Biochemistry, Biophysics, and Structural Biology Commons^™

Analyzing The Impacts Of Loss Of The Fanca Protein On Chromatin State, Mileena Nguyen

Senior Honors Projects

No abstract provided.

Nutritional Data And Corresponding Performance Impacts Of Uri Student-Athletes, Abigael Fenbert

Senior Honors Projects

This research project investigates the diets of various sport athletes at the University of Rhode Island. The question that this project aims to answer is if our athletes are meeting recommended daily values nutritionally, and if not, why? Research continues to grow regarding how performance implications are tied to varying nutritional disparities for athletes. Various studies show malnourishment leads to performance decline, increased injury risk, and improper recovery. This is influenced by factors such as deficits in caloric intake, macronutrient and micronutrient availability, and dehydration. For college athletes, a lack of food availability and nutritional knowledge leaves them especially predisposed …

Characterization Of Protein Aggregation Using A Solid-State Nanopore Device, Mitu Chandra Acharjee

Graduate Theses and Dissertations

Protein aggregation has been linked to many chronic and devastating neurodegenerative human diseases and is also strongly associated with aging. In the case of neurodegenerative diseases, α, β tubulins and tau proteins dissociate in a neuron cell and aggregate both intra and extra-cellularly. Tau and tubulin aggregations were found as one of the major causes of many neurodegenerative diseases, such as Parkinson’s, Picks, Alzheimer’s, Huntington, and Prion. Finding the state and mechanism of protein aggregation is significant. In this work, tau and tubulin aggregations were detected in ionic solutions using the solid-state nanopore technique. Besides tau and tubulin, aggregations of …

Investigating The Effects Of Catalytic Activity In Mycobacterium Tuberculosis Indole-3-Glycerol Phosphate Synthase In Wildtype, N189l, And E57d Variants, Sarah S. Cho

Theses, Dissertations and Culminating Projects

Indole-3-glycerol phosphate synthesis (IGPS) is an enzyme that catalyzes the ring closure in 1-(o-carboxylphenylamino)-1-deoxyribulose 5-phosphate (CdRP). Multiple steps are expected to be involved in formation of the pyrrole ring including dehydration, decarboxylation, cyclization, and condensation. IGPS is an essential protein in the pathogen Mycobacterium tuberculosis and a potential target in the treatment of drug-resistant tuberculosis. In order to better understand the function of Mycobacterium tuberculosis IGPS (mtIGPS), we introduced single-point mutations into active site residues. This was based on the hypothesis that introducing mutations would affect the catalysis in a way where we would be able to obtain more information …

Vertical Metal Distributions In Brownfield Soils Drive Enzyme Activities And Plant Success, Eshariah N. Dyson

Theses, Dissertations and Culminating Projects

The distribution of contaminants in polluted soils can vary through depth. We measured the vertical distributions of heavy metals and enzyme activities in the top 10 cm of side-by-side, vegetated and barren brownfield soils. The data showed metals significantly accumulated in the top 2 cm of barren soil and uniformly distributed through vegetated soil. When planted, germination rate was significantly lower in the previously barren soil, with the metal layer intact, compared to mixed barren soil. These data suggest a feedback loop in which plant roots redistribute metals, diluting metal-rich regions, yet germination remains initially limited by a metal cap. …

Characterization Of A Putative Helicase In Rifampicin Resistance Of Mycobacterium Abscessus:, Aavrati Saxena

Legacy Theses & Dissertations (2009 - 2024)

Mycobacterium abscessus (Mab), a non-tuberculous environmental mycobacterium is one of the emerging pathogens. The number of Mab infections has doubled in the past decade. It is also an opportunistic pathogen usually infecting immunocompromised individuals and causing numerous skin and soft tissue infections. It commonly causes lung infections in people who are already infected with one or other lung infections such as tuberculosis. The treatment of Mab infections is difficult because of its intrinsic resistance to most of the antibiotics available. This project studies Rifampicin (RIF) resistance in Mab, as RIF is a well-established treatment for other mycobacterial infections including tuberculosis, …

Ampa And Kainate Receptor-Potentiating Rna Aptamers, Janet L. Lynch

Legacy Theses & Dissertations (2009 - 2024)

