Plant Biology Commons^™

Comparative Analyses Of Two Geraniaceae Transcriptomes Using Next-Generation Sequencing, Jinxin Zhang, Tracey A. Ruhlman, Jeffrey P. Mower, Robert K. Jansen

Center for Plant Science Innovation: Faculty Publications

Background: Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum.

Results: Normalized cDNA libraries of G. maderense and …

Arabidopsis 56–Amino Acid Serine Palmitoyltransferase- Interacting Proteins Stimulate Sphingolipid Synthesis, Are Essential, And Affect Mycotoxin Sensitivity, Athen N. Kimberlin, Saurav Majumder, Gongshe Han, Ming Chen, Rebecca E. Cahoon, Julie M. Stone, Teresa M. Dunn, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Maintenance of sphingolipid homeostasis is critical for cell growth and programmed cell death (PCD). Serine palmitoyltransferase (SPT), composed of LCB₁ and LCB₂ subunits, catalyzes the primary regulatory point for sphingolipid synthesis. Small subunits of SPT (ssSPT) that strongly stimulate SPT activity have been identified in mammals, but the role of ssSPT in eukaryotic cells is unclear. Candidate Arabidopsis thaliana ssSPTs, ssSPTa and ssSPTb, were identified and characterized. Expression of these 56–amino acid polypeptides in a Saccharomyces cerevisiae SPT null mutant stimulated SPT activity from the Arabidopsis LCB₁/LCB₂ heterodimer by >100-fold through physical interaction with LCB …

Pseudomonas Syringae Pv. Syringae Uses Proteasome Inhibitor Syringolin A To Colonize From Wound Infection Sites, Johana C. Misas-Villamil, Izabella Kolodziejek, Emerson Crabill, Farnusch Kaschani, Sherry Niessen, Takayuki Shindo, Markus Kaiser, James R. Alfano, Renier A. L. Van De Hoorn

Center for Plant Science Innovation: Faculty Publications

Infection of plants by bacterial leaf pathogens at wound sites is common in nature. Plants defend wound sites to prevent pathogen invasion, but several pathogens can overcome spatial restriction and enter leaf tissues. The molecular mechanisms used by pathogens to suppress containment at wound infection sites are poorly understood. Here, we studied Pseudomonas syringae strains causing brown spot on bean and blossom blight on pear. These strains exist as epiphytes that can cause disease upon wounding caused by hail, sand storms and frost. We demonstrate that these strains overcome spatial restriction at wound sites by producing syringolin A (SylA), a …

Functional Modeling Identifies Paralogous Solanesyl-Diphosphate Synthases That Assemble The Side Chain Of Plastoquinone-9 In Plastids, Anna Block, Rikard Fristedt, Sara Rogers, Jyothi Kumar, Brian Barnes, Joshua Barnes, Christian Elowsky, Yashitola Wamboldt, Sally Ann Mackenzie, Kevin Redding, Sabeeha S. Merchant, Gilles J. Basset

Center for Plant Science Innovation: Faculty Publications

Background: Plastid isoforms of solanesyl-diphosphate synthase catalyze the elongation of the prenyl side chain of plastoquinone-9.

Results: Corresponding mutants display lower levels of plastoquinone-9 and plastochromanol-8 and display intact levels of vitamin E.

Conclusion: Plastochromanol-8 originates from a subfraction of non-photoactive plastoquinol-9 and is not essential for seed longevity.

Significance: Viable plastoquinone-9 mutants are invaluable tools for understanding plastid metabolism.

