Biochemistry, Biophysics, and Structural Biology Commons^™

Antimicrobial Studies Of Novel Pyrazole And Thiazole-Based Antibacterial Agents, Hansa Raj Kc

Student Theses and Dissertations

In recent years, the rise of antibiotic-resistant bacteria has become a global concern, resulting in fewer effective antibiotics. Several conventional antibacterial agents are ineffective against these, necessitating novel molecules with enhanced efficacy and diverse actions. We developed pyrazole and thiazole-based antibacterial agents and demonstrated that they have significant potency (minimum inhibitory concentration as low as 0.39 µg/mL) against antibiotic-resistant and susceptible bacteria, as well as promising anti-biofilm and anti-persister activity. In vivo toxicity tests on Caenorhabditis elegans showed no significant harm to this model host organism at low compound concentrations. These compounds rescued C. elegans from methicillin-resistant Staphylococcus aureus (MRSA) …

Improvement Of Single-Crystal Structures Of Very Heavy Element Compounds By Refining Anomalous Dispersion Parameters, Florian Meurer, Gregory Morrison, Birgit Hischa, Hans Conrad Zur Loye, Christoph Hennig, Michael Bodensteiner

Faculty Publications

Refining the anomalous dispersion parameters of the four uranium compounds NaUF5, NaU2F9, Cs2(UO2)TiO4, and Cs2(UO2)Ti2O6 gave insights into the crystallographic model improvement of very heavy atoms. We found that the values for the dispersive and absorptive parts, f′ and f″, closely followed the X-ray absorption spectra on their L3, L2, and L1 edges. The obtained values are sensitive to the chemical environment at each crystallographically independent position. An incorrect treatment of the anomalous dispersion correction can lead to a wrong crystallographic model. The above-mentioned, already published structures were improved by this process. General guidelines were given for the crystal structure …

Unraveling The Role Of Hid-1: Insights Into Sgii Regulation, Breanna L. Sellers

Electronic Theses and Dissertations

The regulated secretory pathway is important for the secretion of hormones and neuropeptides from large dense core vesicles (LDCVs). Dysregulation of the biogenesis of LDCVs can result in metabolic and neurological diseases. Recent studies have suggested that the peripheral membrane protein HID-1 plays a role in the sorting and storage of granins which contribute to LDCV biogenesis. To further understand how HID-1 influences the regulation of granins, we investigated potential HID-1 interactors. We determined that while HID-1 is likely functioning in the same pathway as USP25, a deubiquitinating enzyme (DUB), the cause of reduced cellular SgII levels is likely not …

Sequence Specificity Of Non-Structural Protein 15 From Sars-Cov-2, John Vincent Mcguire

Electronic Theses and Dissertations

The SARS-CoV-2 virus was recently able to cause a global pandemic, largely due to the asymptomatic period that occurs during initial infection. During this period, patients are infectious but do not exhibit symptoms, resulting in the unintentional spread of the virus. This occurs because the virus effectively avoids detection by the immune system during the early stages of infection, and as symptoms are the result of immune system activation, they never manifest. Non-structural Protein 15 (Nsp15) is one of the tools the virus uses to remain undetected, via its degradation of Pathogen-Associated Molecular Patterns (PAMPs) that would otherwise be recognized …

Soft Sets Extensions: Innovating Healthcare Claims Analysis, Daniela Gifu, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In the dynamic arena of healthcare research, where the complexities of data often rival the intricacies of biological systems, the ability to model and analyze such multifaceted datasets is crucial. This comprehensive review delves into the evolution and application of Soft Sets and their extensions, including HyperSoft Sets, SuperHyperSoft Sets, IndetermSoft Sets, IndetermHyperSoft Sets, and TreeSoft Sets, in healthcare claims data analysis.

