Biology Commons^™

Patch-Scale Effects Of An Invasive Ecosystem Engineer On The Structure And Function Of A Eutrophic Stream, Samuel J. Hochhalter

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Recent theoretical and technological advances in ecosystem science have dramatically expanded the ways in which scientists can pursue and explore ecological questions. For my thesis research, I integrated the recent theoretical concept of organisms as ecosystem engineers with the relatively recent development of stable isotope tracer tests to ask the question: how does the invasive common carp affect stream ecosystem structure and function? To investigate the structuring role of carp, I measured autotroph seasonal distribution and abundance and macroinvertebrate seasonal abundance and diversity within two stream reaches in Spring Creek, Utah, USA; one with low carp biomass (LCB) and one …

Linking Space Use And Behavior In Clark's Nutcracker: An Explanation For Seasonal Variation In Space Use, Teresa J. Lorenz

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Clark's Nutcrackers (Nucifraga columbiana) are important seed dispersers for at least 10 species of conifer in western North America and are obligate mutualists for the subalpine tree, whitebark pine (Pinus albicaulis). Despite the important role they play in forest regeneration, space use by nutcrackers has not been formally studied. Several hypotheses exist to explain their year-round space use patterns. I tested one hypothesis that Clark's Nutcrackers migrate altitudinally between summer and autumn in one population in the Cascade Range, Washington. In 2006 and 2007, I compared seasonal differences in summer and autumn space use by 26 …

Prediction Of Protein Function And Functional Sites From Protein Sequences, Jing Hu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

High-throughput genomics projects have resulted in a rapid accumulation of protein sequences. Therefore, computational methods that can predict protein functions and functional sites efficiently and accurately are in high demand. In addition, prediction methods utilizing only sequence information are of particular interest because for most proteins, 3-dimensional structures are not available. However, there are several key challenges in developing methods for predicting protein function and functional sites. These challenges include the following: the construction of representative datasets to train and evaluate the method, the collection of features related to the protein functions, the selection of the most useful features, and …

Cognitive Inference And Resulting Behaviors In Response To Ambiguous Threat In The Coyote, Canis Latrans, Sarah Shawnee Dawson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

While antipredator strategies have been a focus of behavioral research for decades, scientists generally study the responses of prey toward overt, explicit threat. However, risk can also be significant when a threat is covert, such as when an ambush predator may be nearby or a secondary threat remains after a predator's departure. Little is known about the mechanism that prey use to assess risk in a predator's absence. Tests were conducted to determine the manner in which coyotes respond to these ambiguous threats. Specifically, I tested whether coyotes respond to prior anthropogenic activity that has occurred near their only food …

Effects Of Targeted Grazing And Prescribed Burning On Fire Behavior And Community Dynamics Of A Cheatgrass (Bromus Tectorum)-Dominated Landscape, Joel M. Diamond

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Studies were conducted to determine the effectiveness of using targeted grazing and prescribed burning as tools to reduce fire hazards and cheatgrass (Bromus tectorum) dominance on rangelands in the northern Great Basin. A field study, with four grazing-burning treatments (graze and no-burn, graze and burn, no-graze and burn, and no-graze and no-burn), was conducted on a B. tectorum-dominated site near McDermitt, Nevada from 2005-2007. Cattle removed 80-90% of standing biomass in grazed plots in May 2005 and 2006 when B. tectorum was in the boot (phenological) stage. Grazed and ungrazed plots were burned in October 2005 and …

Predicting The Growth Potential Of A Shallow, Warm-Water Sport Fishery: A Spatially Explicit Bioenergetics Approach, Samuel Kirk Dahle

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Capturing the range of fish consumption and growth potential of large, heterogeneous lentic systems can be challenging due to strong gradients in productivity, the diversity of habits types present, and in some cases, site-specific water quality issues. Cutler Reservoir (Utah, USA) displays a high degree of spatial and temporal variation in physical conditions and potential water quality limitations for fish, including high summertime water temperature and large, diel fluctuations in dissolved oxygen concentrations. The combination of bioenergetics modeling and GIS spatial analysis offers a promising interface for quantifying the fish consumptive and growth potential across a spatially and temporally heterogeneous …

Speciation, Species Concepts, And Biogeography Illustrated By A Buckwheat Complex (Eriogonum Corymbosum), Mark W. Ellis

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The focus of this research project is the complex of infraspecific taxa that make up the crisp-leaf buckwheat species Eriogonum corymbosum (Polygonaceae), which is distributed widely across southwestern North America. This complex provides an ideal taxonomic group for research into population relationships and speciation. To avoid unnecessary debates about taxonomic validity or contentious issues regarding appropriate species definitions, the historical evolution of the species concept is first reviewed in detail, demythologizing an often-assumed species problem. Following that review, the E. corymbosum complex is examined specifically.

