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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

The Effect Of Cysteine-Reactive Catechol Antioxidants On Alcohol Dehydrogenase As A Model For Oxidative Stress In Neurodegenerative Disease, Rachel Smith May 2019

The Effect Of Cysteine-Reactive Catechol Antioxidants On Alcohol Dehydrogenase As A Model For Oxidative Stress In Neurodegenerative Disease, Rachel Smith

Undergraduate Honors Theses

The cellular mechanisms underlying age-related neurodegeneration, especially in disease states, are poorly understood. Oxidative stress has been heavily implicated as one factor both produced by and contributing to the progression of neurodegenerative diseases such as Alzheimer’s disease. In particular, it can destroy a cell’s ability to produce energy through aerobic and anaerobic respiration, thus leading to the death of individual cells and brain tissues as a whole. This study focuses on the relationship between oxidative stress and energy production in disease states. In particular, we examine the ability of catechol molecules to take on pro-oxidative properties and modify ...


Efficacy Of Intranasal Administration: A Clinical Approach To Attention, Jacob Feldmann May 2018

Efficacy Of Intranasal Administration: A Clinical Approach To Attention, Jacob Feldmann

Undergraduate Honors Theses

Orexins are a class of neuropeptides that are associated with homeostatic functions, such as food intake, sexual behavior, and the sleep/wake cycle. Orexins also play a pivotal role in cognitive processes such as attention and memory. In the present experiment, we employed a visual attention task to assess the effects of intranasal administration of orexin A in rats. This task required the rats to discriminate between trials when a visual light was illuminated from trials when the light was not illuminated. We tested the efficacy of this administration technique to see its viability as a therapeutic in attention disorders ...


An Analysis Of Oxidative Damage To Lactate Dehydrogenase In Context Of Neurodegeneration And Catechol-Based Phenolic Antioxidant Chemistry, Lydia Boike Dec 2017

An Analysis Of Oxidative Damage To Lactate Dehydrogenase In Context Of Neurodegeneration And Catechol-Based Phenolic Antioxidant Chemistry, Lydia Boike

Undergraduate Honors Theses

Lactate dehydrogenase, a redox-active enzyme with five reactive cysteine residues, reversibly converts pyruvate to lactate during anaerobic glycolysis. In the case of certain disease states, when oxygen levels are low or increased oxidative stress damages mitochondrial respiration, cells must rely heavily on anaerobic glycolysis for ATP production. This is true of Alzheimer’s disease, Parkinson’s disease, ALS, and many cancers. Diseased cells upregulate anaerobic glycolytic enzymes - particularly LDH – to produce enough energy to survive. Upregulated LDH plays a key role because as it produces lactate, it also replenishes NAD+, allowing for high levels of glycolysis to continue uninterrupted. Despite ...


Beyond "Self-Eating": The Role Of The Pseudophosphatase Mk-Styx In Regulating Autophagy, Patrick Christian May 2017

Beyond "Self-Eating": The Role Of The Pseudophosphatase Mk-Styx In Regulating Autophagy, Patrick Christian

Undergraduate Honors Theses

Cells carry out their day to day functions through the cellular work horses, proteins. Proteins work together like bees in a hive, each having its own specific task to accomplish. This specificity creates a fine-tuned division of labor where different types of proteins work together, completing their own work for the overall functioning of the cell. This division of labor can be mapped out nicely with cellular pathways. One such pathway is the stress response pathway. One of the major “workers” in this pathway is MK-STYX [MAPK (mitogen-activated protein kinase) phosphoserine/threonine/tyrosine-binding protein]. MK-STYX is a pseudophosphatase, a member ...


Plateau Potential Fluctuations And Intrinsic Membrane Noise, Daniel Scott Borrus May 2017

Plateau Potential Fluctuations And Intrinsic Membrane Noise, Daniel Scott Borrus

Undergraduate Honors Theses

This thesis focuses on subthreshold membrane potential fluctuations in the plateau potentials of bistable neurons. Research involved with plateau potentials typically finds one of the resting membrane potentials to be more susceptible to voltage fluctuations. This difference in the amplitude of the membrane potential fluctuations is most often attributed to the voltage-dependent membrane conductance. Occasionally, however, the typically quieter resting membrane potential exhibits larger voltage fluctuations than the expected one. It has been proposed that this increased membrane potential noise is the result of the stochastic gating of the voltage-gated ion channels. In this thesis, we use a simple bistable ...


Metabolism And Oxidative Stress: Understanding The Role Of Reactive Cysteines In Pyruvate Kinase, Mary Cate Duff May 2017

Metabolism And Oxidative Stress: Understanding The Role Of Reactive Cysteines In Pyruvate Kinase, Mary Cate Duff

Undergraduate Honors Theses

Reactive oxygen species (ROS) play a critical role in intracellular signaling mechanisms. These small molecules initiate reversible, post-translational modifications of redox-sensitive proteins. Pyruvate kinase (PK) is a key glycolytic enzyme whose activity is modulated by ROS; oxidation inhibits its catalytic function through a reaction at a critical cysteine near the active site. PK’s central role in moderating glycolytic flux makes it highly regulated through both structural and allosteric effectors. This research explores the extent of cysteine modification of PK under various models of intracellular conditions. PK was treated with oxidants and allosteric regulators, and changes in the enzyme’s ...


Metabolism And Oxidative Stress: Understanding The Role Of Reactive Cysteines In Pyruvate Kinase, Mary Cate Duff May 2017

Metabolism And Oxidative Stress: Understanding The Role Of Reactive Cysteines In Pyruvate Kinase, Mary Cate Duff

Undergraduate Honors Theses

Reactive oxygen species (ROS) play a critical role in intracellular signaling mechanisms. These small molecules initiate reversible, post-translational modifications of redox-sensitive proteins. Pyruvate kinase (PK) is a key glycolytic enzyme whose activity is modulated by ROS; oxidation inhibits its catalytic function through a reaction at a critical cysteine near the active site. PK’s central role in moderating glycolytic flux makes it highly regulated through both structural and allosteric effectors. This research explores the extent of cysteine modification of PK under various models of intracellular conditions. PK was treated with oxidants and allosteric regulators, and changes in the enzyme’s ...


Optogenetic Investigations Of The Prebötzinger Complex: Support For The Dbx1 Core Hypothesis, Francis D. Pham May 2017

Optogenetic Investigations Of The Prebötzinger Complex: Support For The Dbx1 Core Hypothesis, Francis D. Pham

Undergraduate Honors Theses

The preBötzinger complex (preBötC) is the central pattern generator for inspiratory behaviors. Previous studies on perinatal mice and in vitro suggest that Dbx1-derived neurons within the preBötC form the core oscillator. Here, we provide support for the Dbx1 core hypothesis and show that Dbx1-derived neurons are essential for respiratory rhythmogenesis in adult mice. Using optogenetic strategies, we transiently hyperpolarized Dbx1 neurons of the preBötC in vitro and in adult mice. In both cases, the inspiratory rhythm was disrupted. It is possible that axons from Dbx1 neurons projecting into the preBötC were also hyperpolarized, leading to disfacilitation. To determine if this ...


Utilization Of Unnatural Amino Acids In Novel Bioconjugates And Probing Applications, Christina A. Howard Apr 2017

Utilization Of Unnatural Amino Acids In Novel Bioconjugates And Probing Applications, Christina A. Howard

Undergraduate Honors Theses

Bioconjugations are utilized in many fields including materials science, biochemistry and medicine, despite the limited chemistries available in biomolecules. Unnatural amino acids can be used to expand the chemical diversity in proteins, affording a greater variety of functional groups for bioconjugations which. The site-specific incorporation of unnatural amino acids confers greater control and specificity over the reactions. Applications of unnatural amino acid based bioconjugations will be explored in this thesis. Optimization of solid supported immobilization of GFP and the extension of the technology to a carboxylesterase will be described. Fluorescent labeling of a medically relevant enzyme, Utag, will be optimized ...


Investigating Biological Properties Utilizing Synthetic Methods, Lindsay E. Chatkewitz Apr 2017

Investigating Biological Properties Utilizing Synthetic Methods, Lindsay E. Chatkewitz

Undergraduate Honors Theses

The growing field of bioorganic chemistry employs interesting tools and methods that can be used to study the intersection of chemistry and biology. This thesis aims to explore bioorganic chemistry, highlighting techniques that encourage the study of biology from a chemical perspective. The development of a photocaged, alkyne-containing unnatural amino acid (UAA) as well as a photocaged selenocysteine UAA highlight the diversity of of what can potentially be incorporated into proteins while also concentrating on the diversity of the functions of UAAs. Development of copper-free microwave mediated azide-alkyne cycloaddition reactions and development of an optimized aqueous Glaser-Hay reaction focuses on ...


