Life Sciences Commons^™

Virulence Of Photorhabdus Spp.: Examining The Roles Of Environment, Evolution, And Genetics In Insect Mortality, Dana Blackburn

Theses and Dissertations

Entomopathogenic nematodes (EPNs) (genera Heterorhabditis and Steinernema) kill their invertebrate hosts with the aid of a mutualistic bacterium. The bacteria (Xenorhabdus spp. for steinernematids and Photorhabdus spp. for heterorhabditids) are primarily responsible for killing the host and providing the nematodes with nutrition and defense against secondary invaders. Photorhabdus is a Gram-negative bacterium in the Enterobacteriaceae family with high virulence towards their insect hosts. To achieve high mortality rates Photorhabdus produces a variety of virulence factors such as toxins, lipases, proteases, secretion systems, and fimbriae. EPNs are amenable to laboratory rearing and mass production for biocontrol applications against insects …

Water Use Of Four Commonly Planted Landscape Tree Species In A Semi-Arid Suburban Environment, Michael Cameron Bunnell

Theses and Dissertations

Native plant communities and agricultural land are commonly converted to urban areas as cities across the Western United States continue to grow and expand. This expansion is typically accompanied by afforestation where a common goal among communities is to maximize shade tree composition. Planted forests in these regions are commonly composed of introduced tree species native to mesic environments and their ability to persist is dependent on consistent irrigation inputs. Many potential ecosystem services may be derived from planting trees in urban and suburban areas; however, there are also costs associated with extensive afforestation, and shade tree cover may have …

Diversification And Speciation Across Sundaland And The Philippines: The Effects Of 30 Million Years Of Eustatic Flux, Luke J. Welton

Theses and Dissertations

I highlight two squamate lineages endemic to Southeast Asia, the Asian water monitors (Varanus salvator Complex) and the Angle-headed lizards (Agamidae: Gonocephalus), and elucidate their systematic affinities and historical biogeography. My results represent novel phylogenetic inferences, with biogeographic histories and diversification events corresponding to major climatic fluctuations over the past 30 million years. Additionally, I solidify the taxonomy and systematics of the Varanus salvator Complex, and enumerate more than a dozen Gonocephalus lineages as candidate species in need of taxonomic scrutiny. Lastly, I investigate contemporary and historical patterns of dispersal throughout Sundaland, and between Sundaland and the Philippines.

Differences In Patterns Of Reproductive Allocation Between The Sexes In Nicrophorus Orbicollis, Ashlee N. Smith, J. Curtis Creighton, Mark C. Belk

Faculty Publications

Organisms are selected to maximize lifetime reproductive success by balancing the costs of current reproduction with costs to future survival and fecundity. Males and females typically face different reproductive costs, which makes comparisons of their reproductive strategies difficult. Burying beetles provide a unique system that allows us to compare the costs of reproduction between the sexes because males and females are capable of raising offspring together or alone and carcass preparation and offspring care represent the majority of reproductive costs for both sexes. Because both sexes perform the same functions of carcass preparation and offspring care, we predict that they …

Repeated Trait Evolution Driven By Divergent Natural Selection At Early And Late Stages Of Speciation, Spencer J. Ingley

Theses and Dissertations

Speciation – the process by which new species arise – is of fundamental importance in the biological sciences. The means by which new species arise, and the relationship among living species, has been a topic that has captivated both lay and scientific observers for centuries. In recent years, the study of speciation has enjoyed increased attention, resulting in significant advances in our understanding of how species form. Although our understanding of the processes that contribute to speciation has increased dramatically in recent years, our knowledge of how reproductive barriers accumulate as speciation proceeds is still limited. Thus, studies that evaluate …

Delimiting Species And Varieties Of Cycladenia Humilis (Apocynaceae), Holly Kathryn Brabazon

Student Works

Taxonomic delimitation of rare species is vital for accurate assessments of diversity and for their conservation. Cycladenia humilis, the sole species of Cycladenia, is an enigmatic perennial widely dispersed across the western United States. Within this species there are three currently recognized varieties: C. humilis var. humilis in Northern California, C. humilis var. venusta in Southern California, and C. humilis var. jonesii in Utah and Northern Arizona. Some populations occur geographically in areas between the typical distribution of each variety and the presently accepted taxonomy inadequately addresses these populations. Using five nDNA regions, we seek to clarify relationships between current …

Delimiting Species And Varieties Of Cycladenia Humilis (Apocynaceae), Holly Kathryn Brabazon

Theses and Dissertations

Taxonomic delimitation of rare species is vital for accurate assessments of diversity and for their conservation. Cycladenia humilis, the sole species of Cycladenia, is an enigmatic perennial widely dispersed across the western United States. Within this species there are three currently recognized varieties: C. humilis var. humilis in Northern California, C. humilis var. venusta in Southern California, and C. humilis var. jonesii in Utah and Northern Arizona. Some populations occur geographically in areas between the typical distribution of each variety and the presently accepted taxonomy inadequately addresses these populations. Using five nDNA regions, we seek to clarify relationships between current …

Discovery And Confirmation Of Novel Serum Biomarkers Diagnosing Alzheimer’S Disease, Tyler Mower, Dr. John Kauwe

Journal of Undergraduate Research

Background: Alzheimer’s disease (AD) remains challenging to diagnose, especially early disease. Useful serum AD biomarkers would be of great utility in clinical settings and in drug development efforts. We used a novel serum proteomic approach to interrogate the lowmolecular- weight proteome for AD biomarkers.

Experimental design: A discovery study used sera from 58 any-stage AD cases and 55 controls analyzed by capillary liquid chromatography-tandem mass spectrometry. Promising biomarkers were retested in a second, blinded confirmatory study (AD cases=68, controls=57). Several biomarkers replicated and multi-marker sets were modeled.

Results: The initial study found 59 potential AD biomarkers. Thirteen recurred in more …

The Emerald Ash Borer: Beautifully Deadly, Preston Arnold, Dr. S. M. Bybee, Dr. N. P. Lord

Journal of Undergraduate Research

The Jewel Beetles (Coleoptera: Buprestidae) contain ~15,000 of the most stunning yet least understood species in the animal kingdom (Fig. 1; Bellamy and Nelson, 2002). Although it is the 8th largest beetle family and contains many species of biological interest and economic importance, the family is poorly studied. To date, only one molecular phylogeny has been published for the family, and the six subfamilial classifications are still in flux (Evans et al. 2014). Of particular interest within the family Buprestidae is the Emerald Ash Borer; (EAB; Agrilus planipennis) a destructive pest of great economic importance (Fairmare). The EAB was …

Replication Of Gene-Gene Interactions In Large Alzheimer Disease Dataset, Kevin Boehme, Dr. John "Keoni" Kauwe

Journal of Undergraduate Research

Alzheimer’s disease (AD) is a common and complex neurodegenerative disease. It is the most common cause of dementia and is characterized by the accumulation of amyloid plaques and neurofibrillary tangles. To date, many genetic loci have been found that modify AD risk, but collectively, they explain only a fraction of the heritability of the disease. It is hypothesized that rare variants with large effects as well as epistatic interactions account for much of the unexplained heritability in AD.

Importance Of Rare Genetic Variants In Alzheimer’S Disease (Ttc3), Devan Bursey, Dr. John S. K. Kauwe

Journal of Undergraduate Research

Alzheimer’s is a neurodegenerative disease caused by the formation of amyloid plaques and neurofibrillary tangles. Most current research on Alzheimer’s disease has focused on using genome-wide association studies to identify common genetic variants however; past research has shown that rare genetic variants play an important role in the development of Alzheimer’s disease. For example, studies have shown that rare genetic variants in APP, PSEN1, and PSEN2 drastically increase an individual’s risk for Alzheimer’s disease (Tanzi). My research focused on specific rare genetic variant in the TTC3 gene (S1966X). This rare variant has a point mutation that causes a premature stop …

Entomophilic Nematode Diversity And Distribution In Beaver Dam Wash Area, Westen Achibald, Dr. Byron Adams