Glutamate receptors act to bring about excitatory transmission in the central nervous system. The receptors are divided into two groups: ionotropic and metabotropic glutamate receptors. Ionotropic glutamate receptors are ion channels which are activated by an agonist such as glutamate or kainate. The main receptors in the ionotropic glutamate receptor family are the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA), kainate and N-methyl-D-aspartate (NMDA) receptors. In the central nervous system ionotropic glutamate receptors are found both pre- and postsynaptically. It has been found that most AMPA and NMDA receptors are postsynaptic receptors while the kainate receptors can be pre- or postsynaptic. Underactivity of these …

Component Causes Of Infectious Bovine Keratoconjunctivitis - The Role Of Moraxella Species In The Epidemiology Of Infectious Bovine Keratoconjunctivitis, John Dustin Loy, Matthew Hille, Gabriele Maier, Michael L. Clawson

School of Veterinary and Biomedical Sciences: Faculty Publications

Moraxella bovis can cause infectious bovine keratoconjunctivitis (IBK).

The role of M bovoculi in IBK is not fully understood.

M bovis and M bovoculi appear to undergo genetic recombination with each other or other members of the Moraxellaceae.

Recombination complicates their classification and potential role(s) in IBK pathogenesis.

MALDI-TOF MS is used to identify M bovis, 2 major strains or genotypes of M bovoculi, M ovis, and other members of the Moraxellaceae.

Classification and determination of pathogenesis potential within Moraxella species may be better understood through whole genome sequencing.

The Hybridizing Ions Treatment (Hit) Method Development And Computational Study On Sars-Cov-2 E Protein., Shengjie Sun

Open Access Theses & Dissertations

Fast and accurate calculations of the electrostatic features for highly charged biomolecules such as DNA, RNA, highly charged proteins, are crucial but challenging tasks. Traditional implicit solvent methods calculate the electrostatic features fast, but they are not able to balance the high net charges in the biomolecules effectively. Explicit solvent methods add unbalanced ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which require more expensive computing resources. Here we developed a novel method, the Hybridizing Ions Treatment (HIT) method, which hybridizes the implicit solvent method with the explicit method to realistically calculate the electrostatic potential for highly …

College Of Natural Sciences Newsletter, May 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 5.

Page 1 Dean's Message
Page 2 - 3 Awards & Recognition
Page 4 Research Spotlight: Dr. Xiaoyang Zhang
Page 5 Upcoming Retirements
Page 6 - 7 Geography Alumni Social, Recent Media Coverage
Page 8 Open PRAIRIE Data
Page 9 - 11 Spring 2021 Dean's List and Academic Recognitions

Construction And Analysis Of Three Multi-Partite Synthetic Microbial Communities, Alexander J. Lazzara, Jacob K. Fanning

Honors Theses

Microbial Communities are of interest to molecular biologists hoping to understand the nature of metabolic interactions between co-existing, or possibly mutualistic, organisms. These interactions are ubiquitous in nature, but understanding the molecular mechanisms involved remains challenging and not well understood. Here, we design three tri-partite microbial circuits based on possible interactions among involved microbes, which are discussed and may suggest mutualistic interactions. Carbon and nitrogen molecular pathways and the intracellular metabolism of each microbe is discussed. We present minimal growth media that will ensure that organisms utilize available resources, which may originate from metabolic processes in neighboring microbes, simulating a …

Functionality Of Red Blood Cells After Cryo-Preservation., Charles Andrew Elder

College of Arts & Sciences Senior Theses

One of the most common medical procedures performed in US hospitals is blood transfusions. Unfortunately, the red blood cells (RBCs) for transfusion have a limited shelf life after donation due to detrimental storage effects on morphological and biochemical properties. Inspired by nature, I am developing a biomimetics approach to preserve RBCs for long-term storage using compounds that occur in animals that have developed a natural propensity to survive in a frozen or desiccated state for decades. Trehalose was employed as a cryoprotective agent when added to the extracellular freezing solution. The highest percent of RBCs with intact membranes after freezing …

Biochemical And Computational Characterization Of Small Regulatory Rnas In The Eastern Oyster, Crassostrea Virginica, Isabelle Townsend

Honors Theses

RNA interference (RNAi) is a process by which gene expression is regulated using small non-coding RNAs (ncRNAs). Three classes of ncRNAs, including micro-RNA (miRNA), short-interfering RNA (siRNA), and Piwi-interacting RNA (piRNA), are readily distinguishable in eukaryotic systems based on unique characteristics such as read sizes, overlap signatures, and mode of biogenesis. In this study, a method for purification of small RNAs was explored in the eastern oyster, Crassostrea virginica. This method involved the use of Sepharose beads for anion exchange chromatography to enhance purification of Argonaute associated small RNAs. Following RNA extraction and purification, small RNA libraries were created …

