Biochemistry Commons^™

Characterization Of Endothelial Nitric Oxide Synthase Serine-600 Phosphorylation, Kevin Patel

Master of Science in Chemical Sciences Theses

Endothelial nitric oxide synthase (eNOS) is part of a family of three nitric oxide synthase (NOS) enzymes that catalyze the production of nitric oxide (NO). NO is a gaseous, free-radical signaling molecule that has a variety of cellular and physiological functions that range from maintaining cardiovascular homeostasis to neurotransmission. The function of NO greatly depends on the concentration and is cell type specific. eNOS is the most regulated of the three NOS isoforms and the mechanisms of regulation can be through protein-protein interactions and posttranslational modifications. A connection with eNOS and the cell cycle has begun to form with recent …

Investigation Of The Electrode Polarization Effect For Biosensor Applications, Anil Koklu

Mechanical Engineering Research Theses and Dissertations

My research focuses on electrokinetic transport. Particularly, in this dissertation, we focus on fabrication and testing of micro electrodes with nanostructured surfaces to minimize the electrode polarization (EP) effects for biosensor applications. In the first study, electrochemical deposition of gold nanoparticles on to planar gold electrodes was used to generate rough surfaces. Dendritic nanostructures that reduced EP up to two orders of magnitude was obtained by optimizing the deposition conditions. These structures also enhanced dielectrophoresis (DEP) response of our bio-chips, making them usable in physiological buffers. In further studies we discovered a universal scaling of EP in the frequency domain, …

Parallel Multipole Expansion Algorithms And Their Biology Applications, Jiahui Chen

Mathematics Theses and Dissertations

N-body pairwise interactions are ubiquitous in scientific areas such as astrophysics, fluids mechanics, electrical engineering, molecular biology, etc. Computing these interactions using direct sum of an O(N) cost is expensive, whereas multipole expansion methods, such as the fast multipole method (FMM) or treecode, can reduce the cost to O(N) or O(N log N). This thesis focuses on developing numerical algorithms of Cartesian FMM and treecode, as well as using these algorithms to directly or implicitly solve biological problems involving pairwise interactions. This thesis consists of the following topics. 1) A cyclic parallel scheme is developed to handle the load balancing …

How To Untie A Protein Knot., Sitao Yin, Brittiny Dhital, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

The origin of protein backbone threading through a topological knot remains elusive. To understand the evolutionary origin of protein knots, in this issue of StructureKo et al. (2019) used circular permutation to untie a knotted protein. They showed that a domain-swapped dimer releases the knot and the associated high-energy state for substrate binding.

Iron-Sulfur Cluster Assembly; In Vivo Analysis Of The Methanogenic Suf System, Evan Dunkle

LSU Master's Theses

Iron-sulfur (Fe-S) clusters are among the most ancient and prevalent of all biological cofactors. Their assembly into associated proteins is a tightly regulated process with many organisms employing multiple cluster assembly pathways. Much is known about Fe-S cluster assembly in aerobic organisms such as Escherichia coli (E. coli) but little is known in regards to cluster assembly in more ancient organisms such as methanogens. Methanogens are members of the domain of Archaea and are defined by their ability to generate methane as a byproduct of their main energy generating pathway. Methanogens also have significantly higher Fe-S cluster content …

Podophyllum Peltatum: Relationship Of Colony Size And Age, Emily Holst, Heidi Keswick, David P. Warners

Student Papers and Reports

No abstract provided.

Stormwater Capture Via Green Infrastructure In The Plaster Creek Watershed, Kyle Dankert, Ana Singh, Deanna Geelhoed, David P. Warners

Student Papers and Reports

No abstract provided.

Elements Of An Effectiveresearch Presentation, Rachel Willand Charnley

Chemistry and Biochemistry Faculty Presentations and Other Materials

No abstract provided.

Temporal Gene Expression Of Mesenchymal Cells In The Pediatric Lung, Quinlen F. Marshall, Soumyaroop Bhattacharya, Gautam Bandyopadhyay, Ravi Misra, Thomas Mariani, Gloria Pryhuber

Chemistry Student Work

INTRODUCTION: The newborn lung undergoes vast biochemical and physiological changes during adaptation from the intrauterine to the extrauterine environment. Lung morphogenesis continues from birth into early childhood, mediated by dynamic gene expression and a diversity of pulmonary cell types (Whitsett, JA. et al. Physiol. Rev, 2019). Murine models demonstrate that pulmonary mesenchymal cells exhibit remarkable heterogeneity in function and morphology during development, however, confirmation of their role is lacking in human neonates and early childhood (Guo, M. et al. Nat. Comm, 2019). In addition, many current human genomic studies of lung maturation suffer from limited sample size, limiting …

Green Team: Ecological Restoration Of Plaster Creek, Yeri Kim, Benjamin Steenwyk, Rachel Warners, David P. Warners, Gail Heffner

Student Papers and Reports

No abstract provided.

