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Automating And Implementing Complex, Multistep Sample Preparation Processes To Generate Reproducible Proteomic And Phosphoproteomic Data, Brian Todd Mullis

Theses and Dissertations

Phosphorylation is the most common post-translational modification that occurs within the cell and is intricately involved in many biological processes. It is important to understand the roles that protein kinases and phosphatases play by mapping protein phosphorylation as many disease states stem from aberrant signaling events. With the advent of modern mass spectrometry (MS), researchers are now provided with more complex phosphorylation patterns from thousands of proteins in each mass spectrometric analysis. Further developments in quantification techniques, such as stable isotope labeling with amino acids in cell culture (SILAC) and label-free quantitation, have allowed researchers to reliably quantify changes to …

Bibliometric Analysis Of Named Entity Recognition For Chemoinformatics And Biomedical Information Extraction Of Ovarian Cancer, Vijayshri Khedkar, Charlotte Fernandes, Devshi Desai, Mansi R, Gurunath Chavan Dr, Sonali Tidke Dr., M. Karthikeyan Dr.

Library Philosophy and Practice (e-journal)

With the massive amount of data that has been generated in the form of unstructured text documents, Biomedical Named Entity Recognition (BioNER) is becoming increasingly important in the field of biomedical research. Since currently there does not exist any automatic archiving of the obtained results, a lot of this information remains hidden in the textual details and is not easily accessible for further analysis. Hence, text mining methods and natural language processing techniques are used for the extraction of information from such publications.Named entity recognition, is a subtask that comes under information extraction that focuses on finding and categorizing specific …

Design And Synthesis Of Selective Estrogen Receptor Agonists, Edward Edward Wetzel

Dissertations (1934 -)

Estrogens are hormones that regulates many different physiological functions. A decline in estrogen leads to significant issues that decrease the quality of life. Past treatments of menopausal symptoms included the administration of estrogen. However, side effects such as an increased risk of breast cancer, made this an unattractive therapeutic option. When a new estrogen receptor (ERβ) was discovered, it provided new hope for hormone replacement therapy (HRT). ERβ was shown to inhibit tumor growth, whereas ERα regulates breast cancer proliferation in certain types of breast cancer. The therapeutic benefits of targeting ERβ are vast; herein we focus on the benefits …

Synthetic And Mechanistic Studies Of Ruthenium Catalyzed C-C, C-H And C-N Bond Activation Reactions, Nuwan Asanka Pannilawithana

Dissertations (1934 -)

Transition metal-catalyzed selective CH, CC and CN bond activation reactions represent a challenging and synthetically important field in organic chemistry. In particular, transition-metal catalytic unreactive bond activation protocols are applicable in various stereoselective and atom economical complex organic molecule synthesis. Recently, significant research efforts have been made for utilizing catalytic CH and CC bond cleavage methods in the further development of commercially valuable pharmaceuticals and agrochemicals. The well-defined cationic Ru–H complex was found to be an effective catalyst for mediating the coupling reaction of 1,2-disubstituted indoles with α,β-unsaturated aldehydes and ketones, in which the regioselective Cα–Cβ activation of the carbonyl …

Scope And Mechanistic Studies Of Ruthenium Catalyzed C-N Bond Activation Reactions, Pandula Taepith Kirinde Arachchige

Dissertations (1934 -)

Primary aliphatic amines which are ubiquitous in natural products, traditionally considered as inert to substitution reactions. Recent studies clearly demonstrated that the aliphatic deaminative coupling chemistry can be used to make valuable scaffolds through C–N bond activation on transition metal complexes. The catalytic system generated in situ from the tetranuclear Ru–H complex with a catechol ligand (2-9/2-16) and independently synthesized ruthenium catecholate complex 2-11 was found to be effective for the direct deaminative coupling of primary amines. The catalytic system formed in-situ from the reaction of cationic Ru–H complex 2-10 with 3,4,5,6-tetrachloro-1,2-benzoquinone 2-12 was found to mediate a regioselective deaminative …

Food Security As A Factor Of Sustainable Development Of The Country, Timur Nurimbetov

Karakalpak Scientific Journal

The article examines the state of the food market and the trends in ensuring the country’s food security. The article also analyzes the regional characteristics of the agricultural products market in the Republic of Karakalpakstan. The saturation level of regional food markets has been studied. Scientific conclusions and practical recommendations on the supply of food to the population have been made.

