Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

BACKGROUND: BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. RESULTS: W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. CONCLUSION: W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum

Sex differences in constitutive autophagy

Sex bias has been described nowadays in biomedical research on animal models, although sexual dimorphism has been confirmed widely under pathological and physiological conditions. The main objective of our work was to study the sex differences in constitutive autophagy in spinal cord and skeletalmuscle tissue fromwild type mice. To examine the influence of sex on autophagy, mRNA and proteins were extracted from male and female mice tissues.The expressions of microtubule-associated protein 1 light chain 3 (LC3) and sequestosome 1 (p62), markers to monitor autophagy, were analyzed at 40, 60, 90, and 120 days of age.We found significant sex differences in the expression of LC3 and p62 in both tissues at these ages. The results indicated that sex and tissue specific differences exist in constitutive autophagy.These data underlined the need to include both sexes in the experimental groups to minimize any sex bias

Competition controls the rate of transition between the peripheral pools of CD4+CD25− and CD4+CD25+ T cells

Recent reports have hinted that it is possible to regenerate CD4+CD25+ regulatory T cells (Treg) from CD4+CD25− cells, a phenomenon termed conversion. We evaluated the relative contribution of this process to the Treg pool by transferring purified populations of CD4+ T cells into T cell-deficient mice. We report that conversion of CD25− cells into the CD4+CD25+Treg pool is minor if other bona fide CD25+ Tregs are present. Moreover, in the same hosts, the loss of CD25 expression by a population of Tregs also decreases in the presence of co-injected CD4+CD25− cells. Thus, the rate of exchange between CD25− and CD25+ T-cell populations is determined by the presence or absence of T-cell competitors. Our results attest for the role of competition in the contribution of different T-cell subsets for the regeneration of the peripheral CD4+ T-cell pool during lymphopeni

Experimental modulation of capsule size in Cryptococcus neoformans

Experimental modulation of capsule size is an important technique for the study of the virulence of the encapsulated pathogen Cryptococcus neoformans. In this paper, we summarize the techniques available for experimental modulation of capsule size in this yeast and describe improved methods to induce capsule size changes. The response of the yeast to the various stimuli is highly dependent on the cryptococcal strain. A high CO(2) atmosphere and a low iron concentration have been used classically to increase capsule size. Unfortunately, these stimuli are not reliable for inducing capsular enlargement in all strains. Recently we have identified new and simpler conditions for inducing capsule enlargement that consistently elicited this effect. Specifically, we noted that mammalian serum or diluted Sabouraud broth in MOPS buffer pH 7.3 efficiently induced capsule growth. Media that slowed the growth rate of the yeast correlated with an increase in capsule size. Finally, we summarize the most commonly used media that induce capsule growth in C. neoformans

Influences from “other influencers” for physical activity practice in teenagers

OBJETIVO Examinar la influencia social (apoyo social, influencia social e influencia como modelo) de los “otros significativos” (padre, madre, amigos, profesor de educación física) en la práctica de actividad física según género y ciclo, en sujetos adolescentes. MATERIAL Y MÉTODOS 831 sujetos de la provincia de Huesca (45,7% hombres y 54,3% mujeres) de entre 12 y 16 años. Contestaron a una adaptación del cuestionario “Four by one-day Physical Activity Questionaire” y al “Cuestionario de influencias sobre la Actividad Física y la Salud”. RESULTADOS La influencia del profesor de educación física como modelo y la influencia social de los amigos explicaron el 11,2% de la actividad física realizada. Se obtuvieron diferencias significativas para los referentes de género en todos los tipos de influencias sociales DISCUSIÓN El apoyo e influencia social diferenciado por parte de los progenitores, en función del género o edad de sus hijos, parece demostrar la importancia que tienen los referentes de género y los estereotipos sexuales, en la influencia sobre la práctica de actividad física en población adolescente.OBJECTIVE To estimate the social influence (social support, social influence and model) that exert "significant others" (father, mother, friends, physical education teacher) on physical activity by gender and cycle, among a representative sample of students in the province of Huesca enrolled in secondary education. MATERIALS AND METHOD The sample analysis was composed by 831 individuals from Huesca High School (45,7% men, 54,3% women), between 12 and 16 years old. Physical activity was assessed using an adapted version of “Four by one-day Physical Activity Questionaire” and “Cuestionario de influencias sobre la Actividad Física y la Salud”. RESULTS The physical activity teacher as a model and the social influence of friend explained 11,2% of the done physical activity. Significant differences in the social influences were obtained depending on the sex. DISCUSSION The influence of the physical activity teacher and the support from the friends appear as positive factors for the physical activity practic

Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations.

