Biochemistry, Biophysics, and Structural Biology Commons^™

Evidence Of Linear Lattice Expansion And Covalency Enhancement In Rutile Tio2 Nanocrystals, Guangshe Li, Juliana Boerio-Goates, Brian F. Woodfield, Liping Li

Faculty Publications

Lattice variations and bonding characteristics in rutile TiO2 nanocrystals were examined by x-ray diffraction and x-ray photoelectron spectroscopy. With a reduction in the physical dimensions, rutile TiO2 nanocrystals show a linear lattice expansion and an anomalous covalency enhancement in apparent contradiction to the ionicity increase in BaTiO3 and CuO nanocrystals as reported recently by S. Tsunekawa et al. [Phys. Rev. Lett. 2000, 85, 3440] and V. R. Palkar et al. [Phys. Rev. B 1996, 53, 2167]. A surface defect dipole model is proposed to explain these physical phenomena in terms of the strong interactions among the surface dipoles that produce …

Examination Of Technologies For Student-Generated Work In A Peer-Led, Peer-Review Instructional Environment, Brian P. Coppola, Alan L. Kiste

Chemistry and Biochemistry

There is a growing literature demonstrating the effectiveness of using computer environments to assist students’ in visualizing science and mathematics concepts. However, with many of these computerized learning environments, students do not have the option of manipulating the environment. Instead, they are presented with pre-made visualizations. Enabling students to display their understanding through multiple representational forms is more interesting. In our peer-led, peer-review environment, students generate a complex, literature-based, multimedia text on which their final examination is based. However, there are great time and personnel costs in this design. Collaborating with SRI Inc., we are addressing these demands via the …

Capillary Liquid Chromatography Using Micro Size Particles, Yanqiao Xiang

Theses and Dissertations

High speed and/or high efficiency separations can be realized using small particles (~ 1 µm) in liquid chromatography (LC). However, due to the large pressure drop caused by small particles, conventional LC pumping systems cannot satisfy the pressure requirements needed to drive the mobile phase through the column. Use of ultrahigh pressure, elevated temperature, or both can overcome these pressure limitations and allow the use of very small particles for high speed and/or high efficiency separations.

In this dissertation, the use of ultrahigh pressures with and without elevated temperatures in capillary LC is described. Very fast separations of various samples …

A High -Order Finite Difference Method For Solving Bioheat Transfer Equations In Three-Dimensional Triple -Layered Skin Structure, Haofeng Yu

Doctoral Dissertations

Investigations on instantaneous skin burns are useful for an accurate assessment of burn-evaluation and for establishing thermal protections for various purposes. Meanwhile, hyperthermia with radiation is important in the treatment of cancer, and it is essential for developers and users of hyperthermia systems to predict, and interpret correctly the biomass thermal and vascular response to heating. In this dissertation, we employ the well-known Pennes' bioheat transfer equation to predict the degree of skin burn and the temperature distribution in hyperthermia cancer treatment.

A fourth-order compact finite difference scheme is developed to solve Pennes' bioheat transfer equation in a three-dimensional single …

Emissions From Miombo Woodland And Dambo Grassland Savanna Fires, Parikhit Sinha, Peter V. Hobbs, Robert J. Yokelson, Donald R. Blake, Song Gao, Thomas W. Kirschsetter

Chemistry and Biochemistry Faculty Publications

[1] Airborne measurements of trace gases and particles over and downwind of two prescribed savanna fires in Zambia are described. The measurements include profiles through the smoke plumes of condensation nucleus concentrations and normalized excess mixing ratios of particles and gases, emission factors for 42 trace gases and seven particulate species, and vertical profiles of ambient conditions. The fires were ignited in plots of miombo woodland savanna, the most prevalent savanna type in southern Africa, and dambo grassland savanna, an important enclave of miombo woodland ecosystems. Emission factors for the two fires are combined with measurements of fuel loading, combustion …

Thickness Dependence Of Magneto-Transport In Cu-Co Granular Thin Films, Jian Qing Wang, Ngocnga Dao, Ham H. Kim, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

This work explores the thickness dependence of magneto-transport properties in granular thin films with different thickness. These results are compared with silver-based film series studied earlier. It was observed that the thickness dependence of the GMReffect was sensitive to the surface chemistry of the films. The extraordinary Hall effect (EHE) in these films was measured and found to be different from the Ag-based system. In the Cu-based system, the EHE is a weak function of film thickness over the range studied. When the variation of the spontaneous magnetization is taken into account the effective EHE has a universal thickness dependence

Velocity And Temperature Characterization Of The First Vacuum Stage Expansion In An Inductively Coupled Plasma - Mass Spectrometer, William Neil Radicic

Theses and Dissertations

The inductively coupled plasma - mass spectrometer (ICP-MS) is the analytical instrument of choice for trace element detection and quantification. Despite the popularity of ICP-MS, significant degradation in sensitivity and precision occurs as the result of matrix and instrument-induced effects. The sources of these effects are not well understood, characterized, or correlated to particular plasma operating condition settings or matrix compositions and involve both neutral and charged species. The purpose of this study is to characterize the behavior of metastable Ar (I) atom and Ca (II) ion through the measurement of Doppler velocities and fluorescence line width "temperatures."

