Biochemistry Commons^™

Dynamic Polarizabilities Of Rare-Earth-Metal Atoms And Dispersion Coefficients For Their Interaction With Helium Atoms, Xi Chu, Alexander Dalgarno, Gerrit C. Groenenboom

Chemistry and Biochemistry Faculty Publications

The dynamic scalar and tensor polarizabilities of the rare-earth-metal atoms are calculated with time-dependent density functional theory. The frequency-dependent polarizabilities at imaginary frequencies are used to determine the isotropic and orientation-dependent van der Waals coefficients for the interactions of the rare-earth-metal atoms with helium atoms. The static polarizabilities are compared with other theoretical values and with experimental results. The agreement is satisfactory in most cases but there are some exceptions where the discrepancy between theory and experiment is significant. The derived isotropic van der Waals coefficients range between 37 and 50 E(H)a(0)(6) and the orientation-dependent coefficients between 2 and -1 …

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.

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 …

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 …

The Biophysical Analysis Of The Human Telomeric Repeat (Ttaggg)4 And Characterization Of Porphyrin Binding In Potassium Solutions, Cosimo Antonacci

Seton Hall University Dissertations and Theses (ETDs)

.

In Vivo Imaging Of Transport And Biocompatibility Of Single Silver Nanoparticles In Early Development Of Zebrafish Embryos, Kerry J. Lee, Prakash D. Nallathamby, Lauren M. Browning, Christopher J. Osgood, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Real-time study of the transport and biocompatibility of nanomaterials in early embryonic development at single-nanoparticle resolution can offer new knowledge about the delivery and effects of nanomaterials in vivo, and provide new insights into molecular transport mechanisms in developing embryos. In this study, we directly characterized the transport of single silver nanoparticles into an in vivo model system (zebrafish embryos) and investigated their effects on early embryonic development at single-nanoparticle resolution in real time. We designed highly purified and stable (not aggregated and no photodecomposition) nanoparticles and developed single-nanoparticle optics and in vivo assays to enable the study. We …

Dna Multiplex Hybridization On Microarrays And Thermodynamic Stability In Solution: A Direct Comparison, Daniel J. Fish, M. Todd Horne, Greg P. Brewood, Jim P. Goodarzi, Saba Alemayehu, Ashwini Bhandiwad, Robert P. Searles, Albert S. Benight

Chemistry Faculty Publications and Presentations

Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH degrees , DeltaS degrees and DeltaG degrees of melting transitions in solution were evaluated directly using differential scanning calorimetry. Quantitative comparison with results from 63 multiplex microarray hybridization experiments provided a linear relationship for perfect match and most mismatch duplexes. Examination of outliers suggests that both duplex length and relative position of tandem mismatches could be important factors contributing to …

The Application Of Electrospray Ionization Coupled To Ultrahigh Resolution Mass Spectrometry For The Molecular Characterization Of Natural Organic Matter, Rachel L. Sleighter, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Mass spectrometry has recently played a key role in the understanding of natural organic matter (NOM) by providing molecular-level details about its composition. NOM, a complex assemblage of organic molecules present in natural waters and soils/sediments, has the ability to bind and transport anthropogenic materials. An improved understanding of its composition is crucial in order to understand how pollutants interact with NOM and how NOM cycles through global carbon cycles. In the past, low-resolution (> 3000) mass analyzers have offered some insights into the structure of NOM, but emerging ultrahigh resolution (> 200000) techniques such as electrospray ionization (ESI) coupled …

Synthesis And Optical Properties Of Four Oligothiophene-Ruthenium Complexes And Synthesis Of A Bidentate Ligand For C-F Bond Activation, Joseph S. Bair

Theses and Dissertations

Photovoltaic cells and fluorescence sensing are two important areas of research in chemistry. The combination of photon-activated electron donors with electron acceptors provides a strong platform for the study of optical devices. A series of four oligothiophene-ruthenium complexes has been synthesized. Variation in oligothiophene length and bipyridine substitution allowed comparison of these variables on electronic properties. The longer oligothiophenes display lower energy absorption and emission compared to the shorter ones. Aromatic conjugation appears more complete with para-, rather than meta-, substitution. Oligothiophenes and Ru(bpy)32+ are highly fluorescent individually, but fluorescence is quenched when connected. Bonds of carbon to fluorine are …

Development Of Polymer Monoliths For The Analysis Of Peptides And Proteins, Binghe Gu

