Digital Commons Network^™

Cost-Effective Engineering Of A Small-Scale Bioreactor, John Tansey, Sadie R. Bartholomew

Chemistry Faculty Scholarship

Several methods exist for increasing the scale of cell culture in the laboratory. While these methods provide significant increases in biomass, they are often prohibitively expensive for many laboratories. We have engineered a small-scale bioreactor with a novel means of introducing oxygen through the catalytic breakdown of hydrogen peroxide using a manganese oxide catalyst. We have also adapted and modified an existing assay for dissolved oxygen to be compatible with culture conditions. In this system we have been able to culture CHO cells at densities of up to 10⁷ cells/mL without the use of automated feedback systems.

Review: A Creationist Review And Preliminary Analysis Of The History, Geology, Climate, And Biology Of The Galápagos Islands, Timothy R. Brophy

Faculty Publications and Presentations

No abstract provided.

Replica Exchange With Dynamical Scaling, Steven W. Rick

Chemistry Faculty Publications

A replica exchange method is presented which requires fewer replicas and is designed to be used for large systems. In this method, dynamically scaled replicas are placed between conventional replicas at broadly spaced temperatures. The potential of the scaled replicas is linearly scaled by a dynamicalvariable which varies between 0 and 1. When the variable is near either end point the replica can undergo exchanges with one of its neighboring replicas. Two different versions of the method are presented for a model system of a small peptide in water. The scaled replica can replace manyreplicas and the method can be …

Fragmentation Of Methyl Chloride Studied By Partial Positive And Negative Ion Yield Spectroscopy, D. Ceolin, Maria Novella Piancastelli, Renaud Guillemin, Wayne C. Stolte, S-W Yu, Oliver Hemmers, Dennis W. Lindle

Environmental Studies Faculty Publications

The authors present partial-ion-yield experiments on the methyl chloride molecule excited in the vicinity of the Cl2p and C1s inner shells. A large number of fragments, cations produced by dissociation or recombination processes, as well as anionic species, have been detected. Although the spectra exhibit different intensity distributions depending on the core-excited atom, general observations include strong site-selective fragmentation along the C–Cl bond axis and a strong intensity dependence of transitions involving Rydberg series on fragment size.

Basic Research Needs For Geosciences: Facilitating 21st Century Energy Systems, U.S. Department Of Energy, Office Of Basic Energy Sciences, Donald J. Depaolo, Franklin M. Orr Jr.

Publications (YM)

Executive Summary

Serious challenges must be faced in this century as the world seeks to meet global energy needs and at the same time reduce emissions of greenhouse gases to the atmosphere. Even with a growing energy supply from alternative sources, fossil carbon resources will remain in heavy use and will generate large volumes of carbon dioxide (CO₂). To reduce the atmospheric impact of this fossil energy use, it is necessary to capture and sequester a substantial fraction of the produced CO₂. Subsurface geologic formations offer a potential location for long-term storage of the requisite large …

The Structure And Function Of Small Nucleolar Ribonucleoproteins, Steve Reichow, Tomoko Hamma, Adrian R. Ferré-D’Amaré, Gabriele Varani

Chemistry Faculty Publications and Presentations

Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequencespecific methylation and pseudouridylation of RNA, the two most abundant types of modifications of cellular RNAs. In eukaryotes, these protein–RNA complexes localize to the nucleolus and are called small nucleolar RNPs (snoRNPs), while in archaea they are known as small RNPs (sRNP). The C/D class of sno(s)RNPs carries out ribose- 20-O-methylation, while the H/ACA class is responsible for pseudouridylation of their RNA targets. Here, we review the recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs. Structures of each of the …

Development Of Enzymatic Biofuel Cell Based On Carbon Nanotube Electrodes On Porous Silicon, Fan Yang

Theses

The work presented in this thesis has focused on designing and characterizing biofuel cell electrodes using porous silicon (p-Si) as the substrate or current collecting platform on which carbon nanotubes (CNTs), both single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MiWNTs), were synthesized directly, followed by enzyme catalyst immobilization on the CNTs. Laccase and glucose oxidase (GOx) were used as enzymatic biocatalysts, which were immobilized on the CNT walls and tips using an electrochemical technique. Cyclic voltammetry showed well-defined redox peaks which indicated that the enzyme (GOx and laccase) were successfully immobilized on the CNTs. The amperometric responses of the …

