Biology Commons^™

Bulked-Segregant Analysis Coupled To Whole Genome Sequencing (Bsa-Seq) For Rapid Gene Cloning In Maize, Harry Klein, Yuguo Xiao, Phillip A. Conklin, Rajanikanth Govindarajulu, Jacob A. Kelly, Michael J. Scanlon, Clinton J. Whipple, Madelaine Bartlett

Faculty & Staff Scholarship

Forward genetics remains a powerful method for revealing the genes underpinning organismal form and function, and for revealing how these genes are tied together in gene networks. In maize, forward genetics has been tremendously successful, but the size and complexity of the maize genome made identifying mutant genes an often arduous process with traditional methods. The next generation sequencing revolution has allowed for the gene cloning process to be significantly accelerated in many organisms, even when genomes are large and complex. Here, we describe a bulked-segregant analysis sequencing (BSA-Seq) protocol for cloning mutant genes in maize. Our simple strategy can …

Bioinformatic Workflows For Generating Complete Plastid Genome Sequences—An Example From Cabomba (Cabombaceae) In The Context Of The Phylogenomic Analysis Of The Water-Lily Clade, Michael Gruenstaeudl, Nico Gerschler, Thomas Borsch

Biological Sciences Faculty Publications

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and …

The Role Of Red Leaf Coloration In Prey Capture For Pinguicula Planifolia, Jenna Annis, Janice Coons, Charles Helm, Brenda Molano-Flores

Faculty Research & Creative Activity

Anthocyanins in the leaves of carnivorous plants are suggested to play a role inprey capture. In this study, we investigated the role of red leaf coloration (an indicator of anthocyanins)on prey capture using Pinguicula planifolia (Chapman’s Butterwort). Overall,red leaves had less prey (i.e., Collembola) than green leaves, suggesting that red colorationdoes not enhance prey capture for Chapman’s Butterwort. However, the frequent presenceof Collembola on leaves suggests that this plant species could be relying on other cues toattract prey (e.g., olfactory cues).

Nutrient Conservation Trait Responses Of Low Resource Adapted Chaparral Shrubs To Increased Resource Availability, Reina Lee Nielsen

Masters Theses

Traits that increase mean nutrient retention times are essential to plant performance in low resource environments, where multiple stressors (low water and nutrients) are present. Although physiological responses to either water or nutrient stress are well understood, fewer studies have investigated the interaction of these stressors from a phylogenetically-controlled, whole-plant perspective. This research focused on three, phylogenetically-controlled pairs of shrubby evergreen species from the California chaparral that either grow on or off serpentine soils, which differ in nutrient availability. Using greenhouse and field studies, the responses of these plants to altered water and nutrient availability were evaluated. The greenhouse study …

The Effects Of Ultraviolet Light On Anthocyanin Accumulation In The Adventitious Roots Of Sedum Wrightii (Crassulaceae), Lila D. Kerr, Dennis A. Gravatt, Robert J. Wiggers

Faculty Publications

Several studies have supported the idea that anthocyanin accumulation may be a possible protection mechanism in plants against DNA damage caused by ultraviolet radiation (UV). This study explored the accumulation of anthocyanins in the adventitious root tips of Sedum wrightii using the following treatments: UVA, UVA+low UVB, and UVA+high UVB. Following exposure to UV radiation, samples were analyzed for anthocyanin accumulation using an ethanol extraction procedure. Using ELISA, additional root samples were analyzed for indicators of DNA damage: cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone dimers (6-4 PPs). The anthocyanin concentrations were significantly higher in the UVA + high …

Phytobiome And Transcriptional Adaptation Of Populus Deltoides To Acute Progressive Drought And Cyclic Drought, Benjamin Garcia, Jessy Labbé, Piet Jones, Piet Jones, Paul Abraham, Ian Hodge, Ian Hodge, Sharlee Climer, Sara Jawdy, Lee Gunter, Gerald Tuskan, Xiaohan Yang, Timothy Tschaplinski, Daniel Jacobson, Daniel Jacobson

Computer Science Faculty Works

Plant drought stress causes systematic changes to photosynthesis, metabolism, growth, and potentially the phytobiome. Additionally, drought affects plants in both a species-specific and water-deficit-driven manner, causing the response to drought to be dependent both on how drought is being experienced and on any adaptation to prior drought exposure. Thus, understanding the effect of drought on plants requires assessing drought response in multiple conditions, such as progressive acute drought and recurrent cyclic drought, and at different levels of severity. In this study, we have utilized RNA sequencing to identify changes to the plant transcriptome and the phytobiome during both acute progressive …

