Biochemistry, Biophysics, and Structural Biology Commons^™

The Effect Of Age On The Mating Call Of The Tungara Frog, Zaizhen Xu

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

A Proteomic Analysis To Identify Changes In Bacterial Protein Expression Following Overexpression Of A Spider Silk Protein, Jamie (Ju Yeon) Park, Jaeyoung (Kate) Lee, David Chanyang Eum, Minji Jung, Sungkyung Lee

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Proteomic Analysis Of The Expression Of Masp1 Dragline Silk Protein In E. Coli, Sophie Rae Pazzo, Rajan Amit Patel, Kamrin Athwal, Edward Kim

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

The Role Of Npun_F0875 In Hormogonium Development And Motility, Daniel Sepulvida, Austin Wong

Pacific Undergraduate Research and Creativity Conference (PURCC)

No abstract provided.

Extracting Dna From Embalmed Tissue To Study Genetic Predisposition To Degenerative Disc Disease, Conner Lynn

Undergraduate Theses

INTRODUCTION. According to a prominent study, 80-90% of people will show some evidence of degenerative disc disease (DDD) by age 50. Researchers have proposed that a Q326W substitution in the COL9A2 gene increases susceptibility to DDD. The role of collagen IX in intervertebral discs is not completely known, but due to its increased flexibility compared to other types of collagens, it is thought to connect collagen II with other components of the cartilage which are important to the integrity of the disc. Collagen II can be found within the nucleus pulposus and the inner portion of the annulus fibrosis. Researchers …

Computational Investigations Into Binding Dynamics Of Tau Protein Antibodies: Using Machine Learning And Biophysical Models To Build A Better Reality, Katherine Lee

University Scholar Projects

Misregulation of post-translational modifications of microtubule-associated protein tau is implicated in several neurodegenerative diseases including Alzheimer’s disease. Hyperphosphorylation of tau promotes aggregation of tau monomers into filaments which are common in tau-associated pathologies. Therefore, tau is a promising target for therapeutics and diagnostics. Recently, high-affinity, high-specificity single-chain variable fragment (scFv) antibodies against pThr-231 tau were generated and the most promising variant (scFv 3.24) displayed 20-fold increased binding affinity to pThr-231 tau compared to the wild-type. The scFv 3.24 variant contained five point mutations, and intriguingly none were in the tau binding site. The increased affinity was hypothesized to occur due …

Design, Synthesis, And Analysis Of Paired Coiled-Coil Peptidic Molecular Building Blocks Used For Linearly Controlled Self-Assembly Of Α-Helical Coiled-Coil Heterodimer Peptide Pairs, Jason Distefano

Chemistry Theses

Molecular building blocks are fundamental to biological synthesis and processes and have been utilized in advanced materials, drugs and drug delivery systems, and biotechnology. Proteins have been used as molecular building blocks for the construction of complex, well-ordered structures. Coiled-coil protein domains are essential subunits used for the oligomerization of protein complexes, gene expression, and structural elements of biological materials. The synthesis and assembly of proteins utilizing coiled-coil motifs are of great scientific interest due to their potential applications in disease treatment, biomechanical motors, nanoscale delivery systems, etc. However, assembling protein complexes with specific morphology is still challenging because …

Halogen Bonding: A Computational Chemistry Investigation Of The Interaction Between Thyroid Hormone And Deiodinase, William Rice

Honors Theses

Halogen bonding is a noncovalent interaction that continues to garner interest among the scientific community. Investigation of halogen bonds in biological contexts typically revolves around rational drug design for developing therapeutics. However, halogen bonding may be occurring naturally in our body every day. Thyroid hormone and its regulating enzyme, iodothyronine deiodinase, show promising results for a halogen bonding interaction that happens during catalysis. Prior work has examined the interaction between the iodine of thyroid hormone and the selenium of iodothyronine deiodinase. However, this study is the first of its kind to use computational chemistry methods to analyze the halogen bond …

The Socioeconomic & Environmental Factors Influencing Prevalence Of Zoonotic Pathogens In Rats: A Meta-Analysis, Katelyn Wing

