Biomedical subjects

Richard N Zare

Publications and source records attributed to Richard N Zare.

At least 19 recordsLinked to original sources

PubMed2003

PAH sorption mechanism and partitioning behavior in lampblack-impacted soils from former oil-gas plant sites.

This study assessed polycyclic aromatic hydrocarbon (PAH) association and aqueous partitioning in lampblack-impacted field soils from five sites in California that formerly housed oil-gas process operations. Lampblack is the solid residue resulting from the decomposition of crude oil at high temperatures in the gas-making operation and is coated or impregnated with oil gasification byproducts, among which PAHs are the compounds of the greatest regulatory concern. A suite of complementary measurements investigated the character of lampblack particles and PAH location and the associated effects on PAH partitioning between lampblack and water. PAH analyses on both whole samples and density-separated components demonstrated that 81-100% of PAHs in the lampblack-impacted soils was associated with lampblack particles. FTIR, 13C NMR, and SEM analyses showed that oil-gas lampblack solids comprise primarily aromatic carbon with soot-like structures. A free-phase aromatic oil may be present in some of the lampblack soils containing high PAH concentrations. Comparable long-term aqueous partitioning measurements were obtained with an air-bridge technique and with a centrifugation/alum flocculation procedure. Large solid/water partition coefficient (Kd) values were observed in samples exhibiting lower PAH and oil levels, whereas smaller Kd values were measured in lampblack samples containing high PAH levels. The former result is in agreement with an oil-soot partitioning model, and the latter is in agreement with a coal tar-water partitioning model. Lampblack containing high PAH levels appears to exhaust the sorption capacity of the soot-carbon, creating a free aromatic oil phase that exhibits partitioning behavior similar to PAHs in coal tar. This study improves mechanistic understanding of PAH sorption on aged lampblack residuals at former oil-gas sites and provides a framework for mechanistic assessment of PAH leaching potential and risk from such site materials.

Carbon↗

PubMed2003

Determination of glutamine and serine in rat cerebrospinal fluid using capillary electrochromatography with a modified photopolymerized sol-gel monolithic column.

Capillary electrochromatographic separations of amino acid mixtures were studied using two modified porous photopolymerized sol-gel monolithic columns. One was modified with dimethyloctadecylchlorosilane (DMOS), and the other was modified with DMOS, followed by chlorotrimethylsilane to end-cap residual silanol groups. Prior to separation, amino acids were derivatized with 4-fluoro-7-nitro-2,1,3-benzoxadiazole using as a mobile phase 50 mM phosphate (pH 2.5), water, and acetonitrile in the ratio of 1:1:8. Five derivatized amino acids (Asn, Phe, Ala, Ile, and Leu) were separated within 7 min. Theoretical plate numbers varied between 58700 and 105000/m. This separation method with the end-capped monolithic column was applied to rat cerebrospinal fluid. The dominant amino acid found was Gln at a concentration of 420 microM along with small quantities of Ser (54 microM).

Animals↗

PubMed2003

Cavity ring-down spectroscopy as a detector for liquid chromatography.

We have demonstrated the use of cavity ring-down spectroscopy (CRDS) as a detector for high performance liquid chromatography (HPLC). For this use, we have designed and implemented a Brewster's angle flow cell such that cavity ring-down spectroscopy can be performed on microliter volumes of liquids. The system exhibits a linear dynamic range of 3 orders of magnitude (30 nM to 30 microM quinalizarin at 470 nm) for static measurements and 2 orders of magnitude (0.5 microM to 50 microM) for HPLC measurements. For the static measurements, the baseline noise is 2.8 x 10(-6) AU rms and 1.0 x 10(-5) AU peak-to-peak, and for the HPLC separations, it is 3.2 x 10(-6) AU rms and 1.3 x 10(-5) AU peak-to-peak. The baseline noise is determined after the data are smoothed by an 11-point boxcar average. The peak areas detected from HPLC separations are reproducible to within 2-3%. The HPLC mass detection limit for a molecule with epsilon = 9 x 10(3) M(-1) cm(-1) in a 300-microm path length cell (illuminated volume, 0.5 microL) is reported as 2.5 x 10(-8) g/mL. These results were obtained using a simple pulsed CRDS system and are comparable to, if not better than, a high-quality commercial UV-vis absorption detector for the same path length.