Journal of Undergraduate Research

The Beaver Dam Wash National Conservation Area is considered an important biodiversity hotspot for the Western United States. The wash is an ecotone on the Northeastern edge of the Mojave Desert and is directly adjacent to both the Colorado Plateau and the Great Basin. Thus, this area contains various species of flora and fauna from each of the surrounding biomes. Prior research of the Beaver Dam Wash has documented high aboveground biodiversity for a desert ecosystem however no research has been conducted on belowground diversity. For this reason we chose to characterize the diversity and distribution of entomophilic nematodes, as …

Environmental And Adaptive Buffers That Mediate The Response Of Subalpine Ecosystems To Environmental Change, Lafe G. Conner

Student Works

This document reports the results of 4 studies of subalpine ecosystem ecology, describing ways that spatial heterogeneity in soils and plant communities mediate ecosystem responses to environmental change. Ecosystem responses to environmental change are also mediated by regional climate patterns and interannual variability in weather. In the first chapter we report the results of an experiment to test for the mediating effects of associational resistance in a forest community that experienced wide-spread beetle kill. We found that Engelmann spruce were more likely to survive a beetle outbreak when growing in low densities (host dilution) and not through other types of …

Environmental And Adaptive Buffers That Mediate The Response Of Subalpine Ecosystems To Environmental Change, Lafe G. Conner

Theses and Dissertations

This document reports the results of 4 studies of subalpine ecosystem ecology, describing ways that spatial heterogeneity in soils and plant communities mediate ecosystem responses to environmental change. Ecosystem responses to environmental change are also mediated by regional climate patterns and interannual variability in weather. In the first chapter we report the results of an experiment to test for the mediating effects of associational resistance in a forest community that experienced wide-spread beetle kill. We found that Engelmann spruce were more likely to survive a beetle outbreak when growing in low densities (host dilution) and not through other types of …

Bioinformatics For The Comparative Genomic Analysis Of The Cotton (Gossypium) Polyploid Complex, Justin Thomas Page

Theses and Dissertations

Understanding the composition, evolution, and function of the cotton (Gossypium) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). Specifically, read-mapping (a fundamental part of next-generation sequence analysis) cannot adequately differentiate reads as belonging to one genome or the other. These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we developed PolyCat to categorize reads according to their genome of origin based on homoeo-SNPs that differentiate the two genomes. We re-sequenced the genomes of extant diploid relatives of tetraploid cotton …

Rare Genetic Variant To The Protection Of Alzheimer’S Disease, Josue David Gonzalez Murcia, John Kauwe

Journal of Undergraduate Research

Alzheimer’s disease is one of the top 10 causes of death in the world and the 6th leading cause of death in the United States, with 5.5 million people diagnosed with the disease. Alzheimer’s cannot be cured, prevented or slowed. Most research with Alzheimer’s disease has been done on SNPs that have a relatively high frequency in the population this has helped facilitate researchers in finding a broad genetic pathway in the development of Alzheimer’s disease (Naj et al. 2011; Harold et al. 2009). Our research will focus on a very rare SNP, with a much lower frequency than previously …

Transferring Hypothetical Deductive Reasoning, Jordan Hatch, Jamie L. Jensen

Journal of Undergraduate Research

The purpose of our project was to understand if hypothetical deductive (HD) reasoning skills exist in each discipline and if so, whether they are transferable between disciplines. HD reasoning is the method of scientific investigation used most commonly by scientists. It includes formulating hypotheses, devising experiments, making predictions, and analyzing results (iSTAR 2013). Many science classes boast scientific reasoning as a main learning outcome, but does reasoning transfer between disciplines and thus benefit the person as a whole? We hypothesized that most, if not all, disciplines use HD reasoning. In addition, we hypothesized that because this skill is context independent …

Did Tardigrades Survive The Last Glacial Maximum In Antarctica?, Caj Johansson, Byron Adams

Journal of Undergraduate Research

The current belief of the majority of glaciologists is that during the last glacial maximum (LGM), 17,000-22000 years ago, the entire Antarctic continent was completely covered in ice (Convey, 2008). This would mean that all terrestrial organisms would have died out during this time, essentially leaving Antarctica without life. If this hypothesis is true then all terrestrial organisms found currently in Antarctica arrived after the LGM (the past 12-18,000 years), a very short time frame for speciation to occur. Tardigrades are microscopic terrestrial animals that are most closely related to Arthropods and Nematodes (Edgecombe, 2011 but see also Longhorn, 2007). …

