Other Chemistry Commons^™

Peptide Arrays For Detecting Naphthenic Acids In Oil Sands Process Affected Water, Kamaljit Kaur, Subir Bhattacharjee, Rajesh G. Pillai, Sahar Ahmed, Sarfuddin Azmi

Pharmacy Faculty Articles and Research

Naphthenic acids (NAs) are water-soluble components of petroleum. The characterization and quantification of NAs by analytical methods have proved quite challenging, whilst the toxic effects of these water-soluble compounds on a variety of organisms adversely affecting reproduction and steroid production is becoming apparent. In this study, we report a fluorescence-based competitive binding method for rapid sensing of the presence of NAs using cellulosic peptide array strips as sensors. The peptide array was designed from sequences derived from the estrogen receptor (ER). Several of these peptides were able to detect the presence of NAs at low micromolar (∼5 mg L^{−1 …}

Acquisition Of An Electrochemical System Instrument For The Development Of Sensors, Elmer-Rico E. Mojico

Cornerstone 1 Reports : Expansion and Enhancements of the Thinkfinity Platform

No abstract provided.

Revisiting The Fundamentals In The Design And Control Of Nanoparticulate Colloids In The Frame Of Soft Chemistry, Vuk Uskoković

Pharmacy Faculty Articles and Research

This review presents thoughts on some of the fundamental features of conceptual models applied in the design of fine particles in the frames of colloid and soft chemistry. A special emphasis is placed on the limitations of these models, an acknowledgment of which is vital in improving their intricacy and effectiveness in predicting the outcomes of the corresponding experimental settings. Thermodynamics of self-assembly phenomena illustrated on the examples of protein assembly and micellization is analyzed in relation to the previously elaborated thesis that each self-assembly in reality presents a co-assembly, since it implies a mutual reorganization of the assembling system …

Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede

Faculty Publications, Chemistry

The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …

Dynamic Light Scattering And Microelectrophoresis: Main Prospects And Limitations, Vuk Uskoković

Pharmacy Faculty Articles and Research

Microelectrophoresis based on the dynamic light scattering (DLS) effect has been a major tool for assessing and controlling the conditions for stability of colloidal systems. However, both the DLS methods for characterization of the hydrodynamic size of dispersed submicron particles and the theory behind the electrokinetic phenomena are associated with fundamental and practical approximations that limit their sensitivity and information output. Some of these fundamental limitations, including the spherical approximation of DLS measurements and an inability of microelectrophoretic analyses of colloidal systems to detect discrete charges and differ between differently charged particle surfaces due to rotational diffusion and particle orientation …

Short-Term Associations Between Pm2.5, Black Carbon, Delta-C, And Cardiovascular Diseases In A Large Developing Megacity, Daniel Malashock

Legacy Theses & Dissertations (2009 - 2024)

Introduction: Association between ambient air pollution and cardiovascular disease (CVD) have been demonstrated by many epidemiological studies in developed countries, however few studies have been performed in developing countries of Asia.

Design Of Novel Inhibitors For Infectious Diseases Using Structure-Based Drug Design: Virtual Screening, Homology Modeling And Molecular Dynamics, Divya Ramamoorthy

USF Tampa Graduate Theses and Dissertations

The main aim of the study in this thesis was to use structure-based protocols to design new drugs for enzymes, DXS and DXR in the non mevalonate pathway. Another aim of this study was to identify the dimer interface in E.coli FabH as an allosteric binding site for designing new class of anti-infective drugs. We have attempted to identify potential inhibitors for DXS by docking the NCI Diversity set compounds, compound libraries available from GSK-MMV and St. Jude's Children's research center. FabH dimer interface has been identified as a potential target using SiteMap, Alanine mutagenesis and docking studies.

The first …

Use And Development Of Computational Tools In Drug Discovery: From Small Molecules To Cyclic Peptides, Daniel Navarrete Santiago

USF Tampa Graduate Theses and Dissertations

The scope of this work focuses on computationally modeling compounds with protein structures. While the impetus of drug discovery is the innovation of new therapeutic molecules, it also involves distinguishing molecules that would not be an effective drug. This can be achieved by inventing new tools or by refining old tools. Virtual screening (VS, also called docking), the computational modeling of a molecule in a receptor structure, is a staple in predicting a molecule's affinity for an intended target. In our Virtual Target Screening system (also called inverse-docking), VS is used to find high-affinity targets, which can potentially explain absorption, …

