Life Sciences Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

Interaction Between Predation Environment And Diet Constrains Body Shape In Utah Chub, Gila Atraria (Cypriniformes: Cyprinidae), Trevor J. Williams, Jerald B. Johnson, Mark C. Belk

Faculty Publications

Evolution typically occurs in response to a suite of selective pressures. Yet, many studies of natural selection in the wild only investigate a single selective agent at a time. This can be problematic when selective agents act in non-additive ways. Here we evaluate the interactive effects of diet and predation on the evolution of body shape in the cyprinid fish Utah chub (Gila atraria). We found that both factors and the interaction between them are significant predictors of body shape. This interaction is likely a result of different forms of selective pressures, where predation is a stabilizing selective …

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 …

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 …

Splice Site Predictor, Mark Wadsworth, Dr. Perry G. Ridge

Journal of Undergraduate Research

With the advent of nextgeneration sequencing, one of the unintended consequences is the sheer number of genomic variations requiring interpretation. Mutations in splice sites have been shown to contribute to the development of cancer [1], and dementia [2] among other potentially deadly disorders. Roughly 14 million people are diagnosed with cancer every year [3], and roughly 7 million with dementia [4]. Since these diseases cause an incredible amount of suffering, scientists in all fields are driven to search for ways to identify and treat them. These have been particularly difficult to interpret and have been largely ignored by the bioinformatics …

Flies As Bioindicators Of Grazing Pressures In Mongolia, Rebecca Clement, C. Riley Nelson

Journal of Undergraduate Research

For over fifty thousand years, humans have affected their surrounding environments in a negative way. As the human population continues to increase, concerns about extinction and other human-influenced problems including climate change, habitat degradation, pollution and introduction of invasive species are becoming more and more difficult to ignore (Oreskes, 2004). Mongolia, with its low population density and richly diverse biogeographical landscape, has retained much of the biota that has been lost in surrounding more populous Asian countries. Much of the fauna is relatively unknown. A growing concern in Mongolia is the commercialization of grazing. Although grazing has been an integral …

Damselflies Of Patagonia: A Phylogeographic Study Utilizing Epic, Taylor King, Seth Bybee

Journal of Undergraduate Research

While working on my original project, “In Situ Hybridization of Opsins in Odonata,” I encountered abundant setbacks that led to refocusing my efforts on a similar project. Patagonian Odonata is one of the most well known insect groups in South America. Within the order Odonata there are two main suborders, encompassing dragonflies and damselflies. It is composed of 36 species in 18 different genera, with 60% of the species and 40% of the genera endemic to the region. We selected two damselfly species, Rhionaeshna variegata and Cyanallagma interruptum to perform the first phylogeographic study of Patagonian Insects. They are the …

Proposal Of A New Genus And A New Species Of Chrysomelid Beetle, E. Russell Anderson, Shawn Clark

Journal of Undergraduate Research

The beetle family Chrysomelidae contains many species and genera which are of agricultural importance, which can cause millions of dollars of damage. While studying Triarius, a genus largely overlooked among Chrysomelidae because of its low agricultural impact, we have recognized that Triarius vittipennis (Horn, 1893) differs markedly from other species in several characters that we regard as key. Accordingly, we propose a new genus to accommodate T. vittipennis, as well as a new Mexican species which we are describing and naming now. Additionally, we are describing a second new species, which we place in the genus Triarius.

Effects Of Age And Prior Reproduction On The Cost Of Reproduction In Two Species Of Burying Beetles, Ethan Damron, Dane Jo, Mark Belk

Journal of Undergraduate Research

Understanding how much energy an organism allocates to breeding to maximize reproduction over their lifetime, or the cost of reproduction, is a central idea to understanding the variations in patterns of reproduction among living organisms (Creighton et al., 2009). In most studies of cost of reproduction, age is confounded with prior reproductive experience. As individuals age, they tend to reproduce making it difficult to disentangle these two factors when evaluating costs of reproduction. It is not clear whether reproduction early in life costs the same as reproduction later in life and how much of that difference might be due to …

Comparative Transcriptomics Of Patagonian Lizards (Liolaemus) And Central-American Casque-Headed Lizards (Coroytophanidae), Megan Mcghie, Jack Sites Jr.

