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Full-Text Articles in Chemistry

Developing A New Sensing Technology For Double-Stranded Dna Detection Utilizing Engineered Zinc Finger Proteins And Nanomaterials, Dat Thinh Ha Oct 2018

Developing A New Sensing Technology For Double-Stranded Dna Detection Utilizing Engineered Zinc Finger Proteins And Nanomaterials, Dat Thinh Ha

Masters Theses & Specialist Projects

A specific double-stranded DNA sensing system is of great interest for diagnostic and other biomedical applications. Zinc finger domains, which recognize double-stranded DNA, can be engineered to form custom DNA-binding proteins for recognition of specific DNA sequences. As a proof of concept, a sequence-enabled reassembly of TEM-1 β- lactamase system (SEER-LAC) was previously demonstrated to develop zinc finger protein (ZFP) arrays for the detection of a double-stranded bacterial DNA sequence. Here, we implemented the SEER-LAC system to demonstrate the direct detection of pathogenspecific DNA sequences present in E. coli O157:H7 on the lab-on-a chip. ZFPs customdesigned to detect shiga toxin …


Folding Of Gα Subunits: Implications For Disease States, Matthew Najor, Brian D. Leverson, Jesse L. Goossens, Saad Kothawala, Kenneth W. Olsen, Duarte Mota De Freitas Oct 2018

Folding Of Gα Subunits: Implications For Disease States, Matthew Najor, Brian D. Leverson, Jesse L. Goossens, Saad Kothawala, Kenneth W. Olsen, Duarte Mota De Freitas

Chemistry: Faculty Publications and Other Works

G-proteins play a central role in signal transduction by fluctuating between “on” and “off” phases that are determined by a conformational change. cAMP is a secondary messenger whose formation is inhibited or stimulated by activated Giα1 or Gsα subunit. We used tryptophan fluorescence, UV/vis spectrophotometry, and circular dichroism to probe distinct structural features within active and inactive conformations from wild-type and tryptophan mutants of Giα1 and Gsα. For all proteins studied, we found that the active conformations were more stable than the inactive conformations, and upon refolding from higher temperatures, activated wild-type subunits recovered significantly more native structure. We also …


Modulating Restriction Endonuclease Activities And Specificities Using Neutral Detergents, Lori H. Conlan, Thomas J. José, Kevin C. Thornton, Cynthia M. Dupureur Aug 2018

Modulating Restriction Endonuclease Activities And Specificities Using Neutral Detergents, Lori H. Conlan, Thomas J. José, Kevin C. Thornton, Cynthia M. Dupureur

Educator Preparation & Leadership Faculty Works

It is well known that type II restriction enzyme activities and specificities can be modulated by altering solution conditions. The addition of co-solvents such as dimethyl sulfoxide (DMSO), alcohols and polyols can promote star activity, which is the cleavage of non-cognate sequences. While neutral detergents are often used to control protein aggregation, little is known about the effect of neutral detergents on restriction enzyme activities and specificities. We report here that BamHI, BglI, BglII, EcoRI, EcoRV, HindIII, MluI, PvuII, SalI and XhoI restriction endonucleases are remarkably tolerant of high concentrations …


P62-Dependent Phase Separation Of Patient-Derived Keap1 Mutations And Nrf2, E. W. Cloer, P. F. Siesser, E. M. Cousins, D Goldfarb, D. D. Mowrey, Joseph S. Harrison, S. J. Weir, N. V. Dokholyan, M. B. Major Aug 2018

P62-Dependent Phase Separation Of Patient-Derived Keap1 Mutations And Nrf2, E. W. Cloer, P. F. Siesser, E. M. Cousins, D Goldfarb, D. D. Mowrey, Joseph S. Harrison, S. J. Weir, N. V. Dokholyan, M. B. Major

College of the Pacific Faculty Articles

Cancer-derived loss-of-function mutations in the KEAP1 tumor suppressor gene stabilize the NRF2 transcription factor, resulting in a pro-survival gene expression program that alters cellular metabolism and neutralizes oxidative stress. In a recent genotype-phenotype study, we classified 40% of KEAP1 mutations as ANCHOR mutants. By immunoprecipitation, these mutants bind more NRF2 than wild-type KEAP1 and ubiquitylate NRF2, but are incapable of promoting NRF2 degradation. BioID-based protein interaction studies confirmed increased abundance of NRF2 within the KEAP1 ANCHOR mutant complexes with no other statistically significant changes to the complexes. Discrete molecular dynamic simulation modeling and limited proteolysis suggest that the ANCHOR mutations …


Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman Aug 2018

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This …


Design And Synthesis Of Circadian Clock Modulators And The Study Of Lov Domain Protein Lkp2 In Arabidosis Thaliana And Brassica Rapa, Aditi Nagar Aug 2018

Design And Synthesis Of Circadian Clock Modulators And The Study Of Lov Domain Protein Lkp2 In Arabidosis Thaliana And Brassica Rapa, Aditi Nagar

Chemistry Theses and Dissertations

Circadian rhythms are self-autonomous endogenous clocks synchronized with the rotation of the Earth. With the Earth’s rotation and revolution on its axis, the internal clock undergoes oscillation in the period of ~24 hour and governs day to day activities in most organisms. In humans, it regulates the day to day physiological activities. Today’s modern lifestyle has an impact on health: shift work, jet lag, and irregular eating habits contribute to the misalignment of the endogenous circadian oscillator, thereby, increasing the risk of many metabolic disorders including diabetes, irregular blood pressure, sleep disorders, obesity, depression, and cancer. The primary goal of …


Ultrafast Laser Filament-Induced Fluorescence Spectroscopy Of Uranyl Fluoride, P. J. Skrodzki, M. Burger, L. A. Finney, F. Poineau, S. M. Balasekaran, J. Nees, K. R. Czerwinski, I. Jovanovic Aug 2018

Ultrafast Laser Filament-Induced Fluorescence Spectroscopy Of Uranyl Fluoride, P. J. Skrodzki, M. Burger, L. A. Finney, F. Poineau, S. M. Balasekaran, J. Nees, K. R. Czerwinski, I. Jovanovic

Chemistry and Biochemistry Faculty Research

Uranyl fluoride (UO2F2) is a compound which forms in the reaction between water and uranium hexafluoride, a uranium containing gas widely used for uranium enrichment. Uranyl fluoride exhibits negligible natural background in atmosphere; as a result, its observation implies the presence and active operation of nearby enrichment facilities and could be used as a tracer for treaty verification technologies. Additionally, detection of UO2F2 has a potential application in guiding remediation efforts around enrichment facilities. Laser-induced fluorescence (LIF) has been proposed in the past as a viable technique for the detection and tracking of UO2F2. We demonstrate that ultrafast laser filamentation …


Manganese Oxide/Hemin-Functionalized Graphene As A Platform For Peroxynitrite Sensing, Haitham F. Kalil, Shaimaa Maher, Tiyash Bose, Mekki Bayachou Aug 2018

Manganese Oxide/Hemin-Functionalized Graphene As A Platform For Peroxynitrite Sensing, Haitham F. Kalil, Shaimaa Maher, Tiyash Bose, Mekki Bayachou

Chemistry Faculty Publications

Peroxynitrite (ONOO−, PON) is a powerful oxidizing agent generated in vivo by the diffusion-limited reaction of nitric oxide (NO) and superoxide (O2˙−) radicals. Under oxidative stress, cumulated peroxynitrite levels are associated with chronic inflammatory disorders and other pathophysiological conditions. The accurate detection of peroxynitrite in biological systems is important, not only to understand the genesis and development of diseases, but also to explore and design potential therapeutics. Herein, a manganese oxide/hemin-modified graphene interface is explored as a platform for peroxynitrite amperometric detection. Hemin-functionalized reduced graphene oxide was further modified with manganese oxide nanoparticles to provide a …


Development Of Rapid, Homogeneous Assay For Investigating Isopeptide Bond Formation Using Fluorescence Polarization/Depolarization Measurements, Samuel Patricc Kasson Aug 2018

Development Of Rapid, Homogeneous Assay For Investigating Isopeptide Bond Formation Using Fluorescence Polarization/Depolarization Measurements, Samuel Patricc Kasson