Catalytic Cleavage Of Phosphate Ester Bonds By Boron Chelates, David A. Atwood

Chemistry Faculty Patents

Novel chemical compounds are disclosed having the general formula L{YX_m}_n, wherein X is selected from the Group 13 elements, Y is a halide, and L is a chelating ligand containing at least one binding atom contacting the Group 13 element, the atom being selected from the group consisting of C, N, O, and S, and m and n are integers having a value of at least 1. L may be a Schiff base type ligand, such as a salen ligand. The compositions of the present invention may be bidentate, quadridentate, or greater. The compositions may be …

High-Resolution Structure Of A Beta-Peptide Bundle, Douglas S. Daniels, E. James Petersson, Jade X. Qiu, Alanna S. Schepartz

Chemistry Faculty Publications

We recently reported that β-peptides can form discrete hetero-oligomers in aqueous solution. Here we describe the structure of such an oligomer as determined by X-ray crystallography. The structure of Zwit-1F reveals a homo-octamer of two cupped “hands” composed of both parallel and antiparallel 314-helices. The core of the assembly is composed entirely of solvent-excluded β3-homoleucine residues. The Zwit-1F assembly shares many of the physical characteristics of natural proteins.

Examination Of The New Α-(2′Z-Fluoro)Vinyl Trigger With Lysine Decarboxylase: The Absolute Stereochemistry Dictates The Reaction Course, Kannan R. Karukurichi, Roberto De La Salud-Bea, Wan Jin Jahng, David B. Berkowitz

David Berkowitz Publications

The first examination of a terminal α-fluorovinyl trigger in an amino acid decarboxylase active site is reported. To investigate the enantiospecifity of inactivation with this new AADC trigger, an enantioselective synthesis of L-α-(2′Z-fluoro)vinyllysine and its D-antipode has been developed. Control of stereochemistry is achieved through introduction of the amino acid side chain via alkylation of a chiral vinylglycine-derived dienolate. Facial selectivity is conferred by a trans-2′(β- naphthyl)-2′-propylcyclohexyl ester auxiliary, available in both antipodal forms (Comins protocol). The alkylation employs a new electrophile, N-p-methoxybenzyl-N-(2′- trimethylsilylethanesulfonyl)-4-iodobutylamine, for convergent installation of the lysine side chain. Vinyl to 2′-fluorovinyl interconversion then provides L- …

Searching For Smart Durable Coatings To Promote Bone Marrow Stromal Cell Growth While Preventing Biofilm Formation, Fereydoon Namavar, John D. Jackson, J. Graham Sharp, Ethan E. Mann, Kenneth W. Bayles, Chin Li Cheung, Connie A. Feschuk, Shailaja Varma, Hani Haider, Kevin L. Garvin

Barry Chin Li Cheung Publications

There is a great need to develop methods to regulate cellular growth in order to enhance or prevent cell proliferation, as needed, to either improve health or prevent disease. In this work we evaluated the adhesion, survival and growth of bone marrow stromal cells on the surface of several new ion beam engineered nano-crystals of ceramic hard coatings such as zirconium, titanium, tantalum and cerium oxides. Cell adhesion and growth on the ceramic coatings were compared to adhesion and growth on a nano-crystalline silver coating which is known to possess antibacterial properties. The initial results of a study to determine …

13C Nmr Analysis Of Biologically Produced Pyrene Residues By Mycobacterium Sp. Kms In The Presence Of Humic Acid, J. Karl C. Nieman, Richard C. Holz, Ronald C. Sims

Chemistry Faculty Research and Publications

Cultures of the pyrene degrading Mycobacterium sp. KMS were incubated with [4-¹³C]pyrene or [4,5,9,10-¹⁴C]pyrene with and without a soil humic acid standard to characterize the chemical nature of the produced residues and evaluate the potential for bonding reactions with humic acid. Cultures were subjected to a “humic acid/humin” separation at acidic pH, a duplicate separation followed by solvent extraction of the humic acid/humin fraction, and a high pH separation. ¹³C NMR analysis was conducted on the resulting solid extracts. Results indicated that the activity associated with solid extracts did not depend on pH and that …

Intellectual Property Management In Health And Agricultural Innovation: A Handbook Of Best Practices, Vol. 2, Anatole Krattiger, Richard T. Mahoney, Lita Nelsen, Jennifer A. Thomson, Alan B. Bennett, Kanikaram Satyanarayana, Gregory D. Graff, Carlos Fernandez, Stanley Kowalski

Law Faculty Scholarship

Prepared by and for policy-makers, leaders of public sector research establishments, technology transfer professionals, licensing executives, and scientists, this online resource offers up-to-date information and strategies for utilizing the power of both intellectual property and the public domain. Emphasis is placed on advancing innovation in health and agriculture, though many of the principles outlined here are broadly applicable across technology fields. Eschewing ideological debates and general proclamations, the authors always keep their eye on the practical side of IP management. The site is based on a comprehensive Handbook and Executive Guide that provide substantive discussions and analysis of the opportunities …

