Biochemistry, Biophysics, and Structural Biology Commons^™

Structural Insights From Hiv-Antibody Co-Evolution And Related Immunization Studies, Jeffrey O. Zhou , '19, Therese Ton , '19, Julia W. Morriss , '19, Diep Nguyen , '19, Daniela Fera

Chemistry & Biochemistry Faculty Works

Human immunodeficiency virus type 1 (HIV-1) is a rapidly evolving pathogen and causes the acquired immunodeficiency syndrome (AIDS) in humans. There are ~30-35 million people infected with HIV around the world, and ~25 million have died since the first reported cases in 1981. Additionally, each year 2-3 million people become newly infected and more than one million die of AIDS. An HIV-1 vaccine would help halt an AIDS pandemic, and efforts to develop a vaccine have focused on targeting the HIV-1 envelope, Env, found on the surface of the virus. A number of chronically infected individuals have been shown to …

Transcriptomics Of Learning, Pablo Iturralde

Theses

Learning is a basic and important component of behavior yet we have very little empirical information about the interaction between mechanisms of learning and evolution. In our work, we are testing hypotheses about the neurogenetic mechanisms through which animal learning abilities evolve. We are able to test this directly by using experimentally evolved populations of flies, which differ in learning ability. These populations were previously evolved within the lab by creating worlds with different patterns of change following theoretically predicted effects on which enhanced learning will evolve. How has evolution acted to modulate genes and gene expression in the brain …

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

Chemistry: Faculty Publications and Other Works

A series of four- and five-coordinate Ni(II) complexes Cz^tBu(Pyr^iPr)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

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

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 …

Dynamics And Interactions Of Membrane Proteins, Azamat Galiakhmetov

Dissertations (1934 -)

Membrane proteins are members of the class of proteins that perform their functions while being associated with a lipid bilayer. In the cell, they serve as transporters, receptors, anchors and enzymes. The domain organisation of these proteins suggests importance of lipid membrane and protein-lipid interactions for protein function. The requirement of a membrane mimic and the level of its resemblance to a native one for protein investigation makes the studies of membrane proteins a challenging project. My research work is focusing on the biophysical and biochemical studies of membrane proteins. This dissertation outlines two separate projects, each with their own …

Strategies For The Modulation Of Protease Activated Receptors (Pars), Disha M. Gandhi

Dissertations (1934 -)

Protease-activated receptors (PARs) are class A G protein-coupled receptors (GPCRs) with 4 subtypes (PAR 1 – 4) and with a unique mode of action. PARs are cleaved by extracellular proteases at the N-terminus, creating a new tethered ligand that activates the receptor and transduces biological signals into the cell. PARs have been implicated in various productive and pathological signals, including those related to thrombosis, inflammation, reperfusion injury, and cancer cell metastasis. Despite the fact that PARs are attractive as drug targets, their intramolecular mode of activation makes it challenging to modulate them with drugs in a selective manner, and only …

Characterizing The Recognition Motif And Novel Substrates Of Carm1, Sitaram Gayatri

Dissertations and Theses (Open Access)

A limited pool of proteins attains vast functional repertoire due to posttranslational modifications (PTMs). Arginine methylation is a common posttranslational modification, which is catalyzed by a family of nine protein arginine methyltransferases or PRMTs. These enzymes deposit one or two methyl groups to the nitrogen atoms of arginine side-chains. Elucidating the substrate specificity of each PRMT will promote a better understanding of which signaling networks these enzymes contribute to. Although many PRMT substrates have been identified, and their methylation sites mapped, the optimal target motif for each of the nine PRMTs has not been systematically addressed. Here we describe the …

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 …

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 …

Lipid Transport Required To Make Lipids Of Photosynthetic Membranes, Evan Labrant, Allison C. Barnes, Rebecca Roston

Department of Biochemistry: Faculty Publications

Photosynthetic membranes provide much of the usable energy for life on earth. To produce photosynthetic membrane lipids, multiple transport steps are required, including fatty acid export from the chloroplast stroma to the endoplasmic reticulum, and lipid transport from the endoplasmic reticulum to the chloroplast envelope membranes. Transport of hydrophobic molecules through aqueous space is energetically unfavorable and must be catalyzed by dedicated enzymes, frequently on specialized membrane structures. Here, we review photosynthetic membrane lipid transport to the chloroplast in the context of photosynthetic membrane lipid synthesis. We independently consider the identity of transported lipids, the proteinaceous transport components, and membrane …

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 …

Utilization Of Papaya’S Sap (Carica Papaya L.) And Water Lettuce (Pistia Stratiotes) To Reduce Protein Amount On Liquid Tofu Waste, Muhammad Dzulfikar Farkhan, Naila Aliyahandra Anzani, Nabila Fikria Santoso