Journal Article↗

PubMed2003

Surface plasmon resonance detection for capillary electrophoresis separations.

A miniaturized surface plasmon resonance sensor has been used as an on-line detector for capillary electrophoresis separations. The capillary was modified slightly to shield the sensor electronics from the high voltages applied during the separation. A three-component mixture of high refractive index materials was separated and detected at the millimolar level by an untreated gold-sensing surface. A simple protein immobilization procedure was used to functionalize the surface for selective protein detection. A hybrid buffer system was developed, in which both the deposition of immobilized protein layers and the electrophoretic delivery of protein analytes were optimized. The detection system has a reproducibility of 15%, a dynamic range of 3 orders of magnitude, and a detection limit for IgG of 2 fmol.

Journal Article↗

PubMed2003

Flow injection analysis in a microfluidic format.

A microfluidic flow injection analysis system has been designed and evaluated. The system incorporates within a single two-layer poly(dimethylsiloxane) monolith multiple pneumatically driven peristaltic pumps, an injection loop, a mixing column, and a transparent window for fluorescence detection. Central to this device is an injection system that mimics the operation of a standard six-port, two-way valve used in conventional liquid chromatography and flow injection experiments. Analyte and carrier solutions continuously flow through this injection system allowing for measurements and sample changes to be performed rapidly and simultaneously. Injection volumes of 1.25 nL generated peak area reproducibility of better than 3% relative standard deviation. The flow injection device was evaluated with fluorescent dyes and demonstrated a detection limit of 400 zmol for fluorescein. A rudimentary sample selection system allowed calibration curves to be rapidly produced, often in less than 10 min. The hydrolysis of fluorescein diphosphate by alkaline phosphatase demonstrates that chemical assays can be carried out with this device in a manner characterized by short analysis times and low sample consumption.

Alkaline Phosphatase↗

PubMed2003

Ultratrace kinetic measurements of the reduction of methylene blue.

The kinetics of methylene blue reduction by ascorbic acid in acetonitrile was investigated by cavity ring-down spectroscopy. Because of our high sensitivity we were able to use very low concentrations (1-10 nM) of the dye. Under these conditions, we observed a second-order loss of dye as well as a competing back reaction with dissolved oxygen. The use of an inexpensive diode laser and a relatively simple setup should make ultratrace kinetic studies more accessible.

Acetonitriles↗

PubMed2003

Effects of modulation defects on Hadamard transform time-of-flight mass spectrometry (HT-TOFMS).

In any Hadamard multiplexing technique, discrepancies between the intended and the applied encoding sequences may reduce the intensity of real spectral features and create discrete, artificial signals. In our implementation of Hadamard transform time-of-flight mass spectrometry (HT-TOFMS), the encoding sequence is applied to the ion beam by means of an interleaved comb of wires (Bradbury-Nielson gate), which shutters the ion beam on and off. By isolating and exaggerating individual skewing effects in simulating the HT-TOFMS process, we determined the nature of errors that arise from various defects. In particular, we find that the most damaging defects are: mismatched voltages between the wire sets and the acceleration voltage of the instrument, which cause positive and negative peaks throughout mass spectra; insufficient deflection voltage, which reduces the intensity of real peaks and causes negative peaks that are spread across the entire mass range; and voltage errors as the wire sets return from their deflection voltage to their transmission value, which yield significant reductions in peak intensities, create artificial peaks throughout mass spectra, and broaden real peaks by causing positive peaks to grow in the bins adjacent to them. Because the magnitude of the modulation defects grows as the applied modulation voltage is increased, Bradbury-Nielson gates with finer wire spacing, and hence stronger effective fields for a given applied voltage, were produced and installed. Operating at 10 to 15 V where errors in the electronics are essentially absent, the most finely spaced gate (100 microm) yielded signal-to-noise ratios that were more than two times higher than those achieved with more widely spaced gates. As an alternative method for minimizing skewing effects, HT-TOFMS data were post processed using an exact knowledge of the modulation defects. Nonbinary matrices that mimic the actual encoding process were built by measuring voltage versus time traces and then translating these traces to transmission versus time. Use of these matrices in the deconvolution step led to marked improvements in spectral resolution but require full knowledge of the encoding defects.

