Life Sciences Commons^™

An Automated Method For Rapid Identification Of Putative Gene Family Members In Plants, Ronald L. Frank, Ajay Mane, Fikret Erçal

Biological Sciences Faculty Research & Creative Works

Background: Gene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences following duplication (adaptive selection) appears to be a common mechanism of evolution in plants and can be accompanied by purifying selection on the coding region. Such negative selection can be detected by a bias toward synonymous over nonsynonymous substitutions. However, the process of identifying this bias requires many steps usually employing several different software programs. We …

A Fourier Transformation Based Method To Mine Peptide Space For Antimicrobial Activity, Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, Mohamed O. Elasri, Youping Deng

Faculty Publications

Background

Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every living organism, it is possible to discover new candidate peptides using the available genomic and proteomic data. High throughput computational techniques could also be used to virtually scan the entire peptide space for discovering out new candidate antimicrobial peptides.

Result

We have identified a unique indexing method based on biologically distinct characteristic features of known antimicrobial peptides. Analysis of the entries in the antimicrobial peptide databases, based on our indexing method, using Fourier transformation …

Smokejumper Obituary: Henry, Edward L. (Missoula 1953), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Smokejumper Obituary: Casieri, Al (Missoula 1952), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Ecophysiology Of Two Native Invasive Woody Species And Two Dominant Warm-Season Grasses In The Semiarid Grasslands Of The Nebraska Sandhills, Kathleen D. Eggemeyer, Tala Awada, David A. Wedin, F. Edwin Harvey, Xinhua Zhou

School of Natural Resources: Faculty Publications

Populations of Pinus ponderosa and Juniperus virginiana are expanding into semiarid Sandhills grasslands in Nebraska. To evaluate the physiological basis of their success, we measured the seasonal course of leaf gas exchange, plant water status, and carbon isotope discrimination in these two native trees and two native C₄ grasses (Schizachyrium scoparium and Panicum virgatum). Compared to the trees, grasses had higher net photosynthetic rates (A_net) and water use efficiency (WUE) and more negative predawn and midday water potentials (Ψ) in June and July. While leaf Ψ and rates of leaf gas exchange declined for all …

Nitrate Accumulation And Movement Under Deficit Irrigation In Soil Receiving Cattle Manure And Commercial Fertilizer, D. D. Tarkalson, J. O. Payero, S. M. Ensley, Charles A. Shapiro

Department of Agronomy and Horticulture: Faculty Publications

Nitrate leaching from agricultural soils can increase groundwater nitrate concentrations. The objectives of the study were to assess the accumulation and movement of nitrate in the soil profile over a 2-year period under def¬icit irrigation conditions following a one time application of N in cattle feedlot manure and commercial fertilizer to corn at rates to achieve yield goals expected under conditions of full irrigation. Cattle manure and ammonium nitrate were applied in 2002 at the University of Nebraska recommended rate (1M and 1F, respectively) and cat¬tle manure was applied at twice the recommended rate (2M) for N for the 2002 …

Waterfowl Management Plan, Lake Restoration Task Force, Wade Worthen, Wes Dripps

Furman Lake Restoration Book Gallery

A six page document submitted by The Lake Restoration Task Force. The document lists the members of the task force, gives an overview of waterfowl overpopulation at the Furman Lake, goals for the future, and the strategy to solve this problem. The document provides a specific implementation plan and concludes with an assessment of the plan.

Testing An Ecophysiological Mechanism Of Morphological Plasticity In Pupfish And Its Relevance To Conservation Efforts For Endangered Devils Hole Pupfish, Sean C. Lema, Gabrielle A. Nevitt

Biological Sciences

Imperiled species that have been translocated or established in captivity can show rapid alterations in morphology and behavior, but the proximate mechanisms of such phenotypic changes are rarely known. Devils Hole pupfish (Cyprinodon diabolis) are endemic to a single desert pool and are characterized by a small body, large head and eyes, and lack of pelvic fins. To lessen the risk of extinction, additional populations of C. diabolis were established in artificial refuges. Yet, pupfish in these refuges rapidly shifted to a larger body, smaller head and eyes, and greater body depth. Here we examined how food availability …