Influence Of Laterial State Of Pair Impurity Complex On Recombination Processes In Semiconductors, L Yu Leyderman, R A. Ayukhanov, Abat Uteniyazov, E S. Esenbaeva, Sh X. Annayeva

Karakalpak Scientific Journal

The paper analyzes the question of the possible influence of the lateral state of a paired impurity complex on the recombination processes. It is shown that the lateral state of the paired impurity complex does not affect the recombination processes of nonequilibrium carriers - they go through that component of the impurity complex that exchanges carriers with both bands (in this particular case, through the component). The second component of the complex () can apparently play some role in the processes of carrier attachment.

Exploring The Roles Of Herc2 And The Nedd4l Hect E3 Ubiquitin Ligase Subfamily In P53 Signaling And The Dna Damage Response, Nicholas A. Mathieu, Rafael H. Levin, Donald E. Spratt

Chemistry

Cellular homeostasis is governed by the precise expression of genes that control the translation, localization, and termination of proteins. Oftentimes, environmental and biological factors can introduce mutations into the genetic framework of cells during their growth and division, and these genetic abnormalities can result in malignant transformations caused by protein malfunction. For example, p53 is a prominent tumor suppressor protein that is capable of undergoing more than 300 posttranslational modifications (PTMs) and is involved with controlling apoptotic signaling, transcription, and the DNA damage response (DDR). In this review, we focus on the molecular mechanisms and interactions that occur between p53, …

Organization Of Compact Spinning Technology In Textile Clusters, Baxtiyar Aralbaevich Paluanov, Abdimalik Pirmatovich Pirmatov

Karakalpak Scientific Journal

The article proposes a system of continuous supply of raw cotton in continuous spinning technology and methods of maximizing the preservation of the natural properties of the fiber and obtaining high-quality yarn.

Imaging Of Neurotransmitters And Small Molecules In Brain Tissues Using Laser Desorption/Ionization Mass Spectrometry Assisted With Zinc Oxide Nanoparticles., Chaochao Chen, Steven R Laviolette, Shawn N Whitehead, Justin B Renaud, Ken K-C Yeung

Chemistry Publications

Inorganic nanostructured materials such as silicon, carbon, metals, and metal oxides have been explored as matrices of low-background signals to assist the laser desorption/ionization (LDI) mass spectrometric (MS) analysis of small molecules, but their applications for imaging of small molecules in biological tissues remain limited in the literature. Titanium dioxide is one of the known nanoparticles (NP) that can effectively assist LDI MS imaging of low molecular weight molecules (LMWM). TiO₂ NP is commercially available as dispersions, which can be applied using a chemical solution sprayer. However, aggregation of NP can occur in the dispersions and the aggregated NP …

Adsorption And Transport Of Colloids At Interface And In Bulk, Jingyun Lee

LSU Doctoral Dissertations

Colloids are suspensions of microscopic insoluble particles dispersed in a continuum phase such as liquid or gas. Colloids are found in our everyday life from food and cosmetic industries to pharmaceutical and biomedical applications. Depending on a global minimum of the free-energy landscape, colloidal suspensions can be classified as two major classes: equilibrium or active colloidal system. This Ph.D dissertation presents strategies to engineer equilibrium self-assembled structures and out-of-equilibrium active matter using various interparticle forces.

First, we introduce the means to promote the equilibrium self-assembled structures driven by adsorption of colloids at interface. Typically, adsorption of colloids at interface is …

Determination Of Atrazine In Glacier Creek Using Gas Chromatography-Mass Spectrometry, Spencer Witte

UNO Student Research and Creative Activity Fair

Atrazine is a commonly used herbicide in agriculture that has been shown to cause adverse health-effects on biological organisms. Glacier Creek Preserve (GCP), a prairie preserve near Omaha, NE, contains restored prairie and agricultural land uses within a single watershed. Surface water samples were collected at various locations of GCP from May to July to quantify atrazine concentrations. Sample preparation included filtering with a 0.45 micron filter and solid-phase extraction (SPE) with a reversed-phase cartridge. The analyte was eluted off the cartridge with ethyl acetate and analyzed by gas chromatography-mass spectrometry (GC/MS). Quantitation was performed with an internal standard calibration …

Pressure- And Temperature-Dependent Inelastic Neutron Scattering Study Of The Phase Transition And Phonon Lattice Dynamics In Para-Terphenyl, Qingan Cai, Michael Mcintire, Luke L. Daemen, Chen Li, Eric Chronister

Chemistry and Biochemistry Faculty Research

Inelastic neutron scattering has been performed on para-terphenyl at temperatures from 10 to 200 K and under pressures from the ambient pressure to 1.51 kbar. The temperature dependence of phonons, especially low-frequency librational bands, indicates strong anharmonic phonon dynamics. The pressure- and temperature-dependence of the phonon modes suggest a lack of phase transition in the region of 0-1.51 kbar and 10-30 K. Additionally, the overall lattice dynamics remains similar up to 200 K under the ambient pressure. The results suggest that the boundary between the ordered triclinic phase and the third solid phase, reported at lower temperatures and higher pressures, …

Noncovalent Bonds Through Sigma And Pi-Hole Located On The Same Molecule. Guiding Principles And Comparisons, Wiktor Ziekiewicz, Mariusz Michalczyk, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems …

Telsam-Target Protein Fusions Can Form Diffraction-Quality Crystals Without Direct Inter-Polymer Contacts, Moriah Longhurst

Undergraduate Honors Theses

X-ray diffraction is a robust method for determining the detailed 3D structures of specific proteins. However, this requires the formation of well-ordered protein crystals, a process that is time-consuming, expensive, and only has about a 10-30% success rate. New methods are needed to enable the efficient crystallization of challenging proteins. One such technique is explored here, which utilizes a protein polymer (the sterile alpha motif domain of the human protein translocation Ets leukemia, or TELSAM) as a crystallization chaperone to form a more ordered crystal lattice of target proteins and drive crystallization. This method was successfully used to crystallize, collect …

Alternative View Of Oxygen Reduction On Porous Carbon Electrocatalysts: The Substance Of Complex Oxygen-Surface Interactions, Giacomo De Falco, Marc Florent, Jacek Jagiello, Yongqiang Cheng, Luke L. Daemen, Anibal J. Ramirez-Cuesta, Teresa J. Bandosz

Publications and Research

Electrochemical oxygen reduction reaction (ORR) is an important energy-related process requiring alternative catalysts to expensive platinum-based ones. Although recently some advancements in carbon catalysts have been reported, there is still a lack of understanding which surface features might enhance their efficiency for ORR. Through a detailed study of oxygen adsorption on carbon molecular sieves and using inelastic neutron scattering, we demonstrated here that the extent of oxygen adsorption/interactions with surface is an important parameter affecting ORR. It was found that both the strength of O2 physical adsorption in small pores and its specific interactions with surface ether functionalities in the …

Investigations Of The Structure And Protein-Protein Interactions Of Chlamydia Trachomatis Scc4, Thilini Oshadhi Senarath Ukwaththage

LSU Doctoral Dissertations

Chlamydia trachomatis (CT) is the most common, sexually transmitted bacterial disease (STD) in the world. In the developmental cycle of CT, specific chlamydia chaperone 4 (Scc4) is a unique protein with essential and multiple roles. Hence, Scc4 is significant as a virulence target for therapeutic approaches to treat chlamydial infections. A novel approach was discovered to purify tag free Scc4 by utilizing a 6X-histidine-tag on Scc1 in the co-expressed Scc4:Scc1 complex by capturing the complex on nickel-charged immobilized metal affinity chromatography resin, followed by dissociation of Scc4 with sarkosyl. Using triple resonance NMR experiments, backbone and sidechain resonances …

Novel Synthetic Transformations Targeting Δ-Valerolactone And Isocoumarin, Joshua Paul Van Houten

LSU Doctoral Dissertations

The purpose of this dissertation is to describe the efforts undertaken to develop synthetic methodology targeting δ-valerolactone and isocoumarin. At the onset, an introduction to the δ-valerolactone and isocoumarin is given. Relevant examples of δ-valerolactone being utilized in the production of materials of biological and industrial application are then discussed. Following, current methods for forming δ-valerolactone are presented. After, an introduction to isocoumarin is begun. Current methods for producing isocoumarin are then discussed.

