Biology Commons^™

Loss Of The Giant Salmonfly Pteronarcys Californica And Changes In Stonefly Diversity In The Provo River, Utah (Plecoptera), Jackson Birrell, C. Riley Nelson

Journal of Undergraduate Research

Plecoptera (stoneflies) are important insects in aquatic ecosystems worldwide. They cover a wide array of functional feeding groups and provide various ecosystem services (1). Stoneflies are sensitive to reductions in water quality, allowing managers to use their presence or absence to denote if a watershed is healthy or impaired. They are therefore known as bioindicators of stream health (2). Plecoptera are also appreciated by fly fisherman throughout the world. Despite their ecological, conservational and cultural importance, stoneflies are in decline. Their sensitivity to anthropogenic disturbances including pollution, river damming, urbanization and climate change make them particularly vulnerable and have lead …

Provo River Restoration: Success Or Failure?, Jared Meek, C Riley Nelson

Journal of Undergraduate Research

The Provo River in central Utah flows from its headwaters in the Uinta Mountains, down the heavily agricultural Heber Valley, through the urban center of Provo and Orem, and out into Utah Lake. Beginning in the 1950s, the Provo River underwent significant alterations as part of a large-scale water reclamation project throughout central Utah1, including the channelization and straightening of its middle section. In addition to these alterations, the river had two dams constructed along its course: the Deer Creek Dam (1941) and the Jordanelle Dam (1993). To remedy the ecological impairment that these manipulations caused, the Utah Reclamation Mitigation …

Phylogeny Of Hetaerina (Odonata: Calopterygidae), Samantha Smith, Seth Bybee

Journal of Undergraduate Research

Damselflies (Zygpotera) exhibit diverse mating behaviors, with the family Calopterygidae known for its pigmented wings and territorial behavior (Cordoba-Aguilar, Cordero-Rivera 2005). The genus Hetaerina, or rubyspot damselflies, has been used in numerous studies due to mating behaviors, morphology and a high density along certain streams (Anderson 2010, 2011; Contreras-Garduno 2006; Cordoba-Aguilar 2009; Grether 1996, 1997; Raihani 2008; Regions 2011). Despite use in studies, relationships between species of Hetaerina remain unclear. Over the past ten years, the taxonomy of Hetaerina and their sister genus Mnesarete has been in flux with species being transferred between the two genera and into Ormenophlebia and …

Biotic Filtering In Endophytic Fungal Communities, Kevin Daniel Ricks

Theses and Dissertations

Plants can be colonized by complex communities of endophytic fungi. This thesis presents two studies, both of which investigate biotic filtering in endophytic fungal communities. Chapter 1. Endophytic fungi can be acquired horizontally via propagules produced in the environment such as in plant litters of various species. Given that litters from different plant species harbor distinct endophytic fungal communities and that endophytic fungi may be dispersal-limited, the structure of the endophytic fungal community of a given plant may be determined by proximity to particular inoculum sources. Community assembly may also be affected by biotic filtering by the plant. Therefore, a …

Genomewide Evaluation Of Cis-Elements And Cognate Transcription Factors In Nicotiana Attenuata Predicts 27 Unique Transcription Factor-Binding Site Pairs, Ashton Omdahl

Undergraduate Honors Theses

Nicotiana attenuata has been widely studied for its ecological plant-herbivore relationships and response to environmental stress. The jasmonate signaling pathway regulated by jasmonate ZIM-domiain (JAZ) repressor proteins that modulate defense response levels has been of particular focus in this research. While our understanding of the genes associated with defense response and their regulation continues to expand, the transcriptional regulation of these genes is largely uncharacterized. In an effort to provide insight into these relationships, we performed genomewide analysis of transcript level data in order to predict transcription factors (TFs), their respective binding sites (TFBS), and the genes they regulate. We …

