Digital Commons Network^™

Genomic Selection In Preliminary Yield Trials In A Winter Wheat Breeding Program, Vikas Belamkar, Mary J. Guttieri, Waseem Hussain, Diego Jarquin, Ibrahim El-Basyoni, Jesse Poland, Aaron J. Lorenz, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Genomic prediction (GP) is now routinely performed in crop plants to predict unobserved phenotypes. The use of predicted phenotypes to make selections is an active area of research. Here, we evaluate GP for predicting grain yield and compare genomic and phenotypic selection by tracking lines advanced. We examined four independent nurseries of F_3:6 and F_3:7 lines trialed at 6 to 10 locations each year. Yield was analyzed using mixed models that accounted for experimental design and spatial variations. Genotype-by-sequencing provided nearly 27,000 high-quality SNPs. Average genomic predictive ability, estimated for each year by randomly masking lines as missing …

Adolescent Sexual Risk Taking: The Distribution Of Youth Behaviors And Perceived Peer Attitudes Across Neighborhood Contexts, Tara D. Warner

Department of Sociology: Faculty Publications

Purpose: Sexual activity is a normative part of adolescent development, yet early sexual debut and sex with multiple partners undermine health and well-being. Both structural (e.g., poverty) and social (e.g., norms) characteristics of neighborhoods shape sexual risk taking, yet scholarship remains focused on urban areas. Thus, this study explores sexually permissive attitudes and sexual risk taking across a wider expanse of neighborhood types. Methods: Among 8,337 nonsexually active respondents in Wave I (1994–1995 [ages 11–18]) of the National Longitudinal Study of Adolescent to Adult Health (Add Health), a hierarchical linear model and a hierarchical generalized linear model were used to …

Tick–Tock Goes The Croc: A High-Density Eeg Study Of Risk-Reactivity And Binge-Drinking, John E. Kiat, Jacob E. Cheadle

Department of Sociology: Faculty Publications

Links between individual differences in risk processing and high-risk behaviors such as binge-drinking have long been the focus of active research. However, investigations in this area almost exclusively utilize decision-making focused paradigms. This emphasis makes it difficult to assess links between risk behaviors and raw risk reactivity independent of decision and feedback processes. A deeper understanding of this association has the potential to shed light on the role of risk reactivity in high-risk behavior susceptibility. To contribute toward this aim, this study utilizes a popular risk-taking game, the crocodile dentist, to assess links between individual differences in decision-free risk-reactivity and …

Age Of Migration And The Incidence Of Cognitive Impairment: A Cohort Study Of Elder Mexican-Americans, Marc A. Garcia, Adriana M. Reyes, Brian Downer, Joseph L. Saenz, Rafael A. Samper-Ternent, Mukaila Raji

Department of Sociology: Faculty Publications

Background and Objectives: To explore nativity and age of migration differentials in the incidence of cognitive impairment among older Mexican-Americans. Research Design and Methods: We employ maximum-likelihood discrete time hazard models to estimate risk ratios of cognitive impairment in a sample of 2,708 Mexican-Americans 65 and older who were cognitively healthy at baseline over a follow-up period of up to 20 years. Results: Late-life immigrant women have a 46% higher risk of cognitive impairment compared to U.S.-born Mexican- American women. Conversely, midlife immigrant men have a 29% lower risk of cognitive impairment compared to U.S.- born Mexican-American men. The incidence …

Life Expectancies With Depression By Age Of Migration And Gender Among Older Mexican Americans, Catherine García, Marc A. Garcia, Chi-Tsun Chiu, Fernando I. Rivera, Mukaila Raji

Department of Sociology: Faculty Publications

Background and Objectives: Prior studies examining depression among older Mexican Americans suggest both women and immigrants are at higher risk of depressive symptomatology than males and U.S.-born Mexican Americans. We use data from the Hispanic Established Populations for the Epidemiologic Study of the Elderly to examine whether life expectancy with depression and without depression varies by nativity, age of migration, and gender.

