Microbiology Commons^™

Preservation Of Oncorhynchus Clarkii By Comparison Of Biomarkers, Chase Paulson, Dr. R. Paul Evans

Journal of Undergraduate Research

The purpose of this project is to analyze biomarkers present in cutthroat and cutbow (a mixture of cutthroat and rainbow trout) trout of the Payson Hatchery compared to typical cutthroat and rainbow markers to better understand if cutthroat trout are being preserved locally and in the Western United States.

The Effect Of The Overexpression Of Irf% In B-Cells On Inflammatory And Co-Stimulatory Activity, Reika Takita, Brian Poole

Journal of Undergraduate Research

Systemic Lupus Erythematosus is a chronic autoimmune disease characterized by inflammatory tissue damage inflicted by the body's rogue immune system (1). Although treatment is available for the disease, the pathogenesis of SLE remains unclear (2). However, researchers suspect the disease to be associated with environmental, genetic, and hormonal factors (1).

Antibiotic Resistance In Staphylococcus Aureus From Commercially Available Meat, Samuel Schriever, Bradford Berges

Journal of Undergraduate Research

Bacteria can be found everywhere. While some bacteria can help humans to make medicine and clean up environmental disasters, other bacteria can cause horrible disease. After the discovery of antibiotics in the early twentieth century humans have been using them to treat human and animal disease. At first antibiotics very effective at clearing bacterial infections. Bacteria that were able to survive the antibiotics were able to spread and become more common. Bacteria have the ability to share genes and those genes are very favorable for the bacteria that have them. Today, animals are given more antibiotics than humans are. This …

Engineering A Cancer Specific 3rd Generation Car Immunotherapy, Josie Tueller, K. Scott Weber

Journal of Undergraduate Research

This project aimed to develop a cancer-specific immunotherapy that will target and destroy cancer cells without killing healthy cells. Current cancer treatments struggle to successfully target cancer cells and commonly target all rapidly dividing cells (both healthy and cancerous). Chimeric antigen receptor (CAR) immunotherapy aims to harness T cells, the body’s natural defense system, to fight cancer by giving T cells via molecular engineering a non-native protein which targets cancer. We successfully produced a T cell that can effectively kill cancer cells while leaving normal cells untouched while minimizing the toxic side effects normally experienced by patients. Future steps involve …

Examining How The Cd5 Co-Receptor Alters T Helper Cell Activation In Response To Bacterial Infection, Garrett Hamblin, Scott Weber

Journal of Undergraduate Research

Properly functioning helper T cells are crucial in a response to an infection. The adaptive immune response is orchestrated by T helper cells and their function is dependent upon interactions between the T cell receptor (TCR), peptide MHC (pMHC) and co-receptors. Upon TCR interaction with a foreign antigen, a calcium signaling cascade is initiated, which determines T cell activation, survival, proliferation and differentiation. CD5 is a T cell co-receptor that is a negative regulator of T cell activation. T cells with higher CD5 expression respond better to foreign antigen than those with lower CD5 expression. Cell-surface expression of CD5 is …

Association Of Essential Tremor And Parkinson’S Disease Development, Alexander Gosch, Mary David

Journal of Undergraduate Research

Essential tremor (ET) is a neurological disorder characterized by symmetrical tremor of the upper limbs. Parkinson’s disease (PD) is a similar disorder, also characterized by tremor, with a few differences: ET tremor is mostly seen during action, while PD tremor is more prevalent while at rest. PD is characterized by problems with walking and balance, while ET is characterized primarily by tremor without balance problems. PD symptoms generally improve with the use of the drug levodopa while ET responds better to the drugs propranolol and primidone.

Development Of A Model For Adult T Cell Leukemia/Lymphoma In Htlv-1 Infected Humanized Mice, Kayleigh Ingersoll, Dr. Brad Berges

Journal of Undergraduate Research

Human T-lymphotropic virus type-1 (HTLV-1) is a virus that is linked to Adult T-cell leukemia/lymphoma (ATLL), causing cancer in T cells. There are an estimated 10-20 million people worldwide infected with HTLV-1. HTLV-1 is transmitted through contact of bodily fluid and usually occurs through breastfeeding, sexual transmission, and sharing needles. ATLL develops in only about 5% of infected persons after decades of infection. An ATLL diagnosis is grim as there is no cure, and most patients do not respond or only have a limited response to treatments. Current treatments include antiretrovirals or chemotherapy, but there has been little to no …

Identifying Novel Regulators Of Cellular Respiration, Sam Nicholes, Julianne Grose

Journal of Undergraduate Research

The impetus behind my project was to contribute in a small but meaningful way to the growing body of research for cures and treatments for cancer. Cancer is fundamentally unwanted cell growth and proliferation. Metabolic processes that take place on the cellular level are the key to finding solutions to the many worldwide problems of cancer. My project looked at some of these metabolic processes in order to help identify the control mechanisms that cause these processes to function normally or to behave aberrantly. The goal was to identify a cellular pathway that could be used as a potential target …

Borrelia Burgdorferi Invasion Of B Lymphocytes, Jacob Bailey, Richard Robinson

Journal of Undergraduate Research

The goal of this project was to determine if Borrelia Burgdorferi’s linear plasmid 36 is required for intracellular localization in B lymphocytes. A more complete understanding of the intracellular localization of B. burgdorferi may provide the means to effective Lyme treatment. It has been proposed that intracellular localization of Lyme spirochetes may be, at least in part, responsible for Post Treatment Lyme Disease. As the spirochetes are safe within human cells, Borrelia are able to evade host immune system responses and be protected from antibiotic treatment. A more complete understanding of the intracellular localization of B. burgdorferi may provide the …

Autoimmunity-Promoting B Cell Effects Of The Risk Factor Irf5, Brian Poole

Journal of Undergraduate Research

The academic objectives of this proposal were met. Using the funding provided by the MEG, we generated data that were used to publish two peer-reviewed journal articles:

Final Report For The 2015 Meg Entitled: Development Of Real-Time Polymerase Chain Reaction (Q-Pcr) Assays For The Detection And Identification Of Human Tick-Borne Pathogens, Richard Robison

Journal of Undergraduate Research

1. Develop singleplex q-PCR assays to identify the tick-borne pathogens Borrelia burgdorferi, Borrelia hermsii, Bartonella henselae, and Babesia microti. Primer generation software will be used to design primer and probe sequences that will theoretically perform optimally in PCR reactions. All sequences will be subjected to BLAST searches to confirm their specificity for a particular organism. Once primer sequences have been obtained, they will be synthesized by Integrated DNA Technologies, Inc. (IDT). These primers will be evaluated in q-PCR reactions using target DNA from multiple isolates and SyberGreen to detect nucleic acid amplification. Parameters for each reaction will be optimized using these …

The Chemotherapeutic Potential Of Resveratrol-Based Treatments, Connor Peck, Kim O'Neill

Journal of Undergraduate Research

Cancer is one of the most prevalent and deadly diseases in the world. In 2012 alone, there were approximately 14 million new cases of cancer and over 8 million cancer-related deaths worldwide. Despite extensive research in past decades, the burden of cancer continues to increase.

One of the most common treatments for cancer is chemotherapy, the use of various chemical substances that exhibit anti-cancer activity. Unfortunately, chemotherapy can be quite toxic and often produces inadequate results. There remains a great need for improved chemotherapeutic treatment strategies in order to improve outcomes for cancer patients.