Ms Environmental Biology Capstone Project, Meghan Mcgill

Regis University Student Publications (comprehensive collection)

This study aims to provide a deeper understanding of the role of competition in food webs, and more specifically, in trophic cascades induced by biodiversity loss. Trophic cascades are food web disturbances that result from the removal of an important species, often a predator, and lead to dramatic changes in herbivore and plant populations. It is critical to understand the mechanisms that drive and mitigate trophic cascades, because global biodiversity loss is increasing. Previous research suggests that biodiversity, specifically intraguild biodiversity with members in the same trophic level, is an important factor in reducing the negative effects of trophic cascades. …

What Drives Species Richness In Colorado's Alpine Tundra, Michael Kintgen

Regis University Student Publications (comprehensive collection)

Despite years of research, drivers of vascular plant species richness in Colorado’s alpine tundra habitats are largely unknown. Factors such as slope aspect, Pleistocene glaciation, nutrient levels, latitude and longitude, snow depth, and disturbance have been studied. Despite this research, few patterns have emerged. Research in Colorado has been conducted on a few well studied mountains. Aridity is one factor that has not been well studied but shows promise in explaining species richness. In Patagonia and the Swiss Alps, increasing aridity correlates with higher species richness. Here, a full species assessment was conducted on nine mountains previously under researched or …

Ms Environmental Biology Capstone Project, Annamaria Marcel

Regis University Student Publications (comprehensive collection)

Due to the worldwide decline of biodiversity, protected nature reserves are necessary for species facing extinction. Many frog species have been experiencing rapid population decline and extinction due to the threat of the fungus Batrachochytrium dendrobatidis (Bd), which inflicts the highly transmittable and deadly disease chytridiomycosis. Chytridiomycosis causes increased skin tissue growth which disrupts respiration and the maintenance of water balance, which can ultimately lead to death. Certain ecological and geographical characteristics have been studied in order to assess their influence on Bd’s prevalence. Specifically, it is hypothesized that high elevations, lotic habitats, and low species richness have a positive …

Floral Symmetry Genes Elucidate The Development And Evolution Of Oil-Bee Pollinated Flowers Of Malpighiaceae And Krameriaceae, Farahnoz N. Khojayori

Theses and Dissertations

Specialization on insect and animal pollinators is thought to be the driving force for the evolution of floral traits. Specifically in the New World (NW), the oil-bee pollination syndrome has led to the convergence of floral characters in two distantly related families of core eudicots, Malpighiaceae and Krameriaceae. Both families display a flag-like structure that establishes a zygomorphic flower and floral oil rewards in epithelial elaiophores. These traits work concomitantly to attract and reward female oil-bees that help fertilize these flowers and in return receive oils. The underlying genetics of floral zygomorphy were studied in several clades of core eudicots, …

Black Cohosh Seed Germination And Conservation, W. John Hayden

Biology Faculty Publications

Like many plant enthusiasts, I have spent a considerable amount of time planting seeds. Every year I grow many vegetables—my garden always includes some annual bedding plants—and I sow seeds of cover crops (winter wheat, winter rye, and buckwheat) by the tens of thousands. While I have committed vast numbers of propagules to moist soil, I cannot say that I have watched every single one sprout. Nevertheless, I certainly have observed the germination process many, many times for lots of different seeds. For these seeds of garden plants, germination is quite rapid, just a few days to maybe as much …

Transcriptome Analysis Of Root Development In Wheat Triticum Aestivum Using High Throughtput Sequencing Technologies, Ghana Challa

Electronic Theses and Dissertations

Root provides plant water, nutrients and anchorage from soil. Most our knowledge of molecular mechanisms of root development is from the dicot model plant Arabidopsis, but very few studies have done in monocot crop systems like rice, maize, and wheat. We are studying very short root (VSR) phenotype in wheat, and lack of a sequenced reference genome in wheat prompted us to sequence and assemble the root transcriptome of the reference cultivar Chinese Spring (CS). A root transcriptome was assembled from the sequenced reads generated from root tip and the mature root tissues of CS. Approximately 169 million reads were …

Expression Analyses And Identification Of Key Molecular Participants In Plant Responses To Environmental Cues, Praveena Kanchupati

Electronic Theses and Dissertations

Plants constantly engage and interact with the environment and respond to the changes in conditions like temperature, water, and photoperiod, by regulating expression of genes of multiple regulatory and signaling pathways. Insight into these pathways and their participants has provided and will provide candidates to improve various agronomically important traits in crops through marker-assisted breeding and genetic manipulation. With this aim in mind, in the present study, I attempted to identify key candidate genes that are involved in the regulation of; i) plant response to low temperature stress, ii) plant roots’ response to soil moisture content and iii) flowering time. …