Graduate Theses/Dissertations

Autocatalytic intramolecular isopeptide bonds have been found in nature in certain gram-positive bacterial pilus structures. Recently, splitting of these domains that are capable of autocatalytic intramolecular isopeptide bond formation have been applied to create stable, selective, bio-orthogonal Catcher/Tag systems. The CnaB2 domain found in the FbaB pilus structure of Streptococcus pyogenes, has yielded the Catcher/Tag, Protein/Peptide systems termed SpyCatchter and SpyTag. Recent study has focused on tag optimization, stability and bio-orthogonality evaluation, along with applications in bioconjugation. I have recombinantly expressed SpyCatcher and SpyTag-fused proteins in E.coli, and conjugated them to fluorescent probes in order for use in fluorescence polarization/depolarization …


Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor Aug 2018

Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor

Electronic Theses and Dissertations

Metabolomics, the study of small molecules in biological systems, has enjoyed great success in enabling researchers to examine disease-associated metabolic dysregulation and has been utilized for the discovery biomarkers of disease and phenotypic states. In spite of recent technological advances in the analytical platforms utilized in metabolomics and the proliferation of tools for the analysis of metabolomics data, significant challenges in metabolomics data analyses remain. In this dissertation, we present three of these challenges and Bayesian methodological solutions for each. In the first part we develop a new methodology to serve a basis for making higher order inferences in metabolomics, …


Fluorescently Labeled Sirnas And Their Theranostic Applications In Cancer Gene Therapy, Stephen David Kozuch Aug 2018

Fluorescently Labeled Sirnas And Their Theranostic Applications In Cancer Gene Therapy, Stephen David Kozuch

Seton Hall University Dissertations and Theses (ETDs)

Gene therapy has emerged as a promising precision nano-medicine strategy in the treatment of numerous diseases including cancer. At the forefront of its utility are the applications of short-interfering RNA (siRNA), that silence oncogenic mRNA expression leading to cancer cell death through the RNA interference (RNAi) pathway. Despite the therapeutic potential, siRNAs are limited by poor pharmacological properties, which has hindered their translation into the clinic. Recent studies, however, have highlighted the applications of modified siRNAs, including the use of fluorescent probes and siRNA nanostructures in cancer detection and treatment. The siRNAs reported in this thesis are designed to target …


Nickel Exposure Reduces Enterobactin Production In Escherichia Coli, Clorissa L. Washington-Hughes, Geoffrey T. Ford, Alsten D. Jones, Kimberly Mcrae, Franklin Wayne Outten Jul 2018

Nickel Exposure Reduces Enterobactin Production In Escherichia Coli, Clorissa L. Washington-Hughes, Geoffrey T. Ford, Alsten D. Jones, Kimberly Mcrae, Franklin Wayne Outten

Faculty Publications

Escherichia coli is a well- studied bacterium that can be found in many niches, such as industrial wastewater, where the concentration of nickel can rise to low- millimolar levels. Recent studies show that nickel exposure can repress pyochelin or induce pyo-verdine siderophore production in Pseudomonas aueroginosa. Understanding the mo-lecular cross- talk between siderophore production, metal homeostasis, and metal toxicity in microorganisms is critical for designing bioremediation strategies for metal- contaminated sites. Here, we show that high- nickel exposure prolongs lag phase duration as a result of low- intracellular iron levels in E. coli. Although E. coli cells respond to low- …


Conjugation Of Nanomaterials And Nematic Liquid Crystals For Futuristic Applications And Biosensors, Thomas George, Amit Choudhary, Guoqiang Li Jul 2018

Conjugation Of Nanomaterials And Nematic Liquid Crystals For Futuristic Applications And Biosensors, Thomas George, Amit Choudhary, Guoqiang Li

Chemistry & Biochemistry Faculty Works

The established role of nematic liquid crystals (NLCs) in the recent rapid development of displays has motivated researchers to modulate the electro-optical properties of LCs. Furthermore, adding nanomaterials into NLCs has led to enhancements of the properties of NLCs, like reduced threshold of the operating voltage, variation in pretilt angle, reduced switching time, etc. These enhanced properties, due to interfacial dynamics, are enabling wider applications of NLCs and nanomaterials. The recent literature of nanomaterial-doped NLCs is rich with various kinds of nanomaterials in a variety of NLCs. The light has been focused on the most widely used and studied gold …


Cross Photoreaction Of Glyoxylic And Pyruvic Acids In Model Aqueous Aerosol, Sha-Sha Xia, Alexis J. Eugene, Marcelo I. Guzman Jul 2018

