Determining The Nucleic Acid Binding Affinities Of Crispr-Associated Ding (Casding),
2021
Utah State University
Determining The Nucleic Acid Binding Affinities Of Crispr-Associated Ding (Casding), Matt Armbrust
Fall Student Research Symposium 2021
CRISPR-Cas systems are adaptive prokaryotic immune systems that enable host cells to defend against attack from foreign nucleic acids such as phage infections or plasmids. CRISPR-Cas systems are diverse and encompass 2 classes, 6 types, and 33 subtypes. The Type IV-A CRISPR-Cas system from Pseudomonas aeruginosa strain 83 is composed of five different genes (csf1, csf2, csf3, cas6, and dinG). Type IV-A systems are poorly understood, and currently there is little research detailing their biological and biochemical mechanism of immunity. CasDinG, an ancillary protein within the Type IV-A system, is required for an immune response in vivo. However, the role …
Single-Variable Porous Nanomaterial Series From Polymer Structure-Directing Agents,
2021
University of South Carolina
Single-Variable Porous Nanomaterial Series From Polymer Structure-Directing Agents, Morgan Stefik
Faculty Publications
Block polymer structure-directing agents (SDA) enable the production of porous nanoscale materials. Most strategies rely upon polymer equilibration where diverse morphologies are realized in porous functional materials. This review details how solvent selectivity determines the polymer SDA behaviors, spanning from bulk-type to solution-type. Equilibrating behavior of either type, however, obscures nanostructure cause-and-effect since the resulting sample series convolve multiple spatial variations. Solution-type SDA behaviors include both dynamic and persistent micelles. Persistent micelle templates (PMT) use high solvent selectivity for kinetic entrapment. PMTs enable independent wall thickness control with demonstrated 2 Å precision alterations. Unimodal PMT pore size distributions have spanned …
Charting A New Frontier Integrating Mathematical Modeling In Complex Biological Systems From Molecules To Ecosystems,
2021
University of Notre Dame
Charting A New Frontier Integrating Mathematical Modeling In Complex Biological Systems From Molecules To Ecosystems, Katharine A. White, Kira D. Mcentire, Nicole R. Buan, Lecia Robinson, Elisar Barbar
Department of Biochemistry: Faculty Publications
Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, and ecological) have transformed how we understand, categorize, and predict complex biological systems. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. Simultaneously, thanks to increased computational power, mathematicians, engineers, and physical scientists have developed sophisticated models of biological systems at different scales. Novel modeling schemes can offer deeper understanding of principles in biology, but there is still a disconnect between modeling and experimental biology that limits our ability to fully realize …
Elucidation Of The Cellular Mechanisms Underlying Missense Mutations In Low Density Lipoprotein Receptor Related Protein 6 (Lrp6) Associated With Cardiovascular Diseases,
2021
United Arab Emirates University
Elucidation Of The Cellular Mechanisms Underlying Missense Mutations In Low Density Lipoprotein Receptor Related Protein 6 (Lrp6) Associated With Cardiovascular Diseases, Huda Issa Samha
Theses
Low-density Lipoprotein Receptor Related Protein 6 (LRP6) is a member of the Low-Density Lipoprotein Receptors family (LDLRs) which is involved in the clearance of LDL from the bloodstream and the signaling of the canonical wingless signaling pathway. Several genetic variants in the LRP6 gene have been conclusively associated with cardiovascular diseases (CVDs) and metabolic syndrome. However, the structural and functional implications of those variations have not been fully elucidated. The CVD-associated LRP6 variants could be retained and possibly subjected to Endoplasmic Reticulum Associated Degradation (ERAD), a quality control and adaptive process employed by cells to eliminate misfolded proteins to maintain …
Genetically Engineered Thermosynechococcus Elongatus Bp1: Assessment Of Potential Biorisks And Biofuel Production,
2021
Old Dominion University
Genetically Engineered Thermosynechococcus Elongatus Bp1: Assessment Of Potential Biorisks And Biofuel Production, Thu Ho Anh Nguyen-Jones
Chemistry & Biochemistry Theses & Dissertations
According to the International Energy Outlook 2019, released by the U.S. Energy Information Administration, it is projected that the energy consumption will increase up to 50% between 2018 and 2050 worldwide. As fossil fuel being a finite source of energy with the risk of depletion, many countries are now facing an energy security crisis. Therefore, it is important to develop other renewable and sustainable energy sources that will allow countries to shift away from depending on fossil fuels. Among several types of renewable energy, biofuel production using genetically engineered cyanobacteria is capturing much interest due to its many advantages. Different …