Apparatus And Method For Growing Crystal, And Apparatus And Method For Analyzing Crystal: United States Patent No. 7,156,917 B2, Hideaki Moriyama, Norio Sugi, Kazunori Kawasaki, Shoji Muramatsu

Hideaki Moriyama Publications

An apparatus for growing a biological macromolecular crystal by vaporizing biological macromolecular solution into an oversaturated state. The apparatus includes a first sealed room that receives first crystallizing agent solution, and a communicating tube that communicates with the first sealed room and has a small sectional area for suppressing convection of air. A plurality of droplets of solution dissolving a biological macromolecule and a crystallizing agent therein are held in the communicating tube with the plurality of droplets being separated from each other.

Investigating The Spring Bloom In San Francisco Bay: Links Between Water Chemistry, Metal Cycling, Mercury Speciation, And Phytoplankton Community Composition, Allison C. Luengen

Environmental Science

Investigating the spring bloom in San Francisco Bay: Links between water chemistry, metal cycling, mercury speciation, and phytoplankton community composition This dissertation addresses the relationship between two problems facing estuaries nationwide: nutrient enrichment and metal contamination. The focus is on the southern reach of San Francisco Bay, where high nutrient concentrations can control the magnitude of the predictably occurring spring phytoplankton bloom. The bloom in this study, in spring 2003, was one of the largest blooms on record, exceeding 150 μg L ^-1 of chlorophyll α. As the bloom grew, diatoms (e.g. Thalassiosira punctigera ) depleted dissolved nutrients from the …

Purification And Study Of Phosphoglucose Isomerase In Cauliflower, Shanti Shrestha

Capstone Research Projects

Phosphoglucose isomerase (PGI), an important enzyme in the glycolytic pathway, catalyzes the conversion of glucose-6-phosphate to fructose-6-phosphate and vice versa. The purpose of this research was to isolate PGI from cauliflower using a shortened procedure through column chromatography and characterize it through absorbance readings, enzyme activity measurements, and SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). PGI was successfully isolated from cauliflower using ion-exchange chromatography. Absorbance and enzyme activity were determined at 280nm and 340nm respectively. There appeared to be one main absorbance peak for the protein at fraction 31, as well as a maximum peak for enzyme activity. SDS-PAGE was conducted …

Intellectual Property Management In Health And Agricultural Innovation: Executive Guide, Anatole Krattiger, Richard T. Mahoney, Lita Nelsen, Jennifer A. Thomson, Alan B. Bennett, Kanikaram Satyanarayana, Gregory D. Graff, Carlos Fernandez, Stanley Kowalski

Law Faculty Scholarship

Prepared by and for policy-makers, leaders of public sector research establishments, technology transfer professionals, licensing executives, and scientists, this online resource offers up-to-date information and strategies for utilizing the power of both intellectual property and the public domain. Emphasis is placed on advancing innovation in health and agriculture, though many of the principles outlined here are broadly applicable across technology fields. Eschewing ideological debates and general proclamations, the authors always keep their eye on the practical side of IP management. The site is based on a comprehensive Handbook and Executive Guide that provide substantive discussions and analysis of the opportunities …

Intellectual Property Management In Health And Agricultural Innovation: A Handbook Of Best Practices, Vol. 1, Anatole Krattiger, Richard T. Mahoney, Lita Nelsen, Jennifer A. Thomson, Alan B. Bennett, Kanikaram Satyanarayana, Gregory D. Graff, Carlos Fernandez, Stanley Kowalski

Law Faculty Scholarship

Prepared by and for policy-makers, leaders of public sector research establishments, technology transfer professionals, licensing executives, and scientists, this online resource offers up-to-date information and strategies for utilizing the power of both intellectual property and the public domain. Emphasis is placed on advancing innovation in health and agriculture, though many of the principles outlined here are broadly applicable across technology fields. Eschewing ideological debates and general proclamations, the authors always keep their eye on the practical side of IP management. The site is based on a comprehensive Handbook and Executive Guide that provide substantive discussions and analysis of the opportunities …

Investigations On The Structure Of Dimethyl Sulfoxide And Acetone In Aqueous Solution, Sylvia E. Mclain, Alan K. Soper, Alenka Luzar

