Digital Commons Network^™

Rna Sequence Determinants Of A Coupled Termination-Reinitiation Strategy For Translation Of Downstream Orf In Helminthosporium Victoriae Virus 190s And Other Victoriviruses (Family Totiviridae), Hua Li

Theses and Dissertations--Plant Pathology

Double-stranded RNA fungal virus Helminthosporium victoriae virus 190S (genus Victorivirus, family Totiviridae) contains two large open reading frames (ORFs) that overlap in the tetranucleotide AUGA. Translation of the downstream ORF, which encodes the RNA-dependent RNA polymerase (RdRp), was previously proposed to depend on ribosomal reinitiation following termination of the upstream ORF, which encodes the capsid protein. In this study, I provided evidence to confirm that coupled termination-reinitiation (stop-restart) is indeed used. A dual-fluorescence method was established to define the RNA sequence determinants for RdRp translation. Stop-restart depends on a 32-nt stretch of RNA sequence immediately upstream of the …

Ether Bridge Formation And Chemical Diversification In Loline Alkaloid Biosynthesis, Juan Pan

Theses and Dissertations--Plant Pathology

Loline alkaloids, found in many grass-Epichloë symbiota, are toxic or feeding deterrent to invertebrates. The loline alkaloids all share a saturated pyrrolizidine ring with a 1-amine group and an ether bridge linking C2 and C7. The steps in biosynthesis of loline alkaloids are catalyzed by enzymes encoded by a gene cluster, designated LOL, in the Epichloë genome. This dissertation addresses the enzymatic, genetic and evolutionary basis for diversification of these alkaloids, focusing on ether bridge formation and the subsequent modifications of the 1-amine to form different loline alkaloids.

Through gene complementation of a natural lolO mutant and comparison …

Beta Diversity Of Urban Floras Among European And Non-European Cities, Frank A. La Sorte, Myla F.J. Aronson, Nicholas S.G. Williams, Laura Celesti-Grapow, Sarel Cilliers, Bruce D. Clarkson, Rebecca W. Dolan, Andrew Hipp, Stefan Klotz, Ingolf Kühn, Pter Pyšek, Stefan Siebert, Marten Winter

Scholarship and Professional Work - LAS

Aim- Cities represent an ideal study system for assessing how intensive land-use change and biotic interchange have altered beta diversity at broad geographic extents. Here we test the hypothesis that floras in cities located in disparate regions of the globe are being homogenized by species classified as invasive (naturalized species that have spread over a large area) or as a European archaeophyte (species introduced into Europe before ad 1500 from the Mediterranean Basin). We also test the prediction that the global influences of European activities (colonization, agriculture, commerce) have supported this outcome.

Location- One hundred and ten cities …

The Complete Plastid Genome Sequence Of Iris Gatesii (Section Oncocyclus), A Bearded Species From Southeastern Turkey, Carol A. Wilson

Aliso: A Journal of Systematic and Floristic Botany

Iris gatesii is a rare bearded species in subgenus Iris section Oncocyclus that occurs in steppe communities of southeastern Turkey. This species is not commonly cultivated, but related species in section Iris are economically important horticultural plants. The complete plastid genome is reported for I. gatesii based on data generated using the Illumina HiSeq platform and is compared to genomes of 16 species selected from across the monocotyledons. This Iris genome is the only known plastid genome available for order Asparagales that is not from Orchidaceae. The I. gatesii plastid genome, unlike orchid genomes, has little gene loss and rearrangement …

Morphology And Genetic Affinities Of A Novel Chattonella Isolate (Raphidophyceae) Isolated From Iran’S South Coast (Oman Sea), Gilan Attaran Fariman, Christopher John Stanley Bolch

Turkish Journal of Botany

The morphology and genetic affinity of a novel raphidophyte belonging to the genus Chattonella Biecheler is described for the first time from the Oman Sea along the south-east coast of Iran. While morphologically very similar to Chattonella subsalsa Biecheler, the Iranian isolates contain a distinct red eyespot. A comparison of LSU-rDNA and rDNA-ITS show that the Iranian isolate is genetically distinct from other Chattonella subsalsa strains isolated from across a wide global range and indicates that the Iranian isolates represent a distinct species related to Chattonella subsalsa.