Mutational Analyses Of A Fork Head Associated Domain Protein, Dawdle, In Arabidopsis Thaliana, Lakshmi Ayiloor Narayanan, Dipaloke Mukherjee, Shuxin Zhang, Bin Yu, David Chevalier

Center for Plant Science Innovation: Faculty Publications

DAWDLE (DDL) gene encodes a protein that contains an N-terminal arginine-rich domain and a C-terminal Fork Head Associated (FHA) domain in Arabidopsis thaliana. DDL protein is believed to function in microRNA biogenesis by mediating the recruitment of pri-microRNA to DICER-LIKE 1 and also stabilizing the microRNA. The aim of this study was to conduct a structure-function analysis to identify the regions in DDL that are of functional significance. Targeted Induced Local Lesions in Genome screen was performed in the Columbia erecta-105 background of Arabidopsis resulting in the identification of eight point mutations spanning DDL. The mutants were characterized by …

Cdc5, A Dna Binding Protein, Positively Regulates Posttranscriptional Processing And/Or Transcription Of Primary Microrna Transcripts, Shuxin Zhang, Meng Xie, Guodong Ren, Bin Yu

Center for Plant Science Innovation: Faculty Publications

CDC5 is a MYB-related protein that exists in plants, animals, and fungi. In Arabidopsis, CDC5 regulates both growth and immunity through unknown mechanisms. Here, we show that CDC5 from Arabidopsis positively regulates the accumulation of microRNAs (miRNAs), which control many biological processes including development and adaptations to environments in plants. CDC5 interacts with both the promoters of genes encoding miRNAs (MIR) and the DNA-dependent RNA polymerase II. As a consequence, lack of CDC5 reduces the occupancy of polymerase II at MIR promoters, as well as MIR promoter activities. In addition, CDC5 is associated with the DICER–LIKE1 complex, …

Evaluating The Success Of Seed Sowing In A New England Grassland, Chad C. Jones, Glenn D. Dreyer, Nels Barrett

Botany Faculty Publications

Grassland habitat is declining in the northeastern United States, leading to a decline in associated native species. Consequently, there is considerable interest by land managers in conserving and restoring grassland habitats in the Northeast. However, unlike the Great Plains and Europe, quantitative monitoring of restoration sites is uncommon, making it difficult to improve new restoration projects. Here we evaluate a grassland restoration in Waterford, Connecticut to determine if mechanical clearing of woody vegetation combined with sowing 23 native grasses and forbs led to successful establishment of these species. We also compared cover, diversity, and colonization by exotic and woody species …

Micropropagación De Hedeoma Drummondii Benth, Su Lin Zamora-Hierro, Ana Laura López-Escamilla

Estudios científicos en el estado de Hidalgo y zonas aledañas

La especie Hedeoma drummondii Benth (Lamiaceae) es una planta útil de Hidalgo, México, con uso medicinal, comestible y con potencial de insecticida por el contenido de pulegona en sus aceites esenciales extraídos. En parte por su valor, la especie ha sido sobrecolectada en el medio silvestre, por lo que es necesario establecer estrategias como la micropropagación para la conservación de la misma y para la obtenció sus aceites esenciales. Este trabajo es un reporte de los avances en el cultivo de H. drummondii. Semillas de H. drummondii se desinfectaron superficialmente y se colocaron en cuatro medios de cultivo diferentes: …

Comparative Studies Of Differential Gene Calling Using Rna-Seq Data, Ximeng Zheng, Etsuko N. Moriyama

Center for Plant Science Innovation: Faculty Publications

Background: With its massive amount of data, gene-expression profiling by RNA-Seq has many advantanges compared with microarray experiments. RNA-Seq analysis, however, is fundamentally different from microarray data analysis. Techniques developed for analyzing microarray data thus cannot be directly applicable for the digital gene expression data. Several statistical methods have been developed for identifying differentially expressed genes specifically from RNA-Seq data over the past few years.
Results: In this study, we examined the performance of differential gene-calling methods using RNA-Seq data in practical situations. We focused on two representative methods: one parametric method, DESeq, and one nonparametric method, NOISeq. …

A Novel Function Prediction Approach Using Protein Overlap Networks, Shide Liang, Dandan Zheng, Daron M. Standley, Huarong Guo, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Construction of a reliable network remains the bottleneck for network-based protein function prediction. We built an artificial network model called protein overlap network (PON) for the entire genome of yeast, fly, worm, and human, respectively. Each node of the network represents a protein, and two proteins are connected if they share a domain according to InterPro database.
Results: The function of a protein can be predicted by counting the occurrence frequency of GO (gene ontology) terms associated with domains of direct neighbors. The average success rate and coverage were 34.3% and 43.9%, respectively, for the test genomes, …

