ThermoPhyl : a software tool for selecting phylogenetically optimized conventional and quantitative-PCR taxon-targeted assays for use with complex samples

The ability to specifically and sensitively target genotypes of interest is critical for the success of many PCR-based analyses of environmental or clinical samples that contain multiple templates.Next-generation sequence data clearly show that such samples can harbour hundreds to thousands of operational taxonomic units; a richness which precludes the manual evaluation of candidate assay specificity and sensitivity using multiple sequence alignments. To solve this problem we have developed and validated a free software tool which automates the identification of PCR assays targeting specific genotypes in complex samples. ThermoPhyl uses user-defined target and non-target sequence databases to assess the phylogenetic sensitivity and specificity of thermodynamically optimised candidate assays derived from primer design software packages. ThermoPhyl takes its name from its central premise of testing Thermodynamically optimal assays for Phylogenetic specificity and sensitivity and can be used for two primer (traditional PCR) or two primers with an internal probe (e.g. TaqMan® qPCR) applications and potentially for oligonucleotide probes.Here we describe the use of ThermoPhyl for traditional PCR and qPCR assays. PCR assays selected using ThermoPhyl were validated using 454 pyrosequencing of a traditional specific PCR assay and with a set of four genotype-specific qPCR assays applied to estuarine sediment samples

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

Creating a Minimum Data Set on ageing in sub-Saharan Africa

The World Health Organisation, together with representatives of four sub-Saharan African countries (Ghana, South Africa, Tanzania, Zimbabwe) and other stakeholders, launched a project in 1999 to establish a Minimum Data Set on ageing and older persons in Africa. The project focusses on identifying what data are needed to build knowledge on the situation of older Africans and forging the centralised, in-country collation and dissemination of this information. This paper summarises the current state of the project and touches on issues of data availability and quality, while exploring methods for data collection, integration, collation and dissemination

Geostatistical modelling of a coal seam for resource risk assessment

The evaluation of a coal seam for profitable extraction requires the estimation of its thickness and quality characteristics together with the spatial variability of these variables. In many cases the only data available for the estimation are from a limited number of exploration and feasibility drill holes. Spatial variability can be quantified by geostatistical modelling, which provides the basis for estimation (kriging). In cases where the spatial variability of the seam thickness and quality characteristics has a significant impact on how the coal is extracted and stored, geostatistical simulation may be preferable to geostatistical kriging methods. The aim of this paper is to present an improved approach to resource risk assessment by propagating the uncertainty in semi-variogram model parameters into the spatial variability of coal variables. We show that a more realistic assessment of risk is obtained when the uncertainty of semi-variogram model parameters is taken into account. The methodology is illustrated with a coal seam from North-western Spain. © 2012 Elsevier B.V.E. Pardo-Igúzquiza, P.A. Dowd, J.M. Baltuille, M. Chica-Olm

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

Additional file 1: Table S1. Taxonomic listing of all bacterial genera and species detected as contaminants of DNA extraction and processing kits in the present study and previously reported

Set‐Based Design and the Ship to Shore Connector

The Ship to Shore Connector (SSC), a replacement for the Landing Craft, Air Cushion (LCAC), is the first government‐led design of a ship in over 15 years. This paper will discuss the changes that a government‐led design presents to the design approach, including schedule, organization structure, and design methodology. While presenting challenges, a government‐led design also afforded the opportunity to implement a new technique for assessing various systems and ship alternatives, set‐based design (SBD). The necessity for implementing SBD was the desire to design SSC from a blank sheet of paper and the need for a replacement craft in a short time frame. That is, the LCACs need to be replaced and consequently the preliminary design phase of the SSC program will only be 12 months. This paper will describe SBD and how it was applied to the SSC, the challenges that the program faced, and an assessment of the new methodology, along with recommendations that future design programs should consider when adopting this approach.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90054/1/j.1559-3584.2011.00332.x.pd

The rehydration transcriptome of the desiccation-tolerant bryophyte Tortula ruralis: transcript classification and analysis

BACKGROUND: The cellular response of plants to water-deficits has both economic and evolutionary importance directly affecting plant productivity in agriculture and plant survival in the natural environment. Genes induced by water-deficit stress have been successfully enumerated in plants that are relatively sensitive to cellular dehydration, however we have little knowledge as to the adaptive role of these genes in establishing tolerance to water loss at the cellular level. Our approach to address this problem has been to investigate the genetic responses of plants that are capable of tolerating extremes of dehydration, in particular the desiccation-tolerant bryophyte, Tortula ruralis. To establish a sound basis for characterizing the Tortula genome in regards to desiccation tolerance, we analyzed 10,368 expressed sequence tags (ESTs) from rehydrated rapid-dried Tortula gametophytes, a stage previously determined to exhibit the maximum stress induced change in gene expression. RESULTS: The 10, 368 ESTs formed 5,563 EST clusters (contig groups representing individual genes) of which 3,321 (59.7%) exhibited similarity to genes present in the public databases and 2,242 were categorized as unknowns based on protein homology scores. The 3,321 clusters were classified by function using the Gene Ontology (GO) hierarchy and the KEGG database. The results indicate that the transcriptome contains a diverse population of transcripts that reflects, as expected, a period of metabolic upheaval in the gametophyte cells. Much of the emphasis within the transcriptome is centered on the protein synthetic machinery, ion and metabolite transport, and membrane biosynthesis and repair. Rehydrating gametophytes also have an abundance of transcripts that code for enzymes involved in oxidative stress metabolism and phosphorylating activities. The functional classifications reflect a remarkable consistency with what we have previously established with regards to the metabolic activities that are important in the recovery of the gametophytes from desiccation. A comparison of the GO distribution of Tortula clusters with an identical analysis of 9,981 clusters from the desiccation sensitive bryophyte species Physcomitrella patens, revealed, and accentuated, the differences between stressed and unstressed transcriptomes. Cross species sequence comparisons indicated that on the whole the Tortula clusters were more closely related to those from Physcomitrella than Arabidopsis (complete genome BLASTx comparison) although because of the differences in the databases there were more high scoring matches to the Arabidopsis sequences. The most abundant transcripts contained within the Tortula ESTs encode Late Embryogenesis Abundant (LEA) proteins that are normally associated with drying plant tissues. This suggests that LEAs may also play a role in recovery from desiccation when water is reintroduced into a dried tissue. CONCLUSION: The establishment of a rehydration EST collection for Tortula ruralis, an important plant model for plant stress responses and vegetative desiccation tolerance, is an important step in understanding the genome level response to cellular dehydration. The type of transcript analysis performed here has laid the foundation for more detailed functional and genome level analyses of the genes involved in desiccation tolerance in plants

Socioeconomic disparities in the seroprevalence of cytomegalovirus infection in the US population: NHANES III

http://deepblue.lib.umich.edu/bitstream/2027.42/61298/1/Dowd,Socioeconomicdisparitiesintheseroprevalenceofcytomegalovirus.pd