Micropropagation Of Erodium Sibthorpianum Subsp. Sibthorpianum, An Endemic Threatened Species Of Uludağ Mountain (Bursa-Turkey), Betül Akin, İsmai̇l Kocaçalişkan, Gürcan Güleryüz

Turkish Journal of Botany

Uludağ Mountain is one of the Important Plant Areas of Turkey. Its native plant species are threatened by various human and environmental factors. In this study, 2 different micropropagation techniques, with Murashige Skoog (MS) and modified MS (ModMS) media, were used for Erodium sibthorpianum Boiss. subsp. sibthorpianum. Mineral composition was developed according to the plant requirements. Shoot tips were cultured on these media. Seedlings, obtained from in vitro germinated seeds, were used as explant sources in micropropagation studies. The highest percentage of shoot induction (11.33 shoots/explant) was determined in 1 ppm 6-benzyl amino purine and plant growth regulator-free MS medium …

Impact Of Climate Change On Wheat Production In Kentucky, Kathleen Russell, Chad Lee, Rebecca L. Mcculley, David Van Sanford

Plant and Soil Sciences Research Report

Summary:

• From 2002 to 2012, Kentucky winter wheat ranged in value from $52 million to $209 million.
• Climate change and variability have the potential to significantly impact this important economic enterprise within our state.
• This report summarizes the current state of knowledge of the potential of climate change to impact wheat production in Kentucky and surrounding states.

Quantitative Trait Locus Analysis Of Unsaturated Fatty Acids In A Recombinant Inbred Population Of Soybean, Xianzhi Wang, Guo-Liang Jiang, Marci Green, Roy A. Scott, D. L. Hyten, P. B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Soybean [Glycine max (L.) Merr.] is an important oilseed crop which produces about 30 %of the world’s edible vegetable oil. The quality of soybean oil is determined by its fatty acid composition. Soybean oil high in oleic and low in linolenic fatty acids is desirable for human consumption and other uses. The objectives of this study were to identify quantitative trait loci (QTLs) for unsaturated fatty acids and to evaluate the genetic effects of single QTL and QTL combinations in soybean. A population of recombinant inbred lines derived from the cross of SD02-4-59 X A02-381100 was evaluated for fatty …

Detection And Confirmation Of Quantitative Trait Loci For Soybean Seed Isoflavones, Christopher J. Smallwood, Catherine N. Nyinyi, Dean A. Kopsell, Carl E. Sams, Dennis R. West, Pengyin Chen, Stella K. Kantartzi, P. B. Cregan, D. L. Hyten, Vincent R. Pantalone

Department of Agronomy and Horticulture: Faculty Publications

Interest in soybean [Glycine max (L.) Merr.] isoflavones has increased in recent years owing to numerous reported health benefits. Consequently, quantitative trait loci (QTL) detection for marker-assisted breeding for isoflavones is being examined for genetic gains. This study sought to detect QTL for soybean isoflavones in a population of 274 recombinant inbred lines derived from a cross between ‘Essex’ and ‘Williams 82’ that were subdivided and tested by maturity (early, mid, and late). The field tests were conducted in three environments in 2009 (Knoxville, TN; Harrisburg, IL; and Stuttgart, AR). The population was genotyped with 480 polymorphic single nucleotide …

Transcriptomic And Physiological Characterization Of The Fefe Mutant Of Melon (Cucumis Melo) Reveals New Aspects Of Iron-Copper Crosstalk, Brian M. Waters, Samuel A. Mcinturf, Keenan Amundsen

Department of Agronomy and Horticulture: Faculty Publications

Iron (Fe) and copper (Cu) homeostasis are tightly linked across biology. In previous work, Fe deficiency interacted with Cu-regulated genes and stimulated Cu accumulation. The C940-fe (fefe) Fe-uptake mutant of melon (Cucumis melo) was characterized, and the fefe mutant was used to test whether Cu deficiency could stimulate Fe uptake. Wild-type and fefe mutant transcriptomes were determined by RNA-seq under Fe and Cu deficiency. FeFe-regulated genes included core Fe uptake, metal homeostasis, and transcription factor genes. Numerous genes were regulated by both Fe and Cu. The fefe mutant was rescued by high Fe or by …

