Digital Commons Network^™

Trip: Tracking Rhythms In Plants, An Automated Leaf Movement Analysis Program For Circadian Period Estimation, Kathleen Greenham, Ping Lou, Sara E. Remsen, Hany Farid, C Robertson Mcclung

Dartmouth Scholarship

Background: A well characterized output of the circadian clock in plants is the daily rhythmic movement of leaves. This process has been used extensively in Arabidopsis to estimate circadian period in natural accessions as well as mutants with known defects in circadian clock function. Current methods for estimating circadian period by leaf movement involve manual steps throughout the analysis and are often limited to analyzing one leaf or cotyledon at a time.

Methods: In this study, we describe the development of TRiP (Tracking Rhythms in Plants), a new method for estimating circadian period using a motion estimation algorithm that can …

Environmental Data: Soil Moisture, Julia I. Chapman, Eric B. Borth, Ryan W. Mcewan

Data Files: Drew Woods Permanent Plots

Volumetric soil water content measured on May 2, 2015 at Drew Woods State Nature Preserve in Darke County, OH. Data key is provided in a supplemental file.

Herbaceous 2015, Julia I. Chapman, Margaret E. Maloney, Ryan W. Mcewan

Data Files: Drew Woods Permanent Plots

Herbaceous vegetation data collected in 2015 at Drew Woods State Nature Preserve in Darke County, OH. Data key is provided in a supplemental file.

Section Abstracts: Botany

Virginia Journal of Science

Abstracts of the Botany Section for the 93rd Annual Meeting of the Virginia Academy of Science, May 21-23, 2015, James Madison University, Richmond, Virginia

Transcriptomic Insights Into The Morphological Variation Present In Bromeliaceae, Victoria A. Gilkison

Masters Theses & Specialist Projects

The Bromeliaceae family utilizes a wide range of adaptations to inhabit a variety of environments including dry ones. Many attribute the large adaptive radiation of Bromeliaceae throughout the Neotropics to three main features: absorptive trichomes, tank reservoirs, and CAM photosynthesis. Based on leaf morphology and arrangement, root type, and nutrient acquisition, Pittendrigh (1948) conservatively separated bromeliads into four main classes. These four main classes are designated Type I bromeliads, Type II bromeliads, Type III bromeliads and Type IV bromeliads. We used RNA-sequencing of leaf mRNA to investigate similarities and differences in gene expression which can be related back to the …

Accessing Chilling Conditions For Perennial Fruit Crop Production In Kentucky, Yao Xue

Masters Theses & Specialist Projects

Temperate Region fruit and nut trees, and many other perennial plants, require cool winter temperatures (chilling hours) to ensure leaf and flower bud production in the following season. Temperate Regions are characterized by variable winter and spring temperatures. Failure of meeting sufficient chilling requirement results in deformed fruits, unequal maturation, and other plant deformities, thereby reducing quality and yields. Chilling requirements are expressed as number of accumulated hours within a range of approximately 32º to 45ºF or 0º to 7.2ºC. These requirements are specific for level of temperature, length of temperature period, and species and cultivar of plants. Information on …

Heterologous Expression Of Arabidopsis Thaliana Purple Acid Phosphatase Gene (Atpap15) In Crops For Phytoremediation Of Sites Contaminated With Excess Phosphorus, Jane Jeruto Bartonjo

Masters Theses & Specialist Projects

AtPAP15 is one of the purple acid phosphatases expressed by Arabidopsis thaliana that has been extensively studied. Purified AtPAP15 has been shown to exhibit both phytase and phosphomonoesterase activities in acidic pH with maximal activity at pH 4.5. AtPAP15 is a phosphorus starvation inducible (PSI) gene that is expressed highly during phosphorus deficient conditions. In the current study, AtPAP15 was overexpressed in Nicotiana tabaccum under cauliflower mosaic virus (CaMV35S) constitutive promoter. After PCR confirmation of the gene, plants were transferred to the greenhouse and allowed to grow in pots. The pots contained Sta-Green potting mix (Lowe’s Inc., Mooresville, North Carolina,U.S.). …

