Microbiology Commons^™

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.

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 …

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.

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.

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, …

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).

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 …

Analysis Of The Kinetics And Recombinatorial Mechanisms Of Hiv-1 Evolution In Vivo In Humanized Mice, Bradford Berges

Journal of Undergraduate Research

Several of my students have moved on to future positions, as follows: Medical school: Sterling Adams, German Cuadra, Art Lee (still interviewing), and Tyler White (still interviewing) Graduate school: Steve Hallam

See below in the ‘academic deliverables’ section for further details on presentations, grant funding awarded directly to students, and publications.

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 …

Discovery And Characterization Of Bacteriophage To Control Mrsa, Jacob B. Hatch, Bradford Berges

Journal of Undergraduate Research

About 20% of humans are carriers of Staphylococcus aureus (SA). There were an estimated 11,000 deaths in the United States in 2005 attributed to SA, with the majority caused by MRSA (Methicillin Resistant Staphylococcus Aureus) isolates [1]. Many MRSA isolates have developed resistance to all but one antibiotic drug: vancomycin. However, other bacteria have developed resistance to vancomycin, suggesting that in time MRSA will likewise become non-responsive to this last available drug and MRSA infections will be untreatable. This project looks to find an alternate method of MRSA treatment. Bacteriophage (phage) are viruses that infect bacterial cells in order …

The Role Of Pas Kinase And The Gut Microbiome In Metabolism And Diabetes Onset In Mice, Andrew Rees, Laura Bridgewater

Journal of Undergraduate Research

Diabetes and obesity are among the most prevalent health concerns in the modern world. However, prevention of their onset and control of their symptoms are still largely limited by our understanding of how these diseases arise. Recent research has indicated that the composition of the gut microbiome is one of the important factors in development of these diseases (5). However, current thinking is not definitive on the relative importance of genetic factors, diet and the gut microbiome, among other factors (5,6). PAS Kinase provided a model through which we could compare the relative affects of genetics, gut microbiome and diet …

Identification Of The Function Of A Unique B4 Mycobacteriophage Protein Via In Silico And In Vivo Analysis, Cameron Sargent, Dr. Julianne Grose

Journal of Undergraduate Research

Once the leading cause of death in the United States, tuberculosis still burdens the world as the second deadliest infectious disease worldwide, latently infecting one-third of the world population and causing 1.5 million deaths in 2013 [1]. Tuberculosis is particularly lethal largely because the pathogen Mycobacterium tuberculosis has several characteristics that make detecting, treating, and studying the disease unusually hard. Among these traits, M. tuberculosis has a complex cell wall that limits the effect of many antibiotics and makes genetic manipulation of the bacterium, a necessity for effective research, nearly impossible through conventional transformation techniques [2]. Recently, Howard Hughes Medical …

Single Nucleotide Polymorphisms And Accelerated Telomere Shortening, Rebecca Winner, Dr. Brent Nielsen

Journal of Undergraduate Research

Telomeres are protective deoxyribonucleic acid caps on the ends of chromosomes which help prevent the chromosome itself from shortening during replication. As a person ages, normal telomere shortening occurs due to chromosome replication. However, accelerated telomere shortening is abnormal and has been linked to several factors such as disease, depression, and anxiety.

This project aims to determine if underlying genetic factors that contribute to increased incidence of depression will produce accelerated telomere shortening as seen in subjects with a history of depression. SNP’s in genes that code for 5-HTT, a serotonin receptor, and DRD2, a dopamine receptor, have been shown …

Role Of The Viral Lana Protein In Human Cancers Caused By Kaposi’S Sarcoma-Associated Herpesvirus, Gregory Low, Brad Berges

Journal of Undergraduate Research

The purpose of our experiment was to ascertain the importance of the LANA protein encoded by the Kaposi’s Sarcoma-Associated Herpesvirus (KSHV). LANA is believed to be essential for the survival of KSHV in human cells. KSHV causes a variety of cancers including Kaposi’s sarcoma (KS), multicentric Castleman’s disease (MCD), and primary effusion lymphoma (PEL). These cancers most often appear in the immunocompromised and can be fatal. The mortality rate of PEL is ~60% after one year, KS 5-year mortality rate is ~30%, and MCD 5-year mortality rate is 35%. No known vaccine or anti-viral drug treatment is currently licensed for …

The Use Of Bacteriophage For Surface Sterilization Of Methicillin-Resistant Staphylococcus Aureus In Poultry Facilities, Trevor Wienclaw, Bradford Berges

Journal of Undergraduate Research

Staphylococcus aureus (SA) is potentially dangerous pathogen that can infect humans and animals alike¹. The primary treatment for such infections has been antibiotics, but even shortly after antibiotics began to be used, antibiotic-resistant strains, known as MRSA, were discovered. These resistant strains have since spread, and now account for over half of all clinical isolates⁴. A similar scenario developed in the livestock industry. Antibiotics have been used to treat diseased animals and to promote growth in healthy animals. This use lead to development of MRSA among these animals. These animals may merely be carriers or they …