Microbial Communities And Their Impact On Bioenergy Crops In Dynamic Environments, Brandon Monier

Electronic Theses and Dissertations

Native perennial grasses, such as prairie cordgrass (PCG, Spartina pectinata Link), and switchgrass (SG, Panicum virgatum L.) have a great potential as bioenergy crops, because they require fewer inputs, produce more energy, and reduce greenhouse gas emissions in comparison to annual cropping systems such as corn and soybean. SG has been selected by the U.S. Department of Energy for development as bioenergy crop, but studies have shown that PCG can outcompete switchgrass in terms of biomass production. These crops can also form associations with a wide variety of plant growth promoting microbes including arbuscular mycorrhial (AM) fungi. In CHAPTER 2, …

Regulation Of Local Auxin Metabolism During Soybean Nodule Development, Suresh Damodaran

Electronic Theses and Dissertations

Legume-rhizobia symbiosis leads to the development of secondary root organs called nodules. Rhizobia bacteria housed inside nodules assimilate atmospheric nitrogen and convert them into plant usable forms thereby reducing the need for fertilizer application in crop legumes like soybean. Nodule development is a coordinated process orchestrated by multiple plant hormones. In soybean, the auxin responsive gene expression was detected in nodule primordia and in the periphery of mature nodules, primarily in nodule vasculature. Auxin hypersensitivity reduces nodule formation in soybean and also polar auxin transport inhibition at the site of nodule development is not crucial for determinate nodule formation. Therefore, …

Identification Of Qtl Modifying The Activity Of The Tcb1-S Locus And Characterization And Sequencing Of Two Plutonium-Beryllium Induced Reduced Gametophyte Transmission Mutants In Maize, Merritt Bryer Burch

Electronic Theses and Dissertations

This thesis is split into two independent projects both involving the male gametophyte generation of maize. The first project looks at how pollen interacts with the female gametophyte to reduce its transmission in cross-incompatible reactions controlled by the unilateral cross-incompatibility system, teosinte crossing barrier 1. The second project explores two plutonium-beryllium induced male gametophyte mutants and attempts to uncover their genetic basis.

Identification of QTL Modifying the Activity of the Tcb1-s Locus
Teosinte crossing barrier 1 (Tcb1) is a unilateral cross-incompatibility system present in maize that provides a pre-zygotic pistil barrier to plants carrying Tcb1-s (strong allele) from pollen …

The Role Of Environmental Filtering In Structuring Appalachian Tree Communities: Topographic Influences On Functional Diversity Are Mediated Through Soil Characteristics, Julia I. Chapman, Ryan W. Mcewan

Biology Faculty Publications

Identifying the drivers of community assembly has long been a central goal in ecology, and the development of functional diversity indices has provided a new way of detecting the influence of environmental gradients on biotic communities. For an old-growth Appalachian forest, we used path analysis to understand how patterns of tree functional diversity relate to topography and soil gradients and to determine whether topographic effects are mediated through soil chemistry. All of our path models supported the idea of environmental filtering: stressful areas (high elevation, low soil moisture, low soil nutrients) were occupied by communities of low functional diversity, which …

Natural And Anthropogenic Drivers Of Tree Evolutionary Dynamics, Brandon M. Lind

Theses and Dissertations

Species of trees inhabit diverse and heterogeneous environments, and often play important ecological roles in such communities. As a result of their vast ecological breadth, trees have become adapted to various environmental pressures. In this dissertation I examine various environmental factors that drive evolutionary dynamics in threePinusspecies in California and Nevada, USA. In chapter two, I assess the role of management influence of thinning, fire, and their interaction on fine-scale gene flow within fire-suppressed populations of Pinus lambertiana, a historically dominant and ecologically important member of mixed-conifer forests of the Sierra Nevada, California. Here, I find evidence …

Quantitative Effects Of Soil Salinity On The Symbiosis Of Wild Lima Bean (Phaseolus Lunatus L.) And Bradyrhizobium In Costa Rica, Daniel J. Ballhorn, Emily R. Wolfe, Jess Tyler, Wren Ronan, Scott Sands-Gouner, Curran Shaw, Mehmet Ali Balkan, Stefanie Kautz