Do Differently Managed Dairy Cows With Production-Related Metabolic Diseases Have Similar Protein And Fat Species In Colostrum And Milk?, Holly Martin, Dr. Beverly Roeder

Journal of Undergraduate Research

Production-related metabolic diseases (PRMDs) in dairy cows threaten the livelihood of the animals as well as the productivity and success of the dairy industry. Because dairy cows supply an important food source for humans, understanding, managing, and preventing these diseases protects this source. Management and prevention of these diseases would increase production and profit margins for the dairy industry.

Testing The Validity Of The Lctsr 12-Point Grading System, Ted Poirczynski, Jamie Jensen

Journal of Undergraduate Research

The Lawson Classroom Test of Scientific Reasoning (LCTSR) is a 24-question, multiple-choice test designed to assess students’ scientific reasoning ability. The test consists of 12 scenarios, each of which focuses on testing a specific reasoning pattern. Each scenario is followed by two questions; the first question assesses a student’s ability to apply the specific reasoning pattern being tested, whereas the second asks the student to explain the reasoning behind his or her response to the first question. This dual question approach is designed to verify that students are employing the correct reasoning patterns to reach the correct answers.

Genome-Wide Association Study Of Cerebrospinal Fluid Prostatic Acid Phosphatase Levels, Lyndsay A. Staley, John S. K. Kauwe

Journal of Undergraduate Research

In genome wide association studies (GWAS), the use of endophenotypes, or intermediate traits, have been found to provide novel insights into understanding the genetics of complex human disease and the pathways and proteins associated with them. Cerebrospinal fluid (CSF) has been shown to contain analytes that may provide promising insight into disease pathways that may not be identified using blood or other biological fluids. The analytes were selected from the Rules Based Medicine, Inc. (RBM) (Austin, TX) Human Discovery Panel 1.0, which includes a range of signaling, structural, and trafficking proteins that have previously shown relationships with human disease pathology. …

Diverging Predation Environment Between Two Sister Species Of Live Bearing Fish: Boldness, Activity, And Exploration., David Money, Jerald B. Johnson

Journal of Undergraduate Research

Our study takes advantage of a unique species pair within Brachyrhaphis, Brachyrhaphis roseni and B. terrabensis,, which provides insight into how divergence proceeds once speciation is complete. Brachyrhaphis roseni and B. terrabensis are sister species that occur in the same river drainages throughout northwestern Panama. A similar pattern occurs between these two species as occurs within other species of Brachyrhaphis, such that B. roseni lives in the presence of ambush predators (e.g., Hoplias microlepis and Gobiomorus dormitor) in lower elevation streams, and B. terrabensis, lives in largely predator-free, higher elevation streams. Therefore, using B. roseni and …

Effects Of Phosphorous Availability On Nematode Growth And Morphology In Vitro, Ammon Perkes, Byron Adams

Journal of Undergraduate Research

The Growth Rate Hypothesis (GRH) proposes that since high-growth protein synthesis in organisms requires phosphorous-rich rRNA, growth is correlated with and dependent on phosphorous availability to said organisms. The limitation imposed by phosphorus availability thus becomes a selective factor that drives evolution. (Elser et al, 2002). This project seeks to test the GRH in vitro using Plectus murrayi a species of Antarctic nematodes. Previous research in the McMurdo Dry Valleys in Antarctica found a correlation between life history in P. murrayi, including growth, and phosphorous availability. (Adhikari et al, in prep). We seek to replicate this difference in vitro …

Firefly Evolution And Signaling Systems, Michael Swindle, Michael Whiting

Journal of Undergraduate Research

The goal of this project was to expand and clarify the relationships between the various subfamilies of fireflies. Lampyridae (the scientific name for fireflies) is a family within the beetle order, Coleoptera, and include about 2000 species across the world. Lampyridae is currently recognized as having nine separate subfamilies, but the relationships between these groups are unclear. This project was meant to determine clear relationsips between these groups and further determine the location of key species, such as Pterotus obscuripennis, whose phylogenetic position has remained uncertain after many attempts to place it firmly within a specific subfamily. However, this …

