Biochemistry, Biophysics, and Structural Biology Commons^™

Calorimetric Study Of Block-Copolymers Of Poly(N-Butyl Acrylate) And Gradient Poly(N-Butyl Acrylate-Co-Methyl Methacrylate), A I. Buzin, M Pyda, P Costanzo, K Matyjaszewski, B Wunderlich

Chemistry and Biochemistry

The nanophase separation in diblock and triblock copolymers consisting of immiscible poly(n-butyl acrylate) (block A) and gradient copolymers of methyl methacrylate (MMA) and n-butyl acrylate (n BA) (block M/A) were investigated by means of their heat capacity, C_p, as a function of the composition of the blocks M/A and temperature. In all copolymers studied, both blocks are represented by their C_p and glass transition temperature, T_g, as well as the broadening of the transition-temperature range. The low-temperature transition of the blocks A is always close to that of the …

Impact Of Sea Grass Density On Carbonate Dissolution In Bahamian Sediments, David J. Burdige, Richard C. Zimmerman

OES Faculty Publications

Carbonate dissolution has been widely observed in shallow water tropical sediments. However, sediment budgets C have generally not been closed with respect to the amount of acid required to produce the observed carbonate dissolution. Recently it has been suggested that enhanced oxygen transport into sediments through the roots and rhizomes of sea grasses might play a role in resolving this mass balance problem. We conducted studies of sea grass-carbonate sediment interactions around Lee Stocking Island, Exuma Islands, Bahamas to further examine this problem. Our studies showed that alkalinity, total dissolved inorganic carbon (ΣCO₂) and Ca²⁺ increased with …

Intrasteric Inhibition Of Atp Binding Is Not Required To Prevent Unregulated Autophosphorylation Or Signaling By The Insulin Receptor, Mark Frankel, Ararat J. Ablooglu, Joseph W. Leone, Elena Rusinova, J. B. A. Ross, Robert L. Heinrikson, Ronald A. Kohanski

Chemistry and Biochemistry Faculty Publications

Receptor tyrosine kinases may use intrasteric inhibition to suppress autophosphorylation prior to growth factor stimulation. To test this hypothesis we made an Asp1161Ala mutant in the activation loop that relieved intrasteric inhibition of the unphosphorylated insulin receptor (IR) and its recombinant cytoplasmic kinase domain (IRKD) without affecting the activated state. Solution studies with the unphosphorylated mutant IRKD demonstrated conformational changes and greater catalytic efficiency from a 10-fold increase in kcat and a 15-fold-lower K_{m ATP} although K_{m peptide} was unchanged. Kinetic parameters of the autophosphorylated mutant and wild-type kinase domains were virtually identical. The Asp1161Ala mutation increased the …

Complex Effects Arising In Smoke Plume Simulations Due To Inclusion Of Direct Emissions Of Oxygenated Organic Species From Biomass Combustion, Sherri A. Mason, Richard J. Field, Robert J. Yokelson, Michael A. Kochivar, Mark R. Tinsley, Darold E. Ward, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

Oxygenated volatile organic species (oxygenates), including HCOOH, H₂CO, CH₃OH, HOCH₂CHO (hydroxyacetaldehyde), CH₃COOH, and C₆H₅OH, have recently been identified by Fourier transform infrared measurements as a significant component of the direct emissions from biomass combustion. These oxygenates have not generally been included in the hydrocarbon-based initial emission profiles used in previous photochemical simulations of biomass combustion smoke plumes. We explore the effects of oxygenates on this photochemistry by using an established initial emission hydrocarbon profile and comparing simulation results obtained both with and without addition of the above six …

Shape Imprinting Due To Variable Disulfide Bonds In Polyacrylamide Gels, Andrew B. Greytak, Alexander Y. Grosberg, Toyoichi Tanaka

Faculty Publications

Through the use of variable disulfide crosslinkers, we have created polyacrylamide gels whose shape can be altered after polymerization. N,N'-bisacryloylcystamine is incorporated as a crosslinker, along with a smaller amount of a permanent crosslinker. After polymerization, the disulfide bonds are cleaved into thiols through reduction. By reoxidizing the thiols with the gel held in a new macroscopic shape, a new set of disulfide bonds is formed, and the gel is forced to adopt the new shape. Retension of the new shape improves with greater distortion from the original shape, as well as with increased concentration of variable …

