Impact Of Drought On Chemical
Composition And Sugar Yields From
Dilute-Acid Pretreatment And
Enzymatic Hydrolysis Of Miscanthus,
A Tall Fescue Mixture, And
Switchgrass,
2018
Idaho National Laboratory
Impact Of Drought On Chemical Composition And Sugar Yields From Dilute-Acid Pretreatment And Enzymatic Hydrolysis Of Miscanthus, A Tall Fescue Mixture, And Switchgrass, Amber Hoover, Rachel Emerson, Allison Ray, Daniel Stevens, Sabrina Morgan, Marnie Cortez, Robert Kallenbach, Matthew Sousek, Rodney Farris, Dayna Daubaras
Department of Agronomy and Horticulture: Faculty Publications
Environmental factors like drought impact the quality of biomass entering a bioconversion process. Drought often reduces the sugar content in lignocellulosic biomass, which could have economic impacts, particularly when compounded with losses in dry biomass yield; however, the effects on conversion efficiency are not completely understood. This study investigated how drought may impact biomass composition and sugar yields from dilute-acid pretreatment and enzymatic hydrolysis of Miscanthus, a tall fescue mixture, and switchgrass from Nebraska, Missouri, and Oklahoma, respectively, grown as part of Regional Feedstock Partnership field trials. Samples were grown and harvested in 2010 during non-drought conditions and in …
Impaired Phloem Loading In Zmsweet13a,B,C Sucrose Transporter
Triple Knock-Out Mutants In Zea Mays,
2018
Heinrich-Heine-Universitat Dusseldorf
Impaired Phloem Loading In Zmsweet13a,B,C Sucrose Transporter Triple Knock-Out Mutants In Zea Mays, Margaret Bezrutczyk, Thomas Hartwig, Marc Horschman, Si Nian Char, Jinliang Yang, Bing Yang, Wolf B. Frommer, Davide Sosso
Department of Agronomy and Horticulture: Faculty Publications
Crop yield is critical for human nutrition, yet the underlying machinery that ultimately determines yield potential is still not understood. Crop productivity under ideal conditions is determined by the efficiency with which plants intercept light, convert it into chemical energy, translocate photosynthates and convert these to storage products in harvestable organs (Zhu et al., 2010). In many crops, sucrose is the primary form for translocation inside the conduit (i.e. the phloem). A combination of SWEETmediated efflux from phloem parenchyma and subsequent secondary active sucrose import by SUT sucrose/H+ symporters is thought to create the driving force for pressure gradient-driven …
Tetracycline And Sulfonamide
Antibiotic Resistance Genes In Soils
From Nebraska Organic Farming
Operations,
2018
University of Texas at El Paso
Tetracycline And Sulfonamide Antibiotic Resistance Genes In Soils From Nebraska Organic Farming Operations, Marylynn Cadena, Lisa M. Durso, Daniel N. Miller, Heidi M. Waldrip, B. L. Castleberry, Rhae A. Drijber, Charles S. Wortmann
Department of Agronomy and Horticulture: Faculty Publications
There is widespread agreement that agricultural antibiotic resistance should be reduced, however, it is unclear from the available literature what an appropriate target for reduction would be. Organic farms provide a unique opportunity to disentangle questions of agricultural antibiotic drug use from questions of antibiotic resistance in the soil. In this study, soil was collected from 12 certified organic farms in Nebraska, evaluated for the presence of tetracycline and sulfonamide resistance genes (n = 15 targets), and correlated to soil physical, chemical, and biological parameters. Tetracycline and sulfonamide antibiotic resistance genes (ARGs) were found in soils from all 12 …
Characterization Of Neofabraea Actinidiae And N. Brasiliensis As Causal Agents Of Apple Bull’S-Eye Rot In Southern Brazil,
2018
Universidade do Estado de Santa Catarina
Characterization Of Neofabraea Actinidiae And N. Brasiliensis As Causal Agents Of Apple Bull’S-Eye Rot In Southern Brazil, Amauri Bogo, Carla C. Comparin, Rosa M. Valdebenito Sanhueza, Patricia Ritschel, Ricardo T. Casa, Fábio N. Silva, Sydney E. Everhart
Department of Plant Pathology: Faculty Publications
The causal agents of apple bull’s-eye rot in southern Brazil have recently been described as Neofabraea actinidiae and N. brasiliensis. Isolates of both species were evaluated for response of mycelial growth index (MGI) to different temperatures, enzyme production, mycelial growth inhibition and effective concentrations (EC50 and EC100) of the fungicides triflumizole, pyrimethanil and thiophanate methyl, as well as aggressiveness on fruits of ‘Fuji’ hybrid and ‘Pink Lady’. There was significantly lower mycelium growth in N. brasiliensis compared with N. actinidiae at all temperatures tested. Neither species grew at 3 and 32°C. There were minor differences in …
Elucidating The Role Of Highly
Homologous Nicotiana Benthamiana Ubiquitin
E2 Gene Family Members In Plant Immunity
Through An Improved Virus‑Induced Gene
Silencing Approach,
2018
University of Nebraska-Lincoln,