Molecular Characterization Of Galectin From Amblyomma Americanum In Context Of Α-Gal Syndrome, Sumar Beauti

Honors Theses

The lone star tick Amblyomma americanum is a vector of various disease-causing pathogens and tick-borne alpha-gal syndrome (AGS) with rapidly expanding populations in the south- and northeast regions of the United States. This study aimed to molecularly characterize galectin and determine its involvement in galactose-α-1,3-galactose (α-gal) synthesis, transport, reproductive fitness, and microbial homeostasis in this tick. The lone star tick galectin possesses two conserved carbohydrate recognition domains and shares homology with other Ixodid tick galectins. Time and tissue-dependent expression data shows that galectin is constantly expressed in salivary glands, midgut, and ovary tissues. An RNA interference approach was used to …

The Effect Of The Apolipoprotein A1 (Apoa1): The Stability And Folding In Potassium Chloride Environment, Alexandra Paladian

Honors Theses

Healthy levels of potassium chloride (KCl) can significantly affect the workings of the cholesterol level of the human body and how they pertain to an individual person. The search for a better salt additive for the human diet can provide a better option for people who experience high cholesterol levels and heart disease. The study focuses on the experimental design of the Molecular Dynamic (MD) simulation of the Apolipoprotein A1 (APOA1) in the potassium ion solution environment to determine the stability and folding of the protein. The study also compares its data to the previous experimental design of chloride ions …

Molecular Dynamic Simulation Of The Complex Folding Patterns Of Apolipoprotein A1 In Various Concentrations Of Potassium Chloride, Hannah Holmberg

Honors Theses

Apopliprotein or ApoA-1 is a complex lipoprotein that functions in the removal of cholesterol from the blood, removing cholesterol from the area around white blood cells and promoting the excretion of lipids through the lymphatic system. Previous research has found that ApoA-1 shows both folded and unfolded conformations depending on the concentration of NaCl in solution in the water around it. The protein was studied using molecular dynamics simulations. Once this state of equilibrium was reached, various structural properties of the protein were measured including the radius of gyration and the radial distribution function. The goal of the project was …

Discovery Of Novel Ubiquitin- And Methylation-Dependent Interactions Using Protein Domain Microarrays, Jianji Chen

Dissertations and Theses (Open Access)

Post-translational modifications (PTMs) drive signal transduction by interacting with "reader" proteins. Protein domain microarray is a high throughput platform to identify novel readers for PTMs. In this dissertation, I applied two protein domain microarrays identifying novel readers for histone H2Aub1 and H2Bub1, and H3TM K4me3. Ubiquitinations of histone H2A at K119 (H2Aub1) and histone H2B at K120 (H2Bub1) function in distinct transcription regulation and DNA damage repair pathways, likely mediated by specific "reader" proteins. There are only two H2Aub1-specific readers identified and no known H2Bub1-specific readers. Using a ubiquitin-binding domain microarray, I discovered the phospholipase A2-activating protein (PLAA) PFU domain …

A Genomic Approach To Assessing The Fkbp52-Regulated Androgen Receptor Cistrome And Transcriptome, Nina Raquelle Ortiz

Open Access Theses & Dissertations

Androgen receptor (AR)-regulated genes contribute to the initiation and progression of prostate cancer. Receptor signaling persists and plays a pivotal role in late-stages of the disease, for which there is currently no treatment. Thus, there is a need to understand the mechanisms regulating AR function as a means to identify drug targets for potential therapeutics. The FKBP52 cochaperone has emerged in recent years as a regulator of AR activity that is functionally linked in the AR signaling pathway. FKBP52 is a known positive regulator of AR and believed to interact with AR at its binding function 3 surface (BF3), a …

Applying Computational Methods To Study The Interactions Between Sars-Cov-2 And Hace2, Yixin Xie

Open Access Theses & Dissertations

The ongoing outbreak of COVID-19 has been a serious threat to human health worldwide. The virus SARS-CoV-2 initiates its infection to the human body via the interaction of its spike (S) protein with the human Angiotensin-Converting Enzyme 2 (ACE2) of the host cells. Here we implemented multi-scale computational approaches to study the binding mechanisms of human ACE2 and S proteins of both SARS-CoV and SARS-CoV-2. Electrostatic features, including electrostatic potential, electric field lines and electrostatic forces of SARS-CoV and SARS-CoV-2 were calculated and compared in detail. The results demonstrate that SARS-CoV and SARS-CoV-2 S proteins are both attractive to ACE2 …

