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Graduate Student Directory

Sakhawat Ali

Sakhawat Ali
PhD Student
Research Lab: Grose
Research Description: My research focus is to investigate the role of PAS kinase in the regulation of NAD kinase and cellular NAD(P) levels. NAD kinase controls the cellular levels of NAD(P)(H), the sole source of cellular energy metabolism, and is required for over 300 reactions in the cell including macromolecular biosynthesis (nucleotides, proteins and fatty acids) as well as reactions that neutralize reactive oxygen species (ROS) produced as a result of high metabolic activity in highly proliferating cancerous cells. Due to the clear central importance of NAD(P)(H) in cellular proliferation, we propose that NAD kinase is a key potential target in cancer treatment.

Rajesh Bogati

Rajesh Bogati
Masters Student
Research Lab: Erickson

Lucy Bowden

Lucy Bowden
PhD Student
Research Lab: Berges
Research Description: My research involves Staphylococcus aureus, the most common pathogen involved in implant-associated infection. I am working with an innovative carbon nanotube-based material to investigate the differences in biofilm development on conventional flat materials such as titanium and those with a varied topography, such as the carbon nanotube material. The topography of a surface impacts the extent to which bacteria are able to attach and proliferate. With the growing threat of antibiotic resistance, materials that can resist the development of bacterial communities by their intrinsic structural design are an intriguing non-antibiotic alternative in our fight against bacterial infection.

Olivia Brown

Olivia Brown
PhD Student
Research Lab: Robison
Research Description: I am passionate about understanding and combating the significant threat posed by B. anthracis, the causative agent of anthrax. My research focuses on the unraveling the intricate interactions between B. anthracis and bacteriophages, as well as understanding the genomic variation and functional implications of the pagA gene, a virulence factor. Through this research journey, I hope to contribute knowledge about host-pathogen interactions and cultivate a deeper appreciation for the world of microbiology and infectious disease.

Tyler Brown

PhD Student
Research Lab: Wilson
Research Description: My research is centered on Staphylococcus aureus' ability to survive in a host that employs various nutritional immunity factors. We are especially interested in iron utilization and how Staph accesses sequestered host iron sources.

Will Brugger

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PhD Student
Research Lab: Davis
Research Description: My research focuses on uncovering potential links between multiple sclerosis patients’ response to treatment and their underlying genetics through ancestry-aware bioinformatics.

Diana Calvopina

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PhD Student
Research Lab: Griffitts
Research Description: I am studying a molecular machine that makes the antimicrobial peptide Micrococcin. This molecular machine is made of 3 proteins, and we call it the IJN machine. We want to understand more about the IJN complex, so we can use it to make alternative peptides with biological properties, and potential medical applications such as antibiotics.

John Carter

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PhD Student
Research Lab: Johnson
Research Description: I study chromatin architecture by looking at nucleosome positioning and its relation to the underlying DNA sequence in the genome.

Abby Cheever

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PhD Student
Research Lab: O'Neill
Research Description: Cell therapies are currently revolutionizing how we treat disease. CAR T cells are one of these therapies, where a chimeric antigen receptor (CAR) is engineered with a highly specific binding domain that activates the T cell's cytotoxic abilities. This allows for specific targeting and elimination of cancer cells. We are developing cell therapies based on the CAR T cell concept that can effectively target and treat cancers and autoimmune diseases.

Charity Conlin Jennings

Charity Conlin Jennings
PhD Student
Research Lab: Kenealey
Research Description: My research focuses on whey proteins. Specifically, I am trying to quantify the different proteins in whey by using a differential scanning calorimeter to evaluate their thermal properties. I am using each protein's enthalpy value and denaturation temperature to quantify the proteins in a mixture.