Are You What You Eat? Selective Sequestration Of Toxic Milkweed Cardenolides In The Monarch Butterfly, Jacob Brammer Apr 2017

Are You What You Eat? Selective Sequestration Of Toxic Milkweed Cardenolides In The Monarch Butterfly, Jacob Brammer

Undergraduate Honors Theses

The Monarch butterfly, Danaus plexippus, is projected to face substantial quasi-extinction risk over the next 20 years after decades of population decline (Semmens et al., 2016). The butterfly shares an exciting and oft-studied chemical relationship with its larval food source, milkweed. Monarchs have the ability not only to tolerate the plant’s toxic cardenolide defenses, but also to sequester them into their own tissue for defense against predators and parasites. Recent work demonstrating a strong correlation between the cardenolides of the milkweed host and the eventual parasite load of the metamorphosed adult motivated us to further investigate the passage of ...


Utilizing Synthetic Tools To Address Biological Issues, Marshall Scott Padilla May 2016

Utilizing Synthetic Tools To Address Biological Issues, Marshall Scott Padilla

Undergraduate Honors Theses

With the advent of chemoselective reactions and unnatural amino acids (UAAs), the fields of molecular biology and organic synthesis are merging. Researchers are developing synthetic tools and producing small molecules that are able to affect and investigate large biomolecules and complex living systems. This thesis undertakes a survey of synthetic techniques to develop novel tools that can be employed to address a variety of relevant biological questions. Specifically, we are investigating alternatives and improvements to caging groups, including photoreversible azobenzene UAAs and an UAA caging group possessing a bioorthogonal handle. Also, we are developing a novel system to undergo copper-free ...


Investigation Of Unnatural Amino Acids As A Means To Modulate Protein Function, Taylor Harrison Jacobs May 2016

Investigation Of Unnatural Amino Acids As A Means To Modulate Protein Function, Taylor Harrison Jacobs

Undergraduate Honors Theses

In order to elucidate the biological processes that occur in everyday life, chemical biologists have developed technologies that allow the study of a various biological systems. Bioorthogonal chemistry is an ever-growing technology that involves performing chemical reactions with biological systems that do not rely on existing biological chemistries. In this work we attempt to develop and characterize novel bioorthognal chemistries that further expand the utility of this field. Additionally, we explore the utility of fluorescent probes in labeling applications. Finally, we attempt to create novel methods of control for a gene-editing protein using light as a mechanism of regulation.


The Pseudophosphatase Mk-Styx Colocalizes To Aggresomes, Veronica L. Nagle May 2016

The Pseudophosphatase Mk-Styx Colocalizes To Aggresomes, Veronica L. Nagle

Undergraduate Honors Theses

MK-STYX [MAPK (mitogen-activated protein kinase) phosphoserine/threonine/tyrosine-binding protein] is a pseudophosphatase member of the dual-specificity family subfamily of protein tyrosine phosphatases. MK-STYX lacks the essential cysteine in its signature motif required for catalytic activity. However, mutations to “restore” the signature motif result in a catalytically active phosphatase, MK-STYXactive (F1). We reported that MK-STYX interacts with G3BP-1 [Ras-GAP (GTPAse-activating protein) SH3 (Src homology 3) domain binding protein-1], and inhibits stress granule (SG) formation implicating the pseudophosphatase MK-STYX in the stress response pathway. SGs are large structures in which untranslated mRNAs accumulate and may serve as sites of mRNA sorting ...


