Biochemistry, Biophysics, and Structural Biology Commons^™

Targeted And Screening Based Approaches To Analyze Drm Transcriptional Repressor Complex Activity In Caenorhabditis Elegans, Emily Washeleski

Dissertations, Master's Theses and Master's Reports

The molecular machinery that control the eukaryotic cell cycle, specifically the processes that mediate the switch between cellular division or quiescence, are essential for cellular and organismal viability. However, how the same machinery integrates with developmental or differentiation programs is less well understood. In Caenorhabditis elegans, the 8-subunit DRM complex (for Dp, Rb and MuvB), whose subunits belong to the Synthetic Mulitivulva (SynMuv) B class genes, is a central regulator of the cell cycle but also prevents inappropriate cell fate specification. The conserved mammalian DREAM complex (for Dp, Rb, E2F, And MuvB) is best known as a transcriptional repressor …

The Triangular Interaction Between Dietary Polyphenols, Gut Microbiota, And Metabolic Syndrome, Emily Bayliss

Senior Honors Theses

Type 2 diabetes mellitus (T2DM) is a growing global health concern characterized by peripheral insulin resistance as well as impaired insulin secretion from pancreatic β-cells. Emerging evidence suggests that the gut microbiome, specifically gut dysbiosis, an imbalance in the gut microbiome, is a critical modulator of the pathophysiology of T2DM. Dietary polyphenols, a diverse group of bioactive compounds that are abundant in plant-based foods, have recently gained attention for their potential to attenuate metabolic disorders through their antioxidant and anti-inflammatory properties as well as through modulating the composition and activity of gut microbes, thereby attenuating dysbiosis. However, the diabetic state …

Investigating The Impacts Of Azole Antifungals On Growth Of Cryptococcus Neoformans, Gnanambika Sindhe

All Theses

Cryptococcus neoformans, an opportunistic fungal pathogen is responsible for cryptococcosis, leading to approximately 181,000 deaths annually, predominantly in regions such as Sub-Saharan Africa. Fluconazole, a widely used fungistatic azole, is often administered due to its relative affordability and lower toxicity. However, resistance to fluconazole in C. neoformans can arise through aneuploidy, complicating treatment efforts. This study aims to deepen our understanding of resistance mechanisms to azole drugs by comparing fluconazole with other azoles, including both clinical and agricultural azole antifungals. Disk diffusion assays were performed to evaluate the ability of C. neoformans to develop resistance to these compounds, focusing …

Tracing The Journey Of Dissolved Organic Matter: From Leaf Litter Photodegradation To Microbial Processing In Tropical Streams, Samantha Nicole Sullivan

Chemistry & Biochemistry Theses & Dissertations

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, …

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops, Keith Skolnick M.D., Anu Valiaveedu

Mako: NSU Undergraduate Student Journal

Many preoperative and postoperative cataract patients struggle with comprehending the use of prescription medication as directed. Language barriers and low health literacy levels are major factors contributing to improper use of prescriptions. To increase patients comprehension, the Fort Lauderdale Eye Institute employed an educational intervention consisting of a live presentation and an instructional video. Results found that 44% of patients were hesitant to ask questions to clinical staff, 32% felt overwhelmed, and nearly 70% lacked confidence in using their prescribed eye drops. Following the intervention, 91% of patients reported increased confidence in their medications, and most indicated that the video …

Effect Of Histidine Tag On The Enzymatic Activity Of Pseudolysin And Its Interaction With The Streptomyces Metalloprotease Inhibitor (Smpi) Protein, Adewale Adeboye Adewole

Electronic Theses and Dissertations

Pseudolysin (PLN) protein is a major virulent factor in Pseudomonas aeruginosa infection. PLN belongs to the family of zinc-dependent metalloproteases. It is naturally inhibited by a smaller protein called streptomyces metalloprotease inhibitor (SMPI), secreted by Streptomyces nigrescens. Previous and current studies demonstrate that the interaction between PLN and SMPI offers unique mechanistic insights for drug development against infections caused by P. aeruginosa. This study investigated the effect of N-terminal Histidine (His) tag on the enzymatic activity of PLN and its interaction with SMPI. His-tagged PLN and SMPI proteins were expressed in bacteria and purified by affinity chromatography …

Role Of Cellular Proteins In The Regulation Of Herpes Simplex Virus Type 1 Gene Expression And Dna Replication, Joseph R. Heath