The International Student Science Fair 2018

ABSTRACT

Liquid waste from tofu production is one of the causes of environmental pollution. This condition happens because liquid tofu waste contain protein. Protein is metabolized by bacteria formed ammonia which emits foul odor. On this research, the protein amount in liquid tofu waste is reduced by the application of papaya’s sap and water lettuce. This research is divided into several steps. First, collecting the liquid tofu waste. second, tapping the papaya’s sap. Third, poured the papaya’s sap into the tofu waste. the next step is keep the mixture between tofu waste and papaya’s sap rest for 6, 18, and …

Aβ42 Protofibrils Interact With, And Are Trafficked Through, Microglial-Derived Microvesicles, Lisa Gouwens, Mudar Ismail, Victoria Rogers, Nathan Zeller, Evan Garrad, Fatima Amtashar, Nyasha Makoni, David Osborn, Michael Nichols

Chemistry & Biochemistry Faculty Works

Microvesicles (MVs) and exosomes comprise a class of cell-secreted particles termed extracellular vesicles (EVs). These cargo-holding vesicles mediate cell-to-cell communication and have recently been implicated in neurodegenerative diseases such as Alzheimer’s disease (AD). The two types of EVs are distinguished by the mechanism of cell release and their size, with the smaller exosomes and the larger MVs ranging from 30 to 100 nm and 100 nm to 1 μm in diameter, respectively. MV numbers are increased in AD and appear to interact with amyloid-β peptide (Aβ), the primary protein component of the neuritic plaques in the AD brain. Because microglial …

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

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 …

Synthesis Of Candidate Natural Killer T Cell Ligands, Teron Haynie, Shenglou Deng, Paul B. Savage

Undergraduate Honors Theses

Natural Killer T (NKT) cells are a subset of T cells that express an invariant T cell receptor (TCR) that recognizes lipid antigens in context of the CD1d molecule. CD1d presents both exogenous and endogenous glycolipids on the surface of antigen presenting cells (APCs). Multiple exogenous lipids capable of NKT cell stimulation have been characterized, but confirmed endogenous ligands are relatively few in number. Recently, a-galactosylceramides were shown to be endogenous NKT cell ligands. We have observed that a-galactosylceramides cyclize in acidic conditions. Since the biosynthetic pathway of lipid presentation via CD1d likely passes through the acidic lysosome, we propose …

Codon Usage Revisited: Lack Of Correlation Between Codon Usage And The Number Of Trna Genes In Enterobacteria, Joaquín Rojas, Gabriel Castillo, Lorenzo Eugenio Leiva, Sara Elgamal, Omar Orellana, Michael Ibba, Assaf Katz

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

It is widely believed that if a high number of genes are found for any tRNA in a rapidly replicating bacteria, then the cytoplasmic levels of that tRNA will be high and an open reading frame containing a higher frequency of the complementary codon will be translated faster. This idea is based on correlations between the number of tRNA genes, tRNA concentration and the frequency of codon usage observed in a limited number of strains as well as from the fact that artificially changing the number of tRNA genes alters translation efficiency and consequently the amount of properly folded protein …

Transcriptional Correlates Of Proximal-Distal Identify And Regeneration Timing In Axolotl Limbs, S. Randal Voss, David Murrugarra, Tyler B. Jensen, James R Monaghan

Neuroscience Faculty Publications

Cells within salamander limbs retain memories that inform the correct replacement of amputated tissues at different positions along the length of the arm, with proximal and distal amputations completing regeneration at similar times. We investigated the possibility that positional memory is associated with variation in transcript abundances along the proximal-distal limb axis. Transcripts were deeply sampled from Ambystoma mexicanum limbs at the time they were administered fore arm vs upper arm amputations, and at 19 post-amputation time points. After amputation and prior to regenerative outgrowth, genes typically expressed by differentiated muscle cells declined more rapidly in upper arms while cell …

Investigating The Role Of Gold Nanoparticle Shape And Size In Their Toxicities To Fungi, Kangze Liu, Zhonglei He, Hugh Byrne, James Curtin, Furong Tian Technological University Dublin

Articles

Gold nanoparticles (GNPs) are increasingly being used in a wide range of applications, and such they are being released in greater quantities into the environment. Consequently, the environmental effects of GNPs, especially toxicities to living organisms, have drawn great attention. However, their toxicological characteristics still remain unclear. Fungi, as the decomposers of the ecosystem, interact directly with the environment and critically control the overall health of the biosphere. Thus, their sensitivity to GNP toxicity is particularly important. The aim of this study was to evaluate the role of GNP shape and size in their toxicities to fungi, which could help …

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.