Determination Of Human Shedding Propensity Based On Str Results, Genevieve Trapani

Student Theses

Trace DNA evidence may be discovered at a crime scene after having been deposited by a person of interest via active or passive transfer. Based on previous studies, passive transfer of one’s DNA is influenced by their shedding propensity, or probability of depositing a detectable amount of DNA through touch. Determining the shedding propensity of a person of interest can aid in trace DNA interpretation in forensic casework. This study explored STR profile quality and the presence of a DNA mixture for different skin surface locations, including fingertips before and after handwashing. As expected, unwashed fingers showed a higher prevalence …

A Computational Analysis Of Selective Metabolism Of Bupropion By Cytochrome P450 2b6, Alyssa Santos

Honors Scholar Theses

Bupropion is an antidepressant and smoking cessation aid that is extensively metabolized by cytochrome P450 (CYP) 2B6. It is a highly lipophilic chiral drug that undergoes stereoselective metabolism with preference for the (S)-enantiomer. Despite chemical reasons for why bupropion can be metabolized by other CYP isozymes, clinically, bupropion is preferentially metabolized by CYP2B6, and at certain concentrations, CYP2E1, CYP2C19, and CYP3A4. A computational analysis with simulated molecular docking was performed using two different scoring algorithms to analyze the specific amino acid interactions between bupropion and various CYP isozymes. Trials were run using one stereoisomer of bupropion (R …

Vertical Transmission Of Zika Virus In An Opossum Model, Dionn Carlo Silva

Theses and Dissertations

This study will identify Brazilian ZIKV infection in the offsprings of mated, inoculated Monodelphis domestica females. Unlike non-human primates (NHP) and transgenic mice, M. domestica provides an opportunity to study ZIKV infection in a novel animal model possibly useful for in-utero studies. M. domestica has also been used in cancer and dietary research with varying degrees of success. ZIKV infection will be identified using antibody staining and in situ hybridization. The expected result of this study is that ZIKV will be identified in various tissues and reveal that ZIKV is transmitted vertically in this animal model. The significance of this …

Developmental Activation Of Mitochodnrial Opa1 Processing Is Retinoic Acid-Independent, Shaynah St. Vallier

Theses and Dissertations

Mitochondria exist as an organellar network within most eukaryotic organisms, and are critical to biochemical energy production and cellular stress response. Mitochondrial bioenergetic function is directly linked to the complex morphological state of its network, existing in a balance of fusion (interconnected state) or fission (fragmented state). The optic atrophy-1 (OPA1) protein plays a major role in regulating mitochondrial inner membrane fusion, whereas the OMA1 metallopeptidase is highly involved in the degradation of the OPA1 protein, thus contributing to its fragmented state. Cellular stress such as a disruption in mitochondrial membrane potential activates OMA1 cleavage of OPA1. However, our data …

Soluble Angiotensin-Converting Enzyme 2, Cardiac Biomarkers, Structure, And Function, And Cardiovascular Events (From The Atherosclerosis Risk In Communities Study), Aliza Hussain, Olive Tang, Caroline Sun, Xiaoming Jia, Elizabeth Selvin, Vijay Nambi, Aaron Folsom, Gerardo Heiss, Faiez Zannad, Thomas Mosley, Salim S Virani, Josef Coresh, Eric Boerwinkle, Bing Yu, Jonathan W Cunningham, Amil M Shah, Scott D Solomon, James A De Lemos, Ron C Hoogeveen, Christie M Ballantyne

Faculty, Staff and Students Publications

Membrane-bound angiotensin-converting enzyme 2 is important in regulation of the renin-angiotensin-aldosterone system, but the association of cleaved soluble ACE2 (sACE2) with cardiovascular disease (CVD) is unclear. We evaluated the association of sACE2 with cardiac biomarkers, structure, and function and cardiovascular events in the Atherosclerosis Risk in Communities Study. sACE2 was measured in a subset of 497 participants (mean age 78±5.4 years, 53% men, 27% black); Cox regression analyses assessed prospective associations of sACE2 with time to first CVD event at median 6.1-year follow-up. sACE2 was higher in men, blacks, and participants with prevalent CVD, diabetes, or hypertension. Higher sACE2 levels …

