Digital Commons Network^™

Modified Soy Products And Methods For Reducing Odor And Improving Flavor Of Soy Products, William L. Boatright

Animal and Food Sciences Faculty Patents

A method for reducing odor in soy products and compositions containing soy products by adding or admixing a compound having one or more disulfide bonds to the soy product or composition. The disulfide compound includes a peptide containing at least cystine residue, a peptide or polypeptide containing at least one disulfide bond, L-cystine, D-cystine, DL-cystine and any combination thereof.

Checklist And Atlas Of The Vascular Flora Of West Virginia, Donna I. Ford-Werntz, Paul J. Harmon, William Grafton

WV Flora Datasets

No abstract provided.

Genomeblast: A Web Tool For Small Genome Comparison, Guoqing Lu, Liying Jiang, Resa M. K. Helikar, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko N. Moriyama

Nebraska Center for Virology: Faculty Publications

Background: Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.

Results: GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each …

Svm Classifier: A Comprehensive Java Interface For Support Vector Machine Classification Of Microarray Data, Mehdi Pirooznia, Youping Deng

Faculty Publications

Motivation

Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpose of this study is to create a GUI application that allows SVM users to perform SVM training, classification and prediction.

Results

The GUI provides user-friendly access to state-of-the-art SVM methods embodied in the LIBSVM implementation of Support Vector Machine. We implemented the java interface using standard swing libraries.

We used a sample data from a breast cancer study for testing classification accuracy. We achieved 100% accuracy in classification among the …

Development Of Computations In Bioscience And Bioinformatics And Its Application: Review Of The Symposium Of Computations In Bioinformatics And Bioscience (Scbb06), Youping Deng, Jun Ni, Chaoyang Zhang

Faculty Publications

The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21-22, 2006. Twenty-six peer-reviewed papers were selected for publication in this special issue of BMC Bioinformatics. These papers cover a broad range of topics including bioinformatics theories, algorithms, applications and tool development. The main technical topics contain gene expression analysis, sequence analysis, genome analysis, phylogenetic analysis, gene function prediction, molecular interaction and system biology, genetics and population study, immune strategy, protein structure prediction and proteomics.

Glycosylation Regulates Turnover Of Cyclooxygenase-2., Mary B. Sevigny, Chai-Fei Li, Monika Alas, Millie Hughes-Fulford

Natural Sciences and Mathematics | Faculty Scholarship

Cyclooxygenase-2 (COX-2) catalyzes the rate-limiting step in the prostanoid biosynthesis pathway, converting arachidonic acid into prostaglandin H(2). COX-2 exists as 72 and 74kDa glycoforms, the latter resulting from an additional oligosaccharide chain at residue Asn(580). In this study, Asn(580) was mutated to determine the biological significance of this variable glycosylation. COS-1 cells transfected with the mutant gene were unable to express the 74kDa glycoform and were found to accumulate more COX-2 protein and have five times greater COX-2 activity than cells expressing both glycoforms. Thus, COX-2 turnover appears to depend upon glycosylation of the 72kDa glycoform.

Functional Association Between Three Archaeal Aminoacyl-Trna Synthetases, Mette Praetorius-Ibba, Corinne D. Hausmann, Molly Paras, Theresa E. Rogers, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Aminoacyl-tRNA synthetases (aaRSs) are responsible for attaching amino acids to their cognate tRNAs during protein synthesis. In eukaryotes aaRSs are commonly found in multi-enzyme complexes, although the role of these complexes is still not completely clear. Associations between aaRSs have also been reported in archaea, including a complex between prolyl-(ProRS) and leucyl-tRNA synthetases (LeuRS) in Methanothermobacter thermautotrophicus that enhances tRNA^Pro aminoacylation. Yeast two-hybrid screens suggested that lysyl-tRNA synthetase (LysRS) also associates with LeuRS in M. thermautotrophicus. Co-purification experiments confirmed that LeuRS, LysRS, and ProRS associate in cell-free extracts. LeuRS bound LysRS and ProRS with a comparable K_{D …}