Rachael David Prince

Rachael David Prince
PhD Student
Research Lab: Erickson
Research Description: Escherichia coli, is a gram-negative, rod-shaped bacteria that is capable of causing Extraintestinal pathogenic E. coli (ExPEC) infections, which come from a variety of sources including animals. Some of these isolates cause diseases like urinary tract infections, meningitis, pneumonia, and sepsis syndrome which may even result in death. E.coli possess major virulence factors including capsules. Capsules (K antigens) are composed of polysaccharides that make the outermost layer and protect some bacteria from phagocytosis and complement-mediated death. Several ExPEC strains produce capsules that belong to groups 2 and 3. Unfortunately, there is fewer known studies focusing group 3 capsule and their transcriptional regulations. Our research system includes, over one hundred ExPEC strains, all of which are obtained from clinical isolates of bovine mastitis known as Mastitis-associated E.coli (MAEC). Some strains of E. coli (MAEC) that are linked to mastitis include genes that are linked to ExPEC pathogenicity, including immune evasion and host attachment capabilities. However, we are unsure if the other MAEC strains that have genes related to ExPEC require group 3 capsules to be virulent and cause infections. Thus, the goal of my proposed research is to investigate the importance of group 3 capsule formation and its transcriptional regulations that cause extraintestinal infections in humans.

Maddie Duffy

Madison Duffy
Masters Student
Research Lab: Grose
Research Description: I am studying PAS kinase and ATAXIN-2 to determine their effects on cellular metabolism. We are also looking at how mutations in these genes lead to diseases like ALS, diabetes, and hypothyroidism and what is happening within the cells metabolic pathways to cause disease.

Spencer Ellsworth

Spencer Ellsworth
Masters Student
Research Lab: Grose
Research Description: Improper glucose allocation is at the heart of most metabolic diseases like diabetes, obesity, and cancer. I am studying the proteins involved in this glucose allocation, like PAS kinase and Cbf1, to better understand how the cell makes decisions regarding glucose and what we can do to remedy these diseases.

Kenneth Ewool

Kenneth Ewool
PhD Student
Research Lab: Grose
Research Description: My research work focuses on two different subjects, the Dynamics of PAS kinase and the use of bacteriophages for human benefit. PAS kinase is a kinase that has been found to be at the pivotal point of glucose allocation to either metabolic respiration or lipid biosynthesis. PAS kinase acts on other kinases and transcription factors to bring about this effect. One of these is USF1, a global transcription factor, implicated in the development of dyslipidemias. Much research has been done on the involvement of USF1 in dyslipidemia. However, little to nothing is known about its effects on respiration under the influence of PAS kinase. My research focuses on how respiration is affected by USF1 in mammalian cells and how this can be leveraged for human benefits in metabolic diseases.

Leslie Ewool

Leslie Ewool
Masters Student
Research Lab: Pickett

Iqra Farooq

Iqra Farooq
PhD Student
Research Lab: Nielsen
Research Description: A major goal of my proposed work is to determine changes in plant gene expression in response to inoculation with halophilic bacteria (salt-tolerant), when the plants grow in the presence or absence of salt and to identify the bacterial properties that contribute to plant growth enhancement. For this purpose, I'm working on the Alfalfa crop (salt sensitive) to analyze the response of halophilic bacteria in salty conditions. In Utah, where BYU is located, alfalfa is the major top crop produced. The use of halophilic bacteria inoculant to stimulate alfalfa crop productivity in saline soil would thus be of great benefit.

Jono Gal

Jono Gal
PhD Student
Research Lab: Johnson
Research Description: My research is focused on Arthrospira platensis, a photosynthetic cyanobacterium that is commonly referred to as ’Spirulina.’ This organism contains very high amounts of edible and nutritious protein. It is a growing part of the global food chain, especially in India and China where high population densities demand greater amounts of nutrition. Cultivation of Spirulina is generally done in tubular photobioreactors, and the per acre rate of protein production by tubular photobioreactors has been estimated at 200x that of cattle farming. It also uses less water. Thus, Spirulina offers a means to improve global nutrition in a land and water efficient manner. NASA is also looking at Spirulina as a nutritional source for space missions.