Characterization Of A Novel Clade Of Transporters In Phytophthora, Stephanie Padula, Paul F. Morris Dr, Howard Casey Cromwell Dr., Menaka Ariyaratne, Andrew Wagner

Honors Projects

The oomycete Phytophthora parasitica has a worldwide distribution and is an economically important pathogen of more than 100 species⁴. RNA-seq analysis showed that one gene, PPTG_16698 has the 5^th highest level of expression of all transport proteins in the zoospore stage, and is highly conserved throughout Phytophthora species. This project attempts to characterize the important biological role that PPTG_16698 plays in P. parasitica and other oomycetes. Three strategies have been implemented to accomplish this goal: growth analysis by heterologous expression in yeast, metabolite analysis in yeast, and construction of a GFP fusion protein to enable localization of …

Activation Of Tomato Bushy Stunt Virus Rna-Dependent Rna Polymerase By Cellular Heat Shock Protein 70 Is Enhanced By Phospholipids In Vitro, Judit Pogany, Peter D. Nagy

Plant Pathology Faculty Publications

Similar to other positive-strand RNA viruses, tombusviruses are replicated by the membrane-bound viral replicase complex (VRC). The VRC consists of the p92 virus-coded RNA-dependent RNA polymerase (RdRp), the viral p33 RNA chaperone, and several co-opted host proteins. In order to become a functional RdRp after its translation, the p92 replication protein should be incorporated into the VRC, followed by its activation. We have previously shown in a cell-free yeast extract-based assay that the activation of the Tomato bushy stunt virus (TBSV) RdRp requires a soluble host factor(s). In this article, we identify the cellular heat shock protein 70 (Hsp70) as …

A Gravity Investigation Of The Tobacco Root Batholith Southwest Montana, Stephen Charles Tatum

Masters Theses

The objective of this research was to delineate and profile the Late Cretaceous Tobacco Root batholith in southwestern Montana through the application of the gravitational method. This survey was accomplished by obtaining 232 gravity measurements in four profiles across the batholith. After correcting for known variations in the gravity field, a Bouguer anomaly map of the batholith and surrounding host rocks was created. Four residual gravity profiles and map, created by subtracting the regional gravity from the Bouguer anomaly, reveal a maximum negative gravity anomaly in the center portion of the batholith which is parallel to the trend of the …

Forest Sustainability In An Altered Landscape Requires Human Intervention, Adam C. Labatore

Biology Theses

Recruitment success determines the abundance and composition of plant communities. Successful recruitment can be summarized as a simple dichotomy of establishment versus seed limitations. Establishment limitation occurs when plant populations are inhibited by habitat availability and quality, whereas seed limitation occurs when seeds fail to arrive in necessary densities. Recruitment failure undermines overstory sustainability if the existing trees cannot replace themselves. Preliminary analysis indicated tree recruitment failure at an urban nature preserve with too few tree seedlings to replace mature canopy trees. These data suggested that the urban forest was not sustainable. The overarching goal of the study was to …

Establishing A Permanent Feeding Site: Reniform Nematode Manipulation Of Soybean Genes, Nathan Wayne Redding

All Theses

Reniform nematode, Rotelynchulus reniformis, is a semi-endoparasite capable of infecting more that 300 host plant species in tropical, subtropical, and warm temperate regions. Female nematodes penetrate host roots and introduce effectors that lead to the formation of multinucleate feeding sites called syncytia. The objective of our study was to identify plant genes involved in the process of syncitium formation. We used a split-root system in which half of a plant’s roots were inoculated with R. reniformis while the rest of the root system remained uninfected. Illumina RNA-seq was used to quantify gene expression patterns in replicate samples of infected and …

Effect Of Germination And Parboiling On Milling, Physicochemical, And Textural Properties Of Medium- And Long-Grain Rough Rice, Ashley Han

Graduate Theses and Dissertations

Germinated brown rice is commonly consumed in Asia for its enhanced nutritional properties such as gamma-aminobutyric acid (GABA) and softer cooked texture. However germination decreases milling yield and alters some physicochemical properties, and most germinated rice studies evaluated medium-grain and aromatic rice cultivars. This study compared the effects of germination duration and parboiling on milling, physicochemical, and textural properties of a medium- (Jupiter) and a long-grain (Wells) rice cultivars. Rough rice was soaked in water at 25°C for 12 hr, and then incubated at 30-34°C for varying germination durations, or combined with parboiling at 120°C for 20 min prior to …