Molecular Docking, Pharmacological Profiling, And Molecular Dynamics Simulation Of Potential Antihyperuricemic Agent From Secondary Metabolites Of Dillenia Philippinensis Rolfe (Dilleniaceae), Louie Rince C. Suyo, John P. Paulin, Nicole Clarence Louise L. Gapaz, Markus Brent S. Arevalo, Vince Tyrell P. Yongco, Librado A. Santiago

Karbala International Journal of Modern Science

Crystal accumulation in the joints due to increased serum uric acid (sUA) may lead to an inflammatory condition called gout. Increased sUA is caused by the excessive reabsorption of the urate anion transporter-1 (URAT-1). Therefore, URAT-1 inhibition will promote uric acid excretion and reduce the risk of having gout. Dillenia philippinensis Rolfe, often known as katmon, is an endemic plant in the Philippines with bioactive compounds associated with several therapeutic benefits. The present study represents the first scientific inquiry into the antihyperuricemic potential of compounds isolated from D. philippinensis. This study aimed to assess the interaction of URAT-1 with …

Structural Basis For Substrate Binding And Selection By Human Mitochondrial Rna Polymerase, Karl Herbine, Ashok Nayak, Dmitry Temiakov

Department of Biochemistry and Molecular Biology Faculty Papers

The mechanism by which RNAP selects cognate substrates and discriminates between deoxy and ribonucleotides is of fundamental importance to the fidelity of transcription. Here, we present cryo-EM structures of human mitochondrial transcription elongation complexes that reveal substrate ATP bound in Entry and Insertion Sites. In the Entry Site, the substrate binds along the O helix of the fingers domain of mtRNAP but does not interact with the templating DNA base. Interactions between RNAP and the triphosphate moiety of the NTP in the Entry Site ensure discrimination against nucleosides and their diphosphate and monophosphate derivatives but not against non-cognate rNTPs and …

Informatics-Based Discovery Of New Natural Products, Their Biosynthesis, And Their Biological Roles, Ethan Older

Theses and Dissertations

In this work, genome mining and biosynthetic knowledge are applied for the discovery of new natural products, their biosynthetic pathways, and their promising biological activities and roles through the development of two unique new informatics-based approaches.

In chapter one, an overview of microbial natural product biological functions and biosynthesis is provided. The use of bioinformatics leveraging microbial natural product biosynthetic knowledge is also introduced. This chapter highlights the importance and need for developing innovative approaches to accessing microbial natural products, a vastly untapped source of new molecules with promising biological activities.

In chapter two, a correlational network linking the gene-encoded …

Absolute Quantification Of Human Myosin And Titin Isoforms In Disease By A Mass Spectrometry Approach, Nitha Aima Muntu

Master's Theses

Heart failure (HF) is the leading cause of death worldwide and produces an immense economic burden. Dilated cardiomyopathy (DCM), characterized by contractile weakness and chamber dilation, is a significant cause of HF. The sarcomeric proteins play a crucial role in regulating the contractile properties of the heart. As the primary motor protein, the expression of cardiac myosin isoforms (α-MHC and β-MHC) dictates the performance and cardiac energy utilization of the sarcomere. Titin is the giant spring protein in the sarcomere, and titin isoform expression impacts the passive stiffness of the myocardium. Small changes in the α-MHC/β-MHC and titin isoform ratios …

Investigating The Oncogenic Role Of Nkx3.1 In Prostate Cancer, Audris Budreika

Master's Theses

Prostate cancer is a unique disease in that it is fueled by androgen receptor (AR) signaling. In the clinic, AR signaling is disrupted by removing androgens via chemical castration and employing AR-antagonists such as enzalutamide. Unfortunately, these therapies are short-lived, resistance sets in, and tumors evolve to a form of the disease called castration-resistant prostate cancer (CRPC). At this stage, therapeutic options are virtually exhausted and palliative care is pursued. There is a growing need to characterize other molecular players that cooperate with AR or play a unique role in CRPC on their own. One such potential candidate is the …

Quantification Of Immunometabolite Derived Protein Modifications During Mitochondrial Metabolic Stress, Justin Hunter Cox