Cross Photoreaction Of Glyoxylic And Pyruvic Acids In Model Aqueous Aerosol, Sha-Sha Xia, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

Aerosols of variable composition, size, and shape are associated with public health concerns as well as with light-particle interactions that play a role in the energy balance of the atmosphere. Photochemical reactions of 2-oxocarboxylic acids in the aqueous phase are now known to contribute to the total secondary organic aerosol (SOA) budget. This work explores the cross reaction of glyoxylic acid (GA) and pyruvic acid (PA) in water, the two most abundant 2-oxocarboxylic acids in the atmosphere, under solar irradiation and dark thermal aging steps. During irradiation, PA and GA are excited and initiate proton-coupled electron transfer or hydrogen abstraction …


High-And Low-Temperature Pyrolysis Profiles Describe Volatile Organic Compound Emissions From Western Us Wildfire Fuels, Kanako Sekimoto, Abigail R. Koss, Jessica B. Gilman, Vanessa Selimovic, Matthew M. Coggon, Kyle J. Zarzana, Bin Yuan, Brian M. Lerner, Steven S. Brown, Carsten Warneke, Robert J. Yokelson, James M. Roberts, Joost De Gouw Jul 2018

High-And Low-Temperature Pyrolysis Profiles Describe Volatile Organic Compound Emissions From Western Us Wildfire Fuels, Kanako Sekimoto, Abigail R. Koss, Jessica B. Gilman, Vanessa Selimovic, Matthew M. Coggon, Kyle J. Zarzana, Bin Yuan, Brian M. Lerner, Steven S. Brown, Carsten Warneke, Robert J. Yokelson, James M. Roberts, Joost De Gouw

Chemistry and Biochemistry Faculty Publications

Biomass burning is a large source of volatile organic compounds (VOCs) and many other trace species to the atmosphere, which can act as precursors to secondary pollutants such as ozone and fine particles. Measurements performed with a proton-transfer-reaction time-of-flight mass spectrometer during the FIREX 2016 laboratory intensive were analyzed with positive matrix factorization (PMF), in order to understand the instantaneous variability in VOC emissions from biomass burning, and to simplify the description of these types of emissions. Despite the complexity and variability of emissions, we found that a solution including just two emission profiles, which are mass spectral representations of …


A Series Of 4- And 5-Coordinate Ni(Ii) Complexes: Synthesis, Characterization, Spectroscopic, And Dft Studies, Jack Ghannam, Talal Al Assil, Trey C. Pankratz, Richard L. Lord, Matthias Zeller, Wei-Tsung Lee Jul 2018

A Series Of 4- And 5-Coordinate Ni(Ii) Complexes: Synthesis, Characterization, Spectroscopic, And Dft Studies, Jack Ghannam, Talal Al Assil, Trey C. Pankratz, Richard L. Lord, Matthias Zeller, Wei-Tsung Lee

Chemistry: Faculty Publications and Other Works

A series of four- and five-coordinate Ni(II) complexes CztBu(PyriPr)2NiX (1–3 and 1·THF–3·THF), where X = Cl, Br, and I, were synthesized and fully characterized by NMR and UV–vis spectroscopy, X-ray crystallography, cyclic voltammetry, and density functional theory calculations. The solid-state structures of 1–3 reveal rare examples of seesaw Ni(II) complexes. In solution, 1–3 bind reversibly to a THF molecule to form five-coordinate adducts. The electronic transitions in the visible region (630–680 nm), attributed to LMCT bands, for 1 → 3 exhibit a …


Interrogation Of Protein Function With Peptidomimetics, Olapeju Bolarinwa Jul 2018

Interrogation Of Protein Function With Peptidomimetics, Olapeju Bolarinwa

USF Tampa Graduate Theses and Dissertations

Proteins can be described as the “machineries” responsible for almost all tasks in the levels of organizational complexity in multi-cellular organisms namely: the cells, tissues, organs and systems. Any disorder in the function of a protein at any of these levels could result in disease, and a study of protein function is critical to understanding the pathological features of the disease at the molecular level. A quick glance at these abundantly present proteins reveals two striking features: large diversity of biological function, and the variations in structural complexity, which varies from simple random coils, to turns and helices, and on …