Genetic Mapping Of Yield And Normalized Difference Vegetative Index In Soft Red Winter Wheat (Triticum Aestivum L.), Christopher Keith Addison

Graduate Theses and Dissertations

Wheat is the most widely cultivated cereal crop, being grown on 17% of the global crop land and as such must be adapted to an array of environmental stresses. In order to become a variety, wheat breeding lines must be tested across a range of environments for both high productivity and stability. Quantitative trait loci (QTL) mapping and indices are tools that can aid plant breeders in the selection of superior lines. Soft red winter wheat accounts for 20% of the total wheat production in the United States, being grown in the southeastern U.S. predominantly along the Mississippi River. However, …

Rice Grain Yield And Nitrogen Uptake And Ammonia Volatilization From Urea As Affected By Urea Amendment And Simulated Rainfall, Randy Dempsey

Graduate Theses and Dissertations

The effect of rainfall between urea application and flood establishment on N loss and grain yield of rice (Oryza sativa L.) has not been studied. The first research objective was to compare the effects of simulated rainfall amounts and N-(n-butyl) thiophosphoric triamide (NBPT) urease inhibitor rate on NH3 volatilization and rice growth. Three field experiments were conducted and NH3 volatilization was measured in two experiments for 11 days after urea application (DAU) in semi-open chambers. Urea or NBPT-treated urea (NBPT-Urea) was subjected to six simulated rainfall amounts (0-25 mm) applied 5 to 15 h after urea application and flooded 7 …

A Microhabitat Assessment Of Five Species Of Invasive Plants In The Ozarks And Appalachians, Eric Hearth

Graduate Theses and Dissertations

Invasive species present a threat to native communities and their introduction and expansion can alter community structure and dynamics. Multiple approaches can be employed for invasive species management including prevention and detection. In this study, microhabitat assessments were conducted on colonies of five species of invasive plants, Alliaria petiolata (M. Bieb.) Cavara & Grande, Lespedeza cuneata (Dum. Cours.) G. Don, Lonicera japonica Thunb., Microstegium vimineum (Trin.) A. Camus, and Rosa multiflora Thunb. in the Ozark Plateau and Appalachians. Elevation, soil moisture, soil pH, light ratio, slope, aspect, distance to disturbance, as well as soil nutrient levels were recorded for each …

Methane Emissions From Direct-Seeded, Delayed-Flood Rice Grown On A Clay Soil, Alden Daniel Smartt

Graduate Theses and Dissertations

Due to the production of methane (CH4) under flooded-soil conditions, rice (Oryza sativa L.) cultivation is a major contributor to agricultural CH4 emissions. Studies examining CH4 emissions from rice have only recently been initiated in Arkansas and no data have been collected from rice produced on clay soils in Arkansas. Therefore, research was conducted in 2012 and 2013 at the Northeast Research and Extension Center in Keiser, Arkansas to examine the factors affecting CH4 emissions from rice produced on a Sharkey clay (very-fine, smectitic, thermic Chromic Epiaquerts). The objectives of this study were to determine: 1) the effect of vegetation …

Viral Sensing Of The Subcellular Environment Regulates The Assembly Of New Viral Replicase Complexes During The Course Of Infection, Peter D. Nagy

Plant Pathology Faculty Publications

Replication of plus-stranded RNA [(+)RNA] viruses depends on the availability of coopted host proteins and lipids. But, how could viruses sense the accessibility of cellular resources? An emerging concept based on tombusviruses, small plant viruses, is that viruses might regulate viral replication at several steps depending on what cellular factors are available at a given time point. I discuss the role of phospholipids, sterols, and cellular WW domain proteins and eukaryotic elongation factor 1A (eEF1A) in control of activation of the viral RNA-dependent RNA polymerase (RdRp) and regulation of the assembly of viral replicase complexes (VRCs). These regulatory mechanisms might …

Assessment Of Variation In Susceptibility Of The Fall Armyworm, Spodoptera Frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), To Bacillus Thuringiensis Toxins, Karen Ferreira Da Silva

Department of Entomology: Dissertations, Theses, and Student Research

The fall armyworm, Spodoptera frugiperda, is a polyphagous insect pest affecting multiple crops. Fall armyworm is managed with insecticides and corn hybrids expressing insecticidal proteins derived from Bacillus thuringiensis. The early detection of insect resistance is important for making appropriate management decisions informs IPM and IRM recommendations.

