrique Rabasa Díaz) pp.33.-- Santiago Roqueta (Por Javier Monedero) pp.34Gentil Baldrich, JM.; García- Gutiérrez Mosteiro, J.; Montaner, JM.; Fontbernat, J.; Casado De Amezúa, J.; Linares García, F.; Villanueva Bartrina, L.... (2005). Reseñas de libros. EGA Expresión Gráfica Arquitectónica. 10(10):4-35. https://doi.org/10.4995/ega.2005.10327OJS435101

Glycemic control during consecutive days with prolonged walking exercise in individuals with type 1 diabetes mellitus

Aims: Despite its general benefits for health, exercise complicates the maintenance of stable blood glucose concentrations in individuals with type 1 diabetes. The aim of the current study was to examine changes in food intake, insulin administration, and 24-h glycemic control in response to consecutive days with prolonged walking exercise (~8 h daily) in individuals with type 1 diabetes. Methods: Ten individuals with type 1 diabetes participating in the worlds' largest walking event were recruited for this observational study. Simultaneous measurements of 24-h glycemic control (continuous glucose monitoring), insulin administration and food intake were performed during a non-walking day (control) and during three subsequent days with prolonged walking exercise (daily distance 40 or 50 km). Results: Despite an increase in daily energy (31 ± 18%; p 10 mmol/L) and hypoglycemia (blood glucose 0.05 for all variables). The prolonged walking exercise was associated with a modest increase in glycemic variability compared with the control day (p < 0.05). Conclusion: Prolonged walking exercise allows for profound reductions in daily insulin administration in persons with type 1 diabetes, despite large increments in energy and carbohydrate intake. When taking such adjustments into account, prolonged moderate-intensity exercise does not necessarily impair 24-h glycemic control. © 2016 Elsevier Ireland Ltd

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 &lt;90 ml per minute per 1.73 m2 of body-surface area and albuminuria (ratio of albumin [mg] to creatinine [g], &gt;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 &lt;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&lt;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&lt;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

Canagliflozin and Cardiovascular and Renal Outcomes in Type 2 Diabetes Mellitus and Chronic Kidney Disease in Primary and Secondary Cardiovascular Prevention Groups

Background: Canagliflozin reduces the risk of kidney failure in patients with type 2 diabetes mellitus and chronic kidney disease, but effects on specific cardiovascular outcomes are uncertain, as are effects in people without previous cardiovascular disease (primary prevention). Methods: In CREDENCE (Canagliflozin and Renal Events in Diabetes With Established Nephropathy Clinical Evaluation), 4401 participants with type 2 diabetes mellitus and chronic kidney disease were randomly assigned to canagliflozin or placebo on a background of optimized standard of care. Results: Primary prevention participants (n=2181, 49.6%) were younger (61 versus 65 years), were more often female (37% versus 31%), and had shorter duration of diabetes mellitus (15 years versus 16 years) compared with secondary prevention participants (n=2220, 50.4%). Canagliflozin reduced the risk of major cardiovascular events overall (hazard ratio [HR], 0.80 [95% CI, 0.67-0.95]; P=0.01), with consistent reductions in both the primary (HR, 0.68 [95% CI, 0.49-0.94]) and secondary (HR, 0.85 [95% CI, 0.69-1.06]) prevention groups (P for interaction=0.25). Effects were also similar for the components of the composite including cardiovascular death (HR, 0.78 [95% CI, 0.61-1.00]), nonfatal myocardial infarction (HR, 0.81 [95% CI, 0.59-1.10]), and nonfatal stroke (HR, 0.80 [95% CI, 0.56-1.15]). The risk of the primary composite renal outcome and the composite of cardiovascular death or hospitalization for heart failure were also consistently reduced in both the primary and secondary prevention groups (P for interaction &gt;0.5 for each outcome). Conclusions: Canagliflozin significantly reduced major cardiovascular events and kidney failure in patients with type 2 diabetes mellitus and chronic kidney disease, including in participants who did not have previous cardiovascular disease

High ACSL5 Transcript Levels Associate with Systemic Lupus Erythematosus and Apoptosis in Jurkat T Lymphocytes and Peripheral Blood Cells

Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which increased apoptosis and decreased apoptotic cells removal has been described as most relevant in the pathogenesis. Long-chain acyl-coenzyme A synthetases (ACSLs) have been involved in the immunological dysfunction of mouse models of lupus-like autoimmunity and apoptosis in different in vitro cell systems. The aim of this work was to assess among the ACSL isoforms the involvement of ACSL2, ACSL4 and ACSL5 in SLE pathogenesis. Findings With this end, we determined the ACSL2, ACSL4 and ACSL5 transcript levels in peripheral blood mononuclear cells (PBMCs) of 45 SLE patients and 49 healthy controls by quantitative real time-PCR (q-PCR). We found that patients with SLE had higher ACSL5 transcript levels than healthy controls [median (range), healthy controls = 16.5 (12.3–18.0) vs. SLE = 26.5 (17.8–41.7), P = 3.9×10 E-5] but no differences were found for ACSL2 and ACSL4. In in vitro experiments, ACSL5 mRNA expression was greatly increased when inducing apoptosis in Jurkat T cells and PBMCs by Phorbol-Myristate-Acetate plus Ionomycin (PMA+Io). On the other hand, short interference RNA (siRNA)-mediated silencing of ACSL5 decreased induced apoptosis in Jurkat T cells up to the control levels as well as decreased mRNA expression of FAS, FASLG and TNF. Conclusions These findings indicate that ACSL5 may play a role in the apoptosis that takes place in SLE. Our results point to ACSL5 as a potential novel functional marker of pathogenesis and a possible therapeutic target in SLE.Financial support for the study was provided by the Ministerio de Ciencia e Innovación-Fondos Feder (PN-SAF2009-11491) and Junta de Andalucía (P07-CVI-02551) to A. Alcina and Fondo de Investigación Sanitaria (FIS PI081636, CP10/00526) to F. Matesanz. M. Fedetz and D. Ndagire are holders of a fellowship from Fundación Española de Esclerosis Múltiple (FEDEM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe