Biochemistry Commons^™

Self-Aligned Mechanical Attachment Of Carbon Nanotubes To Silicon Dioxide Structures By Selective Silicon Dioxide Chemical-Vapor Deposition, Jed D. Whittaker, Ghaleb A. Husseini, Matthew A. Linford, Robert C. Davis, Markus Brink

Faculty Publications

A self-aligned thin-film deposition technique was developed to mechanically attach carbon nanotubes to surfaces for the fabrication of structurally robust nanotube-based nanomechanical devices. Single-walled carbon nanotubes were grown by thermal chemical-vapor deposition (CVD) across 150-nm-wide SiO2 trenches. The nanotubes were mechanically attached to the trench tops by selective silicon tetraacetate-based SiO2 CVD. No film was deposited on the nanotubes where they were suspended across the trenches.

Seasonal Variation And Ecosystem Dependence Of Emission Factors For Selected Trace Gases And Pm2.5 For Southern African Savanna Fires, S. Korontzi, Darold E. Ward, Ronald A. Susott, Robert J. Yokelson, C. O. Justice, Peter V. Hobbs, E.A. H. Smithwick, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

[1] In this paper we present the first early dry season (early June-early August) emission factor measurements for carbon dioxide (CO₂), carbon monoxide (CO), methane (CH₄), nonmethane hydrocarbons (NMHC), and particulates with a diameter less than 2.5 μm (PM_2.5) for southern African grassland and woodland fires. Seasonal emission factors for grassland fires correlate linearly with the proportion of green grass, used as a surrogate for the fuel moisture content, and are higher for products of incomplete combustion in the early part of the dry season compared with later in the dry season. Models of …

Comprehensive Laboratory Measurements Of Biomass-Burning Emissions: 1. Emissions From Indonesian, African, And Other Fuels, Ted J. Christian, B. Kleiss, Robert J. Yokelson, R. Holzinger, P. J. Crutzen, Wei Min Hao, B. H. Saharjo, Darold E. Ward

Chemistry and Biochemistry Faculty Publications

[1] Trace gas and particle emissions were measured from 47 laboratory fires burning 16 regionally to globally significant fuel types. Instrumentation included the following: open-path Fourier transform infrared spectroscopy; proton transfer reaction mass spectrometry; filter sampling with subsequent analysis of particles with diameter <2.5 μm for organic and elemental carbon and other elements; and canister sampling with subsequent analysis by gas chromatography (GC)/flame ionization detector, GC/electron capture detector, and GC/mass spectrometry. The emissions of 26 compounds are reported by fuel type. The results include the first detailed measurements of the emissions from Indonesian fuels. Carbon dioxide, CO, CH₄, NH₃, HCN, methanol, and acetic acid were the seven most abundant emissions (in order) from burning Indonesian peat. Acetol (hydroxyacetone) was a major, previously unobserved emission from burning rice straw (21–34 g/kg). The emission factors for our simulated African fires are consistent with field data for African fires for compounds measured in both …

Evaluation Of Adsorption Effects On Measurements Of Ammonia, Acetic Acid, And Methanol, Robert J. Yokelson, Ted J. Christian, Isaac T. Bertschi, Wei M. Hao

Chemistry and Biochemistry Faculty Publications

[1] We examined how adsorption and desorption of gases from inlets and a cell could affect the accuracy of closed-cell FTIR measurements of carbon dioxide (CO₂), carbon monoxide (CO), methane (CH₄), nitric oxide (NO), nitrogen dioxide (NO₂), methanol (CH₃OH), acetic acid (CH₃COOH), and ammonia (NH₃). When standards were delivered to the cell through a stainless steel inlet, temporarily reduced transmission was observed for CH₃OH and NH₃. However, a halocarbon wax coated inlet (normally used on the system) had excellent transmission (comparable to room temperature …

Magnetic Storage Device Using Induced Magnetic Reversal Of A Cobalt Element Array, Hanning Chen, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

The effects of the applied field, cell size, and cutting area on the ‘‘seed’’ induced magnetic reversal of a cobalt element array have been studied by a stochastic dynamic micromagnetics code using the Laudau–Lifshitz–Gilbert equation. Three magnetic reversal mechanisms under different magnitudes of the applied field have been investigated by examining the energy profiles. To minimize the effect of the thermal fluctuations on the switching time, an applied field with magnitude around 0.7 or 0.8 T and an element array with cutting area less than 10 nm X 10 nm are required. By using the smaller cellsize, the switching time …