Standard-Level Herbivory In An Old-Growth Conifer Forest Canopy, David C. Shaw, Kristina A. Ernest, H. Bruce Rinker, Margaret D. Lowman

All Faculty Scholarship for the College of the Sciences

Herbivory is an important ecological process in forest canopies but is difficult to measure, especially for whole stands. We used the Wind River Canopy Crane in Washington State to access 101 randomly-located sample points throughout the forest canopy. This provided a relatively quick and convenient way to estimate herbivory for a whole stand. The overall level of herbivory was estimated at 1.6% of leaf area. The distribution was strongly skewed to the lower canopy where broad-leafed species experienced higher levels of herbivory. Herbivory averaged 0.3% in conifers and 13.5% in broad-leafed species. Fully half of the sample points had no …

Reproduction, Embryonic Development, And Maternal Transfer Of Contaminants In The Amphibian Gastrophryne Carolinensis, William Alexander Hopkins, Sarah Elizabeth Durant, Brandon Patrick Staub, Christopher Lee Rowe, Brian Phillip Jackson

Dartmouth Scholarship

Although many amphibian populations around the world are declining at alarming rates, the cause of most declines remains unknown. Environmental contamination is one of several factors implicated in declines and may have particularly important effects on sensitive developmental stages. Despite the severe effects of maternal transfer of contaminants on early development in other vertebrate lineages, no studies have examined the effects of maternal transfer of contaminants on reproduction or development in amphibians. We examined maternal transfer of contaminants in eastern narrow-mouth toads (Gastrophryne carolinensis) collected from a reference site and near a coal-burning power plant. Adult toads inhabiting …

Identifying Economic Indicators For Ecosystem-Based Management:, Scott Norris

Publications

In America and across the world, the use of ecosystem-based management is

increasing. One of the primary challenges faced in using this method of management is the integration of economic data and environmental information. This report explores the use of a new tool for integrating economic data, ecosystem-based economic indicators, in a case study of Elkhorn Slough National Estuarine Research Reserve, an estuarine environment located in Monterey County, CA. Research and literature reviews were used to detail the economic activities of the area, in order to identify possible indicators,criteria for evaluating the indicators, and potential sources of indicator data. After …

Evidence That Talin Alternative Splice Variants From Ciona Intestinalis Have Different Roles In Cell Adhesion, Richard H. Singiser, Richard O. Mccann

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Talins are large, modular cytoskeletal proteins found in animals and amoebozoans such as Dictyostelium discoideum. Since the identification of a second talin gene in vertebrates, it has become increasingly clear that vertebrate Talin1 and Talin2 have non-redundant roles as essential links between integrins and the actin cytoskeleton in distinct plasma membrane-associated adhesion complexes. The conserved C-terminal I/LWEQ module is important for talin function. This structural element mediates the interaction of talins with F-actin. The I/LWEQ module also targets mammalian Talin1 to focal adhesion complexes, which are dynamic multicomponent assemblies required for cell adhesion and cell motility. Although Talin1 is …

Living In A Land Of Fire, R. J. Whelan, P. Kanowski, M. Gill, A. Andersen

Faculty of Science - Papers (Archive)

Fires are an inherent part of the Australian environment. They cannot be prevented, but the risks they pose — to life, health, property and infrastructure, production systems, and to environment values — can be minimised through systematic evaluation and strategic planning and management. Fires have a fundamental and irreplaceable role in sustaining many of Australia’s natural ecosystems and ecological processes, and they are a valuable tool for achieving many land management objectives. However, if they are too frequent or too infrequent, too severe or too mild, or mistimed, they can erode ecosystem ‘health’ and biodiversity and compromise other land management …

Small Grains And Field Peas: 2007 Variety Recommendations (2006 Crop Performance Results), Cooperative Extension Service, South Dakota State University