Although eight varieties of E. corymbosum are currently recognized based on morphological characters, this group …

Mycorrhizae In Sagebrush-Steppe Community Restoration: Mycorrhizal Dependency Of Invasive And Native Grasses With Intraspecific And Interspecific Competition, Dara S. Scherpenisse

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Mycorrhizae have been used in restoration for decades. However, studies assessing the use of mycorrhizae in Bromus tectorum-invaded areas of the Great Basin are limited. Two greenhouse pot experiments were conducted to assess the role of mycorrhizae in sagebrush restoration.

The first objective (Chapter 2) was to determine the response of Pseudoroegneria spicatum, Elymus elymoides, and B. tectorum to mycorrhizal symbiosis by altering phosphorus, density, species, presence of mycorrhizae and water levels in a 5 factor design. To assess the mycorrhizal response, a variety of morphological and physiological traits were measured, such as tissue P concentration, specific …

Characterization Of The Substrate Specificity And Mechanism Of Protein Arginine Methyltransferase 1, Whitney Lyn Wooderchak

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methyltransferases (PRMTs) posttranslationally modify protein arginine residues. Type I PRMTs catalyze the formation of monomethylarginine (MMA) and asymmetric dimethylarginine (ADMA) via methyl group transfer from S-adenosyl methionine onto protein arginine residues. Type II PRMTs generate MMA and symmetric dimethylarginine. PRMT-methylation affects many biological processes. Although PRMTs are vital to normal development and function, PRMT-methylation is also linked to cardiovascular disease, stroke, multiple sclerosis, and cancer.

Thus far, nine human PRMT isoforms have been identified with orthologues present in yeast, plants, and fish. PRMT1 predominates, performing an estimated 85% of all protein arginine methylation in vivo. Yet, the substrate …

Consequences Of Vegetation Change On The Dynamics Of Labile Organic Matter And Soil Nitrogen Cycling In A Semiarid Ecosystem, Toby D. Hooker

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Sagebrush-dominated ecosystems are being transformed by wildfire, rangeland improvement techniques, and exotic plant invasions. These disturbances have substantial effects on the composition and structure of native vegetation, but the effects on ecosystem C and N dynamics are poorly understood. To examine whether differences in dominant vegetation affect the quantity and quality of plant organic matter inputs to soil, ecosystem C and N pools and rates of plant turnover were compared among historically grazed Wyoming big sagebrush, introduced perennial crested wheatgrass, and invasive annual cheatgrass communities. Since low soil moisture during the summer may inhibit the microbial colonization of plant detrital …

Consumer-Driven Nutrient Recycling In Arctic Alaskan Lakes: Controls, Importance For Primary Productivity, And Influence On Nutirient Limitation, Cody R. Johnson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In lakes, fish and zooplankton can be both sources and sinks of nitrogen (N) and phosphorus (P) through the consumption of organic N and P, and subsequent excretion of bioavailable inorganic forms. These source/sink dynamics, known as consumer-driven nutrient recycling (CNR), may, in turn, control the availability of potentially limiting nutrients for algal primary production. In this dissertation I investigate the importance and controls of CNR as a source of inorganic N and P for primary production (Chapter 2). I then examine zooplankton CNR as a mechanism for increasing nutrient mean resident time (MRT) in the mixed layer of lakes …

Punta Toro Virus Infection In Mice: Strain Differences In Pathogenesis And Regulation Of Interferon Response Pathways, Michelle Mendenhall

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The Adames strain of Punta Toro virus (PTV-A) causes acute hepatic disease in hamsters and mice similar to that seen in natural Rift Valley fever virus (RVFV) infection, while the Balliet strain (PTV-B) is apathogenic. The ability of PTV-A to suppress the interferon (IFN) response has been demonstrated in hamsters and is thought to be a contributing factor to PTV-A's pathogenicity in hamsters. PTV-B is not assumed to exhibit this IFN-antagonistic activity, as it stimulates production of significantly higher IFN-β levels. To elucidate the role of IFN in resistance of mice to PTV-B infection, we utilized mice deficient in a …

Naive Prey Versus Nonnative Predators: A Role For Behavior In Endangered Species Conservation, Stephanie A. Kraft