A Thraustochytrid Diacylglycerol Acyltransferase 2 With Broad Substrate Specificity Strongly Increases Oleic Acid Content In Engineered Arabidopsis Thaliana Seeds, Chunyu Zhang, Umidjon Iskandarov, Elliott T. Klotz, Robyn L. Stevens, Rebecca E. Cahoon, Tara J. Nazarenus, Suzette L. Pereira, Edgar B. Cahoon

Center for Plant Science Innovation: Faculty Publications

Diacylglycerol acyltransferase (DGAT) catalyses the last step in acyl-CoA-dependent triacylglycerol (TAG) biosynthesis and is an important determinant of cellular oil content and quality. In this study, a gene, designated TaDGAT2, encoding a type 2 DGAT (DGAT2)-related enzyme was identified from the oleaginous marine protist Thraustochytrium aureum. The deduced TaDGAT2 sequence contains a ~460 amino acid domain most closely related to DGAT2s from Dictyostelium sp. (45–50% identity). Recombinant TaDGAT2 restored TAG biosynthesis to the Saccharomyces cerevisiae H1246 TAG-deficient mutant, and microsomes from the complemented mutant displayed DGAT activity with C16 and C18 saturated and unsaturated fatty acyl-CoA and diacylglycerol …

Fuzzy Clustering Of Cpp Family In Plants With Evolution And Interaction Analyses, Tao Lu, Yongchao Dou, Chi Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Transcription factors have been studied intensively because they play an important role in gene expression regulation. However, the transcription factors in the CPP family (cystein-rich polycomb-like protein), compared with other transcription factor families, have not received sufficient attention, despite their wide prevalence in a broad spectrum of species, from plants to animals. The total number of known CPP transcription factors in plants is 111 from 16 plants, but only 2 of them have been studied so far, namely TSO1 and CPP1 in Arabidopsis thaliana and soybean, respectively.
Methods: In this work, to study their functions, we applied …

Germinación In Vitro De Laelia Speciosa (Kunth) Schltr., Una Herramienta Para Su Conservación Ex Situ, María Ascención Aguilar-Morales, Ana Laura López-Escamilla

Estudios científicos en el estado de Hidalgo y zonas aledañas

Dentro de la familia Orchideaceae, Laelia speciosa (Kunth) Schltr. es probablemente la orquídea más explotada en México, por lo que es importante establecer estrategias de conservación. El objetivo del presente trabajo fue determinar el mejor medio de cultivo para la germinación in vitro de semillas. Cápsulas maduras e inmaduras de L. speciosa, fueron colectadas en la Reserva de la Biosfera Barranca de Metztitlán, Hidalgo, México y las semillas se sembraron en condiciones in vitro en cuatro tratamientos: Murashige y Skoog (MS) (1962) al 100%; MS al 50%; Knudson C (KC) (1946) al 50% y KC al 100%. A los …

Evaluación De Diferentes Tratamientos Pregerminativos Y Osmóticos En La Germinación De Semillas Prosopis Laevigata (Humb. & Bonpl. Ex Willd) M. C. Johnston, Jorge Alejandro Sobrevilla-Solís, Maritza López-Herrera, Ana Laura López-Escamilla, Leticia Romero-Bautista

Estudios científicos en el estado de Hidalgo y zonas aledañas

El mezquite es un elemento importante en la vegetación de ambientes semiáridos ya que tiene un gran valor ambiental. Biológicamente, las semillas de Prosopis laevigata presentan dificultades de germinación debido a la presencia de una testa impermeable causando una latencia física. El objetivo de esta investigación fue evaluar 10 diferentes tratamientos de escarificación y la combinación de los tratamientos que obtuvieron los mayores porcentajes de germinación, con cuatro soluciones osmóticas para aumentar la germinación de P. laevigata. Los índices de germinación demuestran que los tratamientos de escarificación de índole mecánico, son los de mayor efectividad ya que estos dañan …

