Biochemistry, Biophysics, and Structural Biology Commons^™

Investigating Molecular Mechanisms Behind Bacterial Chondronecrosis With Osteomyelitis (Bco) Pathogenesis In Modern Broilers, Alison Ramser

Graduate Theses and Dissertations

Bacterial chondronecrosis with osteomyelitis (BCO), a leading cause of lameness in broiler chickens, is characterized by infection, inflammation, and bone attrition. There are currently no effective treatments and positive diagnosis is only possible through necropsy evaluations. Lameness is also a rising animal welfare and economic concern, making prevention and detection of BCO all the more critical. These challenges are exacerbated by a lack of mechanistic understanding of BCO’s etiology. The question I asked during my dissertation was how bacteria induce bone attrition in BCO pathology. My research has shown that mitochondrial dysfunction is characteristic of BCO conditions along with autophagy …

Evaluation Of Diaphragmatic Movement In The Respiratory System Of An Emphysema Patient, Aubri Ford

Honor’s College Freeman Research Journal

Respiration is an essential part of life. The diaphragm is the main muscle involved in the process of respiration. However, respiratory diseases such as emphysema alter the function of the diaphragm which sometimes leads to respiratory failure and death. This review compiles studies concerning emphysema and how the morphological changes in the lungs (i.e. hyperinflation) caused by the disease affect the diaphragm. The first major point covers the risks associated with developing the disease as a component of Chronic Obstructive Pulmonary Disease (COPD). Next, the paper outlines the pathophysiology of emphysema within the lungs, the methods used to diagnose emphysema, …

Spike Protein Structural Dynamics Of Sars-Cov-2 Coronaviruses Studied Using Molecular Dynamics, William Strickland

Biological Sciences Undergraduate Honors Theses

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has overwhelmingly impacted the global population, accounting for millions of confirmed infections and deaths over the last year. The virus’s influence on the health and safety of individuals, the economy, and daily life has been disruptive and devastating. While SARS-CoV-2 and SARS-CoV-1, two closely related members of the SARS coronaviruses, have shown the ability to cross the species barrier and infect humans, SARS-CoV-2 has predominantly been the virus responsible for the number of infections presently known. SARS-CoV-2 has also proven to be volatile, as many variants have …

Characterization Of A Protein-Small Molecule Interaction Between Microtubules And Novel Ruthenium-Polypyridyl Complexes, Chloe Hutchison

Chemistry & Biochemistry Undergraduate Honors Theses

Microtubules are cytoskeletal filaments that play a role in essential functions within the cell such as cell motility, intracellular transport, structural support and chromosome segregation. Tubulin is a heterodimeric protein that exhibits GTP dependent polymerization and self- assembles into polar microtubule filaments. Microtubules are dynamic polymers corresponding to their role in separation of duplicated chromosomes during mitosis. As the polymers cycle through rounds of polymerization and depolymerization based on their nucleotide state, the chromosomes are pulled towards the poles in the mitotic cell. Their normal function and dynamics can be disrupted in highly proliferative cells that interrupt cell cycle progression …

An Investigation Into The Roles Of Aldose Reductase And Acetate Kinase In The Metabolism Of Entamoeba Histolytica, Matthew B. Angel

All Dissertations

Entamoeba histolytica is an amoebic parasite that infects an estimated 90 million people worldwide and causes approximately 100,000 deaths per year. As the causative agent of amoebic dysentery, this food- and water-borne pathogen represents a significant public health burden worldwide, particularly in areas with poor sanitation. While treatments for amoebiasis exist, they are often limited in their effectiveness. Thus, efforts to better understand the biology and physiology of this organism are vital to the development of novel treatments for this disease.