A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers

Faculty Publications, Chemistry

A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning …

Dynamic Light Scattering And Zeta Potential Of Colloidal Mixtures Of Amelogenin And Hydroxyapatite In Calcium And Phosphate Rich Ionic Milieus, Vuk Uskoković, Roselyn Odsinada, Sonia Djordjevic, Stefan Habelitz

Pharmacy Faculty Articles and Research

The concept of zeta-potential has been used for more than a century as a basic parameter in controlling the stability of colloidal suspensions, irrespective of the nature of their particulate ingredients – organic or inorganic. There are prospects that self-assembly of peptide species and the protein-mineral interactions related to biomineralization may be controlled using this fundamental physicochemical parameter. In this study, we have analyzed the particle size and zeta-potential of the full-length recombinant human amelogenin (rH174), the main protein of the developing enamel matrix, in the presence of calcium and phosphate ions and hydroxyapatite (HAP) particles. As calcium and phosphate …

Changes In Apparent Molar Water Volume And Dkp Solubility Yield Insights On The Hofmeister Effect, Daryl K. Eggers, A. Y. Payumo, R. M. Huijon, D. D. Mansfield, L. M. Belk, A. K. Bui, A. E. Knight

Faculty Publications, Chemistry

This study examines the properties of a 4 × 2 matrix of aqueous cations and anions at concentrations up to 8.0 M. The apparent molar water volume, as calculated by subtracting the mass and volume of the ions from the corresponding solution density, was found to exceed the molar volume of ice in many concentrated electrolyte solutions, underscoring the nonideal behavior of these systems. The solvent properties of water were also analyzed by measuring the solubility of diketopiperazine (DKP) in 2.000 M salt solutions prepared from the same ion combinations. Solution rankings for DKP solubility were found to parallel the …

Protein Adsorption Onto Organically-Modified Silica Glass Leads To A Different Structure Than Sol-Gel Encapsulation, Daryl K. Eggers, B, Menaa, C. Torres, M. Herrero, V. Rives, A. R.W Gilbert

Faculty Publications, Chemistry

The secondary structures of two proteins were examined by circular dichroism spectroscopy after adsorption onto a series of organically modified silica glasses. The glasses were prepared by the sol-gel technique and were varied in hydrophobicity by incorporation of 5% methyl, propyl, trifluoropropyl, or n-hexyl silane. Both cytochrome c and apomyoglobin were found to lose secondary structure after adsorption onto the modified glasses. In the case of apomyoglobin, the α-helical content of the adsorbed protein ranged from 21% to 28%, well below the 62% helix found in solution. In contrast, these same glasses led to a striking increase in apomyoglobin structure …

Favourable Influence Of Hydrophobic Surfaces On Protein Structure In Porous Organically-Modified Silica Glasses, Daryl K. Eggers, B. Menaa, M. Herrero, V. Rives, M. Lavrenko

Faculty Publications, Chemistry

Organically-modified siloxanes were used as host materials to examine the influence of surface chemistry on protein conformation in a crowded environment. The sol–gel materials were prepared from tetramethoxysilane and a series of monosubstituted alkoxysilanes, RSi(OR′)3, featuring alkyl groups of increasing chain length in the R-position. Using circular dichroism spectroscopy in the far-UV region, apomyoglobin was found to transit from an unfolded state to a native-like helical state as the content of the hydrophobic precursor increased from 0 to 15%. At a fixed molar content of 5% RSi(OR′)3, the helical structure of apomyoglobin increased with the chain length of the R-group, …

Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha

Faculty Publications, Chemistry

Insertion of hydrophobic groups in a silica matrix, by addition of propyl- or trifluoropropyltrimethoxysilane, leads to a surprising increase in the helical content of apomyoglobin following encapsulation by the sol–gel technique

Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou

Faculty Publications, Biological Sciences

The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway. Both of these diseases exhibit symptoms that can be viewed as accelerated aging. The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood. Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity. Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their …

Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol

Faculty Publications, Biological Sciences

Three mammalian nuclear lamin proteins, lamin B1, lamin B2 and the lamin A precursor, prelamin A, undergo canonical farnesylation and processing at CAAX motifs. In the case of prelamin A, there is an additional farnesylation-dependent endoproteolysis, which is defective in two congenital diseases: Hutchinson-Gilford progeria (HGPS) and restrictive dermopathy (RD). These two diseases arise respectively from defects in the prelamin A substrate and the enzyme (ZmpSte24) that processes it. Recent work has shed light on the roles of the lamin proteins and the enzymes involved in their farnesylation-dependent maturation. Other experimental work, including mouse model studies, have examined the possibility …