The results and discussion section of this dissertation will focus on two methods that were explored with the goal of producing α-acyl-δ-valerolactone with two different substitution patterns. …

Designing Ionic Liquid-Derived Polymer Composites From Poly(Ionic Liquid)–Ionene Semi-Interpenetrating Networks, Kathryn E. O'Harra, George E. Timmerman, Jason E. Barra, Kevin Miller

Faculty & Staff Research and Creative Activity

While the solvating power of ionic liquids (ILs) for a variety of solute types including polymers is well-known, the use of ILs as solvents for ionenes—charged polymers with cationic moieties within the backbone—has only recently begun to be explored. IL–ionene combinations offer vast possibilities to make iongels and perhaps even use ILs to exert control over ionene organization (i.e., coil or rod). If the IL solvent is also polymerizable, then poly(IL)–ionene semi-interpenetrating networks (semi-IPNs) can be achieved. This study reports, for the first time, examples of poly(IL)–ionene semi-IPNs formed by dissolving an ionene in a vinyl-functionalized imidazolium IL followed by …

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …

Atomic-Resolution 1.3 Å Crystal Structure, Inhibition By Sulfate, And Molecular Dynamics Of The Bacterial Enzyme Dape, Matthew Kochert, Boguslaw P. Nocek, Thahani S. Habeeb Mohammad, Elliot Gild, Kaitlyn Lovato, Tahirah K. Heath, Richard C. Holz, Kenneth W. Olsen, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

We report the atomic-resolution (1.3 Å) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the …

Representing Methane Emissions From Wet Tropical Forest Soils Using Microbial Functional Groups Constrained By Soil Diffusivity, Debjani Sihi, Xiaofeng Xu, Mónica Salazar Ortiz, Christine S. O'Connell, Whendee L. Silver, Carla López-Lloreda, Julia M. Brenner, Ryan K. Quinn, Jana R. Phillips, Brent D. Newman, Melanie A. Mayes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Tropical ecosystems contribute significantly to global emissions of methane (CH₄), and landscape topography influences the rate of CH₄ emissions from wet tropical forest soils. However, extreme events such as drought can alter normal topographic patterns of emissions. Here we explain the dynamics of CH₄ emissions during normal and drought conditions across a catena in the Luquillo Experimental Forest, Puerto Rico. Valley soils served as the major source of CH₄ emissions in a normal precipitation year (2016), but drought recovery in 2015 resulted in dramatic pulses in CH₄ emissions from all topographic positions. Geochemical parameters …

Anticancer And Antiangiogenic Activities Of Alkaloids Isolated From Lantana Camara By Adsorption On The Magnetic Nanoparticles, Hussein Kadhem Al-Hakeim, Rahman Sahib Al-Zabibah, Huda Falah Alzihari, Ali Khudhair Almensoori, Hazim A. Al-Zubaidi, Loiy Elsir Ahmed Hassan Hassan

Karbala International Journal of Modern Science

Lantana camara L. (L. camara) is a perennial shrub that contains low amounts of alkaloids. In the present study, the magnetic nanoparticles (MNPs) were used to isolate positively charged alkaloids from the methanolic extract of L. camara leaves. The crude alkaloid was fractionated using HPLC to separate the highest peak of the alkaloid fraction (HPAF). The crude alkaloids (CA) and HPAF were tested for their antiproliferative effect against cancer cell lines (MCF-7, HCT-116, and HeLa) and endothelial cells line (EA.hy926) as a standard cell line. Antiangiogenic properties were examined using rat aortic ring assay. …

Mach-Zehnder Quantum Interference Rules In Hydrocarbons With Substituents, Alaa Al-Jobory, Zainelabideen Y. Mijbil

Karbala International Journal of Modern Science

We have investigated the conditions of quantum interferences in hydrocarbons with substituents using density functional theory and tight binding approximation combined with non-equilibrium Green’s function technique. The chosen model systems, namely benzene and tripyridyl–triazine molecules, have elucidated three prominent rules. The ‘first rule’ is the occurrence of inevitable, destructive quantum interference when 1,3-benzene ring incorporates single substituent at the fifth site. The ‘second rule’ is the chaotic occurrence of quantum interferences due the position and/or type of the substituents. The ‘third rule’: the substituents decrease (increase) the probability of destructive (constructive) interferences

Physical-Chemical Characterization And Heavy Metals Assessment Of Waters And Sediments Of Sebou Watershed (Top Sebou, Morocco), Mohamed Kabriti, Eda Mahougnon Léonce, Chaimaa Merbouh, Bensaber Abdelfattah, Abdelmajid Achkir, Abdlhakim Aouragh, Iounes Nadia