Alka Gaur

Alka Gaur
Masters Student
Research Lab:

Austen Gleave

Austen Gleave
Masters Student
Research Lab: Poole

Evan Harris

Evan Harris
Masters Student
Research Lab: Grose

Topher Haynie

Topher Haynie
PhD Student
Research Lab: Weber
Research Description: I am researching antibody approaches to treating disease. Many immunotherapies rely on antibodies as the basis for treatment. Antibody specificity for a target can be utilized for specific targeting strategies such as my work with cancer target TK1. Antibody receptor binding is also critical to many treatments. I aim to improve the efficacy of treatments by studying the antibody and Fc receptor relationships. I am using machine learning approaches to understand the importance of post-translational modification on the structural function of the antibody to bind and cause signaling through the Fc Receptor. Finally, I am implementing software improvements such as automated workflows for Flow Cytometry, a technique that utilizes antibody staining of cells to identify unique cellular populations and characteristics.

Jacob Herring

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PhD Student
Research Lab: Tessem
Research Description: Diabetes is characterized by a decrease in functional β-cell mass. Nuclear hormone receptor 4a1 plays a role in the regulation of functional β-cell mass. My research focuses on the mechanism of Nr4a1 in the β-cell.

Taalin Hoj

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PhD Student
Research Lab: Robison
Research Description: It has been estimated at 70% of bacterial infections are resistant to at least one commonly prescribed antibiotic, prompting CDC to announce that humanity has entered the “post-antibiotic era.” Among the most serious of these infections are caused by carbapenem-resistant Enterobactericeae (CRE), bacteria resistant to even last-line antibiotics. I study mechanisms of resistance in CREs, the stability and evolution of carbapenem resistance, and methods of treating septicemia caused by CREs.

Lydia Howell

Lydia Howell
PhD Student
Research Lab: Davis
Research Description: My dissertation focuses on the potential epidemiological link between infection and complex diseases. To clarify this link, I work with the All of Us dataset and use the large amount of genetic and electronic health record data available there, leveraging statistical methods like GWAS and PheWAS procedures. I am currently investigating the association between infection with tuberculosis or herpes simplex viruses I & II and autoimmune conditions like multiple sclerosis and Parkinson’s disease, since M. tuberculosis and herpesviruses are known to cause long-lasting chronic infections with a disruptive influence on the immune system.

Misha Iqbal

Misha Iqbal
PhD Student
Research Lab: Griffitts
Research Description: My research is centered on the manipulation of DNA end-joining (EJ) systems in E. coli. The primary objective is to develop a molecular toolkit for genome modifications and to engineer E. coli for in vivo cloning through EJ. Additionally, we aim to engineer inaccurate EJ systems to investigate their impact on genome stability. Ultimately, this project aims to assess E. colisurvival rates after exposure to DNA-damaging agents.

Kyson Jensen

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PhD Student
Research Lab: Griffitts
Research Description: The ability of microorganisms to adapt to environmental stressors is the key to their ability to occupy different ecological niches. No one microorganism can specialize to cope with every possible environmental stressor. This principle accounts for much of the diversity and niche specialization we commonly see in bacteria. The overall objective of my project is to understand the mechanism by which microorganisms adapt to environmental stressors, specifically towards toxic heavy metals. We have previously isolated closely related bacterial strains of the genus Mesorhizobium from both regular soils and heavy metal (serpentine) soils in northern California. While isolated strains are closely related, those from serpentine soils are significantly more tolerant to Ni. The aim of this project is to examine and identify molecular contributors to metal tolerance and evaluate how these tolerance mechanisms influence fitness in the absence of metal stress. This work will enhance our understanding of mechanisms of heavy metal tolerance and may provide clues about evolutionary pathways giving rise to this trait.