Distributions Of Trace Gases And Aerosols During The Dry Biomass Burning Season In Southern Africa, Parikhit Sinha, Peter V. Hobbs, Robert J. Yokelson, Donald R. Blake, Song Gao, Thomas W. Kirschsetter

Chemistry and Biochemistry Faculty Publications

[1] Vertical profiles in the lower troposphere of temperature, relative humidity, sulfur dioxide (SO₂), ozone (O₃), condensation nuclei (CN), and carbon monoxide (CO), and horizontal distributions of twenty gaseous and particulate species, are presented for five regions of southern Africa during the dry biomass burning season of 2000. The regions are the semiarid savannas of northeast South Africa and northern Botswana, the savanna-forest mosaic of coastal Mozambique, the humid savanna of southern Zambia, and the desert of western Namibia. The highest average concentrations of carbon dioxide (CO₂), CO, methane (CH₄), O_{3 …}

Trace Gas Measurements In Nascent, Aged, And Cloud-Processed Smoke From African Savanna Fires By Airborne Fourier Transform Infrared Spectroscopy (Aftir), Robert J. Yokelson, Issac T. Bertschi, Ted J. Christian, Peter V. Hobbs, Darold E. Ward, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

[1] We measured stable and reactive trace gases with an airborne Fourier transform infrared spectrometer (AFTIR) on the University of Washington Convair-580 research aircraft in August/September 2000 during the SAFARI 2000 dry season campaign in Southern Africa. The measurements included vertical profiles of CO₂, CO, H₂O, and CH₄ up to 5.5 km on six occasions above instrumented ground sites and below the TERRA satellite and ER-2 high-flying research aircraft. We also measured the trace gas emissions from 10 African savanna fires. Five of these fires featured extensive ground-based fuel characterization, and two were in the …

Perilipin A Is Essential For The Translocation Of Hormone-Sensitive Lipase During Lipolytic Activation. J Cell Biol, John Tansey

Chemistry Faculty Scholarship

A key step in lipolytic activation of adipocytes is the translocation of hormone-sensitive lipase (HSL) from the cytosol to the surface of the lipid storage droplet. Adipocytes from perilipin -null animals have an elevated basal rate of lipolysis compared with adipocytes from wild-type mice, but fail to respond maximally to lipolytic stimuli. This defect is downstream of the -adrenergic receptor–adenylyl cyclase complex. Now, we show that HSL is basally associated with lipid droplet surfaces at a low level in perilipin nulls, but that stimulated translocation from the cytosol to lipid droplets is absent in adipocytes derived from embryonic fibroblasts of …

Thickness Dependence Of Magnetic Blocking In Granular Thin Films With Interacting Magnetic Particles, Jian Qing Wang, Zhi Dong Zhao, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

Interparticle interaction among single domain nanosize magnetic particles embedded in nonmagnetic matrix was studied. Attention was paid to concentrated Cu–Co granular thin films with a fixed magnetic volume fraction (20%). By analyzing theoretical models and comparing with experimental results, a dimensional constraint on the magnetic properties was found. As the film thickness reduces toward the thin limit the interparticle interaction plays important roles in modifying the magnetic behavior. The dipolar interaction energy was calculated among magnetic particles including far-neighbor interaction for films with different thickness values. When magnetization variation is included in the calculation, the resulting calculated interaction energy versus …

Evaluating The Effects Of Enhanced Processivity And Metal Ions On Translesion Dna Replication Catalyzed By The Bacteriophage T4 Dna Polymerase, Edmunds Z. Reineks, Anthony J. Berdis

Chemistry Faculty Publications

The fidelity of DNA replication is achieved in a multiplicative process encompassing nucleobase selection and insertion, removal of misinserted nucleotides by exonuclease activity, and enzyme dissociation from primer/templates that are misaligned due to mispairing. In this study, we have evaluated the effect of altering these kinetic processes on the dynamics of translesion DNA replication using the bacteriophage T4 replication apparatus as a model system. The effect of enhancing the processivity of the T4 DNA polymerase, gp43, on translesion DNA replication was evaluated using a defined in vitro assay system. While the T4 replicase (gp43 in complex with gp45) can perform …

