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Biomedical subjects

Alan Willse

Publications and source records attributed to Alan Willse.

8 recordsLinked to original sources
PubMed2006

Individual odortypes: interaction of MHC and background genes.

Genes of the major histocompatibility complex (MHC) influence the urinary odors of mice. Behavioral studies have shown (1) that mice differing only at MHC have distinct urinary odors, suggesting an MHC odor phenotype or odortype; (2) that the MHC odortype can be recognized across different background strains; and (3) that the MHC odortype is not an additive trait. Very little is known about the odorants underlying this behavioral phenotype. We compared urinary volatile profiles of two MHC haplotypes (H2(b) and H2(k)) and their heterozygous cross (H2(b) x H2(k)) for two different background strains (C57BL/6J and BALB/c) using solid phase micro-extraction (SPME) headspace analysis and gas chromatography/mass spectrometry (GC/MS). Both MHC and background genes substantially influence the volatile profile. Of 148 compounds screened, 108 of them significantly differ between the six genotypes. Surprisingly, for numerous compounds, their MHC associations are moderated by background genes (i.e., there is a significant MHC x background interaction effect in the statistical model relating genotype to relative compound concentration). These interactions account for nearly 30% of the total genetic effect on the volatile profile. MHC heterozygosity further extends the odortype diversity. For many compounds, the volatile expression for the heterozygote is more extreme than the expression for either homozygote, suggesting a heterozygous-specific odortype. The remarkable breadth of effects of MHC variation on concentrations of metabolites and the interaction between MHC and other genetic variation implies the existence of as yet unknown processes by which variation in MHC genes gives rise to variation in volatile molecules in body fluids.

Animals↗
PubMed2006

Small protein biomarkers of culture in Bacillus spores detected using capillary liquid chromatography coupled with matrix assisted laser desorption/ionization mass spectrometry.

Capillary liquid chromatography (cLC) coupled with matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) was used to compare small proteins and peptides extracted from Bacillus subtilis spores grown on four different media. A single, efficient protein separation, compatible with MALDI-MS analysis, was employed to reduce competitive ionization between proteins, and thus interrogate more proteins than possible using direct MALDI-MS. The MALDI-MS data files for each fraction are assembled as two-dimensional data sets of retention time and mass information. This method of visualizing small protein data required careful attention to background correction as well as mass and retention time variability. The resulting data sets were used to create comparative displays of differences in protein profiles between different spore preparations. Protein differences were found between two different solid media in both phase bright and phase dark spore phenotype. The protein differences between two different liquid media were also examined. As an extension of this method, we have demonstrated that candidate protein biomarkers can be trypsin digested to provide identifying peptide fragment information following the cLC-MALDI experiment. We have demonstrated this method on two markers and utilized acid breakdown information to identify one additional marker for this organism. The resulting method can be used to identify discriminating proteins as potential biomarkers of growth media, which might ultimately be used for source attribution.

Amino Acid Sequence↗
PubMed2006

Diagnostic oligonucleotide microarray fingerprinting of Bacillus isolates.

A genome-independent microarray and new statistical techniques were used to genotype Bacillus strains and quantitatively compare DNA fingerprints with the known taxonomy of the genus. A synthetic DNA standard was used to understand process level variability and lead to recommended standard operating procedures for microbial forensics and clinical diagnostics.

Bacillus↗
PubMed2005

Comparing bacterial DNA microarray fingerprints.

Epidemiologic and forensic investigations often require assays to detect subtle genetic differences between closely related microorganisms. Typically, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial samples, where the patterns of DNA fragment sizes are viewed as genotype 'fingerprints'. The limited genomic sample captured on a gel, however, is not always sufficient to discriminate closely related strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if enough independent oligonucleotide probes are used on the microarray, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate a statistical measurement error model to fingerprint 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

Journal Article↗
PubMed2005

Identification of major histocompatibility complex-regulated body odorants by statistical analysis of a comparative gas chromatography/mass spectrometry experiment.

This paper examines the application of gas chromatography/mass spectrometry (GC/MS) in a comparative experiment to identify volatile compounds from urine that differ in concentration between two groups of inbred mice. A complex mixture might comprise several hundred or even thousands of volatile compounds. Because their number and location in a chromatogram are generally unknown, and because components overlap in populous chromatograms, the statistical problems offer significant challenges beyond traditional two-group screening procedures. We describe a statistical procedure to compare two-dimensional GC/MS profiles between groups, which entails (1) signal processing, baseline correction, and peak detection in single ion chromatograms; (2) aligning chromatograms in time; (3) normalizing differences in overall signal intensities; and (4) detecting chromatographic regions that differ between groups. In an application to chemosignaling, we detect differences in GC/MS chromatograms of ether-extracted urine collected from two inbred groups of mice that differ only in genes of the major histocompatibility complex (MHC). Several dozen MHC-regulated compounds are found, including two known mouse pheromones, 2,5-dimethylpyrazine and 2-sec-butyl-4,5-dihydrothiazole.

Animals↗
PubMed2004

Quantitative oligonucleotide microarray fingerprinting of Salmonella enterica isolates.

We report on a genome-independent microbial fingerprinting method using nucleic acid microarrays for microbial forensics and epidemiology applications and demonstrate that the microarray method provides high resolution differentiation between closely related microorganisms, using Salmonella enterica strains as the test case. In replicate trials we used a simple 192 probe nonamer array to construct a fingerprint library of 25 closely related Salmonella isolates. Controlling false discovery rate for multiple testing at alpha = 0.05, at least 295 of 300 pairs of S.enterica isolate fingerprints were found to be statistically distinct using a modified Hotelling T2 test. Although most pairs of Salmonella fingerprints are found to be distinct, forensic applications will also require a protocol for library construction and reliable microbial classification against a fingerprint library. We outline additional steps required to produce such a protocol.

Bayes Theorem↗
PubMed2002

Poisson and multinomial mixture models for multivariate SIMS image segmentation.

Multivariate statistical methods have been advocated for analysis of spectral images, such as those obtained with imaging time-of-flight secondary ion mass spectrometry (TOF-SIMS). TOF-SIMS images using total secondary ion counts or secondary ion counts at individual masses often fail to reveal all salient chemical patterns on the surface. Multivariate methods simultaneously analyze peak intensities at all masses. We propose multivariate methods based on Poisson and multinomial mixture models to segment SIMS images into chemically homogeneous regions. The Poisson mixture model is derived from the assumption that secondary ion counts at any mass in a chemically homogeneous region vary according to the Poisson distribution. The multinomial model is derived as a standardized Poisson mixture model, which is analogous to standardizing the data by dividing by total secondary ion counts. The methods are adapted for contextual image segmentation, allowing for spatial correlation of neighboring pixels. The methods are applied to 52 mass units of a SIMS image with known chemical components. The spectral profile and relative prevalence for each chemical phase are obtained from estimates of model parameters.

Models, Statistical↗