Chemistry Publications

Aqueous solutions of dimethyl sulfoxide (DMSO) and acetone have been investigated using neutron diffraction augmented with isotopic substitution and empirical potential structure refinement computer simulations. Each solute has been measured at two concentrations—1:20 and 1:2 solute:water mole ratios. At both concentrations for each solute, the tetrahedral hydrogen bonding network of water is largely unperturbed, though the total water molecule coordination number is reduced in the higher 1:2 concentrations. With higher concentrations of acetone, water tends to segregate into clusters, while in higher concentrations of DMSO the present study reconfirms that the structure of the liquid is dominated by DMSO-water interactions. …

Synthesis And Characterisation Of Tetra-Tetrazole Macrocycles, Andrew Bond, Adrienne Fleming, Fintan Kelleher, John Mcginley, Vipa Prajapati, Signe Skovsgaard

Articles

The syntheses of tetra-tetrazole macrocycles, containing two bis-tetrazole units linked by a variety of alkyl chain lengths from four to eight carbons, are described. The crystal structures of three of these derivatives are reported, and the molecular conformation in the solid state is compared to that of one previously reported tetra-tetrazole macrocycle and to other bis- and tris(tetrazole)benzene structures. The macrocycle conformation is influenced by the length of the alkyl chain linker, the relative orientation of the tetrazole rings on the benzene ring, and by intermolecular interactions. In the macrocycles based on 1,2-bis(tetrazole)benzene, the adjacent tetrazole rings on the benzene …

Air And Water Free Solid-Phase Synthesis Of Thiol Stabilized Au Nanoparticles With Anchored, Recyclable Dendrimer Templates, John D. Gilbertson, G. Vijayaraghavan, K. J. Stevenson, Bert D. Chandler

Chemistry Faculty Research

Solid-phase synthetic templates for Au nanoparticles were developed using Merrifield resins and polyamidoamine (PAMAM) dendrimers. This synthetic scheme affords the opportunity to prepare metal nanoparticles in the absence of air and water, and it does not necessitate phase transfer agents that can be difficult to remove in subsequent steps. Amine-terminated generation 5 PAMAM (G5NH2) dendrimers were grafted to anhydride functionalized polystyrene resin beads and alkylated with 1,2-epoxydodecane to produce G5C12anch. The anchored dendrimers bound both CoII and AuIII salts from toluene solutions at ratios comparable to those of solution phase alkyl-terminated PAMAM dendrimers. The encapsulated AuIII salts could be reduced …

Synthesis, Characterization, And Spectroscopy Of Model Molybdopterin Complexes, Sharon J. Nieter Burgmayer, Mary Kim, Rebecca Petit, Amy Rothkopf, Shadia Belhamdounia, Ying Hou, Arpad Somogyi, Diana Habel-Rodriguez, Antonio Williams, Martin L. Kirk

Chemistry Faculty Research and Scholarship

The preparation and characterization of new model complexes for the molybdenum cofactor are reported. The new models are distinctive for the inclusion of pterin-substituted dithiolene chelates and have the formulation Tp*MoX(pterin-R-dithiolene) (Tp* = tris(3,5,-dimethylpyrazolyl)borate), X= O, S, R= aryl or –C(OH)(CH₃)₂). Syntheses of Mo(4+) and (5+) complexes of two pterin-dithiolene derivatives as both oxo and sulfido compounds, and improved syntheses for pterinyl alkynes and [Et₄N][Tp*Mo^IV(S)S₄] reagents are described. Characterization methods include electrospray ionization mass spectrometry, electrochemistry, infrared spectroscopy, electron paramagnetic resonance and magnetic circular dichroism. Cyclic voltammetry reveals that the …

Enhancing Fertiliser Use Efficiency For Transplanted Vegetables, Dennis Phillips, Aileen Reid, Gavin D'Adhemar

Horticulture research reports

Horticulture Australia (HAL) Project No. VG04018.

Project VG 04018 ‘Enhancing fertiliser use efficiency for transplanted vegetables’ showed that spraying highly concentrated solutions containing nitrogen over newly transplanted vegetable seedlings for between 14 and 21 days after planting can increase marketable yields by as much as 300% compared to other methods of fertiliser application. Crops that this method has been successfully tested on in this study by the W.A. Department of Agriculture and Food include iceberg and Cos lettuce, broccoli, cauliflower, Chinese cabbage (wombok), celery and cabbage.

