Life Sciences Commons^™

Transformation Of The Dental Faculty To Promote Changes In Dental Educaiton, Clark A. Dana

Theses and Dissertations

This work introduces a series of papers developed to explore the case for change in dental education. Three issues facing dental education are (a) the challenging financial environment of higher education, making dental schools very expensive and tuition-intensive for universities to operate and producing high debt levels for students, which limits access to education and restricts career choices; (b) the profession's apparent loss of vision for taking care of the oral health needs of all components of society and the resultant potential for marginalization of dentistry as a specialized health care service available only to the affluent; and (c) the …

Adversarial Deep Neural Networks Effectively Remove Nonlinear Batch Effects From Gene-Expression Data, Jonathan Bryan Dayton

Theses and Dissertations

Gene-expression profiling enables researchers to quantify transcription levels in cells, thus providing insight into functional mechanisms of diseases and other biological processes. However, because of the high dimensionality of these data and the sensitivity of measuring equipment, expression data often contains unwanted confounding effects that can skew analysis. For example, collecting data in multiple runs causes nontrivial differences in the data (known as batch effects), known covariates that are not of interest to the study may have strong effects, and there may be large systemic effects when integrating multiple expression datasets. Additionally, many of these confounding effects represent higher-order interactions …

Mechanism Of Positive, Non-Additive Litter Decomposition, Na Yin

Theses and Dissertations

Litter decomposition is a fundamental ecosystem process. It is responsible for nutrient cycling and influences carbon (C) sequestration, and soil physical and chemical properties. In nature, litter is usually heterogeneous and may not decompose the way homogeneous litter does. For example, heterogeneous litter decomposition is frequently non-additive. This makes the rate of nutrient cycling as well as fluxes of C into and out of soil C pools impossible to predict. The most frequently proposed mechanisms for positive, non-additive decomposition include the supply of limiting mineral nutrients, the supply of available C (priming), and the improvement of micro-environmental conditions. However, all …

A Race Against Time: Deciphering Evolution And Describing New Species Of Threatened Tropical Stick Insects (Phasmatodea), Michael F. Whiting

Journal of Undergraduate Research

Funding was received in 2016 to support mentored research into the phylogeny and evolution of stick insects. Specific goals include providing students with scientific design experience, field-based research experience, collections-based experience, molecular lab experience, bioinformatics experience, and experience in presentation at national meetings and publication in peer reviewed journals. One particular focus was to describe new stick insect species, but it became clear very quickly that the phylogeny portion of this work was essential before any new species could be described, so we concentrated our efforts on stick insect phylogeny. The following is a brief summary of accomplishments.

Byu Undergraduates Solving The Genetic Causes Of Alzheimer’S Disease, John 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 three undergraduate students (Sheradyn Hamilton, Kristen Cockriel, and Moroni Chalita) 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.

T Cell Immunotherapy Of Infection Disease And Cancer, Scott Weber

Journal of Undergraduate Research

This project was focused on improving the immune response to infectious disease and cancer. We have engineered T cell receptors with 1000-fold increase in affinity and will characterize their value as diagnostics and therapeutics. In addition, we examined changes in T cell function due to the co-receptor CD5. We also examined how T cell responses to infection are dependent upon metabolic and epigenetic regulation.

Development Of Real-Time Polymerase Chain Reaction (Q-Pcr) Assays For The Detection And Identification Of Drug-Resistance Genes In Carbapenem-Resistant Enterobacteriaceae (Cre), Richard A. Robison, Ph.D.

Journal of Undergraduate Research

I. The Specific aims for the project were as follows:

1. Develop q-PCR assays for the various carbapenem-resistance genes, such as KPC, IMP, VIM, and NDM-1, and then multiplex them into single assays that can be used to quickly characterize an isolate.

Increasing The Accuracy Of Molecular Biomarkers Via Evidence-Based Algorithm Selection, Stephen R. Piccolo

Journal of Undergraduate Research

In making medical decisions, physicians need observable criteria that they can use to make accurate diagnoses, determine optimal treatments, and estimate a patient’s prognosis. The promise of precision medicine is that molecular-level observations can more accurately predict such information than traditional observations. I worked with undergraduate students at Brigham Young University to develop ways to improve the accuracy of such predictions by optimizing computer algorithms to handle the complexity of large, molecular data sets.

Combating Obesity Through Gut Microbiome Targeted Bacteriophage Therapy, Gongze Zhao, Dr. Laura Bridgewater

Journal of Undergraduate Research

The human gut consists of approximately 1.5 kg of bacteria, and 50% of the biomass in our fecal matter is bacterial cells (Nicholson, 2005). Diet is a major factor in shaping the composition of the gut microbiota, (Zhang, 2010) which in turn influences the body by producing metabolites that enter the circulation through different pathways. In 2013, by using Koch’s postulates, scientists were able to demonstrate that the gram-negative opportunistic pathogen E. cloacae B29 can cause obesity and chronic inflammation in its host (Fei & Zhao, 2013). Bacteriophage (phage) are viruses that infect bacteria. Phages bind to their bacterial host …

Chemokine Receptor Ccbp2-V41a And Its Role In Inflammation And Alzheimer’S Disease, Allen Weinert, Scott Weber

Journal of Undergraduate Research

The leading cause of dementia in elderly patients is Alzheimer’s disease (AD), a degenerating and fatal neurodegenerative condition. AD is a proteopathic disease caused by extensive accumulation of amyloid beta plaques and neurofibrillary tangles. A recent genomewide association study analyzing 59 AD-associated cerebrospinal fluid (CSF) samples statistically associated chemokine receptor mutant CCBP2-V41A with increased CSF protein levels of the proinflammatory chemokine CCL2. CCBP2 is a known binding partner of CCL2. We hypothesized that CCBP2-V41A receptor alters CSF levels of CCL2 and that raised CCL2 levels alters immune cell function, resulting in amyloid beta deposition in the brain (Figure 1).

Determining The Role Of Cd5 In Regulatory T Cell Function, Charles Teames, Scott Weber

Journal of Undergraduate Research

Regulatory T cells (Tregs) inhibit the immune response and play a key role in preventing autoimmunity. Unfortunately, Tregs also often prevent an effective immunological response against cancer. CD5 is a T cell surface protein known to regulate the threshold for T cell activation. CD5 is known to influence Treg development, but it is unclear exactly how CD5 impacts the function of Tregs.

Past studies have indicated that mice lacking CD5, known as CD5 knockouts, produce more Tregs than wild type mice (1). It is thought that Tregs from these CD5 knockouts may be more effective in preventing T cells from …

Guided Evolution To Expand The Host Range In Phages, Jamison Walker, Sandra Hope

Journal of Undergraduate Research

My project proposal included the use of Darwin’s theory of evolution by natural selection to determine if genetic mutations will arise in Bacteriophages that would allow them to infect related strains in a species of bacteria. Bacteriophages naturally have a target host range that they can infect. Within species of bacteria, the phage has tail receptors that allow it to infect specific strains. The other strains of the bacteria will be unaffected by the phage. In phage therapy, multiple phages with varied host ranges are chosen to combat this problem. Some phages are more effective than others in killing a …

Damselfies Of Vanuatu, Madison Lallatin, Seth Bybee

Journal of Undergraduate Research

Vanuatu is a string of active volcanic islands in Micronesia near Fiji and Australia. The islands undergo regular submersion and emersion from the ocean, and the most recent emergence was 2 million years ago (Hamilton et al. 2010). As a result, all organisms on the islands of Vanuatu have migrated there, likely from other islands, within the past 2 million years. Fiji is one likely candidate for contributing species, being geographically close to Vanuatu and exhibiting similar species. Fourteen of us went to Vanuatu for 6 weeks on a study abroad led by Dr. Seth Bybee to collect and observe …

Tk1 As A Biomarker Of Chemosensitivity And Metastatic Potential In Breast Tumors, Eric Olsen, Kim O'Neill

Journal of Undergraduate Research

Breast cancer is the most common form of cancer in women, accounting for 23% of total cancer cases and 14% of cancer deaths. Breast carcinoma is not a simple disease. It is comprised of many different biological forms with distinct phenotypes and prognoses. Hormone receptor expression, such as ER, PR, and HER2, along with more universal clinical manifestations like pathological stage, grade, and lymph node invasion are often used for patient prognosis. The heterogeneous nature of breast tumors makes prognosis and response to therapies difficult to determine, and further research is needed to classify breast tumors and their response to …

Could Tk1 Suppress The Immune System And Promote Tumor Development?, Joshua Keller, Roman Kovtun, Kim O'Neill

