Digital Commons Network^™

The Plant Ontology Database: A Community Resource For Plant Structure And Developmental Stages Controlled Vocabulary And Annotations, Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth Kellogg, Susan Mccouch, Anuradha Pujar, Leonore Reiser, Seung Rhee, Martin Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware

Biology Department Faculty Works

The Plant Ontology Consortium (POC, http://www.plantontology.org ) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC …

Comparison Of Plant Growth-Promotion With Pseudomonas Aeruginosa And Bacillus Subtilis In Three Vegetables, A. O. Adesemoye, M. Obini, E. O. Ugoji

Department of Plant Pathology: Faculty Publications

Our objective was to compare some plant growth-promoting rhizobacteria (PGPR) properties of Bacillus subtilis and Pseudomonas aeruginosa as representatives of their two genera. Solanum lycopersicum L. (tomato), Abelmoschus esculentus (okra), and Amaranthus sp. (African spinach) were inoculated with the bacterial cultures. At 60 days after planting, dry biomass for plants treated with B. subtilis and P. aeruginosa increased 31% for tomato, 36% and 29% for okra, and 83% and 40% for African spinach respectively over the non-bacterized control. Considering all the parameters tested, there were similarities but no significant difference at P < 0.05 between the overall performances of the two organisms.

Geographic Variation In The Pollination Biology Of Passiflora Lutea (Passifloraceae), J. Burks Holland, J. Lanza

Journal of the Arkansas Academy of Science

Like most species of Passiflora, P. lutea is reported to produce one-day flowers with complicated floral movements and requires deposition of non-self pollen for fruit production. Medium sized bees are the most likely pollinators in central Texas. We report on a series of observations and experimental manipulations that compare the reproductive biology of P. lutea in central Arkansas to that reported previously from plants about 800 km distant in central Texas. We observed floral movements and floral visitors, compared fruit production of flowers available to pollinators versus flowers from which pollinators were excluded, and compared fruit production of flowers that …

Algae In Agricultural Fields From St. Francis County, Arkansas, T. Smith

Journal of the Arkansas Academy of Science

On August 9th, 2007, two agriculture fields (rice and sorghum fields) were sampled for freshwater algae in St. Francis County. The purpose of this study was to document the algal species in the rice and sorghum fields and compare the similarities of species composition. There were a total of 53 species identified. Overall, diatoms and cyanobacteria were equally dominant with both represented by 21 species (39.6% of the total) and 11 green algal species (20.8%) were present. The sorghum field was dominated by Chlorogloeopsis fritschii and Chroococcus limneticus, while Anabeana cylindrica was abundant in the rice field.

Discrete Return Lidar-Based Prediction Of Leaf Area Index In Two Conifer Forests, Jennifer L. R. Jensen, Karen S. Humes, Lee A. Vierling, Andrew T. Hudak

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Leaf area index (LAI) is a key forest structural characteristic that serves as a primary control for exchanges of mass and energy within a vegetated ecosystem. Most previous attempts to estimate LAI from remotely sensed data have relied on empirical relationships between field-measured observations and various spectral vegetation indices (SVIs) derived from optical imagery or the inversion of canopy radiative transfer models. However, as biomass within an ecosystem increases, accurate LAI estimates are difficult to quantify. Here we use lidar data in conjunction with SPOT5-derived spectral vegetation indices (SVIs) to examine the extent to which integration of both lidar and …

The Small Glycine-Rich Rna Binding Protein Atgrp7 Promotes Floral Transition In Arabidopsis Thaliana, Corinna Streitner, Selahattin Danisman, Franziska Wehrle, Jan C. Schoning, James R. Alfano, Dorothee Staiger

Center for Plant Science Innovation: Faculty Publications

The RNA binding protein AtGRP7 is part of a circadian slave oscillator in Arabidopsis thaliana that negatively autoregulates its own mRNA, and affects the levels of other transcripts. Here, we identify a novel role for AtGRP7 as a flowering-time gene. An atgrp7-1 T-DNA mutant flowers later than wild-type plants under both long and short days, and independent RNA interference lines with reduced levels of AtGRP7, and the closely related AtGRP8 protein, are also late flowering, particularly in short photoperiods. Consistent with the retention of a photoperiodic response, the transcript encoding the key photoperiodic regulator CONSTANS oscillates with a similar pattern …