Brandon Lopez

Brandon Lopez.jfif
Masters Student
Research Lab: Berges
Research Description: I research Vpr, a protein encoded by HIV-1. My research focuses on the effect that single nucleotide mutations have on AIDS progression. I do this by looking at apoptosis levels and cytokine release in infected cells. I am also in the process of determining a pathway that causes these changes by looking at protein localization in individual cells and Vpr expression levels of cell secretion and within virions.

Kayla Maas

Kayla Maas
Masters Student
Research Lab: Robison
Research Description: The Major Facilitator Superfamily (MFS) is one of the largest families of membrane transporters found in living organisms. A large majority found across different genera of bacteria have yet to be characterized and researched. These uncharacterized transporters may be a contributing factor to antibiotic resistance. More knowledge of these transport systems in bacteria may be essential for gaining an advantage in the war against antibiotic resistance. This knowledge could be used for the development of inhibitors which may block multidrug transporters to allow traditional antibiotics to become effective again. My project is focused on cloning an uncharacterized MFS transporter from Pseudomonas aeruginosa and studying its activity against different substrates.

Michael Moran

Michael Moran
Masters Student
Research Lab: Robison

Carlos Moreno

PhD Student
Research Lab: Weber
Research Description: My research focuses primarily on the role of an inhibitory co-receptor called CD5 found on the surface of T cells in the context of periodontitis and cancer immunotherapy development. CD5 has been shown to attenuate T cell receptor signaling and inhibit T cell activation. Additionally, the Weber lab has shown that the metabolic profile of CD4+ T cells deficient in CD5 is altered. Specifically, the rates of glycolysis and oxidative phosphorylation in CD5 knockout T cells are increased and several intracellular metabolites are significantly different. Also, preliminary data indicates that CD5KO T cells have increased levels of cytokine production post-stimulation. We aim to determine whether CD5 may serve as a potential therapeutic target in the treatment of periodontitis, and we are generating chimeric antigen receptor (CAR) T cells deficient in CD5 and characterizing their functionality.

Melinda Moss

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PhD Student
Research Lab: Griffitts (MMBIO) & Taylor (NDFS)
Research Description: Lactose is a by-product of cheese and whey protein manufacturing that is generally considered a low-value ingredient in the food industry. Rare sugars on the other hand are highly valued due to their low-glycemic index and reduced calories, and in recent years a lot of work has been done to find and understand the enzymes that can convert abundant sugars like fructose to rare sugars. The goal of my project is to optimize the conversion of dairy lactose to rare sugars by cloning and expressing the enzymes required to hydrolyze the lactose and subsequently convert the resulting glucose and galactose into the rare sugars allulose and tagatose respectively.

Nagama Parveen

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Masters Student
Research Lab: Erickson
Research Description: We are currently studying Mastitis-associated E. coli strains in our lab which are capable of causing ExPEC infections in people and show significant resistance to a range of antibiotics. Finding a safe substitute for antibiotics is imperative in order to slow the spread of antibiotic-resistant bacteria and lower the number of diseases that affect humans. A potentially promising line of study is the application of gallium nitrate, which can impede bacterial growth by disrupting the equilibrium of iron in the cell. Our research involves the examination of different Mastitis-associated E. coli strains to assess their sensitivity to gallium nitrate. Additionally, we are exploring gallium resistance mechanisms within these strains and investigating any potential alterations to their genomes. This work is aimed at shedding light on the sensitivity of E. coli to gallium, understanding mechanisms of gallium resistance, and elucidating any genomic changes that may occur in response to gallium exposure.

Hyrum Pech

Hyrum Pech.jfif
Masters Student
Research Lab: Chaston
Research Description: I am studying the genetics behind bacterial interactions in the fruit fly microbiota. In particular, I'm interested in learning about and characterizing the genes that are necessary for acetic acid bacteria to benefit from lactic acid produced by lactic acid bacteria. I am also comparing how these interactions behave differently when happening on agar plates and when happening inside of the fruit fly gut.