Hydrogen Sulfide Gas Detection Via Multivariate Optical Computing, Bin Dai, Christopher Michael Jones, Megan Pearl, Mickey Pelletier, Michael L. Myrick Jul 2018

Hydrogen Sulfide Gas Detection Via Multivariate Optical Computing, Bin Dai, Christopher Michael Jones, Megan Pearl, Mickey Pelletier, Michael L. Myrick

Faculty Publications

Hydrogen-sulfide gas is a toxic, colorless gas with a pungent odor that occurs naturally as a decomposition by-product. It is critical to monitor the concentration of hydrogen sulfide. Multivariate optical computing (MOC) is a method that can monitor analytes while minimizing responses to interferences. MOC is a technique by which an analogue calculation is performed entirely in the optical domain, which simplifies instrument design, prevents the drift of a calibration, and increases the strength and durability of spectroscopic instrumentation against physical perturbation when used for chemical detection and identification. This paper discusses the detection of hydrogen-sulfide gas in the ultraviolet …


Characterizing The Activity Of Antimicrobial Peptides Against The Pathogenic Bacterium Clostridium Difficile In An Anaerobic Environment, Adenrele Mojeed Oludiran Jul 2018

Characterizing The Activity Of Antimicrobial Peptides Against The Pathogenic Bacterium Clostridium Difficile In An Anaerobic Environment, Adenrele Mojeed Oludiran

Chemistry & Biochemistry Theses & Dissertations

Clostridium difficile is an anaerobic Gram-positive pathogen with high treatment costs and mortality and very high antibiotic tolerance. Antimicrobial host-defense peptides (HDPs) produced naturally by animal immune systems are promising candidates to develop novel therapies for bacterial infection because they cause oxidative stress that damages multiple targets in bacterial cells, so it is difficult for bacteria to evolve resistance to these attacks.

Piscidins, fish-derived HDPs that can also form complexes with copper (Cu) to enhance their activities, are very active against multiple bacterial species in an aerobic environment. We examined their activity against C. difficile and other species in an …


Advances In Amino Acid Analysis For Marine Related Matrices And Its Application To Coastal Shelf Settings In The Canadian Arctic, Rachel M. Mcmahon Jul 2018

Advances In Amino Acid Analysis For Marine Related Matrices And Its Application To Coastal Shelf Settings In The Canadian Arctic, Rachel M. Mcmahon

OES Theses and Dissertations

Amino acids comprise up to 50% of organic matter in cellular material and are a major fraction of oceanic organic carbon. Amino acids are also considered highly labile during organic matter recycling, making them useful proxies for organic carbon cycling. Nevertheless, analysis of individual amino acids has been burdened by lengthy derivatization and complex analysis since the 1950s. In this thesis, I describe the modification of advanced analytical techniques, developed in the biomedical field, for analysis of marine matrices which allow the determination of at least 40 amino acids without the need for lengthy sample preparation and derivatization, twice the …


Glucosamine From Hydrolysis Of 3d Printing Chitosan For Osteoarthritis Treatment, Ruj Dansriboon, Laphon Premcharoen Jun 2018

Glucosamine From Hydrolysis Of 3d Printing Chitosan For Osteoarthritis Treatment, Ruj Dansriboon, Laphon Premcharoen

The International Student Science Fair 2018

This project aims to introduce a new way for osteoarthritis treatment which is expected to increase in the future. Glucosamine is the main subject for a treatment, which can be derived by hydrolyzing chitosan. This project also includes extraction of chitosan from shrimp waste to make a worthy use of food waste from industry. In this project, 3D printer is applied to print chitosan gel since 3D printing is adjustable to form various shapes of the gel.

The research process begins with the extraction of chitosan from shrimp shells. For the next step, the percent of deacetylation of chitosan was …


N-Glycosylation In The Protease Domain Of Trypsin-Like Serine Proteases Mediates Calnexin-Assisted Protein Folding, Hao Wang, Shuo Li, Juejin Wang, Shenghan Chen, Xue-Long Sun, Qingyu Wu Jun 2018

N-Glycosylation In The Protease Domain Of Trypsin-Like Serine Proteases Mediates Calnexin-Assisted Protein Folding, Hao Wang, Shuo Li, Juejin Wang, Shenghan Chen, Xue-Long Sun, Qingyu Wu