Pain And Stress In The Premature Infant, John Bryle Chong Tan

Loma Linda University Electronic Theses, Dissertations & Projects

Procedural pain and stress in premature neonates is currently assessed utilizing tools that lack objectivity and accuracy. This results in untreated or mismanaged pain. My dissertation utilized physiological methods and biochemical markers that identified pain in premature neonates and its effect on energy metabolism. The painful procedure that I examined is the retinopathy of premature (ROP) examination, a necessary and routine eye examination in the neonatal intensive care unit (NICU) that detects and identifies infants at risk for blindness due to retinal detachment. The effects of the ROP exam on peripheral and deep tissue oxyhemoglobin saturation and urinary purine degradation …

Multicomponent Analysis Using A Confocal Raman Microscope, Zhengyuan Tang, Sinead J. Barton, Thomas E. Ward, John P. Lowry, Michelle M. Doran, Hugh Byrne, Bryan M. Hennelly

Articles

Measuring the concentration of multiple chemical components in a low volume aqueous mixture by Raman spectroscopy has received significant interest in the literature. All of the contributions to date focus on the design of optical systems that facilitate the recording of spectra with high signal-to-noise ratio, by collecting as many Raman scattered photons as possible. In this study, the confocal Raman microscope set-up is investigated for multicomponent analysis. Partial Least Squares Regression is used to quantify physiologically relevant aqueous mixtures of glucose, lactic acid, and urea. The predicted error is 17.81 mg/dL for glucose, 10.6 mg/dL for lactic acid and …

An Introductory Study Of Solid Materials For Capture And Catalysis Of Waste Stream Chemicals, Steven Kyle Butler

Theses and Dissertations

Heterogeneous catalysts are key materials in research and industry. Herein we study two materials in different stages of development toward being applied as heterogeneous catalysts. First, MoO3SnO2 was synthesized and studied as a catalytic system similar to Sn-beta zeolites. While the Mo-based catalyst did not show similar activity to Sn-beta, it did show interesting reactivity in activating carbonyls and oxidizing organic substrates. Second, a method was developed for grafting amines onto carboxylic acid functionalized carbon nanotubes for CO2 capture. The method was successful for grafting monomer ethylamine groups onto CNT and can be further developed to allow for polymeric amine …

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

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 …

Identification Of A Tola Protein Binding Site For Bacterial Toxins, Monica Ferrante

Honors Projects

Group A colicins are proteinaceous bacteriocins encoded by plasmids that exploit the cellular envelope protein TolA to translocate the cell wall barrier and cellular envelope of the bacterium Escherichia coli. These colicins offer protocols for studying certain protein-protein interactions involved in such membrane transport functions. Previous experimentations suggest the carboxyl-terminal domain of TolA protein contains specific amino acid binding regions required for the translocation of group A colicins into E. coli. The amino acid sequence of this domain varies between E. coli and other gram-negative bacterial species. It has been suggested that this diversity could be utilized to …

Cyclic Urethane: A Versatile Handle For Synthetic Peptide Applications, Hader E. Elashal

Seton Hall University Dissertations and Theses (ETDs)

While peptides have impeccable potential due to their biological and therapeutic abilities, they are inherently limited in clinical practice due to their instability towards proteolysis and poor bioavailability. In the past few years peptidomimetics have emerged as a powerful class of compounds that overcomes the shortcomings associated with peptides. Peptidomimetics essentially mimic a natural peptide or protein in its chemical composition, structure and its ability to perform a biologically relevant role. In addition to increased stability and bioavailability, peptidomimetics can also have increased receptor binding affinity and selectivity, thereby making these mimics lead compounds in the field of drug design …

Effect Of Bmp Treatment On Periostin Gene Expression In Pre-Osteoblastic Mc3t3-E1 Mouse Cells, Vincent Lee Khang

UNLV Theses, Dissertations, Professional Papers, and Capstones

Periostin is a secreted, extracellular matrix (ECM) protein widely expressed within collagen-rich fibrous connective tissues of the body including the periodontal ligament (PDL), bone, skin, heart, and cornea. Periostin has been shown to serve many important regulatory functions including cell adhesion, cell motility, wound healing and of particular importance to the dental field, differentiation of osteoblasts. The deletion of periostin compromises osteoblast attachment to bone matrix and induces a reduction in mineralization and expression of bone markers, including type I collagen, osteocalcin, osteopontin and alkaline phosphatase. Periostin has also been shown to play a significant role in collagen fibrillogenesis by …