The Dynamin-Like Protein Vps1 Stimulates Endosome-To-Golgi Fusion In Vitro, Jared Christopher Smothers

Graduate Theses/Dissertations

Intracellular membrane fusion events can be reconstituted by exploiting isolated organelles from cellular hosts or artificial membranes made of purified phospholipid components. Artificial construction of membranes provides two significant advantages. First, cellular isolation of the endosome-derived vesicles and TGN (trans-Golgi Network) compartments needed for the fusion assay would be extremely challenging. Second, reconstituting the membranes provides the added benefit of controlling size and lipid compositions to functionally mimic the individual membrane architectures and introduce only the purified proteins that are under investigation. For these reasons, I have developed the first simultaneous lipid and content mixing fusion assays that measures the …

Does Thermotolerance In Daphnia Depend On The Mitochondrial Function?, Rajib Hasan

Electronic Theses and Dissertations

Thermotolerance limit in aquatic organism is set by the ability to sustain aerobic scope to sudden temperature shifts. This study tested the genetic and plastic differences in thermotolerance of Daphnia that can be explained by the differences in the ability to retain mitochondrial integrity at high temperatures. Five genotypes with different biogeographic origins were acclimated to 18^ᵒC and 25^ᵒC. We developed a rhodamine 123 in-vivo assay to measure mitochondrial membrane potential and observed higher fluorescent in heat damaged tissues as the disruption of the mitochondrial membrane potential. Significant effects on temperature tolerance were observed with CCCP …

Amyloidogenicity Of Naturally Occurring Full-Length Animal Iapp Variants, Larry M. Palato, Shannon Pilcher, Alissa Oakes, Arleen Lamba, Jaris Torres, Litza I. Ledesma Monjaraz, Crystabel Munoz, Edward Njoo, Dillon J. Rinauro, Kate Alexandra Menefee, Angela Tun, Betssy L. Jauregui, Sarah Shapiro, Olivia H. Nossiff, Eileen Olivares, Kevin Chang, Viviane Nguyen, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

Aim: To identify naturally occurring variants of IAPP capable of inhibiting the aggregation of human IAPP and protecting living cells from the toxic effects of human IAPP. Background: The loss of insulin-producing β-cells and the overall progression of type 2 diabetes appears to be linked to the formation of toxic human IAPP (hIAPP, Islet Amyloid Polypeptide, amylin) amyloid in the pancreas. Inhibiting the initial aggregation of hIAPP has the potential to slow, if not stop entirely, the loss of β-cells and halt the progression of the disease. Objective: To identify and characterize naturally occurring variants of IAPP capable of inhibiting …

The Gsk-3Β-Fbxl21 Axis Regulates Tcap Via Ubiquitin-Mediated Proteasomal Pathway In The Cytoplasm, Jiah Yang

Dissertations and Theses (Open Access)

Protein turnover is one of the most essential mechanisms controlling circadian rhythms. F-Box and Leucine Rich Repeat Protein21 (FBXL21) is a circadian E3 ligase which shows oscillatory mRNA transcripts and protein levels. It was previously found to perform subcellular compartment-specific E3 ligase activities targeting the core clock proteins CRYPTOCHROME(CRY)1/2. Here we identified a new sarcomeric target substrate, Telethonin(TCAP), which also shows circadian oscillation in its mRNA transcript and protein expression and, importantly, interaction with FBXL21 in an anti-phasic manner. Via computational and pharmacological tests, we identified Glycogen Synthase Kinase-3β(GSK-3β) as a regulator of FBXL21. Biochemical and molecular characterizations demonstrated that …

The Distinct Expressions Of Integrins Αdβ2 And Αmβ2 Differently Regulate Macrophage Migration In 3d Matrix In Vitro And In Tissue During Inflammation, Kui Cui

Electronic Theses and Dissertations

Chronic inflammation is an essential mechanism during the development of cardiovascular and metabolic diseases. The outcome of diseases depends on the balance between the migration and accumulation of macrophages in damaged tissues. Macrophage motility is highly regulated by adhesive receptors, integrins. Namely, intermediate expression of integrin supports macrophage migration, while a high integrin density inhibits it. Our studies are focused on evaluation of the contribution of related integrins α_Dβ₂ and α_Mβ₂ to macrophage migration and development of chronic inflammation.

