Agricultural Science Commons^™

Microarray Based Comparison Of Two Escherichia Coli O157:H7 Lineages, Scot E. Dowd, Hiroshi Ishizaki

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

Background: Previous research has identified the potential for the existence of two separate lineages of Escherichia coli O157:H7. Clinical isolates tended to cluster primarily within one of these two lineages. To determine if there are virulence related genes differentially expressed between the two lineages we chose to utilize microarray technology to perform an initial screening.

Results: Using a 610 gene microarray, designed against the E. coli O157 EDL 933 transcriptome, targeting primarily virulence systems, we chose 3 representative Lineage I isolates (LI groups mostly clinical isolates) and 3 representative Lineage II isolates (LII groups mostly bovine isolates). Using standard dye …

Current Trends In Quarantine Entomology, Peter A. Follett, Lisa G. Neven

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

With world trade in agricultural commodities increasing, the introduction of exotic insects into new areas where they become pests will increase. The development and application of quarantine treatments or other mitigation approaches to prevent pest introduction in traded commodities raise many research and regulatory issues. The probit 9 standard for quarantine treatment efficacy has given way to risk-based alternatives. Varietal testing may have merit for some treatments or commodities but not for others. Development of generic treatments to control broad groups of insects or insects in all commodities can expedite new trade in agricultural products. Area-wide pest management programs lower …

Comparative Mapping Of Bovine Chromosome 27 With Human Chromosome 8 Near A Dairy Form Qtl In Cattle, E. E. Connor, M. S. Ashwell, R. Schnabel, J. L. Williams

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

In the absence of a complete and annotated bovine genome sequence, detailed human-bovine comparative maps are one of the most effective tools for identification of positional candidate genes contributing to quantitative trait loci (QTL) in cattle. In the present study, eight genes from human chromosome 8 were selected for mapping in cattle to improve breakpoint resolution and confirm gene order on the comparative map near the 40 cM region of the BTA27 linkage map where a QTL affecting dairy form had previously been identified. The resulting map identified ADRB3 as a positional candidate gene for the QTL contributing to the …

Application Of Machine Learning In Snp Discovery, Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curtis P. Van Tassell

Department of Agronomy and Horticulture: Faculty Publications

Background: Single nucleotide polymorphisms (SNP) constitute more than 90% of the genetic variation, and hence can account for most trait differences among individuals in a given species. Polymorphism detection software PolyBayes and PolyPhred give high false positive SNP predictions even with stringent parameter values. We developed a machine learning (ML) method to augment PolyBayes to improve its prediction accuracy. ML methods have also been successfully applied to other bioinformatics problems in predicting genes, promoters, transcription factor binding sites and protein structures. Results: The ML program C4.5 was applied to a set of features in order to build a SNP classifier …

Effects Of Substrate And Temperature On Growth Of Aspergillus Flavus In Peanuts From Georgia, Premila Achar, Andres Sachez

Faculty Articles

We investigated the effects of different substrates (potato dextrose agar [PDA], nutrient agar [NA], and corn meal agar [CMA]) and temperatures on growth and aflatoxin production in Aspergillus flavus. Contaminated peanuts from retailers at different locations in Georgia were used throughout the experiment and 200 seeds were selected from each sample. PDA, NA, and CMA served as the substrate to express the mold from the contaminated seeds. Seeds were plated equidistantly on each of the media and incubated at 10° C, 27° C, 30° C, and 37° C, respectively. Seeds incubated on moist filter paper served as control. Neither growth …

Chemical Composition And Response To Dilute-Acid Pretreatment And Enzymatic Saccharification Of Alfalfa, Reed Canarygrass, And Switchgrass, Bruce S. Dien, Hans-Joachim G. Jung, Kenneth P. Vogel, Michael D. Casler, Joann F. S. Lamb, Loren Iten, Robert C. Mitchell, Gautum Sarath

Department of Agronomy and Horticulture: Faculty Publications

Alfalfa stems, reed canarygrass, and switchgrass; perennial herbaceous species that have potential as biomass energy crops in temperate regions; were evaluated for their bioconversion potential as energy crops. Each forage species was harvested at two or three maturity stages and analyzed for carbohydrates, lignin, protein, lipid, organic acids, and mineral composition. The biomass samples were also evaluated for sugar yields following pretreatment with dilute sulfuric followed by enzymatic saccharification using a commercial cellulase preparation. Total carbohydrate content of the plants varied from 518 to 655 g kg^-1 dry matter (DM) and cellulose concentration from 209 to 322 g kg …