Propagación In Vitro De Mammillaria Schiedeana Schiedeana (Cactaceae), Subespecie Endémica Y Amenazada De Extinción De La Barranca De Metztitlán, Hidalgo, Daniela Soria-Campos, Ana Laura López-Escamilla, Laura Patricia Olguín-Santos

Estudios científicos en el estado de Hidalgo y zonas aledañas

Se reporta por primera vez la micropropagación de la subespecie Mammillaria schiedeana schiedeana, cactácea mexicana considerada como amenazada de extinción por la Norma Oficial Mexicana. Se obtuvo la formación de brotes por activación areolar utilizando explantes longitudinales procedentes de brotes regenerados de un ciclo previo de cultivo y a partir de plántulas germinadas in vitro los cuales se sembraron en medio basal Murashige y Skoog (MS) suplementado con 6-bencilaminopurina (BA) y ácido α-naftalenacético (ANA) a diferentes concentraciones. La producción de brotes en el medio de proliferación se evaluó después de dos meses. La mejor concentración para la formación de …

Plantas Medicinales De Omitlán, Hidalgo, México, I. Fuentes-Cervantes, Miguel Ángel Villavicencio-Nieto, Blanca Estela Pérez-Escandón

Estudios científicos en el estado de Hidalgo y zonas aledañas

Se seleccionó la cabecera municipal de Omitlán, Hidalgo, con el objetivo de evaluar el uso de plantas medicinales, documentar la importancia de dichas especies y estimar el estado actual del conocimiento tradicional en la comunidad. Por medio de entrevistas se detectaron las especies de plantas de uso medicinal, las cuales fueron recolectadas e identificadas, y se llevó a cabo el análisis de datos. Se registraron 134 etnoespecies de plantas, se identificaron 102 especies, las cuales están distribuidas en 53 familias y 89 géneros. La familia y género mejor representados son Asteraceae y Sedum. En el promedio de menciones por …

Smaller, Faster Stomata: Scaling Of Stomatal Size, Rate Of Response, And Stomatal Conductance, Paul Drake, Raymond H. Froend, Peter Franks

Research outputs 2013

Maximum and minimum stomatal conductance, as well as stomatal size and rate of response, are known to vary widely across plant species, but the functional relationship between these static and dynamic stomatal properties is unknown. The objective of this study was to test three hypotheses: (i) operating stomatal conductance under standard conditions (gop) correlates with minimum stomatal conductance prior to morning light [gmin(dawn)]; (ii) stomatal size (S) is negatively correlated with gop and the maximum rate of stomatal opening in response to light, (dg/dt)max; and (iii) gop correlates negatively with instantaneous water-use efficiency (WUE) despite positive correlations with maximum rate …

Synthesis, Characterization, And Properties Of Mononuclear And Dinuclear Ruthenium(Ii) Complexes Containing Phenanthroline And Chlorophenanthroline, Anwar A. Bhuiyan, X. Du

Journal of the Arkansas Academy of Science

The study of photophysical and photochemical properties of ruthenium complexes is of great interest for fundamental practical reasons. Ruthenium complexes have been investigated for use in artificial photosynthesis. This paper deals with the synthesis and spectroscopic investigation of custom-designed ruthenium complexes containing phenanthroline and chloro-phenanthroline ligands. These complexes maybe useful for biological electron-transfer studies. The heteroleptic ruthenium monomer complex Ru(phen)2(Cl-phen) (where phen = 1,10-phenanthroline and Cl-phen=5-chloro-1,10-phenanthroline) was prepared in a two-step procedure previously developed in our laboratory. This monomer complex was used to prepare the ruthenium homometallic dimer complex, (phen)2Ru(phen-phen)Ru(phen)2, by utilizing the Ni-catalyzed coupling reaction. Both complexes were purified …

2013 Virginia Wildflower Of The Year: Redbud, Cercis Canadensis, W. John Hayden

Biology Faculty Publications

Redbuds are small trees or shrubs that may attain heights of 10 m or so. Leaves are alternate and two-ranked, simple, entire, deciduous, broadly cordate, with an acute apex, 611 cm long, 712 cm wide, and palmately veined. Petioles have two swollen pulvini, one at its connection with the stem, the other at its junction with the leaf blade.