Phase Modulation At 125 Khz In A Michelson Interferometer Using An Inexpensive Piezoelectric Stack Driven At Resonance, Barbara M. Hoeling, Andrew D. Fernandez, Richard C. Haskell, Daniel C. Petersen

All HMC Faculty Publications and Research

Fast phase modulation has been achieved in a Michelson interferometer by attaching a lightweight reference mirror to a piezoelectric stack and driving the stack at a resonance frequency of about 125 kHz. The electrical behavior of the piezo stack and the mechanical properties of the piezo-mirror arrangement are described. A displacement amplitude at resonance of about 350 nm was achieved using a standard function generator. Phase drift in the interferometer and piezo wobble were readily circumvented. This approach to phase modulation is less expensive by a factor of roughly 50 than one based on an electro-optic effect.

Process For Immobilizing Waste Using Bagasse (Us Patent 6174275), Michael A. Janusa

Faculty Publications

No abstract provided.

Use Of Py-Gc/Ms Analysis Techniques In Animal Waste Management: A Preliminary Survey Of Dairy Manures, Daniel L. Vaughn, Michael A. Kruge

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The increasing practice of industrial-scale agriculture tends to concentrate large masses of animal waste in relatively compact areas, potentially leading to excessive release of polluting nutrients into waterways during major storms. Anaerobic treatment conditions are generally favored to conserve nitrate N as an agricultural commodity. However, overall N contents in waste are often in excess of crop fertilization needs: storing excess N in soluble nitrate form increases pollution potential. Thus the perceived needs of agriculture and society-at-large become at odds. Organic nitrogen forms (e.g., proteins) are more environmentally stable and are less subject to unintentional release. Although U.S. farmers tend …

Control Of Phytoplankton Growth By Iron And Silicic Acid Availability In The Subantarctic Ocean: Experimental Results From The Saz Project, D. A. Hutchins, Peter N. Sedwick, G. R. Ditullio, P. W. Boyd, B. Queguiner, F. B. Griffiths, C. Crossley

OES Faculty Publications

Subantarctic Southern Ocean surface waters in the austral summer and autumn are characterized by high concentrations of nitrate and phosphate but low concentrations of dissolved iron (Fe, similar to0.05 nM) and silicic acid (Si, <1 muM). During the Subantarctic Zone AU9706 cruise in March 1998 we investigated the relative importance of Fe and Si in controlling phytoplankton growth and species composition at a station within the subantarctic water mass (46.8degreesS, 142degreesE) using shipboard bottle incubation experiments. Treatments included unamended controls; 1.9 nM added iron (+Fe); 9 muM added silicic acid (+Si); and 1.9 nM addediron plus 9 muM added silicic acid (+Fe+Si). We followed a detailed set of biological and biogeochemical parameters over 8 days. Fe added alone clearly increased community growth rates and nitrate drawdown and altered algal community composition relative to control treatments. Surprisingly, small, lightly silicified pennate diatoms grew when Fe was added either with or without Si, despite the extremely low ambient silicic acid concentrations. Pigment analyses suggest that lightly silicified chrysophytes (type 4 haptophytes) may have preferentially responded to Si added either with or without Fe. However, for many of the parameters measured the +Fe+Si treatments showed large increases relative to both the +Fe and +Si treatments. Our results suggest that iron is the proximate limiting nutrient for chlorophyll production, photosynthetic efficiency, nitrate drawdown, and diatom growth, but that Si also exerts considerable control over algal growth and species composition. Both nutrients together are needed to elicit a maximum growth response, suggesting that both Fe and Si play important roles in structuring the subantarctic phytoplankton community.