We found that integrin α_Dβ₂ is upregulated on M1-macrophages in vitro and …

Obscurin Mediates Ankyrin Complex Formation In The Heart, Janani Subramaniam

Dissertations and Theses (Open Access)

Distinctly organized domains of receptors, ion channels, transporters, signaling molecules, cell adhesion molecules, and contractile proteins are crucial to cardiac function. Interactions between adaptor proteins such as ankyrins and cytoskeletal proteins such as obscurin play a pivotal role in organizing these functional domains in cardiomyocytes. Therefore, dysfunction of both ankyrin as well as obscurin lead to a host of cardiovascular diseases such as arrhythmias and cardiomyopathies. Alternative splicing of ankyrin yields numerous isoforms that interact with obscurin at various sub-cellular domains. And while some of these obscurin-ankyrin complexes have been studied, many others have not been characterized. Further, previous studies …

Investigations Of The Structure-Function Relationship In Kainate Receptors Using FöRster Resonance Energy Transfer, Douglas Litwin

Dissertations and Theses (Open Access)

Kainate receptors belong to the family of ion channels known as the ionotropic glutamate receptors. Ionotropic glutamate receptors mediate the majority of excitatory synaptic transmission, modulate the release of presynaptic glutamate, and facilitate dendrite formation. Kainate receptors are unique among the ionotropic glutamate receptors in being modulated by sodium ions. They have also been implicated in the development of higher learning and epilepsy. In recent years a wealth of structural data has become available for the AMPA and NMDA classes; however, the structural characterization of kainate receptors has been limited. The work in this dissertation utilizes luminescence resonance energy transfer …

Investigation Of Protein Dynamics And Communication In Adomet-Dependent Methyltransferases: Non-Ribosomal Peptide Synthetase And Protein Arginine Methyltransferase, Kyle M. May

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For many enzymes to function correctly they must have the freedom to display a level of dynamics or communication during their catalytic cycle. The effects that protein dynamics and communication can have are wide ranging, from changes in substrate specificity or product profiles, to speed of reaction or switching activity on or off. This project investigates the protein dynamics and communication in two separate systems, a non-ribosomal peptide synthetase (NRPS), and a protein arginine methyltransferase (PRMT).

PRMT1, the enzyme responsible for 80% of arginine methylation in humans, has been implicated in a variety of disease states when functioning incorrectly. For …

Investigation Of The Molecular Determinants And Extrinsic Factors That Regulate Prmt Product Specificity, Tamar B. Cáceres

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein arginine methylation is an important modification of proteins, involved in many cellular processes. Some examples are transcription, RNA editing, cellular communication, DNA repair, viral replication and chromatin remodeling. In recent years, the significance of protein arginine methyltransferases (PRMTs) in human diseases has been increasingly studied, especially in cardiovascular disease and cancer. Although the importance of these enzymes is recognized, the understanding of how exactly PRMTs function is still limited. Very little information is available to explain how or why any of the different PRMTs interact with other proteins or, what determines where in that protein to place their methyl …

A Universal Mechanism For N2 Binding To And Differing Reactivity Of The E4(4h) State Of Mo-, V-, And Fe-Nitrogenases, Derek Franklin Harris

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As a basic building block in many biological molecules, the element nitrogen (N) is essential for life. Dinitrogen (N₂) is abundant in Earth’s atmosphere, but this form is biologically unavailable. To be biologically available, N₂ must undergo a reduction reaction to the fixed form, ammonia (NH₃). The industrial Haber-Bosch process, which accounts for approximately 50% of the worlds fixed nitrogen, uses energy from fossil fuels to achieve high pressures and temperatures to catalyze the reaction. The energy used by Haber-Bosch accounts for approximately 2% of the world’s annual supply. The remainder of fixed nitrogen is …

Biophysical And Structural Characterization Of Shigella Atpase Spa47 Oligomerization Provides Insight Into Type Three Secretion System Activation And Virulence, Jamie L. Burgess

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Several bacterial pathogens including Shigella (shigellosis), Escherichia coli (urinary tract infections), Pseudomonas (lung infections), Salmonella (food poisoning), and Yersinia (plague) critically rely on a complex type three secretion system (T3SS) for infection. With the rise in multi-antibiotic resistant strains of several of these pathogens, we turn to the T3SS as a promising target for the development of novel therapeutics. The Dickenson lab at Utah State University has been the first to identify and characterize the ATPase Spa47, the energy source of the Shigella infection system. We show that Spa47 is necessary for proper T3SS formation and function, being ultimately responsible …

Reduced Alphabet Of Prebiotic Amino Acids Optimally Encodes The Conformational Space Of Diverse Extant Protein Folds, Armando D. Solis

Publications and Research

Background

There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding.