Research Design and Methods: Sullivan-based life tables were used to estimate depression life expectancies among Mexican Americans aged 65 years and older residing in the Southwestern United States. Depression is based on the 20-item Center for Epidemiological Studies …

Tomato Spotted Wilt Virus Nss Protein Supports Infection And Systemic Movement Of A Potyvirus And Is A Symptom Determinant, Hernan Garcia-Ruiz, Sergio M. Gabriel Peralta, Patricia A. Harte-Maxwell

Department of Plant Pathology: Faculty Publications

Plant viruses are inducers and targets of antiviral RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressor proteins that interfere with antiviral RNA silencing. The NSs protein is an RNA silencing suppressor in orthotospoviruses, such as the tomato spotted wilt virus (TSWV). The mechanism of RNA silencing suppression by NSs and its role in virus infection and movement are poorly understood. Here, we cloned and tagged TSWV NSs and expressed it from a GFP-tagged turnip mosaic virus (TuMV-GFP) carrying either a wild-type or suppressor-deficient (AS9) helper component proteinase (HC-Pro). When expressed in cis, NSs restored pathogenicity and promoted …

Intermolecular Rna Recombination Occurs At Different Frequencies In Alternate Forms Of Brome Mosaic Virus Rna Replication Compartments, Hernan Garcia-Ruiz, Arturo Diaz, Paul Ahlquist

Department of Plant Pathology: Faculty Publications

Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV) replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to …

Metagenomic Analysis Of Viruses Associated With Maize Lethal Necrosis In Kenya, Mwathi Jane Wamaitha, Deepti Nigam, Solomon Maina, Francesca Stomeo, Anne Wangai, Joyce Njoki Njuguna, Timothy A. Holton, Bramwel W. Wanjala, Mark Wamalwa, Tanui Lucas, Appolinaire Djikeng, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Background: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA. Methods: We used next-generation sequencing to identify viruses associated to maize lethal necrosis in Kenya through a metagenomics analysis. Symptomatic and asymptomatic leaf samples …

Susceptibility Genes To Plant Viruses, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Plant viruses use cellular factors and resources to replicate and move. Plants respond to viral infection by several mechanisms, including innate immunity, autophagy, and gene silencing, that viruses must evade or suppress. Thus, the establishment of infection is genetically determined by the availability of host factors necessary for virus replication and movement and by the balance between plant defense and viral suppression of defense responses. Host factors may have antiviral or proviral activities. Proviral factors condition susceptibility to viruses by participating in processes essential to the virus. Here, we review current advances in the identification and characterization of host factors …

Profile Of Genetically Modified Plants Authorized In Mexico, Mayra Teresa Garcia Ruiz, Aaron N. Knapp, Hernan Garcia Ruiz

Department of Plant Pathology: Faculty Publications

Mexico is a center of origin for several economically important plants including maize, cotton, and cocoa. Maize represents more than a food crop, has been declared a biological, cultural, agricultural and economic patrimony, and is linked to the national identity of Mexicans. In this review, we describe the historic and current use of genetically modified plants in Mexico and factors that contributed to the development of the biosafety regulation. We developed a database containing all permit applications received by the government to release genetically modified plants. A temporal and geographical analysis identified the plant species that have been authorized for …

Genomic-Enabled Prediction Models Using Multi-Environment Trials To Estimate The Effect Of Genotype × Environment Interaction On Prediction Accuracy In Chickpea, Manish Roorkiwal, Diego Jarquin, Muneendra K. Singh, Pooran M. Gaur, Chellapilla Bharadwaj, Abhishek Rathore, Reka Howard, Samineni Srinivasan, Ankit Jain, Vanika Garg, Sandip Kale, Annapurna Chitikineni, Shailesh Tripathi, Elizabeth Jones, Kelly R. Robbins, José Crossa, Rajeev K. Varshney

Department of Agronomy and Horticulture: Faculty Publications

Genomic selection (GS) by selecting lines prior to field phenotyping using genotyping data has the potential to enhance the rate of genetic gains. Genotype × environment (G × E) interaction inclusion in GS models can improve prediction accuracy hence aid in selection of lines across target environments. Phenotypic data on 320 chickpea breeding lines for eight traits for three seasons at two locations were recorded. These lines were genotyped using DArTseq (1.6 K SNPs) and Genotyping-by-Sequencing (GBS; 89 K SNPs). Thirteen models were fitted including main effects of environment and lines, markers, and/or naïve and informed interactions to estimate prediction …

