Biochemistry Commons^™

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 …

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, …

Flux Crystal Growth Of A Series Of Calcium Rare Earth Silicate Chlorides Calnsio4Cl (Ln = Pr, Nd, Sm, Eu, Gd, And Tb): Mixed Anion Materials With A Spodiosite-Type Structure, Maria Goncalves, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

A series of calcium rare earth silicate chlorides, CaLnSiO4Cl (Ln = Pr, Nd, Sm, Eu, Gd, and Tb), was obtained as single crystals from flux crystal growth. The structures were determined by single crystal X-ray diffraction and were found to be related to the spodiosite/Wagnerite mineral structure, Ca2PO4F. The obtained compositions are variations of the spodiosite structure that result from two simultaneous elemental substitutions. Replacing one calcium for one rare earth element and the simultaneous replacement of one VO4³⁻ or PO4³⁻ with one SiO4⁴⁻. CaEuSiO4Cl was found to luminesce, and its photoluminescence spectrum is reported.

Water Circulation Beneath A Hovering Suas For Water Quality Monitoring Applications, Erin E. Hackett, Boone Fleenor, Jensine C. Coggin, Duvall Dickerson-Evans, Nikolaos Vitzilaios, Whitney E. Schuler, Paige K. Williams, Michael L. Myrick

Faculty Publications

Water quality has traditionally been measured via in situ sensors and satellites. The latter has limited applicability for smaller inland water bodies, while the former requires significant logistics, labor, and expense for routine sampling, and reactive/spurious sampling is often not feasible as a result (e.g., sampling pre-/post-storm). Consequently, small uncrewed aircraft system-based (sUAS-based) sampling has emerged as a potential solution to bridge these sampling gaps and challenges. But sampling from an sUAS is complicated by the need to pump water from depth, rather than suspending a sensor from the sUAS, due to concern over sampling sUAS-impacted waters. Here, we measure …

Thermodynamic Assessment Of The Li, Na, K, Cs | F, I Reciprocal Salt For Msr Applications, Clara M. Dixon, Mina Aziziha, Amir Mofrad, Jorge Paz Soldan Palma, Ronald E. Booth, Aiswarya Padinhare Manissery, Jack A. Wilson, Hans Conrad Zur Loye, Hunter B. Tisdale, Juliano Schorne-Pinto, Theodore M. Besmann

Faculty Publications

Gibbs energy models necessary to describe the thermochemical behavior of cesium and iodine in molten FLiNaK (46.5LiF-11.5NaF-42KF mol%), a proposed molten salt reactor coolant and fuel solvent, have been developed as they are of concern due to their high radiotoxicity and volatility. The six constituent pseudo-binary systems LiI-CsI, LiI-KI, LiI-NaI, NaI-KI, KI-CsI and NaI-CsI were evaluated using available phase equilibria and mixing enthalpy measurements. The models for the ternary reciprocal salt systems Li,Cs|F,I, Li,K|F,I, Li,Na|F,I, Na,K|F,I, Na,Cs|F,I and K,Cs|F,I were obtained by interpolation of the optimized pseudo-binary systems and parameters fit as necessary based on observed behavior. The additive (common …

Functional Characterization Of The Hssb1 K94q Mutation, Isaiah Singleton

All Theses

Genome stability depends on precise DNA repair pathways such as homologous recombination (HR), where human single-stranded DNA-binding protein 1 (hSSB1) stabilizes single-stranded DNA (ssDNA) intermediates and recruits repair complexes. Post-translational modifications, including acetylation, are known to regulate hSSB1 activity, but their molecular effects remain poorly defined. This study examined the role of lysine 94 (K94) acetylation using a glutamine substitution mutant (K94Q) that mimics the acetylated state. Recombinant hSSB1 wild type (WT) and hSSB1_K94Q were expressed in Escherichia coli and purified using Ni–NTA affinity chromatography. Biochemical analyses, including electrophoretic mobility shift assays (EMSA), single-strand annealing assays, and displacement loop …

