Biomedical subjects

James D Winefordner

Publications and source records attributed to James D Winefordner.

7 recordsLinked to original sources

PubMed2006

Absorption spectrometry by narrowband light in optically saturated and optically pumped collision and Doppler broadened gaseous media under arbitrary optical thickness conditions.

This work examines absorption spectrometry by narrowband light in gaseous media with arbitrary optical thickness when the light induces optical saturation or optical pumping. Two quantities are defined: the observed absorbance, A(obs), and the true absorbance, A(true). The former is the absorbance that is measured under the existing conditions, whereas the latter represents the absorbance one would measure if the light acted solely as a probe of the populations of the various levels, and it is therefore directly proportional to the concentration or density of absorbers. A general integral equation for the propagation of light in media of arbitrary optical thickness in which the light influences the populations of the levels involved is derived. This expression is transcendental in the observed absorbance and cannot be solved analytically. It is shown that an analytical expression can be derived by investigating the inverse relationship, i.e., A(true) = f(A(obs)). Inasmuch as collision and Doppler broadened media react differently to optical saturation, they are considered separately. It is shown that a nonlinear response results if the medium is optically saturated (or pumped) and not optically thin. Expressions for the error introduced if the technique of standard additions is uncritically applied to such a system are derived.

Journal Article↗

PubMed2005

Desorption/ionization on porous silicon mass spectrometry studies on pentose-borate complexes.

Desorption/ionization on porous silicon mass spectrometry (DIOS-MS) was used to investigate the binding affinities between aldopentose isomers and boron. Boron has been recognized for its importance in pentose synthesis and stabilization in prebiotic conditions. Boron may also account for the fact that ribose, among other aldopentoses, is the favored building block in RNA synthesis. This research started with the detection of aldopentoses in the positive mode through cationization and the aldopentose-borate complexes in the negative mode. Then two competition schemes, one using a pentose structure analogue and the other using 13C-labeled ribose, were designed to compare the relative binding affinities of four aldopentoses (xylose, lyxose, arabinose, and ribose) to boron. Both approaches determined the binding preference to be ribose > lyxose > arabinose > xylose. This work illustrates the potential of DIOS-MS in the analyses of nonvolatile, small molecules in delicate chemical equilibria. Without externally introduced matrices, background signals are not a limiting factor. Furthermore, the possible dramatic change of pH associated with the matrix introduction, which may disturb the equilibria of interest, is avoided.

Boron↗

PubMed2004

MALDI-TOFMS compared with other polyphasic taxonomy approaches for the identification and classification of Bacillus pumilus spores.

To verify the efficacy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) protein profiling for identifying and differentiating bacterial species, several strains of Bacillus pumilus were examined in a thorough taxonomic study incorporating a polyphasic approach. Sixteen isolates of putative B. pumilus isolated from spacecraft assembly facilities, the Mars Odyssey spacecraft, and the International Space Station, were characterized for their biochemical and molecular profiles using the Biolog system, DNA techniques, and MALDI-TOFMS protein profiling. MALDI-TOFMS protein profiling was more accurate than Biolog metabolic profiling, more discriminating than 16S rDNA sequence analysis, and complemented the results of gyrB sequence analysis and DNA-DNA hybridization for the identification of the B. pumilus spores. This is the first report whereby MALDI-TOFMS generated protein profiles from a set of microbes is compared directly with DNA-DNA hybridization yielding a positive correlation. Unique, cluster-specific biomarker peaks have been identified in the spores of the B. pumilus examined in this study. MALDI-TOFMS protein profiling is a rapid and simple analysis and has been demonstrated as a useful taxonomic tool for differentiating spores of the genus Bacillus. For practical purposes, it would be ideal (and necessary) to have a publicly available, standardized MALDI profile database, to facilitate the use of the technique as a diagnostic method to differentiate bacterial species.

Bacillus↗

PubMed2004

Species differentiation of a diverse suite of Bacillus spores by mass spectrometry-based protein profiling.