Karbala International Journal of Modern Science

The main purpose of this study was to investigate the impact of human activities, geochemical background and seasons on pollutant pathway. Surface water, groundwater and sediments were assessed to highlight and confirm those impacts. Sixteen physico-chemical parameters were measured (T°, pH, O2, salinity, conductivity, BOD5, COD, SM, Cl-, NO2-, NO3-, NH4+, TAC, TH, SO₄²- and PO43-) and twelve metallic trace elements were analyzed (Ar, Cr, Zn, Mn, Ni, Fe, Al, Cd, Cu, Pb, K and Na). Five sampling campaigns were carried out in 18 sampling points for over one year, between July 2018 and July 2019 in the upstream part …

Molecular Structure Vibrational & Electronic Properties Of Some Isatin Derivatives, Fatma K. Fkandermili Prof, Fatma M. Aldibashi S, Hakan S. Sayiner Prof

Karbala International Journal of Modern Science

Abstract

In this study, Natural Bonding Orbitals (NBOs) were applied to isatin, 5‑fluoroisatin, 5‑chloroisatin, 5‑methylisatin and 5‑methoxyisatin using the Lee-Yang-Parr correlation functional B3LYP with 6‑311++G(2d,2p) basis set. Natural bonding analysis was performed to consider the transfer interactions of intra-molecular charge, pre-hybridization and electron density within the isatin, 5‑fluoroisatin, 5‑chloroisatin, 5‑methylisatin and 5‑methoxyisatin. In natural bonding orbital analysis, the wave functions of the electrons were explicated in sets of occupied Lewis type terms, (bonds or lone pairs) and sets of unoccupied non‑Lewis (anti‑bond and Rydberg) localized natural bonding orbitals. The electron density between these orbitals was correlated to stabilize the interaction …

Editorial Board

Karbala International Journal of Modern Science

No abstract provided.

Beneficial Impacts Of Incorporating The Non-Natural Amino Acid Azulenyl-Alanine Into The Trp-Rich Antimicrobial Peptide Bucathl4b., Areetha R D'Souza, Matthew R Necelis, Alona Kulesha, Gregory A. Caputo, Olga V Makhlynets

College of Science & Mathematics Departmental Research

Antimicrobial peptides (AMPs) present a promising scaffold for the development of potent antimicrobial agents. Substitution of tryptophan by non-natural amino acid Azulenyl-Alanine (AzAla) would allow studying the mechanism of action of AMPs by using unique properties of this amino acid, such as ability to be excited separately from tryptophan in a multi-Trp AMPs and environmental insensitivity. In this work, we investigate the effect of Trp→AzAla substitution in antimicrobial peptide buCATHL4B (contains three Trp side chains). We found that antimicrobial and bactericidal activity of the original peptide was preserved, while cytocompatibility with human cells and proteolytic stability was improved. We envision …

Thermodynamics Of Ligand Binding And Global Structural Stability Of Human Serum Albumin, Matthew Walter Eskew

Dissertations and Theses

Protein structure is integral to its function. For the past 70 years differential scanning calorimetry has been used to measure protein structural stability. More recently it has been used to study macromolecular interactions. Interactions between proteins and ligands can manifest on differential scanning calorimetry melting curves or thermograms. Utilizing differential scanning calorimetry thermograms to detect or diagnose diseases has been a major goal in disease diagnostics. However, correlating specific ligand-protein interactions, as manifested in a thermogram, with a disease-specific plasma thermogram, has proven elusive.

Modified human serum albumin was utilized to develop a process to capture and retrieve ligands from …

Effective Microwave-Assisted Approach To 1,2,3-Triazolobenzodiazepinones Via Tandem Ugi Reaction/Catalyst-Free Intramolecular Azide–Alkyne Cycloaddition, Maryna O. Mazur, Oleksii S. Zhelavskyi, Eugene M. Zviagin, Svitlana V. Shishkina, Vladimir I. Musatov, Maksim A. Kolosov, Elena H. Shvets, Anna Yu. Andryushchenko, Valentyn A. Chebanov

Department of Chemistry: Faculty Publications

A novel catalyst-free synthetic approach to 1,2,3-triazolobenzodiazepinones has been developed and optimized. The Ugi reaction of 2-azidobenzaldehyde, various amines, isocyanides, and acids followed by microwave-assisted intramolecular azide–alkyne cycloaddition (IAAC) gave a series of target heterocyclic compounds in moderate to excellent yields. Surprisingly, the normally required ruthenium-based catalysts were found to not affect the IAAC, only making isolation of the target compounds harder while the microwave-assisted catalyst-free conditions were effective for both terminal and non-terminal alkynes