Biology Faculty Publications and Presentations

Global climate change and local anthropogenic activities are increasing soil salinization with permanent negative effects on agricultural and ecosystem productivity. While salt stress is known to affect plant performance, its effects on the association with key microbial plant symbionts, such as legume-associated nitrogen-fixing rhizobia, are less understood. In this field study conducted in Costa Rica (Puntarenas), we used sympatrically-occurring wild lima bean (Phaseolus lunatus L.) and Bradyrhizobium to quantify biomass production of unfertilized rhizobial (R+) and fertilized rhizobia-free (R-) plants at different levels of experimentally manipulated salinity in native soil. In response to salt stress, nodulation was significantly reduced even …

Birds And Vegetation Structure Of Isolated Juniper And Oak Communities In The Trans-Pecos Chihuahuan Desert., Kayla Garza

Open Access Theses & Dissertations

Birds of the Trans-Pecos region are historically understudied, with most literature covering birds of desert grasslands and scrub in New Mexico and Northern Mexico. A multitude of vegetation communities within the Chihuahuan Desert have also been neglected due to this gap in the research, for reasons including lack of access to public or preserve land in West Texas, and rough terrain. Indio Mountains Research Station (IMRS), is located 42-km southwest of Van Horn, Texas and encompasses many different vegetation communities, including juniper-oak habitats of arroyo and canyon systems. The purpose of this study was to document the bird species utilizing …

The Role Of Climate In The Dynamics Of Annual Plants In A Chihuahuan Desert Ecosystem, Danielle D. Ignace, Nancy Huntly, Peter Chesson

Biology Faculty Publications

Question: What is the role of temporal climate fluctuations in the dynamics of desert winter annual plants in the Portal Bajada, and in the sustained irruption of the non-native annual plant species, Erodium cicutarium?

Field site: Portal Bajada, San Simon Valley, Arizona, USA.

Methods: We counted plants at flowering over a 21-yeaer period on twelve permanent plots and related these numbers to weather data collected at an on-site weather station, supplemented by observations from the National Climate Data Center. Specific summary climate variables considered most relevant to annual plant biology were developed as candidate predictors of plant response variables. …

Jeweled Spider Flies (Eulonchus Tristis) Are Important Pollinators Of Iris Bracteata, A Rare Siskiyou Mountain Endemic, Jean-Paul E. Ponte

Cal Poly Humboldt theses and projects

Little is known about the pollination biology of the Pacific Coast Irises (Iris: series Californicae, hereafter PCI), especially who visits and pollinates their flowers. In general, Iris flowers are considered bee-pollinated, however, flies in the genus Eulonchus (Acroceridae) are known to visit some PCI members. Therefore, I assessed the relative importance of Eulonchus and other insect visitors to the pollination of a rare PCI species native to the Siskiyou Mountains, I. bracteata.

Methods. I quantified pollinator importance for all flower visitors at sites in northern California and southern Oregon as the product of average visit rate and …

Conflicting Hydraulic Effects Of Xylem Pit Structure Relate To The Growth-Longevity Tradeoff In A Conifer Species, Beth Roskilly

Graduate Student Theses, Dissertations, & Professional Papers

Consistent with a ubiquitous life history tradeoff, trees exhibit a negative relationship between growth and longevity among and within species. However, the mechanistic basis of this life history tradeoff is not well understood. In addition to tradeoffs among multiple traits based on resource allocation conflicts, life history tradeoffs may arise from tradeoffs based on single traits under opposing selection. While a myriad of factors likely contribute to the growth-longevity tradeoff in trees, we hypothesized that conflicting functional effects of xylem structural traits contribute to the growth-longevity tradeoff. We tested this hypothesis by examining the extent to which xylem morphological traits …

The Three Creeks Allotment Consolidation: Changing Western Federal Grazing Paradigms, Taylor Payne

Human–Wildlife Interactions

The federal government owns approximately 47% of all land in the western United States. In the state of Utah, about 64% of the land base is managed by the federal Bureau of Land Management (BLM) and the U.S. Forest Service (USFS). The government has historically issued permits to owners of private lands to allow the owners to graze their livestock on public lands. The permits (allotments) are generally of 10-year duration and allow for an annual season of use. In some cases, continued and repeated historical annual grazing practices may not be ideal for permit holders and their communities nor …

Establishing Relationships Among Environmental Stressors, Host Immune Status, And Wasting Disease Susceptibility In The Dominant Seagrass Species Thalassia Testudinum, Paige Joy Duffin