Mutations In Arabidopsis Yellow Stripe-Like1 And Yellow Stripe-Like3 Reveal Their Roles In Metal Ion Homeostasis And Loading Of Metal Ions In Seeds, Brian M. Waters, Heng-Hsuan Chu, Raymond J. Didonato, Louis A. Roberts, Robynn B. Eisley, Brett Lahner, David E. Salt, Elsbeth L. Walker

Department of Agronomy and Horticulture: Faculty Publications

Here, we describe two members of the Arabidopsis (Arabidopsis thaliana) Yellow Stripe-Like (YSL) family, AtYSL1 and AtYSL3. The YSL1 and YSL3 proteins are members of the oligopeptide transporter family and are predicted to be integral membrane proteins. YSL1 and YSL3 are similar to the maize (Zea mays) YS1 phytosiderophore transporter (ZmYS1) and the AtYSL2 iron (Fe)-nicotianamine transporter, and are predicted to transport metal-nicotianamine complexes into cells. YSL1 and YSL3 mRNAs are expressed in both root and shoot tissues, and both are regulated in response to the Fe status of the plant. β-Glucuronidase reporter expression, driven by …

Pumpkin Cultivar Evaluation, Northern Indiana, 2006, Elizabeth T. Maynard

Purdue Fruit and Vegetable Research Reports

"Pumpkins grown for Halloween and other decorative purposes continue to be an important crop for many Midwestern vegetable farmers. Breeders are developing new varieties with improved appearance and disease resistance. A trial was conducted to evaluate varieties."

Supersweet Sweet Corn Cultivar Evaluation For Northern Indiana, 2006, Elizabeth T. Maynard

Midwest Vegetable Trial Reports

The Indiana Agricultural Statistics Service reported sweet corn for fresh market sales was harvested from 5,200 acres in Indiana in 2005 and had a total value of $7.6 million. Sweet corn fields are located throughout the state. In Northern Indiana bicolor corn is most commonly grown. Varieties with improved eating quality are of interest to both producers and consumers. Producers are also interested in yield, ear size and appearance, and agronomic characteristics. This paper reports on twenty sh2 sweet corn cultivars known as ‘supersweet’ or ‘enhanced’ or ‘augmented supersweet’ that were evaluated at the Pinney-Purdue Ag Center, Wanatah, IN.

Pumpkin Cultivar Evaluation, Northern Indiana, 2006, Elizabeth T. Maynard

Midwest Vegetable Trial Reports

"Pumpkins grown for Halloween and other decorative purposes continue to be an important crop for many Midwestern vegetable farmers. Breeders are developing new varieties with improved appearance and disease resistance. A trial was conducted to evaluate varieties."

Sugar-Enhanced Sweet Corn Cultivar Evaluation For Northern Indiana, 2006, Elizabeth T. Maynard

Midwest Vegetable Trial Reports

The Indiana Agricultural Statistics Service reported sweet corn for fresh market sales was harvested from 5,200 acres in Indiana in 2005 and had a total value of $7.6 million. Sweet corn fields are located throughout the state. In Northern Indiana bicolor corn is most commonly grown. Varieties with improved eating quality are of interest to both producers and consumers. Producers are also interested in yield, ear size and appearance, and agronomic characteristics. This paper reports on eighteen sweet corn cultivars with homozygous se or mixed se and sh2 (synergistic) genetics that were evaluated at the Pinney-Purdue Ag Center, Wanatah, IN.

On-Farm Evaluation Of Tomato Cultivars For Disease Resistance, 2006, Dan Egel, Butch Zandstra, Elizabeth T. Maynard

Midwest Vegetable Trial Reports

Bacterial spot of tomatoes (Xanthomonas campestris pv. vesicatoria) causes lesions on leaves, stems and fruit. Under conditions of hot, humid, rainy weather, defoliation can result in a loss of yield. In addition, lesions on fruit result in a direct loss of marketability. This disease is managed primarily with applications of fixed copper bactericides, crop rotations, greenhouse sanitation and healthy seed/transplants. Even in properly managed commercial fields, however, bacterial spot can cause yield losses. Although there are no varieties with complete resistance to bacterial spot, we report here the results of an on-farm trial that indicates some varieties may have partial …

Sugar-Enhanced Sweet Corn Cultivar Evaluation For Northern Indiana, 2006, Elizabeth T. Maynard

Purdue Fruit and Vegetable Research Reports

The Indiana Agricultural Statistics Service reported sweet corn for fresh market sales was harvested from 5,200 acres in Indiana in 2005 and had a total value of $7.6 million. Sweet corn fields are located throughout the state. In Northern Indiana bicolor corn is most commonly grown. Varieties with improved eating quality are of interest to both producers and consumers. Producers are also interested in yield, ear size and appearance, and agronomic characteristics. This paper reports on eighteen sweet corn cultivars with homozygous se or mixed se and sh2 (synergistic) genetics that were evaluated at the Pinney-Purdue Ag Center, Wanatah, IN.

