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

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

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

The response of Asterochloris erici (Ahmadjian) Skaloud et Peksa to desiccation: a proteomic approach

18 p.The study of desiccation tolerance of lichens, and of their chlorobionts in particular, has frequently focused on the anti-oxidant system that protects the cell against photo-oxidative stress during dehydration/rehydration cycles. In this study, we used proteomic and transcript analyses to assess the changes associated with desiccation in the isolated phycobiont Aste-rochloris erici. Algae were dried either slowly (5?6 h) or rapidly (<60 min), and rehydrated after 24 h in the desiccated state. To identify proteins that accumulated during the drying or rehydration processes, we employed two-dimensional (2D) difference gel electrophoresis (DIGE) coupled with individual protein identi?cation using trypsin digestion and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Proteomic analyses revealed that desiccation caused an increase in relative abundance of only 11?13 proteins, regard-less of drying rate, involved in glycolysis, cellular protection, cytoskeleton, cell cycle, and targeting and degradation. Tran-scripts of ?ve Hsp90 and two b-tubulin genes accumulated primarily at the end of the dehydration process. In addition, transmission electron microscopy (TEM) images indicate that ultrastructural cell injuries, perhaps resulting from physical or mechanical stress rather than metabolic damage, were more intense after rapid dehydration. This occurred with no major change in the proteome. These results suggest that desiccation tolerance of A. erici is achieved by constitu-tive mechanisms.Ministerio de Ciencia e InnovaciónGeneralitat ValencianaUnited States Department of Agricultur

Sporobolus stapfianus: Insights into desiccation tolerance in the resurrection grasses from linking transcriptomics to metabolomics

Predominant clusters of SDATs that share distinct patterns of abundance during dehydration: A. Predominant patterns of abundance for transcripts in clusters that exhibited increased abundance during dehydration. B. Predominant patterns of abundance for transcripts in clusters that exhibited a decreased abundance during dehydration. (PDF 226 kb

The Impossibility of a Perfectly Competitive Labor Market

Using the institutional theory of transaction cost, I demonstrate that the assumptions of the competitive labor market model are internally contradictory and lead to the conclusion that on purely theoretical grounds a perfectly competitive labor market is a logical impossibility. By extension, the familiar diagram of wage determination by supply and demand is also a logical impossibility and the neoclassical labor demand curve is not a well-defined construct. The reason is that the perfectly competitive market model presumes zero transaction cost and with zero transaction cost all labor is hired as independent contractors, implying multi-person firms, the employment relationship, and labor market disappear. With positive transaction cost, on the other hand, employment contracts are incomplete and the labor supply curve to the firm is upward sloping, again causing the labor demand curve to be ill-defined. As a result, theory suggests that wage rates are always and everywhere an amalgam of an administered and bargained price. Working Paper 06-0

Plant Adaptation to Drought --- Interdisciplinary Research at the University of Missouri [abstract]

Only abstract of poster available.Track V: BiomassDrought is the most important cause of crop failure in Missouri and limits plant productivity in large parts of the US and the world. Drought induces severe reductions in average annual crop yields on a regional scale and can have devastating effects at the farm level. Regional droughts can also strikingly reduce net primary productivity of natural ecosystems. Research on plant adaptation to drought is a long-standing, important component of MU faculty members, who comprise a strong, collaborative team of university and USDA-ARS scientists and are among the international leaders in drought research. Group members represent expertise from a broad range of disciplines, including plant physiology, agronomy, forestry, plant breeding, molecular biology, biotechnology, entomology, plant pathology, and soil science. Areas of research span from basic to applied aspects of plant adaptation to drought, fostering the translation of basic discoveries of underlying mechanisms to the delivery of more drought-tolerant crops at the doorsteps of American farmers. In addition to local collaborations, the team interacts with other scientists in the state of Missouri (e.g. Danforth Plant Sciences Center and Washington University in St. Louis) and at the national and international levels (including Australia, England, India, Mexico [CIMMYT], and The Philippines [International Rice Research Institute]). Active research projects conducted by the drought community at MU include research funded by state, federal, commodity group (e.g. Missouri Soybean Merchandising Council, United Soybean Board, Cotton Inc.) and private (Monsanto, Syngenta) sources. Of particular note, members of the group were recently awarded over $1.5 million from the Missouri Life Sciences Research Board to establish “rainout shelters” that will allow control of precipitation under field conditions. The ability to manage the timing, duration, and intensity of water deficit stress under field conditions is essential to examine plant responses to drought and interactions of drought and biotic stresses in mid-western environments. The track record of excellence in drought research and the broad range of expertise of the interdisciplinary group provide fertile grounds for creative and productive research endeavors that are directed to optimize crop and woody plant biomass production