In this study, we demonstrate the versatility of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOFMS) protein profiling for the species differentiation of a diverse suite of Bacillus spores. MALDI-TOFMS protein profiles of 11 different strains of Bacillus spores, encompassing nine different species, were evaluated. Bacillus species selected for MALDI-TOFMS analysis represented the spore-forming bacterial diversity of typical class 100K clean room spacecraft assembly facilities. A one-step sample treatment and MALDI-TOFMS preparation were used to minimize the sample preparation time. A library of MALDI-TOFMS spectra was created from these nine Bacillus species, the most diverse protein profiling study of the genus reported to date. Linear correlation analysis was used to successfully differentiate the MALDI-TOFMS protein profiles from all strains evaluated in this study. The MALDI-TOFMS protein profiles were compared with 16S rDNA sequences for their bacterial systematics and molecular phylogenetic affiliations. The MALDI-TOFMS profiles were found to be complementary to the 16S rDNA analysis. Proteomic studies of Bacillus subtilis 168 were pursued to identify proteins represented by the biomarker peaks in the MALDI-TOFMS spectrum. Four small, acid-soluble proteins (A, B, C, and D), one DNA binding protein, hypothetical protein ymf J, and four proteins associated with the spore coat and spore coat formation (coat JB, coat F, coat T, and spoIVA) were identified. The ability to visualize higher-molecular-mass coat proteins (10 to 25 kDa) as well as smaller proteins (<10 kDa) with MALDI-TOFMS profiling is critical for the complete and effective species differentiation of the Bacillus genus.

Bacillus↗

PubMed2003

Comparison of nonintensified and intensified CCD detectors for laser-induced breakdown spectroscopy.

The performance and sensitivity of an intensified CCD array system and a nonintensified CCD array detector system are compared for laser-induced breakdown spectroscopy (LIBS). LIBS measurements were recorded in a calcium-based aerosol-seeded gas stream at ambient pressure. The signal-to-noise ratio based on the 393.37-nm calcium emission line was calculated as a function of detector delay with respect to the plasma-initiating laser pulse. Both ensemble-averaging and single-shot spectral analyses were performed. For all conditions, the intensified CCD system provided an enhanced signal-to-noise ratio compared with the nonintensified CCD system.

Journal Article↗

PubMed2003

Measurement and modeling of ozone and nitrogen oxides produced by laser breakdown in oxygen-nitrogen atmospheres.

The production of ozone nad nitrogen oxides was studied during multiple laser breakdown in oxygen-nitrogen mixtures at atmospheric pressure. About 2000 laser shots at 10(10) W cm-2 were delivered into a sealed reaction chamber. The chamber with a long capillary was designed to measure absorption of O3, NO, and NO2 as a function of the number of laser shots. The light source for absorption measurements was the continuum radiation emitted by the plasma during the first 0.2 microsecond of its evolution. A kinetic model was developed that encompassed the principal chemical reactions between the major atmospheric components and the products of laser breakdown. In the model, the laser plasma was treated as a source of nitric oxide and atomic oxygen, whose rates of production were calculated using measured absorption by NO, NO2, and O3. The calculated concentration profiles for NO, NO2, and O3 were in good agreement with measured profiles over a time scale of 0-200 s. The steady-state concentration of ozone was measured in a flow cell in air. For a single breakdown in air, the estimated steady-state yield of ozone was 2 x 10(12) molecules, which agreed with the model prediction. This study can be of importance for general understanding of laser plasma chemistry and for elucidating the nature of spectral interferences and matrix effects that may take place in applied spectrochemical analysis.

Flow Injection Analysis↗

PubMed2002

Monitoring atmospheric particulate matter through cavity ring-down spectroscopy.

Cavity ring-down spectroscopy was explored as a means to measure atmospheric optical extinction. Ambient air was sampled through a window on the campus of the University of Florida and transported to a ring-down cell fashioned from standard stainless steel vacuum components. When a copper vapor laser operating at 10 kHz is employed, this arrangement allowed for nearly continuous monitoring of atmospheric extinction at 510 and 578 nm. We have characterized the system performance in terms of detection limit and dynamic range and also monitored a change in atmospheric extinction during a nearby wildfire and fireworks exhibition. The sensitivity and compatibility with automation of the technique renders it useful as a laboratory-based measurement of airborne particulate matter.

Air Pollution↗