Blood-Based Clinical Markers For Early Dementia Detection: Insights From Ad-Detect-Cohort, Benard Aliwa, Jasmit Shah, Olivera Nesic Taylor,, Samuel Nguku, Juzar Hooker, Dilraj Sokhi, Sylvia Mbugua, Litha Musili, Rachel Maina, Harrison Kaleli, Levi Muyela, Anne Njoki Gitere, Anne Nyambura, Zul Merali, Karen Blackmon, Chinedu Momoh

Brain and Mind Institute

Background: Over 55 million people worldwide live with dementia, with more than60% residing in low- and middle-income countries. Alzheimer’s disease, the mostcommon form of dementia, accounts for 60–70% of cases. Early and accurate diagnosisremains a global challenge, necessitating novel approaches to mitigate the diseaseburden. Biomarkers hold significant promise in improving diagnostic accuracy andpredicting disease progression. Validated biomarkers for the preclinical stages ofdementia are crucial for advancing diagnosis and therapeutic strategies. We aimedto identify potential clinical markers for early dementia detection and assess theirpredictive accuracy in identifying high-risk individuals.

Method: We analyzed blood samples from dementia cases (n = 30) and …

Bacillus Subtilis: A Bacterium That Can Potentially Degrade Low-Density Polyethylene (Ldpe) And Polyethylene Terephthalate (Pet), Migdalia Flores

Theses and Dissertations

The widespread application and disposal of plastics, such as low-density polyethylene (LDPE) and polyethylene terephthalate (PET), have raised significant environmental health concerns. Because of each plastic’s stability and durability, these plastics exhibit limited natural degradation in the environment. Recently, the environmentally friendly biodegradation of plastics by living microorganisms has attracted more attention, as they can assist in the natural degradation process. In this study, the bacterial strain Bacillus subtilis ATCC6051 was used to degrade LDPE and PET for 60 days. To measure the degradation of low-density (LDPE) and polyethylene terephthalate (PET), the dry weight was taken, and physical characteristics were …

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 …

Exploring Glycosomes As Therapeutic Targets For Trypanosoma Brucei, Sabrina Sutton Pizarro

All Dissertations

Trypanosoma brucei is a protozoan parasite which causes human African trypanosomiasis and the livestock wasting disease, nagana. These parasites have highly specialized peroxisomes, called glycosomes, which house a variety of essential metabolic pathways, including glycolysis. Glycolysis is the sole means of energy production in the infective life stage of T. brucei making glycosomes and the glycolytic pathway promising targets for therapeutic strategies. In this work, we have studied the glycosome as a therapeutic target from multiple perspectives. The first portion of this work addresses drug trafficking. The efficacy of small-molecule inhibitors of glycosomal enzymes is restricted by the rate of …

Engineered An Ultrasmall Curcumin Oral Nanoformulation Restores Intestinal Integrity And Gut Microbiota Dysbiosis, Vivek Sharma, Prateeksha Prateeksha, Balwant Paliya, Sateesh Gupta, Sarvendra Singh, Anand Anunay, Sushil Agrahari, Shailendra Singh, Chandana Rao, Saroj Barik, Brahma Singh

Department of Biochemistry and Molecular Biology Faculty Papers

Antibiotic therapy for bacterial infections often disrupts gut microbiota (GM) and intestinal integrity, inducing chronic inflammation and inflammatory bowel diseases. An effective therapeutic intervention is urgently needed to alleviate the aforementioned adverse effects of antibiotics. Curcumin (CUR) reveals great potential to restore intestinal integrity and GM dysbiosis due to its strong antiinflammatory and prebiotic effects. However, the weak solubility and stability of CUR result in limited bioavailability and a short half-life, which restricts its clinical uses. An ultra-small CUR oral nanoformulation was created using a carboxylated galactomannan (cGM), facilitated by hydrogen bonding between the phenolic hydroxyl groups of CUR and …