Journal Article↗

PubMed2003

Formation of carbon-carbon bonds in the photochemical alkylation of polycyclic aromatic hydrocarbons.

The reaction of polycyclic aromatic hydrocarbons (PAHs) with alkanes was examined in the presence of ultraviolet (UV) light under model prebiotic Earth and interstellar medium (ISM) conditions. We observed the formation of alkylated PAHs from a variety of PAHs and alkanes, which was caused by the absorption of UV light by the PAH molecule. Photoalkylation occurred in PAHs and alkanes in solution, in thin films in contact with simulated ocean water, and in matrices simulating ISM conditions. Photoalkylation occurred readily, with significant product yields within 5 h of irradiation. Because alkanes and PAHs are presumed to be part of the organic inventory in the ISM and on the early Earth, we propose that this photoalkylation reaction is a plausible pathway for the formation of carbon-carbon bonds in both these environments.

Alkanes↗

PubMed2002

Functional immobilization of a ligand-activated G-protein-coupled receptor.

G-protein-coupled receptors (GPCRs) mediate the majority of cellular responses to hormones and neurotransmitters. They are the largest family of receptors in the human genome and constitute the largest class of targets for drug discovery. To facilitate studies of GPCR activation and interactions with other proteins, we developed a simple method to immobilize a functional, detergent-solubilized GPCR on gold and glass surfaces. The beta(2) adrenergic receptor (beta(2)AR), a prototypical GPCR, was purified and labeled with a reporter fluorophore at a conformationally sensitive site. The detergent-soluble fluorescent beta(2)AR was immobilized through its amino-terminal FLAG epitope on a surface layered with biotinylated bovine serum albumin, avidin, and biotinylated M1 antibody. Agonist activation of the beta(2)AR was monitored in real time by fluorescence microscopy. This approach will make it possible to study conformational dynamics of single immobilized receptors and to generate arrays of functional GPCRs for novel high-throughput screening strategies.

Animals↗

PubMed2002

Coupled electrorotation of polymer microspheres for microfluidic sensing and mixing.

We show that coupled electrorotation (CER) of microscopic particles using microfabricated electrodes can be used for localized sensing and mixing. The effective use of microelectromechanical systems and micro total analysis systems requires many types of control. These include the abilityto (1) manipulate objects within microchannels by noncontact means, (2) mix fluids, and (3) sense local chemical parameters. Coupled electrorotation, in which the interactions between induced electric dipoles of adjacent particles lead to particle rotation, addresses aspects of all three challenges simultaneously. CER is a simple means of controlling the rotation of dielectric objects using homogeneous external radio frequency electric fields. CER is sensitive to several chemical and physical parameters such as the solution conductivity, pH, and viscosity. As a step toward integrating CER devices into microfluidic systems, a simple chip was designed to induce local mixing and to detect local changes in salt concentration, pH, and viscosity.

Journal Article↗

PubMed2002

Analysis of biomolecular interactions using a miniaturized surface plasmon resonance sensor.

