Biochemistry, Biophysics, and Structural Biology Commons^™

Analysis Of Differential Gene Expression In Androgen-Independent Clones Derived From The Mycap Pca Cell Line, Jessie L. Tignor, Melanie Sinanian, Richard Inho Joh, David Gewirtz, Jason Reed

UROP Posters

Androgen deprivation therapy (ADT) is a primary treatment strategy for prostate cancer (PCa), yet many tumors eventually develop androgen independence, leading to treatment resistance. To investigate the molecular changes underlying this transition, we analyzed differential gene expression in four androgen-independent (AI) clones derived from the Myc-CaP prostate cancer cell line using RNA sequencing. Gene expression profiles were compared to the parental Myc-CaP line, and differentially expressed genes (DEGs) were identified using DESeq2 and edgeR. The AI clones exhibited significant downregulation of senescence-associated genes, including Ezh2 and lamin B1, suggesting a loss of senescence-related chromatin repression. Additionally, upregulation of Wnt pathway …

Electrochemical Detection Of Prostate Cancer—Associated Mirna-141 Using A Low-Cost Disposable Biosensor, Alexander Hunt, Gymama Slaughter

Center for Bioelectronics Publications

Prostate cancer is the second leading cause of cancer-related deaths among men in the United States. The early detection of aggressive forms is critical. Current diagnostic methods, including PSA testing and biopsies, are invasive and often yield false results. MicroRNA-141 (miRNA-141) has emerged as a promising non-invasive biomarker due to its elevated levels in the urine of patients with metastatic prostate cancer. Here, a low-cost, paper-based electrochemical biosensor for the sensitive detection of miRNA-141 in synthetic urine is reported. The device employs inkjet-printed gold electrodes on photopaper, functionalized with thiolated single-stranded DNA-141 capture probes for specific target recognition. The biosensor …

Technological Development Of In-Cell Nmr: Microfluidic, Metabolomic, And Fluxomic Approaches, Nicholas Sciolino

Electronic Theses & Dissertations (2024 - present)

In the fields of structural biology, metabolomics, and fluxomics, there is a driving, technique-based concern when it comes to high-resolution spectrometry and its marriage to biological and physiological relevance. Sample preparation often involves cellular perturbation, lysate separation schemes, combinations with non-biological reagents, and timeline slack. Conceptually, the farther we get from the cell, the greater the potential disparity between what exists in vivo and our in vitro manipulations. This is particularly true when seeking to collect data on transfected targets of interest, and on sensitive metabolic equilibria that occur on the order of minutes. The question remains: if we are …

Conserved A-Rich Regions In The 3’ Utr Of Zika Virus Differentially Affect Viral Gene Expression, Kristen Kaytes

Electronic Theses & Dissertations (2024 - present)

Following its discovery in 1947, Zika virus garnered little attention in the global stage until a rapidly spreading epidemic brough the virus to the global stage in 2015. Continuous advances in research have begun to further the understanding of the molecular biology of Zika virus, however much is still unknown. Much of our understanding of the virus comes from cross reference to other viruses within the same family, such as Dengue virus and West Nile virus. A commonality of these viruses is that they resemble cellular mRNAs and have a single-stranded positive-sense RNA genome that contains a 5’-cap but lacks …

Investigating Rna Dysfunction Of Inherited Neuromuscular And Neurodevelopmental Disease, Jacob H. Schroader

Electronic Theses & Dissertations (2024 - present)

ITPase deficiency is a rare but fatal, autosomal recessive enzyme deficiency involving encephalopathy, microcephaly, congenital cataracts, hypotonia, developmental delay, and dilated cardiomyopathy. Within a decade since the original description of the severe form in humans, there are huge gaps in the field regarding the underlying molecular mechanisms driving pathogenesis resulting from ITPase deficiency. Past studies have focused on characterization of the organism level ITPase-deficient phenotype, but the molecular and cellular characterization remains to be fully described. Due to the biochemical function and established biological role of the ITPase enzyme, investigation into the consequences of inosine accumulation and misincorporation into RNA …

Synthesis And Assessment Of Biobased Acrylated Epoxidized Soybean Oil Resins For Stereolithography 3d Printing Of Microfluidic Devices, Natalie S. Romero Figueroa

College of Graduate Studies: Theses & Dissertations

This research focuses on the development and characterization of a biobased photocurable resin synthesized from soybean oil for use in stereolithography (SLA) 3D printing of microfluidic devices. The study explores a sustainable alternative to petroleum-based resins by performing an acrylation reaction on epoxidized soybean oil (ESO) to produce acrylated epoxidized soybean oil (AESO), which was then formulated into a photocurable resin with the addition of a photo initiator. The fabrication process involved designing microfluidic molds in SolidWorks and printing them using an Elegoo Mars 4 SLA printer under various exposure and layer thickness parameters. The printed samples consisted of microchannels …