E. histolytica lacks the enzymes for many common metabolic pathways such as the citric acid cycle and oxidative phosphorylation …

Studying Acetylation Of Aconitase Isozymes By Genetic Code Expansion, Jessica Araujo

Graduate Theses and Dissertations

The tricarboxylic acid (TCA) cycle is a very important, centrally located, energy-producing pathway that connects numerous other metabolic and regulatory pathways. Enzymes of this cycle have been more recently implicated in various cancers and neurometabolic disorders, however, the exact mechanism by which this happens becomes quite complex when considering the potential modification of these enzymes and the presence of multiple forms of the enzymes and therefore there is much to be studied in this area.

Aconitase has become a recent enzyme of interest as its substrate, citrate, has been found to play a major role in many vital processes within …

Describing The Effect Of Thin Layer Sediment Placement On Coastal Microbial Communities Using Foraminifera Diversity, Elizabeth B. Billings

Senior Honors Projects

Salt marshes are rich ecosystems that play an important role in aquatic food systems and prevent erosion while also providing essential habitats for wildlife. Climate change has resulted in rising sea levels and erosion of these coastal wetlands. Thin Layer Sediment Placement (TLP) is a restoration effort being implemented to mitigate the effects of climate change on coastal ecosystems. The TLP process raises elevation of the marsh and provides substrates for vegetative growth by spraying dredged sediment over existing marsh. The impacts of TLP on microbial populations is not widely understood, therefore metrics are required to study the effects of …

A Pathogen Outside Its Host: F. Tularensis Survival In Water, Aisling Macaraeg

Senior Honors Projects

Francisella tularensis is a Gram-negative pathogenic bacterium and is the causative agent for tularemia. While our understanding of F. tularensis survival in the environment is limited, it is clear they can persist in freshwater aquatic environments for long periods of time. Currently, there is a gap in knowledge with the understanding of the genes involved with the long-term survival of F. tularensis in an aquatic environment. In the laboratory setting, it has been found that lower temperatures seem to allow longer survival. The aim of this project is to identify laboratory conditions that allow F. tularensis to survive longterm in …

Characterization Of The Role Of The Replicase And Quasispecies Diversity In Flaviviral Evolution And Host Adaptation, Haley Caldwell

Legacy Theses & Dissertations (2009 - 2024)

Flaviviruses include several emerging and re-emerging arboviruses that cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses adapt to different hosts and rapidly alternate between hosts. Different aspects of flaviviral biology impact host switching, viral fitness, and the generation of viral diversity during genome replication by the NS3 and NS5 proteins. Together these factors may impact host plasticity.

Essential Amino Acid (Eaa) Regulation Of Skeletal Muscle Protein Turnover With Age, Mary Komp

Graduate Theses and Dissertations

Skeletal muscle (SM) is vital for both long term health and quality of life. Recent research suggests an increase in catabolic signals with age triggers pathologic conditions, such as sarcopenia. Although results from in vitro studies model how EAA can regulate muscle protein synthesis (MPS), the relevance of these models to muscle protein breakdown (MPB) and the presence of physiological EAA concentrations remains to be established. Therefore, the objective of this study was to determine the effects of a low, normal, and supra physiological dose of EAA (0.2, 1.0, and 3.0 x EAA) in a young (passages 2-10) and aging …

Multicopy Suppression Of Ribosomal Protein Deletion Mutants, Jacqualine Cerbone

Senior Honors Projects

To suppress the ribosome assembly defective phenotype of a ribosomal protein uS17- deficient mutant, various ribosomal proteins were used to act as multicopy suppressors. Ribosomal protein uS17 is a highly conserved component of the 30S (small) ribosomal subunit and is important for 30S subunit assembly. Mutants with a deletion of rpsQ (the gene encoding uS17) are viable but have a severe 30S subunit assembly defect and a temperature-sensitive (ts) phenotype. While fully assembled 30S subunits do form, incomplete ("20S") particles lacking several proteins accumulate. We hypothesized that increasing the intracellular concentration of one or more of the proteins missing from …