Efficacy Of Foliar Fungicides And Application Timing Of Stratego Yld On Field Corn In Nebraska, 2013, C. M. Schleicher, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

A foliar fungicide efficacy timing trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. Corn hybrid NK ‘N68B’, rating of “fair” (7 out of 9) for gray leaf spot (GLS), not rated for common rust (CR), and “excellent” (2 out of 9) for southern rust (SR), was planted on 15 May in 30-in. rows at a target population of 31,763 plants/A. The trial area was disked with corn as the previous year’s crop. Nine treatments and a nontreated control were replicated six times in a randomized complete block design. Each plot was four …

Evaluation Of Foliar Fungicide And Application Timing On Field Corn Following Hail Event At Scal In Nebraska, 2013, C. M. Schleicher, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

A foliar fungicide efficacy timing trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE to determine the potential effect of foliar fungicides and their application timing on lodging and yield after a late season hail event. Novartis corn hybrid N6800 GT with CruiserMaxx 250 seed treatment was planted on 24 May in 30 in. rows with a target population of 32,000 plants/A. Force 3G (4 oz/1,000 row ft) was applied in-furrow at planting. Lexar (3 qt/A) + Roundup UltraMax (32 fl oz/A) was applied on 5 Jun. The trial area had corn as …

Efficacy Evaluation Of Fortix And Headline Amp Application Timing In Field Corn In Nebraska, 2013, C. M. Schleicher, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

A foliar fungicide efficacy timing trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. Corn hybrid NK ‘N68B’, rating of “fair” (7 out of 9) for gray leaf spot (GLS), not rated for common rust (CR), and “excellent” (2 out of 9) for southern rust (SR), was planted on 15 May in 30-in. rows at a target population of 31,763 plants/A. The trial area was disked with corn as the previous year’s crop. Nine treatments were replicated six times in a randomized complete block design. Each plot was four rows (10 ft) wide …

Efficacy Evaluation Of Foliar Fungicide Application Timing In Field Corn In Nebraska, 2012, C. M. Schleicher, T. A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

A foliar fungicide efficacy trial was conducted at the University of Nebraska-Lincoln South Central Agricultural Laboratory near Clay Center, NE. DeKalb corn hybrid DKC 64-83, rating of “good” (6 out of 9) for gray leaf spot (GLS), “very good” (4 out of 9) for common rust (CR), and “good” (5 out of 9) for southern rust (SR), was planted on 26 Apr in 30-in. rows at a target population of 30,600 plants/A. The trial area was disked with corn as the previous year’s crop. Six foliar fungicide treatments and a non-treated control were replicated six times in a randomized complete …

What’S New In Plant Pathology, Loren Giesler, Tamra A. Jackson-Ziems, Casey Schleicher, Kevin Korus

Department of Plant Pathology: Faculty Publications

Extension Plant Pathology Team Update

Plant and Pest Diagnostic Clinic Update

Disease Management Products

Table 1. Foliar Fungicide Label Updates

Table 2. New Products

Impacts Of Drought On Disease Development And Management, Stephen Wegulo, Loren Giesler, Robert Harveson, Tamra A. Jackson-Ziems, Bo Liu, Kevin Korus

Department of Plant Pathology: Faculty Publications

Drought conditions such as those that occurred in Nebraska in 2012 can impact the development of plant diseases. In general drought slows down or prevents the development of plant diseases caused by pathogens that thrive under moist conditions. However, some diseases are favored by drought. This is because when plants are stressed due to lack of moisture or excessive heat, they become more susceptible to these diseases. This article presents examples of diseases of agronomic crops favored by drought and how to manage them. Data are provided on the effect of dry or wet conditions on the profitability of applying …

Grain Storage Management To Minimize Mold And Mycotoxins, Thomas W. Dorn, Tamra A. Jackson-Ziems

Department of Plant Pathology: Faculty Publications

As most dryland corn producers are aware, the dry and hot growing season in 2012 resulted in reduced corn yields with moderately lower test weights. Along with the reduced test weights are concerns about potential mycotoxin contamination in the drought-stressed grain.