Using The Balanced Scorecard For Ranch Planning And Management:Setting Strategy And Measuring Performance, Barry H. Dunn, Roger N. Gates, Jack Davis, Agustin Arzeno

SDSU Extension Circulars

The key to business success—whether operating a ranch or a Fortune 500 company—lies in management and planning. It’s the ability to have foresight, to carefully evaluate and choose appropriate new concepts and technologies, and to implement a well thought- out plan that complements all aspects of the business. The highly-respected former CEO and chairman of General Electric Jack Welch put it this way: Good business leaders create a vision, articulate the vision, passionately own the vision, and relentlessly drive it to completion. How does that description apply to you? Are you a visionary business leader for your ranch enterprise? Or …

Low Cell Ph Depresses Peak Power In Rat Skeletal Muscle Fibres At Both 30°C And 15°C: Implications For Muscle Fatigue, Shannon T. Knuth, H. L. W. Dave, Jim R. Peters, Robert H. Fitts

Biological Sciences Faculty Research and Publications

Historically, an increase in intracellular H⁺ (decrease in cell pH) was thought to contribute to muscle fatigue by direct inhibition of the cross-bridge leading to a reduction in velocity and force. More recently, due to the observation that the effects were less at temperatures closer to those observed in vivo, the importance of H⁺ as a fatigue agent has been questioned. The purpose of this work was to re-evaluate the role of H⁺ in muscle fatigue by studying the effect of low pH (6.2) on force, velocity and peak power in rat fast-and slow-twitch muscle fibres …

Diapause In Aquatic Invertebrates:What's Known And What's Next In Research And Medical Application?, Victor R. Alekseev, Jiang-Shiou Hwang, Mei-Hui Tseng

Journal of Marine Science and Technology–Taiwan

Dormancy is a profound and ancient adaptation found in a wide spectrum of plants and animals of all habitats. In diapause the switch between active and dormant states is driven by hormonal mechanism that usually includes a photoperiodic pace-maker. Temperature, food limitation and some other stress factors as well are shown as driven by diapause induction in aquatic invertebrates. In the last decade, diapause studies from a wide variety of topics have demonstrated that diapause switch mechanisms may be developed to create novel applications in biotechnology. Resting eggs accumulated in the surface lake sediments represent a “bank” of zooplankton species …

Girls' Perception Of Physical Environmental Factors And Transportation: Reliability And Association With Physical Activity And Active Transport To School, Kelly R. Evenson, Amanda Birnbaum, Ariane L. Bedimo-Rung, James Sallis, Carolyn C. Voorhees, Kimberly Ring, John P. Elder

Department of Public Health Scholarship and Creative Works

Background

Preliminary evidence suggests that the physical environment and transportation are associated with youth physical activity levels. Only a few studies have examined the association of physical environmental factors on walking and bicycling to school. Therefore, the purpose of this study was (1) to examine the test-retest reliability of a survey designed for youth to assess perceptions of physical environmental factors (e.g. safety, aesthetics, facilities near the home) and transportation, and (2) to describe the associations of these perceptions with both physical activity and active transport to school.

Methods

Test and retest surveys, administered a median of 12 days later, …

Microarray Profiling Of Skeletal Muscle Sarcoplasmic Reticulum Proteins, Jospeh S. Schulz, Nathan Palmer, Jon Steckelberg, Steven J. Jones, Michael G. Zeece

Department of Animal Science: Faculty Publications

Microarrays were developed to profile the level of proteins associated with calcium regulation in sarcoplasmic reticulum (SR) isolated from porcine Longissimus muscle. The microarrays consisted of SR preparations printed onto to glass slides and probed with monoclonal antibodies to 7 target proteins. Proteins investigated included: ryanodine receptor, (RyR), dihydropyridine receptor, (DHPR), triadin (TRI), calsequestrin (CSQ), 90 kDa junctional protein (JSR90), and fast-twitch and slow-twitch SR calcium ATPases (SERCA1 and SERCA2). Signal from a fluorescentlylabeled detection antibody was measured and quantitated using a slide reader. The microarray developed was also employed to profile Longissimus muscle SR proteins from halothane genotyped animals. …