Electronic Theses and Dissertations

Herpes simplex virus type 1 (HSV-1) is a ubiquitous human pathogen that infects the majority of the human population. To facilitate infection, this virus relies on a combination of host and viral factors. Previous studies have revealed a number of host proteins that associate with the HSV-1 genome throughout infection but their putative role(s) in this process remain undefined. This study aims to examine two such proteins to determine their contributions to HSV-1 gene expression and DNA replication. The first of these factors is Ints3, a subunit of the Integrator complex. This protein complex functions in transcription regulation, and Ints3 …

In Silico Prediction Of Cytotoxic T-Cell Epitopes From Helicobacter Pylori Virulence Factors Using An Immunoinformatics Approach, Demy Valerie Chacon, Kiana Alika Co, Daphne Noreen Enriquez, Aubrey Love Labarda, Reanne Eden Manongsong, Edward Kevin B. Bragais

Biology Faculty Publications

Background: Helicobacter pylori infects approximately half of the global population, leading to gastric and duodenal ulcers. Despite the availability of antibiotics, challenges such as patient reluctance, high treatment costs, and antibiotic resistance limit their effectiveness, making vaccination a promising alternative. This study used immunoinformatics to identify candidate epitopes for a multiepitope vaccine construct against H. pylori.

Material and methods: The protein variability server was utilized for conservation analysis. The epitopes were screened for antigenicity, allergenicity, toxicity, cross-reactivity, and population coverage. Selected epitopes were docked with their corresponding human leukocyte antigen (HLA) alleles, and thermodynamic quantities were determined. Five virulence …

Investigating A Link Between Dna Repair And Dna Replication In Escherichia Coli Using A Bacterial Two-Hybrid System, Lo Cooper

University Honors Theses

Cells rely on nucleotide excision repair (NER) to remove bulky DNA lesions, such as those caused by UV light. In Escherichia coli, NER involves the UvrABC complex, and includes two main pathways, global genomic repair and transcription-coupled repair (TCR). While TCR, which preferentially removes lesions that block RNA polymerase on the transcribed strand of active genes, is well studied, less is known about whether a similar coupling between repair proteins and replisomes blocked by damaged DNA exists. Such a process has been suggested by a high throughput interactome study, using the replisome subunit HolC as bait and the damage …

Evaluation Of Nature-Based Engineering Stream Restoration Of Plaster Creek Through Leisure Creek Condominium Association, Julie Wildschut, Rebecca Evenhouse, Andrea Lubberts, Dave Warners, Haley Weesies

Faculty and Professional Research

When land that was once covered with vegetation and soil becomes dominated by impervious concrete and rooftops, the amount of water infiltrated by the ground plumets. As a result, most suburban areas contribute to the impairment of streams by adding excess water, nutrients, and pollutants to nearby waterways each time it rains. One harmful result of this is the erosion of stream banks. The rapid influx of water that occurs after rain events can destabilize and erode stream banks, resulting in excess sediment in the water. One location where this happened very prominently was a section of Plaster Creek which …

Characterization Of Sars-Cov-2 Replication And Transcription Complexes Via Structural And Evolutionary Approaches, Amelie Ghirardo, Ben Shabatian, Avishai Aghelian, Kyle Tau, Eleonora Gianti

Undergraduate Research

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused around 700M cases and over 7M COVID-19-related deaths recorded worldwide (World Health Organization, March 2025). Aiming to effectively combat this and other disease-causing Coronaviruses (CoV), unprecedented research efforts led to the development of new vaccines and antiviral therapies. Due to emergence of variants of concern (VOCs) with increased transmissibility, immune evasion from vaccination, and potential to resist the available treatments, SARS-CoV-2 continues to represent a major threat to global health. Hence, there is a pressing need to discover new antivirals with broad-spectrum efficacy against multiple SARS-CoV-2 variants and related CoVs. This project …

Novel Chloroviruses With Unique Glycans On Their Major Capsid Proteins, Cayden J. Homolka

Honors Program: Senior Projects (Public)