Chemistry Faculty Publications

Trypsin-like serine proteases are essential in physiological processes. Studies have shown that N-glycans are important for serine protease expression and secretion, but the underlying mechanisms are poorly understood. Here, we report a common mechanism of N-glycosylation in the protease domains of corin, enteropeptidase and prothrombin in calnexin-mediated glycoprotein folding and extracellular expression. This mechanism, which is independent of calreticulin and operates in a domain-autonomous manner, involves two steps: direct calnexin binding to target proteins and subsequent calnexin binding to monoglucosylated N-glycans. Elimination of N-glycosylation sites in the protease domains of corin, enteropeptidase and prothrombin inhibits corin and enteropeptidase cell surface …


Comparison Between Tetrel Bonded Complexes Stabilized By Σ And Π Hole Interactions, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner Jun 2018

Comparison Between Tetrel Bonded Complexes Stabilized By Σ And Π Hole Interactions, Wiktor Zierkiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH4, TH3F, and TH2F2 (T = Si, Ge, Sn) and the latter by TH2=CH2, THF=CH2, and TF2=CH2, all paired with NH3 as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of …


Facially Amphiphilic Polyionene Biocidal Polymers Derived From Lithocholic Acid, Mitra S. Ganewatta, Md Anisur Rahman, Louis Mercado, Tinom Shokfai, Alan W. Decho, Theresa M. Reineke, Chuanbing Tang Jun 2018

Facially Amphiphilic Polyionene Biocidal Polymers Derived From Lithocholic Acid, Mitra S. Ganewatta, Md Anisur Rahman, Louis Mercado, Tinom Shokfai, Alan W. Decho, Theresa M. Reineke, Chuanbing Tang

Faculty Publications

Bacterial infections have become a global issue that requires urgent attention, particularly regarding to emergence of multidrug resistant bacteria. We developed quaternary amine-containing antimicrobial poly(bile acid)s that contain a hydrophobic core of lithocholic acid in the main-chain. Interestingly, by choosing appropriate monomers, these cationic polymers can form core-shell micelles. These polymers exhibited biocidal activity against both Gram-positive and Gram-negative bacterial species. It is demonstrated that the micelles can deliver hydrophobic antibiotics that functionally have dual antimicrobial activities. Cytotoxicity assays against HeLa cells showed dosage-dependent toxicity for polymers with longer linkers.


Fluorescent Probes And Functionalized Nanoparticles For Bioimaging: Synthesis, Photophysical Properties And Applications, Xinglei Liu May 2018

Fluorescent Probes And Functionalized Nanoparticles For Bioimaging: Synthesis, Photophysical Properties And Applications, Xinglei Liu

Dissertations

The development of new organic molecular probes with excellent photophysical properties and high fluorescence quantum yields is of considerable interest to many research areas including one- and two-photon fluorescence microscopy, fluorescence-based sensing methodologies, and cancer therapy. Series of organic linear-/non-linear optical molecules including squaraine derivatives, and fluorene derivatives as well as other bioconjugates are designed and synthesized during the doctoral study for the aim of ion detection (Chapter 5), photo dynamic therapy, and deep-tissue imaging (Chapter 4). These optical probes are capable of absorbing light in the near infrared (NIR) window and thus have deeper penetration and cause less photodamage …


Design And Assessment Of Small Molecules As Free Radical Scavengers And Potential Multi-Target Therapeutic Agents Against Alzheimer’S Disease, Diabetes And Cancer, William Horton May 2018

Design And Assessment Of Small Molecules As Free Radical Scavengers And Potential Multi-Target Therapeutic Agents Against Alzheimer’S Disease, Diabetes And Cancer, William Horton

Graduate Doctoral Dissertations

Complex diseases such as Alzheimer’s disease (AD), diabetes and cancer are difficult to manage with single target treatment approaches and unfortunately, they are wide-spread. For example, over 16 million people are expected to have AD in the US by 2050, thus new therapeutic approaches have to be developed. Multi-functional drug candidates have gained increasing popularity in treating complex diseases. The impact of oxidative stress in almost every disease progression makes them essential components in therapies for complex diseases. Endogenous systems typically maintain redox homeostasis within the cell, but in the diseased state these systems fail to alleviate oxidative stress. Supplementation …