Arabidopsis Lipins, Pdat1 Acyltransferase, And Sdp1 Triacylglycerol Lipase Synergistically Direct Fatty Acids Toward Β-Oxidation, Thereby Maintaining Membrane Lipid Homeostasis, Jilian Fan, Chengshi Yan, Rebecca Roston, John Shanklin, Changcheng Xu

Department of Agronomy and Horticulture: Faculty Publications

Triacylglycerol (TAG) metabolism is a key aspect of intracellular lipid homeostasis in yeast and mammals, but its role in vegetative tissues of plants remains poorly defined. We previously reported that PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE1 (PDAT1) is crucial for diverting fatty acids (FAs) from membrane lipid synthesis to TAG and thereby protecting against FA-induced cell death in leaves. Here, we show that overexpression of PDAT1 enhances the turnover of FAs in leaf lipids. Using the trigalactosyldiacylglycerol1-1 (tgd1-1) mutant, which displays substantially enhanced PDAT1- mediated TAG synthesis, we demonstrate that disruption of SUGAR-DEPENDENT1 (SDP1) TAG lipase or PEROXISOMAL TRANSPORTER1 (PXA1) severely decreases …

Rapid Fluctuations In Mid-Latitude Siliceous Plankton Production During The Middle Eocene Climatic Optimum (Odp Site 1051, Western North Atlantic), Jakub Witkowski, Steven M. Bohaty, Kirsty M. Edgar, David M. Harwood

ANDRILL Research and Publications

The Middle Eocene Climatic Optimum (MECO; ~ 40 million years ago [Ma]) is one of the most prominent transient global warming events in the Paleogene. Although the event is well documented in geochemical and isotopic proxy records at many locations, the marine biotic response to the MECO remains poorly constrained. We present new high-resolution, quantitative records of siliceous microplankton assemblages from the MECO interval of Ocean Drilling Program (ODP) Site 1051 in the subtropical western North Atlantic Ocean, which are interpreted in the context of published foraminiferal and bulk carbonate stable isotope (δ¹⁸O and δ¹³C) records. …

Characterization Of Putative Defense Genes In Nonvascular Plants, Blaine Harlan

Undergraduate Honors Thesis Collection

Vascular plants have many known defenses against herbivory and pathogen infection. One inducible defense system that has been extensively studied in vascular plants is systemic acquired resistance (SAR), which is a plant-wide response that results in resistance to a wide range of pathogens Many genes that play a role in SAR have been characterized. Although several studies of plant-pathogen interactions in non-vascular plants have occurred, it was not until recently that the existence of SAR was shown in these plants. The goal of the present study was to confirm the presence of homologous defense genes in moss, and to study …

Nelsonioideae (Lamiales: Acanthaceae): Revision Of Genera And Catalog Of Species, Thomas F. Daniel, Lucinda A. Mcdade

Aliso: A Journal of Systematic and Floristic Botany

A taxonomic account of Acanthaceae subfamily Nelsonioideae based on morphological and phylogenetic data treats five genera with 172 species: Anisosepalum (3), Elytraria (21), Nelsonia (2), Saintpauliopsis (1), and Staurogyne (145). Two other currently recognized genera, Gynocraterium and Ophiorrhiziphyllon, are included within Staurogyne, and the new combinations, Staurogyne guianensis and S. macrobotrya, are proposed. Probable apomorphic and other diagnostic macro- and micromorphological characters are discussed relative to the subfamily and genera. Characters of the inflorescence, androecium (especially pollen), and seed show important phylogenetic and diagnostic signal. A key to genera, generic descriptions and discussions, illustrations, and distribution maps …

Chemical Control Of Turfgrass Diseases 2014, Paul Vincelli, Gregg Munshaw

Agriculture and Natural Resources Publications

Turfgrasses under intensive management are often subject to outbreaks of infectious diseases. Diseases usually are most damaging when weather or cultural conditions favor the disease-causing agent but not plant growth and vigor. Cultural conditions that predispose turfgrass to diseases include close mowing, inadequate or excessive nitrogen fertility, light or frequent irrigation, excessive thatch, poor drainage, and shade.