Spectroscopic Studies Of The Interaction Between Phosphorus Heterocycles And Cytochrome P450,
2021
University of South Carolina - Columbia
Spectroscopic Studies Of The Interaction Between Phosphorus Heterocycles And Cytochrome P450, Dumei Ma, Libo Zhang, Yingwu Yin, Yuxing Gao, Qian Wang
Faculty Publications
P450 fatty acid decarboxylase OleT from Staphylococcus aureus (OleTSA) is a novel cytochrome P450 enzyme that catalyzes the oxidative decarboxylation of fatty acids to yield primarily terminal alkenes and CO2 or minor α- and β-hydroxylated fatty acids as side-products. In this work, the interactions between a series of cycloalkyl phosphorus heterocycles (CPHs) and OleTSA were investigated in detail by fluorescence titration experiment, ultraviolet–visible (UV–vis) and 31P NMR spectroscopies. Fluorescence titration experiment results clearly showed that a dynamic quenching occurred when CPH-6, a representative CPHs, interacted with OleTSA with a binding constant value of 15.2 …
Molecular Mechanism Of Dna Bisintercalator Antibiotic Resistance,
2021
University of Texas at El Paso
Molecular Mechanism Of Dna Bisintercalator Antibiotic Resistance, Priyanka Rajendra Gade
Open Access Theses & Dissertations
Class II UvrA is an ATP-binding cassette protein and a homolog of class I UvrA, the DNA lesion detection component of the universal prokaryotic nucleotide excision repair system. We show that Ecm16, a class II UvrA protein from Streptomyces lasalocidi, specifically recognizes DNA duplex that contains the DNA bisintercalator antibiotic echinomycin. Heterologous expression of Ecm16 in Escherichia coli renders host cells resistant to echinomycin. Interestingly, Ecm16’s antibiotic resistance activity does not require the DNA repair proteins UvrA/B/C/D, indicating that it operates independently of the cell’s nucleotide excision repair pathway. Unlike UvrA, Ecm16 uses the insertion domain to regulate its ATPase …
Site-Specific Effects Of Lysine Acetylation On Aminoacyl-Trna Synthetase,
2021
University of Arkansas, Fayetteville
Site-Specific Effects Of Lysine Acetylation On Aminoacyl-Trna Synthetase, Hao Chen
Graduate Theses and Dissertations
Aminoacyl-tRNA synthetases (AARSs) are an ancient and highly conserved family of enzymes which can catalyze a two-steps aminoacylation reaction to charge tRNAs with their cognate amino acids, thus playing crucial roles in ribosomal protein synthesis. Naturally, the accurate amino acids and tRNA recognition of these synthetases are essential to the fidelity of translation process. To assure the correct recognition, some of these synthetases have evolved with an editing function to help remove the mischarged tRNAs. In addition to these functions, AARSs are also involved in various biological processes ranging from transcription to translation. Currently, a series of proteomic studies have …
Engineering Fluorescently Labeled Human Fibroblast Growth Factor One Mutants And Characterizing Their Photophysics Properties Towards Designing Fret Assays,
2021
University of Arkansas, Fayetteville
Engineering Fluorescently Labeled Human Fibroblast Growth Factor One Mutants And Characterizing Their Photophysics Properties Towards Designing Fret Assays, Mamello Mohale
Graduate Theses and Dissertations
Human fibroblast growth factor one (hFGF1) belongs to a family of 22 FGF members produced by fibroblast cells. Cell signaling during physiological processes of angiogenesis and wound healing occurs when hFGF1 binds to its receptor (FGFR). However, when heterogenous homeostasis is not maintained, fibroblast cells exhibit excessive proliferation which can lead to a myriad of cancers. smFRET is an ultrasensitive distant dependent (1-10 nm) technique capable of resolving such heterogeneity in structural dynamics and binding affinities (Kd). Therefore, we successfully designed and characterized fluorescently labeled hFGF1 tracers which span the visible light region of the electromagnetic spectrum for use in …
Enzymatic Degradation Of Microcystin-Lr By Microcystinase (Mlra),
2021
University of Arkansas, Fayetteville
Enzymatic Degradation Of Microcystin-Lr By Microcystinase (Mlra), Faisal Alqhtani
Graduate Theses and Dissertations