For the …

Evaluating The Contributions Of Desolvation And Base-Stacking During Translesion Dna Synthesis, Xuemei Zhang, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA polymerases catalyze the insertion of a nucleoside triphosphate into the growing polymer chain using the template strand as a guide. Numerous factors such as hydrogen bonding interactions, base-stacking contributions, and desolvation play important roles in controlling the efficiency and fidelity of this process. We previously demonstrated that 5-nitro-indolyl-2′-deoxyriboside triphosphate, a non-natural nucleobase with enhanced base-stacking properties, was more efficiently inserted opposite a non-templating DNA lesion compared to natural templating nucleobases (E. Z. Reineks and A. J. Berdis, Biochemistry, 2004, 43, 393–404). The catalytic enhancement was proposed to reflect increased base-stacking interactions of the non-natural nucleobase with the polymerase and …

N9 Alkylation And Glycosylation Of Purines; A Practical Synthesis Of 2-Chloro-2'-Deoxyadenosine, Minghong Zhong

Theses and Dissertations

(a) The Robins reagent [2-acetamido-6-O-(diphenylcarbamoyl)purine] was utilized for glycosylation under Lewis acid conditions. Regioselectivity of glycosylation depends on the glycosyl donor and its 2-O- or 2-N-protecting group. Regioselective N9 glycosylation of 2-acetamido-6-O-(diphenylcarbamoyl)purine with problematic glucosamine has been accomplished by protecting the amino function as a phthalimido group with consequent stabilization of the oxocarbenium cation, and lowering the activation energy by introduction of trichloroacetimidate at the anomeric carbon.

(b) 6-Heteroaryl functions [6-(1,2,4-triazol-4-yl) and 6-(imidazol-1-yl)] were introduced into purine derivatives for regioselective N9 alkylation. The regiospecificity of alkylation mainly results from steric effects due to the coplanar conformation of the two linked …

Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber

Faculty Publications

n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 µA/µm and 4.9 µA/V, respectively, with device yields of >85%.

Role Of Iron In The Mechanism Of Asbestos-Induced Apoptosis In Human Lung And Pleural Target Cells, Aleksander Baldys

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Occupational exposure to asbestos has been associated with increased incidence of pulmonary interstitial fibrosis, mesothelioma of the pleura, and bronchogenic carcinoma. Although the mechanism by which asbestos causes cancer remains unknown, iron associated with asbestos is thought to play a role in the pathogenic effects of fibers.

The aim of this research was to examine and compare the asbestos-induced signaling phenomena in relevant human lung and pleural target cells, and to determine the role of iron from asbestos fibers in these events. Exposure of human airway epithelial (A549) cells, human pleural mesothelial (MET5A) cells, and normal human small airway epithelial …

Identification Of An Il-17-Producing Nk1.1neg Inkt Cell Population Involved In Airway Neutrophilia, Paul B. Savage, Marie-Laure Michel, Alexandre Castro Keller, Christophe Paget, Masakazu Fujio, Francois Trottein, Chi-Huey Wong, Elke Schneider, Michael Dy, Maria C. Leite-De-Moraes

Faculty Publications

Invariant natural killer T (iNKT) cells are an important source of both T helper type 1 (Th1) and Th2 cytokines, through which they can exert beneficial, as well as deleterious, effects in a variety of inflammatory diseases. This functional heterogeneity raises the question of how far phenotypically distinct subpopulations are responsible for such contrasting activities. In this study, we identify a particular set of iNKT cells that lack the NK1.1 marker (NK1.1neg) and secrete high amounts of interleukin (IL)-17 and low levels of interferon (IFN)-{gamma} and IL-4. NK1.1neg iNKT cells produce IL-17 upon synthetic ({alpha}-galactosylceramide [{alpha}-GalCer] or PBS-57), as well …