Rab10: The Future Of Alzheimer’S Disease, Keni Reid, Dr. John Kauwe

Journal of Undergraduate Research

Alzheimer’s disease is a brain disorder caused by an irreversible degeneration of nerve cells. It is developed in response to a growth of proteins, tau tangles or amyloid plaques, which disrupt communication between neurons in the brain. Because the nerve cells no longer function, they die. It is estimated that as many as 5.1 million Americans may have Alzheimer’s disease and about one to four family members act as caregivers for each individual with Alzheimer’s disease. Many lives are affected by Alzheimer’s which has driven further and extensive research for solutions. However, despite much effort, the genetics of Alzheimer’s remains …

Metastatic Colon Adenocarcinoma Has A Significantly Elevated Expression Of Il-10 Compared With Primary Colon Adenocarcinoma Tumors, Michelle H. Townsend, Abigail M. Felsted, Stephen R. Piccolo, Richard A. Robison, Kim Oneill

Faculty Publications

Classical anti-inflammatory cytokines are known to play a role in both cancer progression as well as cancer elimination. We evaluated the anti-inflammatory cytokines IL-10 and TGF-β in patients with colon adenocarcinoma and metastatic colon adenocarcinoma using immunohistochemical assays to determine the expression of the cytokines between various malignant tissues. We found tissues stained with TGF-β showed no significant upregulation within malignant tumors when compared with normal tissue controls. We observed high levels of TGF-β presence in most tissues similar to GAPDH expression. Within both colon adenocarcinoma and metastatic carcinomas there was a significant variability among patients in the expression of …

Small Mammal Diversity, Rattlesnake Demographics, And Resource Utilization In The Great Basin: Implications For Management And Stable Isotope Proxies, Bryan T. Hamilton

Theses and Dissertations

Plant carbon isotopes were used to track assimilation of riparian resources by small mammals. Voles and shrews derived significant portions of their carbon from riparian vegetation. Deer and harvest mice were abundant in riparian habitat but assimilated little riparian vegetation indicating that the riparian corridor provided resources other than food. This is first use of stable carbon isotopes to trace riparian resources into a vertebrate community. Conifer encroachment in sagebrush ecosystems negatively affects many wildlife populations. Conifer removal is recommended across millions of hectares in the Great Basin. However the effects of conifer encroachment and conifer removal are unknown for …

Analysis Of Whole Exome Sequence Data In Affected Cousin Pairs From High-Risk Alzheimer's Pedigrees, Lyndsay Ann Staley

Theses and Dissertations

Genetic factors account for about half of Alzheimers Disease (AD) risk and only about a quarter of that heritability is accounted for by known variants. Family based approaches to understanding AD genetics may be an effective way to identify additional risk factors. Here we report the results of whole exome sequencing (WES) and analyses done on pairs of AD affected cousins from 19 families from the Utah Population Database (UPDB) with a statistical excess of AD risk. WES variants passing quality control were additionally filtered by population frequency (minor allele <<> 0.01) and concordance between cousin pairs, resulting in 564 variants …

The Evolutionary Significance Of Body Size In Burying Beetles, Ashlee Nichole Momcilovich

Theses and Dissertations

Body size is one of the most commonly studied traits of an organism, which is largely due to its direct correlation with fitness, life history strategy, and physiology of the organism. Patterns of body size distribution are also often studied. The distribution of body size within species is looked at for suggestions of differential mating strategies or niche variation among ontogenetic development. Patterns are also examined among species to determine the effects of competition, environmental factors, and phylogenetic inertia. Finally, the distribution of body size across the geographic range of a species or group of closely related is looked at …

Does Body Size Affect Fitness The Same Way In Males And Females? A Test Of Multiple Fitness Components, Ashlee N. Smith, Mark C. Belk

Faculty Publications

Body size generally has an important relationship with fitness, whereby larger body size leads to an increase in fitness through competition, reproductive output and survivorship. However, the traits through which body size increases fitness often differ between the sexes. We tested for the effects of body size on fitness in both sexes using three separate experiments on competitive ability, reproductive output and starvation resistance in the burying beetle Nicrophorus marginatus. Results varied between sexes as follows: (1) larger body size increased competitive ability differentially between sexes; (2) female body size, but not male body size, significantly affected reproductive output …