Dna Extrusion Size Determines Pathway Choice During Cag Repeat Expansion, Mayuri Bhatia, Ashutosh S. Phadte, Anna Lakhina, Anthony R. Monte Carloi Iii, Sarah Barndt, Anna Pluciennik

Department of Biochemistry and Molecular Biology Faculty Papers

DNA triplet repeat expansion causes several primarly neurological disorders like Huntington's disease, myotonic dystrophy type 1, and fragile-X related disorders. There is general consensus that recognition of extrahelical extrusions or hairpin-loop structures (formed by strand slippage) by the DNA mismatch repair protein MutSβ leads to repeat expansion by a mutagenic process. By contrast, the FAN1 nuclease attenuates triplet repeat expansion, the molecular basis of which was explained by our recent finding that FAN1 nuclease cleaves and initiates removal of extrahelical extrusions. Here we show that extrusions containing two or more triplet repeats are subject to recognition and processing by either …

Synthesis Of Disulfide Triazole Phosphorus Fire Retardant Via Photochemical Conditions, Jason Liu

Undergraduate Research Symposium Lightning Talks

The development of fire retardants is critical to enhancing fire safety and advancing fire science. The novel synthesis of a disulfide triazole phosphorus thiolacid fire retardant under photochemical conditions, along with relevant testing on plume generation performance, aims to answer our research goals.The proposed specific synthesis and conditions provide for a more efficient and environmentally greener route compared to conventional methods, utilizing photochemical click reactions. Furthermore, the addition of sulfur element to conventionally sole phosphorus-based FR reduces the chance of leaching by increasing the molecular weight of the compound and overcoming the obstacle of low molecular weight problems while also …

Liver-Directed Base Editing Of Abcc6 Prevents Ectopic Calcification In A Variant-Humanized Mouse Model Of Pseudoxanthoma Elasticum, Lauren C. Testa, Dora Obiri-Yeboah, Hooda Said, Ping Qu, Michael A. Levine, Mohamad-Gabriel Alameh, Kiran Musunuru, Qiaoli Li, Xiao Wang

Department of Biochemistry and Molecular Biology Faculty Papers

Pseudoxanthoma elasticum (PXE) is an autosomal recessive connective tissue disorder characterized by ectopic calcification of elastic fibers throughout the skin, retina, and arteries. It is caused by pathogenic variants in ABCC6 , which encodes a transmembrane transporter that primarily localizes to hepatocytes. Loss of ABCC6 function in hepatocytes leads to systemic deficiency of inorganic pyrophosphate (PPi), a potent inhibitor of calcification; such depletion of PPi from the circulation is responsible for multisystemic ectopic calcification seen in PXE. Therefore, liver-targeted variant correction by genome editing and subsequent restoration of systemic PPi may offer a one-and-done therapeutic approach for PXE. The ABCC6 …

Electrochemical Breath Sensors In Medical Diagnostics: Emerging Trends And Future Directions, Natalie E. Strom, Courtney J. Weber, Olja Simoska

Faculty Publications

With the rising prevalence of metabolic diseases, infections, and mental health disorders, there is a growing demand for noninvasive diagnostic tools that enable early detection and continuous health monitoring. In this context, exhaled breath biomarkers provide insight into physiological and pathological processes. Electrochemical breath sensors (EBSs) have emerged as a promising platform for rapid, real-time, and cost-effective disease tracking via the detection of volatile breath biomarkers, such as NH₃, NO, and CO₂. Recent advancements in electrode materials, biological recognition elements, and sensor architectures—spanning nanomaterials, enzymes, aptamers, and molecularly imprinted polymers—have enhanced the analytical performance of EBSs. …

Electrochemical Breath Sensors In Medical Diagnostics: Emerging Trends And Future Directions, Natalie E. Strom, Courtney J. Weber, Olja Simoska