Effects Of Iron, Silicate, And Light On Dimethylsulfoniopropionate Production In The Australian Subantarctic Zone, G. R. Ditullio, P. N. Sedwick, D. R. Jones, P. W. Boyd, A. C. Crossley, D. A. Hutchins

OES Faculty Publications

Shipboard bottle incubation experiments were performed to investigate the effects of iron, light, and silicate on algal production of particulate dimethylsulfoniopropionate (DMSP_p) in the Subantarctic Zone (SAZ) south of Tasmania during March 1998. Iron enrichment resulted in threefold to ninefold increases in DMSP_p concentrations relative to control treatments, following 7 and 8-day incubation experiments. Additions of Fe and Si preferentially stimulated the growth of lightly-silicified pennate diatoms and siliceous haptophytes, respectively, to which we attribute the increased DMSP_p production in the incubation bottles. Both of these algal groups were previously believed to be low DMSP_{p …}

Analysis Of Wine For Penicillin, Gary Morris, James Yuan, Roy Williams

Chemistry & Biochemistry Faculty Publications

This study addresses the question of whether the antibiotic Penicillin, which is produced by the common mold Penicillium notatum, could possibly become a contaminate of wine during the fermentation process. The significance of this study is related to the potential health effects this agent might produce in those consumers who have an allergic response to Penicillin. It has been estimated that between 6% and 8% of the American population is subject to this type of allergic response. A method is developed for the detection of penicillin in wines using high-pressure liquid chromatography. We demonstrate that penicillin G hydrolyzes rapidly …

Identification Of The Domains Of Urer, An Arac-Like Transcriptional Regulator Of The Urease Gene Cluster In Proteus Mirabilis, Carrie A. Poore, Christopher Coker, Jonathan D. Dattelbaum, Harry L.T. Mobley

Chemistry Faculty Publications

Proteus mirabilis urease catalyzes the hydrolysis of urea to CO₂ and NH₃, resulting in urinary stone formation in individuals with complicated urinary tract infections. UreR, a member of the AraC family, activates transcription of the genes encoding urease enzyme subunits and accessory proteins, ureDABCEFG, as well as its own transcription in the presence of urea. Based on sequence homology with AraC, we hypothesized that UreR contains both a dimerization domain and a DNA-binding domain. A translational fusion of the leucine zipper dimerization domain (amino acids 302 to 350) of C/EBP and the C-terminal half of UreR …

Chemical Constituents Of Desmos Dumosus, Roxb., Mazdida Sulaiman

Student Works (2000-2009)

The chemical content of the 'leaves and bark of Des mos dumosus has been carried out in this study. The leaves yielded nine isoquinoline type of alkaloids and two flavones. The isoquinoline alkaloids isolated were pronuciferine 37, stepharine 39, nomuciferine 40, (-) - 3 - hydroxynomuciferine 41, norlirioferine 42, asimilobine 43, liriodenine 44, lysicamine 45 and O - methylmoschatoline 46. The flavones were 5 - hydroxy - 6,7 - dimethoxyflavone 47 and 5 - hydroxy - 7,8 - dimethoxyflavone 48. The same flavones, 47 and 48 and the alkaloids 45 and 46 were also present in the bark of this …

Nonsteroidal Anti-Inflammatory Drugs, Acetaminophen, Cyclooxygenase 2, And Fever, Daniel L. Simmons, David Wagner, Kenneth Westover

Faculty Publications

Nonsteroidal anti-inflammatory drugs (NSAIDs) are frequently used antipyretic agents that most probably exert their antifever effect by inhibiting cyclooxygenase (COX)–2. Thus, COX-2–selective drugs or null mutation of the COX-2 gene reduce or prevent fever. Acetaminophen is antipyretic and analgesic, as are NSAIDs, but it lacks the anti-inflammatory and anticoagulatory properties of these drugs. This has led to the speculation that a COX variant exists that is inhibitable by acetaminophen. An acetaminophen-inhibitable enzyme is inducible in the mouse J774.2 monocyte cell line. Induction of acetaminophen-inhibitable prostaglandin E2 synthesis parallels induction of COX-2. Thus, inhibition of pharmacologically distinct COX-2 enzyme activity by …

Measurements Of Excess O3, Co2, Co, Ch4, C2h4, C2h2, Hcn, No, Nh3, Hcooh, Ch3cooh, Hcho, And Ch3oh In 1997 Alaskan Biomass Burning Plumes By Airborne Fourier Transform Infrared Spectroscopy (Aftir), Jon G. Goode, Robert J. Yokelson, Darold E. Ward, Ronald A. Susott, Ronald E. Babbitt, Mary Ann Davies, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