Methods And Materials For Making And Using Transgenic Dicamba-Degrading Organisms, Donald P. Weeks, Xiao-Zhuo Wang, Patricia L. Herman

Department of Biochemistry: Faculty Publications

The invention provides isolated and at least partially-purified dicamba-degrading enzymes, isolated DNA molecules coding for dicamba-degrading enzymes, DNA constructs coding for dicamba-degrading enzymes, transgenic host cells comprising DNA coding for dicamba-degrading enzymes, and transgenic plants and plant parts comprising one or more cells comprising DNA coding for dicamba-degrading enzymes. Expression of the dicamba-degrading enzymes results in the production of dicamba-degrading organisms, including dicamba-tolerant plants. The invention further provides a method of controlling weeds in a field containing the transgenic dicamba-tolerant plants of the invention and a method of decontaminating a material containing dicamba comprising applying an effective amount of a …

Multiplatform Genome-Wide Identification And Modeling Of Functional Human Estrogen Receptor Binding Sites, Chin-Yo Lin, Vinsensius B. Vega, Koon Siew Lai, Li Say Kong, Min Xie, Xiaodi Su, Huey Fang The, Jane S. Thomsen, Ai Li Yeo, Wing Kin Sung, Guillaume Bourque, Edison T. Liu

Faculty Publications

Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. Results: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms …

R. B. Warren Arena Dedication

Department of Animal Science: Departmental News

Richard “R.B.” Warren was a member of the Animal Science Department, University of Nebraska-Lincoln, from 1956 to 1990. A Kansas native, R.B. graduated with a B.S. degree in Agriculture from Kansas State University and married Doris Kite in 1948. He completed an M.S. degree in Animal Breeding from Oklahoma State University in 1950 and served on the Animal Science faculty at Michigan State University for six years before coming to Nebraska. R.B. Warren enthusiastically developed young leaders for the animal industry through motivation, quality learning, skill development and personal mentoring. His legacy included one of the finest youth horse extension …

Two Glucose-Sensing Pathways Converge On Rgt1 To Regulate Expression Of Glucose Transporter Genes In Saccharomyces Cerevisiae, Jeong-Ho Kim, Mark Johnston

Faculty Publications

The yeast Saccharomyces cerevisiae deploys two different types of glucose sensors on its cell surface that operate in distinct glucose signaling pathways: the glucose transporter-like Snf3 and Rgt2 proteins and the Gpr1 receptor that is coupled to Gpa2, a G-protein α subunit. The ultimate target of the Snf3/Rgt2 pathway is Rgt1, a transcription factor that regulates expression of HXT genes encoding glucose transporters. We have found that the cAMP-dependent protein kinase A (PKA), which is activated by the Gpr1/Gpa2 glucose-sensing pathway and by a glucose-sensing pathway that works through Ras1 and Ras2, catalyzes phosphorylation of Rgt1 and regulates its function. …

Reflections On Wallace, Charles H. Smith

DLPS Faculty Publications

An unpublished paper has recently come to light, which shows that even at an early age, Alfred Russel Wallace was bold enough to approach the scientific establishment with his ideas.

A Unifying Approach For Haplotype Analysis Of Quantitative Traits In Family-Based Association Studies: Testing And Estimating Gene-Environment Interactions With Complex Exposure Variables, Stijn Vansteelandt, Christoph Lange

COBRA Preprint Series

We propose robust and e±cient tests and estimators for gene-environment/gene-drug interactions in family-based association studies. The methodology is designed for studies in which haplotypes, quantitative pheno- types and complex exposure/treatment variables are analyzed. Using causal inference methodology, we derive family-based association tests and estimators for the genetic main effects and the interactions. The tests and estimators are robust against population admixture and strati¯cation without requiring adjustment for confounding variables. We illustrate the practical relevance of our approach by an application to a COPD study. The data analysis suggests a gene-environment interaction between a SNP in the Serpine gene and smok- …