SDSU Extension Circulars

Variety selection is a fundamental element in a sound crop production program. This report contains variety recommendations, descriptions, and yield data for the spring-seeded small grains – hard red spring wheat, oat, and barley, along with the fall-seeded small grain –hard red winter wheat. Key factors in variety selection include yield, yield stability, maturity, straw strength, height, test weight, quality, and disease resistance. Yield is an important factor; however, a variety with good disease resistance, straw strength, and high grain quality may be more profitable in some cases than the highest yielding variety. Disease resistance information is based on reactions …

Use Of Hidden Markov Models For Qtl Mapping, Karl W. Broman

Johns Hopkins University, Dept. of Biostatistics Working Papers

An important aspect of the QTL mapping problem is the treatment of missing genotype data. If complete genotype data were available, QTL mapping would reduce to the problem of model selection in linear regression. However, in the consideration of loci in the intervals between the available genetic markers, genotype data is inherently missing. Even at the typed genetic markers, genotype data is seldom complete, as a result of failures in the genotyping assays or for the sake of economy (for example, in the case of selective genotyping, where only individuals with extreme phenotypes are genotyped). We discuss the use of …

Linking Bioturbation And Sensory Biology: Chemoreception Mechanisms In Deposit-Feeding Polychaetes, Sara M. Lindsay, Paul Rawson

University of Maine Office of Research Administration: Grant Reports

Soft-sediment benthic habitats are ubiquitous in the marine environment and typically feature macrofaunal assemblages that include large numbers of deposit-feeding invertebrates such as polychaetes, bivalves, gastropods, crustaceans, holothurians, and hemichordates. Via their feeding, modulated in part by chemoreception, these organisms have profound effects on the ecology, biology, geology, and chemistry of their habitats. Very little is known, however, concerning the physiology and molecular biology of chemoreception in deposit feeders.

This research is a comprehensive investigation of the sensory mechanisms coordinating chemoreception in deposit feeding spionid polychaetes. It directly addresses this lack of information and will therefore have a significant impact …

Intsormil’S Global Impact: A Revolution In West African Sorghum Production, Intsormil

INTSORMIL Impacts and Bulletins

Sorghum and pearl millet are the staple grains for millions of people around the world, especially those residing in the semiarid margins of agricultural sustainability. For this reason, INTSORMIL has been working in the semiarid regions of Africa and Central America where it has been helping sorghum and millet farmers achieve the status of surplus grain production and the economic, social and health benefits thus provided. What impact has INTSORMIL had on the lives of these sorghum and millet farmers?

To determine the global impact of the USAID funded INTSORMIL program, Battelle, an independent agency, was chosen to conduct an …

A Comparative Study Of The Fractionation Of Regular Buttermilk And Whey Buttermilk By Microfiltration, Pierre Morin, Yves Pouliot, Rafael Jiménez-Flores

Dairy Science

The use of a ceramic microfiltration (MF) membrane for the fractionation of buttermilk and whey buttermilk obtained from pilot scale churning of cream and whey cream from industrial sources has been studied. Whey buttermilk contained comparable amounts of phospholipids compared to regular buttermilk but its protein content was lower due to the absence of caseins. However, it was found that lipid content of whey cream did vary significantly between lots resulting in important variations in the fat content of whey buttermilk. A twofold MF concentration of regular buttermilk doubled its phospholipids content whereas that of whey buttermilk was increased by …

Influence Of Ph And Heat Treatment Of Whey On The Functional Properties Of Whey Protein Concentrates In Yoghurt, Isabelle Sodini, Jerry Mattas, Phillip S. Tong

Dairy Science

Our aim was to investigate how two conditions of whey processing, pH and heat treatment, affect the physical properties of stirred yoghurts fortified to 45 g protein kg⁻¹ with whey protein concentrates (WPC). Cheddar whey was heated at pH 6.4 or pH 5.8 at 72 °C for 15 s, eventually heated further at 82 or 88 °C for 78 s, ultrafiltered, and spray dried. Resulting WPC contained 38% protein; the denaturation level of the whey protein was 10–53%. There were significant (P