Abraham Quaye

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PhD Student
Research Lab: Poole
Research Description: Hemorrhagic enteritis is a viral disease of turkeys characterized by bloody diarrhea and immunosuppression caused by turkey hemorrhagic enteritis virus (THEV). An avirulent THEV strain called VAS that does not cause the disease in turkeys but retains some immunosuppressive ability is currently used as a live vaccine. Due to the immunosuppressive traits of VAS, vaccinated turkeys are more susceptible to secondary bacterial infections than unvaccinated cohorts, leading to substantial economic losses. My research focuses on identifying the VAS genes mediating its immunosuppressive traits and studying the mechanism of action of such genes. Ultimately, we hope to engineer a novel THEV strain with no immunosuppressive characteristics to be used as an improved vaccine.

Luke Ramirez

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Masters Student
Research Lab: Johnson
Research Description: I am currently researching how Post Translational Modifications (PTMs) on histone N-terminal tails affect the rate of transcription elongation. I am using an RNA aptamer that when transcribed forms a secondary structure that binds a fluorophore and can be detected using real time polymerase chain reaction.

Josh Ramsey

Joshua Ramsey
Masters Student
Research Lab: Berges

Naomi Rapier-Sharman

PhD Student
Research Lab: Pickett
Research Description: Balanced inflammation is a crucial process for protecting our bodies against threats. However, when inflammation becomes dysregulated, illnesses such as cancers and autoimmune diseases can develop. I'm using bioinformatics to compare gene expression in cancer and autoimmune disease to gain more insights about inflammation, and hopefully improve current treatments. In addition to a broad transcriptomic survey of inflammation, I'm specifically investigating anti-inflammatory lifestyle modification as a potential cancer-prevention treatment.

Miranda Sharp

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Masters Student
Research Lab: Davis
Research Description: I am studying gene variants in PASK, USF1, and ATXN2 and the relationship to BMI, activity and sleep in humans. These genes have been linked to diseases such as obesity and because it is a worldwide problem, we look to find an answer to why some people have a harder time with obesity then others. We are utilizing the new All of Us data set from NIH to gather genomic, survey, Fitbit, and electronic heath records to analyze the associations between the genes and these measurable traits.

Sidney Sithole

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PhD Student
Research Lab: Berges
Research Description: My research revolves around understanding the factors that make certain individuals susceptible to developing AIDS after contracting HIV, while others do not. While several host factors also contribute to HIV progression, my research focus is on HIV genetics, specifically HIV vpr, which has been implicated in playing an important role in HIV progression. A single nucleotide mutation in HIV vpr has been associated with individuals that either rapidly progress (rapid progressors (RP)) or delay progression (Long-Term Non Progressors (LTNP)) towards AIDS. Using molecular tools, my research will unfold the mechanisms employed by HIV Vpr that result in either a RP or LTNP phenotype. Since HIV is a human-specific pathogen that does not cause disease in most conventional small animal models, we have validated the use of a “humanized mice” model to study HIV progression. A humanized mouse refers to a mouse that has undergone a transplantation of human cells. Specifically, we transplant mice with human hematopoietic stem cells, resulting in the production of diverse human blood cell types and the development of a human immune system within the mouse. Consequently, the mouse is capable of generating antibody and cellular immune responses originating from humans. With this model, I will better understand the role of HIV Vpr in AIDS progression by studying different methods and mechanisms of cell death such as apoptosis and necrosis exhibited by different HIV vpr polymorphisms in vivo.  

Madi Wagley

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Masters Student
Research Lab: Berges
Research Description: I am working in the Berges virology lab as part of an ongoing project studying the role of HIV protein Vpr. My research centers around the HIV strain R77Q, which contains a mutation in Vpr and is associated with slower disease progression. I am observing the differences in Vpr interaction with host transcriptional factors between wild-type and R77Q virus to understand better the mechanisms this mutation affects and how this may contribute to slower disease progression in HIV.
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