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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

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 …

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 …

The Role Of Nutrition And Hormone Signaling In Extended Larval Development And Obesity In Starvation-Selected Drosophila Melanogaster, Jennifer M. Clark

UNLV Theses, Dissertations, Professional Papers, and Capstones

Brief periods of starvation are a common stressor that most animals encounter in the wild and must be able to survive in order to maximize their fitness. Starvation resistance of the adult fruit fly, Drosophila melanogaster, is thought to be primarily conferred by adult fat stores, body size, metabolic rate, behavior, and activity levels. Additionally, flies selected for starvation resistance also often show delayed pupariation, which is usually indicative of altered hormone signaling. How starvation selection extends development and if it contributes to adult starvation resistance remains incompletely studied. Identifying the targets of starvation selection that cause extended development 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 …

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 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 …

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 …

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 …

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 …

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 …

Studies Of The Dutpase Of The Western Corn Rootworm, Carlos A. Riera-Ruiz

School of Biological Sciences: Dissertations, Theses, and Student Research

The western corn rootworm (WCR), Diabrotica virgifera virgifera, is a major corn pest in the United States and Europe. WCR has developed resistance to multiple management strategies, including Cry proteins. Even though the biology and ecology have been thoroughly studied in WCR, their genome and molecular mechanisms are understudied. This work focuses on the ubiquitous enzyme deoxyuridine triphosphatase (dUTPase) encoded by the DUT gene. dUTPase hydrolyzes dUTP into dUMP and pyrophosphate. It contributes to genome stability by keeping the uracil-to-thymine ratio at a certain level. In WCR, two dUTPase isoforms were predicted using transcriptome analyses. These two potential isoforms …

Biochemical Characterization Of Small Molecule Inhibitor Binding On A Ras Related Gtpase And Its Effector Interactions, Djamali Muhoza

Graduate Theses and Dissertations

The Ras superfamily of GTPases has 167 proteins that are involved in various cellular processes such as proliferation, transformation, migration, and inhibition of cell death. Mutations, abnormal expression, and function of these proteins are observed in many diseases, including several forms of cancer. Even though these GTPases were among the first discovered oncogenes, no successful Ras drug candidate has successfully passed clinical trials. Drugs targeting these proteins have failed mainly because of the complexity of their regulation, their high affinity to GTP, and their structure’s dynamic nature. Recently, novel promising targeting approaches have renewed interest in the Ras drug discovery …

Machine Learning Models For Deciphering Regulatory Mechanisms And Morphological Variations In Cancer, Saman Farahmand

Graduate Doctoral Dissertations

The exponential growth of multi-omics biological datasets is resulting in an emerging paradigm shift in fundamental biological research. In recent years, imaging and transcriptomics datasets are increasingly incorporated into biological studies, pushing biology further into the domain of data-intensive-sciences. New approaches and tools from statistics, computer science, and data engineering are profoundly influencing biological research. Harnessing this ever-growing deluge of multi-omics biological data requires the development of novel and creative computational approaches. In parallel, fundamental research in data sciences and Artificial Intelligence (AI) has advanced tremendously, allowing the scientific community to generate a massive amount of knowledge from data. Advances …

Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli, Carson Ercanbrack

Chemistry & Biochemistry Undergraduate Honors Theses

The primary purpose of this project is to evaluate the genes that play a role in the oxidative stress response in Escherichia coli. In doing so, the entire genome of E. coli was subject to throughput in which individual genes were determined to have a role in the bacteria’s oxidative stress response. Moreover, this project focused on the validation of the genes that were able to pass the initial throughput stage. The genes were subject to two forms of validation. In the first validation technique, candidate genes were overexpressed and minimum inhibitory concentrations of hypochlorous acid were taken. Following, a …

Understanding The Non-Classical Secretion Mechanism Of Interleukin-1 Alpha, Clay Martin

Chemistry & Biochemistry Undergraduate Honors Theses

The Interleukin 1 family is a unique collection of cytokines in that they are primarily associated with both acute and chronic inflammation, which is associated with many diseases. In classical protein secretion, a protein, typically with an N-terminal signal peptide, is synthesized on a ribosome of a cell either in the cytoplasm or on the rough endoplasmic reticulum, transported to and merges with the Golgi apparatus, and is then sent to bind with either a lysosome or the cell membrane or is released from the cell via exocytosis. Thus, a non-classical secretion mechanism is any mechanism that differs from this. …

Reaction Pathways Initiated By One-Electron Oxidation Of Guanine: Reaction Pathways Leading To Stable End Products, Zach Cutright

Undergraduate Honors Theses

8-hydroxyguanine (8-oxoG) is one of the most important products resulting from the oxidation of guanine in DNA. 8-oxoG is known as a biomarker of oxidative stress such as lung cancer. 2,5-diamino-4H-imidazol-4-one (Iz) and its hydrolysis product 2,2-diamino-4-[(2-deoxy-β-D-erythro-pentofuranosyl)-amino]-2,5-dihydrooxazol-5-one (Oz) are also important products of oxidation of guanine in DNA. Recently, novel types of dimer intermediates related to 8-oxoG and Iz have been identified in our research lab. Using high performance liquid chromatography (HPLC), LC-MS, and NMR coupled with educated hypotheses, it is possible to identify the products, X1 and X2, resulting from the oxidation of guanine and decipher the mechanisms leading …

Analyzing The Effects Of E-Hook Peptides On Kinesin-1, Ashton Ward Murrah, Baylee Hope Howard

Honors Theses

Cancer is the second leading cause of death in the United States. Cancerous growth is a result of oncogenes, or mutated genes that increase the rate of cell division in an uncontrolled manner. Cell division, which consists of mitosis and cytokinesis phases, is dependent upon the active movement of kinesin motor proteins along microtubules to rearrange the cytoskeleton for equitable distribution of genetic material to daughter cells. As kinesins are vital to this process, if we could prevent kinesin from binding to the microtubules, cell division would cease.

The goal of this study is to develop a method to prevent …

Detailed Analysis Of The Role Of Mtr4 Arch Domain In Rna Binding And Helicase Activity, Keith J. Olsen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The central dogma of biology states that DNA is transcribed into RNA, which is translated into protein. However, this concept portrays RNA purely as an intermediary step from DNA to protein. RNA plays an essential and vital role in a cell, including; regulating protein and RNA levels, act as a template for protein synthesis, cell differentiation, regulatory processes, and signaling molecules. If cells do not adequately monitor and regulate RNA levels, it can lead to disease states and even cell death. The main protein complex that regulates the maturation and degradation of RNA in the nucleus is the RNA nuclear …

Remote Performance Modulation Of Ultrafiltration Membranes By Magnetically And Thermally Responsive Polymer Chains, Arijit Sengupta, Anh Vu, Xianghong Qian, Sumith R. Wickramasinghe

Chemical Engineering Faculty Publications and Presentations

Ultrafiltration membranes, that respond to an external magnetic field and local temperature have been developed. Surface-initiated activator-generated electron transfer (AGET) atom transfer radical polymerization (ATRP) has been used to graft poly(N-isopropylacrylamide) (PNIPAm) from the surface of 300 kDa regenerated cellulose membranes. The polymerization initiator was selectively attached to the entire membrane surface, only the outer membrane surface or only the inner pore surface. A superparamagnetic nanoparticle was attached to the end of the polymer chain. The DI water flux as well as the flux and rejection of bovine serum albumin were investigated in the absence and presence of a 20 …

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 …