Nanotechnology-Based Approaches To Mitigate Environmental Pollutants -- Induced Neurological Disorders, Jyoti Ahlawat

Open Access Theses & Dissertations

Neurodegenerative diseases such as Parkinson's disease (PD), Alzheimerâ??s Disease (AD) and Huntingtonâ??s Disease (HD) have no cure despite intensive research efforts geared towards therapeutics development. In the USA, patients with PD and AD alone cost the nation ~ $200 billion annually in patient care and lost productivity. Therefore, there remains an urgent and unmet need to develop novel drugs and drug carriers with the potential to slow down, halt and ideally reverse the course of neurodegenerative disorders. The dissertation focuses on developing approaches towards targeting PD using multifactorial mechanisms including the targeting of protein aggregation and oxidative stress. This is …

Investigation Of The Binding Domain Interfaces Of The C-Terminus Of The Albino3 Insertase And The 43kda Chloroplast Signal Recognition Particle Subunit Via Single Molecule Förster Resonance Energy Transfer, Amanda Tomanek

Chemistry & Biochemistry Undergraduate Honors Theses

Fluorescent labeling is a technique used for visualizing functional groups contained in biomolecules by fluorescence imaging. This technique was used in this project to analyze post-translational targeting of light-harvesting chlorophyll-binding proteins (LHCP), which are the core complexes that harvest sunlight to drive photosynthetic electron transfer. This protein is synthesized in the cytosol and post-translationally targeted to the stroma of chloroplasts. CpSRP43 is a signal recognition particle (SRP) subunit unique to chloroplasts, which has been shown to interact with the stroma-soluble C-terminus of the thylakoid-bound Albino3 insertase (Alb3-Cterm). In the chloroplast stroma, targeting to thylakoids is performed via the cpSRP pathway …

Characterization Of Fgf1/Fgf2 Heterodimer With Mutation R136e, Brett Haley

Biological Sciences Undergraduate Honors Theses

Fibroblast growth factors are a family of heparin binding proteins that are involved in a broad spectrum of physiological functions, such as angiogenesis, cell proliferation, cell differentiation, and wound healing. Fibroblast growth factor 1 (FGF-1) is a member of the FGF superfamily and can bind universally to fibroblast growth factor receptors. Fibroblast growth factor 2 (FGF-2) is similar in structure to FGF-1 but has been shown to have a potent effect on angiogenesis. A physiologically stable dimerization of these two growth factors could prove to induce desirable effects in the instance of wound healing. In this study, we have designed …

Regulation Of The Reaction Between Cytochrome C And Cytochrome C Oxidase In The Mitochondria, Anders Nowell

Biological Sciences Undergraduate Honors Theses

Cytochrome c (Cc) is a multifunction protein that has important life and death functions in the cell. In the electron transport chain (ETC), Cc transfers electrons from cytochrome bc₁ to cytochrome c oxidase (CcO), which helps build the electrochemical gradient that drives ATP synthase. The reaction of Cc with CcO is very important in ETC regulatory processes. Previous research shows phosphorylation sites in Cc that affect the binding with CcO, with measurable effects on k_d, k_f, and K_D. These effects result in changes in mitochondrial membrane potentials, respiration, and reactive oxygen species (ROS) …

Modeling Developmental, Molecular, And Behavioral Effects Of An Apolipoprotein-E4 Fragment On The Embryogenesis Of Zebrafish, Madyson Mccarthy

Boise State University Theses and Dissertations

Although the increased risk of developing sporadic Alzheimer’s disease (AD) associated with the inheritance of the apolipoprotein E4 (APOE4) allele is well characterized, the molecular underpinnings of how ApoE4 imparts risk remains unknown. Enhanced proteolysis of the ApoE4 protein with a toxic-gain of function has been suggested and a 17 kDa amino-terminal ApoE4 fragment (nApoE4_1-151) has been identified in post-mortem human AD frontal cortex sections. Recently, we demonstrated in vitro, exogenous treatment of nApoE4_1-151 in BV2 microglial cells leads to uptake, trafficking to the nucleus and increased expression of genes associated with cell toxicity …

Biophysical Insights Into The Transport Properties Of Lysenin Channels, Andrew Merlin Bogard

Boise State University Theses and Dissertations

The defense work focused on deciphering novel functionalities of lysenin channels with respect to adjustment of their regulation and transport properties in response to environmental changes. Lysenin is a pore-forming toxin extracted from the earthworm E. fetida, which self-assembles into large pores in artificial and natural lipid membranes containing sphingomyelin. Prior investigations on their functionality identified strong regulation by voltage and ligands as fundamental traits of lysenin, similar to ion channels. In addition, stochastic sensing, controlled switching, and hysteretic conductance have been added to the list of intricate biophysical properties of lysenin channels as potential enablers of biotechnological and biomedical …

Macronutrient Availability Shapes Host Response To Infection And Feeding Behavior, Weston Gerald Perrine

Graduate Theses and Dissertations

Macronutrients in the diet are vital to the physiological processes necessary for an organism to effectively clear a pathogen. Diet can be important to a host’s susceptibility to infection and severity of pathology, though results can vary across host-pathogen systems (Sen et al. 2016). Manipulating the ratio of specific macronutrients in the diet is an effective method to begin understanding how individual macronutrients, rather than food types, have on immune responses. Using an avian host-pathogen system, I explored the effects of dietary macronutrient composition, specifically lipid and protein content, on disease pathology and behavior of canaries (Serinus canaria) infected with …

Role Of E168d In M. Tuberculosis Igps Catalysis, Hedda Booter

Theses, Dissertations and Culminating Projects

Mycobacterium tuberculosis is a bacterium that affects the lungs and causes tuberculosis, infecting over 10 million people worldwide each year. Owing to the organism’s evolving drug resistance, existing antibiotics no longer combat the disease. The need to discover new drug targets has never been greater. Previous findings suggest that the protein IGPS (indole-3-glycerol phosphate synthase) in M. tuberculosis (MtIGPS) may be a target in the treatment of the disease. MtIGPS catalyzes the fourth step in the tryptophan biosynthetic process. The ability to create their own tryptophan is a major advantage that many bacteria have. The role of E168, in the …

Cannabinoids And Retinal Fibrotic Disorders., Lucy June Sloan

Electronic Theses and Dissertations

Retinal fibrosis is detrimental to vision. Retinal pigment epithelial (RPE) cells contribute to several retinal fibrotic diseases. Upon exposure to TGF-β, a key fibrotic cytokine, RPE cells trans-differentiate to myofibroblasts marked by the integration of α-SMA fibers into F-actin stress fibers, which confer strong contractility. Myofibroblasts produce and contract the collagen-rich fibrotic scar and disrupt retinal architecture. In this study, we investigated the in vitro effects of the putative endocannabinoid compound N-oleoyl dopamine (OLDA) on TGF-β2 induced porcine RPE cell contraction and α-SMA expression. Using an in vitro collagen matrix contraction assay, we found that OLDA inhibited TGF-β2 induced contraction …

Novel Regulators Of Cellular Secretion Alter The Tumor Microenvironment To Drive Metastasis, Rakhee Bajaj

Dissertations and Theses (Open Access)

Lung cancer is a highly aggressive disease responsible for ~25% of all cancer-related deaths, due in part to its proclivity to metastasize. Treating metastasis holds potential for improving patient survival but requires a deeper investigation into the underlying mechanisms. Some of these processes that can regulate metastasis are: (1) Oncogenic targets of epithelial micro-RNAs (miRNAs) are epigenetically de-repressed upon loss of the miRNAs during epithelial-to-mesenchymal transition (EMT) and in cancer. EMT confers plasticity and fitness to cancer cells promoting their survival through the metastatic cascade. This cascade and EMT are initiated by loss of the miRNA200 family (miR-200) and the …