Preparation Of 2s,3s-N-Isobutyl-N-(2-Hydroxy-3-Amino-4-Phenylbutyl)-P-Nitrobenzenesulfonylamide Hydrochloride And Other Derivatives Of 2-Hydroxy-1,3-Diamines, Aslam A. Malik, Hasan Palandoken, Joy A. Stringer, Roland P. Carlson, John Leach, Thomas G. Archibald, Robert G. Miotke

Chemistry and Biochemistry

The present invention provides a new process for the preparation of 2S,3S-N-isobutyl-N-(2-hydroxy-3-amino-4phenylbutyl)- p-nitrobenzenesulfonylamide hydrochloride, wherein this compound is prepared directly from the chloromethylalcohol. Importantly, the process of the present invention results in higher yields of 2S,3S-N-isobutyl-N-(2hydroxy -3 -amino -4-phenylbutyl) -pnitrobenzenesulfonylamide hydrochloride without sacrificing its purity. The processes of the present inventin can be used to prepare not only the 2S,3S-derivative, but also the 2R,3S-, 2S,2R- and the 2R,3R-derivatives.

Clean, High-Yield Preparation Of S,S- And R,S- Amino Acid Isosteres, Aslam A. Malik, Todd E. Clement, Hasan Palandoken, James Robinson Iii, Joy A. Stringer

Chemistry and Biochemistry

The present invention provides compounds and methods that can be used to convert the intermediate halomethyl ketones (HMKs), e.g., chloromethyl ketones, to the corresponding S,S- and R,S-diastereomers. More particularly, the present invention provides: (1) reduction methods; (2) inversion methods; and (3) methods involving the epoxidation of alkenes. Using the various methods of the present invention, the R,S-epoxide and the intermediary compounds can be prepared reliably, in high yields and in high purity.

Tropospheric Carbon Monoxide Measurements From The Scanning High-Resolution Interferometer Sounder On 7 September 2000 In Southern Africa During Safari 2000, W. W. Mcmillan, M. L. Mccourt, H. E. Revercomb, R. O. Knuteson, Ted J. Christian, B. G. Doddridge, Peter V. Hobbs, J. V. Lukovich, P. C. Novelli, S. J. Piketh, L. Sparling, D. Stein, R. J. Swap, Robert J. Yokelson

Chemistry and Biochemistry Faculty Publications

[1] Retrieved tropospheric carbon monoxide (CO) column densities are presented for more than 9000 spectra obtained by the University of Wisconsin-Madison (UWis) Scanning High-Resolution Interferometer Sounder (SHIS) during a flight on the NASA ER-2 on 7 September 2000 as part of the Southern African Regional Science Initiative (SAFARI 2000) dry season field campaign. Enhancements in tropospheric column CO were detected in the vicinity of a controlled biomass burn in the Timbavati Game Reserve in northeastern South Africa and over the edge of the river of smoke in south central Mozambique. Relatively clean air was observed over the far southern coast …

Emissions Of Trace Gases And Particles From Savanna Fires In Southern Africa, Parikhit Sinha, Peter V. Hobbs, Robert J. Yokelson, I. T. Bertschi, Donald R. Blake, Isobel J. Simpson, Song Gao, Thomas W. Kirschsetter, Tica Novakov

Chemistry and Biochemistry Faculty Publications

[1] Airborne measurements made on initial smoke from 10 savanna fires in southern Africa provide quantitative data on emissions of 50 gaseous and particulate species, including carbon dioxide, carbon monoxide, sulfur dioxide, nitrogen oxides, methane, ammonia, dimethyl sulfide, nonmethane organic compounds, halocarbons, gaseous organic acids, aerosol ionic components, carbonaceous aerosols, and condensation nuclei (CN). Measurements of several of the gaseous species by gas chromatography and Fourier transform infrared spectroscopy are compared. Emission ratios and emission factors are given for eight species that have not been reported previously for biomass burning of savanna in southern Africa (namely, dimethyl sulfide, methyl nitrate, …

Evolution Of Gases And Particles From A Savanna Fire In South Africa, Peter V. Hobbs, Parikhit Sinha, Robert J. Yokelson, Ted J. Christian, Donald R. Blake, Song Gao, Thomas W. Kirschsetter, Tica Novakov, Peter Pilewskie

