Microbiology Commons^™

Analysis Of Nucleosome Isolation And Recovery: From In Silico Invitrosomes To In Vivo Nucleosomes, Collin Brendan Skousen

Theses and Dissertations

There are a vast number of factors that influence nucleosome formation, and consequently gene regulation. These factors include histone modifications, nucleotide composition, transcriptional region elements, and specific nucleotide motifs, among others. Although the amount we know now is limited, we are creating new techniques and discoveries to assist us in continued understanding of chromatin. To make a significant contribution to the field of chromatin, I conducted two hypothesis driven sets of experiments that address the topic of chromatin structure. First, I created a technique for tissue specific nucleosome isolation with the goal of observing the effect of single nucleotide polymorphisms …

The Role Of Viral Interleukin-6 In Tumor Development Of Kaposi's Sarcoma-Associated Herpesvirus Lymphomas, Rebecca A. Fullwood

Theses and Dissertations

Kaposi's sarcoma herpesvirus (KSHV) is a cancer-causing virus, primarily affecting AIDS patients. KSHV is found in 3-10% of the U.S. population and can cause a range of cancers in the highly immunosuppressed; these cancers include Kaposi's sarcoma, pleural effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). The current techniques for treating these cancers are relatively ineffective, largely due to their inefficiency at targeting tumors formed by the infection. One protein produced by KSHV, the viral homolog of interleukin-6 (vIL-6), is thought to play a major role in tumor development post-infection. Here a novel animal model is implemented to study the …

A Cryab Interactome Reveals Clientele Specificity And Dysfunction Of Mutants Associated With Human Disease, Whitney Katherine Hoopes

Theses and Dissertations

Small Heat Shock Proteins (sHSP) are critical molecular chaperones that function to maintain protein homeostasis (proteostasis) and prevent the aggregation of other proteins during cellular stress. Any disruption in the process of proteostasis can lead to prevalent diseases ranging from cancer and cataract to cardiovascular and Alzheimer's disease. CryAB (αB-crystallin, HspB5) is one of ten known human sHSP that is abundant in the lens, skeletal, and cardiac muscle. This protein is required for cardiac function and muscle cell integrity. When the cell experiences physiological stress, including heat shock, CryAB moves to the cytoskeleton to act as a chaperone and prevent …

Genetic And Biochemical Analysis Of The Micrococcin Biosynthetic Pathway, Philip Ross Bennallack

Theses and Dissertations

Declining antibiotic discovery and flourishing antibiotic resistance have led to a modern antibiotic crisis which threatens to compromise our ability to treat infectious disease. Consequently, there is significant interest in developing new antibiotics with novel modes of action and chemical properties. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural compounds with the appealing attributes of being derived directly from a genetic template while possessing numerous exotic chemical features that contribute to stability and antimicrobial activity. Abundant in nature, their diverse range of biological activities makes them excellent prospects for antibiotic development. Thiopeptides, a RiPP family rich in chemical complexity, …

Characterizing Interaction Between Pask And Pbp1/ Atxn2 To Regulate Cell Growth And Proliferation, Nidhi Rajan Choksi

Theses and Dissertations

Pbp1 is a component of glucose deprivation induced stress granules and is involved in P-body-dependent granule assembly. We have recently shown that Pbp1 plays an important role in the interplay between three sensory protein kinases in yeast: AMP-regulated kinase (Snf1 in yeast), PAS kinase 1 (Psk1 in yeast), and the target of rapamycin complex 1 (TORC1), to regulate glucose allocation during nutrient depletion. This signaling cascade occurs through the SNF1-dependent phosphorylation and activation of Psk1, which phosphorylates and activates poly(A)- binding protein binding protein 1 (Pbp1), which then inhibits TORC1 through sequestration at stress granules. In this study we further …

The Activity Of Alkaline Glutaraldehyde Against Bacterial Endospores And Select Non-Enveloped Viruses, Justen Thalmus Despain

Theses and Dissertations

Alkaline glutaraldehyde (GTA) has been used as a high level chemical disinfectant and sterilant for many years and is known to kill a broad spectrum of organisms ranging from vegetative eukaryotes to bacterial endospores. Although the mechanism of sporicidal action has been studied on numerous occasions, GTA's exact mechanism(s) of action are still debated. In addition to the uncertainty of GTA's mechanism(s) of action, GTA has also shown significant variability in the time required to kill endospores and naked viruses. A better knowledge of the lethal mechanism(s) of GTA is needed to understand this discrepancy in kill times for GTA …