Reduced Macrophage Apoptosis Is Associated With Accelerated Atherosclerosis In Low-Denstiy Lipoprotein Receptor-Null Mice, Michael Sinensky, J. Liu, D. P. Thweke, Y. R. Su, M. F. Linton, S. Fazio

Faculty Publications, Biological Sciences

Objective— The majority of apoptotic cells in atherosclerotic lesions are macrophages. However, the pathogenic role of macrophage apoptosis in the development of atherosclerosis remains unclear. Elevated expression of Bax, one of the pivotal proapoptotic proteins of the Bcl-2 family, has been found in human atherosclerotic plaques. Activation of Bax also occurs in free cholesterol-loaded and oxysterol-treated mouse macrophages. In this study, we examined the effect of Bax deficiency in bone marrow-derived leukocytes on the development of atherosclerosis in low-density lipoprotein receptor-null (LDLR−/−) mice. Methods and Results— Fourteen 8-week-old male LDLR−/− mice were lethally irradiated and reconstituted with either wild-type (WT) …

Phosphoproteomic Studies Of Smooth Muscle Contraction: Investigation Of Differential Phosphorylation In Relaxed/Contracted Rat Aortic Smooth Muscle Tissue Using Maldi-Tof Ms, Tonya M. Pekar

Theses, Dissertations and Capstones

Many human disorders are associated with the malfunction of smooth muscle tissue, or are related to the capabilities of its proper function—asthma, glaucoma, renal inefficiency, hypertension, and cardiovascular disease. Dysfunctional proteins are frequently implicated as the source of such disorders. As the second highest cause of death in the United States, the epidemic of cardiovascular disease makes the study of smooth muscle of utmost concern.

The capabilities of proteomics and mass spectrometry allow the entire proteome complement of a cell or tissue type to be analyzed at once. This investigation employs such techniques in an effort to better understand the …

Familial Als-Associated Mutations Decrease The Thermal Stability Of Distinctly Metallated Species Of Human Copper/Zinc Superoxide Dismutase, Daryl K. Eggers, J. A. Rodriguez, J. S. Valentine, J. A. Roe, A. Tiwari, R. H. Brown, L. J. Hayward

Faculty Publications, Chemistry

We report the thermal stability of wild type (WT) and 14 different variants of human copper/zinc superoxide dismutase (SOD1) associated with familial amyotrophic lateral sclerosis (FALS). Multiple endothermic unfolding transitions were observed by differential scanning calorimetry for partially metallated SOD1 enzymes isolated from a baculovirus system. We correlated the metal ion contents of SOD1 variants with the occurrence of distinct melting transitions. Altered thermal stability upon reduction of copper with dithionite identified transitions resulting from the unfolding of copper-containing SOD1 species. We demonstrated that copper or zinc binding to a subset of “WT-like” FALS mutants (A4V, L38V, G41S, G72S, D76Y, …

Complexes Between Nascent Polypeptides And Their Molecular Chaperones In The Cytosol Of Mammalian Cells, Daryl K. Eggers, W. J. Welch, W. J. Hansen

Faculty Publications, Chemistry

Folding of newly synthesized proteins in vivo is believed to be facilitated by the cooperative interaction of a defined group of proteins known as molecular chaperones. We investigated the direct interaction of chaperones with nascent polypeptides in the cytosol of mammalian cells by multiple methods. A new approach using a polyclonal antibody to puromycin allowed us to tag and capture a population of truncated nascent polypeptides with no bias as to the identity of the bound chaperones. In addition, antibodies that recognize the cytosolic chaperones hsp70, CCT (TRiC), hsp40, p48 (Hip), and hsp90 were compared on the basis of their …

Expression Of Prelamin A Confers Sensitivity Of Dna Biosynthesis To Lovastatin On F9 Teratocarcinoma Cells, Michael Sinensky, T. Mclain, K. Fantle

Faculty Publications, Biological Sciences

No abstract provided.