Journal of Undergraduate Research

Introduction This project aimed help identify some of the genomic basis of various phenotypic-genotypic relationships among reptiles. These include the genetic basis of adaption in the following aims: (1) the evolution of hemoglobin subunits and its relationship to high altitudes/hypoxia and (2) comparative analyses on parity modes (oviparity, viviparity, and parthenogenesis). For these purposes, we analyzed published data versus the new data form two charismatic groups of lizards: (1) four species of the temperate Patagonian genus Liolaemus and (2) one species from each of the Neotropical genera Corytophanes and Basiliscus (family: Corytophanidae). Both clades have relative limited or no genomic/transcriptomic …

Examining Gene-Expression Patterns Across Rare Colon Cancer Syndromes To Identify Early Diagnosis And Treatment Options, Douglas Hawkes, Stephen Piccolo

Journal of Undergraduate Research

Colon cancer often runs in families. Individuals in these families have a relatively high lifetime risk of developing colon cancer and often develop aggressive tumors at a relatively young age. Currently, genetic testing is the standard way to diagnose hereditary colon cancer; however, many people who develop hereditary colon tumors do not have a mutation in the tested genes. Thus a better diagnostic approach, as well as a better understanding of how to target the underlying molecular causes of hereditary colon cancer, are needed.

Individuals who have a potentially high hereditary risk for colon cancer sometimes do not receive a …

Phylogeny And Species Boundaries In The “Flying Dragons” Of The Draco Maculatus Species Complex (Family Aamiedae), Randy Klabacka, Dr. Jack W. Sites

Journal of Undergraduate Research

Indo-Burma, comprising most of Mainland Southeast Asia east of India and north of Peninsular Malaysia, is a biodiversity hotspot within Southeast Asia that has been called a contender for the “hottest of hotspots” (Mittermeier, 1999). A remarkable majority of this species diversity remains hidden from human recognition in two areas: (1) undiscovered in natural habitat, and (2) conspicuously masquerading under known taxa. While solutions to the former require continued field work, solutions for the latter require further study of already identified taxa for hidden diversity therein. Indo-Burma is the endemic home to the “spotted flying dragon” (Draco maculatus; …

In-Class Participation And Performance Gender Gaps In Introductory Biology Courses: The Instructor Gender Effect, Nicholas Nelson, Liz Bailey

Journal of Undergraduate Research

It is well known that undergraduate women are underrepresented in STEM disciplines, which includes the sciences, technology, engineering, and mathematics (NSF 20011). However, the explanation for this phenomenon is not completely understood. Much research has been done recently and suggests that the “why?” is very complicated and multi-faceted (Smith 2012, Gayles 2014). Reasons can include female students’ sense of belonging, perception of ability, access to a positive mentor, and others (Smith 2012). While biology programs are unique in that female enrollment often exceeds that of males, gender inequities are still seen as postgraduates enter their careers (Handelsman et.al 2005). Because …

Meta-Analysis Of Flipped Classroom, Dr. Jamie Jensen, Ratchapong Kaosucharit

Journal of Undergraduate Research

The “Flipped Classroom” is a learning model in which content attainment is shifted forward to out-side of class, and then followed by instructor-facilitated concept application activitiesa in class (Jensen, 2015). It is one of the most rapidly emerging and popular learning models to date. It has become increasingly popular within many educational settings including medical schools. Currently, the flipped classroom has gained such reputation that there are 12,000 educators around the globe who support and implement the flipped classroom model in their institutions, including BYU (Jensen, 2015). The flipped classroom has unique characteristics that differ from traditional classrooms. While the …

Do Antartctic Tardigrades Survive Better When They Are Wet Or Dry When Exposed To Freese/Thaw Cycling?, Katelyn Hendricks, Byron Adams

Journal of Undergraduate Research

: Substantial amounts of evidence prove that there are drastic climate changes taking place everywhere on Earth. Antarctica, the home to microscopic tardigrades, or water bears, is no exception. Tardigrades have distinct roles and adaptations that allow them to survive the harsh climates of their environment. Because of climate change in Antarctica, there is a clear increase in the presence of liquid water and freeze/thaw cycles. This correlation raises the question of whether or not the increase of freeze/thaw cycles in Antarctica could result in increased tardigrade mortality. Normally, tardigrades experience the majority of their freeze-thaw cycles in a desiccated …

How Well Can Machine-Learning Algorithms Predict Biomedical Outcomes Based On Gene-Expression Data?, Anna Guyer, Stephen Piccolo

Journal of Undergraduate Research

Biomedical data are increasing in size and complexity. To make sense of these data, biomedical researchers often use “machine-learning” algorithms, which are developed by the computer-science community. Our goal was to perform a systematic comparison of many of these algorithms across 100 data sets to identify which algorithms perform best for this type of data. To help meet this goal, we also planned to carefully curating data from the public domain for others to use in their own comparisons.

Unlike DNA, which changes little from cell to cell, gene-expression levels vary dramatically across different types of tissues and under different …