Microcystin-LR (MC-LR) is affecting the water supply worldwide. Hence, a way to eliminate this toxin is an essential target. In this study, successful cloning of the mlrA gene and producing MlrA enzyme that can degrade the cyclic MC-LR to linearized MC-LR was done. MlrA protein was expressed in Escherichia coli BL-21 (E. coli). Also, enhancing the MlrA yield by adding nickel to LB media was a success in producing more MlrA enzyme from the same volume. Even though the enzyme showed no activity after adding Ni, the enzyme was expressed at a higher yield. Furthermore, it was to investigate adding …
Impact Of Pank1 Deletion On Mitochondrial Acetylation And Cardiac Function During Pressure Overload.,
2021
University of Louisville
Impact Of Pank1 Deletion On Mitochondrial Acetylation And Cardiac Function During Pressure Overload., Timothy N. Audam
Electronic Theses and Dissertations
Recent studies have associated elevated protein acetylation levels with heart failure in humans. Although mechanisms promoting elevated acetylation levels are not fully known, excess acetyl-CoA may drive enzyme-independent acetylation of cardiac proteins. Accumulation of acetyl-CoA depends on the availability of sufficient CoA, whose production is regulated by pantothenate kinases in the CoA biosynthetic pathway. We show that cardiac proteins are hyperacetylated during heart failure in humans and tested in mice whether limiting CoA abundance would improve ventricular remodeling during pressure overload-induced hypertrophy. We limited cardiac CoA levels by deleting the rate-limiting enzyme in CoA biosynthesis, Pank1 (one of three PANK-encoding …
Characterization Of The Multifunctional Enzyme Proline Utilization A,
2021
University of Nebraska-Lincoln
Characterization Of The Multifunctional Enzyme Proline Utilization A, Yizi Mao
Department of Biochemistry: Dissertations, Theses, and Student Research
Proline is a unique and important amino acid. Proline is a proteogenic amino acid and its metabolism is involved in many critical cellular functions. Therefore, proline metabolism is tightly regulated, and dysfunction of proline metabolism is related to human diseases. The first step of proline oxidization to ∆1-pyrroline-5-carboxylic acid (P5C) is catalyzed by proline dehydrogenase (PRODH). P5C is then non-enzymatically hydrolyzed to glutamate-γ-semialdehyde (GSA), which can be further oxidized to glutamate by P5C dehydrogenase (P5CDH/GSALDH). In Gram-negative bacteria, the PRODH and P5CDH enzymes are expressed as one polypeptide called proline utilization A (PutA). In some Gram-negative bacteria an …
Mechanisms Of Stress Survival In Gram Positive Bacterial Pathogens,
2021
Old Dominion University
Mechanisms Of Stress Survival In Gram Positive Bacterial Pathogens, Asia Poudel
Chemistry & Biochemistry Theses & Dissertations
Anaerobic Gram-positive bacteria are not a well-characterized group but include many human pathogens that are resilient against stresses caused by the human immune system or by antibiotic treatment. This dissertation investigated the survival mechanisms of two clinically relevant Gram-positive organisms, Clostridioides difficile and Cutibacterium acnes under extracellular stresses. The response of the opportunistic skin pathogen Cutibacterium acnes to nanosecond electric pulses is characterized and found that growth in a biofilm, which usually protects bacteria from stress, renders this species more killable by this treatment. In addition, the stringent response (SR), a conserved bacterial stress survival mechanism, is studied in the …
Development And Validation Of A Method For The Determination Of Designer Benzodiazepines In Hair By Liquid Chromatography Tandem Mass Spectrometry (Lc-Ms/Ms),
2021
CUNY John Jay College
Development And Validation Of A Method For The Determination Of Designer Benzodiazepines In Hair By Liquid Chromatography Tandem Mass Spectrometry (Lc-Ms/Ms), Laura C. Defreitas
Student Theses
In recent years, new designer benzodiazepines have become a challenge in forensic toxicology. These substances are analogues of the classic benzodiazepines, but their pharmacology is not well known, and many of them have been associated with overdoses and deaths. As a result, there has been a surge in efforts to develop ways to accurately test for these compounds in different biological matrices. This study focused to develop and validate a method for determining 17 new designer benzodiazepines in hair by liquid chromatography tandem mass spectrometry (LC-MS/MS). Hair samples were decontaminated, pulverized, and 20 mg of the sample was incubated in …
Lipidomic Analysis Of Various Developmental Stages Of Physcomitrium Patens,
2021
East Tennessee State University
Lipidomic Analysis Of Various Developmental Stages Of Physcomitrium Patens, Deepshila Gautam
Electronic Theses and Dissertations