Molecular Evolution Of Odonata Opsins, Odonata Phylogenomics And Detection Of False Positive Sequence Homology Using Machine Learning, Anton Suvorov

Theses and Dissertations

My dissertation comprises three related topics of evolutionary and computational biology, which correspond to the three Chapters. Chapter 1 focuses on tempo and mode of evolution in visual genes, namely opsins, via duplication events and subsequent molecular adaptation in Odonata (dragonflies and damselflies). Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Odonata have the largest opsin repertoire of any insect currently known. In particular our results suggest that both the blue sensitive (BS) and long-wave sensitive (LWS) opsin classes were subjected to strong positive …

Evolution Belief Trends, Jamie Jensen

ScholarsArchive Data

This is the essay code frequencies along with the raw survey data for both Cohort 1 and Cohort 2 for the following paper:

Bradshaw, WS, Phillips, AJ, Bybee, SM, Gill, RA, Peck, SL, Jensen, JL. 2018. A longitudinal study of attitudes toward evolution among Mormon undergraduates. PLOSONE.

Pvaast Anallysis Of Alzheimer’S Disease Sequencing Project Pedigree Data, Kristen Crofts, John S. K. Kauwe

Journal of Undergraduate Research

Alzheimer’s disease is a progressive brain disorder affecting more than 10 percent of Americans over the age of 65 (1). This disease destroys memory and thinking skills and is a leading cause of dementia. Although research in recent years has provided substantial information related to risk factors associated with Alzheimer’s disease, a great deal of information still remains unknown. PVAAST is a software tool that can analyze genome sequence data of Alzheimer’s patients in a creative way by also analyzing the patients’ pedigree information. With the combined information from family members, it is more feasible to identify genetic mutations related …

Classifying Cancer Genome Aberrations By Their Mutually Exclusive Effects On Transcription, Jonathan B. Dayton, Stephen R. Piccolo

Faculty Publications

Background

Malignant tumors are typically caused by a conglomeration of genomic aberrations—including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemotherapies and targeted drug treatments are effective against tumors that harbor certain genomic aberrations. However, predictive aberrations (biomarkers) have not been identified for many tumor types and treatments. One way to address this problem is to examine the downstream, transcriptional effects of genomic aberrations and to identify characteristic patterns. Even though two tumors harbor different genomic aberrations, the transcriptional effects of those aberrations may be similar. These patterns could be used to inform treatment …

Understanding Community And Ecophysiology Of Plant Species On The Colorado Plateau, Hannah Elizabeth Yokum

Theses and Dissertations

The intensification of aridity due to anthropogenic climate change is likely to have a large impact on the growth and survival of plant species in the southwestern U.S. where species are already vulnerable to high temperatures and limited precipitation. Global climate change impacts plants through a rising temperature effect, CO2 effect, and land management. In order to forecast the impacts of global climate change, it is necessary to know the current conditions and create a baseline for future comparisons and to understand the factors and players that will affect what happens in the future. The objective of Chapter 1 is …

Why Does It Take Two To Tango? Lifetime Fitness Consequences Of Parental Care In A Burying Beetle, Ashlee N. Smith, J. Curtis Creighton, Mark C. Belk

Faculty Publications

In species that require parental care, each parent can either care for their offspring or leave them in the care of the other parent. For each parent this creates three possible parental care strategies: biparental care, uniparental (male or female) care, and uniparental desertion by either the male or female. The burying beetle, Nicrophorus orbicollis, typically exhibits biparental care of offspring, and thus provides a unique system that allows us to compare the fitness benefits of these parental care strategies in an unconfounded way. In this study, we assess the lifetime fitness of biparental care, uniparental care, and uniparental …

Elevated Expression Of Hypoxanthine Guanine Phosphoribosyltransferase Within Malignant Tissue, Michelle H. Townsend, Abigail M. Felsted, Zachary E. Ence, Stephen R. Piccolo, Richard A. Robison, Kim L. O'Neill

