Biology Commons^™

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.

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.

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 …

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 …

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).

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 …

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 …

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 …

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.

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 …

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 …

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. …

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 …

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 …

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].

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 …

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 …

Functional And Transcriptomic Characterization Of Carboplatin-Resistant A2780 Ovarian Cancer Cell Line, Tamara Viscarra, Kurt Buchegger, Ignacio Jofre, Ismael Riquelme, Louise Zanella, Michel Abanto, Alyssa C. Parker, Stephen R. Piccolo, Juan Carlos Roa, Carmen Ili, Priscilla Brebi

Faculty Publications

Background

Ovarian cancer is a significant cancer-related cause of death in women worldwide. The most used chemotherapeutic regimen is based on carboplatin (CBDCA). However, CBDCA resistance is the main obstacle to a better prognosis. An in vitro drug-resistant cell model would help in the understanding of molecular mechanisms underlying this drug-resistance phenomenon. The aim of this study was to characterize cellular and molecular changes of induced CBDCA-resistant ovarian cancer cell line A2780.

Methods

The cell selection strategy used in this study was a dose-per-pulse method using a concentration of 100 μM for 2 h. Once 20 cycles of exposure to …

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 …

Potential New Biomarkers For Endometrial Cancer, Michelle H. Townsend, Zac E. Ence, Abigail M. Felsted, Alyssa C. Parker, Stephen R. Piccolo, Richard A. Robison, Kim L. O'Neill

Faculty Publications

Abstract

Background: Incidence of endometrial cancer are rising both in the United States and worldwide. As endometrial cancer becomes more prominent, the need to develop and characterize biomarkers for early stage diagnosis and the treatment of endometrial cancer has become an important priority. Several biomarkers currently used to diagnose endometrial cancer are directly related to obesity. Although epigenetic and mutational biomarkers have been identified and have resulted in treatment options for patients with specific aberrations, many tumors do not harbor those specific aberrations. A promising alternative is to determine biomarkers based on differential gene expression, which can be used to …

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 …

Biogeography And Natural History Of Tiger Moths And Spongillaflies Of Intermountain North America With Experimental Studies Of Host Preference In The Lichen-Feeder Cisthene Angelus (Insecta: Lepdioptera: Erebidae: Arctiinae And Neuroptera: Sisyridae), Makani Layne Fisher

Theses and Dissertations

The Intermountain West is comprised of impressive land formations, numerous ecoregions, and a unique biota. The area has many flora and fauna that have been investigated, but the region is generally considered undersampled when it comes to insects. However, I propose the matter to be a lack of shared experience in identifying key insect species and the underutilization of professional and personal collections. These impediments are highlighted by two insect groups in the Intermountain West: spongillaflies and tiger moths. Spongillaflies can be difficult to recognize for the general entomologist and have rarely been recorded in the Intermountain West. My colleagues …

Evolution Of The Photopigments In The Largest And Most Complex Terrestrial Animal Eyes, Seth M. Bybee

Journal of Undergraduate Research

Evaluation of how well the academic objectives of the proposal were met The proposal had three main aims: 1). Produce a phylogenetic estimate of aeshnid dragonfly evolution from transcriptomes. 2). Use the phylogeny from Aim I and the photopigments isolated from the transcriptome data to examine the evolution of aeshnid color visual systems and 3) Using independent and complimentary methods (in situ hybridization, qPCR and transcriptome data) to examine both the distribution and level of expression for each photopigment for one focal species (Anax junius). Goals one and two were both successful, however goal three became bogged down and only …

Sequencing Complete Genome Of Cutthroat Trout Subspecies For Purposes Of Improving Classification Of Cutthroat Trout Species, Emily Brown, Dr. Dennis Shiozawa

Journal of Undergraduate Research

Since the 1800s, biologists have studied cutthroat trout native to Western North America. Their early work and classification were based on the standards of the day: meristics, the observation and counting of physical features, and morphology. Further improvements came through later studies that added geographic distribution to their phylogenetic classification. Without the foresight of DNA genotyping methods, “traditional taxonomic assessments often failed to accurately capture phylogenetic diversity.” Many discrepancies have since arisen as genetic methods shed new light on cutthroat trout subspecies phylogenies. Current mtDNA work has identified errors in historical classifications of several of these subspecies in the Colorado, …

Lctsr: The New Path To Academic Success, Faith Hathenbruck, Dr. Jamie Jensen

Journal of Undergraduate Research

The Lawson’s Classroom Test of Scientific Reasoning¹(LCTSR) is a content-independent measure of scientific reasoning abilities including conservation, proportional reasoning, identifying and controlling variables, probabilistic reasoning, correlational reasoning, and hypothetico-deductive reasoning. A relationship has been seen between scores on this test and a student’s decision to major in a STEM degree² as well as with their performance in science, technology, engineering and mathematics, also known as STEM, courses³. Thus, the LCTSR can be a clever tool in predicting a student’s performance and persistence in STEM degrees. This test, however, has more potential than just predicting STEM …

A User Friendly Tool To Allow Easy Access To Big Biological Data, Pj Tatlow, Stephen Piccolo

Journal of Undergraduate Research

Over the course of the past year I have been able to put a lot of work into creating a tool for scientists, those with computational background and without, that provides a simple web interface for downloading data from large, publically available datasets. It allows users to select a dataset that we have pre-processed, enter filters based on the samples they want to research, and download only that portion of the data. This will save researchers a lot of time, as well as reduce their reliance on bioinformaticians.

Genetic Basis For Elevated Rheumatic Heart Disease Susceptibility In Samoa, John Bowen Allen

Theses and Dissertations

Rheumatic heart disease is an inflammatory heart disease that affects millions of people around the world. Especially high rates of the disease can be found in Oceania, including the island nation of Samoa. Genetic studies of immune response genes have provided insight into a possible genetic link to increased susceptibility to rheumatic heart disease, including the genes that code for the toll-like receptor (TLR) protein family. One of the functions of TLR proteins is to recognize the presence of bacteria via identification of bacterial flagella. My evaluation of a Samoan family identified a variant in the TLR-5 gene that would …

Evolutionary Relationships In Anax Dragonflies, Rebecca Clement, Dr. Seth Bybee

Journal of Undergraduate Research

Anax dragonflies are found worldwide, with many species migrating across continents. One species of Anax, A. junius, makes annual migrations travelling thousands of miles each fall from Canada to Mexico (May 2013). Researchers from all over the world use Anax to learn about vision, insect musculature and insect migration. For example, A. junius is a favorite of many research projects in North America (Bybee et al. 2012), while A. imperator is often used by European collaborators (Sharkey et al. 2015), and A. parthenope by Asian collaborators (Futahashi et al. 2015). However, despite widespread interest in Anax, relationships among species remain …

Predicting Bacteriophage Gene Function Through Secondary Structure Blast, Corinne Sexton, Perry Ridge

Journal of Undergraduate Research

Bacteriophages are viruses that specifically target bacteria. With antibiotic resistance on the rise, some researchers are looking to bacteriophages as a viable treatment alternative. Phage therapy would be effective for a host of reasons, some of which are because phages are 1) highly specific to their host bacteria, 2) very effective in lysing bacteria targets, 3) non toxic to humans, and 4) easy to manufacture and cost effective. (Oliveira 2015) Additionally, bacteriophages could be used effectively to treat bacterial infections in plants and animals of agricultural importance.