Chloroviruses, of the family Phycodnaviridae, are large, dsDNA viruses with a genome of 290 to 410 kb. These virus genomes are so large that they are classified as “giant viruses”. Within this genome, up to 16 tRNAs and 330 to 450 proteins are encoded. Among the massive amounts of genes and proteins are unique carbohydrate synthesis/metabolism genes, which are responsible for the glycosylation of chloroviruses major capsid proteins. In most viruses, these proteins are glycosylated by the host enzymes located in the endoplasmic reticulum. Instead, Chloroviruses encode their own glycosylation machinery; essentially decorating themselves. Furthermore, these chlorovirus glycans are unlike …

Navigating The Challenges Of Coccidioides Surveillance: Insights From The Environment Of El Paso County, Texas, Tanzir Hossain

Open Access Theses & Dissertations

Coccidioidomycosis, or Valley fever, is a fungal infection resulting from the inhalation of spores from the Coccidioides species (C. immitis and C. posadasii), native to arid areas of the Western Hemisphere. Coccidioidomycosis presents considerable health hazards and can be fatal. It affects between 206,000 and 360,000 individuals annually, leading to 700 to 1,100 fatalities in the United States alone. In response to these issues, extensive research has concentrated on therapeutic goals for this infectious disease. Nonetheless, more limited research has focused on the environmental detection of its causative fungi, which is crucial for forecasting treatment needs and formulating preventive strategies. …

Exploring The Role Of Lysine Acetylation During Biofilm Formation In Bacillus Subtilis, Jennifer Nguyen, Briana Ericka Reid, Valerie Carabetta

Rowan-Virtua Research Day

Biofilms are structured communities of bacterial cells encased in a self-produced extracellular matrix, composed of polysaccharides, extracellular DNA, and proteins. Bacteria in a biofilm pose significant challenges in healthcare due to their resistance to disinfectants and tolerance to antibiotics. In some species, histone-like proteins were found to be important structural components of the biofilm. Nε-Lysine acetylation is a widespread post-translational modification (PTM) in bacteria, which can alter a protein’s function. The histone-like protein HBsu in Bacillus subtilis is acetylated at seven sites in vivo. We hypothesized that the acetylation state of HBsu may alter biofilm structure or the genetic programming, …

Implications Of Type Iv Pilus Retraction For Dna Uptake By Acinetobacter Baumannii, Yafan Yu

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Horizontal gene transfer (HGT) via natural competence allows bacteria to incorporate extracellular DNA (eDNA) into their genomes, facilitating genetic diversity and adaptation. In Acinetobacter species, natural competence depends on DNA binding and uptake mediated by type IV pili (T4P). T4P are dynamic extracellular filaments composed primarily of the major pilin subunit PilA, along with a few minor subunits. T4P drive a range of cellular functions including twitching motility, biofilm formation, and DNA uptake, with some functions dependent on pilus retraction and others not. However, how Acinetobacter T4P bind DNA and how T4P/eDNA interactions impact biofilm formation remain unclear. Here, I …

Expanding Inducible Epithelial Resistance Against Pneumonia: Novel Virus, Novel Receptor, Michael Longmire

Dissertations and Theses (Open Access)

Pneumonia is the leading infectious cause of death worldwide and presents a continuing risk among immunocompromised patients. Our work has been focused for many years on the phenomenon of inducible epithelial resistance, where activation of the innate immune response in the airway epithelium is necessary and sufficient to produce a pathogen-killing but self-protective environment to prevent severe disease. Inducible resistance is pathogen-agnostic and has been demonstrated against an array of respiratory infections. We achieve this using a combination of pattern recognition receptor agonists – Pam2CSK4 and ODN M362 being the current formulation – which produce synergistic levels of pathogen reduction …

Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma

Dartmouth College Ph.D Dissertations

Clostridium thermocellum, a thermophilic anaerobic bacterium, holds promise as a biocatalyst for conversion of lignocellulosic biomass into biofuels. This microbe has been subjected to various metabolic engineering strategies, including the deletion of genes encoding secondary fermentation products such as H₂, formate, acetate, and lactate, as well as the expression of heterologous genes to redirect carbon flux toward ethanol production. Despite these efforts, achieving economically viable ethanol titers remains a challenge. We hypothesized that studying how intracellular metabolite concentrations change as fermentation stops could reveal metabolic bottlenecks or regulatory mechanisms limiting ethanol production at high titers. However, metabolomics studies at …

Biochemical And Structural Insights Into The Yersinia Effector Yopm And Its Negative Regulation Of The Pyrin Inflammasome, Bethany Wairimu Mwaura