Fragmentation Studies Of Lysine And Lysine Analog Containing Tetrapeptides, Zachariah Imran Hasan May 2016

Fragmentation Studies Of Lysine And Lysine Analog Containing Tetrapeptides, Zachariah Imran Hasan

Undergraduate Honors Theses

The fragmentation patterns of lysine and lysine-analog containing tetrapeptides were analyzed in this study using collision induced dissociation (CID) in an ESI-ion trap mass spectrometer. Understanding the fragmentation mechanisms of lysine-containing peptides is integral to improving bottom-up proteomics techniques and peptide sequencing and searching algorithms. Lysine and its non-protein amino acid (NPAA) analogs ornithine, DABA, and DAPA have been shown to affect fragmentation patterns based on their basicities in dipeptides and tripeptides. Studies have shown the occurrence of sequence scrambling due to macrocyclization of pentapeptides during fragmentation, which can result in inaccurate database matching. This study of the twenty tetrapeptides ...


Physical Modeling Of Vortical Cross-Step Filtration In The Oral Cavity Of American Paddlefish (Polyodon Spathula), Hannah Brooks May 2016

Physical Modeling Of Vortical Cross-Step Filtration In The Oral Cavity Of American Paddlefish (Polyodon Spathula), Hannah Brooks

Undergraduate Honors Theses

This thesis explores the filter-feeding mechanisms of the American paddlefish, Polyodon spathula. The data indicate that paddlefish use a filtration method termed cross-step filtration, which utilizes vortices formed behind the branchial arches by the incoming water flow. Videos of these vortices were obtained and quantified for the first time inside the oral cavities of preserved paddlefish. Since the paddlefish can move the branchial arches within the oral cavity, the effects of changing branchial arch angle on vortex characteristics were studied in 3D models. The vortices in three models with different arch angles were quantified. The data demonstrated that a change ...


Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens Apr 2016

Creating A Computational Model Of Prion Disease In The Human Neocortex, Christina Alexandra Stephens

Undergraduate Honors Theses

One way to study disease is to model specific biological reactions or processes involved in the generation of the disease in terms of a system of differential equations. The equations, called kinetic rate laws, are often non-linear and high order, making them difficult to solve. By approximating equations in complex biological networks as linear first order reactions, we can solve large sets of equations using computational software, such as MATLAB, to determine general trends in the change of molecular concentrations over time. These trends can tell us details about the disease and direct us toward areas worthy of further investigation ...


Characterizing Importin Binding To Thyroid Hormone Receptor Α1, Emma Lynn Mcgregor Apr 2016

Characterizing Importin Binding To Thyroid Hormone Receptor Α1, Emma Lynn Mcgregor

Undergraduate Honors Theses

Thyroid hormone, or T3, is essential in many bodily functions, from early development to the maintenance of health in adults. It is crucial for growth and skeletal development, development of the nervous system, cell differentiation, and maintenance of metabolic balance. The thyroid hormone receptor, TR, is a major mediator of thyroid hormone action. TR is a transcription factor and able to activate or repress transcription depending on the binding of its ligand, T3. There are two isoforms of TR, encoded by different genes: TRα and TRβ. Each of these isoforms have multiple alternative splicing products.

While TR’s ...


Development Of Novel Chemical Techniques To Address Biological Questions, Johnathan C. Maza May 2015

Development Of Novel Chemical Techniques To Address Biological Questions, Johnathan C. Maza

Undergraduate Honors Theses

The current biological toolkit has been vital in advancing our understanding of the world. That being said, the toolkit has limitations. As such, chemical biologists have been developing novel means to probe biological systems using chemical techniques. Bioorthogonal chemistry represents a new avenue to address biological questions that cannot be answered using current techniques. Herein, we describe a novel technique to probe proteins-of-interest using unnatural amino acid (UAA) mutagenesis. We have found that our UAAs allow us to access bioorthogonal chemistries for the conjugation of fluorophores to UAA-containing proteins. Additionally, we have extended these findings towards the application of protein ...


Development Of A Site-Selective Protein Immobilization Methodology Utilizing Unnatural Amino Acids, Benjamin K. Raliski May 2015

Development Of A Site-Selective Protein Immobilization Methodology Utilizing Unnatural Amino Acids, Benjamin K. Raliski

Undergraduate Honors Theses

Proteins are nature’s catalysts and have evolved over millennia to be highly selective and efficient. As a result, many have sought to incorporate proteins into artificial systems to varying degrees of success. Immobilization of proteins onto solid supports can increase the stability of proteins in conditions that would normally induce denaturation but immobilization strategies can present their own challenges by using reactions that lack selectivity and can potentially disrupt protein function themselves. This work develops a new methodology for protein immobilization that uses an unnatural amino acid site-selectively incorporated into a protein as the functional handle for immobilization. As ...