Fluorescence Detectors For Proteins And Toxic Heavy Metals, Uchenna Prince Paul

Theses and Dissertations

An inexpensive detector for proteins is described. The detection technique was based on two-photon excitation intrinsic protein fluorescence using a visible 532 nm diode-pumped nano laser as the excitation source. Proteins that exhibit intrinsic fluorescence must contain at least one tryptophan, tyrosine, or phenylalanine residue in their amino acid sequences. The detector was characterized and was found to have a detection limit of 4 micro-molar for tryptophan, 22 micro-molar for tyrosine and 500 micro-molar for phenylalanine. Bovine serum albumin, a serum protein with 3 tryptophan residues in its amino acid sequence was also used to characterize the detector. It was …

Analysis Of Clinically Important Compounds Using Electrophoretic Separation Techniques Coupled To Time-Of-Flight Mass Spectrometry, Zlatuse Durda Peterson

Theses and Dissertations

Capillary electrophoretic (CE) separations were successfully coupled to time-of-flight mass spectrometric (TOFMS) detection for the analysis of three families of biological compounds that act as mediators and/or indicators of disease, namely, catecholamines (dopamine, epinephrine, norepinephrine) and their O-methoxylated metabolites (3-methoxytyramine, norepinephrine, and normetanephrine), indolamines (serotonin, tryptophan, and 5-hydroxytryptophan), and angiotensin peptides. While electrophoretic separation techniques provided high separation efficiency, mass spectrometric detection afforded specificity unsurpassed by other types of detectors.

Both catecholamines and indolamines are present in body fluids at concentrations that make it possible for them to be determined by capillary zone electrophoresis coupled to TOFMS without employing any …

A Subgroup Algorithm To Identify Cross-Rotation Peaks Consistent With Non-Crystallographic Symmetry, Ryan H. Lilien, Chris Bailey-Kellogg, Amy C. Anderson, Bruce R. Donald

Dartmouth Scholarship

Molecular replacement (MR) often plays a prominent role in determining initial phase angles for structure determination by X-ray crystallography. In this paper, an efficient quaternion-based algorithm is presented for analyzing peaks from a cross-rotation function in order to identify model orientations consistent with proper non-crystallographic symmetry (NCS) and to generate proper NCS-consistent orientations missing from the list of cross-rotation peaks. The algorithm, CRANS, analyzes the rotation differences between each pair of cross-rotation peaks to identify finite subgroups. Sets of rotation differences satisfying the subgroup axioms correspond to orientations compatible with the correct proper NCS. The CRANS algorithm was first …

Heterogeneous Chemistry Involving Methanol In Tropospheric Clouds, A. Tabazadeh, Robert J. Yokelson, H. B. Singh, Peter V. Hobbs, J. H. Crawford, L. T. Iraci

Chemistry and Biochemistry Faculty Publications

In this report we analyze airborne measurements to suggest that methanol in biomass burning smoke is lost heterogeneously in clouds. When a smoke plume intersected a cumulus cloud during the SAFARI 2000 field project, the observed methanol gas phase concentration rapidly declined. Current understanding of gas and aqueous phase chemistry cannot explain the loss of methanol documented by these measurements. Two plausible heterogeneous reactions are proposed to explain the observed simultaneous loss and production of methanol and formaldehyde, respectively. If the rapid heterogeneous processing of methanol, seen in a cloud impacted by smoke, occurs in more pristine clouds, it could …

Comprehensive Laboratory Measurements Of Biomass-Burning Emissions: 2. First Intercomparison Of Open-Path Ftir, Ptr-Ms, And Gc-Ms/Fid/Ecd, Ted J. Christian, B. Kleiss, Robert J. Yokelson, R. Holzinger, P. J. Crutzen, Wein Min Hao, T. Shirai, Donald R. Blake

Chemistry and Biochemistry Faculty Publications

No abstract provided.

Altered Phosphorylation Of [Beta]-Catenin In Glucocorticoid Treated 235-1 Rat Pituitary Tumor Cells, Susie K. Saunders

Theses, Dissertations and Capstones

Beta-catenin is an essential cell adhesion and signaling protein, associated with high prolactin levels in rat pituitary tumor cells. It has been shown that phosphorylation affects the location and activity of b-catenin. Glycogen synthase kinase (GSK3-b) is a serine-threonine kinase that phosphorylates b-catenin on N-terminal residues, targeting it for proteasomal degradation. Studies have shown that C-terminal tyrosine phosphorylation decreases the association of b-catenin with cadherin. In 235-1 rat pituitary tumor cells, our lab has shown that the glucocorticoid analog dexamethasone (Dex) decreases the half- life of b-catenin while increasing the activity of GSK3-b. The current study was undertaken to examine …

Distributions Of Z-Dna And Nuclear Factor I In Human Chromosome 22: A Model For Coupled Transcriptional Regulation, P. Christoph Champ, Sandor Maurice, Jeff Vargason, Tracy Camp, P. Shing Ho