New And Current Microbiological Tools For Ecosystem Ecologists: Towards A Goal Of Linking Structure And Function, Rebecca E. Drenovsky, Kevin P. Ferris, Katharine M. Batten, Krassimira Hristova

Biology

Interest in the relationships between soil microbial communities and ecosystem functions is growing with increasing recognition of the key roles microorganisms play in a variety of ecosystems. With a wealth of microbial methods now available, selecting the most appropriate method can be daunting, especially to those new to the field of microbial ecology. In this review, we highlight those methods currently used and most applicable to ecological studies, including assays to study various aspects of the carbon and nitrogen cycles (e.g., pool dilution, acetylene reduction, enzyme analyses, among others), methods to assess microbial community composition (e.g., phospholipid fatty acid analysis …

Ultrastructural Alterations In Arabidopsis Thaliana Dj1c Null Mutant Cotyledons, Han Chen, J. L. Frey, Tara Nazarenus, Christian Elowsky, Julie M. Stone

Center for Plant Science Innovation: Faculty Publications

Increasing evidence suggests that deficits in mitochondrial function, oxidative and nitrosative stress, accumulation of aberrant or misfolded proteins, and ubiquitin-proteasome system dysfunction may represent the principal molecular pathways that commonly underlie the pathogenesis of neurodegenerative Parkinson’s disease (PD). Mutations in human DJ-1 lead to early onset PD. The subcellular distribution of DJ-1 (PARK7) is primarily cytoplasmic with smaller quantities found associated with mitochondria. Postulated functions include roles in the oxidative stress response, either as a redox sensor protein that can prevent the aggregation of alpha-synuclein or as an antioxidant. Homologs of DJ-1 are found in all kingdoms of life. To …

A History Of Woodland Dynamics In The Owyhee’S: Encroachment, Stand Closure, Understory Dynamics, And Tree Biomass, Rick Miller, Jaime Ratchford, Dustin Johnson

Reports

Piñon and juniper woodlands in the cold desert of the Intermountain West occupy over 44.6 million acres (Miller and Tausch 2001). These woodlands are commonly associated with sagebrush communities forming a mosaic of shrub-steppe and woodland across the region. Numerous studies have documented the recent expansion (since the late 1800’s) of these woodlands that has resulted in the replacement of shrub-steppe communities. Recent debate has challenged the degree of expansion in terms of percent of new areas occupied by trees and the increase in total population of piñon and juniper since the late 1800’s. Various interest groups have become concerned …

Discovery: The Student Journal Of Dale Bumpers College Of Agricultural, Food And Life Sciences - Volume 9 2008, Several Authors

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Center For Grassland Studies Newsletter, Winter 2008, Volume 14, No. 1

Center for Grassland Studies: Newsletters

Contents:

Organic Matter -- Should It Matter? A Golf Course Perspective by Roch Gaussoin, Department of Agronomy and Horticulture, UNL

UNL-USDA Study: Major Net Energy Gain from Switchgrass-based Ethanol

Using the Corn Stalk Grazing Calculator as a Decision Aid by Aaron Stalker, Department of Animal Science and Matt Stockton, Department of Agricultural Economics, West Central Research and Extension Center, UNL, North Platte

Avian Response to Invasive Tree Removal on Remnant Prairie Pastures in Southeast Nebraska by Elizabeth Forbus and Craig Allen, School of Natural Resources, UNL

Conserving Wildlife and A Way of Life: Conservancy Launches Grass Exchange Program

Instructions For Authors, Discovery Editors

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Terrestrial Habitat Use Of Marbled Salamanders Ambystoma Opacum: A Site Specific Approach, Frank Piccininni

Theses, Dissertations and Capstones

Habitat destruction, fragmentation and degradation have contributed heavily to the decline of amphibian populations such as Marbled Salamanders (Ambystoma opacum). Often, ambystomatid water resources are conserved without consideration for the equally important terrestrial habitat. This is partly due to a lack of information regarding the relationship between ecological succession, plant community composition, microhabitat and salamander abundance. Three sampling transects consisting of drift fence arrays, vegetation assessments and microhabitat surveys were extended 100 m into the terrestrial habitat surrounding a seasonal wetland at Beech Fork State Park in Wayne County, West Virginia. Principal components analysis was used to identify …