UNF Graduate Theses and Dissertations

A growing body of evidence supports the observation that marine disease outbreaks, especially those caused by opportunistic pathogens, are increasing in frequency and severity. One genus of such pathogens, Labyrinthula, has been identified as the causative agent of seagrass wasting disease, an epidemic that has historically plagued seagrass beds around the world. It is suspected that pathogenicity is intimately linked to the ability of the host to initiate defense responses, but a lack of compelling evidence prevents any meaningful application of preliminary observations. This body of work investigated the roles of host genotype, host immune status, and environmental stressors …

Comparison Of Photosynthesis Among Three Chaparral Species In The Family Anacardiaceae, Catelyn T. Price, Sarah A. Holmes, Brandon T. Harris, Stephen D. Davis, Karagan L. Smith, Talia A. Cao

Featured Research

Recent argumentative data showed a lack of niche differentiation amongst three Banksia species in Australia conducted by Lamont and Bergl, and the Anacardiaceae family in the native chaparral of the Santa Monica Mountains are supposed to be significantly similar¹. Because of this we wanted to test if there would be a significant difference between the stomatal conductance, photosynthesis, and water potential in samples of the Rhus ovata, Rhus integrifolia, and Malosma laurina (Rhus laurina) species. We tested this idea by collecting the stomatal conductance and photosynthetic rates of each plant species in the same general location with …

Post-Drought Recovery In The Chaparral Shrub Ceanothus Spinosus, Katie C. Lindley, Kylie N. Smith, Nina R. Duchild, Stephen D. Davis, Karagan L. Smith, Talia A. Cao

Featured Research

This study investigated the abilities of Ceanothus spinosus, or greenbark ceanothus, to recover after a historic drought. This plant is one of the hardiest in the Santa Monica Mountains, providing soil stabilization and nutrients to other organisms in the ecosystem. In a previous investigation done during the drought, it was found that C. spinosus subjects growing in their natural habitat experienced significant dieback, with predawn water potentials falling as low as -7 MPa and native embolisms at an average of 47.17% (Ross et al., 2016). Other parameters tested were stomatal conductance, photosynthetic rate, and chlorophyll fluorescence. Compared to the …

The Rate Of Fungal Pathogen Growth (Botryosphaeria Dothidea) 
In Stems Of The Chaparral Shrub Rhus Integrifolia, Jayla D. Simmons, Edward J. Ayala, Kamara J. Satcher, Stephen D. Davis, Karagan L. Smith, Talia A. Cao

Featured Research

The fungus Botryosphaeria dothidea will grow between one to five millimeters after a week on the chaparral species Rhus integrifolia. To test this, we inoculated six individual shrub located behind the greenhouse on Campus Walk Road . On each shrub we selected two branches, receiving adequate and equal sunlight and inoculated one branch with the fungus B. dothidea and the other with a plain gel in order to compare the growth with a control group. The data we collected at the end of the one week period was similar to our initial hypothesis. The shortest growth was on the …

Testing For The Presence Of Botryosphaeria Dothidea In Ceanothus Spinosus, Brandon R. Grinovich, Chelsea N. Puncochar, Katarina L. Carter, Stephen D. Davis, Rodney L. Honeycutt, Talia A. Cao, Karagan L. Smith

Featured Research

Botryosphaeria dothidea is an opportunistic fungus found in some of the cavitated branches of the vegetation in the Santa Monica Mountains. In this study, we focused on finding the presence of Botryosphaeria dothidea in Ceanothus spinosus located on Pepperdine University’s campus. We wanted to test this hypothesis because we observed a large amount of dieback in the Ceanothus spinosus population and wanted to identify a possible contributor. Because of the large number of cavitated branches the Ceanothus spinosus contained, we hypothesized they contained fungus. To test this, we took twenty samples of twenty different Ceanothus spinosus, isolated the fungus …

Phyllotactic Regularity Requires The Paf1 Complex In Arabidopsis, Kateryna Fal, Mengying Liu, Assem Duisembekova, Yassin Refahi, Elizabeth S. Haswell, Olivier Hamant

Biology Faculty Research

In plants, aerial organs are initiated at stereotyped intervals, both spatially (every 137° in a pattern called phyllotaxis) and temporally (at prescribed time intervals called plastochrons). To investigate the molecular basis of such regularity, mutants with altered architecture have been isolated. However, most of them only exhibit plastochron defects and/or produce a new, albeit equally reproducible, phyllotactic pattern. This leaves open the question of a molecular control of phyllotaxis regularity. Here, we show that phyllotaxis regularity depends on the function of VIP proteins, components of the RNA polymerase II-associated factor 1 complex (Paf1c). Divergence angles between successive organs along the …