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

Variabilidad en la presentación del Síndrome de Brown-McLean

Case report: We report two aphakic patients with Brown-McLean syndrome. Discussion: One patient was affected by Marfan syndrome, after having undergone lens subluxation surgery and aphakia 23 years previously. The other patient was aphakic due to cataract surgery with complications three years before. Our cases demonstrate that this syndrome can show a variety of clinical characteristics, but peripheral corneal edema is always present. A full understanding of the clinical signs of presentation is of great importance in order to detect this syndrom

A1298C polymorphism in the MTHFR gene predisposes to cardiovascular risk in rheumatoid arthritis

8 páginas, 1 figura, 3 tablas.-- et al.[Introduction]: We determined the contribution of the methylene tetrahydrofolate reductase (MTHFR) 677 C>T and 1298 A>C gene polymorphisms to the susceptibility to rheumatoid arthritis (RA). We also assessed whether these two MTHFR gene polymorphisms may be implicated in the development of cardiovascular (CV) events and subclinical atherosclerosis manifested by the presence of endothelial dysfunction, in a series of Spanish patients with RA. [Methods]: Six hundred and twelve patients fulfilling the 1987 American College of Rheumatology classification criteria for RA, seen at the rheumatology outpatient clinics of Hospital Xeral-Calde, Lugo and Hospital San Carlos, Madrid, were studied. Patients and controls (n = 865) were genotyped using predesigned TaqMan SNP genotyping assays. [Results]: No significant differences in allele or genotype frequencies for the MTHFR gene polymorphisms between RA patients and controls were found. Also, no association between the MTHFR 677 C>T polymorphism and CV events or endothelial dysfunction was observed. However, the MTHFR 1298 allele C frequency was increased in patients with CV events after 5 years (38.7% versus 30.3%; odds ratio = 1.45; 95% confidence interval = 1.00 to 2.10; P = 0.04) and 10 years (42.2% versus 31.0%; odds ratio = 1.62; 95% confidence interval = 1.08 to 2.43; P = 0.01) follow up. Moreover, patients carrying the MTHFR 1298 AC and CC genotypes had a significantly decreased flow-mediated endothelium-dependent vasodilatation (4.3 ± 3.9%) compared with those carrying the MTHFR 1298 AA genotype (6.5 ± 4.4%) (P = 0.005). [Conclusions]: Our results show that the MTHFR 1298 A>C gene polymorphism confers an increased risk for subclinical atherosclerosis and CV events in patients with RA.The present study was supported by two grants from Fondo de Investigaciones Sanitarias PI06-0024 and PS09/00748 (Spain). This work was partially supported by RETICS Program RD08/0075 (RIER) from the Instituto de Salud Carlos III.Peer reviewe

Utilización de bolsas ANKOM® en la determinación de la digestibilidad de la materia seca in vitro en conejos.

La metodología de digestibilidad in vitro de la materia seca (DMSiv) desarrollada por Ramos et al. (1992) para predecir la digestibilidad de la materia seca y valor nutricional de diferentes alimentos comúnmente utilizados en la alimentación de conejos, ha sido estandarizada y validada por diferentes laboratorios (Villamide et al. 2008 y Carabaño et al. 2008), demostrándose su fiabilidad, reproducibilidad y repetibilidad. Uno de los puntos críticos de las metodologías gravimétricas es la filtración con crisol, ya que las propiedades físicas junto con la composición química de diversas materias primas dificultan este proceso y aumentan la variabilidad en los resultados (Mertens, 2002). Por otra parte la digestión individual de las muestras limita la capacidad de análisis. Con la finalidad de corregir estas limitaciones se propuso como alternativa el uso de bolsas ANKOM ® , ya utilizadas en el análisis secuencial de Van Soest (Kenneth et al., 1999), digeridas colectivamente en un mismo recipiente. Además de la utilización de bolsas, como novedad se incluyó al final de la digestibilidad un lavado adicional de las bolsas. El objetivo de este trabajo fue determinar la validez de esta modificación en la digestibilidad in vitro ileal (dos pasos) y fecal (tres pasos