Enhancing The Mechanical Properties Of Sla 3d-Printed Bio-Resin From Linseed Oil Using Cellulose And Lignin Biopolymers, Chukwunonso A. Ikedionu

College of Graduate Studies: Theses & Dissertations

Abstract

This research explores the development of bio resin from linseed oil by the process of epoxidation and acrylation to produce acrylated epoxidized linseed oil (AELO). Lignin and cellulose biopolymers were added as reinforcement at varying weight fractions of 1 wt.%, 2.5 wt.%, and 5 wt.%, and their mechanical performance was compared against pure AELO. The formulations were printed using an Elegoo SLA 3D printer to create standardized test specimens like tensile bars, compression cylinders, and hardness blocks, which were all prepared according to the ASTM testing standard.

The results indicate that reinforcement effects depend on both filler type and …

Development Of Dna Nanoswitches With Aptamer Based Detection For Thrombin, Camryn A. Beckles

Electronic Theses & Dissertations (2024 - present)

Bio-transducers are devices capable of converting the binding signals from molecular recognition events into readable signals for analytical detection. There is a need for modular bio-transducers that can specifically detect a wide range of analytes using a unified readout technique, as this approach could dramatically reduce costs of healthcare diagnostics and environmental monitoring.

To create such a modular transducer, the molecular recognition properties of aptamers will be used and integrated with the already established biosensing capabilities of DNA nanoswitches that reconfigure their shape in the presence of their target molecule. In this design, the detector strands of the nanoswitch will …

Characterization Of Adaptive Quorum Sensing In Pseudomonas Aeruginosa, Kayla Simanek

Electronic Theses & Dissertations (2024 - present)

Pseudomonas aeruginosa is an opportunistic pathogen that is highly antibiotic resistant and causes tens of thousands of infections each year. It persists in hospitals by forming biofilms on medical equipment like ventilators and catheters, making it difficult to eradicate. Biofilm formation, among other virulence factors of P. aeruginosa, is regulated through quorum sensing, a mechanism of bacterial communication. Quorum sensing is primarily coordinated through LuxI-R type systems comprised of an autoinducer synthase and receptor, respectively. Canonically, the first system to be expressed is LasI-R, and LasR upregulates the second arm of the quorum sensing network, the RhlI-R system. Research …

Physiological Structure, Activity, And Interactions Of The Formin, Human Diaphanous Homologue 1, Aaron Premo

Electronic Theses & Dissertations (2024 - present)

Human Diaphanous Homologue 1 (DIAPH1) is a 143 kDa functional protein that plays a critical role in the regulation of actin dynamics within eukaryotic cells. As a formin, DIAPH1 facilitates the assembly of actin filaments from globular actin monomers, a process essential for cellular structure, motility, and other fundamental cellular processes. Beyond its structural role in actin polymerization, DIAPH1 is implicated in several diseases, including diabetes, cancer, and inflammation, as well as complications like hearing loss. Despite its significance in human health, the functional and structural properties of DIAPH1, particularly in human cells, remain less explored compared to related proteins, …

Using Rna Sequencing To Examine Encephalic Gene Expression In Cactus Mice, Sarah A. Nicholls

Honors Theses and Capstones

Many of the exact mechanisms by which desert-adapted animals avoid dehydration-induced complications are unknown, though there are likely ties to the general mammalian dehydration response, a multisystem process spearheaded by the brain. Peromyscus eremicus, the cactus mouse, can survive its whole life without intaking water and is commonly used as a model to study desert adaptations. In this study, we have used bulk transcriptomics to characterize the differential gene expression across hydrated and dehydrated P. eremicus in five major regions of the brain: the cerebral cortex (referred to throughout much of this paper as the cortex), hippocampus, thalamus, midbrain, …

Optimization Of Small-Scale Bioreactors For Increased Pdna Production And Yield, Laura M. Hills

Honors Theses and Capstones

No abstract provided.