Honors Theses

Background/Question/Methods

Global rat populations are increasing at an alarming rate across the world. In turn, this increases the risk of human-rat interactions and the potential spread of zoonotic pathogens and parasites. Rats are the second most common host of disease and can have detrimental effects in urban ecosystems. Rattus rattus and R. norvegicus are the two most abundantly distributed species of rats and are the target organism for this study. The aim of this study is to understand the connection between environmental and socioeconomic factors that influence the rate of zoonotic disease in rats. We developed two hypotheses to gain …

The Role Of Free Radicals In The Activation Of Epidermal Growth Factor Receptors In Murine Microglial Cells, Eliana John

Honors Theses

Regulation of cellular processes is important for proper functioning. Environmental factors, including stress, can interfere with cellular regulation. One of the diseases caused by cellular regulation disturbance is cancer and mutations in EGF-related genes highly correlate with worse outcomes in cancer. The Epidermal Growth Factor (EGF) pathway is involved in the regulation of cell growth and differentiation. Phosphorylation of the receptors activates this pathway, leading to cell growth and regulation. This study examines the impact of oxidative stress on EGF pathway activation. Previous studies using breast cancer lines have indirectly shown a decrease in Epidermal Growth Factor Receptor (EGFR) activation …

Prenatal Exposure To A Climate-Related Disaster Results In Changes Of The Placental Transcriptome And Infant Temperament, Jessica Buthmann, Dennis Huang, Patrizia Casaccia, Sarah O'Neill, Yoko Nomura

Advanced Science Research Center

Maternal stress during pregnancy exerts long-term effects on the mental well-being of the offspring. However, the long-term effect of prenatal exposure on the offspring’s mental status is only partially understood. The placenta plays a vital role in connecting the maternal side to the fetus, thereby serving as an important interface between maternal exposure and fetal development. Here, we profiled the placental transcriptome of women who were pregnant during a hurricane (Superstorm Sandy), which struck New York City in 2012. The offspring were followed longitudinally and their temperament was assessed during the first 6–12 months of age. The data identified a …

Exploring Indicator Displacement Assays For Phosphate Detection In Seawater, Francis Radics

Chemistry & Biochemistry Student Scholarship

Francis Radics ’22
Major: Biochemistry
Faculty Mentor: Dr. John Breen, Chemistry and Biochemistry

Indicator displacement assays are based on the optical signal modulation of a noncovalently bound indicator upon dissociation by an analyte species. Our work has focused on exploring the lower detection limits for luminescent displacement assays for inorganic phosphate in seawater using complex ions containing two di(2-picolyl)amine ligands (also called DPA or bis(2-pyridylmethyl)amine), each coordinating a zinc cation. Following the work of B.D. Smith and coworkers, we have prepared three ligands by covalently attaching two DPA moieties, 2,6-bis(chloromethyl) benzene, and 2,6-bis(chloromethyl)-4-methylphenol, and 1,2-phenylenedimethylamine, for assays with 6,7-dihydroxy-4-methanesulfonic acid …

Investigation Of Cotinine Concentration Found In Saliva Of Smokers And Vapers In Demographic Sectors, Seth A. Sims

Honors Theses

A simple and reproducible method for investigation of cotinine and nicotine levels in saliva was developed by utilizing gas chromatography mass spectrometry (GCMS) and simple extraction techniques. This method allowed for accurate detection of cotinine in saliva samples collected within a 50-mile radius of Searcy, AR. The observed cotinine levels proportionately depict nicotine levels, which were then compared with participants’ demographics, displaying trends among different communities. This research hopes to provide insight into vaping popularity as well as a reproducible method that future research can utilize.