Brenneria quercina and Serratia spp. isolated from Spanish oak trees: molecular characterization and PCR development

Brenneria quercina has been reported as one of the causal agents of oak decline in Spain. To investigate the bacterial variability of this pathogen from different Spanish oak forests, a collection of 38 bacterial isolates from seven geographic locations and from different oak species was analysed by sequencing 16S rDNA and rep-PCR fingerprinting. All Spanish isolates of B. quercina were grouped by rep-PCR into a homogenous cluster that differed significantly from B. quercina reference strains from California. 16S rDNA analysis revealed that 34 out of 38 isolates were Brenneria . However, four isolates belonged to the genus Serratia , suggesting that this bacterium could cause cankers in oak trees. The information obtained by rep-PCR fingerprint analysis was used to develop PCR primers for the sensitive and specific detection of B. quercina from infected plant tissues. Pathogenicity tests performed with Brenneria and Serratia isolates showed that both were able to grow and cause cankers in oak trees

Il10 Deficiency Rebalances Innate Immunity to Mitigate Alzheimer-Like Pathology

SummaryThe impact of inflammation suppressor pathways on Alzheimer’s disease (AD) evolution remains poorly understood. Human genetic evidence suggests involvement of the cardinal anti-inflammatory cytokine, interleukin-10 (IL10). We crossed the APP/PS1 mouse model of cerebral amyloidosis with a mouse deficient in Il10 (APP/PS1+Il10−/−). Quantitative in silico 3D modeling revealed activated Aβ phagocytic microglia in APP/PS1+Il10−/− mice that restricted cerebral amyloidosis. Genome-wide RNA sequencing of APP/PS1+Il10−/− brains showed selective modulation of innate immune genes that drive neuroinflammation. Il10 deficiency preserved synaptic integrity and mitigated cognitive disturbance in APP/PS1 mice. In vitro knockdown of microglial Il10-Stat3 signaling endorsed Aβ phagocytosis, while exogenous IL-10 had the converse effect. Il10 deficiency also partially overcame inhibition of microglial Aβ uptake by human Apolipoprotein E. Finally, the IL-10 signaling pathway was abnormally elevated in AD patient brains. Our results suggest that “rebalancing” innate immunity by blocking the IL-10 anti-inflammatory response may be therapeutically relevant for AD

Leucaena leucocephala in ruminant nutrition

It is a common situation in extensive ruminant production systems in tropical countries to have low production indicators due to nutrient deficiencies in the diet. An economic alternative to increase animal production is the incorporation of legumes (fodder and fruits) in the diet. This review, presents an analysis of the positive and negative effects of Leucaena leucocephala consumption by ruminants, with particular emphasis on the secondary compound mimosine. Leucaena due to its high nutrient content, rumen by-pass protein supply and its possible effect on the reduction of greenhouse gas (attributed to tannins) has become one of the legumes most commonly used in ruminant feeding practices. However, in countries where leucaena has been introduced, its use is still limited to levels below 30% inclusion in the diet, due to the secondary compound mimosine and its isomers (3,4 and 2,3 DHP), which can induce toxicity, even when animals are inoculated with rumen fluid containing the bacteria Synergistes jonesii reported as responsible for degrading these compounds in the rumen. In the Yucatan Peninsula, Mexico, ruminants consuming leucaena can tolerate more than 50% inclusion in the diet, without having a negative impact on production, attributed intake to mimosine and its isomers. We conclude that in animals not adapted, the intake would be limited to low inclusion levels (less than 30% inclusion in the diet), mainly because of mimosine and its derivatives. The decrease in intake or diet digestibility seem to better explain the reduction in methane production, however, in vivo studies are required to clearly establish the mechanism of action. It has been reported the presence of different bacteria to S. jonessi that would have the ability to degrade mimosine and its derivatives, however, the activity of these bacteria and its effectiveness must be confirmed in vivo