Theses and Dissertations

The immunometabolite itaconate accumulates during lipopolysaccharide (LPS) stimulation of macrophages and microglia. Itaconate non-enzymatically reacts with cysteine residues to generate 2,3-dicarboxypropylcysteine (2,3-DCP), referred to as protein dicarboxypropylation. The tricarboxylic acid (TCA) cycle metabolite fumarate non-enzymatically reacts with the amino acid cysteine to form S-(2-succino)-cysteine (2SC), resulting in irreversible protein succination. Since fumarate and itaconate levels dynamically change in activated immune cells, the levels of both 2SC and 2,3-DCP reflect the abundance of these metabolites and their capacity to modify protein structure and function. I generated esters of 2SC and 2,3-DCP from protein hydrolysates and used stable isotope dilution liquid chromatography-tandem …

Design Of An Artificial Transcription Factor For Inducing Potent Interferon-Γ Signals, Ashley King

Theses and Dissertations

Cytokines are small immune signaling proteins responsible for cellular communication and their levels are tightly regulated throughout immune recognition and defense. Interferon gamma is a key cytokine responsible for upregulation of antigen presentation and supports the differentiation of pro-inflammatory effector cells. Due to its role in regulation, excess interferon gamma is cleared from the body limiting the success of interferon gamma immunotherapies. This study reports the design and validation of an artificial transcription factor (ATF) that induces endogenous interferon gamma expression. The transcription factor contains zinc finger proteins to recognize the interferon gamma gene and an activation domain to promote …

Characterizing The Role Of The Escherchia Coli Monothiol Glutaredoxin, Grxd, As An Iron-Sulfur Cluster Carrier Protein, Claire Elizabeth Fisher

Theses and Dissertations

Iron-sulfur (Fe-S) clusters are important cofactors with a primary role of electron transport that are required by proteins involved in wide range of biological pathways such as respiration, photosynthesis, and DNA repair. In Escherichia coli (E. coli), the assembly and transfer of these clusters to their target apo-protein is a highly coordinated process encoded by the multiprotein systems iscRSUAhscBAfdx and sufABCDSE operons. These clusters are assembled on a scaffold protein, where they are then transferred to a carrier protein that will deliver the cluster to the target apo-protein. The Isc and Suf systems contain their own carrier proteins IscA …

Investigation Of P27 Tumor Suppressor Gene (Cdkn1b) Polymorphisms In Dogs With Malignant Mammary Tumors, Gizem Kırmızıoğlu, Iraz Akış

The Thai Journal of Veterinary Medicine

Mammary tumors are the most common neoplasm in dogs, with a high mortality rate. The development of canine mammary tumors (CMT) is multifactorial, but different incidence rates between breeds suggest the effects of genetic risk factors. Many CMT-associated candidate genes were reported, mainly involved in cell cycle control. This study aims to investigate p27 tumor suppressor gene polymorphisms in dogs with mammary tumors and analyze the association between variations and CMTs. For this purpose, case and control groups were formed from 22 dogs diagnosed with malignant mammary tumors and 10 dogs with healthy mammary glands. The whole canine p27 gene …

Assimilating Satellite-Derived Snow Cover And Albedo Data To Improve 3-D Weather And Photochemical Models, Colleen Jones, Huy Tran, Trang Tran, Seth Lyman

Chemistry and Biochemistry Faculty Publications

During wintertime temperature inversion episodes, ozone in the Uinta Basin sometimes exceeds the standard of 70 ppb set by the US Environmental Protection Agency. Since ozone formation depends on sunlight, and less sunlight is available during winter, wintertime ozone can only form if snow cover and albedo are high. Researchers have encountered difficulties replicating high albedo values in 3-D weather and photochemical transport model simulations for winter episodes. In this study, a process to assimilate MODIS satellite data into WRF and CAMx models was developed, streamlined, and tested to demonstrate the impacts of data assimilation on the models’ performance. Improvements …

Macromolecular Crowding Effects On Enzymes That Display Non-Hyperbolic Kinetics, Kelsey A. Aldrich