Characterization Of The Influence Of A Small Molecule Inhibitor On Ras-Related Proteins Interactions, Emilio Duverna

Graduate Theses and Dissertations

The Ras superfamily of small G proteins are involved in cell-signaling processes that, if not regulated, may lead to cell multiplication, apoptosis inhibition, and tumorigenesis. They function as molecular switches, which through GTP/GDP exchange cycle, switch on or off cellular activities. Overexpression and/or hyperactivity of these proteins have been linked to many diseases including various cancers. CDC42, a member of the Rho subfamily of the Ras superfamily of small G proteins, participates in the regulation of many cellular processes including cell adhesion, mitosis, and cytoskeletal rearrangements. CDC42 binds to and activates many effector proteins including CDC42-activated kinase (ACK). Abnormal activities …

Evaluation Of Current Methods To Detect Cellular Leucine-Rich Repeat Kinase 2 (Lrrk2) Kinase Activity, Belén Fernández, Vinita G. Chittoor-Vinod, Jillian H. Kluss, Kaela Kelly, Nicole Bryant, An Phu Tran Nguyen, Syed A. Bukhari, Nathan J. Smith, Antonio Jesús Lara Ordóñez, Elena Fdez, Marie-Christine Chartier-Harlin, Thomas J. Montine, Mark A. Wilson, Darren J. Moore, Andrew B. West, Mark R. Cookson, R. Jeremy Nichols, Sabine Hilfiker

Department of Biochemistry: Faculty Publications

Background: Coding variation in the Leucine rich repeat kinase 2 gene linked to Parkinson’s disease (PD) promotes enhanced activity of the encoded LRRK2 kinase, particularly with respect to autophosphorylation at S1292 and/or phosphorylation of the heterologous substrate RAB10.

Objective: To determine the inter-laboratory reliability of measurements of cellular LRRK2 kinase activity in the context of wildtype or mutant LRRK2 expression using published protocols.

Methods: Benchmark western blot assessments of phospho-LRRK2 and phospho-RAB10 were performed in parallel with in situ immunological approaches in HEK293T, mouse embryonic fibroblasts, and lymphoblastoid cell lines. Rat brain tissue, with or without adenovirus-mediated …

Regulation Of C-C Chemokine Receptor 7 (Ccr7) Ligand-Mediated Internalization And Chemotaxis By G Protein-Coupled Receptor Kinase Family 4 (Grk-4, 5, 6) In Human Pediatric T-Cell Acute Lymphoblastic Leukemia (T-All), Eduardo Elias Chaib

Open Access Theses & Dissertations

Background and Significance: The Hispanic population is disproportionally affected by T-ALL (T-cell acute lymphoblastic leukemia) when compared to other races in the US. C-C Chemokine Receptor 7 (CCR7) in T-ALL is used during disease progression, and may lead to migration of cancerous cells into the Central Nervous System (CNS) of patients. Goals and Objectives: This project aims to find relevant rates and risk factors for T-ALL for the Hispanic population in the US/Mexico border region. The other aim is to assess the effect of the G protein-coupled Receptor Kinase 4 (GRK-4) family proteins on migration and receptor internalization through CCR7 …

Lipid Rafts, Exosomal Vesicles And Anti-Giardial Therapies, Brian Ivan Grajeda

Open Access Theses & Dissertations

Giardia lamblia, a protozoan parasite, is a major cause of waterborne infection, worldwide. While the trophozoite form of this parasite induces pathological symptoms in the gut, the cyst forms transmit the infection via contaminated water. Since Giardia is a non-invasive parasite, the actual mechanism by which it causes infection remains elusive. We have previously reported that Giardia assembles cholesterol and GM1 glycolipid-enriched lipid rafts (LRs) that participate in encystation and cyst production. To further delineate the role of LRs in pathogenesis, we isolated LRs from Giardia and subjected them to proteomic analysis. Various cellular proteins including the virulent proteins—e.g., giardins, …

