Effects Of Crowding Agents On I-Motif Dna,
2021
University of Mississippi
Effects Of Crowding Agents On I-Motif Dna, Hayden Brines
Honors Theses
Deoxyribonucleic acid (DNA) is a well-known double stranded, helical, biological molecule. In addition to its more commonly known structure, DNA can also form more complicated structures like G-quadruplexes and i-motifs (iM). The iMs are formed by cytosine rich DNA and are a four stranded structure that is typically looped around itself. The iM formation is typically pH-dependent and is favored in more acidic conditions; the pKa value is approximately 6.5. This pKa value allows for potential in vivo formation, since the cells have a pH of approximately 7.3. Due to this, iMs are thought to be powerful, innovative molecules for …
Chemical And Co-Solute Effects Of Polyethylene Glycol On I-Motif Formation,
2021
University of Mississippi
Chemical And Co-Solute Effects Of Polyethylene Glycol On I-Motif Formation, Lindsey Rutherford
Honors Theses
DNA typically forms Watson and Crick double helix structures in which adenine, thymine, guanine, and cytosine pair with their complimentary DNA base. However, DNA i-motif structures can form in cytosine rich DNA, typically under slightly acidic conditions (~pH 6). DNA i-motifs are four stranded secondary structures in which cytosine pairs with cytosine to form a quadruplex. The i-motifs are typically formed in acidic conditions because of the protonation in the C•C base pair between one of the three hydrogen bases. Recent studies have suggested i-motifs can also form under neutral conditions, which is more realistic for a cell. It is …
Covalent Modification Of Genetically Engineered Polymers With Bodipy Fluorophores,
2021
University of Mississippi
Covalent Modification Of Genetically Engineered Polymers With Bodipy Fluorophores, Emilie Smith
Honors Theses
Osteoarthritis and other debilitating diseases cause chronic pain that is difficult to manage. Nonsteroidal Anti-inflammatory Drugs (NSAIDs) are the current standard of treatment for many long-term pain management, but there are potential systemic effects when using NSAIDs long-term. Therefore, it isnecessary to have an alternative option for NSAID delivery that doesn’t include these systemic effects. Hydrogels can be that alternative option. Hydrogels’ distinct characteristics allow them to be viable in the body, degrade under unique conditions, and be modified through many different chemistries. Additionally, hydrogels can be engineered and their properties optimized for the use as a drug depot inside …
Remote Performance Modulation Of Ultrafiltration Membranes By Magnetically And Thermally Responsive Polymer Chains,
2021
Bhabha Atomic Research Centre
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 …
Pectin And Alginate Extraction To Treat Liquid Cafo Manure,
2021
Bowling Green State University
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 …
Ampa And Kainate Receptor-Potentiating Rna Aptamers,
2021
University at Albany, State University of New York
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 …
Nutritional Data And Corresponding Performance Impacts Of Uri Student-Athletes,
2021
University of Rhode Island
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 …
The Biochemical Characterization Of Aza197 And A Ras Related Protein Cdc42,
2021
University of Arkansas, Fayetteville
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,
2021
University of Tennessee at Chattanooga
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,
2021
University of Tennessee at Chattanooga
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,
2021
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
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 …
Rna G-Quadruplex Structures: Functions In Noncoding Rnas And Disease,
2021
Duquesne University
Rna G-Quadruplex Structures: Functions In Noncoding Rnas And Disease, Emily Benner
Electronic Theses and Dissertations
Paraspeckles are a relatively newly identified subnuclear body whose function is still largely unknown. They are membraneless organelles found within mammalian nuclei originally identified as being comprised of different paraspeckle proteins (PSPs), and later proven to also contain RNA. This study investigates the long non-coding RNA nuclear enriched abundant transcript 1 (NEAT1), which has been found to be indispensable in the formation of paraspeckles, with each containing up to 50 NEAT1 molecules. NEAT1 has two isoforms, the shorter NEAT1_1, and the longer NEAT1_2. The focus of this work will be on the NEAT1_2, which acts as a scaffold in the …
Validation Of Anti-Oxidative Stress Genes From Genome-Wide Screening Of Escherichia Coli,
2021
University of Arkansas, Fayetteville
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 …
Investigating A Novel Function For Phosphoserine Aminotransferase 1 (Psat1) In Epidermal Growth Factor Receptor (Egfr)-Mediated Lung Tumorigenesis.,
2021
University of Louisville
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 …
Studies Of The Dutpase Of The Western Corn Rootworm,
2021
University of Nebraska-Lincoln
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,
2021
University of Arkansas, Fayetteville
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 …
Understanding The Non-Classical Secretion Mechanism Of Interleukin-1 Alpha,
2021
University of Arkansas, Fayetteville
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. …
Simulation Of The Interaction Between Striated Muscle Unc-45 And Transcription Factor Gata-4,
2021
Stephen F. Austin University
Simulation Of The Interaction Between Striated Muscle Unc-45 And Transcription Factor Gata-4, Drake Alexander Duncan
Electronic Theses and Dissertations
Striated Muscle UNC-45, also known as UNC-45b, is an important protein that acts as a chaperone for myosin in cardiac and skeletal muscles, binding to myosin at its C-terminal UCS domain and regulating its assembly into thick filaments and sarcomeric structures. The UCS domain contains a large loop that is believed to be the first point of interaction between myosin and UNC-45b. GATA-4 is an essential transcription factor that facilitates transcription of several genes in cardiac development, particularly alpha-heavy chain myosin in heart tissue. Recently, studies have shown that there is interaction of GATA-4 with UNC-45b and that GATA-4 binds …
Detailed Analysis Of The Role Of Mtr4 Arch Domain In Rna Binding And Helicase Activity,
2021
Utah State University
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 …
Characterizing Oligomeric State Changes Of Protein Arginine Methyltransferase 1 As A Mechanism For Regulating Activity,
2021
Utah State University
Characterizing Oligomeric State Changes Of Protein Arginine Methyltransferase 1 As A Mechanism For Regulating Activity, Ariana N. Ortolano
All Graduate Theses and Dissertations, Spring 1920 to Summer 2023
If you imagined a living cell as a factory, enzymes would be the workers with each individually performing a very specific and important job. If a job is not done correctly it could be detrimental to the performance of assembly lines and devastate a businesses’ existence. For enzymes, their jobs occur on a biological level by catalyzing reactions inside the cell, which can include altering another protein and the pathway it is involved in. Protein arginine methyltransferases, or PRMTs, is an example of an enzyme that modifies protein substrates. It does this by adding one or two methyl groups onto …