Dartmouth College Ph.D Dissertations

Bacteria utilize sophisticated secretion systems to inject effectors into host cells in order to facilitate their survival and replication in the host. Some pathogenic species of Gram-negative bacteria use a conserved contact-dependent T3SS to inject a wide array of effectors. While the effectors diverge in their structures, functions and cell-localization, the T3SS is well conserved. Several effectors discussed in this thesis target key host inflammasome responses. The focus of this work is how the Yersinia effector YopM inhibits the pyrin inflammasome. During Yersinia infection, two effectors, YopE and YopT inadvertently activate the pyrin inflammasome while targeting RhoA to avoid phagocytosis. …

How The Biotic And Abiotic Factors In The Belle Forest Cave And Arboretum Soil Dictates Tree Species Prevalence, Amya A. Bingham

SPARK Symposium Presentations

A plethora of factors in the soil impact a plant’s health, including the presence of different biotic and abiotic factors. These include things like temperature, elevation, pH, microbial respiration and the presence of water, clay, loam, silt, sand, nitrogen, potassium, and phosphorus. Different soils will have varying amounts of these, which may dictate what is able to grow in them, and therefore also the surrounding area. This research project explores how the aforementioned biotic and abiotic factors affect the soil at the Belle Forest Cave and Arboretum. Three samples will be taken from four spots along a transect at this …

College Of Natural Sciences Newsletter, Spring 2025, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message from Dr. Sen Subramanian
Page 2 Student Spotlights
Page 3 Kaushik honored, Three-Minute Thesis, & Ice Cores revealed
Page 4 Alumni Spotlight
Page 5 Day of Scholars
Page 6 Cyanide research, Record Research Expenditures, Adhikari awarded Miller Research Award
Page 8 Hanson Receives NSF Grant
Page 9 Snow Lab Research Team
Page 10 Faculty Awards
Page 11 Drone Day
Page 13 Khalaf Awarded Presidential Award

Induced Mutagenesis In West Nile Virus Non-Structural Protein 3 With A Discussion Of The Mutation's Effects On Viral Properties, Caden Connealy

Honors Program: Senior Projects (Public)

West Nile Virus (WNV), a member of the Flaviviridae family and introduced to the Western hemisphere in 1999, presents a unique and emerging threat to human health. Infection in humans is often mild but can occasionally result in severe neurological impairment and even death. West Nile Virus non-structural protein 3 (NS3) plays an important role in the process of viral genome amplification. More specifically, the C-terminal domain of the protein folds into a helicase enzyme, which is responsible for the “unwinding” of double-stranded RNA intermediates and RNA secondary structure on the WNV genome. This is a vitally important step in …

College Of Natural Sciences 2024 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Dean's Message
Page 3 Department Highlights
Page 4 One Day for State
Page 5 New Students in Wecota
Page 6-8 Faculty Excellence
Page 9 SDSU Physics Students Recognized
Page 9 Prairie Doc Watch Party
Page 10-11 Student Excellence
Page 11 Connections Abroad
Page 12-13 CNS’s Research Centers
Page 14 Connections Abroad
Page 14 Dean Wolf-Hall Retired
Page 15 Outreach Program
Page 15 Events and Traditions
Page 16 Student Spotlight
Page 17 Alumni Spotlight
Page 18-19 SDSU Alum at Paris Paralympics
Page 20 Work Anniversaries & Programs

Exploring Oxylipins In Host–Microbe Interactions And Their Impact On Infection And Immunity, Robert J. Neff, Christopher D. Radka

Markey Cancer Center Faculty Publications

Plasma lipids are essential components of biological systems, transported through interactions with proteins to maintain cellular functions. These lipids exist in various forms, such as fatty acids, glycerolipids, glycerophospholipids, sphingolipids, sterols, and prenol lipids, derived from dietary intake, adipose tissue, and biosynthesis. While the association between certain fatty acids and cardiovascular diseases has been widely recognized, polyunsaturated fatty acids (PUFAs) exhibit cardioprotective effects, reducing risks of arrhythmias and heart-related mortality. This is due to their role in the production of eicosanoids, which modulate inflammation. Chronic inflammation, particularly in obesity, is significantly influenced by fatty acids, with saturated fatty acids promoting …

Transcription Factor Binding And Discovery Of Novel Gene In The Opportunistic Human Pathogen, Pseudomonas Aeruginosa, Alaina Westee