Small Heat Shock Protein 27 And Its Role In Human Disease, Bianka Andrea Holguin

Open Access Theses & Dissertations

Small heat shock protein 27 (Hsp27) is a ubiquitously expressed molecular chaperone with roles in many physiological processes. As an ATP-independent molecular chaperone, Hsp27 protects substrates from irreversible aggregation and holds them in a folding competent state for later recycling into the proteome. Hsp27 proteins form dimers that are assembled into large oligomeric complexes. Phosphorylation of Hsp27 dissembles the oligomers into chaperone active dimers. Several missense mutations of Hsp27 are causative for the neurodegenerative disorders Charcot-Marie-Tooth disease 2F and distal Hereditary Motor Neuropathy IIB. Here I show that the oligomerization and chaperoning ability of Hsp27 are altered by the Hsp27 …

The Electrostatic Features Of Dengue Virus Capsid Assembly, Alan Eduardo Lopez Hernandez

Open Access Theses & Dissertations

Dengue virus causes serious diseases and considerable deaths each year all around the globe. Dengue virus undergoes assembly in a capsid, matures and becomes viral. Revealing mechanisms of the viral capsid protein may lead to the discovery of novel drugs that prevent this assembly to happen and stop the virus from spreading. Here I present a computational work which is focused on the stability and assembly of the dengue viral capsid. The E and M proteins conform a heterotetramer, which consists of two copies of E and M proteins. The heterotetramers form a highly ordered capsid. In the electrostatic analysis …

Combining Pharmacokinetics And Vibrational Spectroscopy: Mcr-Als Hard-And-Soft Modelling Of Drug Uptake In Vitro Using Tailored Kinetic Constraints, David Perez-Guaita, Guillermo Quintas, Zeineb Farhane, Roma Tauler, Hugh Byrne

Articles

Raman microspectroscopy is a label-free technique which is very suited for the investigation of pharmacokinetics of cellular uptake, mechanisms of interaction, and efficacies of drugs in vitro. However, the complexity of the spectra makes the identification of spectral patterns associated with the drug and subsequent cellular responses difficult. Indeed, multivariate methods that relate spectral features to the inoculation time do not normally take into account the kinetics involved, and important theoretical information which could assist in the elucidation of the relevant spectral signatures is excluded. Here, we propose the integration of kinetic equations in the modelling of drug uptake and …

Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie

Open Access Theses & Dissertations

Computational biology is an interdisciplinary area that applies computational approaches in biological big data, including protein amino acid sequences, genetic sequences, etc., which is widely used to analyze protein-protein interactions, make predictions in drug discovery, develop vaccines, etc. Popular methods include mathematical modeling, molecular dynamics simulations, data science mythology, etc. With the help of computational algorithms and applications, drug development is much faster than traditional processes, as it reduces risks early on in a drug discovery process and helps researchers select target candidates that have the highest potential for success. In my doctoral research, I applied multi-scale computational approaches to …

Zinc-Mediated Regulatory Function Of Psd-95 On Nmdar At Post-Synapses, Luis F. Acosta

Theses and Dissertations

Postsynaptic density-95 (PSD-95) is a membrane-associated guanylate kinase that mediates localization of receptors in the excitatory postsynaptic density. It has been reported that PSD-95 mediates postsynaptic localization of NMDA receptors and anchors postsynaptic AMPAR receptors mainly through its postsynaptic membrane targeting by its N-terminal palmitoylation. Recent studies have shown that Ca2+/calmodulin blocks palmitoylation of PSD-95 by binding at the N-terminus of PSD-95, which promotes dissociation of PSD-95 from the postsynaptic membrane and causes loss of surface AMPARs in cultured neurons. Another metal ion zinc is found in various areas of the brain. As an endogenous neuromodulator, zinc plays a role …