Genetic Basis For Rheumatic Heart Disease In High Risk Families In Western Samoa, Eleni Tukuafu, John S.K. Kauwe

Journal of Undergraduate Research

Rheumatic heart disease (RHD) is the most common form of acquired cardiovascular disease among children worldwide and results in 233,000 deaths annually. Although genetic and environmental factors are known to contribute to RHD, not much is known about genes that increase susceptibility. RHD results from untreated rheumatic fever (RF). RF develops when a Streptococcus pyogenes infection, such as streptococcal pharyngitis, goes untreated. About 34% of children with an untreated Streptococcus pyogenes infection develop rheumatic fever. Only 1/3 of those children acquire RHD¹. This suggests that there is a genetic basis for why some children are prone to the …

Molecular Phylogenetics Of Basal Insect Groups: A Team Mentored Experience, Michael F. Whiting

Journal of Undergraduate Research

Funding was received from the BYU ORCA mentorship program during 2012-2013 to support undergraduates performing research in my lab on insect evolution, under the mentorship of postdoctoral researchers, graduate students, and myself. During 2013- 2014, this funding provided direct support for 6 undergraduates who are in various stages of completing research projects. The following report focuses on undergraduate achievements, but also provides summary data for graduate students and other lab participants.

Evolution And Biogeography Of Mesoamerican Small Mammals: With Focus On The Genus Handleyomys And Related Taxa, Ana Villalba Almendra

Theses and Dissertations

Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. For mammals, the patterns of diversification of Mesoamerican taxa still are controversial. Reasons for this include the region's complex geologic history, and the relatively recent timing of such geological events. Previous studies, however, support the view that substantial migration between North (NA) and South America (SA) occurred prior or/and during the Great American Biotic Interchange (GABI) ~3.5 Ma. This was followed by repeated periods of isolation during Pleistocene climatic oscillations, which produced most of the diversification in the region. From a North American origin, …

Byu Undergraduates Execute A Familial Study Of Non-Demented Individuals In High-Risk Alzheimer’S Disease Pedigrees, John S.K. Kauwe

Journal of Undergraduate Research

Successful enrollment in and completion of graduate programs requires a constellation of skills. Students must be prepared to plan and execute experiments, present their findings both verbally and in manuscript form and interact effectively with senior scientists in the field of their choice. In this MEG I will mentor four undergraduate students (Kevin Boehme, Lyndsay Staley, Kaitlin Bell and Mark Wadsworth) as they develop skills in study design, data analysis, manuscript preparation, presentation and networking while identifying genetic factors that protect individuals from Alzheimer’s disease.

Linking Water And Carbon Cycles To Train Students To Meet 21st Century Grand Challenges In Environmental Science, Richard Gill

Journal of Undergraduate Research

The central aim of this proposal is to provide opportunities for students from diverse academic backgrounds to work collaboratively on a number of federally funded environmental change experiments across four of Utah’s ecosystems—Mojave Desert, Great Basin Shrub Steppe, Subalpine Tall Forb, and Colorado Plateau Grassland. This proposal funded 4 students from life sciences and engineering.

The Central Aim Of This Proposal Is To Provide Opportunities For Students From Diverse Academic Backgrounds To Work Collaboratively On A Number Of Federally Funded Environmental Change Experiments Across Four Of Utah’S Ecosystems—Mojave Desert, Great Basin Shrub Steppe, Subalpine Tall Forb, And Colorado Plateau Grassland. This Proposal Funded 4 Students From Life Sciences And Engineering., Mark C. Belk

Journal of Undergraduate Research

The proposal was to compare life history characteristics and the cost of reproduction tradeoff among populations of a burying beetle (Nicrophorus orbicollis). We conducted two major experiments with the MEG funding directed toward this goal. Both experiments required that we collect beetles from the wild and then raise their offspring in the lab to document responses. First, we compared lifetime reproductive output among two populations at two distinct temperatures. Second, we evaluated parentage of offspring (using newly developed molecular techniques) after manipulation of parental care.