The Pmrhfijklm Operon In Yersinia Pseudotuberculosis Enhances Resistance To Ccl28 And Promotes Phagocytic Engulfment By Neutrophils, Lauren Elizabeth Johnson

Theses and Dissertations

Yersinia pseudotuberculosis is a foodborne pathogen that is the ancestral strain to Yersinia pestis, the causative agent of Plague. Y. pseudotuberculosis invades a host through the intestinal epithelium. The bacteria resist mucosal innate immune defenses including antimicrobial chemokines and phagocytic cells, and replicate in local lymph nodes. They cause Tuberculosis-like symptoms, including necrosis of local tissue and granuloma formation. Like all bacteria, Y. pseudotuberculosis has a net negative charge, which contributes to its susceptibility to some cationic antimicrobial peptides. Y. pseudotuberculosis is able to reduce this negative charge by adding 4-amino-4-deoxy-L-arabinose (L-Ara4N) to the lipid A portion of lipopolysaccharide. The …

Characterization Of Five Brevibacillus Bacteriophages And Their Genomes, Michael Allen Sheflo

Theses and Dissertations

Brevibacillus laterosporus (B. laterosporus) is a pathogen difficult to distinguish from Paenibacillus larvae (P. larvae), and contributes to Colony Collapse Disorder (CCD) of honeybees. To develop a biocontrol agent to limit its presence, bacteriophages were isolated from Utah County soil samples and used to infect B. laterosporus isolated from Utah County honey and larvae samples. Since CCD is prevalent in Utah beehives, bacteriophage that infect and lyse B. laterosporus may be isolated and characterized. Pathogens were isolated from soil samples, and 16S rRNA gene tests initially identified the strains as P. larvae. Bacteriophages were isolated, purified, and amplified sufficiently to …

Human Herpesvirus 6a Infection And Immunopathogenesis In Humanized Rag2-/-Γc-/- Mice And Relevance To Hiv/Aids And Autoimmunity, Anne Tanner

Theses and Dissertations

Human herpesvirus 6A (HHV-6A) has yet to be definitively linked to a specific disease. This is due in part to the ubiquitous nature of the virus. Humanized Rag2^-/-γc-/- (Rag-hu) mice were tested to determine if these were a suitable animal model to study the virus. Both cell-free and cell-associated virus was used for infection and both were found to be efficient at infecting the mice. Viral DNA was found in the plasma and cellular blood fractions, bone marrow, lymph node, and thymus, indicating successful infection and propagation of the virus in vivo. The CD3+CD4- population was depleted, while the …

The Role Of The Transcriptional Antiterminator Rfah In Lipopolysaccharide Synthesis, Resistance To Antimicrobial Peptides, And Virulence Of Yersinia Pseudotuberculosis And Yersinia Pestis, Jared Michael Hoffman

Theses and Dissertations

RfaH is a unique bacterial protein that enhances transcription of a select group of long operons in many Gram-negative bacteria. Operons regulated by RfaH possess an upstream operon polarity suppressor sequence, which recruits the RfaH protein to the RNA polymerase during transcription of genes, most of which are involved in the synthesis of cell-surface features. These include synthesis of the lipopolysaccharide (LPS) core and O-antigen in Salmonella and Escherichia coli, as well as F-plasmid conjugation pilus and capsule in E. coli. LPS is an important virulence factor in many Gram-negative bacteria, and protects Y. pseudotuberculosis against host antimicrobial …

The Path To Understanding Salt Tolerance: Global Profiling Of Genes Using Transcriptomics Of The Halophyte Suaeda Fruticosa, Joann Diray Arce

Theses and Dissertations

Salinity is a major abiotic stress in plants that causes significant reductions in crop yield. The need for improvement of food production has driven research to understand factors underlying plant responses to salt and mechanisms of salt tolerance. The aim of improving tolerance in traditional crops has been initiated but most crops can only tolerate a limited amount of salt in their systems to survive and produce biomass. Studies of naturally occurring high salt-tolerant plants (halophytes) are now being promoted for economic interests such as food, fodder or ecological reasons. Suaeda fruticosa, a member of the family Chenopodiaceae, belongs …

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 …

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.

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 …

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 …

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 …

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 …

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 …

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 …

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. …