Theses and Dissertations

Several novel polymer monoliths for the analysis of peptides and proteins were synthesized using polyethylene glycol diacrylate (PEGDA) as crosslinker. Photo-initiated copolymerization of polyethylene glycol methyl ether acrylate and PEGDA yielded an inert monolith that could be used for size exclusion liquid chromatography of peptides and proteins. This macroscopically uniform monolith did not shrink or swell in either water or tetrahydrofuran. More importantly, it was found to resist adsorption of both acidic and basic proteins in aqueous buffer without any organic solvent additives. A strong cation-exchange polymer monolith was synthesized by copolymerization of 2-acrylamido-2-methyl-1-propanesulfonic acid (AMPS) and PEGDA. A ternary …

Development Of Methods For The Study Of Phosphoproteins, Zhaoyuan Chen

Theses and Dissertations

Characterization of phosphoproteins-including detection, identification of phosphoproteins and identification of phosphorylation sites-is mostly done with radiolabeling and proteomic techniques. Three main topics related to phosphoprotein characterization are included in this dissertation. First, large-scale characterization of the CHO (Chinese hamster ovary) cell phosphoproteome was done using two dimensional gel electrophoresis (2DE) separation, visualization of phosphoproteins by radiolabeling or a phosphoprotein specific dye, followed by MALDI-TOF identification. Because radiolabeling of phosphoproteins is very sensitive and straightforward to quantify, such analysis can give a clear picture of the relative phosphosphorylation of proteins present in a sample. But there are also limitations to this …

Capillary Electrophoresis Of Proteins With Selective On-Line Affinity Monoliths, Jenny Marcela Armenta Blanco

Theses and Dissertations

The analysis of proteins in biological fluids by capillary electrophoresis (CE) is of interest in clinical chemistry. However, due to low analyte concentrations and poor concentration limits of detection (CLOD), protein analysis by this technique is frequently challenging. Coupling preconcentration techniques with CE greatly improves the CLOD. An on-line preconcentration-CE method that can selectively preconcentrate any protein for which an antibody is available would be very useful for the analysis of low abundance proteins and would establish CE as a major tool in biomarker discovery. To accomplish this, an on-line protein G monolithic preconcentrator CE system for enrichment and separation …

Biochemical Investigations Of Macular Degeneration: The Significance Of Protein Oxidation Including Novel Methods For Its Study, Sarah Warburton

Theses and Dissertations

The retinal pigment epithelium (RPE) is a monolayer of cells located directly behind the photoreceptor cells in the retina. These cells are involved in a variety of functions that support the visual process in the eye, namely 1) they form a blood-retina barrier which separates the neural retina from the choroid's blood supply, 2) the apical processes of RPE cells diurnally phagocytose the outer segments of photoreceptor cells, and 3) they participate in the renewal of the photopigment 11-cis retinal. Age-related macular degneration (AMD) is the leading cause of blindness in people over the age of 50 years in North …

Characterization Of Cucurbituril Complex Ions In The Gas Phase Using Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Haizhen Zhang

Theses and Dissertations

Host-guest interactions have been well studied in the new century to obtain fundamental insights into supramolecular chemistry. Most of the pioneering works have been done using techniques such as NMR, X-ray crystallography, IR spectroscopy and so on. However, none of these techniques is universal for the investigation of all types of supramolecules, and usually they have one or more limiting factors such as relatively large sample consumption, matrix effects from solvents, etc. Electrospray mass spectrometry has been widely used to investigate host-guest interactions in the gas phase. A particular advantage of gas phase host-guest research is that the experimental results …

Periodic Boundary Condition Induced Breakdown Of The Equipartition Principle And Other Kinetic Effects Of Finite Sample Size In Classical Hard-Sphere Molecular Dynamics Simulation, Randall B. Shirts, Scott R. Burt, Aaron M. Johnson

Faculty Publications

We examine consequences of the non-Boltzmann nature of probability distributions for one-particle kinetic energy, momentum, and velocity for finite systems of classical hard spheres with constant total energy and nonidentical masses. By comparing two cases, reflecting walls (NVE or microcanonical ensemble) and periodic boundaries (NVEPG or molecular dynamics ensemble), we describe three consequences of the center-of-mass constraint in periodic boundary conditions: the equipartition theorem no longer holds for unequal masses, the ratio of the average relative velocity to the average velocity is increased by a factor of [N/(N–1)]^1/2, and the ratio of average collision energy to average kinetic energy is …

Microfabrication And Evaluation Of Planar Thin-Film Microfluidic Devices, Bridget Ann Peeni