We used an airborne Fourier transform infrared spectrometer (AFTIR), coupled to a flow-through, air-sampling cell, on a King Air B-90 to make in situ trace gas measurements in isolated smoke plumes from four, large, boreal zone wildfires in interior Alaska during June 1997. AFTIR spectra acquired near the source of the smoke plumes yielded excess mixing ratios for 13 of the most common trace gases: water, carbon dioxide, carbon monoxide, methane, nitric oxide, formaldehyde, acetic acid, formic acid, methanol, ethylene, acetylene, ammonia and hydrogen cyanide. Emission ratios to carbon monoxide for formaldehyde, acetic acid, and methanol were 2.2±0.4%, 1.3±0.4%, and …

Investigations On The Use Of Ion Mobility Spectrometry For Clinical Chemistry Applications, Henri Parson Patten

Theses and Dissertations in Biomedical Sciences

The major objective of this research is to examine ion mobility spectrometry as a rapid screening tool for specific application to clinical chemistry research and laboratory use. Methodology was developed for target analytes representing several classes of physiologically active substances, including anesthetics, illicit drugs, and their metabolites. The IMS characteristics of animal tissues and other compounds such as amino acids and proteins were determined. Quality assurance and control procedures were developed for specific quality data objectives. Criteria were established relating to use of IMS for assessing the precision and accuracy of data, qualitative screening, and semi-quantitative analyses.

It was found …

Studies On The Roles Of Atp In Nitrogenase Catalysis, Wei Wu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogenase is the enzyme that catalyzes the reduction of nitrogen to ammonia in a reaction requiring MgATP hydrolysis. Two component proteins of nitrogenase are the iron protein (Fe protein) and the molybdenum-iron protein (MoFe protein).

Nitrogenase contains two nucleotide binding sites. During catalysis, the Fe protein binds two MgATP first. The conformational changes induced upon MgATP binding allow the Fe protein to associate with the MoFe protein. After the formation of the Fe protein-MoFe protein complex, a single electron is transferred from the Fe protein to the MoFe protein, an event that is coupled to MgATP hydrolysis in the Fe …

Biochemical Composition Of Particles And Dissolved Organic Matter Slong An Estuarine Gradient: Sources And Implications For Dom Reactivity, Antonio Mannino, H. Rodger Harvey

OES Faculty Publications

The chemical composition of high molecular weight dissolved organic matter (DOM) and particulate organic matter (POM) was examined along the salinity gradient of the Delaware Estuary. DOM was collected and fractionated by tangential-flow ultrafiltration into 1-30 kDa (HDOM; high molecular weight) and 30 kDa to 0.2 μm (VHDOM; very high molecular weight) and compared to particles collected in parallel. Polysaccharides comprised 12-43% of particulate organic carbon (POC), 30-56% of VHDOM carbon, and 7.5-19% of HDOM carbon. Hydrolyzable amino acids comprised 17-38% of POC, 5.4-12% of VHDOM carbon, and 1.5-4.2% of HDOM carbon. Only 7-43% of dissolved organic nitrogen in VHDOM …

Applications Of The Atomic Force Microscope Within The Fields Of Haematology And Cytogenetics, Margaret O'Reilly-Crowley

Theses

Atomic force microscopy [AFM] has become a rapidly developing interdisciplinary field of research in recent years. The technique, including instrumentation and specimen preparation methods, is now more sophisticated and its application has increased dramatically. The key advantage of AFM is in providing three-dimensional images of samples imaged. Both size and shape of samples imaged can be obtained allowing their subsequent quantification. Red blood cells [RBCs] and chromosomes were imaged in this work. A brief overview of the current status of biomedical AFM, has been presented in the review.