Gene Expression Profiling Of Iron Deficiency Chlorosis Sensitive And Tolerant Soybean Indicates Key Roles For Phenylpropanoids Under Alkalinity Stress, Brian M. Waters, Keenan Amundsen, George L. Graef

Department of Agronomy and Horticulture: Faculty Publications

Alkaline soils comprise 30% of the earth and have low plant-available iron (Fe) concentration, and can cause iron deficiency chlorosis (IDC). IDC causes soybean yield losses of $260 million annually. However, it is not known whether molecular responses to IDC are equivalent to responses to low iron supply. IDC tolerant and sensitive soybean lines provide a contrast to identify specific factors associated with IDC.We used RNA-seq to compare gene expression under combinations of normal pH (5.7) or alkaline pH (7.7, imposed by 2.5mM bicarbonate, or pH 8.2 imposed by 5mM bicarbonate) and normal (25μM) or low (1μM) iron conditions from …

Reduction In Musca Domestica Fecundity By Dsrna-Mediated Gene Knockdown, Neil D. Sanscrainte, Hanayo Arimoto, Christy M. Waits, Lucy Y. Li, Dana Johnson, Chris Geden, James Becnel, Alden S. Estep

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

House flies (Musca domestica) are worldwide agricultural pests with estimated control costs at $375 million annually in the U.S. Non-target effects and widespread resistance challenge the efficacy of traditional chemical control. Double stranded RNA (dsRNA) has been suggested as a biopesticide for M. domestica but a phenotypic response due to the induction of the RNAi pathway has not been demonstrated in adults. In this study female house flies were injected with dsRNA targeting actin-5C or ribosomal protein (RP) transcripts RPL26 and RPS6. Ovaries showed highly reduced provisioning and clutch reductions of 94±99% in RP dsRNA treated flies but …

Experimental Droughts With Rainout Shelters: A Methodological Review, David L. Hoover, Kevin R. Wilcox, Kristina E. Young

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

Forecast increases in the frequency, intensity, and duration of droughts with climate change may have extreme and extensive ecological consequences. There are currently hundreds of published, ongoing, and new drought experiments worldwide aimed to assess ecological sensitivity to drought and identify the mechanisms governing resistance and resilience. To date, the results from these experiments have varied widely, and thus, patterns of drought sensitivities and the underlying mechanisms have been difficult to discern. Here we examined 89 published drought experiments, along with their associated historical precipitation records to (1) identify where and how drought experiments have been imposed, (2) determine the …

Detection Of Exogenous Double-Stranded Rna Movement In In Vitro Peanut Plants, P. C. Faustinelli, I. L. Power, R. S. Arias

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

New technologies are needed to eliminate mycotoxins and/or fungal pathogens from agricultural products. RNA interference (RNAi) has shown potential to control fungi associated with crops. In RNAi, double-stranded RNA (dsRNA) targets homologous mRNA for cleavage, and can reach the mRNA of pathogens in contact with the plant. The key element in this process is the movement of RNA signals cell-to-cell and over long distances within the plant, and between host plants and parasites.

• In this study, we selected a regulatory gene in the aflatoxin biosynthesis pathway, aflS/ aflR, necessary for the production of aflatoxins in Aspergillus spp. We …

Bioconversion Of Pelletized Big Bluestem, Switchgrass, And Low-Diversity Grass Mixtures Into Sugars And Bioethanol, Bruce S. Dien, Robert B. Mitchell, Michael J. Bowman, Virginia L. Jin, Joshua Quarterman, Marty R. Schmer, Vijay Singh, Patricia J. Slininger

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

Three crops of warm-season grasses are being developed for biomass production on northern rain-fed marginal farmland: big bluestem (BBS), switchgrass (SG), and a low diversity mixture of grasses (LDM). In this study, biomass harvested from established fields were compared for pelletization and subsequent conversion to sugars and ethanol. Each biomass was successfully pelletized to similar bulk densities without adding a binder at a commercial feed operation. Pelletizing increased the bulk density by 407% on average and was equally effective on all three biomass samples (528–554 kg/m³). Chemical analysis of the samples indicated that glucan and xylan contents were …