On-Farm Evaluation Of Tomato Cultivars For Disease Resistance, 2006, Dan Egel, Butch Zandstra, Elizabeth T. Maynard

Purdue Fruit and Vegetable Research Reports

Bacterial spot of tomatoes (Xanthomonas campestris pv. vesicatoria) causes lesions on leaves, stems and fruit. Under conditions of hot, humid, rainy weather, defoliation can result in a loss of yield. In addition, lesions on fruit result in a direct loss of marketability. This disease is managed primarily with applications of fixed copper bactericides, crop rotations, greenhouse sanitation and healthy seed/transplants. Even in properly managed commercial fields, however, bacterial spot can cause yield losses. Although there are no varieties with complete resistance to bacterial spot, we report here the results of an on-farm trial that indicates some varieties may have partial …

Supersweet Sweet Corn Cultivar Evaluation For Northern Indiana, 2006, Elizabeth T. Maynard

Purdue Fruit and Vegetable Research Reports

The Indiana Agricultural Statistics Service reported sweet corn for fresh market sales was harvested from 5,200 acres in Indiana in 2005 and had a total value of $7.6 million. Sweet corn fields are located throughout the state. In Northern Indiana bicolor corn is most commonly grown. Varieties with improved eating quality are of interest to both producers and consumers. Producers are also interested in yield, ear size and appearance, and agronomic characteristics. This paper reports on twenty sh2 sweet corn cultivars known as ‘supersweet’ or ‘enhanced’ or ‘augmented supersweet’ that were evaluated at the Pinney-Purdue Ag Center, Wanatah, IN.

Comparative Staging Of Embryo Development In Chicken, Turkey, Duck, Goose, Guinea Fowl, And Japanese Quail Assessed From Five Hours After Fertilization Through Seventy-Two Hours Of Incubation, N. Sellier, J.-P. Brillard, V. Dupuy, M. R. Bakst

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

Normal tables of chicken embryo development are used to define specific stages of morphogenetic progression from the first cleavage divisions through hatching. Although established for the turkey and Pekin duck, the application of the normal tables of chicken embryo development to other birds of commercial and research importance needs be examined. Chicken, turkey, Japanese quail, and Pekin duck blastoderms from oviductal eggs showed differences in the rate of development that were inversely correlated with egg size. Oviposited eggs from these and additional species (goose, Muscovy and mule ducks, and Guinea fowl) were examined after 24 to 72 h of storage …

Effect Of Fenbendazole On Turkey Semen Quality, M. R. Bakst, M. Kramer, J. Long

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

Fenbendazole (FBZ) is an anthelmintic recently approved to treat and control nematode infections in growing turkeys. When administered to growing turkeys there are no detrimental side effects. However, when we used FBZ to treat nematodes in mature breeder toms, we observed a decrease in semen quality and a subsequent precipitous decline in fertility to less than 20% within 6 wk of administration. An experiment was designed to determine the impact of FBZ administration on aspects of spermatogenesis and semen quality. We discovered that although sperm viability and concentration was not significantly affected by FBZ, this drug significantly reduced sperm mobility. …

Spermatogenesis In The Turkey (Meleagris Gallopavo): Quantitative Approach In Immature And Adult Males Subjected To Various Photoperiods, Jérôme Noirault, Jean-Pierre Brillard

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

The objectives of this study were to identify and quantitate the germ cell populations of the testes in sexually mature male turkeys (Trial 1), determine the duration of meiosis based on BrdU labeling and stereological analyses (Trial 2), and examine the impact of various photoperiods on germinal and somatic cell populations in immature and adult males (Trial 3). In Trial 1, both testes within a male had similar stereological components (P > 0.05) for all parameters analyzed. In Trial 2, the duration of Type-1 spermatocytes and round spermatids in turkeys lasted 4.5 ± 0.5 and 2.0 ± 0.5 days, respectively. In …