Comparative Biochemical Analysis Of Uhrf Proteins Reveals Molecular Mechanisms That Uncouple Uhrf2 From Dna Methylation Maintenance, Robert M. Vaughan, Bradley M. Dickson, Evan M. Cornett, Joseph S. Harrison, Brian Kuhlman, Scott B. Rothbart May 2018

Comparative Biochemical Analysis Of Uhrf Proteins Reveals Molecular Mechanisms That Uncouple Uhrf2 From Dna Methylation Maintenance, Robert M. Vaughan, Bradley M. Dickson, Evan M. Cornett, Joseph S. Harrison, Brian Kuhlman, Scott B. Rothbart

College of the Pacific Faculty Articles

UHRF1 is a histone- and DNA-binding E3 ubiquitin ligase that functions with DNMT1 to maintain mammalian DNA methylation. UHRF1 facilitates DNMT1 recruitment to replicating chromatin through a coordinated mechanism involving histone and DNA recognition and histone ubiquitination. UHRF2 shares structural homology with UHRF1, but surprisingly lacks functional redundancy to facilitate DNA methylation maintenance. Molecular mechanisms uncoupling UHRF2 from DNA methylation maintenance are poorly defined. Through comprehensive and comparative biochemical analysis of recombinant human UHRF1 and UHRF2 reader and writer activities, we reveal conserved modes of histone PTM recognition but divergent DNA binding properties. While UHRF1 and UHRF2 diverge in their …


Characterization Of A Catalyst-Based Conversion Technique To Measure Total Particulate Nitrogen And Organic Carbon And Comparison To A Particle Mass Measurement Instrument, Chelsea E. Stockwell, Agnieszka Kupc, Bartlomiej Witkowski, Ranajit K. Talukdar, Yong Liu, Vanessa Selimovic, Kyle J. Zarzana, Kanako Sekimoto, Carsten Warneke, Rebecca A. Washenfelder, Robert J. Yokelson, Ann M. Middlebrook, James M. Roberts May 2018

Characterization Of A Catalyst-Based Conversion Technique To Measure Total Particulate Nitrogen And Organic Carbon And Comparison To A Particle Mass Measurement Instrument, Chelsea E. Stockwell, Agnieszka Kupc, Bartlomiej Witkowski, Ranajit K. Talukdar, Yong Liu, Vanessa Selimovic, Kyle J. Zarzana, Kanako Sekimoto, Carsten Warneke, Rebecca A. Washenfelder, Robert J. Yokelson, Ann M. Middlebrook, James M. Roberts

Chemistry and Biochemistry Faculty Publications

The chemical composition of aerosol particles is a key aspect in determining their impact on the environment. For example, nitrogen-containing particles impact atmospheric chemistry, air quality, and ecological N deposition. Instruments that measure total reactive nitrogen (Nr Combining double low line all nitrogen compounds except for N2 and N2O) focus on gas-phase nitrogen and very few studies directly discuss the instrument capacity to measure the mass of Nr-containing particles. Here, we investigate the mass quantification of particle-bound nitrogen using a custom Nr system that involves total conversion to nitric oxide (NO) across platinum and molybdenum catalysts followed by NOĝ'O3 chemiluminescence …


Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield May 2018

Organic Compound Emissions From A Landfarm Used For Oil And Gas Solid Waste Disposal, Seth N. Lyman, Marc L. Mansfield

Chemistry and Biochemistry Faculty Publications

Solid or sludgy hydrocarbon waste is a byproduct of oil and gas exploration and production. One commonly-used method of disposing of this waste is landfarming. Landfarming involves spreading hydrocarbon waste on soils, tilling it into the soil, and allowing it to biodegrade. We used a dynamic flux chamber to measure fluxes of methane, a suite of 54 non-methane hydrocarbons, and light alcohols from an active and a remediated landfarm in eastern Utah, U.S.A. Fluxes from the remediated landfarm were not different from a PTFE sheet or from undisturbed soils in the region. Fluxes of methane, total non-methane hydrocarbons, and alcohols …


Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson May 2018

Structure Of Frequency-Interacting Rna Helicase From Neurospora Crassa Reveals High Flexibility In A Domain Critical For Circadian Rhythm And Rna Surveillance, Yalemi Morales, Keith J. Olsen, Jacqueline M. Bulcher, Sean J. Johnson

Chemistry and Biochemistry Faculty Publications

The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH …