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Computational Identification Of Micro Rna In Musa Sp Est Sequences., Tan Yew Seong

Student Works (2010-2019)

MicroRNAs (miRNAs) are small single-stranded non-protein-coding RNAs of about 22 nucleotides that play an important role in post-transcriptional gene regulation in animals and plants by targeting mRNAs for direct cleavage of mRNAs or repression of mRNA translation. In this study, a homology search based approach has been used for identifying the novel miRNA genes of Musa sp. using the BLAST program with a total of 42,978 Musa sp. expressed sequence tags (EST) were compared to a total of 959 previously known plant miRNA sequences. Forty-seven candidate miRNA with homology to previously known miRNAs were identified. By using the mFold3.1 program, …

Sfa Gardens Newsletter, Winter 2010, Sfa Gardens, Stephen F. Austin State University

SFA Gardens Newsletters

No abstract provided.

Phosphorus For High Rainfall Pastures, Mike Bolland, Bill Russell, David Weaver

Bulletins 4000 -

Soil testing for phosphorus provides a reliable indication of when the level of phosphorus in a soil is likely to be adequate for pasture production in the next growing season. It is a waste of money to apply phosphorus fertiliser when soil testing indicates none is required, or to acidified soils, or to undergrazed pastures, or to pastures dominated by poorly productive species.

Legumes have higher phosphorus requirement than grasses.

Critical soil test phosphorus values do not change when nitrogen fertiliser is applied.

Seed Morphology Of Ebenus L. Species Endemic To Turkey, Fatma Bayrakdar, Zeki̇ Aytaç, Zeki̇ye Suludere, Selami̇ Candan

Turkish Journal of Botany

In the present study, seed surface morphology of species of the genus Ebenus L. in Turkey, all of which are endemic, was studied. E. plumosa var. speciosa has the biggest and E. laguroides var. laguroides has the smallest seeds. The seed shapes are spheroid in E. reesei, orbiculate in E. pisidica, and oblong-spheroid in others. Ornamentation is striate in E. macrophylla, rugose in E. haussknechtii, and reticulate or multi-reticulate in others. Microphylle is subterminal in all Turkish Ebenus species.

Russia’S Agricultural Imports: Will The High Growth Of The 2000s Continue?, William M. Leifert, Olga Liefert, Mathew Shane

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

Russia’s agricultural imports during the 2000s have grown substantially, from €7.4 billion in 2000 to €19.2 billion in 2007 (Figure 1). The import growth has made Russia the second largest agricultural importer among emerging market economies, after China. The main imports are meat, highly processed products, fruits and vegetables (Figure 2). Russia’s agricultural exports have also grown during this time, though from a much lower base in value terms (and with most of the increase coming just from grain).

Europe has benefited strongly from the rise in Russia’s agricultural imports. During this decade, Russia has been the EU’s second largest …

Drivers Impacting The Adoption Of Sustainable Agricultural Management Practices And Production Systems Of The Northeast And Southeast United States, G. F. Sassenrath, J. M. Halloran, D. Archer, R. L. Raper, J. Hendrickson, P. Vadas, J. Hanson

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

Agricultural production responds to social, political, economic, environmental, and technological drivers that influence producers’ decisions and shape the individual systems through modification of management practices, crop and livestock mix, and marketing strategy. We use an interview and discussion approach with producer panels to examine production systems in the eastern United States and explore key drivers impacting their unique characteristics and development. The internal social driver that values the farming lifestyle is a principle factor that leads people to choose farming. Irrespective of location, farming is first and foremost a lifestyle choice. The choice of type of production system is partly …

Cloning, Expression, And Immunogenicity Of Flavobacterium Columnare Heat Shock Protein Dnaj, Oscar Olivares-Fuster, Jeffery S. Terhune, Craig A. Shoemaker, Covadonga R. Arias

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

The Flavobacterium columnare heat shock protein (HSP) gene dnaJ* was isolated, cloned, expressed, and used as an antigen in a recombinant vaccine strategy for channel catfish Ictalurus punctatus. The F. columnare dnaJ* sequence was obtained from genomovars I and II and showed intraspecies variability. Recombinant protein was expressed and purified from Escherichia coli cultures and injected intraperitoneally (12 lg of purified DnaJ/fish) into fingerling channel catfish. In addition, induced (expressing the recombinant DnaJ) and uninduced (no recombinant protein being produced) E. coli cultures were also used to immunize fish. At 28 d postimmunization, antibody response was evaluated and the …

Comparisons Of Sperm Storage Tubule Distribution And Number In 4 Strains Of Mature Broiler Breeders And In Turkey Hens Before And After The Onset Of Photostimulation, M. R. Bakst, A. M. Donoghue, D. E. Yoho, J. R. Moyle, S. M. Whipple, M. J. Camp, G. Q. Liu, R. K. Bramwell

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

The biological basis of sustained fertility in broiler and turkey hens is their capacity to store sperm in the oviductal sperm storage tubules (SST) located in the uterovaginal junction. The objectives of this study were to determine if the numbers of SST varied between 4 strains of broiler breeders and determine the number of SST in the turkey before (less than 9 d of photostimulation) and after (up to 22 d of photostimulation and laying) photostimulation. No statistical differences were observed in SST numbers in the 4 strains of broilers examined or in turkey hens before and after the onset …

Identification Of Protein Carbonyls In Serum Of The Fetal And Neonatal Pig, Thomas J. Caperna, Amy E. Shannon, Le Ann Blomberg, Wesley M. Garrett, Timothy G. Ramsay

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

Oxidation of serum proteins leads to non-reversible carbonyl formation which alters their function and is associated with stress-related disease processes. The primary objective of this study was to quantify and identify oxidized serum proteins in fetal and newborn piglets. Protein carbonyls were converted to hydrazones with dinitrophenyl hydrazine and quantified spectrophotometrically. For identification, serum protein carbonyls were derivatized with biotin hydrazide, separated by 2D PAGE and stained with FITCavidin. Biotin-labeled proteins were excised from gels and identified by mass spectrometry. At birth, carbonyls were determined to be ∼600 pmole/mg serum protein. Fetuses at 50 and 100 days of gestation had …

Volatiles Emitted From Eight Wound-Isolated Bacteria Differentially Attract Gravid Screwworms (Diptera: Calliphoridae) To Oviposit, M. F. Chaudhury, Steven R. Skoda, A. Sagel, J. B. Welch

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

Bovine blood inoculated with bacteria isolated from screwworm [Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae)]-infested animal wounds was tested as an attractant for oviposition for gravid screwworms. Eight species of gram-negative coliform (Enterobacteriaceae) bacteria mixed with bovine blood singly or all species combined and incubated for various times produced volatiles that attracted gravid flies in a cage bioassay in varying numbers. In 15-min duration tests, volatiles from five species of bacteria (Klebsiella oxytoca, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii) attracted more females than volatiles of the three species (Enterobacter cloacae, Enterobacter …

2010 Across-Breed Epd Table, Larry Kuehn, Mark Thallman

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

The table of adjustment factors to be used to estimate across-breed expected progeny differences (AB-EPDs) for eighteen breeds was presented at the Beef Improvement Federation Annual Meeting in Columbia, MO, on June 30 (see Table 1). Across-breed adjustment factors have been calculated for growth traits and maternal milk since 1993. Adjustment factors for carcass traits have been calculated since 2008; to be included, breeds must have carcass data in the U.S. Meat Animal Research Center (USMARC) database and report their carcass EPDs on an actual carcass basis using an age-adjusted endpoint. Bulls of different breeds can be compared on the …

Effects Of Prescribed Fire And Herbicide Application On Cattle Grazing And Herbage Production From Yellow Bluestem Pastures, S. A. Gunter, R. L. Gillen

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

Forage management practices influence the quantity and quality of forage available to grazing cattle. The objectives of this experiment were to determine the effects of prescribed fire or herbicides on the density of forbs, the production and nutritive value of the herbage, and the performance of beef steers grazing Yellow bluestem [Bothriochloa ischaemum (L.) Keng var. ischaemum (Hack.) Celarier and Harlan] pastures. The experiment was conducted in northwestern Oklahoma from 1998 through 2000, and the untreated pastures (control) were not burned or sprayed. The prescribed-fire treatment (PFT) occurred annually between March 27 and April 10. The herbicide treatment (HT) consisted …

Expression And Self-Assembly Of Virus-Like Particles From Two Genotypes Of Marine Vesiviruses And Development Of An Elisa For The Detection Of Antibodies, Shasta D. Mcclenahan, Karin Bok, Stanislav V. Sosnovtsev, John D. Neill, Kathy A. Burek, Kimberlee B. Beckmen, Alvin W. Smith, Kim Y. Green, Carlos H. Romero

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

Sequences encoding the major and minor capsid proteins (VP1 and VP2) from two marine vesivirus isolates (Steller sea lion viruses V810 and V1415) were engineered for expression of virus-like particles (VLPs) in the baculovirus system. The resulting VLPs were morphologically similar to native vesivirus virions. Purified VLPs were probed in immunoblots with pooled antisera specific for nine San Miguel sea lion virus (SMSV) types, and a predominant protein of approximately 60 kDa was detected. An enzyme linked immunosorbent assay (ELISA) for the detection of antibodies was developed in which the VLPs served as antigen. The VLPs were adsorbed to the …

Optimized Construction Of Microsatellite-Enriched Libraries, Natascha Techen, R. S. Arias, Neil C. Glynn, Zhiqiang Pan, Ikhlas A. Khan, Brian E. Scheffler

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

The construction of microsatellite-enriched libraries is an indispensable tool to search for molecular markers as complete genome sequences are still not available for the majority of species of interest. Numerous protocols are available in the literature for the construction of these libraries; however, sometimes their low efficiency or lack of optimization in the protocols can restrict their efficacy. We have designed and tested various adapters and ligation methods; we also tested oligo-repeat combinations and hybridization temperatures, and created libraries with this new protocol for four organisms: Ipomoea batatas (L.) Lam, Chionanthus retusus Lindley & Paxton, Rotylenchulus reniformis Linford & Olivera …

Potential For Stable Flies And House Flies (Diptera: Muscidae) To Transmit Rift Valley Fever Virus1, Michael J. Turell, David J. Dohm, Christopher J. Geden, Jerome A. Hogsette, Kenneth Linthicum

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

Rift Valley fever (RVF), a disease of ruminants and humans, has been responsible for large outbreaks in Africa that have resulted in hundreds of thousands of human infections and major economic disruption due to loss of livestock and to trade restrictions. As indicated by the rapid spread of West Nile viral activity across North America since its discovery in 1999 and the rapid and widespread movement of chikungunya virus from Africa throughout the Indian Ocean Islands to Asia and Europe, an introduced exotic arbovirus can be rapidly and widely established across wide geographical regions. Although RVF virus (RVFV) is normally …

Efficacy Of Commercial Mosquito Traps In Capturing Phlebotomine Sand Flies (Diptera: Psychodidae) In Egypt, D. F. Hoel, D. L. Kline, Jerome Hogsette, Ulrich R. Bernier, S. S. El-Hossary, H. A. Hanafi, N. Watany, E. Y. Fawaz, B. D. Furman, P. J. Obenauer, D. E. Szumlas

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

Four types of commercial mosquito control traps, the Mosquito Magnet Pro (MMP), the Sentinel 360 (S360), the BG-Sentinel (BGS), and the Mega-Catch Ultra (MCU), were compared with a standard Centers for Disease Control and Prevention (CDC) light trap for efficacy in collecting phlebotomine sand flies (Diptera: Psychodidae) in a small farming village in the Nile River Valley 10 km north of Aswan, Egypt. Each trap was baited with either carbon dioxide (CO₂) from combustion of butane gas (MMP), dry ice (CDC and BGS traps), light (MCU and S360), or dry ice and light (CDC). Traps were rotated through …

A Quantitative Phosphorus Loss Assessment Tool For Agricultural Fields, Michael J. White, Daniel E. Storm, Philip R. Busteed, Michael D. Smolen, Hailin Zhang, Garey A. Fox

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

In the United States, government sponsored conservation programs are under increasing pressure to quantify the environmental benefits of practices they subsidize. To meet this objective, conservation planners need tools to accurately predict phosphorus (P) loss from agricultural lands. Existing P export coefficient based tools are easy to use, but do not adequately account for local conditions. Hydrologic and water quality models are more accurate, but are prohibitively complex for conservation planners to use. Pasture Phosphorus Management (PPM) was developed as a user-friendly P and sediment loss prediction tool based on the Soil and Water Assessment Tool (SWAT), a popular comprehensive …

Comparison Of Broiler Litter And Commercial Fertilizer At Equivalent N Rates On Soil Properties, Ardeshir Adeli, Haile Tewolde, Karamat Sistani, Dennis Rowe

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

A 3-year study was conducted to determine the effects of broiler litter relative to inorganic fertilizer on soil nutrient content and quality in an upland Loring silt loam soil. Treatments included annual broiler litter rates of 0, 2.2, 4.5, 5.6, 6.7, 10.1, and 13.4 Mg ha⁻¹ y⁻¹ and commercial fertilizer rates of 34, 68, 90, 112, 134, and 168 kg nitrogen (N) ha⁻¹ y⁻¹. Broiler litter application linearly increased soil total carbon (C), microbial biomass C, extractable soil phosphorus (P), potassium (K), soil cation exchange capacity (CEC), and the stability of soil aggregate. At the …

Overseeding Unimproved Warm-Season Pasture With Cool- And Warm-Season Legumes To Enhance Forage Productivity, P. W. Bartholomew, R. D. Williams

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

Overseeding forage legumes into existing warm-season pasture may help to reduce cool-season forage deficit on small and resource-limited small farms in the southern Great Plains of the United States. Unimproved warm-season grass pastures were overseeded with Korean lespedeza (Lespedeza stipulacea Maxim) were not overseeded with summer legume. These same plots were subsequently overseeded with hairy vetch (Vicia villosa Roth), crownvetch (Coronilla varia L.), black medic (Medicago lupulina L.) or ladino white clover (Trifolium repens L.) or, not overseeded with cool-season legume. Including lespedeza in a forage mixture increased total forage yield by an average of …

Soil Organic Matter Fractions And Aggregate Distribution In Response To Tall Fescue Stands, I. P. Handayani, Mark S. Coyne, R. S. Tokosh

Plant and Soil Sciences Faculty Publications

The study was conducted to evaluate the influences of tall fescue management on soil organic matter fractions and macro- and microaggregate distribution. Soil samples were collected from four paired adjacent fields consisting of five years of tall fescue mono and poly stands in Western Kentucky. Soil samples from 0 to 15 cm and 15 to 30 cm soil depths were analyzed for soil organic C and N, particulate organic matter C (POM-C) and N (POM-N), macro- and micro aggregate distribution and C-associated with macro- and micro- aggregates. Significant effects were observed between stands for all the properties, except total C, …

Agronomic Performance Of Five Varieties Of Forage Grasses Inroduced In Carmen Pampa, Province Of Nor Yungas, La Paz, Joel Eliseo Bautista Vargas

Theses and Dissertations

This study was done with the objective of evaluating the agronomic performance of five varieties of forage grasses introduced to the community of Carmen Pampa in the province of Nor Yungas, La Paz from 2005-2006. The average temperature during the study was 11.93ºC and the average precipitation was 801.75 mm. The trial was done with a design of randomized blocks having five species and six repetitions. The species studied were: Panicum virgatum, Sorghastrum nutans, Andropogon gerardii, Tripsacum dactyloides, and Eragrostis curvula. Variables evaluated were: plant height (cm), coverage (%), number of plants, bunches of florets, and dry matter yield (kg/ha). …