Measurement of mean cell volume [MCV] of immobilised red blood cells with …

Emissions Of Formaldehyde, Acetic Acid, Methanol, And Other Trace Gases From Biomass Fires In North Carolina Measured By Airborne Fourier Transform Infrared Spectroscopy, Robert J. Yokelson, Jon G. Goode, Darold E. Ward, Ronald A. Susott, Ronald E. Babbitt, D. D. Wade, Issac T. Bertschi, David W. T. Griffith, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

Biomass burning is an important source of many trace gases in the global troposphere. We have constructed an airborne trace gas measurement system consisting of a Fourier transform infrared spectrometer (FTIR) coupled to a “flow-through” multipass cell (AFTIR) and installed it on a U.S. Department of Agriculture Forest Service King Air B-90. The first measurements with the new system were conducted in North Carolina during April 1997 on large, isolated biomass fire plumes. Simultaneous measurements included Global Positioning System (GPS); airborne sonde; particle light scattering, CO, and CO₂; and integrated filter and canister samples. AFTIR spectra acquired within …

Trace Gas Emissions From Laboratory Biomass Fires Measured By Open-Path Fourier Transform Infrared Spectroscopy: Fires In Grass And Surface Fuels, Jon G. Goode, Robert J. Yokelson, Ronald A. Susott, Darold E. Ward

Chemistry and Biochemistry Faculty Publications

The trace gas emissions from six biomass fires, including three grass fires, were measured using a Fourier transform infrared (FTIR) spectrometer coupled to an open-path, multipass cell (OP-FTIR). The quantified emissions consisted of carbon dioxide, nitric oxide, water vapor, carbon monoxide, methane, ammonia, ethylene, acetylene, isobutene, methanol, acetic acid, formic acid, formaldehyde, and hydroxyacetaldehyde. By including grass fires in this study we have now measured smoke composition from fires in each major vegetation class. The emission ratios of the oxygenated compounds, formaldehyde, methanol, and acetic acid, were 1–2% of CO in the grass fires, similar to our other laboratory and …

Micromagnetics Simulation Of Nanoshaped Iron Elements: Comparison With Experiment, Ngocnga Dao, S. R. Homer, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

A micromagnetics simulation has been conducted on nanostructured magnetic elements of iron in order to investigate the effect of the shape of the element on magnetic properties, such as domain formation and hysteresis loops. These results are compared with recent experimental studies. The results display an impressive agreement with both the experimentally observed magnetic domains in individual particles as well as the shape of the hysteresis loops. The simulation results then explain features in the hysteresis loops in terms of vortice formation and motion.

Induced Changes In Solvent Structure By Phospholipid Monolayer Formation At A Liquid–Liquid Interface, R. A. Walker, D. E. Gragson, G. L. Richmond

Chemistry and Biochemistry

Vibrational sum frequency spectroscopy has been used in conjunction with dynamic surface tension measurements to study formation of a 1,2-dilauroyl-sn-phosphatidylcholine (DLPC) monolayer at a water–carbon tetrachloride interface. Surface tension measurements show that an aqueous solution of liquid crystalline phosphocholine vesicles (4.5 μM DLPC) requires several hours to form a tightly packed, fully equilibrated monolayer of DLPC monomers. Vibrational spectra of the interfacial region at different stages in the monolayer formation process indicate that the solvent structure undergoes dramatic re-organization as the monolayer forms. Initial adsorption of DLPC monomers severely disrupts the interfacial hydrogen bonding. Intensity in the OH …

Nitrate Reductase Activity, Nitrate Uptake And Iodine Speciation In The Marine Environment, Chin-Chang Hung

OES Theses and Dissertations

The present method for the determination of new production (NP) by measuring the uptake of added ¹⁵NO₃^– suffers from a number of limitations. In an attempt to improve this situation, this research examined the possibility of estimating ¹⁵NO₃– uptake by measuring the activity of nitrate reductase (NRA). In addition, because it has long been suspected that the biological reduction of IO₃^– to I^– may be mediated by nitrate reductase (NR), this research investigated the ability of NR to catalyze the reduction of iodate to iodide.