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Fish are one of the most imperiled groups of vertebrates worldwide. Threats to fish fall into one of four general categories: physical habitat loss or degradation, chemical pollution, overfishing, and nonnative species introductions. Nonnative predatory fish often have a devastating impact on native prey, especially with endemic fish, whose restricted distribution and often limited evolutionary history with predators make them particularly susceptible to nonnative predators. One reason nonnative fish are often so efficient predators is that the native fish do not recognize the predator as a threat. Although many studies have examined the role of predator odor recognition, no fish …

Greater Sage-Grouse And Energy Development In Northeastern Utah: Implications For Management, Leah Suzanne Smith

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Concern regarding the effect of energy development on greater sage-grouse (Centrocercus urophasianus) is increasing as the search for fossil fuel intensifies. Sage-grouse may be especially sensitive to energy development because they require large, diverse areas of sagebrush (Artemisia spp.) habitat to complete their life cycle. Additionally, the network of pipelines, roads, and wells required by energy development may fragment sagebrush habitat isolating populations and contributing to genetic drift, inbreeding, local extinction, or rapid divergence.

Seep Ridge, located in northeastern Utah, is one area where sage-grouse habitat and energy development plans overlap. Approved leases call for the construction …

An Investigation Of Postzygotic Reproductive Isolation And Phenotypic Divergence In The Bark Beetle Dendroctonus Ponderosae, Ryan R. Bracewell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Understanding reproductive isolation and divergence is the focus of speciation research. Recent evidence suggested that some Dendroctonus ponderosae populations produced hybrids with reproductive incompatibilities, a reproductive boundary undetected by phylogeographic analyses using molecular markers. Additionally, the unique bifurcated distribution of D. ponderosae and the proposed isolation-by-distance gene flow pattern around the Great Basin Desert provided a unique opportunity to investigate the evolution of postmating (postyzygotic) isolation while also understanding phenotypic divergence along latitudinal (climatic) gradients. First, I characterized the strength, biological pattern, and geographic pattern of postzygotic isolation in D. ponderosae by crossing increasingly divergent populations in a common garden …

The Bioactive Properties Of Syringomycin E-Rhamnolipid Mixtures And Syringopeptins, Mekki F. Bensaci

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The need for new antimicrobial agents has become important in the last decade due to emerging resistance to a number of conventional antimicrobial agents. New approaches and sources are needed to generate novel and effective antimicrobials. For example, synergistic combinations between two or more agents may lead to new antimicrobial therapies. Furthermore, the increase in health problems caused by the exposure to agricultural crop pesticides and synthetic fungicides and the emerging development of organic farming has increased the necessity to develop natural products than can be used safely in controlling crop diseases.

In this work, I present the first studies …

Mechanisms Of Induced Cell Death In Bluetongue Virus Challenged Human Cell Lines, Justin Darrel Hoopes

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bluetongue virus (BTV) is a pathogenic member of the Reoviridae family. BTV does not cause disease in humans, but is capable of selectively infecting and killing certain transformed human cell lines. Understanding BTV's oncotrophism may lead to new therapeutics for treating cancer. This study focused on the underlying mechanisms of BTV-induced cell death in carcinoma cell lines. It was our hypothesis that BTV infects human carcinoma transformed cells, produces mRNA and protein, induces a strong inflammatory response, induces mitogen activated protein kinase (MAPK)-based pro-apoptotic signaling, inhibits PKB-based signaling, and eventually kills the cell by inducing apoptosis.

Three carcinoma cell lines …

Taste Sensitivity To 6-N-Propylthiouracil (Prop) As A Biological Marker For Vulnerability To Stress In Mothers And Children, Deann Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Some people are genetically more vulnerable to stress than others, leading them towards poorer outcomes following stressful events. Mothers' vulnerability to stress may, in turn, influence their children, leading their children towards poor outcomes as well. A biological marker of vulnerability to stress may indicate mothers who are at greater risk for experiencing parenting stress, depression, and less support of the infant's emotional development, and infants who are at greater risk for development of poor emotion regulation and behavior problems. Taste sensitivity to propylthiouracil (PROP) is proposed as a biological marker of stress vulnerability in mothers and children. This research …

Microbial Growth Inhibition And Decomposition Of Milk Mineral And Sodium Tripolyphosphate Added To Media Or Fresh Ground Beef, Rossarin Tansawat

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Milk mineral (MM) is a type II antioxidant (metal chelator) that can bind iron and prevent iron catalysis of lipid oxidation. Thus, MM might have microbial growth inhibition effects on iron-dependent bacteria. Objective 1 was to evaluate effects of MM on growth of non-pathogenic iron-dependent bacterial strains (Listeria innocua, Eschericia coli, Pseudomonas fluorescens). MM (1.5 % w/v) did not significantly inhibit growth of Listeria and E. coli. However, growth of Pseudomonas fluorescens was consistently and significantly reduced by ~1 log colony forming units per ml (CFU/ml) with all levels of MM (0.5, 0.75, 1.5 % …