Dryland Performance Of Sweet Sorghum And Grain Crops For Biofuel In Nebraska, Charles S. Wortmann, Adam Liska, Richard B. Ferguson, Drew J. Lyon, R. N. Klein, Ismail M. Dweikat

Department of Agronomy and Horticulture: Faculty Publications

Sweet sorghum [SS; Sorghum bicolor (L.) Moench] is a potential biofuel crop for the Great Plains. Sweet sorghum was compared with corn [Zea mays (L.)] and grain sorghum for potential ethanol yield, energy use effi ciency, and greenhouse gas (GHG) emissions at seven dryland site-years in Nebraska. Seasonal rainfall ranged from approximately 340 to 660 mm. Soils were deep with medium texture at all site-years. Th e eff ects of seeding rate, N rate, and cultivar on SS performance were evaluated. Sweet sorghum sugar yield was not aff ected by seeding rate and N application at six of seven …

Emissions Savings In The Corn-Ethanol Life Cycle From Feeding Coproducts To Livestock, Virgil R. Bremer, Adam Liska, Terry J. Klopfenstein, Galen E. Erickson, Haishun Yang, Daniel T. Walters, Kenneth G. Cassman

Department of Agronomy and Horticulture: Faculty Publications

Environmental regulations on greenhouse gas (GHG) emissions from corn (Zea mays L.)-ethanol production require accurate assessment methods to determine emissions savings from coproducts that are fed to livestock. We investigated current use of coproducts in livestock diets and estimated the magnitude and variability in the GHG emissions credit for coproducts in the corn-ethanol life cycle. The coproduct GHG emissions credit varied by more than twofold, from 11.5 to 28.3 g CO₂e per MJ of ethanol produced, depending on the fraction of coproducts used without drying, the proportion of coproduct used to feed beef cattle (Bos taurus …

Spring Grazing Impacts On The Vegetation Of Reed Canarygrass–Invaded Wetlands, Heidi Hilhouse, Susan J. Tunnell, James L. Stubbendieck

Department of Agronomy and Horticulture: Faculty Publications

The Rainwater Basin region in Nebraska is critically important stopover habitat for spring waterfowl migrations, but the ability of these sites to produce sufficient food for migrating waterfowl is endangered by the invasion of reed canarygrass (Phalaris arundinacea L.). This species produces thick litter layers and abundant aboveground biomass, reducing germination and seedling survival of the annual plant species responsible for much of the seed production in the area. Cattle grazing often is used as a management tool in the Rainwater Basin to slow or reverse reed canarygrass invasion and to improve growing conditions for more desirable plant species. …

Economic Potential Of Substituting Legumes For Synthetic Nitrogen In Warm Season Perennial Grasses Used For Stocker Cattle Grazing, Maru Kering, John Biermacher, Ryan Reuter, Twain Butler, Job D. Springer, James Rogers, John Blanton, Joe Bouton, John A. Guretzky

Department of Agronomy and Horticulture: Faculty Publications

Stocker cattle grazing warm season perennial grasses is an important economic activity in the southern Great Plains. Substantial increases in the price of nitrogen fertilizer is negatively affecting forage producers‟ profitability. Two alternative nitrogen management systems that use annual and perennial legumes have been developed for bermudagrass pastures. The goal of the study is to determine if the legumes systems are more profitable than the conventional practice of applying synthetic sources of nitrogen. Results of the two-year grazing study show that the legume systems could not compete economically with the common practice.