Theses and Dissertations

Over the past 15 years, research in the field of microfluidics has rapidly gained popularity. By seeking to miniaturize and automate separation-based analysis, microfluidic research seeks to improve current methods through decreased cost, analysis time, and sources of contamination. My work has focused on developing a novel fabrication method, based on standard microfabrication techniques, to create thin-film microfluidic devices. This microfabrication format makes it possible to generate devices that provide high efficiencies, enable mass fabrication, and provide a platform capable of integrating the microfluidic and electronic components necessary for a micro-total analysis system (μ-TAS). Device fabrication combines the processes of …

Detection Of Proteins By Two-Photon Excitation Of Native Fluorescence, Li Li

Theses and Dissertations

Proteins are of primary importance to the structure and function of all living cells. Study of proteins relies on the ability to separate a complex mixture so that individual proteins can be more easily processed by other techniques. Since protein samples often exist at low concentration in a small volume, the trend in chemical analysis is toward micro total analysis systems (µTAS) or lab-on-a-chip devices. Among µTAS separation methods, the relatively new electric field gradient focusing (EFGF) technique has shown potential. It focuses and separates analytes based on their electrophoretic migration in an opposing hydrodynamic flow. The detection principles that …

Ferritin: Mechanistic Studies And Electron Transfer Properties, Bo Zhang

Theses and Dissertations

Ferritins are ubiquitous iron storage proteins in living systems. Although much is known about the iron deposition process in ferritin and a mechanism has been developed, several important issues still remain unknown. One lingering question is the less than stoichiometric quantities of hydrogen peroxide detected in previous studies on animal ferritins. Extensive experimental data on identifying the species in competition for peroxide equivalents point to a surprising conclusion that H2O2 generated in the ferroxidase reaction is consumed by amine buffers that are commonly employed in in vitro ferritin studies, while non-nitrogen containing buffers, such as acetate, phosphate, and carbonate, do …

Photoreductive Dissolution Of Ferrihydrite By Methanesulfinic Acid: Evidence Of A Direct Link Between Dimethylsulfide And Iron-Bioavailability, Anne M. Johansen, Jennifer M. Key

All Faculty Scholarship for the College of the Sciences

Within open‐ocean regions where excess macronutrients are present, phytoplankton growth is limited by the bioavailability of iron supplied to these areas primarily within atmospheric aerosols of crustal origin. However, processes that control the abundance of biologically accessible iron in these aerosols are largely unknown. Here we show that dissolution of ferrihydrite, a surrogate iron(oxy)hydroxide phase found in atmospheric waters, is enhanced in the presence of methanesulfinic acid (MSIA, CH₃SO₂H, a dimethylsulfide (DMS) oxidation intermediate) in laboratory irradiation experiments with aqueous suspensions that simulate marine aerosol particles. The increased release of soluble Fe(II) is attributed to a …

Structure-Activity Studies Of Glycosphingolipids As Antigens Of Natural Killer T Cells, Randal Donald Goff

Theses and Dissertations

Glycosphingolipids (GSLs), composed of a polar saccharide head and a lipophilic ceramide tail, are ubiquitous components of the plasma membrane of eukaryotic cells. They serve in many regulatory capacities and have antigenic properties towards natural killer T (NKT) cells of the innate immune system. Critical to the recognition of glycosylceramides by NKT cells are antigen presenting cells (APC), such as dendritic cells, which are responsible for binding, processing, and delivery of ligands to these lymphocytes. This event is mediated by CD1d, a major histocompatibility complex-like protein expressed on the surface of APCs, which binds GSL antigens by the ceramide moiety …

Accumulation Of Phycotoxins In The Mussel Mytilus Galloprovincialis From The Central Adriatic Sea, Maja Pavela-Vrančić, Ivana Ujević, Živana Ninčević Gladan, Ambrose Furey

Physical Sciences Publications

Surveys of DSP (Diarrheic Shellfish Poisoning) toxin profiles in the mussel Mytilus galloprovincialis from coastal waters of the central Adriatic Sea, over the years 1995 to 2001, demonstrate that incidents of shellfish toxicity in this area are dominated by the occurrence of okadaic acid (OA) and a PTX derivative, 7-epi-pectenotoxin-2-seco acid (7-epi-PTX-2SA). Toxin composition and the relative ratio of toxic components in shellfish is in correlation with the occurrence of DSP producing organisms from the Dinophysis species along with Prorocentrum micans and Lingulodinium polyedrum. The occurrence of D. sacculus shortly before the appearance of OA in shellfish implicates its possible …

