Biochemistry, Biophysics, and Structural Biology Commons^™

Validation Of A Deployable Proteomic Assay For The Serological Screening Of Sexual Assault Samples, Catherine O'Sullivan Brown

Electronic Theses and Dissertations

Protein mass spectrometry (MS) has emerged as a technique to supplant traditional serological tests for body fluid identification. It was hypothesized that proteomic techniques would surpass the sensitivity and specificity of traditional serological techniques. An automated workflow coupled with protein MS has been developed for the confirmatory identification of five biological fluids. A developmental validation was completed, assessing parameters such as reproducibility, sensitivity, ion suppression, and limit of detection. Implementation was determined through tandem sample processing by MS, traditional serological tests, and standard DNA profiling methods. The MS approach offered superior detection limits while also providing true confirmatory results, producing …

Synthetic Pathways For Potential Platinum 1,10-Phenanthroline Compounds, Jacob Young

Mahurin Honors College Capstone Experience/Thesis Projects

There are extremely important uses for platinum when it comes to the treatment of cancers and dementias. One potential therapeutic combines platinum with a structure known as phenanthroline. This platinum phenanthroline structure is normally extremely water-insoluble, rendering it difficult to study and use in biological systems. The Williams’ Biochemistry Laboratory endeavored to find a simpler synthetic pathway for a water-soluble phenanthroline product. While unsuccessful in identifying a product as of yet, many synthetic pathways have been ruled out, and more hypothetical pathways are being formulated for testing.

Among the strategies analyzed are varying solvent, reagents, apparatus, methodology, and temperature in …

Analyzing Single Ion Channel Activity In A Lipid Bilayer, David Ruiter, Loren Haarsma

Summer Research

Bilayers of lipid molecules form the basis of the cell membranes in living organisms. An ion channel is a type of molecule that can temporarily open a channel in a lipid bilayer in order to allow specific ions in and out. Problems with ion channels and their interactions with lipid bilayers are associated with several diseases, including osteoporosis. Carefully controlling the type of lipid in the bilayer, and its temperature, gives us tools to study the basic biophysics of these systems

Effects Of Resin Chemistries On The Selective Removal Of Industrially Relevant Metal Ions Using Wafer-Enhanced Electrodeionization, Humeyra B. Ulusoy Erol, Christa N. Hestekin, Jamie A. Hestekin

Chemical Engineering Faculty Publications and Presentations

Wafer-enhanced electrodeionization (WE-EDI) is an electrically driven separations technology that occurs under the influence of an applied electric field and heavily depends on ion exchange resin chemistry. Unlike filtration processes, WE-EDI can be used to selectively remove ions even from high concentration systems. Because every excess ion transported increases the operating costs, the selective separation offered by WE-EDI can provide a more energy-efficient and cost-effective process, especially for highly concentrated salt solutions. This work reports the performance comparison of four commonly used cation exchange resins (Amberlite IR120 Na⁺, Amberlite IRP 69, Dowex MAC 3 H⁺, and …

How Does Atg 10 Regulate The Autophagic Process? An Investigation Into The Atg12-5 Conjugation Pathway, Ayanda Brydie

Senior Honors Theses and Projects

Autophagy is a highly conserved eukaryotic cellular recycling process in which the degradation of proteins and cytoplasmic organelles occurs to recycle broken down products throughout the cell. This process plays a critical role in cell survival and maintenance. Once initiated by either nutrient deficiency (bulk autophagy) or recognition of damaged organelles (selective autophagy) this process is mediated by autophagy-related proteins (Atg proteins). The Atg proteins function to form a double-membrane vesicle, the autophagosome, to target part of the cytoplasm and deliver it to the vesicle for breakdown. In bulk autophagy, the presence of these proteins at the phagophore assembly site …

Purification And Activity Analysis Of A Highly Active Recombinant Catalase From Psychrophilic Bacterium Psychrobacter Cryohaloentis, Andrew Stewart

Honors Program Theses

To date, the genus Psychrobacter includes 37 recognized bacterial species isolated from different sources ranging from Siberian permafrost (P. cryohalolentis) to seal feces (P. lutiphocae). Due to its diverse ecological niches, several species belonging to the genus have different enzymatic activities with potential applications in bioremediation and the food industry. In this study, a bioprospecting approach was used to perform a in depth analysis of a Psychrobacter-like bacterial strain isolated from goose feces (designated as Psychrobacter unknown). The phylogenetic analysis of 16S rRNA gene and homologous sequence studies suggest that the strain may represent a novel species of the Psychrobacter …