Faculty Publications

Hypoxanthine Guanine Phosphoribosyltransferase (HPRT) is a housekeeping enzyme involved in the purine synthesis of guanine and inosine in the salvage pathway. While other salvage pathway enzymes, such as TK1, have been established as biomarkers for both cancer cell proliferation and cancer development, little research been done to evaluate whether HPRT has the same potential as a cancer biomarker. We designed this study to determine if HPRT has value as an identifier of malignancy within the most common types of cancer. We utilized histological samples from lung, colon, prostate, and breast cancer with additional normal tissue to evaluate whether there was …

Byu Undergraduate Explore The Development Of Scientific Reasoning Ability In Stem Majors And Its Correlation To Student Performance And Retention, Jamie Jensen

Journal of Undergraduate Research

This report will outline how effectively we met our academic and mentoring objectives. I have listed below both the academic and mentoring objectives put forth in the original proposal and have outlined how they were met or modified over the course of the past two years. Let me just start out by saying how proud I am of my undergraduate team of researchers. They have been absolutely AMAZING and have taken this project on with incredible autonomy. Although we are a bit behind our anticipated schedule (due to the autonomy that I have tried to foster with the students), the …

Insect Visual Systems And Fossils To Provide Students A Clear Vision Of 21st Century Phylogenetic Systematics, Seth M. Bybee

Journal of Undergraduate Research

Goals one and three were both very successful (more below), however goal two became bogged down and was ultimately abandoned. CT-scanning is a process that requires hundreds or even thousands of fine x-rays through an organism in cross-section to be “stacked” together. Stacking the x-rays together allows researchers to literally explore the internal and external anatomy of organisms in ways never before possible. The most successful scans are those produced when tissues are discrete and have different attributes in terms of pattern, hardness, etc. We focused heavily on fossil specimens embedded in amber. Unfortunately, the cuticle of these specimens were …

Response To Drought Of A Stream Fish Assemblage In A High Elevation Stream In The Intermountain West, Richard M. Simkins

Theses and Dissertations

One of the most influential disturbances for stream fish assemblages is large-scale declines in flow caused by periods of drought. Although stream characteristics are known to influence the response of stream fishes to drought, we asked if ecological traits of stream fishes determine, in part, their population level response to drought. To test for ecological trait-based responses to drought in a stream fish assemblage, we quantified species abundances over a period of 5 years that represented a wet to dry period. We sampled stream fishes in Yellow Creek, Wyoming, USA, a high elevation stream dependent on snow-storage for most of …

Role Of Terrestrial Organic Matter In Food Webs Of The Rocky Intertidal Zone, Douglas O. Fairbanks

Theses and Dissertations

Terrestrial organic matter (TOM) constitutes an important source of energy in many aquatic environments (streams, lakes, wetlands). This is the first study to examine the role of TOM in food webs of the rocky intertidal zone. We compared the consumption of red alder leaves (Alnus rubra) to common marine sources of drifting detritus along the southern Oregon coast (Nereocystis luetkeana, Phyllospadix spp., and Fucus gardneri). We used short term (hours to days) and long term (months) feeding experiments to compare the rate of consumption among each plant species during the Spring and Fall of 2014 …

Bacterial Community Ecology Of The Colon In Mus Musculus, Rachel Marie Nettles

Theses and Dissertations

The gut microbiome is a community of closely interacting microbes living in the gastrointestinal tract. Its structure has direct relevance to health. Disturbances to the microbiome, such as due to antibiotic use, have been implicated in various diseases. The goal of this study was to determine how the gut microbiome reacts to and recovers from disturbance caused by antibiotics. Because diet also influences the microbiome, this study included the interaction between diet and antibiotics. Half of the mice in each diet treatment were given antibiotics to disturb their microbiomes. After cessation of antibiotics, mice were paired in combinations within diets …

Current And Future Prospects Of The Biological Diversity Of Vertebrates In Teh Protected Areas Of A Megadiverse Country: Ecuador, Benjamin Bay, Dr. Jack Sites

Journal of Undergraduate Research

I collected, cleaned, and organized data on animal species in Ecuador, a megadiverse country (harbors a vast proportion of Earth’s species and is home to high numbers of endemic species). These data were crucial for a larger project which modeled the impacts of climate change on species conservation over time. I designed the algorithms that cleaned and organized these large data sets.