Raman Spectroscopy For Rapid Quantification Of Macronutrients In Heirloom Beans, K. Chandler Williams

Graduate Theses, Dissertations, and Problem Reports (ETD)

Quantification of macronutrients in food requires a large investment in facilities and instrumentation as well as ongoing expenses of labor, reagents, and hazardous waste disposal. These costs pose a significant barrier to determining macronutrient quantities in the thousands of uncharacterized landrace and heirloom crops and discourage traditional crop breeding projects from ensuring that their selected crops maintain desirable macronutrient profiles in addition to target agronomic traits. Our objective was to test whether a hand-held Raman spectrometer—a technology which has found use in plant disease diagnostics but remains largely overlooked in nutrient quantification-- could provide a feasible means for quantifying the …

Identification Of A Serine Protease Involved In Spinosad Degradation In The Yellow Fever Mosquito, Aedes Aegypti, Hongxiao Yu, Caixia Peng, Zhaohui Chen, Jie Li, Yunqi Li, Xiaojing Zhu, Yuqi Huang, Linlong Jiang, Pablo Sobrado, Jianqiang Lan, Yingying Guo, Qian Han

Chemistry Faculty Research & Creative Works

Spinosad is a widely used insecticide effective in controlling Aedes aegypti populations, but the molecular mechanisms underlying resistance remain poorly understood. This study explores the role of a serine protease, AeaSP (AAEL002624), in the potential detoxification ability of spinosad. Our results showed the crude protein of Ae. aegypti degraded approximately 48% of spinosad in vitro within 1 h; based on our previous research, AeaSP was believed to be potentially involved in the degradation of spinosad. Subsequently, AeaSP was recombinantly expressed in vitro, and its enzymatic activity was tested using BAEE as a substrate, with a Michaelis constant (KM) of 0.88 …

Exploring The Effects Of Road Salt On Earthworm Species, Alea Mry Koston

Williams Honors College, Honors Research Projects

This study examines the effects of two road salts, sodium chloride (NaCl) and calcium magnesium acetate (CMA), on the health of two earthworm species: Eisenia fetida and Lumbricus terrestris. Over a 4-week period, approximately 168 earthworms were exposed to varying concentrations of either NaCl, CMA, or mixed ratios of both, with a control group included for comparison. The experiment involved monitoring the changes in earthworm weight and measuring their contraction rates to determine physiological responses. Statistical analysis revealed no significant differences in weight or activity between NaCl and CMA treatments for either species. However, higher concentrations of NaCl resulted in …

Elongate Locomotors Show Consistent Torque Patterns Across Substrates, Spencer Bradford, Henry Astley

Williams Honors College, Honors Research Projects

The four main movements found in snakes are understood mainly due to external study; however, muscular forces and resulting torques are poorly known. The main research objective is to study the torque production on different substrates using a snakebot. The study will give a rudimentary model for torque production on different substrates. It can then be compared against biological systems to understand snake movement at a muscular level. This study used a snakebot, allowing direct assessment of the current being run through each of its motors (proportional to torque). Data was then examined using a Principal Component Analysis test for …

Expression And Purification Of Cytochrome P450 46a1 For Resonance Raman Spectroscopy, Lauren Jirles

Williams Honors College, Honors Research Projects

Researchers are targeting cytochrome P450 46A1 (CYP46A1), an enzyme critical for brain cholesterol homeostasis, as a potential therapeutic approach for neurological diseases. CYP46A1 plays a key role in cholesterol turnover in the brain by catalyzing the conversion of cholesterol to 24S-hydroxycholesterol (24HC) and is linked to Alzheimer’s disease pathophysiology. Given its critical role in brain health, CYP46A1 represents a promising target for therapeutic intervention in neurological disorders. The goal of this project was to express the CYP46A1 protein in GC5 E. coli cells and purify the protein using chromatographic techniques including affinity and ion exchange chromatography. Ultraviolet-Visible (UV-Vis) spectroscopy was …

Impact Of Tetrahydrocannabinol (Thc) On Daphnia Magna Heart Rate, Ashley Cosgrave

Williams Honors College, Honors Research Projects

Marijuana (Cannabis) is currently federally illegal within the United States and classified as a Schedule I drug. This leaves a large research gap on the impacts of Tetrahydrocannabinol (THC) use. Daphnia magna are frequently used as a model organism for the human heart and toxicology screenings due to their myogenic heart, similarities in physiological pathways, and sensitivity to toxins. As such, in order to bridge the research gap and uncover potential use of Daphnia magna as a model organism for humans in regard to impact on heart rate, we hypothesized that if Daphnia magna possess CB1 receptors or an equivalent …

Site-Specific Modification Of Antibodies Utilizing Microbial Transglutaminase For Improved Immunoassay Performance, Emily Beitello

