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Dynamic Interplay Between The Co-Opted Fis1 Mitochondrial Fission Protein And Membrane Contact Site Proteins In Supporting Tombusvirus Replication, Wenwu Lin, Zhike Feng, K. Reddisiva Prasanth, Yuyan Liu, Peter D. Nagy 2021 University of Kentucky

Dynamic Interplay Between The Co-Opted Fis1 Mitochondrial Fission Protein And Membrane Contact Site Proteins In Supporting Tombusvirus Replication, Wenwu Lin, Zhike Feng, K. Reddisiva Prasanth, Yuyan Liu, Peter D. Nagy

Plant Pathology Faculty Publications

Plus-stranded RNA viruses have limited coding capacity and have to co-opt numerous pro-viral host factors to support their replication. Many of the co-opted host factors support the biogenesis of the viral replication compartments and the formation of viral replicase complexes on subverted subcellular membrane surfaces. Tomato bushy stunt virus (TBSV) exploits peroxisomal membranes, whereas the closely-related carnation Italian ringspot virus (CIRV) hijacks the outer membranes of mitochondria. How these organellar membranes can be recruited into pro-viral roles is not completely understood. Here, we show that the highly conserved Fis1 mitochondrial fission protein is co-opted by both TBSV and CIRV via ...


Non-Transgenic Crispr-Mediated Knockout Of Entire Ergot Alkaloid Gene Clusters In Slow-Growing Asexual Polyploid Fungi, Simona Florea, Jolanta Jaromczyk, Christopher L. Schardl 2021 University of Kentucky

Non-Transgenic Crispr-Mediated Knockout Of Entire Ergot Alkaloid Gene Clusters In Slow-Growing Asexual Polyploid Fungi, Simona Florea, Jolanta Jaromczyk, Christopher L. Schardl

Computer Science Faculty Publications

The Epichloë species of fungi include seed-borne symbionts (endophytes) of cool-season grasses that enhance plant fitness, although some also produce alkaloids that are toxic to livestock. Selected or mutated toxin-free endophytes can be introduced into forage cultivars for improved livestock performance. Long-read genome sequencing revealed clusters of ergot alkaloid biosynthesis (EAS) genes in Epichloë coenophiala strain e19 from tall fescue (Lolium arundinaceum) and Epichloë hybrida Lp1 from perennial ryegrass (Lolium perenne). The two homeologous clusters in E. coenophiala—a triploid hybrid species—were 196 kb (EAS1) and 75 kb (EAS2), and the E. hybrida EAS cluster was 83 ...


Direct Agroinoculation Of Maize Seedlings By Injection With Recombinant Foxtail Mosaic Virus And Sugarcane Mosaic Virus Infectious Clones, Bliss M. Beernink, Katerina L. Holan, Ryan R. Lappe, Steven A. Whitham 2021 Iowa State University

Direct Agroinoculation Of Maize Seedlings By Injection With Recombinant Foxtail Mosaic Virus And Sugarcane Mosaic Virus Infectious Clones, Bliss M. Beernink, Katerina L. Holan, Ryan R. Lappe, Steven A. Whitham

Plant Pathology and Microbiology Publications

Agrobacterium-based inoculation approaches are widely used for introducing viral vectors into plant tissues. This study details a protocol for the injection of maize seedlings near meristematic tissue with Agrobacterium carrying a viral vector. Recombinant foxtail mosaic virus (FoMV) clones engineered for gene silencing and gene expression were used to optimize this method, and its use was expanded to include a recombinant sugarcane mosaic virus (SCMV) engineered for gene expression. Gene fragments or coding sequences of interest are inserted into a modified, infectious viral genome that has been cloned into the binary T-DNA plasmid vector pCAMBIA1380. The resulting plasmid constructs ...


Vegetable Diseases Of Utah, Claudia Nischwitz, Mair Murray, Nick Volesky 2021 Utah State University

Vegetable Diseases Of Utah, Claudia Nischwitz, Mair Murray, Nick Volesky

All Current Publications

This guide provides a list of vegetable crop diseases that have been documented in Utah along with some that are likely to occur. Plant diseases are caused by pathogens such as fungi, bacteria, viruses, and fungal-like organisms. Diagnosing specific plant diseases takes careful observation of signs, symptoms, and sometimes culturing and molecular testing in a laboratory setting.