An improved method for the determination …

The Mean Spherical Approximation For A Dipolar Yukawa Fluid, Douglas Henderson, Dezso Boda, Istvan Szalai, Kwong-Yu Chan

Faculty Publications

The dipolar hard sphere fluid (DHSF) is a useful model of a polar fluid. However, the DHSF lacks a vapor–liquid transition due to the formation of chain-like structures. Such chains are not characteristic of real polar fluids. A more realistic model of a polar fluid is obtained by adding a Lennard–Jones potential to the intermolecular potential. Very similar results are obtained by adding a Yukawa potential, instead of the Lennard–Jones potential. We call this fluid the dipolar Yukawa fluid (DYF). We show that an analytical solution of the mean spherical approximation (MSA) can be obtained for the DYF. Thus, the …

Reductive Dehydroxy Coupling Of 2-(Hydroxymethyl)Indenes To Prepare Ethano-Bridged Bis(2-Indenyl) Ansa-Titanocenes, Hasan Palandoken, Justin K. Wyatt, Shawn R. Hitchcock, Marilyn M. Olmstead, Michael H. Nantz

Chemistry and Biochemistry

New examples of ansa-titanocenes derived from 1,2-bis(2-indenyl)ethane have been prepared. The titanium-mediated reductive coupling of 2-(hydroxymethyl)indenes provided a convenient method for substrate dimerization. Alkyl substitution of the indene ring at C(3) improved the regioselectivity of the reductive coupling to provide the ethylene bis(2-indenyl)ansa-ligands in 29–62% yield.

Production Of Copper-Complexing Ligands In Response To Elevated Concentrations Of Copper In Marine Synechococcus Spp., Arunsri Chatkaeomorakot Brown

Theses and Dissertations in Biomedical Sciences

Synechococcus spp. (marine cyanobacteria) are extremely sensitive to copper toxicity and can produce high-affinity ligands of unknown structure which form complexes with free cupric ion. These ligands may contribute to the biological control of the levels of free cupric ions in surface seawater. Synechococcus spp. are known to produce metallothioneins (MT) in response to cadmium and zinc stress. In the present study the hypothesis that marine Synechococcus produce MT in response to copper was tested. Three marine Synechococcus spp. i.e., PCC 7001, PCC 73109, and PCC 7003, were exposed to different concentrations of CUSO 4 for various time periods. Size …

Monte Carlo Study Of The Capacitance Of The Double Layer In A Model Molten Salt, Douglas Henderson, Dezso Boda, Kwong-Yu Chan

Faculty Publications

Monte Carlo simulations are reported for charged hard spheres at high density near a charged wall. This system is a simple model for a molten salt double layer. Unfortunately, the reduced temperatures that correspond to experiment are very small. This results in a large Boltzmann factor. As a result, we are unable to obtain meaningful results for such low values and report results only for moderately low values of the reduced temperature. Even so, our results should be a useful benchmark. Further, we are able to give a qualitative answer to an interesting question. We find that at low temperatures …

Relationship Between Udp-Glucose 4-Epimerase Activity And Oligoglucose Glycoforms In Two Strains Of Neisseria Meningitidis, F K. Lee, B W. Gibson, William Melaugh, A Zaleski, M A. Apicella

Chemistry Faculty Publications

Sodium dodecyl sulfate-polyacrylamide gel analysis of lipooligosaccharide (LOS) from Neisseria meningitidis has demonstrated considerable microheterogeneity in the variable region of LOS due to the presence of novel glycoforms. As a step toward understanding the basis for the expression of these novel glycoforms, we have examined the LOS structures and UDP-glucose 4-epimerase (epimerase) activity levels in two strains (NMB and MA-1) and their respective galE mutants. Strain NMB was found to have low epimerase activity and to contain multiple glycoforms, some of which appear to contain only glucose sugars. The galE mutant had only the oligoglucose glycoforms. Strain MA-1 had higher …

Iron-Induced Oxidative Stress In Erythrocyte Membranes Of Non-Insulin-Dependent Diabetic Nigerians, Gbolahan W. Okunade, Odutayo O. Odunuge, Olufunso O. Olorunsogo

Faculty Publications

The presence of higher level of endogenous free radical reaction products in the erythrocyte ghost membrane (EGM) of Non-insulin-dependent diabetes mellitus (NIDDM) subjects compared with that of normal healthy controls has been demonstrated. The EGMs of NIDDM subjects were also shown to be more susceptible to exogenously generated oxidative stress than those of normal healthy individuals. The decreased level of reactive thiol groups in the EGM of NIDDM individuals supported this observation. We propose that the presence of significant levels of non-heme iron in the EGM of NIDDM subjects is an indication of the potential for iron-catalysed production of hydroxy …