Good turf management practices often greatly reduce the impact of disease by promoting healthy plants that are better able to resist infections. Even under good management, however, diseases sometimes cause excessive damage to highly managed turfgrasses. The proper use of fungicides in these …

Plant Community Composition And Structure Monitoring For Agate Fossil Beds National Monument, 2013 Annual Report, Isabel W. Ashton, Michael Prowatzke

United States National Park Service: Publications

Introduction

During the last century, much of the prairie within the Northern Great Plains has been plowed for cropland, planted with non-natives to maximize livestock production, or otherwise developed, making it one of the most threatened ecosystems in the United States. Within Nebraska, greater than 77% of the area of native mixed-grass prairie has been lost since European settlement (Samson and Knopf 1994). The National Park Service (NPS) plays an important role in preserving and restoring some of the last pieces of intact prairies within its boundaries. The stewardship goal of the NPS is to “preserve ecological integrity and cultural …

Sudden Aspen Decline Report For Spruce Beetle Epidemic And Aspen Decline Management Response Eis, Jim Worrall, Suzanne Marchetti, Gerald E. Rehfeldt

Aspen Bibliography

Aspen is an important component of GMUG’s forests. Over 288,000 ha (712,000 acres) of aspendominated forest type (TAA) occur across the GMUG (Table 1). Just over half (55%) of the aspen forest type is outside wilderness and roadless areas.

Four Common Setaria Species Are Alternative Hosts For Clavibacter Michiganensis Subsp. Nebraskensis, Causal Agent Of Goss's Bacterial Wilt And Blight Of Corn, Craig B. Langemeier, Tamra A. Jackson-Ziems, Greg R. Kruger

Department of Plant Pathology: Faculty Publications

Goss’s bacterial wilt and blight, caused by Clavibacter michiganensis subsp. nebraskensis (Cmn), has reemerged as an important disease of Zea mays (corn) in the U.S. Midwest. Results from a 2011 multistate survey indicated that Setaria spp. (foxtail) were often present in corn fields with a history of Cmn. The objective of this research was to determine if Setaria spp. that are common in the Midwest are susceptible to infection by Cmn. In the greenhouse, seedlings of four Setaria spp., including S. viridis (green foxtail), S. faberi (giant foxtail), S. verticillata (bristly foxtail), and S. pumila (yellow foxtail), and Zea mays …

What’S New In Plant Pathology, Tamra A. Jackson-Ziems, Loren Giesler, Robert M. Harveson, Stephen N. Wegulo, Kevin Korus

Department of Plant Pathology: Faculty Publications

Disease Management Products

During the past year several new products have become available for disease management. The new products are summarized in Tables 1 and 2, as well as included in the 2014 Guide for Weed Management in Nebraska with Insecticide and Fungicide Information. In addition, fungicides labeled for use on sorghum and sunflower have also been added to the publication.

Table 1. New Foliar Fungicides

Table 2. New Seed Nematicide

Disease Identification and Management Resources

Ficotylus Laselvae N. Sp. (Tylenchomorpha: Anguinidae) Associated With Ficus Colubrinae In Costa Rica, Robin M. Giblin-Davis, Natsumi Kanzaki, Kerrie A. Davies, Weimin Ye, Yongsan Zeng, Barbara J. Center, Alejandro Esquivel, Thomas O. Powers

Department of Plant Pathology: Faculty Publications

Ficotylus laselvae n. sp. was recovered from under the bracts of figs (syconia) of Ficus colubrinae from La Selva, Costa Rica, during a survey of nematode rainforest biodiversity and is described herein. This is only the second report of an association between the nematode suborder Tylenchina and the sycones of figs. Previous reports of most nematode associates of the sycones of figs have been from the lumen and involved transmission by female fig wasp pollinators (Agaonidae) during pollination/oviposition (e.g., Schistonchus and Parasitodiplogaster spp.). The association between F. laselvae n. sp. and Ficus colubrinae may involve an invertebrate host, …