Unnatural Amino Acids In Proteins For Development Of Novel Biochemical Tools, Jordan Villa May 2015

Unnatural Amino Acids In Proteins For Development Of Novel Biochemical Tools, Jordan Villa

Undergraduate Honors Theses

Unnatural amino acids (UAAs) permit the incorporation of novel biochemical functionalities into proteins. This expansion of the genetic code has enabled enhanced spatial and temporal control of protein activity and conferred novel protein reactivity. This study examines the incorporation of three UAAs: fluoro-tyrosine, ortho-nitrobenzyl-tyrosine, and propargyloxy-phenylalanine towards various applications. Each UAA was successfully incorporated into a protein of interest (GFP or PRMT1) to facilitate the desired manipulation of protein function. The resulting alterations to GFP fluorescence, PRMT1 activity, or immobilization using Glaser-Hay bioconjugation demonstrate the success and practicality of the utilization of UAAs in the development of novel biochemical tools.


Novel Methodologies To Study Protein S-Glutathiolation Using Fluorescence Spectroscopy, Jacob Daniels May 2015

Novel Methodologies To Study Protein S-Glutathiolation Using Fluorescence Spectroscopy, Jacob Daniels

Undergraduate Honors Theses

Protein oxidation and repair is a physiological process that has been implicated in the pathology of diseases such as Alzheimer’s and in the normal aging process. S-glutathiolation, the process by which glutathione reacts at equilibrium with a protein and prevents the protein from undergoing further oxidation, is a critical repair mechanism for oxidized proteins.

In this thesis, we use the technique of fluorescence spectroscopy to develop a methodology to visualize S-glutathiolation in vitro. We report the spectroscopic properties of previously synthesized glutathione derivatives that have successfully labeled proteins during periods of oxidation. We also report the results of labeling ...


Thiols In Glycolysis: Effects Of Cysteine Modification On Pyruvate Kinase Activity, Taylor K. Lain May 2015

Thiols In Glycolysis: Effects Of Cysteine Modification On Pyruvate Kinase Activity, Taylor K. Lain

Undergraduate Honors Theses

Pyruvate kinase (PK), the tenth enzyme in glycolysis, undergoes significant activity changes with thiol modification at cysteine residues. This research explored the extent of these activity changes and of cysteine labeling experienced by PK after direct thiol modification by hydrogen peroxide, Ellman’s reagent, hypochlorous acid, glutathione, and dansyl-labeled glutathione derivatives. Mixed reactions with thiol-modifying agents and the reducing agents dithiothreitol and tris(2-carboxyethyl)phosphine examined the reversibility of labeling and restoration of activity. Results of these studies confirmed that PK activity may be modulated by cellular redox conditions. They determined that some of the residues responsible for labeling were ...


Modeling The Effect Of Cooperativity On Ligand-Driven Fluctuations Of Metabotropic Glutamate Receptors, Jeffrey Y. Liu May 2015

Modeling The Effect Of Cooperativity On Ligand-Driven Fluctuations Of Metabotropic Glutamate Receptors, Jeffrey Y. Liu

Undergraduate Honors Theses

The metabotropic glutamate receptors (mGluRs) are a family of dimeric G-protein coupled receptors (GPCR) that play a significant role in the modulation of synaptic transmission and excitability in neuronal cells [10]. Upon formation of mGluR dimers, protomer binding sites interact cooperatively with ligands, leading to receptor activation [5,9,10]. The dimer typically activates with full receptor occupancy, so the noise output of the system is assumed to scale in proportion to the number of activated dimers [2]. While the characterization of noise is well appreciated, the connection between cooperativity and noise has received less attention [1,2]. We examine ...


Characterization Of Pseudophosphatase Mk-Styx-Induced Neuronal Differentiation In Pc12 Cells, Dallas A. Banks Apr 2015

Characterization Of Pseudophosphatase Mk-Styx-Induced Neuronal Differentiation In Pc12 Cells, Dallas A. Banks

Undergraduate Honors Theses

MK-STYX [MAPK (mitogen activated protein kinase) phosphoserine/threonine/tyrosine binding protein] is a pseudophosphatase member of the MAPK phosphatase family. Though structurally related to the MAPK phosphatases, MK-STYX lacks the nucleophilic cysteine and histidine residues essential for catalysis. Despite its lack of catalytic activity, MK-STYX maintains its ability to bind to phosphorylated proteins, but not dephosphorylating them. This thesis focuses on further characterizing the role of MK-STYX in PC12 neuronal differentiation. The PC12 cell line is widely used as a model to study neuronal differentiation. Our previous data demonstrated that MK-STYX induces neuronal differentiation in PC12 cells. The results presented ...


Spread And Interaction Of Epidemics And Information On Adaptive Social Networks, Yunhan Long Jan 2015

Spread And Interaction Of Epidemics And Information On Adaptive Social Networks, Yunhan Long

Dissertations, Theses, and Masters Projects

The spread of diseases and opinions has profoundly affected the development of human societies. The structure of the underlying social network may change as a result of individuals changing their social connections in response to an ongoing epidemic or opinion spreading, either for self protection or as an expression of personal values. The interaction of spreading processes and the underlying network structure has been a focus of many recent studies. In this dissertation, we construct models to better incorporate heterogeneous responses to disease spread and attempted opinion spread.;We first model the simultaneous spread of an epidemic and awareness about ...


Langevin, Population Density And Moment-Based Modeling Of Local And Global Aspects Of Intercellular Calcium Signaling, Xiao Wang Jan 2015

Langevin, Population Density And Moment-Based Modeling Of Local And Global Aspects Of Intercellular Calcium Signaling, Xiao Wang

Dissertations, Theses, and Masters Projects

Markov chain models of the coupled gating of intracellular calcium (Ca 2+) channels are often used to study the stochastic dynamic of local Ca2+ release events and whole cell Ca2+ homeostasis. However, the runtime of the Markov chain description of Ca2+ channel gating is exponential in the number of Ca2+ channel states and may thus result in a combinatorial state space explosion when the number of channel states is large. This dissertation presents several novel stochastic modeling approaches that capture important aspects of Ca 2+ signaling while improving computational efficiency. This dissertation presents several novel stochastic modeling approaches that capture ...


A Mathematical Model Of Tau Protein Hyperphosphorylation: The Effects Of Kinase Inhibitors As A Theoretical Alzheimer's Disease Therapy, Patrick Neil Blank Jan 2015

A Mathematical Model Of Tau Protein Hyperphosphorylation: The Effects Of Kinase Inhibitors As A Theoretical Alzheimer's Disease Therapy, Patrick Neil Blank

Dissertations, Theses, and Masters Projects

No abstract provided.


Clinical And Physiological Analysis Of Very Long Apneas In Premature Infants, Anne Mennen May 2014

Clinical And Physiological Analysis Of Very Long Apneas In Premature Infants, Anne Mennen

Undergraduate Honors Theses

Apnea is common in premature infants, and in severe cases it may impair development. Data recorded during apnea events by hospital monitors at the University of Virginia Neonatal Intensive Care Unit (NICU) include EKG, chest impedance, and pulse oximetry signals. In previous work, an apnea detection algorithm was developed that filtered the cardiac artifact from the chest impedance signal to improve detection of apneas [1]. An unexpected result was the discovery that Very Long Apneas (VLAs) lasting more than 60 seconds are not rare. We use this findings in our research to provide new information about these apneas and to ...


The Role Of Mk-Styx In The Eif2alpha Stress Response Pathway, Alex Mcfarland Apr 2014

The Role Of Mk-Styx In The Eif2alpha Stress Response Pathway, Alex Mcfarland

Undergraduate Honors Theses

The pseudophosphatase MK-STYX (mitogen activated kinase phosphoserine/threonine/tyrosine binding protein) is a member of the MAPK phosphatases (MKP) dual specificity phosphatase family. However, it has the residues FSX5R, instead of HCX5R in its signature active motif. We previously reported that MK-STYX interacts with the RNA binding protein G3BP1 (Ras-GTPase SH3 domain binding protein-1) in the stress response pathway. During the stress response, mRNA translation is halted. Cytoplasmic compartments known as stress granules form around mRNA and RNA binding proteins, such as G3BP1, until the cell determines their fate. Dephosphorylation of G3BP1 at S149 induces stress ...