Quantitative Proteomics Reveals Extensive Lysine Ubiquitination In The Arabidopsis Root Proteome And Uncovers Novel Transcription Factor Stability States, Gaoyuan Song, Damilola Olatunji, Christian Montes, Natalie M. Clark, Yunting Pu, Dior R. Kelley, Justin W. Walley 2021 Iowa State University

Quantitative Proteomics Reveals Extensive Lysine Ubiquitination In The Arabidopsis Root Proteome And Uncovers Novel Transcription Factor Stability States, Gaoyuan Song, Damilola Olatunji, Christian Montes, Natalie M. Clark, Yunting Pu, Dior R. Kelley, Justin W. Walley

Genetics, Development and Cell Biology Publications

Protein activity, abundance, and stability can be regulated by posttranslational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function and yet we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich peptides containing the di-glycine (diGly) remnant of ubiquitin and coupled that with isobaric labeling to enable quantification, from up to 16-multiplexed samples, for plant tissues. Collectively, we identified 7,130 diGly-modified lysine residues sites arising from 3,178 proteins in Arabidopsis primary roots. These data include ubiquitin proteasome ...


Robotic Agricultural Instrument For Automated Extraction Of Nematode Cysts And Eggs From Soil To Improve Integrated Pest Management, Christopher M. Legner, Gregory L. Tylka, Santosh Pandey 2021 Iowa State University

Robotic Agricultural Instrument For Automated Extraction Of Nematode Cysts And Eggs From Soil To Improve Integrated Pest Management, Christopher M. Legner, Gregory L. Tylka, Santosh Pandey

Plant Pathology and Microbiology Publications

Soybeans are an important crop for global food security. Every year, soybean yields are reduced by numerous soybean diseases, particularly the soybean cyst nematode (SCN). It is difficult to visually identify the presence of SCN in the field, let alone its population densities or numbers, as there are no obvious aboveground disease symptoms. The only definitive way to assess SCN population densities is to directly extract the SCN cysts from soil and then extract the eggs from cysts and count them. Extraction is typically conducted in commercial soil analysis laboratories and university plant diagnostic clinics and involves repeated steps of ...


Known Distribution Of The Soybean Cyst Nematode, Heterodera Glycines, In The United States And Canada In 2020, Gregory L. Tylka, Christopher C. Marett 2021 Iowa State University

Known Distribution Of The Soybean Cyst Nematode, Heterodera Glycines, In The United States And Canada In 2020, Gregory L. Tylka, Christopher C. Marett

Plant Pathology and Microbiology Publications

In the United States and Canada, the most damaging pathogen of soybean, Glycine max, is the soybean cyst nematode (SCN), Heterodera glycines. Plant health professionals working for universities and state and provincial departments of agriculture in the United States and Canada are queried periodically about counties and rural municipalities that are newly known to be infested with SCN in their states and provinces. Such a census was conducted in 2020, and the results were compared with results of the most recent survey, published in 2017. Between 2017 and 2020, 55 new SCN-infested counties were reported from 11 U.S. states ...


Introduction To Special Issue Of Plant Virus Emergence, Michael M. Goodin, Jeanmarie Verchot 2021 University of Kentucky

Introduction To Special Issue Of Plant Virus Emergence, Michael M. Goodin, Jeanmarie Verchot

Plant Pathology Faculty Publications

No abstract provided.


72-H Diurnal Rna-Seq Analysis Of Fully Expanded Third Leaves From Maize, Sorghum, And Foxtail Millet At 3-H Resolution, Xianjun Lai, Claire Bendix, Yan Zhang, James Schnable, Frank G. Harmon 2021 University of Nebraska - Lincoln & Xichang University

72-H Diurnal Rna-Seq Analysis Of Fully Expanded Third Leaves From Maize, Sorghum, And Foxtail Millet At 3-H Resolution, Xianjun Lai, Claire Bendix, Yan Zhang, James Schnable, Frank G. Harmon

Faculty Publications from the Center for Plant Science Innovation

Objectives: The purpose of this data set is to capture the complete diurnal (i.e., daily) transcriptome of fully expanded third leaves from the C4 panacoid grasses sorghum (Sorghum bicolor), maize (Zea mays), and foxtail millet (Setaria italica) with RNA-seq transcriptome profiling. These data are the cornerstone of a larger project that examined the conservation and divergence of gene expression networks within these crop plants. This data set focuses on tem- poral changes in gene expression to identify the network architecture responsible for daily regulation of plant growth and metabolic activities. The power of this data set is fine temporal ...