Erv26p Directs Pro-Alkaline Phosphatase Into Endoplasmic Reticulum–Derived Coat Protein Complex Ii Transport Vesicles, Catherine A. Bue, Christine M. Bentivoglio, Charles Barlowe

Dartmouth Scholarship

Secretory proteins are exported from the endoplasmic reticulum (ER) in transport vesicles formed by the coat protein complex II (COPII). We detected Erv26p as an integral membrane protein that was efficiently packaged into COPII vesicles and cycled between the ER and Golgi compartments. The erv26Δ mutant displayed a selective secretory defect in which the pro-form of vacuolar alkaline phosphatase (pro-ALP) accumulated in the ER, whereas other secretory proteins were transported at wild-type rates. In vitro budding experiments demonstrated that Erv26p was directly required for packaging of pro-ALP into COPII vesicles. Moreover, Erv26p was detected in a specific complex with pro-ALP …

Dna Molecules And Polypeptides Of Pseudomonas Syringae Hrp Pathogenicity Island And Their Uses: U.S. Patent No. Us 7,102,059 B2, Alan Collmer, James R. Alfano, Amy O. Charkowski

Department of Plant Pathology: Faculty Publications

One aspect of the present invention relates to isolated nucleic acid molecules (i) encoding proteins or polypeptides of Pseudomonas CEL and EEL genomic regions, (ii) nucleic acid molecules which hybridize thereto under stringent conditions, or (iii) nucleic acid molecules that include a nucleotide sequence which is complementary to the nucleic acid molecules of (i) and (ii). Expression vectors, host cells, and transgenic plants which include the DNA molecules of the present invention are also disclosed. Another aspect relates to the isolated proteins or polypeptides and compositions containing the same. The nucleic acid molecules and proteins of the present invention can …

In Vivo Mature Immunological Synapses Forming Smacs Mediate Clearance Of Virally Infected Astrocytes From The Brain, Carlos Barcia, Clare Thomas, James Curtin, Gwendalyn King, Kolja Wawrowsky, Marianela Candolfi, Weidong Xiong, Chunyan Liu, Kurt Kroeger, Olivier Boyer, Jerzy Kupiec-Weglinski, David Klatzmann, Maria Castro, Pedro Lowenstein

Articles

The microanatomy of immune clearance of infected brain cells remains poorly understood. Immunological synapses are essential anatomical structures that channel information exchanges between T cell–antigen-presenting cells (APC) during the priming and effector phases of T cells' function, and during natural killer–target cell interactions. The hallmark of immunological synapses established by T cells is the formation of the supramolecular activation clusters (SMACs), in which adhesion molecules such as leukocyte function-associated antigen 1 segregate to the peripheral domain of the immunological synapse (p-SMAC), which surrounds the T cell receptor–rich or central SMAC (c-SMAC). The inability so far to detect SMAC formation in …

Comparative Sequence Analysis And Tissue Localization Of Members Of The Slc6 Family Of Transporters In Adult Drosophila Melanogaster, Matthew S. Thimgan, Jonathan S. Berg, Ann E. Stuart

Biological Sciences Faculty Research & Creative Works

The SLC6 family comprises proteins that move extracellular neurotransmitters, amino acids and osmolytes across the plasma membrane into the cytosol. In mammals, deletion of SLC6 family members has dramatic physiologic consequences, but in the model organism Drosophila melanogaster, little is known about this family of proteins. Therefore, in this study we carried out an initial analysis of 21 known or putative SLC6 family members from the Drosophila genome. Protein sequences from these genes segregated into either well-defined subfamilies, including the novel insect amino acid transporter subfamily, or into a group of weakly related sequences not affiliated with a recognized …

Harina De Sorgo Como Sustituto Del Trigo En Panaderías Rurales De El Salvador, Intsormil