Theses and Dissertations

Immobilization strategies used for fixing antibodies to solid phase surfaces significantly contribute to the antigen capture capacity and influences the performance and sensitivity of immunoassays. Traditional methodologies result in the random orientation and/or the weak attachment of immobilized antibodies. Different formats of immunoassays scope in applicability to many fields of research and everyday use. Improving the efficiency of immobilizing antibodies in immunoassays is a beneficial endeavor to increase assay sensitivity. Here, we investigated the use of enzyme-mediated conjugation of antibodies to facilitate a highly oriented immobilization. Microbial transglutaminase (mTG) catalyzes the covalent bond formation between a plethora of primary amine …

Scalable Fabrication Of High-Payload Dendrimer-Based Nanoparticles For Targeted Atherosclerosis Therapy, Huari Kou, Lin Qi, Da Huang, Jiandong Wu, Honglan Shi, Hu Yang

Chemistry Faculty Research & Creative Works

Nanoparticle-based therapeutics hold promise for the treatment of atherosclerosis, but challenges such as low drug-loading capacity and a lack of scalable, controllable production hinder their clinical translation. Flash nanoprecipitation, a continuous synthesis method, offers a potential solution for scalable and reproducible nanoparticle production. In this study, we employed a custom-designed multi-inlet vortex mixer to perform cross-linking reaction-enabled flash nanoprecipitation, facilitating controlled and scalable synthesis of cross-linked Poly amidoamine (PAMAM) dendrimer nanoparticles. Notably, this approach allows simultaneous nanoparticle cross-linking and drug loading in a single step. The mannose moiety enabled specific targeting of macrophages via mannose receptors, enhancing the localization of …

Discovery Of Photosynthetic Oxic N2-Fixation In Cyanobacteria Using Wet Lab And Machine Learning Approaches, James A. Young Iii

Electronic Theses and Dissertations

No abstract provided.

Inductions Of Long-Term Potentiation With Biomimetic Electromagnetic Fields In Primary Neurons, Cooper E. Kansala

Theses and Dissertations (Comprehensive)

Endogenous brain rhythms guide neural communication and plasticity, raising the question of whether weak, temporally structured electromagnetic fields (EMFs) that mimic these rhythms can modulate neuronal activity in a targeted, biomimetic manner. This thesis investigates whether patterned EMFs designed to reflect the temporal structure of hippocampal long-term potentiation (LTP) are more effective at inducing neural plasticity than conventional sinusoidal fields or no stimulation at all. Cortical neurons cultured from postnatal rats were exposed to patterned EMFs for 30 minutes and assessed across three distinct experimental domains. In Chapter 2, microelectrode array (MEA) recordings revealed that the LTP-patterned field significantly increased …

Evaluation Of The Dnazyme Gr5 For The Determination Of Lead Speciation In Natural Waters, Gaganprit Gill

Theses and Dissertations (Comprehensive)

This thesis explores the development and application of a DNAzyme-based biosensor designed to detect labile metal species in environmental samples. Real time and on-site monitoring of labile metal fractions would make a valuable contribution to environmental management, as these fractions are the most bioavailable and pose significant toxicity risks to aquatic organisms. Conventional methods for detecting labile metals, while effective, are often burdened by high costs, complexity, and lengthy processing times, making them less ideal for rapid and widespread environmental assessments.

The first manuscript of this thesis (chapter 2) establishes the fundamental capabilities of the Pb²⁺-specific DNAzyme GR5 …

Structural Insights Into Peptidoglycan O-Acetylation In Gram-Negative Bacteria, Tyler Malloch

Theses and Dissertations (Comprehensive)

The Centres for Disease Control has acknowledged that we are entering a post-antibiotic era, where increasing numbers of bacterial pathogens are becoming resistant to known antibiotics. One of the most successfully targeted features of bacteria is also the main component of the cell wall, peptidoglycan (PG). PG is a heteropolymer of alternating sugar residues, namely N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) which are joined together by b-(1,4)-glycosidic bonds and crosslinked via stem peptide chains. PG is a target, readily lysed by exogenous and endogenous autolysins, such as lysozyme and lytic transglycosylase, respectively. This event leads to cell death …

Exploring The Interconnections Between Mitochondrial Carrier Proteins Involved In Energy Transfer: The Case Of Uncouplig Proteins 2 And 4, Adenine Nucleotide Translocase, And Phosphate Translocase, Marzieh Tabefam

Theses and Dissertations (Comprehensive)

Mitochondrial carrier (MC) proteins play an essential role in cellular energy metabolism by mediating the transport of solutes and protons across the mitochondrial inner membrane (MIM). This thesis explores the structural and functional characteristics of three groups of MC proteins—Uncoupling Proteins (UCPs), Adenine Nucleotide Translocase (ANT), and Phosphate Translocase (P_iT)—to elucidate their individual and interrelated cooperative roles in mitochondrial proton transport and energy regulation.