Improved Monitoring Of Habs Using Autonomous Underwater Vehicles (Auv), Ian C. Robbins, G. J. Kirkpatrick, Shelley M. Blackwell, J. Hillier, Charles A. Knight, Mark A. Moline

Biological Sciences

Blooms of toxic algae are increasing in magnitude and frequency around the globe, causing extensive economic and environmental impacts. On the west coast of Florida, blooms of the toxic dinoflagellate Karenia brevis (Davis) have been documented annually for the last 30 years causing respiratory irritation in humans, fish kills, and toxin bioaccumulation in shellfish beds. As a result, methods need to be established to monitor and predict bloom formation and transport to mitigate their harmful effects on the surrounding ecosystems and local communities. In the past, monitoring and mitigation efforts have relied on visual confirmation of water discoloration, fish kills, …

Bovine Immune Response To Shiga-Toxigenic Escherichia Coli O157:H7, Mark A. Hoffman, Christian Menge, Thomas A. Casey, William Laegreid, Brad T. Bosworth, Evelyn A. Dean-Nystrom

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Although cattle develop humoral immune responses to Shiga-toxigenic (Stx⁺) Escherichia coli O157:H7, infections often result in long-term shedding of these human pathogenic bacteria. The objective of this study was to compare humoral and cellular immune responses to Stx⁺ and Stx^- E. coli O157:H7. Three groups of calves were inoculated intrarumenally, twice in a 3-week interval, with different strains of E. coli: a Stx2- producing E. coli O157:H7 strain (Stx2⁺O157), a Shiga toxin-negative E. coli O157:H7 strain (Stx^-O157), or a nonpathogenic E. coli strain (control). Fecal shedding of Stx2⁺O157 was …

Outcomes Of The Wetline Review. The Minister For Fisheries Proposed Decision For The Future Management Of The West Coast And Gascoyne Commercial 'Wetline' Fisheries, Department Of Fisheries Western Australia.

Fisheries management papers

This document details my proposed decisions regarding the new management arrangements for the West Coast and Gascoyne commercial “wetline” fisheries. Before finalising my position on the new management arrangements for these fisheries I invite any final comments on the proposed arrangements set out in this document. Although specific issues have been identified, your views are sought on any or all of the matters in the document of significance to you and/or your group.

Lpe Center News, December 2006

Livestock and Poultry Environmental Learning Center Newsletters

In this issue:

• Integrated Nutrient Management and Limits of the P-Index

• Pathogen Resources Available on the Website

• Quick Start Your Search with Dynamic Bibliographies

• Environmental Management Systems for Agriculture

Does Seed-Caching Experience Affect Spatial Memory Performance By Pinyon Jays?, B. Lucas Stafford, Russell P. Balda, Alan Kamil

Papers in Behavior in Biological Sciences

Food-storing birds use spatial memory to find previously cached food items. Throughout winter, pinyon jays (Gymnorhinus cyanocephalus) rely heavily on cached pinyon pine (Pinus edulis) seeds. Because of a recent severe drought, pinyon pine trees had not produced a significant seed crop for several years. Therefore, 1- and 2-year-old birds never had the opportunity to cache and recover seeds and birds 4 or more years of age had not recovered seeds in 3 years. This study examined whether natural but extreme variability in experience might result in differences in abstract spatial memory ability during a non-cache …

Southeast South Dakota Experiment Farm Annual Progress Report, 2006, Agricultural Experiment Station

Agricultural Experiment Station and Research Farm Annual Reports

This document highlights 24 crop and livestock research and demonstration reports from projects conducted at Southeast Research Farm in 2006. It is published by the South Dakota Agricultural Experiment Station and Cooperative Extension Service at South Dakota State University in cooperation with the Southeast South Dakota Experiment Farm Corporation. Reports in this document include information on: temperatures and precipitation data, corn production and performance, soybean research and planting, soil testing, alfalfa yield test, fertilizer testing, herbicide research, crop rotation, sorghum, small grains, livestock research, and pest and weed control.