Faculty Publications - Department of Biological & Molecular Science

An analysis of the human chromosome 22 genomic sequence shows that both Z-DNA forming regions (ZDRs) and promoter sites for nuclear factor-I (NFI) are correlated with the locations of known and predicted genes across the chromosome and accumulate around the transcriptional start sites of the known genes. Thus, the occurrence of Z-DNA across human genomic sequences mirrors that of a known eukaryotic transcription factor. In addition, 43 of the 383 fully annotated chromosomal genes have ZDRs within 2 nucleosomes upstream of strong NFIs. This suggests a distinct class of human genes that may potentially be transcriptionally regulated by a mechanism …

Development Of A Gene Transfer System In Clostridium Scindens Vpi 12708, Rashmi Ramasubbaiah

Masters Theses & Specialist Projects

Clostridium scindens VPI 12708 (previously known as Eubacterium sp. VPI 12708) is a bile-acid dehydroxylating bacterium originally isolated from the feces of a colon cancer patient. Many genes required for bile acid 7-a dehydroxylation are found on a large bile acid inducible operon (bai) that has been extensively studied. However the bai promoter, which directs expression of the bai operon, has yet to be characterized due, in part, to a lack of a functional genetic transfer system for this strain. A spontaneous rifampinresistant Clostridium scindens VPI 12708 mutant was used as a recipient to determine the efficacy of conjugation as …

Evaluation Of Multiple Models To Distinguish Closely Related Forms Of Disease Using Dna Microarray Data: An Application To Multiple Myeloma, Johanna S. Hardin, Michael Waddell, C. David Page, Fenghuang Zhan, Bart Barlogie, John Shaughnessy, John J. Crowley

Pomona Faculty Publications and Research

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is …

Influence Of Short-Term Variations In Food On Survival Of Crassotrea Gigas Larvae: A Modeling Study, Eric N. Powell, Eleanor A, Bochenek, John M. Klinck, Eileen E. Hofmann

OES Faculty Publications

A biochemically-based model was developed to simulate the growth, development, and metamorphosis of larvae of the Pacific oyster, Crassostrea gigas. The model defines larvae in terms of their protein, lipid, carbohydrate, and ash content and includes variation in growth efficiency and egg quality to better simulate cohort population dynamics. Changes in tissue composition occur as the larva grows and in response to the biochemical composition of the food. The premise behind this modeling study was that certain periods of larval life are more critical than others with respect to the availability of food and that food quality is as …

Computational Protein Biomarker Prediction: A Case Study For Prostate Cancer, Michael Wagner, Dayanand N. Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, Bao-Ling Adam, O. John Semmes, George L. Wright Jr.

Mathematics & Statistics Faculty Publications

Background: Recent technological advances in mass spectrometry pose challenges in computational mathematics and statistics to process the mass spectral data into predictive models with clinical and biological significance. We discuss several classification-based approaches to finding protein biomarker candidates using protein profiles obtained via mass spectrometry, and we assess their statistical significance. Our overall goal is to implicate peaks that have a high likelihood of being biologically linked to a given disease state, and thus to narrow the search for biomarker candidates.

Results: Thorough cross-validation studies and randomization tests are performed on a prostate cancer dataset with over 300 patients, obtained …

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 …

Modeling Of The Inverse Heat -Conduction Problem With Application To Laser Chemical Vapor Deposition And Bioheat Transfer, Peng Zhen

Doctoral Dissertations

This dissertation consists of two parts. Part one deals with three-dimensional laser induced chemical vapor deposition (3D-LCVD), whereas part two deals with a Pennes model of a 3D skin structure. LCVD is an important technique in manufacturing complex micro-structures with high aspect ratio. In part one, a numerical model was developed for simulating kinetically-limited growth of an axisymmetric cylindrical rod by pre-specifying the surface temperature distribution required for growing the rod and then by obtaining optimized laser power that gives rise to the pre-specified temperature distribution. The temperature distribution at the surface of the rod was assumed to be at …

Extensive Regional Atmospheric Hydrocarbon Pollution In The Southwestern United States, Lambert A. Doezema

Chemistry and Biochemistry Faculty Works

Light alkane hydrocarbons are present in major quantities in the near-surface atmosphere of Texas, Oklahoma, and Kansas during both autumn and spring seasons. In spring 2002, maximum mixing ratios of ethane [34 parts per 109 by volume (ppbv)], propane (20 ppbv), and n-butane (13 ppbv) were observed in north-central Texas. The elevated alkane mixing ratios are attributed to emissions from the oil and natural gas industry. Measured alkyl nitrate mixing ratios were comparable to urban smog values, indicating active photochemistry in the presence of nitrogen oxides, and therefore with abundant formation of tropospheric ozone. We estimate that 4-6 teragrams of …