Symposium of Student Scholars

Pseudomonas aeruginosa (PA) is a gram-negative, ubiquitously-found bacterium that primarily causes nosocomial, or hospital-borne, infections within immunocompromised patients. Therefore, it has been deemed a critical priority pathogen by the World Health Organization (WHO) and the Center for Disease Control (CDC), generating a need for research on its fundamental biology. The Van Dyke laboratory focuses on proteins called transcription factors, which promote or repress gene expression to regulate an organism’s functioning. We are specifically studying the cadmium-responsive transcription factor, CadR, due to the importance of metals in virulence and the lack of information on PA’s response to metal fluctuations. We intend …

Characterization Of Legionella Pneumophila Effector Protein Ceg10, Emmanuella Ofoka

Masters Theses & Specialist Projects

Legionella pneumophila, the causative agent of Legionnaires' disease, utilizes a Type IV secretion system (T4SS) to transport effector proteins into host cells. This bacterium is said to have over 300 effector proteins. Among these, the Ceg10 effector protein had remained uncharacterized, despite evidence suggesting the importance of bacterial effector proteins in the host-pathogen interaction. This study aimed to perform a structural and functional characterization of Ceg10 through transcriptomic, bioinformatics, and molecular analyses. Transcriptomic profiling of HEK 293T cells expressing Ceg10 revealed significant differential gene expression, with approximately 20 upregulated genes, including leucine-rich repeat, as well as other downregulated genes. …

Microbial And Plant Biodiversity In Appalachian Agroecosystems And Their Implications For Soil Health, Kinsey Reed Close

Graduate Theses, Dissertations, and Problem Reports (ETD)

The sustainability of agricultural landscapes depends on understanding the complex interactions between plants, soil, and microbes. In Appalachia, a region shaped by complex terrain and long histories of human and ecological interaction, small family farms produce hay, livestock, and row crops. These agroecosystems, though often treated as “artificial” by many ecologists, have the potential to support both food production and biodiversity conservation if managed with an understanding of ecological complexity. This dissertation examines how plant and microbial diversity interact with soil and management to influence nutrient cycling, soil health, and long-term resilience in Appalachian agricultural systems. A literature review revealed …

Molecular Interactions Between The Shellfish Pathogen Vibrio Coralliilyticus Re22 And The Probiont Phaeobacter Inhibens S4sm, Jessica Coppersmith

Open Access Dissertations

Oyster larvae aquaculture is an important industry, both economically and environmentally, helping to create sustainable food systems by supplying seed oysters to farms, and also to restoration projects aimed at building coastal resilience and improving water quality by rejuvenating wild populations. However, oyster larvae are highly susceptible to rapid mortality events, crashes, which can seriously impact the industry. One source of these crashes in hatchery systems is vibriosis, caused by pathogenic species of Vibrio bacteria that are ubiquitous in temperate coastal waters, and with rising surface water temperatures their prevalence and virulence are increasing. To prevent these larval crashes from …

Reversible Degradation Of Peptidoglycan By Lytic Transglycosylases, Aaron Devereaux

Theses and Dissertations (Comprehensive)

Antimicrobial resistance continues to be a burden on the global healthcare system with an estimated cost of billions of dollars and millions of deaths each year. Recently, there has been little to no development on new antibiotics to treat bacterial infection, and any that are developed become resisted to within a few years. Both Gram-positive and Gram-negative bacteria contain a mesh-like layer called peptidoglycan (PG) that surrounds their cells providing strength, cell shape, and protection from their environments. This layer is a polymer of N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) connected via a b-1,4-glycosidic bond, with each strand being cross-linked …

Investigating Regulation And The Regulome Of The Nucleic Acid Binding Protein Spovg Within Borrelia Burgdorferi, Timothy C. Saylor

Theses and Dissertations--Medical Sciences

Prior studies indicated Borrelia burgdorferi SpoVG protein was regulated, SpoVG binds specifically to a number of nucleic acids, and SpoVG binds to the non-variable section of the major virulence factor vlsE. Although a direct transcriptional activator or inhibitor was not elucidated, it is shown that SpoVG is regulated based on cell culture density independent of the growth rate of B. burgdorferi, indicating that SpoVG regulation is outside the scope of the alternative sigma factor RpoS. Using a dCas9 CRISPRi construct to target SpoVG resulted in protein expression trending towards upregulation of the BosR-RpoS regulon, and a marked decrease …