In this study, we examined Sicilian-style green olive fermentations upon the addition of Saccharomyces cerevisiae UCDFST 09-448 and/or Pichia kudriazevii UCDFST09-427 or the lactic acid bacteria (LAB) Lactobacillus plantarum AJ11R and Leuconostoc pseudomesenteroides BGM3R. Olives containing S. cerevisiae UCDFST 09-448, a strain able to hydrolyze pectin, but not P. kudriazevii UCDFST 09-427, a nonpectinolytic strain, exhibited excessive tissue damage within 4 weeks. DNA sequencing of fungal internal transcribed spacer (ITS) regions and comparisons to a yeast-specific ITS sequence database remarkably showed that neither S. cerevisiae UCDFST 09-448 nor P. kudriazevii UCDFST 09-427 resulted in significant changes to yeast species diversity. Instead, Candida boidinii constituted the majority (>90%) of the total yeast present, independent of whether S. cerevisiae or P. kudriazevii was added. By comparison, Lactobacillus species were enriched in olives inoculated with potential starter LAB L. plantarum AJ11R and L. pseudomesenteroides BGM3R according to community 16S rRNA gene sequence analysis. The bacterial diversity of those olives was significantly reduced and resembled control fermentations incubated for a longer period of time. Importantly, microbial populations were highly dynamic at the strain level, as indicated by the large variations in AJ11R and BGM3R cell numbers over time and reductions in the numbers of yeast isolates expressing polygalacturonase activity. These findings show the distinct effects of exogenous spoilage and starter microbes on indigenous communities in plant-based food fermentations that result in very different impacts on product quality. IMPORTANCE Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be improved by the deliberate addition of starter culture microbes that accelerate or beneficially modify product outcomes, the impact of either of those microbial additions on community dynamics within the fermentations is not well understood at strain-specific or global scales. Herein, we show how exogenous spoilage yeast or starter lactic acid bacteria confer very different effects on microbial numbers and diversity in olive fermentations. Introduced microbes have long-lasting consequences and result in changes that are apparent even when levels of those inoculants and their major enzymatic activities decline. This work has direct implications for understanding bacterial and fungal invasions of microbial habitats resulting in pivotal changes to community structure and function

Identificación y chequeo de parentesco en la especie canina mediante análisis de ADN

Este trabajo presenta los primeros resultados en España de un estudio de identificación y chequeo de parentesco en la especie canina mediante microsatélites (polimorfismos del ADN). Para este trabajo se han utilizado 79 animales, 48 de los cuales no están emparentados y 31 que pertenecen a 3 familias, en los que Se han analizado 11 microsatélites. Los resultados indican la posibilidad de utilizar estos marcadores en test de paternidad con resultados altamente fiables (99%), si se utilizan más de 7 microsatélites.This work presents the first results in Spain of an study concerning identity and parentage test in dogs by microsatellites (ONA polymorphisms). 79 animals have been used for this work, (48 unrelated dogs and 31 dogs from 3 families). Our main conclusion is the necessity of using more than 7 microsatellites in arder to obtain results with 99% of garanty

Diagnóstico de Leishmaniosis canina mediante la técnica de reacción en cadena de la polimerasa (PCR) : un procedimiento simple para uso en la clínica

Para detectar la presencia de Leishmania ssp, en distintas muestras clínicas de perros sospechosos de padecer esta enfermedad, se ha utilizado la técnica PCR, amplificando para ello un fragmento del gen SSU rRNA, repetido más de 100 veces en el genoma del parásito. El método se ha optimizado para utilizarlo como método de rutina en la clínica. El procesado de las muestras es rápido y simple. El diagnóstico se ha realizado por presencia/ausencia del parásito, utilizando para ello muestras de sangre, médula ósea y ganglio linfático principalmente. En el caso de existir el parásito en el huésped se visualiza una banda nítida de un tamaño de 603 bp y en el caso de que el parásito esté ausente, no se detecta la presencia de esta banda. Los mejores resultados se obtuvieron cuando la muestra de partida fue médula o ganglio linfático. El método presenta la ventaja adicional de detectar portadores asintomáticos, incluidos los titulas de IFI dudosos. La técnica PCR se presenta como test de diagnóstico rutinario, siendo más rápida, eficaz y económica que los métodos de diagnóstico clásicos

Thermoluminescent Characteristics of Li2B4O7 Doped with Mn2+ and Eu3+ Ions

Analysis of thermoluminescent properties were made for two samples; Li2B4O7, Li2B4O7:Mn2+:Eu3+. These samples were prepared by melt quenching method. The glow curves of the samples show two broad peaks at 160º C and 245 ºC, and a high peak at 130ºC for Li2B4O7 doped. The response of the materials were analyzed according to the doses (0.2-80 Gy), fading (0-72 hours) and reproducibility of the experiment (10 times). To determine how the glow curve is formed, thermal bleaching for a dose of 5 Gy were made from room temperature to 300º C. Besides, X-ray diffraction patterns were recorded to identify the structure and grain size of the samples