Lipids maintain fluidity of the cell membrane during the lifetime of all organisms. The moss Physcomitrium patens, an early land plant, enters reproductive phase under cold (15°C) conditions relative to its gametophytes (22°C). Thus, we hypothesized that their lipid content and composition would be distinct. Using ESI-MS/MS, we showed that the content and acyl composition of 11 lipid classes varied during development. Galactolipids were abundant in gametophytes but insignificant in sporophytes; among phospholipids, phosphatidylcholine was predominant in both phases. Although, sporophytes contained around five-fold less lipids than the gametophyte, their phosphatidic acid content, which accumulates during stress, was 18-fold …
Reintegrating Biology Through The Nexus Of Energy, Information, And Matter,
2021
Colorado State University
Reintegrating Biology Through The Nexus Of Energy, Information, And Matter, Kim L. Hoke, Sara L. Zimmer, Adam B. Roddy, Mary Jo Ondrechen, Craig E. Williamson, Nicole R. Buan
Department of Biochemistry: Faculty Publications
Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that compose this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, …
The Flavoprotein Rcla Is A Hypothiocyanous Acid Reductase,
2021
Western Michigan University
The Flavoprotein Rcla Is A Hypothiocyanous Acid Reductase, Irina Chapman
Masters Theses
Reactive chlorine species (RCS) - hypochlorous acid (HOCl), hypothiocyanous acid (HOSCN), and chloramines - are powerful antimicrobial oxidants generated by the innate immune system. Bacteria developed defense mechanisms against RCS, which are highly toxic for invading pathogens. One such defense system involves RclA, an enzyme from the flavin disulfide reductase family, which is massively upregulated upon exposure of Escherichia coli to RCS. Recent research suggests that RclA functions as a Cu(II) reductase to provide resistance against RCS. However, the exact mechanism used by RclA was subject to debate. In this study, we demonstrate that RclA is unlikely to function as …
Deciphering The Role Of Hsp110 Chaperones In Diseases Of Protein Misfolding,
2021
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Deciphering The Role Of Hsp110 Chaperones In Diseases Of Protein Misfolding, Unekwu M. Yakubu
Dissertations and Theses (Open Access)
Molecular chaperones maintain protein homeostasis (proteostasis) by ensuring the proper folding of polypeptides. Loss of proteostasis has been linked to the onset of numerous neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease. Hsp110 is a member of the Hsp70 class of molecular chaperones and acts as a nucleotide exchange factor (NEF) for Hsp70, the preeminent Hsp70-family protein folding chaperone. Hsp110 promotes rapid cycling of ADP for ATP, allowing Hsp70 to properly fold nascent or unfolded polypeptides in iterative cycles. In addition to its NEF activity, Hsp110 possesses an Hsp70-like substrate binding domain (SBD) whose biological roles are undefined. Previous work …
Agonist-Induced Conformational Changes In The Nmda Receptor,
2021
The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences
Agonist-Induced Conformational Changes In The Nmda Receptor, Ryan Durham, Ryan Durham
Dissertations and Theses (Open Access)
NMDA receptors are ligand-gated ion channels that mediate a number of physiological and pathological phenomena within the mammalian central nervous system. Under the typical course of activation, these receptors bind to glycine and glutamate molecules and undergo a series of conformational changes that results in the opening of a cation-permeable pore in the neuronal plasma membrane. Various aspects of NMDA receptor function are not fully understood, including the phenomenon of negative cooperativity between the glycine- and glutamate-binding sites of the receptor and the mechanism controlling partial agonism. Past studies utilizing static structural snapshots of the receptor or isolated domains of …
Effects Of Localized Oxygen Production By Electrolysis On The First-Generation Glucose Sensor Response,
2021
University of Arkansas, Fayetteville
Effects Of Localized Oxygen Production By Electrolysis On The First-Generation Glucose Sensor Response, Nandita Halder
Graduate Theses and Dissertations
Glucose sensors are very important for detecting blood glucose both in vitro and in vivo. First-generation glucose biosensors were based on the glucose oxidase (GOx) enzyme using molecular oxygen as the electron acceptor and therefore oxygen dependent. Unfortunately for in-vivo work, oxygen in the body is variable and limited. Alternative approaches to overcome the oxygen dependency came with their own limitations. The widely used and commercially available ex-vivo glucose test strip uses a mediator in place of oxygen to free it from oxygen dependency. The mediator-based technology, in most cases cannot be transferred to in vivo applications due to the …