Microarray Analysis Of Late-Season Velvetleaf (Abutilon Theophrasti) Effect On Corn, David P. Horvath, Robert Gulden, Sharon A. Clay

Agronomy, Horticulture and Plant Science Faculty Publications

Microarray analysis was used to identify changes in gene expression in corn leaves collected from plants at the V11–14 growth stage that resulted from competition with velvetleaf. The plants were grown in field plots under adequate N (addition of 220 kg N ha¹) and irrigation to minimize N and water stress. Consequently, only differences resulting from competition for micronutrients, light, and perhaps allelopathic stress were anticipated. Genes involved in carbon and nitrogen utilization, photosynthesis, growth and development, oxidative stress, signal transduction, responses to auxin and ethylene, and zinc transport were repressed in corn growing in competition with velvetleaf. …

Characterization Of Microbial Populations In The Subsurface, Mark P. Buttner, Patricia Cruz, Klaus J. Stetzenbach, Amy J. Smiecinski

Publications (YM)

This task is part of a cooperative agreement between the UNLV Research Foundation and the U.S. Department of Energy (#DE-FC28-04RW12237) titled “Yucca Mountain Groundwater Characterization”. The work was conducted in the Harry Reid Center for Environmental Studies, Microbiology Division of the University of Nevada, Las Vegas from October 1, 2004 to September 30, 2006. The overall goal of this research was to investigate the phenomena that affect the fate and transport of radionuclides in the environment. The purpose of this task (ORD-RF-01), “Characterization of Microbial Activity”, was to develop a molecular biological method for the characterization of the microbial population …

Evidence Of Influenza A Virus Rna In Siberian Lake Ice, Scott O. Rogers, Gang Zhang, Dany Shoham, David Gilchinsky, Sergei Davydov, John D. Castello

Biological Sciences Faculty Publications

Influenza A virus infects a large proportion of the human population annually, sometimes leading to the deaths of millions. The biotic cycles of infection are well characterized in the literature, including in studies of populations of humans, poultry, swine, and migratory waterfowl. However, there are few studies of abiotic reservoirs for this virus. Here, we report the preservation of influenza A virus genes in ice and water from high-latitude lakes that are visited by large numbers of migratory birds. The lakes are along the migratory flight paths of birds flying into Asia, North America, Europe, and Africa. The data suggest …

Signaling Through The Trail Receptor Dr5/Fadd Pathway Plays A Role In The Apoptosis Associated With Skeletal Myoblast Differentiation, J. O'Flaherty, Y. Mei, M. Freer, C. M. Weyman

Biological, Geological, and Environmental Faculty Publications

Apoptosis rather than differentiation is a physiological process during myogenesis and muscle regeneration. When cultured myoblasts were induced to differentiate, we detected an increase in caspase 8 activity. Pharmacological inhibition of caspase 8 activity decreased apoptosis. Expression of a dominant-negative mutant of the adapter protein FADD also abrogated apoptosis, implicating a death ligand pathway. Treatment with TRAIL, but not Fas, induced apoptosis in these myoblasts. Accordingly, treatment with a soluble TRAIL decoy receptor or expression of a dominant-negative mutant of the TRAIL receptor DR5 abrogated apoptosis. While TRAIL expression levels remained unaltered in apoptotic myoblasts, DR5 expression levels increased. Finally, …

Interview With Carol Mayer-Reed, Mayer/Reed, 2006 (Audio), Carol Mayer-Reed

All Sustainability History Project Oral Histories

Interview of Carol Mayer-Reed by Robyn Russnogle at on December 1st, 2006.

The interview index is available for download.

Communicator, Dec. 2006, San Jose State University, Department Of Kinesiology

Communicator (Kinesiology)

Volume 19, Issue 2