A commercially available miniaturized surface plasmon resonance sensor has been investigated for its applicability to biological interaction analysis. The sensor was found to exhibit excellent repeatability and linearity for high-refractive index solutions and good reproducibility for the binding of proteins. Its detection limit for the monoclonal antibody M1 was found to be 2.1 fmol, which corresponds to a surface concentration of 21 pg/mm2. Simple surface immobilization procedures relying on biotin/avidin or glycoprotein/lectin chemistry have been explored. Equilibrium dissociation constants for the binding of the FLAG peptide to its monoclonal antibody (M1) and for the binding of concanavalin A to a glycoprotein have been determined. The close agreement of these measurements with values obtained by surface fluorescence microscopy and fluorescence correlation spectroscopy helps to validate the use of this device. Thus, this sensor shows promise as an inexpensive, portable, and accurate tool for bioanalytical applications in laboratory and clinical settings.

Animals↗

PubMed2002

Effect of preparatory conditions on the performance of photopolymerized sol-gel monoliths for capillary electrochromatography.

We prepared different photopolymerized sol-gel (PSG) columns by varying the amount of monomer (methacryloxypropyltrimethoxysilane), porogen (toluene) and catalyst (hydrochloric acid) in the reaction solution containing a photoinitiator (Irgacure 1800). The effects of these variations on the chromatographic behavior of the PSG columns were studied. All of the columns studied exhibited reversed-phase character. The concentration of hydrochloric acid was important for the rigidity of the columns, although it did not affect the separation property. The ratio of monomer solution to porogen was a critical factor in controlling the through-pore size and the surface area of PSG, which were found to significantly affect the separation properties, such as permeability, theoretical plate number, retention time, and separation efficiency, of a mixture of test analytes-thiourea, benzene, and naphthalene. There was no change in the retention order for the test analytes. Short separation times were achieved on PSG columns made from a 10% monomer stock solution and 90% porogen with 1 M hydrochloric acid. Mixtures of polycyclic aromatic hydrocarbons and alkylbenzenes were separated with theoretical plate numbers greater than 100 000 plates/m.

Chromatography, Micellar Electrokinetic Capillary↗

PubMed2002

Coupled electrorotation: two proximate microspheres spin in registry with an AC electric field.

We report a novel approach to micro- and nanoparticle rotation, uniting the fine translational control afforded by optical trapping with the flexibility and simplicity of dipole-field-induced coupled electrorotation (CER). Fluorescence imaging using a microparticle photopatterning technique was combined with optical trapping to quantify both the senses and speeds of rotation for individual pairs of particles. Laser tweezers allowed controlled positioning of a pair of particles within a dipole field while simultaneously providing an axis about which the particles rotated. The particle-particle interactions inherent in CER offer several distinct advantages compared with electrorotation in multipole fields. Results from several investigations highlight the utility of this approach, including quantification of rotation in spheres as small as 750 nm in diameter, observation of rotation rates as high as 1800 rpm, fabrication of coupled electrorotational "antigears", trapping and rotation of sphere dimers, and exploitation of the registry of sphere rotation to probe the dielectric properties of immobile objects.

Electrochemistry↗

PubMed2002

Stable isotope ratios using cavity ring-down spectroscopy: determination of 13C/12C for carbon dioxide in human breath.

We have constructed a cavity ring-down spectrometer employing a near-IR external cavity diode laser capable of measuring 13C/12C isotopic ratios in CO2 in human breath. The system, which has a demonstrated minimum detectable absorption loss of 3.2 x 10(-11) cm(-1) Hz(-1/2), determines the isotopic ratio of 13C16O16O/12C16O16O by measuring the intensities of rotationally resolved absorption features of each species. As in isotope ratio mass spectrometry (IRMS), the isotopic ratio of a sample is compared to that of a standard CO2 sample calibrated to the Pee Dee Belemnite scale and reported as the sample's delta13C value. Measurements of eight replicate CO2 samples standardized by IRMS and consisting of 5% CO2 in N2 at atmospheric pressure demonstrated a precision of 0.22/1000 for the technique. Delta13C values were also obtained for breath samples from individuals testing positive and negative for the presence of Helicobacter pylori, the leading cause of peptic ulcers in humans. This study demonstrates the ability of the instrument to obtain delta13C values in breath samples with sufficient precision to serve as a useful medical diagnostic.