A Patient-Derived Ipsc Model To Study Glutamate Deficiency By Shank-3 Mutation In Autism Spectrum Disorder, Tiffany Berry, Courtney Caccia

Biology Student Scholarship

Tiffany Berry ’22, Majors: Biology and Psychology

Courtney Caccia ’22, Majors: Biology and Psychology

Faculty Mentor: Dr. Charles Toth, Biology

The use of human stem cell lines derived from persons with Autism Spectrum Disorder (ASD) provides a unique opportunity to model brain growth and potential to regain brain activity for treatment. Our lab has previously used stem cells to derive 3D cardiomyocytes to examine cardiovascular disease as well as kidney organoids and macrophages to study kidney disease. Using techniques our lab has learned using these stem cell models have prepared us to examine cell communication in mutated neurons. We will …

The Discovery And Analysis Of Mycobacteriophage “Rita”, Anna Fakhri

Chemistry & Biochemistry Student Scholarship

Anna Fakhri ’24
Major: Biochemistry
Faculty Mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Mycobacteriophage “Rita” was isolated on Mycobacterium smegmatis mc2155 from an enriched soil sample from North Easton, Massachusetts. As Rita infects Mycobacterium smegmatis, further study of the phage was completed in order to determine its ability to be utilized in phage therapy for infections caused by pathogenic Mycobacterium, such as Mycobacterium tuberculosis and Mycobacterium abscessus. Once isolated, the phage DNA was analyzed through PCR to determine the phage belonged to cluster F and subcluster F1. The phage DNA was sequenced, and a genome annotation was completed. The annotation …

Evaluating Alternative Ebullition Models For Predicting Peatland Methane Emission And Its Pathways Via Data–Model Fusion, Shuang Ma, Lifen Jiang, Rachel M. Wilson, Jeff P. Chanton, Scott Bridgham, Shuli Niu, Colleen M. Iversen, Avni Malhotra, Jiang Jiang, Xingjie Lu, Jason Keller, Xiaofeng Xu, Daniel M. Ricciuto, Paul J. Hanson, Yiqi Luo

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Understanding the dynamics of peatland methane (CH₄) emissions and quantifying sources of uncertainty in estimating peatland CH₄ emissions are critical for mitigating climate change. The relative contributions of CH₄ emission pathways through ebullition, plant-mediated transport, and diffusion, together with their different transport rates and vulnerability to oxidation, determine the quantity of CH₄ to be oxidized before leaving the soil. Notwithstanding their importance, the relative contributions of the emission pathways are highly uncertain. In particular, the ebullition process is more uncertain and can lead to large uncertainties in modeled CH₄ emissions. To improve model simulations …

Alzheimer's Disease: A Comprehensive Review Including Personal Experience From Retirement Home Patients, Sydney Fox

Honors Theses

Alzheimer’s Disease is a neurodegenerative illness and disease, the most common type of dementia, and the sixth leading cause of death (Sá et al., 2012). The disease was discovered in 1906 and named after Dr. Alois Alzheimer, a psychiatrist and neuropathologist. Over time, a variety of hypotheses have developed regarding the cause behind this multifactorial disease, and these will be disclosed in a later section. Nonetheless, the disease was first observed in changes of the brain tissue of a woman who was said to have die from an unusual mental illness with many abnormal bumps. These bumps are now recognized …

Foldamers Reveal And Validate Therapeutic Targets Associated With Toxic Α-Synuclein Self-Assembly, Jemil Ahmed, Tessa C. Fitch, Courtney M. Donnelly, Johnson A. Joseph, Tyler D. Ball, Mikaela M. Bassil, Ahyun Son, Chen Zhang, Aurélie Ledreux, Scott Horowitz, Yan Qin, Daniel Paredes, Sunil Kumar

Chemistry and Biochemistry: Faculty Scholarship

Parkinson’s disease (PD) is a progressive neurodegenerative disorder for which there is no successful prevention or intervention. The pathological hallmark for PD involves the self-assembly of functional Alpha-Synuclein (αS) into non-functional amyloid structures. One of the potential therapeutic interventions against PD is the effective inhibition of αS aggregation. However, the bottleneck towards achieving this goal is the identification of αS domains/sequences that are essential for aggregation. Using a protein mimetic approach, we have identified αS sequences-based targets that are essential for aggregation and will have significant therapeutic implications. An extensive array of in vitro, ex vivo, and in vivo assays …