Electronic Theses and Dissertations

Macromolecules occupy up to 30% of a cell's volume, yet the in vitro study of biological processes is almost exclusively performed in dilute solutions that fail to approximate the crowded interior of a cell. A growing body of literature has identified that macromolecular crowding has significant effects on a number of biochemical processes, including enzymatic activity. However, changes in kinetic parameters with increased macromolecule concentrations have only been determined for enzymes that follow hyperbolic Michaelis-Menten kinetics, despite the fact that over 25% of enzymes deviate from this model. Here, we perform the first characterization of macromolecular crowding effects on …

Rna Secondary Structures: Structure-Function Studies In Viral And Neurodegenerative Diseases, Caylee Cunningham

Electronic Theses and Dissertations

The studies within this dissertation highlight the importance of RNA structure and function, highlighting potential mechanisms in the pathogenesis of the SARS-CoV-2 virus and hallmarks of ALS. Specifically, the s2m, a 41-nt structure found within the hyper variable region of the 3’ UTR of the SARS-CoV-2 virus, was investigated as this element has no definitive role in viruses but its high conservation in several viral families warrants investigation. We used various biophysical techniques to determine if a palindromic sequence in the terminal loop could participate in dimerization activities, which may have implications in recombination and the longevity of the virus. …

Role Of Pycr2 In Colorectal Cancer, Raju Lama Tamang

Theses & Dissertations

Despite significant progress in clinical management, colorectal cancer (CRC) remains the 3rd most common cause of cancer-related deaths. A positive association of PYCR2 (Pyrroline-5-carboxylate reductase-2), a terminal enzyme of proline metabolism, with CRC aggressiveness was recently reported including by us. However, how PYCR2 promotes colon carcinogenesis remains ill understood. In our studies, comprehensive in-silico and biochemical evaluations were performed along with genetic manipulations and in-vivo tumor growth assays to gain mechanistic understanding. Results showed that PYCR2 expression was significantly upregulated in CRC and associated with poor patient survival specifically among PYCR isoforms (PYCR-1, -2 and -3). Genetic inhibition of PYCR2 …

Determining If Cx45 Acts As An Arrythmogenic Substrate In The Diseased Myocardium, Stephen R. Sobota

Theses & Dissertations

Proper contraction of the heart relies on gap junction channels (GJCs) composed of Cx40 and Cx43 in the atrial and ventricular tissues which mediate electrical conductance in the working myocardium. Also expressed is Cx45, which is limited to the pacemaker system. Studies in diseased human hypertrophic cardiac tissue have shown expression of Cx45 and decrease of Cx43 in the myocardium. Cx43 and Cx45 in vitro form heterometric GJCs, where the channel characteristics (metabolite transfer, electrical conductance, etc.) resemble those of Cx45. There is little-to-no data showing whether GJCs composed of Cx43 and Cx45 in cardiac hypertrophy result in altered conductance. …

Enpp1 Enzyme Replacement Therapy Improves Ectopic Calcification But Does Not Rescue Skeletal Phenotype In A Mouse Model For Craniometaphyseal Dysplasia, Ernst Reichenberger, Kevin O'Brien, Ayano Hatori, Thomas Carpenter, Koen Van De Wetering, Lisa Flaman, Jennifer Howe, Daniel Ortiz, Yves Sabbagh, I-Ping Chen

Jefferson Institute of Molecular Medicine Papers and Presentations

Craniometaphyseal dysplasia (CMD) is a rare genetic bone disorder, characterized by progressive thickening of craniofacial bones and flared metaphyses of long bones. Craniofacial hyperostosis leads to the obstruction of neural foramina and neurological symptoms such as facial palsy, blindness, deafness, or severe headache. Mutations in ANKH (mouse ortholog ANK), a transporter of small molecules such as citrate and ATP, are responsible for autosomal dominant CMD. Knock-in (KI) mice carrying an ANK_F377del mutation (Ank^KI/KI) replicate many features of human CMD. Pyrophosphate (PPi) levels in plasma are significantly reduced in Ank^KI/KI mice. PPi is a potent inhibitor of …

Exploring The Role Of Rb1 In Cellular Differentiation Using Patient-Derived Stem Cells, Ambily Vincent

Theses and Dissertations

The Retinoblastoma (RB1) gene, predominantly recognized as a tumour suppressor, plays a crucial role in early growth and development. Mice lacking the retinoblastoma gene do not survive and exhibit defects in the differentiation of various tissues, underscoring its involvement in cellular differentiation. This suggests that the functions of the RB1 gene extend beyond its role as a tumour suppressor, encompassing cell cycle regulation, maintenance of genomic stability, cellular senescence, and cellular differentiation.