The Small Gtpase Rab-35 Facilitates The Initiation Of Phagosome Maturation And Acts As A Robustness Factor For Apoptotic Cell Clearance, Ryan Haley, Zheng Zhou

Faculty, Staff and Students Publications

We recently identified the novel function of the small GTPase RAB-35 in apoptotic cell clearance in Caenorhabditis elegans, a process in which dying cells are engulfed and degraded inside phagosomes. We have found that RAB-35 functions in two separate steps of cell corpse clearance, cell corpse recognition and the initiation of phagosome maturation. During the latter process, RAB-35 facilitates the removal of phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) from the membranes of nascent phagosomes and the simultaneous production of phosphatidylinositol-3-P (PI(3)P) on these same membranes, a process that we have coined the PI(4,5)P2 to PI(3)P shift. RAB-35 also promotes the recruitment of the …

New Applications For The Kinetic Exclusion Assay (Kinexa), Mark Harrison Smith

Boise State University Theses and Dissertations

This dissertation examines the fundamental principles and applicability of the kinetic exclusion assay (KinExA), developed and marketed by Sapidyne Instruments of Boise, Idaho, since 1995. Chapter One reviews and consolidates the manufacturer’s guidance and many early papers that delineate the practical and theoretical aspects of the technology. In brief, KinExA is a two stage analytical system. In stage one, a number of solutions are prepared, whereby one of the partners is kept constant (the constant binding partner, or CBP), while the other (the titrant) is varied, usually in serial dilution. As the titrant is increased, the free CBP decreases, and …

Understanding The Role Of Ano1 In Oral Cancer, Mallary Forrest

UNLV Theses, Dissertations, Professional Papers, and Capstones

In 2008, the gene ANO1 was discovered to encode a calcium activated chloride channel. This gene is located on the 11q13 locus, a locus that is commonly amplified in many cancers including cancer of the head and neck. ANO1 is situated in close proximity to genes associated with growth and apoptosis. As rapid proliferation and lack of apoptosis are hallmark characteristics of cancer, growth factors and apoptosis mediators are expected to be altered in cancer. But what does a calcium activated chloride channel have to contribute to cancer’s pathogenesis? Is it an active gene in cancer progression or is it …

Investigating A Novel Function For Phosphoserine Aminotransferase 1 (Psat1) In Epidermal Growth Factor Receptor (Egfr)-Mediated Lung Tumorigenesis., Rumeysa Biyik-Sit

Electronic Theses and Dissertations

Phosphoserine aminotransferase 1 (PSAT1) catalyzes the second enzymatic step within the serine synthetic pathway (SSP) and its expression is elevated in numerous human cancers, including non-small cell lung cancer (NSCLC). Epidermal growth factor receptor (EGFR) mutant NSCLC is characterized by activating mutations within its tyrosine kinase domain and accounts for 17% of lung adenocarcinomas. Although elevated SSP activity has been observed in EGFR-mutant lung cancer cells, the involvement of PSAT1 in EGFR-mediated oncogenesis is still unclear. Here, we explore a putative non-canonical function for PSAT1 using biochemical approaches to elucidate unknown interacting proteins and genomic RNA-seq profiling to identify cellular …

Pectin And Alginate Extraction To Treat Liquid Cafo Manure, Clare Sunderman

Honors Projects

For this project, various extraction methods were used to extract pectin from Pastinaca Sativa and alginate from Macrocystis. These extractions were then dried and used in treating 250mL of manure along with a CaCl₂ or FeCl₃ coagulant. It was found that CaCl₂ was not as effective as FeCl₃ in coagulating manure. But the results obtained suggest that pectin and alginate obtained with a simpler extraction method is just as effective as the highly purified and refined pectin and alginate produced for the food industry, in the treatment of CAFO manure. The liquid portion of the …

The Biochemical Characterization Of Aza197 And A Ras Related Protein Cdc42, Alix Montoya-Beltran

Graduate Theses and Dissertations

Eukaryotic cells contain an extensive amount of GTP/GDP binding proteins. Proteins known as Ras GTPase primary function as a binary switch, where they cycle from an on and off state when GTP or GDP are bound, respectively. They are known to play a critical role in many cellular functions where a dysregulation could potentially lead to oncogenic behavior or other malignancies. In our laboratory, our focus is the study of a Ras related protein Cell division control 42 homolog (Cdc42) which belongs to the Rho subfamily. Cdc42 plays a critical role in many biological signaling processes; therefore, its uncontrol gene …