High Throughput Analysis To Study Emerging Pollutants And Nanoparticle Fate In Biological Systems, Xiaolong He

Doctoral Dissertations

”The increasing applications of emerging and fugitive contaminants (EFCs) and engineered nanoparticles (ENPs) attract significant research interest for their potential risks to human health and the environment. In order to assess the health risks of these emerging contaminants, rapid and reliable analytical methods to measure the concentrations and fates of these contaminants are imperative. This dissertation focuses on the developments of advanced analytical methods and their applications to study those emerging contaminants in crop plant and simulated gastric fluid (SGF). Three types of mass spectrometry based methodologies have been developed, one is freeze-thaw/centrifugation extraction followed by high performance liquid chromatography …

Therapeutic Immunoglobulin G Surface Mobility Promotes Antibody-Dependent Cellular Phagocytosis By Arp2/3 And Syk Mediated Rearrangement Of Fcγ Receptors, Seongwan Jo

Electronic Theses and Dissertations

Therapeutic antibodies are rapidly growing class of drugs for treating cancers and immunological disorders by targeting specific antigens or blocking certain pathway to inhibit the tumor growth. In cancer immunotherapy, it was found that Fcγ receptor (FcγR) in immune cells play an important role in antibody dependent cell toxicity against tumor cells. Therefore, understanding FcγR activation mechanism, which requires ligation with immunoglobulin (IgG), is crucial to enhance potency of therapeutic antibodies. One crucial immune responses triggered upon FcγR ligation with IgG is phagocytosis which indicates clearing targets by engulfment. It is known that FcγRs form microclusters which gets rearranged during …

The Quantitative Assessment Of Pond Scum: An Examination Of The Biogeochemistry Of Phosphorus Cycling In The Belgrade Lakes, Abbey M. Sykes

Honors Theses

The internal recycling phosphorus in freshwater lake bottom sediments represents a significant source of hypolimnetic phosphorus (P) release for many of Maine’s lakes. In summer months, Maine lakes often thermally stratify and the lake hypolimnion develops anoxia, leading to a reduction in redox potential at the sediment-water interface. These reducing conditions facilitate the reductive dissolution of ferric iron, and, since phosphorus is often present in freshwater lake sediments as solid FeOOH-PO₄ complexes, results in release of soluble phosphorus into the water column. Our current study presents field and laboratory data from sediment fractionation extractions designed to quantify concentrations of …

Single Molecule Investigations Of Holliday Junction Binding Protein Ruva, Dalton Reed Gibbs

Theses and Dissertations

DNA breaks are inevitable as they mainly occur due to cells’ own reactive oxygen species (ROS). While DNA breaks can be single-stranded or double-stranded, the double-stranded DNA (dsDNA) breaks are more dangerous. If such damage is not repaired, it can lead to genetic instability and serious health issues including cancers. One way dsDNA breaks can be repaired is via a process called homologous recombination (HR), which involves several DNA-binding proteins. Therefore, to have a better insight into the repair mechanism and origin of repair defects, we need a better understanding of how these proteins interact with DNA itself and DNA …

Development Of Chemical Methods For Oligonucleotide Purification, Paramagnetic Labeling And Synthesis Of Dna-Based Advanced Materials, Muhan He

Legacy Theses & Dissertations (2009 - 2024)

This thesis describes a chemical method for alternative oligonucleotide purification that is non-chromatographic and gel-free and allows to routinely synthesize and purify long functional RNA strands. The purification of long RNAs is based on the bio-orthogonal inverse electron demand Diels-Alder (IEDDA) chemistry between trans-cyclooctene (TCO) and tetrazine (Tz). Target oligonucleotide strands are selectively tagged with Tz and can be captured and purified from the failure sequences with immobilized TCO. RNA strands are synthesized on solid support through a photolabile linker to avoid the loss of Tz tag. Purity of the isolated oligonucleotides was evaluated using gel electrophoresis, HPLC and mass …

Missense Mutations In The Gamma Crystallins And Mechanisms Of Lens Opacity, Wenjuan Hou