Chemistry and Biochemistry Faculty Publications

[1] Airborne measurements of particles and gases from a 1000-ha savanna fire in South Africa are presented. These measurements represent the most extensive data set reported on the aging of biomass smoke. The measurements include total concentrations of particles (CN), particle sizes, particulate organic carbon and black carbon, light-scattering coefficients, downwelling UV fluxes, and mixing ratios for 42 trace gases and 7 particulate species. The ratios of excess nitrate, ozone, and gaseous acetic acid to excess CO increased significantly as the smoke aged over ∼40–45 min, indicating that these species were formed by photochemistry in the plume. For 17 other …

Trace Gas And Particle Emissions From Fires In Large Diameter And Belowground Biomass Fuels, Isaac T. Bertschi, Robert J. Yokelson, Darold E. Ward, R. E. Babbitt, Ronald A. Susott, Jon G. Goode, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

[1] We adopt a working definition of residual smoldering combustion (RSC) as biomass combustion that produces emissions that are not lofted by strong fire-induced convection. RSC emissions can be produced for up to several weeks after the passage of a flame front and they are mostly unaffected by flames. Fuels prone to RSC include downed logs, duff, and organic soils. Limited observations in the tropics and the boreal forest suggest that RSC is a globally significant source of emissions to the troposphere. This source was previously uncharacterized. We measured the first emission factors (EF) for RSC in a series of …

Examination Of The Role Of The Clamp-Loader And Atp Hydrolysis In The Formation Of The Bacteriophage T4 Polymerase Holoenzyme, Michael A. Trakselis, Anthony J. Berdis, Stephen J. Benkovic

Chemistry Faculty Publications

Transient kinetic analyses further support the role of the clamp-loader in bacteriophage T4 as a catalyst which loads the clamp onto DNA through the sequential hydrolysis of two molecules of ATP before and after addition of DNA. Additional rapid-quench and pulse-chase experiments have documented this stoichiometry. The events of ATP hydrolysis have been related to the opening/closing of the clamp protein through fluorescence resonance energy transfer (FRET). In the absence of a hydrolysable form of ATP, the distance across the subunit interface of the clamp does not increase as measured by intramolecular FRET, suggesting gp45 cannot be loaded onto DNA. …

Trace Gas Emissions From The Production And Use Of Domestic Biofuels In Zambia Measured By Open-Path Fourier Transform Infrared Spectroscopy, Isaac T. Bertschi, Robert J. Yokelson, Darold E. Ward, Ted J. Christian, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

[1] Domestic biomass fuels (biofuels) were recently estimated to be the second largest source of carbon emissions from global biomass burning. Wood and charcoal provide approximately 90% and 10% of domestic energy in tropical Africa. In September 2000, we used open-path Fourier transform infrared (OP-FTIR) spectroscopy to quantify 18 of the most abundant trace gases emitted by wood and charcoal cooking fires and an earthen charcoal-making kiln in Zambia. These are the first in situ measurements of an extensive suite of trace gases emitted by tropical biofuel burning. We report emission ratios (ER) and emission factors (EF) for (in order …

Structural And Biochemical Analyses Of Dna And Rna Binding By A Bifunctional Homing Endonuclease And Group I Intron Splicing Factor, Jill M. Bolduc, P. Clint Spiegel, Pivali Chatterjee, Kristina L. Brady, Maureen E. Downing, Mark G. Caprara, Richard B. Waring, Barry L. Stoddard

Chemistry Faculty and Staff Publications

We determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 Å resolution. The structure demonstrates the remarkable structural conservation of the (3-sheet DNA-binding motif between highly divergent enzyme subfamilies. DNA recognition by I-AniI was further studied using nucleoside deletion and DMS modification interference analyses. Correlation of these results with the crystal structure provides information on the relative importance of individual nucleotide contacts for DNA recognition. Alignment and modeling of two homologous maturases reveals conserved basic surface residues, distant …

Urer, The Transcriptional Activator Of The Proteus Mirabilis Urease Gene Cluster, Is Required For Urease Activity And Virulence In Experimental Urinary Tract Infections, Jonathan D. Dattelbaum, C. Virginia Lockatell, David E. Johnson, Harry L.T. Mobley