Elucidating The Role Of Highly Homologous Nicotiana Benthamiana Ubiquitin E2 Gene Family Members In Plant Immunity Through An Improved Virus‑Induced Gene Silencing Approach, Bangjun Zhou, Lirong Zeng
Department of Plant Pathology: Faculty Publications
Background: Virus-induced gene silencing (VIGS) has been used in many plant species as an attractive post transcriptional gene silencing (PTGS) method for studying gene function either individually or at large-scale in a high-throughput manner. However, the specificity and efficiency for knocking down members of a highly homologous gene family have remained to date a significant challenge in VIGS due to silencing of off-targets. Results: Here we present an improved method for the selection and evaluation of gene fragments used for VIGS to specifically and efficiently knock down members of a highly homologous gene family. Using this method, we knocked down …
The Tomato U-Box Type E3 Ligase
Pub13 Acts With Group Iii Ubiquitin
E2 Enzymes To Modulate
Fls2-Mediated Immune Signaling,
2018
University of Nebraska-Lincoln,
The Tomato U-Box Type E3 Ligase Pub13 Acts With Group Iii Ubiquitin E2 Enzymes To Modulate Fls2-Mediated Immune Signaling, Bangjun Zhou, Lirong Zeng
Department of Plant Pathology: Faculty Publications
In Arabidopsis and rice, the ubiquitin ligase PUB13-mediated protein degradation plays a significant role in plant pattern-triggered immunity (PTI) and flowering time control. The Arabidopsis PUB13 has been shown to attenuate the pattern recognition receptor FLS2-mediated immune signaling by ubiquitinating FLS2 and consequently promoting its degradation by the 26S proteasome. Nevertheless, the cognate ubiquitin-conjugating enzymes (E2) with which PUB13 acts to modulate FLS2-mediated PTI are unknown. To address this question, we investigate here the tomato (Solanum lycopersicum) homolog of PUB13, SlPUB13 by utilizing the recently characterized complete set of tomato E2s. Of the 13 groups of tomato E2s, …
Proteomic Analysis Of Ubiquitinated
Proteins In Rice (Oryza Sativa)
After Treatment With
Pathogen-Associated Molecular
Pattern (Pamp) Elicitors,
2018
Chinese Academy of Agricultural Sciences
Proteomic Analysis Of Ubiquitinated Proteins In Rice (Oryza Sativa) After Treatment With Pathogen-Associated Molecular Pattern (Pamp) Elicitors, Xiao-Lin Chen, Xin Xie, Liye Wu, Caiyun Liu, Lirong Zeng, Xueping Zhou, Feng Luo, Guo-Liang Wang, Wende Liu
Department of Plant Pathology: Faculty Publications
Reversible protein ubiquitination plays essential roles in regulating cellular processes. Although many reports have described the functions of ubiquitination in plant defense responses, few have focused on global changes in the ubiquitome. To better understand the regulatory roles of ubiquitination in rice pattern-triggered immunity (PTI), we investigated the ubiquitome of rice seedlings after treatment with two pathogen-associated molecular patterns, the fungal-derived chitin or the bacterialderived flg22, using label-free quantitative proteomics. In chitin-treated samples, 144 and 167 lysine-ubiquitination sites in 121 and 162 proteins showed increased and decreased ubiquitination, respectively. In flg22-treated samples, 151 and 179 lysine-ubiquitination sites in 118 and …
Application Of Machine Learning Methodologies For
Predicting Corn Economic Optimal Nitrogen Rate,
2018
Dupont Pioneer
Application Of Machine Learning Methodologies For Predicting Corn Economic Optimal Nitrogen Rate, Zhisheng Qin, D. Brenton Myers, Curtis J. Ransom, Newell R. Kitchen, Sang-Zi Liang, James J. Camberato, Paul R. Carter, Richard B. Ferguson, Fabian G. Fernandez, David W. Franzen, Carrie A. M. Laboski, Brad D. Malone, Emerson D. Nafziger, John E. Sawyer, John F. Shanahan
Department of Agronomy and Horticulture: Faculty Publications
Determination of in-season N requirement for corn (Zea mays L.) is challenging due to interactions of genotype, environment, and management. Machine learning (ML), with its predictive power to tackle complex systems, may solve this barrier in the development of locally based N recommendations. The objective of this study was to explore application of ML methodologies to predict economic optimum nitrogen rate (EONR) for corn using data from 47 experiments across the US Corn Belt. Two features, a water table adjusted available water capacity (AWCwt) and a ratio of in-season rainfall to AWCwt (RAWCwt), were …
Managing Wicked Herbicide-Resistance: Lessons
From The Field,
2018
USDA
Managing Wicked Herbicide-Resistance: Lessons From The Field, Jill Schroeder, Michael Barrett, David R. Shaw, Amy B. Asmus, Harold Coble, David Ervin, Raymond A. Jussaume Jr., Michael D. K. Owen, Ian Burke, Cody F. Creech, A. Stanley Culpepper, William S. Curran, Darrin M. Dodds, Todd A. Gaines, Jeffrey L. Gunsolus, Bradley D. Hanson, Prashant Jha, Annie E. Klodd, Andrew R. Kniss, Ramon G. Leon, Sandra Mcdonald, Don W. Morishita, Brian J. Schutte, Christy L. Sprague, Phillip W. Stahlman, Larry E. Steckel, Mark J. Vangessel