Characterization Of Storage Proteins In Wild (Glycine Soja) And Cultivated (Glycine Max) Soybean Seeds Using Proteomic Analysis, Savithiry S. Natarajan, Chenping Xu, Hanhong Bae, Thomas J. Caperna, Wesley M. Garrett

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

A combined proteomic approach was applied for the separation, identification, and comparison of two major storage proteins, β-conglycinin and glycinin, in wild (Glycine soja) and cultivated (Glycine max) soybean seeds. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) with three different immobilized pH gradient (IPG) strips was an effective method to separate a large number of abundant and less-abundant storage proteins. Most of the subunits of β-conglycinin were well separated in the pH range 3.0-10.0, while acidic and basic glycinin polypeptides were well-separated in pH ranges 4.0-7.0 and 6.0-11.0, respectively. Although the overall distribution pattern of the protein spots …

Separation And Identification Of Soybean Leaf Proteins By Two-Dimensional Gel Electrophoresis And Mass Spectrometry, Chenping Xu, Wesley M. Garrett, Joseph Sullivan, Thomas J. Caperna, Savithiry Natarajan

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

To establish a proteomic reference map for soybean leaves, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 260 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS. Fifty-three of these protein spots were identified by searching NCBInr and SwissProt databases using the Mascot search engine. Sixty-seven spots that were not identified by MALDI-TOF-MS analysis were analyzed with liquid chromatography tandem mass spectrometry (LC-MS/MS), and 66 of these spots were identified by searching against the NCBInr, SwissProt and expressed sequence tag (EST) databases. …

The Best Dna Markers Pennies Can Buy A Specialized Set Of Cattle Markers For Improving Food Safety And Beef Quality, Michael P. Heaton

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

Researchers at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska are developing a set of 100 DNA markers that will provide essential genetic information for improving food safety and beef quality in North American beef and dairy cattle. This powerful set of markers has been thoroughly screened to accomplish both DNA fingerprinting and parentage testing in essentially all U.S. beef and dairy populations, an ability that only a small fraction of known DNA markers have.

One key to success has been the careful sampling of U.S. beef and dairy populations to create a test panel representing the …

Dispersal Of Boll Weevils (Coleoptera: Curculionidae) From Cotton Modules Before Ginning, Thomas W. Sappington, Mark D. Arnold, Alan D. Brashears, Megha N. Parajulee, Stanley C. Carroll, Allen E. Knutson, John W. Norman Jr.

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

We characterized the level of risk of boll weevil, Anthonomus grandis grandis Boheman, reintroduction to an eradication zone posed by dispersal from cotton modules during and after transport to the gin. Mark-release-recapture experiments in August and September in Texas indicated that most weevils disperse rapidly from the module surface, temperature permitting, unless confined under a module tarp, where most died. Nevertheless, 1-5% of released weevils were recovered alive after 24 h on the side and top surfaces of modules, representing potential dispersants. Mortality of boll weevils caged on the top surface of a module was 95-100% after 1-4 d when …

Dispersal Of Newly Eclosed European Corn Borer Adults (Lepidoptera: Crambidae) From Corn Into Small-Grain Aggregation Plots, Brendon J. Reardon, Douglas V. Sumerford, Thomas W. Sappington

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

Genetically modified, insecticidal Bacillus thuringiensis (Bt) corn, Zea mays L., hybrids are used throughout the Corn Belt for European corn borer, Ostrinia nubilalis(Hübner) (Lepidoptera: Crambidae), control. To slow development of Bt corn resistance, the Environmental Protection Agency requires growers to plant a refuge. Determining the appropriate distance between a refuge and Bt corn, and development of mitigation-remediation strategies such as mass releases of susceptible moths, requires an understanding of adult dispersal and mating behavior. However, much remains unknown about these behaviors. Because mating often occurs in grass near cornfields where adult O. nubilalis aggregate, we planted small-grain plots as …

Impact Of Trap Design, Windbreaks, And Weather On Captures Of European Corn Borer (Lepidoptera: Crambidae) In Pheromone-Baited Traps, Thomas W. Sappington, Brendon J. Reardon, Douglas V. Sumerford