An Introduction To The Biocomplexity Of Sanak Island, Western Gulf Alaska, Hd G. Maschner, M Betts, J Cornell, B Finney, J A. Dunne, Nancy J. Huntly, J W. Jordan, N Misarti, K L. Reedy-Maschner, R Russell

Biology Faculty Publications

The Sanak Biocomplexity Project is a transdisciplinary research effort focused on a small island archipelago 50 km south of the Alaska Peninsula in the western Gulf of Alaska. This team of archaeologists, terrestrial ecologists, social anthropologists, intertidal ecologists, geologists, oceanographers, paleoecologists, and modelers is seeking to understanding the role of the ancient, historic, and modern Aleut in the structure and functioning of local and regional ecosystems. Using techniques ranging from systematic surveys to stable isotope chemistry, long-term shifts in social dynamics and ecosystem structure are present in the context of changing climatic regimes and human impacts. This paper presents a …

Global Chloroplast Phylogeny And Biogeography Of Bracken (Pteridium: Dennstaedtiaceae), Joshua P. Der, J. A. Thomson, J. K. Stratford, Paul G. Wolf

Biology Faculty Publications

Bracken ferns (genus Pteridium ) represent an ancient species complex with a natural worldwide distribution. Pteridium has historically been treated as comprising a single species, but recent treatments have recognized several related species. Phenotypic plasticity, geographically structured morphological variation, and geographically biased sampling have all contributed to taxonomic confusion in the genus. We sampled bracken specimens worldwide and used variable regions of the chloroplast genome to investigate phylogeography and reticulate evolution within the genus. Our results distinguish two major clades within Pteridium , a primarily northern hemisphere Laurasian/African clade, which includes all taxa currently assigned to P. aquilinum , and …

Hydrologic Control Of Nitrogenremoval, Storage And Export In A Mountain Stream, R. O. Hall Jr., Michelle A. Baker, C. D. Arp, B. J. Koch

Biology Faculty Publications

Nutrient cycling and export in streams and rivers should vary with flow regime, yet most studies of stream nutrient transformation do not include hydrologic variability. We used a stable isotope tracer of nitrogen (¹⁵N) to measure nitrate (NO₃^-) uptake, storage, and export in a mountain stream, Spring Creek, Idaho, U.S.A. We conducted two tracer tests of 2-week duration during snowmelt and baseflow. Dissolved and particulate forms of ¹⁵N were monitored over three seasons to test the hypothesis that stream N cycling would be dominated by export during floods, and storage during low flow. Floods …

Changes In A Tropical Forest Support Metabolic Zero-Sum Dynamics, S.K. Morgan Ernest, Ethan P. White, J. H. Brown

Biology Faculty Publications

Major shifts in many ecosystem-level properties of tropical forests have been observed, but the processes driving these changes are poorly understood. Over the past two decades, the forest on Barro Colorado Island, Panama (BCI) exhibited a 20% decrease in the number of trees and a 10% increase in average tree diameter. Here we show that these changes are consistent with a zero-sum constraint operating in this forest. Zero-sum constraints result when the total resource use of an ecosystem is limited by available resources. This causes increases in resource use by some groups of organisms to be compensated for by decreases …

Differences In Nitrate Uptakeamong Benthic Algal Assemblages In A Mountain Stream, Michelle A. Baker, G. De Guzman

Biology Faculty Publications

We evaluated how benthic algal assemblages that vary in composition, richness, and other diversity metrics remove NO 3 -N from the water column of a mountain stream. Ecological theory and empirical studies suggest that ecosystem process rates should increase as richness increases because of niche separation or activity of dominant taxa. Accordingly, we predicted that algal assemblages with highest richness would show the highest rates of NO 3 -N uptake. To test this prediction, we transplanted 225 rocks representing 3 patch types (green, yellow, and brown) that differed macroscopically in algal composition from a lake outflow stream to a lake …

Selective Herbivory By The Woodrat (Neotoma Lepida) On Joshua Trees (Yucca Brevifolia), M P. Stanford, Nancy J. Huntly