The research was conducted on virgin sandy soils of the Swan Coastal Plain near …

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

Characterization Of Power Induced Heating And Damage In Fiber Optic Probes For Near-Field Scanning Optical Microscopy, Nicholas E. Dickenson, E. S. Erickson, O. L. Mooren, R. C. Dunn

Chemistry and Biochemistry Faculty Publications

Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to ~55–60°C as output powers reach ~50 nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of ~450 nW. The sample heating profiles measured for etched NSOM probes are consistent with …

Eddy Correlation Measurements Of The Air/Sea Flux Of Dimethylsulfide Over The North Pacific Ocean, Christa A. Marandino, Warren J. De Bruyn, Scott D. Miller, Eric S. Saltzman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Shipboard measurements of air/sea fluxes and sea surface concentrations of dimethylsulfide (DMS) were made over the tropical and midlatitude North Pacific Ocean. Atmospheric pressure chemical ionization mass spectrometry was used to measure DMS levels in ambient air and in air equilibrated with surface seawater drawn from a depth of 5 m. Air/sea fluxes were obtained using eddy covariance. Corrections and uncertainties involved in the calculation of fluxes from shipboard data are discussed. The surface ocean DMS concentrations measured during this study ranged from 1 to 10 nM, and atmospheric mixing ratios ranged from 20 to 1000 ppt. Air/sea fluxes ranged …

Size Dependent Magnetic Properties And Cation Inversion In Chemically Synthesized Mnfe2o4 Nanoparticles, C. N. Chinnasamy, Aria Yang, S. D. Yoon, Kailin Hsu, M. D. Shultz, E. E. Carpenter, S. Mukerjee, C. Vittoria, V. G. Harris

Chemistry Publications

MnFe2O4nanoparticles with diameters ranging from about 4to50nm were synthesized using a modified coprecipitation method. X-ray diffractograms revealed a pure phase spinel ferrite structure for all samples. Transmission electron microscopy showed that the particles consist of a mixture of both spherical (smaller) and cubic (larger) particles dictated by the reaction kinetics. The Néel temperatures (TN) of MnFe2O4 for various particle sizes were determined by using high temperature magnetometry. The ∼4nm MnFe2O4 particles showed a TN of about 320°C whereas the ∼50nm particles had a TN of about 400°C. The high Néel temperature, compared with the bulk MnFe2O4 TN of 300°C, is …

Polymer Gels: Mimickin G Biological Environments, Joshua Carey

Opportunities for Undergraduate Research Experience Program (OURE)

A comparison of the hydrolysis of pyruvic acid in polymer gels and in aqueous environment will be studied using NMR techniques. Relaxation time and diffusion rates will be determined and compared to show the mimicking capability of the polymer gels to that of biological environments. This will allow for a means in which chemical reactions can be performed in a medium that more closely resembles the rate that the reaction would occur in biological systems.

Emissions From Forest Fires Near Mexico City, Robert J. Yokelson, S. P. Urbanski, E. L. Atlas, D. W. Toohey, E. C. Alvarado, J. D. Crounse, P. O. Wennberg, M. E. Fisher, C. E. Wold, T. L. Campos, K. Adachi, P. R. Buseck, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

The emissions of NOx (defined as NO (nitric oxide) + NO2 (nitrogen dioxide)) and hydrogen cyanide (HCN), per unit amount of fuel burned, from fires in the pine forests that dominate the mountains surrounding Mexico City (MC) are about 2 times higher than normally observed for forest burning. The ammonia (NH3) emissions are about average for forest burning. The upper limit for the mass ratio of NOx to volatile organic compounds (VOC) for these MC-area mountain fires was similar to 0.38, which is similar to the NOx/VOC ratio in the MC urban area emissions inventory of 0.34, but much larger …

The Tropical Forest And Fire Emissions Experiment: Overview And Airborne Fire Emission Factor Measurements, Robert J. Yokelson, T. Karl, Paulo Artaxo, Donald R. Blake, Ted J. Christian, David W. T. Griffith, Alex Guenther, Wei Min Hao

Chemistry and Biochemistry Faculty Publications

The Tropical Forest and Fire Emissions Experiment (TROFFEE) used laboratory measurements followed by airborne and ground based field campaigns during the 2004 Amazon dry season to quantify the emissions from pristine tropical forest and several plantations as well as the emissions, fuel consumption, and fire ecology of tropical deforestation fires. The airborne campaign used an Embraer 110B aircraft outfitted with whole air sampling in canisters, mass-calibrated nephelometry, ozone by UV absorbance, Fourier transform infrared spectroscopy (FTIR), and proton-transfer mass spectrometry (PTR-MS) to measure PM(10), O(3), CO(2), CO, NO, NO(2), HONO, HCN, NH(3), OCS, DMS, CH(4), and up to 48 non-methane …