Biological Control And Microbial Ecology Draft Genome Sequence Data Of Glutamicibacter Sp. Fbe-19, A Bacterium Antagonistic To The Plant Pathogen Erwinia Tracheiphila, Benzhong Fu, Olakunle Olawole, Gwyn A. Beattie 2021 Iowa State University

Biological Control And Microbial Ecology Draft Genome Sequence Data Of Glutamicibacter Sp. Fbe-19, A Bacterium Antagonistic To The Plant Pathogen Erwinia Tracheiphila, Benzhong Fu, Olakunle Olawole, Gwyn A. Beattie

Plant Pathology and Microbiology Publications

Glutamicibacter sp.FBE-19 was isolated based on its strong antagonism to the cucurbit bacterial blight pathogen Erwinia tracheiphila on plates. Members of the Glutamicibacter genus can promote plant growth under saline conditions and antagonize fungi on plates via chitinolytic activity; however, their production of antibacterial compounds has not been examined. Here, we report the genome sequence of strain FBE-19. The genome is 3.85 Mbp with a G+C content of 60.1% and comprises 3,791 genes. Genes that may contribute to its antagonistic activity include genes for the secondary metabolites stenothricin, salinosporamide A, a second β-lactone compound, and ...


Evaluation Of Corn Agronomic Management Practices Following A Rye Cover Crop, Daniel John Quinn 2021 University of Kentucky

Evaluation Of Corn Agronomic Management Practices Following A Rye Cover Crop, Daniel John Quinn

Theses and Dissertations--Plant and Soil Sciences

Fall implementation of a rye (Secale cereale L.) cover crop (RCC) prior to spring corn (Zea mays L.) planting is a management practice used to improve soil conservation, water quality, and limit herbicide dependence. However, corn growth and yield following a RCC is often reduced due to early-season nitrogen (N) stress and decreased plant emergence, which can limit RCC adoption. The objective(s) of this research were to evaluate corn agronomic management practices (e.g., N and seeding rate management, in-furrow (IF) starter use) following a RCC and determine which management practices can be used to limit corn stress following ...


Key Interplay Between The Co-Opted Sorting Nexin-Bar Proteins And Pi3p Phosphoinositide In The Formation Of The Tombusvirus Replicase, Zhike Feng, Nikolay Kovalev, Peter D. Nagy 2020 University of Kentucky

Key Interplay Between The Co-Opted Sorting Nexin-Bar Proteins And Pi3p Phosphoinositide In The Formation Of The Tombusvirus Replicase, Zhike Feng, Nikolay Kovalev, Peter D. Nagy

Plant Pathology Faculty Publications

Positive-strand RNA viruses replicate in host cells by forming large viral replication organelles, which harbor numerous membrane-bound viral replicase complexes (VRCs). In spite of its essential role in viral replication, the biogenesis of the VRCs is not fully understood. The authors identified critical roles of cellular membrane-shaping proteins and PI(3)P (phosphatidylinositol 3-phosphate) phosphoinositide, a minor lipid with key functions in endosomal vesicle trafficking and autophagosome biogenesis, in VRC formation for tomato bushy stunt virus (TBSV). The authors show that TBSV co-opts the endosomal SNX-BAR (sorting nexin with Bin/Amphiphysin/Rvs- BAR domain) proteins, which bind to PI(3 ...


Evaluating The Current Weed Community In Wild Blueberry Fields And Ipm Strategies For Spreading Dogbane (Apocynum Androsaemifolium), Anthony G. Ayers 2020 University of Maine

Evaluating The Current Weed Community In Wild Blueberry Fields And Ipm Strategies For Spreading Dogbane (Apocynum Androsaemifolium), Anthony G. Ayers

Electronic Theses and Dissertations

Lowbush blueberry (Vaccinium angustifolium) is Maine’s third largest crop (USDA 2020 a). From 2017 – 2019 the three seasons yield average was 27,200 tons were harvested from 19,500 acres for a value of $22,468,000 (USDA 2020 c). Lowbush blueberries are managed on a two-year cycle. Every other year, lowbush blueberry fields are pruned to the ground either through the use of a tractor mounted flail mower or a prescribed burn (Yarborough 2009). Pruning is a necessary part of managing lowbush blueberries as the second-year growth produces the highest yield but steadily declines in subsequent years (Drummond ...


Assessment Of Grain Safety In Developing Nations, Jose R. Mendoza 2020 University of Nebraska - Lincoln

Assessment Of Grain Safety In Developing Nations, Jose R. Mendoza

Dissertations, Theses, & Student Research in Food Science and Technology

Grains are the most widely consumed foods worldwide, with maize (Zea mays) being frequently consumed in developing countries where it feeds approximately 900 million people under the poverty line of 2 USD per day. While grain handling practices are acceptable in most developed nations, many developing nations still face challenges such as inadequate field management, drying, and storage. Faulty grain handling along with unavoidably humid climates result in recurrent fungal growth and spoilage, which compromises both the end-quality and safety of the harvest. This becomes particularly problematic where there is little awareness about health risks associated with poor quality grain ...


Polerovirus Genomic Variation And Mechanisms Of Silencing Suppression By P0 Protein, Natalie Holste 2020 University of Nebraska-Lincoln

Polerovirus Genomic Variation And Mechanisms Of Silencing Suppression By P0 Protein, Natalie Holste

Dissertations and Theses in Biological Sciences

The family Luteoviridae consists of three genera: Luteovirus, Enamovirus, and Polerovirus. The genus Polerovirus contains 32 virus species. All are transmitted by aphids and can infect a wide variety of crops from cereals and wheat to cucurbits and peppers. However, little is known about how this wide range of hosts and vectors developed. In poleroviruses, aphid transmission and virion formation is mediated by the coat protein read-through domain (CPRT) while silencing suppression and phloem limitation is mediated by Protein 0 (P0)—a protein unique to poleroviruses. P0 gives poleroviruses a great advantage amongst plant viruses and diversifies polerovirus species, but ...


Boxwood Dieback: Molecular Detection, In-Vitro Fungicide Efficacy, And Host Susceptibility For Managing A New Emerging Disease Caused By Colletotrichum Theobromicola, Harleen Kaur 2020 Louisiana State University and Agricultural and Mechanical College

Boxwood Dieback: Molecular Detection, In-Vitro Fungicide Efficacy, And Host Susceptibility For Managing A New Emerging Disease Caused By Colletotrichum Theobromicola, Harleen Kaur

LSU Master's Theses

Boxwood (Buxus spp. L) is one of the most common and widely planted perennial ornamentals in both home gardens and commercial landscapes. Grown for its evergreen, dark green foliage, boxwood cultivation dates back to 4000 BC in Egypt. Although considered hardy, boxwood is susceptible to several plant pathogens. Recently reported boxwood dieback, a fungal disease caused by Colletotrichum theobromicola, has been spreading at an alarming rate within the United States. Boxwood dieback consists of symptoms that resemble to those caused by Phytophthora root rot, Volutella blight, and some abiotic disorders and can be easily misdiagnosed in nurseries and landscape plantings ...


A New Esophageal Gland Transcriptome Reveals Signatures Of Large Scale De Novo Effector Birth In The Root Lesion Nematode Pratylenchus Penetrans, Paulo Vieira, Jonathan Shao, Paramasivan Vijayapalani, Thomas R. Maier, Clement Pellegrin, Sebastian Eves-van den Akker, Thomas Baum, Lev G. Nemchinov 2020 U.S. Department of Agriculture

A New Esophageal Gland Transcriptome Reveals Signatures Of Large Scale De Novo Effector Birth In The Root Lesion Nematode Pratylenchus Penetrans, Paulo Vieira, Jonathan Shao, Paramasivan Vijayapalani, Thomas R. Maier, Clement Pellegrin, Sebastian Eves-Van Den Akker, Thomas Baum, Lev G. Nemchinov

Plant Pathology and Microbiology Publications

Background: The root lesion nematode Pratylenchus penetrans is a migratory plant-parasitic nematode responsible for economically important losses in a wide number of crops. Despite the importance of P. penetrans, the molecular mechanisms employed by this nematode to promote virulence remain largely unknown.

Results: Here we generated a new and comprehensive esophageal glands-specific transcriptome library for P. penetrans. In-depth analysis of this transcriptome enabled a robust identification of a catalogue of 30 new candidate effector genes, which were experimentally validated in the esophageal glands by in situ hybridization. We further validated the expression of a multifaceted network of candidate effectors during ...


Role Reversal Of Functional Identity In Host Factors: Dissecting Features Affecting Pro-Viral Versus Antiviral Functions Of Cellular Dead-Box Helicases In Tombusvirus Replication, Cheng-Yu Wu, Peter D. Nagy 2020 University of Kentucky

Role Reversal Of Functional Identity In Host Factors: Dissecting Features Affecting Pro-Viral Versus Antiviral Functions Of Cellular Dead-Box Helicases In Tombusvirus Replication, Cheng-Yu Wu, Peter D. Nagy

Plant Pathology Faculty Publications

Positive-stranded (+)RNA viruses greatly exploit host cells to support viral replication. However, unlike many other pathogens, (+)RNA viruses code for only a limited number of genes, making them highly dependent on numerous co-opted host factors for supporting viral replication and other viral processes during their infections. This excessive dependence on subverted host factors, however, renders (+)RNA viruses vulnerable to host restriction factors that could block virus replication. Interestingly, cellular ATP-dependent DEAD-box RNA helicases could promote or inhibit the replication of Tomato bushy stunt virus (TBSV) replication. However, it is currently unknown what features make a particular DEAD-box helicase either pro-viral ...


A Mechanistic Approach To Assessing The Potential For Cover Crops To Serve As Trap Crops For The Soybean Cyst Nematode, Chelsea J. Harbach, Elizabeth Wlezien, Gregory L. Tylka 2020 Iowa State University

A Mechanistic Approach To Assessing The Potential For Cover Crops To Serve As Trap Crops For The Soybean Cyst Nematode, Chelsea J. Harbach, Elizabeth Wlezien, Gregory L. Tylka

Plant Pathology and Microbiology Publications

The effects of cover crops on the biology of the soybean cyst nematode (SCN), Heterodera glycines, are not well established. It is possible that cover crops may reduce SCN population densities by acting as trap crops. Cover crops with potential to serve as trap crops may stimulate hatching and/or attract hatched SCN juveniles and also may be penetrated by large numbers of nematodes that cannot feed. Experiments were conducted to determine if root exudates and soil leachates (RE+SL) from various cover crop plants affected SCN hatching and chemotaxis and if there were significant differences in SCN juvenile root ...


Challenges And Opportunities In Machine-Augmented Plant Stress Phenotyping, Arti Singh, Sarah Jones, Baskar Ganapathysubramanian, Soumik Sarkar, Daren S. Mueller, Kulbir Sandhu, Koushik Nagasubramanian 2020 Iowa State University

Challenges And Opportunities In Machine-Augmented Plant Stress Phenotyping, Arti Singh, Sarah Jones, Baskar Ganapathysubramanian, Soumik Sarkar, Daren S. Mueller, Kulbir Sandhu, Koushik Nagasubramanian

Mechanical Engineering Publications

Plant stress phenotyping is essential to select stress-resistant varieties and develop better stress-management strategies. Standardization of visual assessments and deployment of imaging techniques have improved the accuracy and reliability of stress assessment in comparison with unaided visual measurement. The growing capabilities of machine learning (ML) methods in conjunction with image-based phenotyping can extract new insights from curated, annotated, and high-dimensional datasets across varied crops and stresses. We propose an overarching strategy for utilizing ML techniques that methodically enables the application of plant stress phenotyping at multiple scales across different types of stresses, program goals, and environments.


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