Legacy Theses & Dissertations (2009 - 2024)

Cataract, or clouding of the ocular lens, among the most common types of eye diseases, is the leading cause of blindness worldwide. With the opacity or clouding of the lens, light incident on the lens is scattered rather than being transmitted and is thus prevented from focusing on the retina. The lens becomes cataractous due to a large number of reasons, among which aging and genetic mutations are two of the most common factors. Clouding of the center of the lens or nuclear opacity, is the most frequently observed type of age-onset cataract, as well as inherited, congenital cataract [1, …

College Of Natural Sciences 2021 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Welcome, Table of Contents
Page 3 Our Departments: Highlights From 2021
Page 4 Overview of the College
Page 5 Overview of Bold & Blue
Pages 6, 7 Announcing the First Endowed Professorship in the College of Natural Sciences
Page 8 Spooky Science, Astronomy Outreach, SDSU Chemistry Research Features on Journal Cover
Page 9 Students Win Business Plan Competition With Aims to Improve Shelf Life of Produce, Summer Researchers
Page 10 NIH Grant Helps Unravel Rare Inflammatory Genetic Disorders, International Excellence in South Dakota
Page 11 The Next Frontier of Science Education: Virtual Reality, SDSU Researchers Uncover how Cancer …

An Integrative Analysis On The Role Of Notch1 And Notch3 In Musculoskeletal Disease, Haydee Magdalena Torres

Electronic Theses and Dissertations

Notch signaling is an evolutionarily conserved signaling pathway involved in cell fate decisions and cell renewal of multiple systems, including skeletal and muscle homeostasis. As the multifunctional nuclear complex of Notch1 is essential for its pathological function, identifying these interacting partners represents a potentially broad range of druggable vulnerabilities. We have completed a BioID proteomics study and found a large set of nuclear proteins associated with NOTCH1, including transcriptional regulators and epigenetic modulators, of which Histone Deacetylase 1 (HDAC1) is a promising interacting partner of Notch1. Our Cytoscape analysis predicted HDAC1 to be a top critical node in an activated …

Biocompatible And Multifunctional Trityl Spin Probes For Electron Paramagnetic Resonance Spectroscopy, Teresa D. Gluth

Graduate Theses, Dissertations, and Problem Reports (ETD)

The primary objective of my thesis was to develop and utilize a biocompatible multifunctional trityl spin probe for concurrent measurement of pO₂, pH_e, and [P_i] in vivo by electron paramagnetic resonance (EPR) spectroscopy (Chapter 2). My first goal was to synthesize the proposed probe we are terming HOPE71. Secondly, HOPE71 was characterized by X-band and L-band EPR spectroscopy. Next, the biocompatibility of HOPE71 was assessed through an albumin binding test, cytotoxicity assays, and in vivo intravenous tolerance. Then, the use of HOPE71 to measure the target parameters was demonstrated in a breast cancer …

Structual Analysis Of The Cl-Par-4 Tumor Suppressor As A Function Of Ionic Environment, Krishna K. Raut, Komala Ponniah, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Prostate apoptosis response-4 (Par-4) is a proapoptotic tumor suppressor protein that has been linked to a large number of cancers. This 38 kilodalton (kDa) protein has been shown to be predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at Asp-131 to generate the 25 kDa functionally active cleaved Par-4 protein (cl-Par-4) that inhibits NF-κB-mediated cell survival pathways and causes selective apoptosis in tumor cells. Here, we have employed circular dichroism (CD) spectroscopy and dynamic light scattering (DLS) to assess the effects of various monovalent and divalent salts upon the conformation of cl-Par-4 in vitro. We have …

The Effects Of Increasing Positively Charged Metal Ions Within Synovial Fluid, Kandisi Anyabwile

Williams Honors College, Honors Research Projects

Osteoarthritis is a degenerative joint disease that affects 10% of men and 13% of women over age of 60. It is the degradation of the cartilage between two bones; obesity, age, overuse, or injury are major contributors to the development of this disease. The joint is incapsulated by the synovial sac filled with a viscous solution that aids in lubrication referred to as synovial fluid. If the synovial sac is ruptured due to injury, positive ions (K⁺, Na⁺, Ca²⁺, and Fe³⁺) may affect viscoelastic properties within the sac. The purpose of this …