Isolation And Characterization Of Novel Lytic Phage To Treat Mrsa, Tyler White, Bradford Berges

Journal of Undergraduate Research

The bacterium Staphylococcus Aureus is the cause of a serious skin disease that is known to cause life-threatening infections such as pneumonia, endocarditis, meningitis, sepsis, bacteremia, and toxic shock syndrome [1]. Nonetheless, most SA infections are readily remedied via antibiotic treatment with methicillin. However, over the course of frequent exposure to various antibiotics, the bacteria have evolved a mutant strain (MRSA) that is completely resistant to the drug. In 2005 an estimated 11,000 deaths occurred that can be attributed to SA, with the majority caused by MRSA isolates [2]. Albeit the mutant is named MRSA, isolates of this strain are …

Finding Clues To Phosphate Homeostasis Through Transposon Sequencing, Tanner Dean, William Mccleary

Journal of Undergraduate Research

Though Escherichia Coli is a thoroughly investigated species of bacteria, questions still remain concerning genes involved in phosphate homeostasis. Phosphate homeostasis is the idea that a cell or bacterium adapts to changing environmental phosphate concentrations. Cells need to adapt to changing phosphate conditions because phosphate is essential to the biochemistry of many cellular processes. A cell therefore, must be able to collect and store phosphate when there is excess or scavenge and utilize stored phosphate in times when there are low levels of extracellular phosphate available. This process is not entirely understood in E.coli or other single celled organisms. A …

Creation Of An Eight-Member Plasmid Library For Promoter Swapping To Control Chromosomal Gene Expression In E. Coli, Matt Phillips, Dr. William Mccleary

Journal of Undergraduate Research

The ability to control gene expression in bacteria has been essential in solving problems in many fields, including medicine and environmental protection. Recent advances in genomic and metabolic modeling tools have led to the development of a new technique called promoter swapping which enables researchers to “swap” any native gene promoter with one that has been specifically engineered. Promoter swapping uses viral recombination proteins to swap DNA in the chromosome rather than in plasmids, allowing for constant and permanent expression levels. Our goal was to create eight template plasmids with promoters of increasing strengths to be used in promoter swapping. …

Vibrio Cholera: Detection And Destruction, Amber Brown, Dr. Julianne Grose

Journal of Undergraduate Research

Cholera, the Disease: Cholera is a disease that affects three to five million people each year with approximately 100,000 deaths. Transmitted mainly by the drinking-­‐water supply, it causes an infection in the small intestine leading to severe diarrhea and vomiting. If left untreated, it can cause death within hours. The disease is caused by the bacterium Vibrio cholerae which was first isolated by Filippo Pacini in 1854. Vibrio cholerae is gram negative, comma shaped, and flagellated. It is easily treated with modern water purification techniques, and as such it is most prevalent in developing countries that lack this infrastructure. Countries …

Biofilm Binding Capabilities Of Yersinia Pseudotuberculosis Mutants, Bailey Benson, Dr. David Erickson

Journal of Undergraduate Research

Yersinia pestis — the causative agent of the deadly bubonic plague, which killed over one-third of Europe in the 14th century – spreads quickly from person to person due to its ability to create a biofilm, characterized by bacterial adhesion to themselves and surfaces. The bacteria infects fleas and forms a biofilm in their midgut, which causes the flea to both feed more often and cough up bacteria biofim into each new host. In this way, the formation of a strong biofilm is essential for the rapid spread of the bubonic plague. In my experiment, I analyzed which genes would …

Understanding The Role Of Estrogen In The Mucosal Immune Response, Youna Choi, Dr. Eric Wilson

Journal of Undergraduate Research

Most antigens (foreign substances) enter an organism via mucosal surfaces. Thus, understanding the mechanisms involved in immune protection at these surfaces is of paramount importance. Immune responses are highly dependent on homing mechanisms responsible for directing lymphocyte (white blood cell) migration and accumulation at target tissues. Estrogen control of lymphocyte homing within the uterus has recently been established (2).

Analysis Of Anti-Dengue Antibodies, Lauren Syndergaard, Brian Poole

Journal of Undergraduate Research

Dengue virus is a mosquitoes-borne virus that causes dengue fever. It is found primarily in tropical areas with over a third of the world’s population living in at-risk areas (WHO). The number of infections has grown rapidly in recent years with as many as 50 to 100 million infections occur each year (WHO). Though not widely present in the United States (small outbreaks occur with some regularity in Texas from the Mexican border; Hawaii and Florida relatively recently had cases), many travelers endemic areas contract the virus. Though several are being studied, as yet, there are no vaccines available for …