The purpose of my project was …

Effect Of High Expression Of Irf5 On B Cell Activation After Antigen Stimulation, Kalarelyn Eberting, Brian Poole

Journal of Undergraduate Research

While autoimmune diseases are very prevalent in the United States, little is understood about the cause of autoimmunity, making it difficult to take preventative measures and develop treatments. Previous studies have determined that a common genetic risk factor across many autoimmune diseases leads to B cell overexpression of the transcription factor IRF5 (1,2,4). Researchers have also discovered that high IRF5 levels are strongly associated with autoantibody production, suggesting that IRF5 may play a role in actually causing autoimmunity. At this point, however, it is unclear how IRF5 promotes the production of autoantibodies.

Development Of A Model For Adult T Cell Leukemia In Htlv-1 Infected Humanized Mice, Matthew Smith, Dr. Brad Berges

Journal of Undergraduate Research

Millions of people in the world are infected with human T-lymphotropic virus type-1 (HTLV-1). As the name states, this virus attacks the T cells of the infected organism. Though many of these individuals will remain asymptomatic throughout life, a small percentage will develop adult T cell leukemia/lymphoma (ATLL), a rare and understudied form of cancer. The latency period, or amount of time between infection and detection of cancer, is generally 20-40 years before infected patients begin developing cancer.

Phenome-Wide Association Study Of Y Chromosome Genetic Markers, Matthew Durrant, Mary Davis

Journal of Undergraduate Research

The purpose of this project was to analyze genetic variants on the Y chromosome for significant association with various diseases. In Dr. Mary Davis’ lab we gained access to a unique data set that allows us to analyze many single-nucleotide polymorphisms (SNPs) on the Y chromosome. This was a hypothesis-generating study that has the potential to revolutionize the currently accepted hypothesis that genetic variants on the Y chromosome do not play a significant role in common disease.

Cellular Mechanism Of Thymidine Kinase 1 Secretion, Wei Meng, Kim O'Neill

Journal of Undergraduate Research

Cancer remains the second most common cause of death in the US, accounting for nearly 1 of every 4 deaths. Studies have shown that the early detection of cancer leads to better patient prognosis and a greater five-year survival rate. [1] Diagnostic and prognostic markers play a key role in classifying tumors and determining the best treatment plan for a patient. Among these biomarkers, Thymidine kinase 1 (TK1) has been studied extensively, primarily as a diagnostic biomarker for a variety of cancer types. TK1 plays a role in regulating the intracellular thymidine pools throughout the cell cycle, and thus regulates …

Expression Changes Of Dopamine Type 2 Receptor On The Surface Of Human Monocytes And Lymphocytes After Exposure To Dopamine In Vitro., Brandon Thomas Garcia, Sandra Hope, Scott Steffensen

Journal of Undergraduate Research

Dopamine (DA) is a neurotransmitter in the brain that plays a role in several functions such as reward, motivation, and dependence. The imbalance of DA in the central nervous system (CNS) can lead to several debilitating diseases like Parkinson’s Disease, Alzheimer’s, and Schizophrenia as well as drug dependence. Levels of DA in the brain are often determined by measuring the expression of Dopamine type 2 (D2) receptors by positron emission topography (PET) scans in the Nucleus Accumbens (NAc). This test which is often expensive and unavailable to many people without access to hospitals or regular healthcare.

Development Of Chimeric Antigen Receptor T Cells To Target Cancer, Justin Crandall, Dr. Scott Weber

Journal of Undergraduate Research

Cancer negatively affects the lives of millions of individuals, and remains a difficult ailment to treat. In 2014, approximately 585,720 deaths and 1,665,540 new cases of cancer were reported in the USA alone.1 Treatment of cancer is challenging due to cancer mutating to combat the body’s immune system. An example is shown in major histocompatibility complexes (MHCs) located on the surface of nearly every cell. These are patrolled by T cells to ensure that cells are properly functioning and healthy. With cancer however, these become downregulated allowing the cancer to grow and proliferate since T cells are unable to detect …

Creation Of Twelve Member Plasmid Library For Promoter Swapping To Control Chromosomal Gene Expression In E. Coli, Chris Nielson, William R. Mccleary