Breath Tests↗

PubMed2002

Direct monitoring of absorption in solution by cavity ring-down spectroscopy.

Cavity ring-down spectroscopy is applied to the liquid phase by placing the target solution directly into the optical cavity. We demonstrate that solutions in the cavity can be stirred and more importantly monitored in a flow. We report a minimum detectable absorption of 10(-6) cm(-1) for a range of organic solvents. This detection limit corresponds to picomolar concentrations for strong absorbers.

Journal Article↗

PubMed2002

Hadamard transform time-of-flight mass spectrometry: a high-speed detector for capillary-format separations.

This work demonstrates that with an intrinsic duty cycle of 50% and spectral storage speeds up to 277 spectra s(-1) Hadamard transform time-of-flight mass spectrometry (HT-TOFMS) is a promising detector for any capillary-format separation that can be coupled to MS by electrospray ionization. Complete resolution of the components of a nine-peptide standard was achieved by coupling pressurized-capillary electrophoresis (pCE) to HT-TOFMS. The addition of pressure to the separation capillary decreased analysis times and stabilized the electrospray ionization source. Pulsed-pressurized injection of reserpine was used to experimentally simulate narrower peaks than those obtained in the pCE. HT-TOFMS was able to sample peaks having widths in the millisecond range.

Electrophoresis, Capillary↗

PubMed2002

Observation and interpretation of a time-delayed mechanism in the hydrogen exchange reaction.

Extensive theoretical and experimental studies have shown the hydrogen exchange reaction H+H2 --> H2+H to occur predominantly through a 'direct recoil' mechanism: the H--H bonds break and form concertedly while the system passes straight over a collinear transition state, with recoil from the collision causing the H2 product molecules to scatter backward. Theoretical predictions agree well with experimental observations of this scattering process. Indirect exchange mechanisms involving H3 intermediates have been suggested to occur as well, but these are difficult to test because bimolecular reactions cannot be studied by the femtosecond spectroscopies used to monitor unimolecular reactions. Moreover, full quantum simulations of the time evolution of bimolecular reactions have not been performed. For the isotopic variant of the hydrogen exchange reaction, H+D2 --> HD+D, forward scattering features observed in the product angular distribution have been attributed to possible scattering resonances associated with a quasibound collision complex. Here we extend these measurements to a wide range of collision energies and interpret the results using a full time-dependent quantum simulation of the reaction, thus showing that two different reaction mechanisms modulate the measured product angular distribution features. One of the mechanisms is direct and leads to backward scattering, the other is indirect and leads to forward scattering after a delay of about 25 femtoseconds.

Journal Article↗

PubMed2002

Genetic screening using the colour change of a PNA-DNA hybrid-binding cyanine dye.

As the relationship between human genes and various malfunctions and diseases becomes revealed at an ever-increasing pace, the need arises for the development of rapid genetic screening methods for diagnostic purposes. Genetic diseases show great diversity. Some are caused by a few characteristic localised mutations, while others arise from a large number of variations. Hence, it is unlikely that a single, general diagnostic method that applies to all cases will ever exist. Instead, a combination of methods is frequently applied. Here we propose the use of a dramatic colour change that a cyanine dye, 3,3'-diethylthiadicarbocyanine, displays upon binding to DNA-PNA duplexes. This method could become an inexpensive, fast and simple genetic screening test by visual inspection, with no need for complicated equipment. Our results demonstrate that this diagnostic method may be sufficiently sensitive to discriminate between even a fully complementary and a single mutation DNA sequence.

Base Sequence↗