The only way to know for sure if there are mycotoxins in your grain and which specific mycotoxins are present is to collect representative grain samples and have them tested by a certified laboratory.

Many species of fungi can cause ear rot diseases and molding of grain. Most of these fungi become associated with the grain in the field …

Developing White Ash With Resistance To The Emerald Ash Borer, Kaitlin Joy Palla

Open Access Theses

Hypocotyls isolated from mature embryos germinated on Murashige and Skoog (MS) medium supplemented with 22.2 µM 6-benzyladenine (BA) and 0.5 µM thidiazuron (TDZ) were transformed using Agrobacterium tumefaciens strain EHA105 harboring the pBI121-8D2 vector containing the neomycin phosphotransferase (nptII) gene and a full length, codon-optimized Bacillus thuringiensis Cry8Da protoxin gene (cry8D2). Explants were transformed in a bacterial suspension with 100 µM acetosyringone using 90 s sonication and 10 min vacuum-infiltration. Four independent lines of transformed shoots were selectively regenerated on MS medium with 22.2 µM BA, 0.5 µM TDZ, 50 mg L^-1 adenine sulfate, 10% …

Sub1a-Mediated Submergence Tolerance Response In Rice Involves Differential Regulation Of The Brassinosteroid Pathway, Aaron J. Schmitz, Jing J. Folsom, Yusuke Jikamaru, Pamela C. Ronald, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Submergence 1A (SUB1A), is an ethylene response factor (ERF) that confers submergence tolerance in rice (Oryza sativa) via limiting shoot elongation during the inundation period. SUB1A has been proposed to restrict shoot growth by modulating gibberellic acid (GA) signaling.

Our transcriptome analysis indicated that SUB1A differentially regulates genes associated with brassinosteroid (BR) synthesis during submergence. Consistent with the gene expression data, the SUB1A genotype had higher brassinosteroid levels after submergence compared to the intolerant genotype. Tolerance to submergence can be activated in the intolerant genotype by pretreatment with exogenous brassinolide, which results in restricted shoot elongation …

Confirmation Of Allelopathic Chemicals From Reed Canarygrass (Phalaris Arundinacea L.) Roots, Alexander Richard Tomes

All Graduate Theses, Dissertations, and Other Capstone Projects

Reed Canarygrass (Phalaris arundinacea) is an invasive species and a major threat to grasslands and natural wetlands on nearly every landmass (Morrison and Molofsky 1998). Methanol extracts of whole and macerated Reed Canarygrass roots have been found to reduce the germination and growth of lettuce (Lactuca sativa), radish (Raphanus sativus), and the aquatic plant, Reed Mannagrass (Glyceria maxima) (Veit and Proctor 2009). Linoleic, linolenic and palmitic acids were identified in the methanol extracts of both the whole and macerated Reed Canarygrass roots (Proctor 2011). The purpose of this research was to determine if these chemicals individually and in combination would …

The Role Of Polyadenylation In Seed Germination, Liuyin Ma

Theses and Dissertations--Plant and Soil Sciences

Seed germination has many impacts on the uses of seeds, and is an important subject for study. Seed germination is regulated at both transcriptional and post-transcriptional levels. Therefore, it is important to study how polyadenylation regulates gene expression during seed germination. To this end, a modified Illumina GAIIx sequencing protocol (described in Chapter Two) was developed that allows deep coverage of poly(A) site position and distribution.

Alternative polyadenylation (APA) regulates gene expression by choosing one potential poly(A) site on a precursor RNA consequentially shortening/lengthening the mRNA relative to other possible sites. To further explore this phenomenon, genes affected by APA …