Using Bioinformatics To Increase The Number Of Tumors That Can Be Treated With Existing Drug Treatments, Jonathan Dayton, Stephen Piccolo

Journal of Undergraduate Research

Typically, tens or even hundreds of mutations are observed in the DNA of a single tumor by the time it has been detected1-4. Knowledge of these mutations may be useful in guiding the way the tumor is treated. In some cases, if a tumor has a mutation in a certain gene, this may indicate that the tumor can be treated with a certain drug. For example, the drug Trastuzumab is a targeted therapy for breast cancer patients with mutations in the HER2 gene5. In other cases, a mutation may be able to be targeted by a drug even if the …

Modelling Climate Suitability For Ephedra Viridis In Space And Time, Anne Thomas, Richard Gill

Journal of Undergraduate Research

Climate change is expected to decrease soil moisture in the sensitive, water-limited ecosystems of America’s southwestern deserts, leading to shifts in plant distributions and altering ecosystem function. Studies have already documented the loss of desert grasses and the expansion of desert shrubs on the Colorado Plateau near Canyonlands National Park.i The objective of this work is to identify the climatic and biophysical factors influencing the distribution of an evergreen shrub, Ephedra viridis, and its expansion in plot-scale studies over the past 30 years.ii A gymnosperm and member of the plant division Gnetophyta, this shrub is unique because of its …

Alzheimer’S Risk Genes And Pathways Of Expression, Samantha Jensen, John Kauwe

Journal of Undergraduate Research

Although Alzheimer’s disease (AD) has been the subject of research for nearly 100 years, these decades of research have not led to a unified understanding of the mechanisms behind the disease pathology1 ,2. Recent improvements in whole genome sequencing have made it possible for researchers to find a large number of mutations implicated in AD. Due to a high frequency of false positives and confounding factors, many mutations being investigated for therapies may not even have a causative effect on Alzheimer’s expression. Without concrete knowledge of the interactions of the proteins and genes implicated in the disease, drug development has …

Investigating Species Boundaries And Taxonomy In The California Pincushion Plants, Theresa Saunders, Leigh Johnson

Journal of Undergraduate Research

Species in the genus Navarretia are annual wildflowers found almost exclusively in California. The Navarretia atractyloides group consists of just two species, N. atractyloides and N. hamata, that are more similar to each other morphologically than to any other Navarretia species. The most recent taxonomic investigation of these two species distinguishes between them based on bract shape, stamen attachment to the corolla, and whether the style is included and anthers included to slightly exserted from the corolla tube versus style exserted and anthers long exserted (Day, 1993). However, we have noticed that some specimens that seem to be …

Integrative Analysis To Evaluate Similarity Between Brcaness Tumors And Brca Tumors, Weston Reed Bodily

Theses and Dissertations

The term "BRCAness" is used to describe breast-cancer patients who lack a germline mutation in BRCA1 or BRCA2, yet who are believed to express characteristics similar to patients who do have a germline mutation in BRCA1 or BRCA2. Although it is hypothesized that BRCAness is related to deficiency in the homologous recombination repair (HRR) pathways, relatively little is understood about what drives BRCAness or what criteria should be used to assign patients to this category. We hypothesized that patients whose tumor carries a genomic or epigenomic aberration in BRCA1 or BRCA2 should be classified under the BRCAness category and that …

Transition From Cardiovascular Disease To Cancer As The Leading Cause Of Death In Us States, 1999-2014, Michael C. Harding, Evan Thacker

Journal of Undergraduate Research

In 1900 the three leading causes of death in the United States were pneumonia and influenza; tuberculosis; and gastritis, enteritis, and colitis.¹ However, through a combination of improved sanitation, the discovery of antibiotics, and the advent of vaccination programs, deaths from infectious diseases subsided and soon gave way to chronic diseases.² Shortly after the turn of the century, diseases of the heart became of the number one cause of death, and in the 1940s, cancer began consistently appearing at number two. Since then, heart disease and cancer have remained firmly entrenched as the number one and two causes …