Nebraska Vine Lines, Volume Xi, Issue 3, June/July 2008

Nebraska Vine Lines (2003–2006)

EASTERN FIELD DAY WELL-RECEIVED

Sandell Highlights Weed Management

Excitement Building for the March 2009 Spring Forum - Save the Date March 5-7, 2009

TIMELY PEST MANAGEMENT

TIPS AND TENDRILS

FIELD DAY OPPORTUNITIES

Tentative Program

The Calendar

Around Nebraska in the University of Nebraska Viticulture Program

Future Nebraska Winery & GrapeGrowers Forums

Around the Country

2009

12th Annual Forum – March 5-7, 2009 Great Program Planned – Chien, Pierquet, Fennell, and more! Put this one on your calendar! Holiday Inn, Kearney, NE

More Evidence That Mutation Rate In The Chloroplast Genome Depends On Copy Number, Ashley Dutton

Undergraduate Honors Theses

The conservative nature of the copy variable region (CVR) of the chloroplast genome, also known as the inverted repeat (IR) region, is well established; however the basis for the lower mutation rate has been debated. Two ideas have been proposed to explain the reduced rate: 1) genes in the region are inherently slow to evolve; or 2) the presence of two copies reduces the rate via copy correction. Comparisons of eighty-three genes and twenty introns were made estimating mutation rates, from both the CVR region and single copy (SC) regions in legumes and gymnosperms. In gene and intron comparisons, CVR …

Seed Predation By Acanthoscelides Submuticus And A. Pallidipennis (Coleoptera: Bruchidae) In False Indigo In The Northern Great Plains, Arvid Boe, Paul J. Johnson

Native Plant Focused Publications

False indigo (Amorpha fruticosa L.) is a native North American leguminous shrub frequently found on shores of lakes and banks of rivers and streams in eastern and central United States and is present in 46 of the 48 contiguous states. It is planted for wildlife habitat, streambank erosion control, and ornamental purposes. Over several years, 16 collections of mature pods of false indigo were obtained from shorelines of four lakes and one cultivated planting in the northern Great Plains to determine frequency of pod predation by bruchid beetles. Frequency of pod predation by Acanthoscelides submuticus (Sharp) varied significantly among locations, …

Capturing Genetic Variation During Ecological Restorations: An Example From Kankakee Sands In Indiana, Rebecca W. Dolan, Deborah L. Marr, Andrew Schnabel

Scholarship and Professional Work - LAS

Genetic variation in populations, both natural and restored, is usually considered crucial for response to short term environmental stresses and for long term evolutionary change. To have the best chance of successful long-term survival, restored populations should reflect the extant variation found in remnants, but restored sites may suffer from genetic bottlenecks as a result of founder effects. Kankakee Sands is a large-scale restoration being conducted by The Nature Conservancy (TNC) in northwestern Indiana. Our goal was to test for loss of genetic variation in restored plant populations by comparing them with TNC’s seed source nursery and with local remnant …

Mullewa Research Annexe Spring Field Day Future Farming Systems For North-Eastern Districts 21 August 2008, Department Of Agriculture, Western Australia

Grain and other field crops research reports

Papers:

• Mullewa Research Annexe activities 2008

• Wheat for today and the future

• Consequences of strongly acidic and alkaline soils

• Break crop influence on low rainfall heavy soil

• Chemical fallow options for the north-east agricultural region

• Herbicide tolerance of new wheat varieties

• Lowrainfall oilseed crops for food and biofuel

• Utilising stock to reduce business risk in Binnu! A case study

Codling Moth Areawide Integrated Pest Management, Alan L. Knight

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

Codling moth (CM) is an insidious pest, tunnelling to the core of valuable commodities that are typically marketed with exceptional quality standards for appearance, firmness and sweetness. While there is no mention in the Bible of whether the apple that Eve gave to Adam graded 'Extra fancy', it is likely that if this fruit had been infested with CM, the human race would not be as anxious about returning to a pest-ridden garden of paradise. Nevertheless, since Noah allowed two adult CM to disembark from his boat, the distribution of this pest has closely followed man's cultivation of its hosts …

Impact Of Solar Ultraviolet-B On The Proteome In Soybean Lines Differing In Flavonoid Contents, Chenping Xu, Joe H. Sullivan, Wesley M. Garrett, Thomas J. Caperna, Savithiry Natarajan