While the tumour suppressor function of the RB1 has been extensively studied, its role in cellular differentiation remains incompletely understood. Existing literature, primarily based on animal models, has …

Lysineless Hibit And Nanoluc Tagging Systems As Alternative Tools For Monitoring Targeted Protein Degradation, Hanfeng Lin, Kristin Riching, May Poh Lai, Dong Lu, Ran Cheng, Xiaoli Qi, Jin Wang

Faculty, Staff and Students Publications

Target protein degradation (TPD) has emerged as a revolutionary approach in drug discovery, leveraging the cell’s intrinsic machinery to selectively degrade disease-associated proteins. Nanoluciferase (nLuc) fusion proteins and the NanoBiT technology offer two robust and sensitive screening platforms to monitor the subtle changes in protein abundance induced by TPD molecules. Despite these advantages, concerns have arisen regarding potential degradation artifacts introduced by tagging systems due to the presence of lysine residues on them, prompting the development of alternative tools. In this study, we introduce HiBiT-RR and nLucK0, variants devoid of lysine residues, to mitigate such artifacts. Our findings demonstrate that …

Stem-Loop And Circle-Loop Tads Generated By Directional Pairing Of Boundary Elements Have Distinct Physical And Regulatory Properties, Wenfan Ke, Miki Fujioka, Paul Schedl, James Jaynes

Department of Biochemistry and Molecular Biology Faculty Papers

The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation-dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary …

Integration Of Machine Learning And Quantum Mechanical Calculations For De Novo Drug Design, Ayesh Madushanka Mahamada Kalapuwage

Chemistry Theses and Dissertations

The drug designing process is an intricate and resource-intensive endeavor, spanning approximately 12 years to transform a lead compound into a functional drug. Computer-aided drug design (CADD) plays a fundamental role in this process, mitigating the risk of failures in the later stage and saving valuable time and money. In the last decade, Artificial intelligence (AI) has provided remarkable alternatives for practical challenges, including drug design. Simultaneously, advanced QM calculations have achieved near-experimental accuracy in simulating drug-target interactions. However, introducing QM and AI-based techniques into drug discovery presents considerable challenges. AI techniques require high- quality data and often struggle with …

Assessment Of Tripeptides Self-Assembly & Er Stress On Cell Viability And Exosome Secretion In Mda-Mb231, Azmat Parveen

Theses and Dissertations

This study delves into the effects of tripeptides KYpF and WYpK(NBD) on MDA-MB-231 cells, uncovering KYpF's ability to reduce cell proliferation and exosome secretion in peptide treated cells. Conversely, WYpK(NBD) demonstrated significant toxicity at 10 μM. These insights pave the way for optimizing peptide-based cellular treatments for exosome secretion purposes.

G12/13 Signaling In Asthma, Elizabeth L. Mcduffie, Reynold A Panettieri, Charles P. Scott

Department of Biochemistry and Molecular Biology Faculty Papers

Shortening of airway smooth muscle and bronchoconstriction are pathognomonic for asthma. Airway shortening occurs through calcium-dependent activation of myosin light chain kinase, and RhoA-dependent calcium sensitization, which inhibits myosin light chain phosphatase. The mechanism through which pro-contractile stimuli activate calcium sensitization is poorly understood. Our review of the literature suggests that pro-contractile G protein coupled receptors likely signal through G12/13 to activate RhoA and mediate calcium sensitization. This hypothesis is consistent with the effects of pro-contractile agonists on RhoA and Rho kinase activation, actin polymerization and myosin light chain phosphorylation. Recognizing the likely role of G12/13 signaling in the pathophysiology …

