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

Radiological Assessment on Interest Areas on the Sellafield Nuclear Site via Unmanned Aerial Vehicle

The Sellafield nuclear plant is a 3 km2 site in north-west Cumbria, England, with a long and distinguished history of nuclear power generation, reprocessing and waste storage—with a current working emphasis on decommissioning and clean-up. Important to this safe, efficient and complete remediation of the site, routine monitoring is essential in a wide range of on-site environments and structures to attain: (i) accurately map the evolving distribution of radiation with the best possible accuracy (sensitivity and spatial resolution); in addition to (ii) the contributing radionuclide species and therefore the radiological and chemo-toxicity risk. This work presents the trial deployment of an unmanned aerial vehicle equipped with a lightweight radiation detection system as a novel tool for the assessment of radioactivity at a number of test-sites on the nuclear licenced site. Through the use of this system, it was possible to determine the existence of anthropogenically present radiation at selected facilities. Such a system has been proven to be highly accurate (spatially) and precise (attribution of contamination species observed) within the challenging site environments, capable of measuring and mapping contamination over both high and low dose-rate areas

The use of unmanned aerial systems for the mapping of legacy uranium mines

AbstractHistorical mining of uranium mineral veins within Cornwall, England, has resulted in a significant amount of legacy radiological contamination spread across numerous long disused mining sites. Factors including the poorly documented and aged condition of these sites as well as the highly localised nature of radioactivity limit the success of traditional survey methods. A newly developed terrain-independent unmanned aerial system [UAS] carrying an integrated gamma radiation mapping unit was used for the radiological characterisation of a single legacy mining site. Using this instrument to produce high-spatial-resolution maps, it was possible to determine the radiologically contaminated land areas and to rapidly identify and quantify the degree of contamination and its isotopic nature. The instrument was demonstrated to be a viable tool for the characterisation of similar sites worldwide

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

An integrated approach to use genetic resources for resurrection plants to enhance drought tolerance in breeding-extension programs [abstract]

Only abstract of poster available.Track V: BiomassThe ultimate goals of this project are to gain a basic understanding of the unique gene and gene regulatory networks that are necessary and sufficient for vegetative tissues to withstand dehydration and then rapidly recover upon rehydration and to use the knowledge gained to develop crops, maize and forage grasses that maintain biomass production under drought condition. Our approach is to combine comparative genomics and phylogenetics to identify genes and gene networks that are adaptive and central to the tolerance of cellular dehydration. This involves the use of resurrection species as models for dehydration tolerance coupled with a suite of comparative bioinformatic tools that allows for the phylogenetic assessment of gene expression patterns in response to dehydration and rehydration. Once the key genetic elements have been identified and assessed we will use a transgenic functional assessment of their involvement in the phenotype, both at a molecular and physiological level, of drought tolerance. One of our key resurrection species is the South African grass Sporobolus stapfianus, which is capable of surviving -240 MPa of water deficit (a hundred times lower than most crop plants). This plant not only serves as a model for monocot crops such as maize and switchgrass, our major targets for crop improvement, but also serves as a direct possibility for an alternate forage grass and biomass source. The improvement of biomass production under drought conditions is not only important for sustainable biofuel production but also for food and energy security. Funded by a CSREES-NRI Grant of $450,000 over three years to PI Mel Oliver USDA-ARS-PGRU Columbia, CoPIs Robert Sharp, University of Missouri; John Cushman, University of Nevada, Reno; Paxton Payton, USDA-ARS-PSRU Lubbock