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

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was used to systematically investigate the impact of solar ultraviolet- B (UV-B) radiation on the soybean leaf proteome. In order to investigate the protective role of flavonoids against UV-B, two isolines of the Clark cultivar (the standard line with moderate levels of flavonoids and the magenta line with reduced flavonoids) were grown in the field with or without natural levels of UV-B. The 12-day-old first trifoliates were harvested for proteomic analysis. More than 300 protein spots were reproducibly resolved and detected on each gel. Statistical analysis showed that 67 protein spots were significantly (P < 0.05) affected by solar UV-B. Many more spots were altered by UV-B in the magenta line than in the standard line. Another 12 protein spots were not altered by UV-B but showed significantly (P < 0.05) different accumulations between the two lines, and for most spots the line-specific differences were also observed under UV-B exclusion. Most of the differentially accumulated spots were identified by mass spectrometry. The proteins were quite diverse, and were involved in metabolism, energy, protein destination/storage, protein synthesis, disease/defense, transcription, and secondary metabolism. The results suggest that high levels of flavonoids lead to a reduction in UV-B sensitivity at the proteomic level.

Biotinyl-Methyl 4-(Amidomethyl)Benzoate Is A Competitive Inhibitor Of Human Biotinidase, Keyna Kobza, Kittichai Chaiseeda, Gautam Sarath, James M. Takacs, Janos Zempleni

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

Posttranslational modification of histones by biotinylation can be catalyzed by both biotinidase (BTD) and holocarboxylase synthetase. Biotinylation of histones is an important epigenetic mechanism to regulate gene expression, DNA repair, and chromatin remodeling. The role of BTD in histone biotinylation is somewhat ambiguous, given that BTD also catalyzes removal of the biotin tag from histones. Here, we sought to develop BTD inhibitors for future studies of the role of BTD in altering chromatin structure. We adopted an existing colorimetric BTD assay for use in a novel 96-well plate format to permit high-throughput screening of potential inhibitors. Biotin analogs were chemically …

Chapter 19. Remediation Of Drinking Water For Rural Populations, W. J. Hunter

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

Nitrate is the most common nitrogen contaminant in raw water supplies. In rural areas agricultural activities that involve the use of fertilizers and animal manures are major sources of nitrate contamination. Several processes are currently available that can effectively remove nitrate from raw water. Systems that are suitable for small rural communities include reverse osmosis, ion exchange, and electrodialysis. However, all of these systems move nitrate from raw water and concentrate it in a reject water or brine. Disposal of the reject water can be a major expense as well as an environmental issue. Several emerging systems are under development …

Auditing And Assessing Air Quality In Concentrated Feeding Operations, N. A. Cole, R. Todd, B. Auvermann, D. B. Parker

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

The potential adverse effects of concentrated animal feeding operations (CAFO) on the environment are a growing concern. The air quality issues of most concern to CAFO vary but generally include ammonia, hydrogen sulfide, particulate matter, volatile organic compounds, greenhouse gases, and odors. Air pollutants may be regulated by federal and state laws or by nuisance complaints. The United States Environmental Protection Agency, and poultry, swine, and dairy industries recently agreed to the National Air Emissions Monitoring System to fund research on atmospheric emissions from production farms in the United States. Air quality regulations may be based on actual emissions, atmospheric …

Evaluation Of Beef Cattle Operations Utilizing Different Seasons Of Calving, Weaning Strategies, Postweaning Management, And Retained Ownership, R. E. Kruse, M. W. Tess, E. E. Grings, R. E. Short, R. K. Heitschmidt, W. A. Phillips, H. S. Mayeux

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

Data from a 3-yr study in Montana were utilized to evaluate impacts of season of calving, weaning strategy, and retained ownership of steer calves on enterprise profitability. Calving seasons were late winter (LW), early spring (ES), or late spring (LS). Each season had 2 weaning times: 190 (LW190, ES190) or 240 (LW240, ES240) d for LW and ES, and 140 (LS140) or 190 (LS190) d for LS. Backgrounding options included shipping steers to Oklahoma (OK1), or backgrounding in Montana to a constant age (MT2) or weight (MT3). Steers from OK1 and MT2 were finished in Oklahoma in confinement or via …

Roles Of Micrornas In Plant Abiotic Stress, Development And Viral Infection, Venugopal Mendu