Journal of Undergraduate Research

Metabolic engineering is becoming a very important area of research, allowing researchers to harness metabolic pathways to either eliminate or synthesize desired compounds. Understanding metabolic pathways by altering expression of proteins involved in the pathway helps to uncover thermodynamic bottlenecks which render certain pathways inefficient or infeasible. Altering expression of genes through the use of promoter swapping is a useful research technique used to understand important metabolic and physiologic pathways. Engineered promoters contained in plasmids can be inserted into chromosomal DNA through the utilization of promoter swapping to alter the expression of a given gene in order to better understand …

Thymidine Kinase 1: The Key To Predicting Cancer Recurrence, Rachel Brog, Dr. Kim L. O'Neill

Journal of Undergraduate Research

Currently it is estimated that over 230,000 women will be diagnosed with breast cancer this year in the United States alone. Although treatments are improving, an alarming number of these cases will show cancer recurrence after treatment. A method to consistently predict cancer recurrence is crucial to better treat cancer and improve patient care. Thymidine Kinase 1 (TK1) has been found in abnormally high levels in serum and tissue of cancer patients compared to healthy patients. There is question to why TK1 is present in such high quantities when normally it aids in the DNA salvage pathway during S phase …

The Role Of Pas Kinase And Cbf1 In Cellular Metabolism, Jenny Adele Pattison, Julianne H. Grose

Journal of Undergraduate Research

The most recent National Institute of Health report concludes that 68.8% of American adults are considered to be overweight or obese1. With this trend in obesity, metabolic diseases such as heart disease, stroke, cancer, and diabetes are on the rise. The critical yet basic function of cellular homeostasis is a central component in controlling these diseases. Sensory protein kinases are essential in the phosphorylation of many protein substrates, allowing them to control several metabolic functions and appropriately allocate glucose, maintaining homeostasis in cells. PAS kinase is a sensory protein kinase that is highly conserved and plays a crucial role in …

Bacteriophages As A Biocontrol Agent Of Soft Rot In Potatoes, Trevor Hodson, Don Breakwell

Journal of Undergraduate Research

Pectobacterium carotovorum (Pcc) is a principle causative agent of soft rot in potatoes. It causes losses of up to 60% in potato yields in the USA (Mantsebo et. Al, 2014) and approximately $50-$100 million dollars’ worth of losses yearly in multiple types of crops. Because potatoes grow beneath the soil surface, there is no way of treating the potatoes until they are harvested. Even then, no postharvest methods of controlling this pathogen exist (Wood et. Al, 2013). A spray-able bacteriophage cocktail specific to Pcc could save millions of dollars-worth of crops each year by minimizing soft rot.

Illuminating Novel Genes For Escherichia Coli Growth In Varying Phosphate Conditions Using Tnseq And Illumina Sequencing, Tanner Robinson, Dr. William R. Mccleary

Journal of Undergraduate Research

The purpose of my project is to identify novel genes in the genome of Escherichia coli ( E coli) associated with phosphate homeostasis under high phosphate conditions. The previous efforts that have been employed were great and innovative for their time, but both lacked the technology currently available, and focused solely on lowphosphate response. Other labs have used variations of the TnSeq protocol that I have, to address a variety of questions in many organisms, with great success (Subashchandrabose et al., 2013).

A Phenome Wide Association Study Of Multiple Sclerosis And Comorbidities, Scott Frodsham, Mary Davis

Journal of Undergraduate Research

Genome wide association studies (GWAS) have identified relationships between many different genes and diseases. GWAS studies scan whole genomes of many individuals and then associate genetic variants with diseases that the individuals have. In contrast, a phenome wide association study (PheWAS), looks at the phenotypes of many individuals and associates those phenotypes with one or more genetic variants. Electronic medical records (EMRs) linked to DNA biobanks provide both clinical and genetic data of patients. This study utilizes one such EMRlinked DNA biobank called BioVU from Vanderbilt University.