Faculty Publications

With the rising prevalence of metabolic diseases, infections, and mental health disorders, there is a growing demand for noninvasive diagnostic tools that enable early detection and continuous health monitoring. In this context, exhaled breath biomarkers provide insight into physiological and pathological processes. Electrochemical breath sensors (EBSs) have emerged as a promising platform for rapid, real-time, and cost-effective disease tracking via the detection of volatile breath biomarkers, such as NH₃, NO, and CO₂. Recent advancements in electrode materials, biological recognition elements, and sensor architectures—spanning nanomaterials, enzymes, aptamers, and molecularly imprinted polymers—have enhanced the analytical performance of EBSs. …

Single-Fibril Förster Resonance Energy Transfer Imaging And Deep Learning Reveal Concentration Dependence Of Amyloid Β 42 Aggregation Pathways, Sara Sohail, J. Yoo, H. S. Chung

Chemistry & Biochemistry Faculty Works

Amyloid fibril formation is a highly heterogeneous process as evidenced by polymorphism in fibril structure. It has been suggested that different polymorphs are associated with different diseases or disease subtypes. Detailed characterization of this heterogeneity is a key to understanding the aggregation mechanism and, possibly, the disease mechanism. In this work, we develop Förster resonance energy transfer (FRET) imaging of amyloid fibril formation in real time and investigate the concentration-dependent heterogeneous fibril formation of amyloid β 42 (Aβ42). We incubated a mixture of unlabeled and labeled (5% donor and 5% acceptor) Aβ42, followed aggregation, and characterized individual fibrils in terms …

Analysis Of Mct-1 Expression In Mouse Neural Retina In Response To Chronic Inflammation, Ian W. Ronson

PANDION: The Osprey Journal of Research and Ideas

Chronic inflammation is a current public health concern as it is linked to the etiology and symptoms of numerous diseases, for example diabetic retinopathy (DR). In the case of DR, inflammation leads to dysregulation of the blood retina barrier causing retinal hemorrhage and macular edema leading ultimately to irreversible vision loss. MCT-1 is critical for the survival of photoreceptor cells because MCT-1 forms protein complexes with Basigin, a cell-cell adhesion protein, that enables Müller glial cells to efficiently provide lactate as a high energy fuel source. Previous studies have shown chronic inflammation reduces Basigin expression in the retina and that …

Comparative Analysis Of Citrate Synthase Activity In Skeletal Muscle, Liver, And Adipose Tissue In Beef Cattle, Abigail Webb

Honors Program: Senior Projects (Public)

Mitochondrial efficiency plays a central role in determining how cattle partition nutrients toward muscle growth or adipose deposition, yet little is known about tissue-specific differences in mitochondrial density among tissues or among beef cattle. This study aimed to quantify mitochondrial density in muscle, liver, and adipose tissue samples from beef cattle and evaluate its potential relationship with metabolic efficiency. Tissue samples of semitendinosus muscle (ST), liver, and subcutaneous adipose (SC) were collected, homogenized, and analyzed for citrate synthase (CS) activity using a fluorometric assay as a proxy for mitochondrial density. Preliminary analyses revealed that the semitendinosus muscle displayed the highest …

A New Low-Rate Stable Hydrogel Cathode For Aqueous Zn-Ion Batteries, Roya Rajabi, Shichen Sun, Jamil A. Khan, Morgan Stefik, Kevin Huang

Faculty Publications

Aqueous Zn-ion batteries (ZIBs) are attractive candidates for large-scale energy storage owing to the abundance, low cost, and intrinsic safety of Zn metal. However, their practical application is hindered by poor cycle stability, especially at low current densities, due to cathode dissolution and limited electrochemically active sites (EAS). Herein, a hydrogel-based cathode comprising ammonium vanadate, carbon black, and a Zn-ion-conducting carboxymethyl chitosan–acrylamide hydrogel matrix doped with Zn(ClO4)2 is reported. This design establishes a continuous Zn-ion-conducting network, thereby maximizing EAS density throughout the electrode volume. The ZIB with the hydrogel cathode exhibits outstanding cycling stability, with 77% capacity retention after 2000 …