Biology Commons^™

Association Of Tm2d3 Gene With Lateonset Of Alzheimer’S Disease In Cache County, Eleni Tukuafu, Dr. John S. K. Kauwe

Journal of Undergraduate Research

It is estimated that 5.2 million Americans have Alzheimer’s disease. It is currently the 6th leading cause of death in America, killing around 500,000 seniors every year. A 68% increase of death from Alzheimer’s disease was observed from the year 2000 to 2010. These numbers are expected to continue climbing.

Anatomical Variation Of The Ulnar Collateral Ligament And Implications For Joing Stability And Surgical Rehabilitation, Jakob Gamboa, Dr. Jonathan Wisco

Journal of Undergraduate Research

In 1974, the first ulnar collateral ligament reconstructive surgery was performed on Los Angeles Dodgers’ pitcher, Tommy John. The damaged ligament of the medial elbow was repaired with tendons from the pitcher’s body. Since then, the surgery has been colloquially termed “Tommy John’s Surgery”, and the alarming increase of the rates of the procedure has now become a concern, being recently called an “epidemic” by the American Sports Medicine Institute¹. The procedure possesses risk of complications, and can lead to shortened careers, decreased performance over time², and can carry a heavy financial toll on individuals and …

Testing The Effect Of Antioxidants On The Pathogenesis Of Alzheimer’S Disease Through The Rage/Nf-Kb Inflammatory Pathway, Harrison Snyder, Jonathan Wisco

Journal of Undergraduate Research

The Receptor for Advanced Glycation Endproducts (RAGE) is known to have a role in inflammatory processes. When produced in excess it induces oxidative stress by activating a number of ligand enzymes, resulting in the generation of excessive cytosolic reactive oxidant species. This oxidative stress then stimulates Nuclear Factor Kappa-B (NF-kB), which regulates immune response and inflammation. When RAGE is incorrectly regulated, inflammation occurs in otherwise healthy tissue, a process implicated in neurodegenerative disorders like Alzheimer’s disease. RAGE is found throughout the body and is seen in greater concentration in inflamed tissues; it has also been found in the brain tissue …

Alzheimer’S Disease And The P.V236e Variant In The Apoe Gene, Alton Chad Sorensen, John Kauwe

Journal of Undergraduate Research

I was interested in trying to validate the findings of the publication by Medway et al. concerning the SNP rs199768005 using data from the Cache Country data set. Unfortunately, of the 4703 people from our data set, only 10 were carriers. Using R statistical analysis, I found that the p-value for this SNP with an association to protect for Alzheimer’s Disease (AD) was not significant. It was similarly not significant in its association with Any AD. I also ran other models to include for factors such as education or age in conjunction with this SNP and its association with AD …

Ligament Microstructure Analysis, Michael Gillespie, Jonathan Wisco

Journal of Undergraduate Research

Due to the relatively poor fiber contrast of tendons in comparison with muscles, the anatomical, and therefore, functional relationship of muscle attachments to bones via tendons has not been well mapped. We were interested in mapping the 3D gross anatomical structure of tendons using a MicroScribe 3D digitizer (GoMeasure3D, Amherst, VA), with the goal to compare fibrous architecture between tendons of various types of muscles and muscle classes. We developed a stain made of blue dye and powdered sugar to increase fiber visibility, thus allowing for 3D digitization. This technique was applied to human cadaveric calcaneal tendon and quadriceps tendon.

Analyzing Structural Differences In Quadriceps Femoris Tendon Fibers Using Microscribe Technology, Nathaniel Hainsworth, Jon Wisco

Journal of Undergraduate Research

Not all tendons and ligaments are created equally. Many have different structural characteristics based on functionality or need for stability. This turns out to be true even between different portions of the same tendon. This project’s purpose was to analyze and compare structural differences between tendon fibers of the patellar portion and quadriceps portion of the quadriceps femoris tendon. We hypothesized that there are significant structural differences between these two portions because they act very different biomechanically, as well as different in the amount of tension/strain put on each portion. We mapped individual tendon fibers of both portions using MicroScribe …

Assessment Of Biodiversity On Mount Timpanogos With A Focus On Flies, Diptera: Agromyzidae, Samantha Smith, Dr. Riley Nelson