Journal of Undergraduate Research

Cancer is a widespread disease that affects millions of people worldwide and in many cases is difficult to treat. In order to find new and better treatment, it is important to understand how this disease progresses. Thymidine Kinase 1 (TK1) is a recognized biomarker that is upregulated in cancer cells compared to healthy tissue. Although this protein is normally found inside the cells (cytosol), it becomes upregulated on the surface of malignant cells. Moreover, recent research shows that TK1 expression is further upregulated in breast cancer tissues that undergo a transition from stationary (epithelial) cells to more mobile (mesenchymal) cells. …

Using Remote Video Systems To Measure Effectiveness Of Small Scale Mpas In Saipipi, Samoa, Calvin Quigley, Dr. Richard Gill

Journal of Undergraduate Research

Coral reefs represent an invaluable natural, providing $30 billion dollars of fishing and recreational profits worldwide, and housing nearly a quarter of the oceans species [1, 2]. However, threats such as climate change, ocean acidification, coastal development and overharvesting have destroyed more than a fifth of the worlds coral reefs in recent decades[3]. One of the most common management plans that has been implemented to help protect and restore coral reefs is the establishment of marine protected areas (MPAs)[4]. MPAs have been proven to be effective in helping restore fish populations and coral cover, however the majority of MPAs are …

Quantifying Predictive Value Of Biological Data Types In Machine Learning Models Of Cancer Outcome, Samantha Jensen, Stephen Piccolo

Journal of Undergraduate Research

Precision medicine is a growing movement toward utilizing molecular diagnostics to guide medical decisions. It is particularly useful when applied to cancer treatment, as knowing details about cancer stage, genetic pathology, and tumor type can inform life-saving decisions. Increasingly, physicians may use genetic, proteomic, epigenetic, and expression data to determine treatment strategy and even choose specific chemotherapy drugs1.

Effectiveness Of Hospital Disinfectants Against Clostridium Spores, Bejamin Ogilvie, Richard Robinson

Journal of Undergraduate Research

Clostridium is a genus of anaerobic spore-forming bacteria notable for causing human infections. C. difficile has an especially high impact, affecting roughly 453,000 individuals in the U.S. in 2011 (1). C. tetani and C. perfringens infections occur much less frequently, although they remain clinically important. Disinfecting objects contaminated with Clostridium is challenging, as Clostridium spores are resistant to extreme temperature, desiccation, and most chemicals (2, 3). Clostridium is also frequently found within soil, making it a likely contaminant on almost any piece of medical equipment (3).

Currently, the U.S. EPA only requires sporicidal disinfectant efficacy tests against C. sporogenes, a …

Histone Post-Translational Modifications And Nucleosome Positioning: A New Layer In The Histone Code Hypothesis?, Andrew Earl, Dr. Steven Johnson

Journal of Undergraduate Research

Nucleosomes are the fundamental unit of chromatin organization. They consist of an octamer of histone proteins (two of each H2A, H2B, H3, and H4) wrapped around by 147 base pairs of DNA. Their positioning and occupancy around important genetic elements such as enhancers and promoters are some of the most important means of epigenetic regulation: changes in expression of genes that reflect a change in something other than DNA sequence. For example, highly-expressed genes are generally associated with low nucleosome occupancy, whereas inactive genes are associated with high nucleosome occupancy. It has also been shown that the positioning of nucleosomes …

Cd5 Deficient Mice Exhibit Altered Cognitive Function In Behavioral Studies, Tyler Cox, Dr. Scott Weber

Journal of Undergraduate Research

The immune system plays a role in protecting and maintaining the central nervous system (CNS). 1Dysfunctions within the immune system can affect the CNS and it is associated with diseases such as Multiple Sclerosis, Alzheimer’s and Parkinson’s disease. Having an imbalanced activation of immune cells within CNS results in cognitive impairments. CD5 is a protein on the surface of T cells and certain B cells that inhibits cellular activation and prevents immune cells from reacting too strongly to antigens and causing autoimmunity to our own tissues. Modulating CD5 and the immune system could affect the CNS and cognitive function. Observations …

Characterization Of Mutant Chemokine (C-C) Motif Receptor-Like 2 (Ccrl2) And Its Role In Inflammation And Alzheimer’S Disease, Meganne Ferrel, Dr. John S. K. Kauwe

Journal of Undergraduate Research

Alzheimer’s Disease (AD) is identified as a proteopathic disease that results from an extensive accumulation of amyloid plaques and neurofibrillary tangles in the brain. Several researchers have discovered that cerebrospinal fluid (CSF) contains biomarkers for AD such as Amyloid-beta and tau. Neuritic plaques in AD are surrounded by activated microglia and astrocytes which can initiate complement and inflammation in the presence of amyloid-beta. Macrophage inflammatory protein chemokine (C-C motif) ligand 4 (CCL4) is a biomarker found in CSF. A high level of expression is associated with risk of developing AD. CCL4 is expressed in a subpopulation of reactive astrocytes and …

Morphological Variation In Alfaro Cultratus Across Varying Stream Flow Regimes, Kaitlyn Beard Golden, Jerald B. Johnson

Journal of Undergraduate Research

Alfaro cultratus is a freshwater fish native to Costa Rica.1 The common name for Alfaro cultratus is ‘the knife edge livebearer’. It is named after its sharply keeled ventral surface which allows for movement through river currents with speed and agility. Yet this species is a live-­bearer, meaning it gives birth to free-­swimming young rather than laying eggs. Its shape does not allow for the normal distended abdomen during pregnancy like other live-­bearers. This morphology likely provides advantages in high flow regimes, but produces costs for reproductive investment. To begin looking at this paradoxical evolutionary trait, I looked at the …

Cell Free Single Stranded Dna Concentration In Csf As Biomarker To Diagnose Alzheimer’S Disease, Taylor Avei, Dr. John Kauwe

Journal of Undergraduate Research

The neuropathology of Alzheimer’s Disease (AD) is well-known as a degradation of neural connections in the brain caused by multiple deposits of Amyloid-beta peptide plaques as well as neurofibrillary tangles of tau proteins [1]. Because of this and successful research, both Amyloid-beta 42 and tau protein levels in cerebrospinal fluid currently serve as important biomarkers for the diagnosis of AD according to the New Research Criteria for the Diagnosis of AD provided by the International Working Group (IWG) [2].

Multispecies Character Displacement In Mexican Poeciliopsis Fishes, Andrea J. Roth

Theses and Dissertations

Competition has long been recognized as a central force in shaping evolution, particularly through character displacement. Yet research on character displacement is biased as it has focused almost exclusively on pairs of interacting species while ignoring multispecies interactions. Unfortunately, communities are seldom so simple that only pairs of species interact, and it is not clear if inferences from pairwise interactions are sufficient to explain patterns in nature. A more realistic approach is to ask how traits evolve when multiple species interact. Here I explore the importance of multispecies competitive interactions on trait evolution in four congeneric species of livebearing fishes …

Genetics Beyond The Classroom: An Analysis Of Undergraduate Students’ Understanding Of Genetics And Attitudes Towards Clinical Genetics, Jessica Mcclintock

Undergraduate Honors Theses

Genetics is a field of study that has been difficult for high school students, college students, and the general public to fully grasp, comprehend, and apply to clinical settings. Other studies show that students who are given hands on experiences with difficult concepts, like personalized genomics, have a better attitude towards and retention of those concepts. The purpose of this study was to determine if an in-class lecture specifically discussing clinical genetics concepts and benefits in solving difficult polygenic diseases would increase student attitudes towards genetic testing and prenatal testing and their knowledge of genetics in general. Students were asked …

Effects Of Substrate On Movement Patterns And Behavior Of Stream Fish Through Culverts: An Experimental Approach, Kyla Johnson, Lindsay E. Wait, Suzanne K. Monk, Russell Rader, Rollin H. Hotchkiss, Mark C. Belk

Faculty Publications

Culverts can provide a significant barrier to fish passage by fragmenting fish habitats and impeding the passage success of small-bodied fish. Geographical connectivity is critical to the maintenance of diverse fish assemblages. Culverts with high cross-sectional velocity can cause population fragmentation by impeding passage of small, freshwater fish. Behavioral responses of small fish to high velocities can differ among functional groups, and swimming behavior of many species is not well known. We tested effects of substrate type on swimming behavior in two small, freshwater fish species—southern leatherside chub (Lepidomeda aliciae, a midwater species), and longnose dace (Rhinichthys …