University of Kentucky Doctoral Dissertations

Plant microRNAs play important roles in plant growth and development. Here we investigated the roles of miRNAs in the plant abiotic stress, development and viral infection. MicroRNA membrane array analysis using five different abiotic stress treatments resulted in the identification of 8 novel stress inducible miRNA-families. Functional studies on novel stress inducible miR168 revealed its functional relation with abiotic stress. Over expression of miR168 in Arabidopsis showed upregulation of four stress related miRNAs (miR163, miR167, miR398 and miR408). Analysis of 9 independent transgenic lines showed induction of miR398, an oxidative stress responsive miRNA with a corresponding down regulation of its …

Map-Based Cloning Of An Anthracnose Resistance Gene In Medicago Truncatula, Shengming Yang

University of Kentucky Doctoral Dissertations

Anthracnose, caused by the fungal pathogen Colletotrichum trifolii, is one of the most destructive diseases of alfalfa worldwide. Cloning and characterization of the host resistance (R) genes against the pathogen will improve our knowledge of molecular mechanisms underlying host resistance and facilitate the development of resistant alfalfa cultivars. However, the intractable genetic system of cultivated alfalfa, owing to its tetrasomic inheritance and outcrossing nature, limits the ability to carry out genetic analysis in alfalfa. Nonetheless, the model legume Medicago truncatula, a close relative of alfalfa, provides a surrogate for cloning the counterparts of many agronomically important genes in …

Genetic Variability Of The European Corn Borer, Ostrinia Nubilalis, Suggests Gene Flow Between Populations In The Midwestern United States, Jeffrey T. Krumm, Thomas E. Hunt, Steven R. Skoda, Gary L. Hein, Donald J. Lee, Pete L. Clark, John E. Foster

Department of Entomology: Faculty Publications

The European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae), is a widely distributed and serious economic pest to corn production in the U.S. Genetic variability of O. nubilalis was studied in 18 sub-populations in the upper Midwestern United States using amplified fragment length polymorphism. The relatively low GST values indicate that more variation exists within populations than between populations. High gene flow (Nm) values were indicated across the entire O. nubilalis population; the lowest degree of gene flow was in the northern samples (Nm = 1.96) and the highest degree of gene flow was in the southern samples (Nm = …

Spiderwort Is Vnps Wildflower Of The Year, W. John Hayden

Biology Faculty Publications

The VNPS 2008 Wildflower of the Year (WOY) is spiderwort (Tradescantia virginiana). This herbaceous perennial plant occurs throughout much of the eastern portion of the U.S. and is widespread in Virginia. Spiderwort blooms from April to July. The small flowers occur in clusters at the ends of the stems, atop several elongate bracts. Flowers have three petals that range from purple to rose or, rarely, white. Densely hairy stamens provide, perhaps, the easiest way to recognize spiderworts. Also, stalks of spent flowers droop below the flower cluster yielding an aspect reminiscent of spindly spider legs.

Use Of Passive Integrated Transponders In Hatchling Texas Horned Lizards, Scott E. Henke

The Prairie Naturalist

The Texas horned lizard (Phrynosoma cornutum) is a Texas state-threatened species and acquisition of data related to the species' ecology is essential. To accomplish this task individual animals need to be marked. Many marking techniques are available for lizards, however the majority of techniques have been tested on adults only. Studies involving hatchling and juvenile horned lizards are scarce due to problems associated with marking and relocating individuals in these age classes. I demonstrated that injection of passive integrated transponders (PIT's) can safely be used as a marking method in young Texas horned lizards. Thirty-two captive bred hatchling lizards were …

Mortality Of An American Marten From An Off-Highway Vehicle, Joshua B. Smith, Jonathan A. Jenks

The Prairie Naturalist

While there are several reviews of the effects of OHVs and recreational activity on wildlife populations (Knight and Gutzwiller 1995, Joslin and Youmans 1999), most studies have focused on physiological (Creel et al. 2002) or behavioral (Van Dyke et al. 1986, Riley et al. 2003) responses to disturbance; none have addressed the potential for direct mortality. In 2005, we documented the death from an OHV of a juvenile, female American marten (F299) that had been radiocollared during a study documenting the distribution and abundance of American marten in the Black Hills, South Dakota (Smith 2007); the Institutional Animal Care and …