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

Pheromone-baited traps are often used in ecological studies of the European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae). However, differences in trap captures may be confounded by trap design, trap location relative to a windbreak, and changes in local weather. The objectives of this experiment were, first, to examine differences in O. nubilalis adult (moth) captures among the Intercept wing trap, the Intercept bucket/funnel UNI trap, and the Hartstack wire-mesh, 75-cm-diameter cone trap (large metal cone trap) as well as among three cone trap designs. Second, we examined the influence of the location of the large metal cone trap relative …

Usmarc Beef Carcass Instrument Grading Systems, Tommy Wheeler, Steven Shackelford, Mohammad Koohmaraie

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

Evaluation of Beef Carcass Grades with Image Analysis

Beef Tenderness

Post-Weaning Performance Of Steers From Varying Calving And Weaning Strategies In Montana, E. E. Grings, W. A. Phillips, R. E. Short, H. Mayeux, R. K. Heitschmidt

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

The impact of varied calving and weaning times on post-weaning production of steer calves was evaluated in a 3- yr study. Steers (approximately 12 steers per calving-weaning treatment per year) born in late winter or early spring were weaned at 190 or 240 d of age, and steers born in late spring were weaned at 140 or 190 d of age after grazing with their dams on native range. Steers were pen-fed a growing diet until approximately 375 kg BW. They were then moved to an individual feeding facility and fed a higher-energy diet. Steers were allotted to harvest dates …

Registration Of ‘Choptank’ Wheat, J.M. Costa, C.A. Griffey, H.E. Bockelman, S.E. Cambron, X. Chen, A. Cooper, C. Gaines, Robert A. Graybosch, A. Grybauskas, R.J. Kratochvil, D.L. Long, E. Shirley, L. Whitcher

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

‘Choptank’ (Reg. no. CV-976, PI 639724) is a soft red winter wheat (Triticum aestivum L.) that was jointly developed and released by the Maryland Agricultural Experiment Station, Department of Natural Resource Sciences and Landscape Architecture, and the Virginia Agricultural Experiment Station in 2004. Choptank is named after Maryland’s longest scenic river, which flows 70 miles from the western part of Delaware through Maryland and into the Chesapeake Bay, on Maryland’s Eastern Shore. Choptank has performed well in Maryland, Virginia, and Delaware and provides growers with a high-yielding cultivar with short stature, excellent powdery mildew [caused by Blumeria graminis (DC.) …

Traps And Trapping Techniques For Adult Mosquito Control, Daniel L. Kline

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

An overview is presented of the recent advancements in research activities conducted to evaluate mosquito traps. insecticide-impregnated targets baited with combinations of attractants, and strategies for using mass trapping techniques for adult mosquito population management. Technologies that use semiochemicals (attractants). traps and targets. and mass trapping are relatively new for management of adult mosquito populations. To date. emphasis has been placed primarily on developing barriers of attractant-baited and insecticide-impregnated targets. The most successful continuous use of this type of technology has been at Stevens' Landing. Collier County. Florida, Recently. commercially available traps have been evaluated for their ability to reduce …

Androthrips Ramachandrai (Thysanoptera: Phlaeothripidae): An Introduced Thrips In The United States, David W. Boyd, Jr., David W. Held

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

Androthrips ramachandrai Karny is an exotic thrips, assumed to be predacious, and is associated with gall-inducing thrips. It was first reported in the U.S. from FL, and intercepted in CA from Thailand in 2002. We surveyed Ficus spp. with Gynaikothrips-induced galls in AL, CA, FL, HI, LA, MS, and TX, and document that A. ramachandrai is now established in CA, FL, HI, and TX. It probably has been spread by the ornamental horticulture industry. We outline its biology and compare it to a congener A. flavipes, a documented thrips predator. Androthrips ramachandrai has the potential to be a …

Host Specificity Of Divergent Populations Of The Leaf Beetle Diorhabda Elongata (Coleoptera: Chrysomelidae), A Biological Control Agent Of Saltcedar (Tamarix Spp.), Lindsey R. Milbrath, C. Clark Deloach

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

The leaf beetle, Diorhabda elongata (Brullé) sensu lato, was released in 2001 for the classical biological control of exotic saltcedars, a complex of invasive Tamarix species and hybrids. It did not establish at sites south of 37°N latitude where summer daylengths are below the critical photoperiod of the northern-adapted populations of the beetle that were released. Therefore, we assessed the host specificity of four D. elongata populations collected from more southern latitudes in the Old World (Tunisia, Crete, Uzbekistan, and Turpan, China). All populations were similar to each other and the previously released populations of D. elongata in their …