Development Of An Animal Model In Which To Study Hiv-2, Taalin Rasmussen, Bradford Berges

Journal of Undergraduate Research

Human Immunodeficiency Virus (HIV) attacks and destroys the cells of the immune system necessary to mounting an effective immune response to successfully fight off infection. Unchecked, an HIV infection leads to a gradual deterioration of the immune system, giving rise to many opportunistic infections not normally seen in people with a functioning immune system. There are two subtypes of HIV: HIV-1, which accounts for the most HIV infections worldwide, and HIV-2, which is most commonly seen in West Africa and countries with strong socioeconomic ties to West Africa, such as France, Portugal, Spain, Angola, Mozambique, and Brazil (1). There is, …

Visualizing Hemocyte Extracellular Traps In Galleria Mellonella, Timothy Siebach, Davidson Erickson

Journal of Undergraduate Research

Neutrophil extracellular traps (NETs) were recently found to be an additional method that neutrophils use to combat pathogens. They are composed of nuclear DNA and proteins that possess anti-microbial properties. Some studies suggest that in addition to killing pathogens, NETs also serve as a barrier to prevent pathogens from spreading. Mammalian infection models are known to possess NETs, but these models often raise ethical issues and can be quite costly. Using an insect such as Galleria mellonella is a valuable alternative. Insects possess an intricate innate immune response comparable to mammals in many ways. There is already substantial evidence indicating …

Membrane On The Frontier, Erin Wu, David Erickson

Journal of Undergraduate Research

Antimicrobial chemokines is a type of host defense protein that play an important role in the natural defenses of many organisms such as defending skin and mucosal tissues against bacterial infections.These peptides have a net positive charge, which contributes to membrane permeabilization and/or cell penetration. It has been observed that CCL28, an antimicrobial chemokine, binds to the surface of bacteria, however, it is not known how they bind, or what they do, to cause bacterial death. Research has demonstrated that Yersinia pseudo tuberculosis with mutations in lipopolysaccharide Oantigen and core synthesis genes (rfaD mutation) exhibit increased binding affinity for the …

Identifying Genetic Factors In The Development Of Diabetes In The Wasatch Front Population 2013-2014, Julianne H. Grose

Journal of Undergraduate Research

The academic objectives of this MEG were to train undergraduate and graduate students on the scientific process while providing valuable insight into the genetic factors that may play a role in the development of diabetes in the Wasatch front population. We were able to meet these objectives as evidenced by the training of two graduate students and seven undergraduates and by the identification of a novel genetic allele which most likely contributes to diabetes.

Examining The Relative Contributions Of Genes, Diet, And The Gut Microbiome To The Development Of Obesity And Diabetes, Laura C. Bridgewater

Journal of Undergraduate Research

This project began as a collaboration with Dr. Julianne Grose in MMBIO to study the effect of PAS kinase on diabetes and obesity in a mouse model system. Due to our initial findings, the study has grown to include Dr. Ben Bickman in PDBIO (an expert in metabolism) and Dr. Scott Weber in MMBIO (an immunologist). We have found that PAS kinase knockout mice have an increased metabolic rate—not only in their overall system but also specifically in skeletal muscle. Metabolic rate can have a profound influence on the immune system, so we began working with Dr. Weber to measure …

Final Report For 2013 Meg: Improving The Memory Response Of Pathogen Specific Helper T Cells, Scott Weber

Journal of Undergraduate Research

The following two aims are from my 2013 MEG. We made great progress and completed most of both Aim 1 and Aim 2. Details on the progress for each aim are described below.

Mentoring Environment: This MEG allowed me to expand the size of my lab and increase the amount and quality of mentoring. I met with student each week in lab meeting as well as individually. I also had each student email me a weekly update. Students were given opportunities to do hands on work, be involved in the data analysis and presentation at local and regional meetings.

BYU …