Znf397 Deficiency Triggers Tet2-Driven Lineage Plasticity And Ar-Targeted Therapy Resistance In Prostate Cancer, Yaru Xu, Yuqiu Yang, Zhaoning Wang, Martin Sjöström, Yuyin Jiang, Yitao Tang, Siyuan Cheng, Su Deng, Choushi Wang, Julisa Gonzalez, Nickolas A Johnson, Xiang Li, Xiaoling Li, Lauren A Metang, Atreyi Mukherji, Quanhui Xu, Carla R Tirado, Garrett Wainwright, Xinzhe Yu, Spencer Barnes, Mia Hofstad, Yu Chen, Hong Zhu, Ariella B Hanker, Ganesh V Raj, Guanghui Zhu, Housheng H He, Zhao Wang, Carlos L Arteaga, Han Liang, Felix Y Feng, Yunguan Wang, Tao Wang, Ping Mu

Faculty, Staff and Students Publications

Cancer cells exhibit phenotypical plasticity and epigenetic reprogramming that allows them to evade lineage-dependent targeted treatments by adopting lineage plasticity. The underlying mechanisms by which cancer cells exploit the epigenetic regulatory machinery to acquire lineage plasticity and therapy resistance remain poorly understood. We identified zinc finger protein 397 (ZNF397) as a bona fide coactivator of the androgen receptor (AR), essential for the transcriptional program governing AR-driven luminal lineage. ZNF397 deficiency facilitates the transition of cancer cell from an AR-driven luminal lineage to a ten-eleven translocation 2 (TET2)-driven lineage plastic state, ultimately promoting resistance to therapies inhibiting AR signaling. Intriguingly, our …

The Role Of Efflux Pump Inhibitor In Enhancing Antimicrobial Efficiency Of Silver Nanoparticles And Methylene Blue As An Effective Photodynamic Therapy Agent, Yaran Allamyradov

Masters Theses & Specialist Projects

Efflux pumps are critical active transport systems utilized by cells to expel toxic substances, including antibiotics and photosensitizer complexes, thereby contributing to antimicrobial resistance. Efflux pump inhibitors (EPIs), which are compounds that obstruct the transport of molecules through these pumps, play a pivotal role in enhancing the effectiveness of antimicrobial therapies against pathogens. This study investigates the effects of the EPI reserpine on the photodeactivation rate of pathogens when used in conjunction with silver nanoparticles (Ag NPs) and methylene blue (MB), a common photosensitizer.

Our research reveals that the application of reserpine, in combination with Ag NPs and MB, leads …

Detection Of Cryptosporidium Spp. In Surface Water And Tissues Of Bivalves In Waterways Of Coney Island, New York (Usa), Manasvi Patel

Biochemistry and Molecular Biology

Combined sewer overflows (CSOs) are major sources of pollutants such as microbial pathogens, total suspended solids (TSS), oxygen depleting substances, toxicants, and nutrients. Untreated wastewater contains parasites like Giardia, Cryptosporidium and Entamoeba which impact human health. Cryptosporidium is the leading cause of diarrheal diseases which spreads through contaminated water supplies. Our research on Coney Island in Brooklyn investigated the amount of Cryptosporidium oocysts found in the water and bivalves/shellfish tissue and to supports a parallel study examining both people's use of waterways around Coney Island (for religious ceremonies, fishing, foraging, swimming, etc.) and their perceptions of how polluted the …

Furthering Ascidian Taxonomy Using Molecular Biology, Nicholas Gulnick

Electronic Theses and Dissertations

Ascidians are our closest invertebrate relatives and comprise nearly 3,000 species separated into three orders: Aplousobranchia (most speciose), Stolidobranchia, and Phlebobranchia (least speciose). Ascidians can be classified as either solitary or colonial organisms. Species delimitation using morphological characters alone has had varied results. Well known, widely distributed, morphological species have turned out to be catch all species comprised of several cryptic species. Molecular markers can help mitigate some of the issues presented by strictly using morphological observations, including resolving the status of cryptic species, and accessing the expert knowledge required to identify a species. By incorporating molecular markers and pairing …