Graduate Student Directory

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.

Learn more about Sakhawat here!

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.

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.

PhD Student
Research Lab: Wilson

Research Description: Finding vulnerable points at the intersection of cell wall synthesis and D-amino acid metabolism in Staphylococcus aureus. Historically, the bacterial cell wall has been a major target of antibiotics; today, those same antibiotics are largely ineffective, and our understanding of the bacterial cell wall is still incomplete. Better understanding of the synthesis and structure of the bacterial cell wall may result in new and effective treatment options.

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.

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.

Learn more about Abby here!

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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.

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.

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.

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.

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.

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.

PhD Student
Research Lab: Aanderud

Research Description: Anaerobic digestion is a process in which organic waste is decomposed into gas through a community of bacteria, archaea, and fungi. Anaerobic digestion provides an alternative path for solid waste (such as manure and sewage) that would otherwise be disposed of in a landfill; the gas produced during anaerobic digestion is used as a source of renewable energy. My research makes anaerobic digestion more efficient by implementing a biological pretreatment before anaerobic digestion. The pretreatment process consists of a specialized bacteria which degrades compounds that are recalcitrant to microbial decomposition in the anaerobic digester. I study the effectiveness of the pretreatment process as well as changes in the microbial communities of the anaerobic digester with the implementation of the pretreatment process. Improving the anaerobic digestion process results in less landfill waste and increased sources of renewable energy.

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.

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.

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.

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.

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 causes only subclinical infections in turkeys but retains the immunosuppressive ability is currently used as a live vaccine. Thus, vaccinated turkeys are rendered more susceptible to secondary opportunistic infections than unvaccinated cohorts, leading to substantial economic losses. My research focuses elucidating both host and viral factors involved in bringing about immunosuppression. Specifically, I focus 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. I’m also using RNA sequencing to uncover the host cell pathways and processes affected by VAS leading to immunosuppression. This knowledge will be key to developing effective treatments for infected turkeys.

PhD Student
Research Lab: Pickett

Research Description: Cancers and autoimmune diseases are formidable individually, but are even worse for patients when they strike at the same time. Unfortunately, cancers and autoimmune diseases affecting the same tissue type often co-occur. Naomi is searching for better treatments that target molecular mechanisms shared between cancers and autoimmune diseases. Using patient RNA-Sequencing data, artificial intelligence, and known drug-protein interactions, Naomi's novel algorithm, Immume Imbalance Transcriptomics (IIT), seeks to unwind and target the shared underlying mechanisms of co-occuring cancers and autoimmume diseases to provide new treatment options, starting the co-occuring diseases Systemic Lupus Erythematosus and B-Cell Lymphoma.

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.  

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