Fertilizer Rate Effects On Forage Yield Stability And Nutrient Uptake Of Midland Bermudagrass, John A. Guretzky, Maru K. Kering, Jagadeesh Mosali, Eddie Funderburg, Jon T. Biermacher

Department of Agronomy and Horticulture: Faculty Publications

Our objectives were to document effects of nitrogen (N), phosphorus (P), and potassium (K) fertilizer rates on forage yields and uptake of N, P, and K by Midland bermudagrass [Cynodon dactylon (L.) Pers.] on a Minco fine, sandy loam in southern Oklahoma. After six years of this long-term experiment, forage yield responses to fertilization were mixed and depended on year. Stability analysis indicated forage yields responded positively to N fertilization during favorable weather conditions but negatively during poor weather conditions. Application of 112 kg N ha⁻¹ provided the best yield stability and mean annual forage yield among treatments, …

Factors Affecting The Alkaline Cooking Performance Of Selected Corn And Sorghum Hybrids, Weston B. Johnson, Wajira S. Ratnayake, David S. Jackson, Kyung-Min Lee, Timothy J. Herrman, Scott R. Bean, Stephen Mason

Department of Agronomy and Horticulture: Faculty Publications

Dent com (Zea mays L.) and sorghum (Sorghum hieolor L. Moench) sample sets representative of commonly grown hybrids and diverse physical attributes were analyzed for alkaline cooking performance. The influence of kernel characteristics including hardness, density, starch properties (thermal. pasting, and crystallinity). starch content. protein content. and prolamin content on alkaline cooking performance was also determined. Com nixtamal moisture content was lower for hard, dense kernels with high protein contents; sorghum nixtamal moisture content was lower for kernels with low moisture contents and low starch relative crystallinities. Statistically significant (P < 0.05) regression equations showed that com nixtamal moisture content was influenced by TADD (tangential abrasive dehulling device) index. kernel moisture content. starch content. and protein content; sorghum nixtamal moisture content was influenced by starch relative crystallinity. kernel moisture content, and abrasive hardness index. Pericarp removal was not strongly correlated with kernel characterization tests. Location (environmental) and hybrid (genetic) factors influenced most kernel characteristics and nixtamalization processing variables.

Evaluation Of The Intercom Model For Predicting Growth Of Forest Herbs, Zorica S. Popović, J. L. Lindquist

Department of Agronomy and Horticulture: Faculty Publications

The ecophysiological model INTERCOM was evaluated for its suitability in predicting the growth of perennial forest herbs. A field experiment was conducted to obtain data on photosynthesis and growth parameters of two spring flowering understorey geophytes. Results were used to parameterize the model and its performance was evaluated using the average normalized difference (AE) between predicted and observed biomass and the leaf area index. The model was assumed to provide accurate simulations if the AE was smaller than 0.4. Adjusting the photosynthetic intensity parameters in the model to reflect observed changes in photosynthesis throughout the growing period resulted in the …

Spring Seed Guide 2010: Nebraska Variety And Hybrid Tests -- Soybeans, Teshome Regassa, Robert N. Klein, Bruce Anderson, Charles A. Shapiro, Jim Krall

Department of Agronomy and Horticulture: Faculty Publications

NEBRASKA SOYBEAN VARIETY TESTS 2009

Crop Production Summary: The November 2009 estimated soybean yield for Nebraska was 52 bushels per acre from 4.800 million harvested acres. The total production of soybeans for the state was forecasted at 247 million bushels. These estimates are from the November National Agricultural Statistics Service.

Efficacy Of Singular And Stacked Brown Midrib 6 And 12 In The Modification Of Lignocellulose And Grain Chemistry, Scott E. Sattler, Deanna L. Funnell-Harris, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

In sorghum, brown midrib (bmr) 6 and 12 impair the last two steps of monolignol synthesis. bmr genes were introduced into grain sorghum to improve the digestibility of lignocellulosic tissues for grazing or bioenergy uses following grain harvest. Near-isogenic grain sorghum hybrids (AWheatland X RTx430) were developed containing bmr6, bmr12, and the bmr6 bmr12 double mutant (stacked), and their impacts were assessed in a two-year field study. The bmr genes did not significantly impact grain or lignocellulosic tissue yield. Lignocellulosic tissue from bmr6, bmr12, and stacked hybrids had reduced lignin content and increased in …