Journal of Undergraduate Research

Mount Timpanogos, with an elevation of 3,582 meters, is home to an amazing array of insect species. Through much previous effort, many have studied the insects found in American Fork Canyon leading up to Mount Timpanogos. They have still barely scratched the surface of the abundant biodiversity on the mountain. Varied temperature regimes can cause changes in insects’ life cycle and the length of their feeding period, making the collections at different elevations of Mount Timpanogos during different years of particularly great value (Petitt et al 1991). Thus the value of collections along Mount Timpanogos is two-fold; both to study …

Analysis Of Hmgcr As A Genetic Modifier For Alzheimer’S Disease, Brian Davis, Dr. John S. K. Kauwe

Journal of Undergraduate Research

Alzheimer’s disease (AD) is a chronic neurodegenerative disorder that occurs predominantly later in life and represents the fourth most common cause of death in the developed world. Given the absence of curative treatment, discovering the factors related to the development of AD and the conversion from mild cognitive impairment (MCI) to AD is one of the most urgent medical mysteries affecting the aging population. The search for the identification of genes contributing to AD led to the identification of 695 candidate genes of which a surprising number are directly involved in lipid metabolism at the level of transport, synthesis, storage, …

Association Of Rare Genetics Variants To The Protection Of Alzheimer’S Disease In The Cache County Data Set, 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 …

Expanding The Freshwater Aquatic Invertebrate Identification Guide Cd, Sarah Brown, C. Riley Nelson

Journal of Undergraduate Research

The Freshwater Aquatic invertebrate Identification Guide (FAIIG) was a computer program created by the C. Riley Nelson lab in 2006 to help students with the identification process of various aquatic invertebrates throughout Utah. It has been used in Bio 100 classes at Brigham Young University to help students successfully identify various aquatic invertebrate specimens from rivers and streams in Utah. The goal of this project was to work on expanding the FAIIG program to include aquatic invertebrates in North America west of the Mississippi River. As well as expanding the breadth of content, we also worked on improving the information …

Association Of Rs75932628 (R47h) With Vascular Dementia In The Cache County Study, Emily Sears, Dr. John Kauwe

Journal of Undergraduate Research

Vascular dementia (VaD) is a neurodegenerative disease caused by atherosclerosis, or inadequate blood flow to the brain as a result of the build-up of fat deposits, dead cells, or other cell debris on the inside of arteries. It shortens the lifespan of those affected, and severely impairs their quality of life. VaD is the second most common form of dementia, after Alzheimer’s disease, accounting for 20-30% of dementia cases. Thus far the risk factors that have been determined are non-specific to the brain: high blood pressure, high cholesterol, and high blood sugar (Roman et. al 2003). There has not been …

Assembling Benchmark Datasets For Machine Learning Classification, Parker Hollingsworth, Stephen Piccolo

Journal of Undergraduate Research

Machine learning classification is a type of artificial intelligence that learns from data and makes predictions. There are many different algorithms that can be used to develop predictive models for machine learning. Generally the algorithm looks for patterns in the data and uses those patterns to make predictions on an additional data set. This type of artificial intelligence is being used increasingly in the biomedical community to predict disease diagnosis and prognosis. Although machine learning has shown to provide promising results, it is far from perfect. The accuracy of the predictive model often depends on arbitrary decisions made by researchers. …

Investigation Of Visual Systems In A New Species Of Firefly, Yelena Pacheco, Dr. Seth Bybee

Journal of Undergraduate Research

Fireflies are well known for their bioluminescent flashes causing them to be a particular group of interest concerning insect vision research. Their flashes are used for both sexual communication and as an aposematic warning to predators. Bioluminescent fireflies are known to use either a yellow-green flash or a yellow-orange flash to communicate between sexes in order to find a mate. There have been many studies concerning flash patterns’ role in sexual communication among fireflies; however, the understanding of firefly vision as a whole allows for many more untouched research possibilities. As a member of the Bybee lab I had the …

Presenilin E318g Variant And Alzheimer’S Disease Risk: The Cache Country Study, Ariel Hippen, John Kauwe

Journal of Undergraduate Research

Alzheimer’s disease is the leading cause of dementia in the elderly and the third most common cause of death in the United States. A vast number of genes regulate Alzheimer’s disease, including Presenilin 1 (PSEN1). It is possible that novel variants in the PSEN1 gene have an effect on Alzheimer’s disease status. A recent study suggested that one of these variants, PSEN1 E318G, significantly affects Alzheimer’s disease status in a large case-control dataset, particularly in connection with the APOEε4 allele [1].

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 …

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 …

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 …

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.

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 …

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 …

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.

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). …

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 …

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.

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.