The objective of the first study was to establish baseline susceptibility of fall armyworm populations to the Cry1F Bt insecticidal protein, emphasizing collections from locations where fall armyworm overwinters in the U.S. Fall armyworm neonates were exposed to artificial diet treated with increasing Cry1F concentrations, and mortality and growth inhibition were …

Plant Diversity Affects Performance Of Invasive Thistles In Restored Nebraska Grasslands, Katilyn J. Price

School of Natural Resources: Dissertations, Theses, and Student Research

Invasive plant species threaten native grasslands, affecting nutrient cycling, biodiversity, wildlife habitat, and usable land for production. Consequently, preventing establishment of invasive species is critical before removal becomes difficult and expensive. The purpose of this study was to examine the effects of grassland plant diversity on musk thistle (Carduus nutans) and Canada thistle (Cirsium arvense) establishment and determine which environmental factors (light penetration, soil moisture, plant diversity, and soil nitrogen) account for resistance to invasions. In a field experiment at The Nature Conservancy’s Wood River site (Nebraska), the two invasive thistle species were planted into replicated …

Postharvest Degradation Of Microalgae: Effect Of Temperature And Water Activity, Jacob A. Nelson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Though usually a nuisance in swimming pools and ponds, algae has the potential to be a valuable commodity for use as food and fuel. But before algae butter and biofuel become commonplace, issues with harvesting and storing this new crop need to be overcome. Though there has been ample research into how to grow and use algae, scientists have spent little time figuring out what to do after you pull it out of the water and before you eat it (or turn it into biodiesel). Algae, like all food products, starts to spoil as soon as it is harvested.

This …

Understanding Perceptions Of Genetically Modified Food Among Natural Food Shoppers In Southern Nevada, Christian Murua-Aceves

UNLV Theses, Dissertations, Professional Papers, and Capstones

Today, 85% of corn, 93% of soybeans, and 88% of cotton in the U.S. are genetically modified (GM). Using laboratory methods, genes from one species, such as a plant, can be transferred to an unrelated species, such as an animal. Genetically modified crops may lead to higher yields, have improved food quality, texture, and nutritional value, and have an increased shelf life.

Despite these promising benefits, the potential health risks relating to the consumption of GM food remain inadequately assessed. Genetically modified food is not subjected to rigorous safety testing, such as epidemiologic studies, to identify potential health risks. Two …

Consequences Of Pre-Inoculation With Native Arbuscular Mycorrhizae On Root Colonization And Survival Of Wyoming Big Sagebrush (Artemisia Tridentata Ssp. Wyomingensis) Seedlings After Transplanting, Bill Eugene Davidson

Boise State University Theses and Dissertations

Inoculation of seedlings with arbuscular mycorrhizal fungi (AMF) is a common practice aimed at improving seedling establishment. The success of this practice largely depends on the ability of the inoculum to multiply and colonize the growing root system after transplanting. These events were investigated in Artemisia tridentata ssp. wyomingensis (Wyoming big sagebrush) seedlings inoculated with native AMF. Seedlings were first grown in a greenhouse in sterilized soil (non-inoculated seedlings) or soil containing a mixture of native mycorrhizae (inoculated seedlings). Three-month old seedlings were transplanted to 24 L pots containing soil from a sagebrush habitat (mesocosm experiments) or to a recently …

Nutrient Management For Growing Dandelion (Taraxacum Officinale L.) In Nutrient Film And Deep Flow Hydroponics, Reetinder Gill

Graduate Theses and Dissertations

This research study was conducted to determine an optimal nutrient strategy for dandelion production in nutrient film technique (NFT) and deep flow technique (DFT) systems of hydroponics. It was achieved by growing dandelion at varying levels of nutrient solution concentration and pH in both NFT and DFT systems. Additionally, an optimal nutrient solution concentration and timing of application for dandelion seedling production was also determined.