Biology Faculty Publications

We studied herbivory by the desert woodrat (Neotoma lepida) on Joshua trees (Yucca brevifolia) in the Mojave Desert to determine whether N. lepida fed selectively based on leaf nitrogen content. We measured leaf nitrogen content and the location and amount of herbivory by woodrats on Y. brevifolia trees in southwestern Utah, USA. Neotoma lepida removed the outer tips of leaves (1/3 to 2/3 of total leaf length) but left leaf bases, which had lower nitrogen content, uneaten. Herbivory by N. lepida also was concentrated on rosettes that were oriented south, and these had significantly higher nitrogen content than rosettes that …

Taking Species Abundance Distributions Beyond Individuals, H. Morlon, Ethan P. White, R. S. Etienne, J. L. Green, A. Ostling, D. Alonso, B. J. Enquist, F. He, A. H. Hurlbert, A. E. Magurran, B. A. Maurer, B. J. Mcgill, H. Olff, D. Storch, T. Zillio

Biology Faculty Publications

The species abundance distribution is one of the few “universal” patterns in ecology. Research on this fundamental distribution has been focused to the study of numerical counts, irrespective of the traits of individuals. Here we show that considering a set of Generalized Species Abundance Distributions (GSADs) that encompass several abundance measures, specifically numerical abundance, biomass and resource use can provide novel insights into organizational forces at play in ecological communities. We first leverage a comprehensive dataset to investigate the similarity and difference between GSADs. We then use classical probability theory and allometric scaling laws to explore theoretical linkages among GSADs …

Long-Term Monitoring And Experimentalmanipulation Of A Chihuahuan Desert Ecosystem Near Portal, Arizona, Usa, S.K. Morgan Ernest, T. J. Valone, J. H. Brown

Biology Faculty Publications

Desert ecosystems have long served as model systems in the study of ecological concepts (e.g., competition, resource pulses, top-down/bottom-up dynamics). However, the inherent variability of resource availability in deserts, and hence consumer dynamics, can also make them challenging ecosystems to understand. Study of a Chihuahuan desert ecosystem near Portal, Arizona, USA, began in 1977. At this site, 24 experimental plots were established in 1977 and divided among controls and experimental manipulations. Experimental manipulations over the years include removal of all or some rodent species, all or some ants, seed additions, and various alterations of the annual plant community. While some …

The Taxonomic Designation Of Eriogonum Corymbosum Var. Nilesii (Polygonaceae) Is Supported By Aflp And Cpdna Analyses, M. W. Ellis, J. M. Roper, R. Gainer, J. P. Der, Paul G. Wolf

Biology Faculty Publications

We examined populations of perennial, shrubby buckwheats in the Eriogonum corymbosum complex and related Eriogonum species in the subgenus Eucycla, to assess genetic affiliations of the recently named E. corymbosum var. nilesii. The known populations of this varietyare all located in Clark County, Nevada, U. S. A. We compared AFLP profiles and chloroplast DNA sequences of plants sampled from populations of E. corymbosum var. nilesii with those of plants representing other E. corymbosum varieties and related Eriogonum species from Colorado,Utah, northern Arizona, and northern New Mexico. We found evidence of genetic cohesion among the Clark County populations as well astheir …

Conservation Of Selection On Matk Following An Ancient Loss Of Its Flanking Intron, A. M. Duffy, S. A. Kelchner, Paul G. Wolf

Biology Faculty Publications

The chloroplast gene trnK and its associated group II intron appear to be absent in a large and ancient clade that includes nearly 90% of fern species. However, the maturase protein encoded within the intron (matK) is still present and located on the boundary of a large-scale inversion. We surveyed the chloroplast genome sequence of clade-member Adiantum capillus-veneris for evidence of a still present but fragmented trnK intron. Lack of signature structural domains and sequence motifs in the genome indicate loss of the trnK intron through degradation in an ancestor of the clade. In plants, matK preferentially catalyzes splicing of …

Global Chloroplast Phylogeny And Biogeography Of Bracken (Pteridium: Dennstaedtiaceae), J. P. Der, J. A. Thomson, J. K. Stratford, Paul G. Wolf

Biology Faculty Publications

Bracken ferns (genus Pteridium) represent an ancient species complex with a natural worldwide distribution. Pteridium has historically been treated as comprising a single species, but recent treatments have recognized several related species. Phenotypic plasticity, geographically structured morphological variation, and geographically biased sampling have all contributed to taxonomic confusion in the genus. We sampled bracken specimens worldwide and used variable regions of the chloroplast genome to investigate phylogeography and reticulate evolution within the genus. Our results distinguish two major clades within Pteridium, a primarily northern hemisphere Laurasian/African clade, which includes all taxa currently assigned to P. aquilinum, and a primarily southern …