Viruses As Nanoparticles: Structure Versus Collective Dynamics, S. Sirotkin, A. Mermet, M. Bergoin, V. Ward, James L. Van Etten

James Van Etten Publications

In order to test the application of the “nanoparticle” concept to viruses in terms of low-frequency dynamics, large viruses (140–190 nm) were compared to similar-sized polymer colloids using ultra-small-angle x-ray scattering and very-low-frequency Raman or Brillouin scattering. While both viruses and polymer colloids show comparable highly defined morphologies, with comparable abilities of forming self-assembled structures, their respective abilities to confine detectable acoustic vibrations, as expected for such monodisperse systems, differed. Possible reasons for these different behaviors are discussed.

Viruses Infecting Marine Picoplancton Encode Functional Potassium Ion Channels, Fenja Siotto, Corinna Martin, Oliver Rauh, James L. Van Etten, Indra Schroeder, Anna Moroni, Gerhard Thiel

James Van Etten Publications

Phycodnaviruses are dsDNA viruses, which infect algae. Their large genomes encode many gene products, like small K+ channels, with homologs in prokaryotes and eukaryotes. Screening for K+ channels revealed their abundance in viruses from fresh-water habitats. Recent sequencing of viruses from marine algae or from salt water in Antarctica revealed sequences with the predicted characteristics of K+ channels but with some unexpected features. Two genes encode either 78 or 79 amino acid proteins, which are the smallest known K+ channels. Also of interest is an unusual sequence in the canonical α-helixes in K+ channels. Structural prediction algorithms indicate that the …

Wheat Streak Mosaic Virus Infects Systemically Despite Extensive Coat Protein Deletions: Identification Of Virion Assembly And Cell-To-Cell Movement Determinants, Satyanarayana Tatineni, Frank A. Kovacs, Roy C. French

Department of Plant Pathology: Faculty Publications

Viral coat proteins function in virion assembly and virus biology in a tightly coordinated manner with a role for virtually every amino acid. In this study, we demonstrated that the coat protein (CP) of Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) is unusually tolerant of extensive deletions, with continued virion assembly and/or systemic infection found after extensive deletions are made. A series of deletion and point mutations was created in the CP cistron of wild-type and/or green fluorescent protein-tagged WSMV, and the effects of these mutations on cell-to-cell and systemic transport and virion assembly of WSMV …

Phytophthora Ramorum, Sydney E. Everhart, Javier F. Tabima, Niklaus J. Grünwald

Department of Plant Pathology: Faculty Publications

Phytophthora ramorum is a recently emerged plant pathogen and causal agent of one of the most destructive and devastating diseases currently affecting US horticulture and forests (Rizzo et al. 2002, 2005). This oomycete pathogen was discovered in Marin County, California, in the mid-1990s, causing sudden oak death on coast live oak (Quercus agrifolia) and tanoak (Notholithocarpus densiflorus) and simultaneously discovered in Europe causing foliar blight on Rhododendron and Viburnum (Rizzo et al. 2002; Werres et al. 2001). It is now known to affect more than 100 plant species, including economically important nursery and forest host species …

Comparison Of Herbicide Systems For Dark Fire-Cured Tobacco, William A. Bailey, Tim Lax, Bobby Hill

Plant and Soil Sciences Research Report

Field experiments were conducted at Murray, KY in 2005, 2006, and 2007 to compare dark tobacco tolerance and weed control from various herbicide systems applied prior to transplanting. Herbicide treatments included sulfentrazone at 0.38 lb ai/A (12 oz/A Spartan 4F) applied pretransplant (PT), clomazone at 1 lb ai/A PT (2.67 pt/A Command 3ME), sulfentrazone at 0.38 lb ai/A plus clomazone at 1 lb ai/A PT, pendimethalin at 1.48 lb ai/A (3.6 pt/A Prowl 3.3EC) applied pretransplant incorporated (PTI), pendimethalin at 1.48 lb ai/A PTI followed by sulfentrazone at 0.38 lb ai/A PT, pebulate at 4 lb ai/A PTI (2.67 qt/A …