The Processing Pathway Of Prelamin A, Michael Sinensky, K. Fantle, M. Trujillo, T. Mclain, A. Kupfer, M. Dalton

Faculty Publications, Biological Sciences

The conversion of mammalian prelamin A to mature lamin A proceeds through the removal of 18 amino acids from the carboxyl terminus. The initial step in this processing is the isoprenylation of a CAAX box cysteine. This proteolytic event is distinctive for prelamin A among the known prenylated mammalian proteins. Since the carboxyl terminus of prelamin A is removed during maturation, it is not obvious that this protein would undergo the two reactions subsequent to prenylation observed in other CAAX box proteins-the endoproteolytic removal of the carboxyl-terminal 3 amino acids and the subsequent methylation of the now carboxyl-terminal cysteine. To …

Isoprenylation Is Required For The Processing Of The Lamin A Precursor, Michael Sinensky, L. A. Beck, T. J. Hosick

Faculty Publications, Biological Sciences

The nuclear lamina proteins, prelamin A, lamin B, and a 70-kD lamina-associated protein, are posttranslationally modified by a metabolite derived from mevalonate. This modification can be inhibited by treatment with (3-R,S)-3-fluoromevalonate, demonstrating that it is isoprenoid in nature. We have examined the association between isoprenoid metabolism and processing of the lamin A precursor in human and hamster cells. Inhibition of 3-hydroxy-3-methylglutaryl coenzyme A reductase by mevinolin (lovastatin) specifically depletes endogenous isoprenoid pools and inhibits the conversion of prelamin A to lamin A. Prelamin A processing is also blocked by mevalonate starvation of Mev-1, a CHO cell line auxotrophic for mevalonate. …

Incorporation Of A Product Of Mevalonic Acid Metabolism Into Proteins Of Chinese Hamster Ovary Nuclei, Michael Sinensky, L. A. Beck, T. Hosick

Faculty Publications, Biological Sciences

We have examined the nuclear localization of isoprenylated proteins in CHO-K1 cells labeled with [14C]mevalonate. Nuclear proteins of 68, 70, and 74 kD, posttranslationally modified by an isoprenoid, are also components of a nuclear matrix-intermediate filament preparation from CHO cells. Furthermore, the 68-, 70-, and 74-kD isoprenylated polypeptides are immunoprecipitated from cell extracts with two different anti-lamin antisera. Based on exact two-dimensional comigration with lamin B, both from rat liver lamin and CHO nuclear matrix-intermediate filament preparations, and its immunoprecipitation with anti-lamin antisera, we conclude that the 68-kD isoprenylated protein found in nuclei from [14C]mevalonate-labeled CHO cells is lamin B. …

Adaptative Alteration In Phospholipid Composition Of Plasma Membranes From A Somatic Cell Mutant Defective In The Regulation Of Cholesterol Biosynthesis, Michael Sinensky

Faculty Publications, Biological Sciences

A somatic cell mutant (CR1) of a Chinese hamster ovary cell (CHO-K1) which has previously been shown to be defective in the regulation of cholesterol biosynthesis accumulates more cholesterol than the parental cell line in plasma membranes. Although such an increase in membrane cholesterol should lead to an increase in the order parameter of these membranes, as measured with an electron spin resonance spin probe, the order parameters of mutant and wild-type plasma membranes are identical--apparently because of an adaptive alteration in membrane phospholipid composition. The phospholipid compositions of mutant and wild-type cell plasma membranes are compared and the mutant …

New Header Treatment Aids Weevil Control, J H. Moulden

Journal of the Department of Agriculture, Western Australia, Series 4

A new insecticide formulation supplied in high pressure cylinders simplifies weevil control in headers.

Simplified Sheep Skin Tanning, Department Of Agriculture, Western Australia

Journal of the Department of Agriculture, Western Australia, Series 4

Most people would agree that a white sheepskin rug adds a touch of luxury to any home.

The following method will produce dressed, woolly sheep skins with chemicals and equipment available to any householder.

Progress In Weed Control, Department Of Agriculture, Western Australia

Journal of the Department of Agriculture, Western Australia, Series 4

In May, 1967, the "Journal of Agriculture" printed a special issue on weed control, with the emphasis on chemicals for weed control in cereal crops.

This month, just two years later, enough new information has accumulated to warrant publication of another "theme" issue, this time with important articles on weed control in pastures, chemical firebreaks and chemical ploughing, as well as weed control in linseed and cereal crops.

Citrus Growers : Don't Blow Up Your Colouring Rooms, Department Of Agriculture, Western Australia

Journal of the Department of Agriculture, Western Australia, Series 4

THERE have been several dangerous incidents associated with the use of acetylene in citrus colouring chambers recently, and growers are warned to take care when using this explosive gas.