The Effect Of Protein Dielectric Coefficient On The Ionic Selectivity Of A Calcium Channel, Douglas Henderson, Dezso Boda, Monika Valisko, Bob Eisenberg, Wolfgang Nonner, Dirk Gillespie

Faculty Publications

Calcium-selective ion channels are known to have carboxylate-rich selectivity filters, a common motif that is primarily responsible for their high Ca2+ affinity. Different Ca2+ affinities ranging from micromolar (the L-type Ca channel) to millimolar (the ryanodine receptor channel) are closely related to the different physiological functions of these channels. To understand the physical mechanism for this range of affinities given similar amino acids in their selectivity filters, we use grand canonical Monte Carlo simulations to assess the binding of monovalent and divalent ions in the selectivity filter of a model Ca channel. We use a reduced model where the electrolyte …

Dna-Templated Surface Alignment And Characterization Of Carbon Nanotubes., Huijun Xin

Theses and Dissertations

Carbon nanotubes are appealing materials for nanofabrication due to their unique properties and structures. However, for carbon nanotubes to be used in mass-fabricated devices, precise control of nanotube orientation and location on surfaces is critical. I have developed a technique to align single-walled carbon nanotubes (SWNTs) on surfaces from a droplet of nanotube suspension under gas flow. Fluid motion studies indicate that alignment is likely due to circulation of SWNTs in the droplet. My work provides a facile method for generating oriented nanotubes for nanodevice applications. I have also devised an approach for localizing SWNTs onto 1-pyrenemethylamine-decorated DNA on surfaces. …

Enhanced Electrospray Ionization For Mass Spectrometry And Ion Mobility Spectrometry, Li Zhou

Theses and Dissertations

Electrospray ionization (ESI) has become one of the most commonly used ionization techniques for mass spectrometry (MS) and ion mobility spectrometry (IMS), and efforts continue to improve its performance. ESI-MS is most recognized for its wide application to biomacromolecules where high sensitivity is of paramount importance. However, the major limitation in sensitivity with ESI-MS is due to its low ion transmission efficiency from the ESI source into the sampling orifice and through any stages utilized for transfer of ions from atmosphere to vacuum in the MS. A series of atmospheric pressure ion focusing interfaces were designed and implemented to enhance …

Electric Field Gradient Focusing-Uv Detection For Protein Analysis, Shu-Ling Lin

Theses and Dissertations

Electric field gradient focusing (EFGF) utilizes a hydrodynamic flow and an electric field gradient to focus and concentrate charged analytes and order them in a separation channel according to electrophoretic mobility. Elution can be achieved by decreasing the applied voltage or increasing the hydrodynamic flow. EFGF has the advantages of concentrating a large volume (100 micro-L) of target proteins without significant band broadening and simultaneously removing unwanted components from the sample. Two types of EFGF devices have been investigated to concentrate and separate proteins: a fiber-based EFGF device and a hydrogel-based EFGF device. Using fiber-based EFGF with UV detection, a …

Model Studies Towards The Total Synthesis Of Lyconadin A Via An Acyl Radical Cascade Reaction, Koudi Zhu

Theses and Dissertations

Lyconadin A is an alkaloid possessing a unique structure and antitumor activity. The total synthesis of Lyconadin A was proposed via an acyl radical cascade reaction. To investigate the possibility and stereoselectivity of the cascade cyclization, phenyl selenoester 16 was chosen as a model substrate to study the 7-exo-5-exo radical cyclization. A synthetic route to phenyl selenoester 16 was developed. The 7-exo-5-exo radical cyclization was found to occur with a high yield and excellent stereoselectivty. Attempts were also tried to synthesize another radical precursor 14 albeit with less success. A synthetic pathway to the synthesis of 14 as well as …

The Mechanism Of Assembly Of The G-Protein Beta Gamma Subunit Dimer By Ck2 Phosphorylated Phosducin-Like Protein And The Chaperonin Containing Tcp-1, Christine M. Baker

Theses and Dissertations

Phosducin-like protein (PhLP) binds G-protein beta gamma subunits and is thought to assist in assembly of the G-protein beta gamma dimer. Phosphorylation of PhLP at serine residues 18-20 by the casein kinase 2 (CK2) appears to play an essential role in this process. PhLP has also been shown to interact with the chaperonin containing TCP-1 (CCT) atop its apical domain, not entering the substrate folding cavity. However, the physiological role of the PhLP-CCT interaction in G-protein beta gamma dimer formation remains unclear. This study addresses the mechanism of G-protein beta gamma assembly by exploring the specific roles of CCT and …