Boron Nutrition Of Burley And Dark Tobacco, Laura Ann Frakes Mitchell

Theses and Dissertations--Plant and Soil Sciences

The incidences of suspected Boron (B) deficiency have increased recently in Kentucky tobacco fields, potentially due to recent changes in management practices. The symptoms observed in the field include; hollow stalk, stunted growth, deformed or no bud formation, small slits on the lower leaf midrib and uncontrollable breaking of the midrib approximately two inches from the stalk. B is a micronutrient tobacco needs in minute amounts, however excessive additions of B could cause toxicity. The objectives of this work were to 1) establish critical points for B sufficiency, 2) describe and define B deficiency and toxicity symptoms and 3) develop …

Characterization Of The Role Of Salicylic Acid In Plant-Pathogen Interactions In Moss, Erica Grabinski

Undergraduate Honors Thesis Collection

The central objective of this project is to explore defense systems that are induced in two moss species, Amblystegium serpens and Physcomitrella patens, upon inoculation with the fungus, Pythium irregulare. In vascular plants, systemic defense is associated with the plant hormone salicylic acid (SA). I hypothesize that when the moss are treated exogenously with SA, the organisms will undergo a systemic defense response, which will involve the induction of defense-related genes and increased resistance to future P. irregulare infection, that is directly correlated with the amount of hormone applied. If the role of SA in plant defense in A. serpens …

Saudi Arabian Students In Detroit Use Natural Health Products More So Than Other University Students In Detroit, Samiah Naji Alqahtani

Wayne State University Theses

Natural Health Products (NHP), are defined as products that derive from organisms and may include supplements and herbal/traditional remedies. Prior research indicates that females use NHP more than males. We have unpublished data to show that students use NHP for health maintenance with significantly different use of NHP by Native/Aboriginal students vs. other students. Less is known about Saudi students. We hypothesize that: (1) There are gender differences in NHP used; and (2) There are geo-ethnic differences in NHP used. We also determine the predictor variables that influence NHP use by students. Students from Wayne State University (n=560; 193 …

A Reference Genome For Common Bean And Genome-Wide Analysis Of Dual Domestications, Jeremy Schmutz, Phillip E. Mcclean, Sujan Mamidi, G. Albert Wu, Steven B. Cannon, Jane Grimwood, Jerry Jenkins, Shengqiang Shu, Qijian Song, Carolina Chavarro, Mirayda Torres-Torres, Valerie Geffroy, Samira Mafi Moghaddam, Dongying Gao, Brian Abernathy, Kerrie Barry, Matthew Blair, Mark A. Brick, Mansi Chovatia, Paul Gepts, David M. Goodstein, Michael Gonzales, Uffe Hellsten, D. L. Hyten, Gaofeng Jia, James D. Kelly, Dave Kudrna, Rian Lee, Manon M.S. Richard, Phillip N. Miklas, Juan M. Osorno, Josiane Rodrigues, Vincent Thareau, Carlos A. Urrea Florez, Mei Wang, Yeisoo Yu, Ming Zhang, Rod A. Wing, P. B. Cregan, Daniel S. Rokhsar, Scott A. Jackson

Department of Agronomy and Horticulture: Faculty Publications

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. …

Genome Size And Phylogenetic Relationships Between The Tunisian Species Of The Genus Calligonum (Polygonaceae), Hassen Gouja, Alfredo Garcia Fernández, Teresa Garnatje, Aly Raies, Mohamed Neffati

Turkish Journal of Botany

The species of the genus Calligonum L. (Polygonaceae) that appear in Tunisian deserts play an important role in maintaining local ecosystems and supply important natural resources in these regions. In this study, 31 individuals belonging to the 3 hypothetical species of the genus Calligonum (Calligonum arich Le Houér., Calligonum azel Maire, and Calligonum comosum L'Hér.) were collected from 12 populations in 6 localities of the Tunisian desert and examined to assess the relationship between species. Phylogenetic analyses using 1 nuclear (ITS) and 2 plastid regions (trnL-trnF and rbcL) and genome size assessments are used in this study to evaluate the …