The study develops and applies novel methodologies for the overexpression, purification, and reconstitution of MC proteins into model lipid bilayers mimicking the native mitochondrial inner membrane environment. These methods ensure proteins maintain their native-like …

Development Of Cyan And Blue Thermostable Fluorescent Proteins: Characterization And Structural Analysis, Acacia J. Jurkowski

Graduate Theses/Dissertations

Fluorescent proteins are commonly used as cell markers in living organisms. Modifications by mutation can be used to improve the qualities of these proteins including fluorescence, thermostability, pH stability, and chemical stability. The goal of this project is to use mutagenesis to improve the fluorescence of thermostable cyan and blue proteins derived from the thermal green protein (TGP). The first cyan protein developed by the DeVore lab (CTP 0.0) shifted the fluorescence to cyan but decreased the quantum yield (Φ_F) to 0.056. Further mutations were incorporated to increase the quantum yield through incorporating hydrogen bonding interactions to the …

Functional Characterization Of Vago In Black Tiger Shrimp Penaeus Monodon Ikk-Nf-Κb Signaling Pathway Against Viral Infection, Zittipong Nanakorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Cytokines serve as key regulators in innate antiviral defense. In crustaceans, research on cytokine-mediated immunity remains limited. A previous study in Penaeus monodon has demonstrated that PmVago proteins exhibit cytokine-like function by acting through the inhibitor of kappa B kinase-nuclear factor κB (IKK-NF-κB) cascade to defend against white spot syndrome virus (WSSV). In this study, five PmVago isoforms were identified, each showing differential transcriptional responses to pathogen challenges. Among them, PmVago1 and PmVago4 exhibited strong antiviral responses against WSSV infection. RNA interference of PmVago1 and PmVago4 increased shrimp susceptibility to WSSV infection with enhanced viral replication. Their suppression also disrupted …

Investigating The Lyoprotective Properties Of An Antifreeze Protein From A Broadleaf Desert Shrub, Alexzandria Sheppard

Honors Theses and Capstones

Lyophilization, or freeze-drying, is an important preservation method for protein-based products, such as protein pharmaceuticals. However, the process introduces both freezing and drying stresses that can harm proteins. Here, we have studied the efficacy of AnAFP, a dehydrin-like antifreeze protein isolated from the broadleaf desert shrub Ammopiptanthus nanus, in reducing enzyme damage during freeze-drying, or lyophilization. We have shown that AnAFP can protect the model enzyme lactate dehydrogenase (LDH) from both freezing and dehydration damages during lyophilization with similar or better efficacy than 10% w/v sucrose and superior to that of another known antifreeze protein.

Swinging Lever Mechanism Of Myosin Directly Shown By Time-Resolved Cryo-Em, David P. Klebl, Sean N. Mcmillan, Cristina Risi, Eva Forgacs, Betty Virok, Jennifer L. Atherton, Sarah A. Harris, Michele Stofella, Donald A. Winkelmann, Frank Sobott, Vitold E. Galkin, Peter J. Knight, Stephen P. Muench, Charlotte A. Scarfi, Howard D. White

Department of Biomedical and Translational Sciences Faculty Publications

Myosins produce force and movement in cells through interactions with F-actin¹. Generation of movement is thought to arise through actin-catalysed conversion of myosin from an ATP-generated primed (pre-powerstroke) state to a post-powerstroke state, accompanied by myosin lever swing²,³. However, the initial, primed actomyosin state has never been observed, and the mechanism by which actin catalyses myosin ATPase activity is unclear. Here, to address these issues, we performed time-resolved cryogenic electron microscopy (cryo-EM)⁴ of a myosin-5 mutant having slow hydrolysis product release⁵,⁶. Primed actomyosin was predominantly captured 10 ms after …

Green Chelation Strategy For Deashing Of Algal Biomass, Agyare Asante, George Daramola, Ryan W. Davis, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

This study investigated a green chelation strategy for deashing algal biomass using nitrilotriacetic acid (NTA) and deionized water (DI) to enhance its suitability for biofuel and bioproduct applications. Solid-state algal turf scrubber (SS ATS), green algal turf scrubber (ATS), and Scenedesmus were analyzed, with Scenedesmus selected for detailed evaluation due to its high ash removal efficiency. The objective was to optimize a purification process that minimizes ash and heavy metal content while preserving biochemical integrity. Algal biomass underwent sequential washing with DI, NTA, and NTA+DI under varying temperatures (90-130 °C). Analytical techniques including Fourier Transform Infrared (FTIR) spectroscopy, Inductively Coupled …