Phylogenetic Relationships Of Samydaceae And Taxonomic Revision Of The Species Of Casearia In South-Central Asia, Tharangamala Samarakoon

Dissertations

The flowering plant family Samydaceae was recently reinstated to include 14 genera and about 256 species of tropical trees and shrubs. Preliminary analyses of relationships in the family, however, indicated that the largest genus in the family, Casearia, is not monophyletic and that several smaller groups are probably misplaced. In order to affirm or refute those hypotheses, additional DNA sequence data with broader taxon sampling from the Old World were gathered for phylogenetic analysis. In particular, rapidly evolving plastid (matK, ndhF, psbA-trnH, trnL, and trnL-F) and nuclear (EMB2765 and GBSSI) DNA …

Seasonal Activity And Sampling Methods For The Dectes Stem Borer, Dectes Texanus Leconte, In Nebraska Soybeans, Zachary D. Rystrom

Department of Entomology: Dissertations, Theses, and Student Research

The Dectes stem borer, Dectes texanus Leconte, has caused significant economic damage to soybean fields in south central Nebraska during recent years. Most economic injury occurs when soybean plants become susceptible to late season lodging due to larval girdling. Developing a comprehensive management plan for Dectes stem borer in Nebraska is limited by lack of knowledge of seasonal activity and effective sampling plans to monitor adult populations. Field studies were conducted in 2013 and 2014 to describe Dectes stem borer adult emergence patterns, female ovipositional period and adult densities in soybean fields. Calendar date predictions for adult emergence varied, while …

Microsatellite Variations Of Elite Setaria Varieties Released During Last Six Decades In China, Guanqing Jia, Xiaotong Liu, James C. Schnable, Zhengang Niu, Chunfang Wang, Yuhui Li, Shujun Wang, Suying Wang, Jinrong Liu, Erhu Guo, Hui Zhi, Xianmin Diao

Department of Agronomy and Horticulture: Faculty Publications

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, …

Potential Of Forage Kochia And Other Plant Materials In Reclamation Of Gardner Saltbush Ecosystems Invaded By Halogeton, Rob C. Smith

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Gardner saltbush ecosystems are increasingly being invaded by halogeton, a competitive annual weed that increases soil surface salinity and reduces plant biodiversity. This study was established on the Flaming Gorge National Recreation Area, in the Ashley National Forest near Manila, UT to evaluate the ability of forage kochia, Russian wildrye, tall wheatgrass, Indian ricegrass and Gardner saltbush, in monocultures and binary mixtures with Gardner saltbush, to establish and compete in ecosystems dominated by halogeton. A dormant seeding, with and without prior disking, was conducted to determine the ability of plant materials to establish. A spaced-plant evaluation was used to determine …

Effects Of Plant Stress On Facultative Apomixis In Boechera (Brassicaceae), Mayelyn Mateo De Arias

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In flowering plants, apomixis is asexual reproduction by seeds. Apomixis allows the production of offspring with the same genetic characteristics as the mother plant. Fertilization is not required. Apomixis could become a tool for naturally cloning high-yielding crop hybrids through their own seed. However, apomixis does not occur in major crop plants, except for citrus. In the present study, genes that might cause apomixis in naturally occurring apomictic plants were investigated. Sexual and apomictic species of the genus Boechera were exposed to stressed and non-stressed conditions. Effects of these treatments on the expression of apomixis was then measured. Stress triggered …

Population And Community Dynamics Of Freshwater Decapods In Response To Ecological And Anthropogenic Factors In Subtropical Streams In The Caribbean, Omar Perez-Reyes

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Historically, cities were established in close proximity to the richest agricultural lands and freshwater resources. In tropical islands, urbanization occupies a large percentage of land use along streams and rivers and strongly affects the biota and habitat quality. I studied freshwater decapod population and community dynamics in tropical streams of Puerto Rico across human and elevational gradients. I found that: 1) streams with less urbanization had higher decapod species richness and population sizes than the highly urbanized streams; 2) changes in the food webs in the streams are the result of the influence of changes in land use and environmental …