INTSORMIL Impacts and Bulletins

El grano de sorgo está generando mucho interés en el escenario de la comida sana. Por que? La respuesta es muy sencilla: la harina de grano de sorgo, NO CONTIENE GLUTEN. Esto es muy importante para aquellas personas intolerantes al gluten (padecimiento celíaco). El sorgo contiene un alto contenido de antioxidantes (que ayudan a prevenir el cáncer) y fibra insoluble (lenta digestibilidad), con cantidades relativamente pequeñas de fibra soluble. La proteína y el almidón del endospermo del sorgo son digeridos más lentamente si se les compara con otros cereales. El bajo porcentaje de digestibilidad en los productos preparados a base …

Sorghum Flour As A Substitute For Wheat In El Salvador Village Bakeries, Intsormil

INTSORMIL Impacts and Bulletins

Grain sorghum is generating new excitement on the health food scene. Why? For one reason, flour milled from grain sorghum has NO GLUTEN! That’s important to those people with an intolerance to gluten-containing products (Celiac disease). Sorghum is high in antioxidants (cancer prevention) and insoluble fiber (slowly digested), with relatively small amounts of soluble fiber. The protein and starch in sorghum endosperm are more slowly digested than other cereals. The slower rate of digestibility of sorghum products may be beneficial to diabetics.

So how is sorghum flour used in baking? It can be substituted for wheat, rice or soybean flour …

Direct And Correlated Effects Of Selection On Flight After Exposure To Thermal Stress In Drosophila Melanogaster, Robert A. Krebs, Kimberly A. Thompson

Biological, Geological, and Environmental Faculty Publications

To demonstrate how insects may adapt to ecologically relevant levels of heat stress, we performed artificial selection on the ability of Drosophila melanogaster to fly after an exposure to a high but non-lethal thermal stress. Both tolerance and intolerance to heat stress arose very quickly, as only a few generations of selection were necessary to cause significant separation between high and low lines for heat tolerance. Estimates of heritability based on the lines artificially selected for increased flight ability ranged from 0.024 to 0.052, while estimates of heritability based on the lines selected for the inability to fly after heat …

The Growing Together Guide: A Companion Resource To The New England Environmental Finance Center/Melissa Paly Film, New England Environmental Finance Center

Smart Growth

What local leader or public official wants to be faced with an SOS the “same old story” of public discord and confrontation over growth and development in one’s community? That situation has become a problem for efforts to promote smart growth. Investments are needed in the walkable, compact, traditional‐streetscape and mixed use neighborhoods and developments that are more sustainable and healthy than sprawl, for both people and the landscape. Yet attempts at such change all too often end up mired in costly public controversy and stalemate.

Smokejumper Obituary: Smith, George E. (Idaho City 1962), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

In Situ Muscle Power Differs Without Varying In Vitro Mechanical Properties In Two Insect Leg Muscles Innervated By The Same Motor Neuron, Anna N. Ahn, Kenneth Meijer, Robert J. Full

All HMC Faculty Publications and Research

The mechanical behavior of muscle during locomotion is often predicted by its anatomy, kinematics, activation pattern and contractile properties. The neuromuscular design of the cockroach leg provides a model system to examine these assumptions, because a single motor neuron innervates two extensor muscles operating at a single joint. Comparisons of the in situ measurements under in vivo running conditions of muscle 178 to a previously examined muscle (179) demonstrate that the same inputs (e.g. neural signal and kinematics) can result in different mechanical outputs. The same neural signal and kinematics, as determined during running, can result in different mechanical functions, …

Diversity Of The Ig Repertoire Is Maintained With Age In Spite Of Reduced Germinal Centre Cells In Human Tonsil Lymphoid Tissue, G. R. Kolar, D. Mehta, P. C. Wilson, J. D. Capra

Biological Sciences Faculty Research & Creative Works

Humans and almost all species studied to date exhibit a decreased responsiveness to immunization and increased autoimmunity with age. While this has been observed clinically for decades, only recently has an understanding of the molecular basis for these changes begun to be appreciated. Studies of the B-cell aspects of these changes in ageing mice and the very few reports in ageing humans have not been conclusive. Here we examine the nucleotide sequence of over 1250 VH transcripts from the tonsils of individuals of various ages for changes to the VH4 immunoglobulin repertoire. An exhaustive examination of VH, DH and JH …