Effects Of Triclosan In Breast Milk On The Infant Fecal Microbiome, Candace S. Bever, Amy A. Rand, Malin Nording, Diana Taft, Karen M. Kalanetra, David A. Mills, Melissa A. Breck, Jennifer T. Smilowitz, J. Bruce German, Bruce D. Hammock

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

Triclosan is frequently used for its antimicrobial properties and has been detected in human serum, urine, and breast milk. Animal and molecular studies have shown that triclosan exerts a wide range of adverse health effects at both high (ppm) and low (ppb) concentrations. Since triclosan is of growing concern to human and environmental health, there is a need to improve extraction procedures and to study additional effects from triclosan exposure. In this study, we have improved triclosan extraction from breast milk by using salt (MgSO4) to reduce emulsion formation and increase water polarity and water (~80%) to enhance the overall …

Application Of The Biosafety Ram And Eprotocol Software Programs To Streamline Institutional Biosafety Committee Processes At The Usda-National Animal Disease Center, John P. Bannantine, Karen B. Register, David M. White

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

The National Animal Disease Center (NADC) conducts basic and applied research on endemic animal diseases of high priority that adversely affect US livestock production or trade. Experiments conducted at this center vary in range and scope with a subset involving synthetic or recombinant nucleic acids (DNA), microorganisms, and/or animals. Historically, the NADC used hard copy paper and filing systems to catalog and monitor these types of experiments, but to improve communication, tracking, searching, reporting, and documentation of Institutional Biosafety Committee (IBC) actions, this institution has transitioned to using a commercially available software tool to digitally manage protocols in our ongoing …

Knowledge Gaps That Hamper Prevention And Control Of Mycobacterium Avium Subspecies Paratuberculosis Infection, Herman W. Barkema, Karin Orsel, S.S. Nielsen, A.P. Koets, V.P.M.G. Rutten, J. P. Bannantine, G.P. Keefe, D.F. Kelton, Scott J. Wells, Richard J. Whittington, Colin G. Mackintosh, E.J. Manning, M.F. Weber, C. Heuer, T.L. Forde, C. Ritter, S. Roche, C.S. Corbett, R. Wolf, P.J. Griebel, J.P. Kastelic, J. De Buck

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

In the last decades, many regional and country-wide control programmes for Johne’s disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn’s disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of …

A Simple And Scalable Hydrogel-Based System For Culturing Protein-Producing Cells, Qiang Li, Qiaofeng Wang, Ou Wang, Kaifeng Shao, Haishuang Lin, Yuguo Lei

Department of Chemical and Biomolecular Engineering: Faculty Publications

Recombinant protein therapeutics have become important components of the modern medicine. Majority of them are produced with mammalian cells that are cultured either through adherent culturing, in which cells are cultured on substrates, or suspension culturing, in which cells are suspended and cultured in agitated cell culture medium in a culture vessel. The adherent cell culturing method is limited by its low yield. In suspension culturing, cells need extensive genetic manipulation to grow as single cells at high density, which is time and labor-consuming. Here, we report a new method, which utilizes a thermoreversible hydrogel as the scaffold for culturing …

Nebraska Summary: S1150 Challenger 1050, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Nebraska Summary: S1158 John Deere 6230r, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2202: John Deere 6215r Autoquad-Plus, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2205: Challenger Mt738, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2199a: New Holland Workmaster 60, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2198: John Deere 5125r Pfc, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2199: Case Ih Farmall 60a, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2195: John Deere 5115r Oc, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2197: John Deere 5125r Oc, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …

Test 2193: John Deere 5100r Oc, Nebraska Tractor Test Lab

Nebraska Tractor Tests

ABOUT THE TEST REPORT AND USE OF THE DATA The test data contained in this report are a tabulation of the results of a series of tests. Due to the restricted format of these pages, only a limited amount of data and not all of the tractor specifications are included. The full OECD report contains usually about 30 pages of data and specifications. The test data were obtained for each tractor under similar conditions and therefore, provide a means of comparison of performance based on a limited set of reported data. EXPLANATION OF THE TEST PROCEDURES Purpose The purpose of …