Evaluating Alternative Ebullition Models For Predicting Peatland Methane Emission And Its Pathways Via Data–Model Fusion, Shuang Ma, Lifen Jiang, Rachel M. Wilson, Jeff P. Chanton, Scott Bridgham, Shuli Niu, Colleen M. Iversen, Avni Malhotra, Jiang Jiang, Xingjie Lu, Yuanyuan Huang, Jason Keller, Xiaofeng Xu, Daniel M. Ricciuto, Paul J. Hanson, Yiqi Luo

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Understanding the dynamics of peatland methane (CH4) emissions and quantifying sources of uncertainty in estimating peatland CH4 emissions are critical for mitigating climate change. The relative contributions of CH4 emission pathways through ebullition, plant-mediated transport, and diffusion, together with their different transport rates and vulnerability to oxidation, determine the quantity of CH4 to be oxidized before leaving the soil. Notwithstanding their importance, the relative contributions of the emission pathways are highly uncertain. In particular, the ebullition process is more uncertain and can lead to large uncertainties in modeled CH4 emissions. To improve model simulations of CH4 emission and its pathways, …

Characterization Of Immunity Systems In A Cluster Phages, Katherine Cleary

Chemistry & Biochemistry Student Scholarship

Katherine Cleary ’23
Major: Biochemistry
Faculty Mentor: Dr. Kathleen A. Cornely, Chemistry and Biochemistry

Bacteriophages are viruses that infect bacteria. Bacteriophages may use two different cycles to infect their hosts, which are the lytic cycle and the lysogenic cycle. During the lysogenic cycle, the phage genome integrates into the bacteria chromosome and becomes a part of the host. If a phage remains in the lysogenic cycle, the host is susceptible to infection from other bacteriophages. This process is known as superinfection and it can have a variety of outcomes. Homoimmunity occurs when the phages have similar repressor proteins. Heteroimmunity occurs …

Eukaryotic Initiation Factor 4e (Eif4e) In Complex With Eif4e Binding Protein 1 (4e-Bp1) Binds With Higher Affinity To M7gpppn Cap Of A Subset Of Human Mrnas, Izza F. Nawaz

Theses and Dissertations

Fluorescence anisotropy binding assays were used to analyze the binding of eIF4E in complex with 4E-BP1 onto the 5’ m7G cap of a subset of mRNA that are known to carry cap-independent translation. These studies suggest that 4E-BP1 increases eIF4E binding affinity to 5’cap of both FGF-9 and HIF-1𝝰.

The Various Nervous System Drugs Commonly Used For Treatment And The Disparities In Availability Of These Drugs In Minority Groups, Iman Haurami

Honors Scholars Collaborative Projects

The nervous system is a complex network in our body that is responsible for actions, reflexes, and even sensations. With the brain being part of the CNS, many common nervous system disorders are due to a defect in the central nervous system and the functions of this organ. These disorders include mental health problems, degenerative diseases, seizures, infections, and other possible genetic diseases. Many of these diseases are common in society and constantly researched. Even though these diseases are common, treatment accessibility and effects on people of minority groups are overlooked compared to the focus on majority groups. For drug …

Targeting Platelets Using Ionic Liquid Coated Nanoparticles, Karen Mun Wong

Honors Theses

Platelets are key players in our body’s inflammatory processes upon activation, which can create physiological problems. Researchers are actively seeking solutions by targeting platelets with therapeutics. The objective of the research in this thesis was to investigate a new and potentially less invasive drug delivery platform using nanoparticles. The topic of the project was to explore the world of ionic liquids and their abilities, when coated on nanoparticles, to bind to platelets. A library of choline carboxylic acid-based ionic liquids (ILs) was first synthesized via salt metathesis while PLGA-based nanoparticles were simultaneously being synthesized via the nanoprecipitation method. The ionic …

Effects Of Seasonal Variation Of Abiotic Factors On Edna Detection Of Two Groundwater Crayfish Species, Jared Prine Higgs

Honors Capstone Projects and Theses

No abstract provided.

Using Integrated Rate Equations To Analyze Acid Phosphatase Kinetics, Melissa Gouge

ONU Student Research Colloquium

In an academic setting, enzyme kinetics are introduced by analysis of the initial rates using the Michaelis-Menten model. To better understand enzyme kinetics, a complete time course analysis will provide a larger set of data, including information on feedback or product inhibition. With this, the Lambert W function can be used to analyze the integrated rate equations. We have started our analysis with the enzyme, acid phosphatase. Inorganic phosphorus is a known competitive inhibitor of the acid phosphatase catalyzed hydrolysis of p-nitrophenylphosphate. Using the integrated form of the rate equation allows us to determine the relative relationship of the K …

Fast Photochemical Oxidation And Footprinting Of Proteins Via Trifluoromethyl Radical Chemistry, Elaine Morrow

Honors Theses

Fast photochemical oxidation of proteins (FPOP) is a useful tool in proteomics because of the ability for modifications to occur on the scale of microseconds which reduces the modifications to tertiary and quaternary structure allowing for more accurate labeling of the protein. Labels for FPOP are generated from various radicals in our experiments which include hydroxyl radicals and trifluoromethyl radicals. Hydroxyl radicals are easily generated by using an excimer laser (KrF laser, 248 nm) or a UV flash lamp (as a part of the Fox™ System) by the photolysis of hydrogen peroxide. Trifluoromethyl radicals, however, need hydroxyl radicals to be …

Eukaryotic Initiation Factor 4f Promotes A Reorientation Of Eukaryotic Initiation Factor 3 Binding On The 5 And The 3 Utrs Of Barley Yellow Dwarf Virus Mrna, Paul Powell, Usha Bhardwaj, Dixie Goss

Publications and Research

Viral mRNAs that lack a 5 m 7 GTP cap and a 3 poly-A tail rely on structural elements in their untranslated regions (UTRs) to form unique RNA-protein complexes that regulate viral translation. Recent studies of the barley yellow dwarf virus (BYDV) have revealed eukaryotic initiation factor 3 (eIF3) plays a significant role in facilitating communication be- tween its 5 and 3 UTRs by binding both UTRs simultaneously. This report uses in vitro translation assays, fluorescence anisotropy binding assays, and selective 2 -hydroxyl acylation analyzed by primer ex-tension (SHAPE) footprinting to identify secondary structures that are selectively interacting with eIF3. …

Protein Engineering Of A Spectroscopic Probe Into Malate Dehydrogenase (Mdh), Equoia S. Gibson, Mary E. Ludwig, Olivia H. Thompson, Genevieve M. Woods, Ella M. Young

Celebrating Scholarship and Creativity Day (2018-)

Malate dehydrogenase (MDH) is an enzyme that has a key role in biological processes, like the Krebs cycle. Specifically, it reversibly catalyzes the interconversion of (S)-malate with NAD+ to oxaloacetate and NADH. Once oxaloacetate is synthesized, MDH dispatches it to citrate synthase, but it is not clear how this happens. One theory is that MDH channels it to citrate synthase by forming a metabolon, a mechanism for direct channeling, preventing diffusion of reaction intermediates into a bulk matrix. There is a lack of research in this area due to the absence of a spectroscopic probe necessary to visualize MDH’s conformational …

Biochemical Analysis Of Biofilm Formation In Response To Changes In Concentrations Of D-Alanine, Jasmin Cruz, Akeisha Belgrave, Erica Ward

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

This project involves the biochemical analysis of biofilm formation in response to changes in concentration of D-alanine. I hypothesized that an increase in D-alanine concentration increases the ability for cells to make more cross-links, which increases the viability of bacteria allowing them to make more biofilms. The experiment done showed no significant difference in cell density between four treatment conditions. (Independent Research)

Bci Validation: Yfiler Plus Kit Validation, Chloe Koon

Honors Projects

In order to have access and use the Combined DNA Index System (CODIS), it is required by the Federal Bureau of Investigation's Quality Assurance Standards (FBI-QAS) for Forensic DNA Units to complete comprehensive validation studies on all equipment, materials, and methods used in the process of DNA analysis. This study continues validation previous done within the Ohio Bureau of Criminal Investigation (BCI). YFiler Plus is a DNA amplification kit that is used in cases where it is most useful to examine only male DNA profile(s) within a sample by amplifying loci only on the Y-Chromosome. Components of this study include …