Chemistry Faculty Publications

Proteus mirabilis, a cause of complicated urinary tract infection, produces urease, an essential virulence factor for this species. UreR, a member of the AraC/XylS family of transcriptional regulators, positively activates expression of the ure gene cluster in the presence of urea. To specifically evaluate the contribution of UreR to urease activity and virulence in the urinary tract, a ureR mutation was introduced into P. mirabilis HI4320 by homologous recombination. The isogenic ureR::aphA mutant, deficient in UreR production, lacked measurable urease activity. Expression was not detected in the UreR-deficient strain by Western blotting with monoclonal antibodies raised against UreD. Urease …

Fluorescence Determination Of Tryptophan Side-Chain Accessibility And Dynamics In Triple-Helical Collagen-Like Peptides, K. V. Simon-Lukasik, A. V. Persikov, B. Brodsky, J. A. M. Ramshaw, William Laws, J. B. A. Ross, R. D. Ludescher

Chemistry and Biochemistry Faculty Publications

We report tryptophan fluorescence measurements of emission intensity, iodide quenching, and anisotropy that describe the environment and dynamics at X and Y sites in stable collagen-like peptides of sequence (Gly-X-Y)(n). About 90% of tryptophans at both sites have similar solvent exposed fluorescence properties and a lifetime of 8.5-9 ns. Analysis of anisotropy decays using an associative model indicates that these long lifetime populations undergo rapid depolarizing motion with a 0.5 ns correlation time; however, the extent of fast motion at the Y site is considerably less than the essentially unrestricted motion at the X site. About 10% of tryptophans at …

Constrained Analysis Of Fluorescence Anisotropy Decay: Application To Experimental Protein Dynamics, E. Feinstein, G. Deikus, E. Rusinova, E. L. Rachofsky, J. B. A. Ross, William Laws

Chemistry and Biochemistry Faculty Publications

Hydrodynamic properties as well as structural dynamics of proteins can be investigated by the well-established experimental method of fluorescence anisotropy decay. Successful use of this method depends on determination of the correct kinetic model, the extent of cross-correlation between parameters in the fitting function, and differences between the timescales; of the depolarizing motions and the fluorophore's fluorescence lifetime. We have tested the utility of an independently measured steady-state anisotropy value as a constraint during data analysis to reduce parameter cross correlation and to increase the timescales over which anisotropy decay parameters can be recovered accurately for two calcium-binding proteins. Mutant …

Tetratricopeptide Repeat Motif-Mediated Hsc70-Msti1 Interaction Molecular Characterization Of The Critical Contacts For Successful Binding And Specificity*, Odutayo O. Odunuge, Judith A. Hornby, Chrisiane Bies, Richard Zimmermann, David J. Pugh, Gregory L. Blatch

Faculty Publications

Murine stress-inducible protein 1 (mSTI1) is a cochaperone that is homologous with the human Hsp70/ Hsp90-organizing protein (Hop). Guided by Hop structural data and sequence alignment analyses, we have used site-directed mutagenesis, co-precipitation assays, circular dichroism spectroscopy, steady-state fluorescence, and surface plasmon resonance spectroscopy to both qualitatively and quantitatively characterize the contacts necessary for the N-terminal tetratricopeptide repeat domain (TPR1) of mSTI1 to bind to heat shock cognate protein 70 (Hsc70) and to discriminate between Hsc70 and Hsp90. We have shown that substitutions in the first TPR motif of Lys8 or Asn12 did not affect binding of mSTI1 to Hsc70, …

Protocols For Disease Classification From Mass Spectrometry Data, Michael Wagner, Dayanand Naik, Alex Pothen

Mathematics & Statistics Faculty Publications

We report our results in classifying protein matrix-assisted laser desorption/ionizationtime of flight mass spectra obtained from serum samples into diseased and healthy groups. We discuss in detail five of the steps in preprocessing the mass spectral data for biomarker discovery, as well as our criterion for choosing a small set of peaks for classifying the samples. Cross-validation studies with four selected proteins yielded misclassification rates in the 10-15% range for all the classification methods. Three of these proteins or protein fragments are down-regulated and one up-regulated in lung cancer, the disease under consideration in this data set. When cross-validation studies …