Department of Agronomy and Horticulture: Faculty Publications
Herbicide resistance is ‘wicked’ in nature; therefore, results of the many educational efforts to encourage diversification of weed control practices in the United States have been mixed. It is clear that we do not sufficiently understand the totality of the grassroots obstacles, concerns, challenges, and specific solutions needed for varied crop production systems. Weed management issues and solutions vary with such variables as management styles, regions, cropping systems, and available or affordable technologies. Therefore, to help the weed science community better understand the needs and ideas of those directly dealing with herbicide resistance, seven half-day regional listening sessions were held …
Growth, Fitness, And Overwinter Survival Of A Shattercane (Sorghum Bicolor Ssp. Drummondii) × Grain Sorghum (Sorghum Bicolor Ssp. Bicolor) F2 Population,
2018
University of Nebraska-Lincoln
Growth, Fitness, And Overwinter Survival Of A Shattercane (Sorghum Bicolor Ssp. Drummondii) × Grain Sorghum (Sorghum Bicolor Ssp. Bicolor) F2 Population, Jared J. Schmidt, Melinda K. Yerka, Jeffrey F. Pedersen, John L. Lindquist
Department of Agronomy and Horticulture: Faculty Publications
Although sorghum [Sorghum bicolor (L.) Moench ssp. bicolor] is the fifth most important grain crop in terms of global production, no commercial hybrids carry genetically engineered (GE) traits for resistance to insect pests or herbicides due to regulatory concerns about gene flow to weedy relatives. However, non-GE herbicide resistance currently is being developed in grain sorghum and will likely transfer to related weeds. Monitoring the impact of this new nuclear technology on the evolution and invasiveness of related weeds requires a baseline understanding of the population biology of grain sorghum genes once they transfer to in situ weed …
Genomic Selection In Preliminary Yield Trials In A
Winter Wheat Breeding Program,
2018
University of Nebraska-Lincoln
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 F3:6 and F3:7 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 …
Tomato Spotted Wilt Virus Nss Protein Supports Infection And Systemic Movement Of A Potyvirus And Is A Symptom Determinant,
2018
University of Nebraska-Lincoln
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,
2018
University of Nebraska-Lincoln
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,
2018
KALRO
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,
2018
University of Nebraska-Lincoln
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,
2018
Universidad Autónoma Chapingo
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,
2018
University of Nebraska-Lincoln
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 …
Riparian Vegetation And The Soil Seed Bank Five Years After Dam Removal On The Elwha River, Washington,
2018
Eastern Washington University
Riparian Vegetation And The Soil Seed Bank Five Years After Dam Removal On The Elwha River, Washington, Cody C. Thomas
EWU Masters Thesis Collection
Damming of rivers is widespread and can profoundly impact riparian areas by altering the fluvial processes that drive riparian vegetation communities. Dam removal may reverse these effects; however, very few studies have examined the response of riparian vegetation to large dam removal and associated disturbances, such as the release of sediment. Understanding how dam removal impacts downstream riparian vegetation is crucial as dam removal becomes more common. The Elwha River, Washington, is the location of the largest dam removals to date and provides an unprecedented opportunity to explore questions related to dam removal and riparian vegetation. The objectives of this …
Pushing The Resolution Limit By Correcting The Ewald
Sphere Effect In Single-Particle Cryo-Em
Reconstructions,
2018
Chinese Academy of Sciences
Pushing The Resolution Limit By Correcting The Ewald Sphere Effect In Single-Particle Cryo-Em Reconstructions, Dongjie Zhu, Xiangxi Wang, Qianglin Fang, James L. Van Etten, Michael G. Rossmann, Zihe Rao, Xinzheng Zhang
Department of Plant Pathology: Faculty Publications
The Ewald sphere effect is generally neglected when using the Central Projection Theorem for cryo electron microscopy single-particle reconstructions. This can reduce the resolution of a reconstruction. Here we estimate the attainable resolution and report a “block-based” reconstruction method for extending the resolution limit. We find the Ewald sphere effect limits the resolution of large objects, especially large viruses. After processing two real datasets of large viruses, we show that our procedure can extend the resolution for both datasets and can accommodate the flexibility associated with large protein complexes.