Nonhuman Iapp Variants Inhibit Human Iapp Aggregation, Alissa Oakes, Kate Menefee, Arleen Lamba, Larry M. Palato, Dillon J. Rinauro, Angela Tun, Betssy Jauregui, Kevin Chang, Luiza A. Nogaj, David A. Moffet

Chemistry and Biochemistry Faculty Works

The aggregation of the 37-amino acid polypeptide human islet amyloid polypeptide (hIAPP), as either insoluble amyloid or as small oligomers, appears to play a direct role in the death of human pancreatic β-islet cells in type 2 diabetes. hIAPP is considered to be one of the most amyloidogenic proteins known. The quick aggregation of hIAPP leads to the formation of toxic species, such as oligomers and fibers, that damage mammalian cells (both human and rat pancreatic cells). Whether this toxicity is necessary for the progression of type 2 diabetes or merely a side effect of the disease remains unclear. If …

Using Nmr Spectroscopy And Computational Chemistry To Confirm The Structure Of Novel Antibiotic Nocamycin O, Stephanie Lewis

CMC Senior Theses

In recent years, many medically promising antibiotics have been discovered in nature, especially in insect-microbe symbioses. One of the better-studied examples of this kind of defensive relationship is that of fungus-growing ants and the antibiotic-producing Actinobacteria. These bacteria produce several defensive chemicals with myriad uses, including one antibiotic that inhibits the growth of several bacterial strains, including other Actinobacteria. This antibiotic (known as nocamycin O) is a promising candidate for medicinal use due to its similarities to bacterial RNA polymerase inhibitors tirandamycin and streptolydigin, which inhibit several human pathogens. The determination of the structure of nocamycin O will be an …

Transcriptional Repressor Protein Based Macrolide Biosensor Development With Improved Sensitivity, Jayani A. Christopher

Graduate Research Posters

Macrolide antibiotics are in high demand for clinical applications. Macrolides are biosynthesized via giant assembly line polyketide synthases (PKS) which are arranged in a modular fashion. Combinatorial biosynthetic methods have been used to produce diversified macrolides by reprograming these modules and modifying tailoring enzymes required for post synthetic modifications. However it is challenging due to the size and complexity of PKSs. To overcome this challenge, new enzymes for macrolide diversification could be obtained by directed evolution where a large number of enzyme variants need to be screened. Therefore it is important to develop high throughput screening methods to identify the …

Huntingtin Aggregation At Interfaces Associated With Membranes And Organelles, Adewale Vincent Adegbuyiro

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s Disease (HD) is a genetic neurodegenerative disease caused by the expansion of polyglutamine (polyQ) domain within the first exon (exon1) of the huntingtin (htt) protein. Due to this mutation within the polyQ domain, htt aggregates into various toxic species such as oligomers, fibrils, and other amorphous aggregates. While the aggregation of htt strongly correlates with polyQ length, other factors, e.g. interaction with membranes or organelles and posttranslational modifications (PTMs), modulate aggregation. The first 17 N-terminal amino acids (Nt17) that precede the polyQ in htt-exon1 enhances aggregation and facilitated binding of htt to membranous organelles, promoting morphological changes and disfunction. …

Understanding The Relationship Between Local Environmental Changes And The Function Of The Ph Low Insertion Peptide, Violetta Burns Casamayor

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cancer is the second leading cause of death in the US with over 1.7 million new cases each year. Current cancer treatments tend to also target healthy tissues due to similarities with cancerous ones, resulting in acute side effects. Early detection is the best approach towards defeating cancer, however, modern imaging techniques require sizeable samples, often implying a late stage in the disease. One common attribute of tumors is their acidic microenvironment, which can be taken advantage of.

The pH Low Insertion Peptide (pHLIP) is a membrane-active peptide that can take advantage of the acidic microenvironment surrounding cancer cells. pHLIP …

Conformational Modulation Of Α-Helical N-Acetylated Α-Synuclein, Ricardo Fernandez

Theses and Dissertations

Human N-acetylated α-synuclein (^NAcαSyn) has long been accepted as an intrinsically disordered protein (IDP) predominantly found in terminal nerve regions in healthy subjects. ^NAcαSyn structural fluidity enables the formation of transient or dynamic assemblies. Some of these assemblies may serve functional, yet undefined purposes. ^NAcαSyn is highly susceptible to the surrounding environment, leading to misfolding under high cytosolic oxidative stress conditions, which in turn assemble in the form of toxic oligomers or amyloid fibrils. These ^NAcαSyn inclusions along with their accretion and migration within neurons, are pathological hallmarks of Parkinson’s disease (PD), dementia, and multiple …

In Vitro Screening Of Tp5801 Against Kinases For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

Data from screen of TP-5801 against in vitro kinases

Improvement In 14-3-3 Binding Site Prediction, Katherine K. Mccormack

ScholarsArchive Data

The 14-3-3 family of phospho-binding proteins regulate a variety of major cellular processes through interaction with a network of dynamic proteins. Deregulation of the 14-3-3 interaction network contributes to a variety of degenerative disorders and cancers. Our lab focuses on identifying novel 14-3-3 interactions and understanding how 14-3-3 binding regulates protein function. A major gap in this process is that identifying the phospho-site where 14-3-3 docks on a given protein is time- and resource-consuming. Prediction algorithms have been developed to predict canonical 14-3-3 binding sites, however, there are many non-canonical sites that existing software is unable to predict. To fill …

Kinase Screen Data For Nature Communications Publication, Joshua Andersen

ScholarsArchive Data

A TNK1 peptide encompassing S502 was screened against 245 Ser/Thr kinases. This file contains kinase activity values (against S502) from an n=1 experiment. These data support a manuscript to be published in Nature Communications (Chan and Egbert et al.)

Investigation Of Multidrug Efflux Transporter Acrb In Escherichia Coli: Assembly, Degradation And Dynamics, Prasangi Irosha Rajapaksha

Theses and Dissertations--Chemistry

The Resistant Nodulation Division (RND) super family member, tripartite AcrA-AcrB-TolC efflux pump, is a major contributor in conferring multidrug-resistance in Escherichia coli. The structure of the pump complex, and drug translocation by functional rotation mechanism have been widely studied. Despite of all these data, the dynamics of the assembly process of the pump and AcrB during functional rotation in the process of drug efflux remains poorly understood. My thesis focuses on understanding the pump assembly process, dynamics of AcrB in functional rotation mechanism, and also investigate the mechanism of degradation of AcrB facilitated by a C-terminal ssrA tag.

In the …

Characterization Of Potential Anti-Infective Agents By Targeting Burkholderia Pseudomallei And Escherichia Coli Ispf, Dakota Lane Grote

Graduate Research Theses & Dissertations

With the likelihood of contracting an antibiotic resistant infection increasing, the need for novel anti-infective agents is critical. The development of novel anti-infective agents benefits from the identification of new target pathways necessary for the survival of the pathogen. One such target is the methylerythritol phosphate (MEP) pathway, responsible for the synthesis of the isoprenoid precursors isopentyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) in bacteria and other pathogenic organisms. The MEP pathway is an attractive target because it is specific to a wide range of pathogenic organisms, while humans have a separate pathway, the mevalonate (MVA) pathway, for the biosynthesis …

Developing Synthetic Strategies For Multifaceted Applications Of Stable Gold-Based Complexes, Randall Tyler Mertens

Theses and Dissertations--Chemistry

Development of stable gold-based complexes has been a rapidly advancing field due to the popularity of gold complexes, particularly for use in biomedical research and catalytic transformations. Given that auranofin, a gold(I) complex with FDA approval for the treatment of rheumatoid arthritis is used in the clinic, the development of stable gold-based molecules of clinical relevance is urgently needed. Herein are reported, synthetic strategies used for the development of new classes of gold(I) and gold(III) complexes for advancement in mitochondrial modulation for use as chemotherapeutics as well as application to gold catalysis due to the unique geometry of complexes presented …

Computational Insights On Medicinal Chemistry Targeting Cyp450s, Alexander D. Fenton

Theses and Dissertations--Chemistry

Modern-day medicinal chemistry has provided researchers with a wide variety of tools to not only gather greater insight from their data, but also to generate data in new ways. One such tool is the construction of computational protein models from crystallographic datasets, and their subsequent use to understand the structure-activity relationships of protein-ligand complexes. These models can be utilized for their predictive power to inform the synthesis of, and improvement of, lead compounds. It is the goal of this work to employ such models to the CYP450 enzyme system such that potent and selective inhibitors can be designed, evaluated biologically, …