Results

Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure …

Hybrid Fusion Protein For Inhibition Of Multiple Proteases For Chronic Wound Healing, Graham L. Strauss

USF Tampa Graduate Theses and Dissertations

Many diseases display a multitude of relevant factors that contribute to the persistence of the disease and difficulty treating it. The multifactorial characteristics of some diseases lead to the requirement of combination of treatments in order to restore health. The latter may necessitate the mixing of treatments, medications, and therapeutics to first halt the disease, then assist the human body in returning itself to a state of normality. For example, chronic wounds exhibit this multifactor characteristic in which there exist many factors that lead to the body’s inability to properly heal in a timely manner. This presents a further threat …

Substituted Anthraquinones Represent A Potential Scaffold For Dna Methyltransferase 1-Specific Inhibitors, Rebecca L. Switzer, Jessica Medrano, David A. Reedel, Jill Weiss

Faculty Journal Articles

In humans, the most common epigenetic DNA modification is methylation of the 5-carbon of cytosines, predominantly in CpG dinucleotides. DNA methylation is an important epigenetic mark associated with gene repression. Disruption of the normal DNA methylation pattern is known to play a role in the initiation and progression of many cancers. DNA methyltransferase 1 (DNMT1), the most abundant DNA methyltransferase in humans, is primarily responsible for maintenance of the DNA methylation pattern and is considered an important cancer drug target. Recently, laccaic acid A (LCA), a highly substituted anthraquinone natural product, was identified as a direct, DNA-competitive inhibitor of DNMT1. …

Lignin Biopolymers In The Age Of Controlled Polymerization, Mitra S. Ganewatta, Hasala N. Lokupitiya, Chuanbing Tang

Faculty Publications

Polymers made from natural biomass are gaining interest due to the rising environmental concerns and depletion of petrochemical resources. Lignin isolated from lignocellulosic biomass is the second most abundant natural polymer next to cellulose. The paper pulp process produces industrial lignin as a byproduct that is mostly used for energy and has less significant utility in materials applications. High abundance, rich chemical functionalities, CO2 neutrality, reinforcing properties, antioxidant and UV blocking abilities, as well as environmental friendliness, make lignin an interesting substrate for materials and chemical development. However, poor processability, low reactivity, and intrinsic structural heterogeneity limit lignins′ polymeric applications …

Translational Control Of Antibiotic Resistance, Anne Witzky, Rodney Tollerson Ii, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Many antibiotics available in the clinic today directly inhibit bacterial translation. Despite the past success of such drugs, their efficacy is diminishing with the spread of antibiotic resistance. Through the use of ribosomal modifications, ribosomal protection proteins, translation elongation factors and mistranslation, many pathogens are able to establish resistance to common therapeutics. However, current efforts in drug discovery are focused on overcoming these obstacles through the modification or discovery of new treatment options. Here, we provide an overview for common mechanisms of resistance to translation-targeting drugs and summarize several important breakthroughs in recent drug development.

Electron Transfer Activity Of Mitochondria Neet-Proteins, Yiming Wang

LSU Doctoral Dissertations

Mitochondrial NEET proteins are recently discovered iron-sulfur proteins that are localized within mitochondria. There are three NEET proteins: mitoNEET, a type II diabetes drug pioglitazone binding target, a mitoNEET related protein 1 (Miner1 or NAF-1), and a mitoNEET-related protein 2 (Miner2). While both mitoNEET and Miner1 are mitochondrial outer membrane proteins, Miner2 is a mitochondrial matrix protein. All three NEET proteins bind at least one [2Fe-2S] cluster via CDGSH (Cys-Asp-Gly-Ser-His) motif. In this work, we have investigated the electron transfer activity of mitoNEET, and found that the CDGSH-type [2Fe-2S] clusters of mitoNEET can be reduced by the reduced flavin mononucleotide …

A Small Rna And Dna Binding Protein Contribute To Biofilm Development In Bartonella Henselae, Udoka Okaro

USF Tampa Graduate Theses and Dissertations

A biofilm, which is associated with 80% of chronic infections in humans, is formed when bacteria aggregate, attach to a substrate and secrete a matrix protecting the bacteria from host cell defenses and antibiotics. Bartonella henselae (B. henselae) is the causative agent of cat scratch disease, persistent bacteremia, and one of the most frequently reported causes of blood-culture negative endocarditis (BCNE) in patients. The ability of B. henselae to adhere to the heart valve, form a biofilm and vegetation to cause endocarditis increases the morbidity and mortality rate in infected patients. The presence of a trimeric autotransporter adhesin (TAA) called …

Organic Chemistry With A Biological Emphasis Volume Ii, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

Organic Chemistry With A Biological Emphasis Volume I, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …