Biomedical subjects

Yan Wan

Publications and source records attributed to Yan Wan.

4 recordsLinked to original sources

PubMed2007

Validation of mixed-genome microarrays as a method for genetic discrimination.

Comparative genomic hybridizations have been used to examine genetic relationships among bacteria. The microarrays used in these experiments may have open reading frames from one or more reference strains (whole-genome microarrays), or they may be composed of random DNA fragments from a large number of strains (mixed-genome microarrays [MGMs]). In this work both experimental and virtual arrays are analyzed to assess the validity of genetic inferences from these experiments with a focus on MGMs. Empirical data are analyzed from an Enterococcus MGM, while a virtual MGM is constructed in silico using sequenced genomes (Streptococcus). On average, a small MGM is capable of correctly deriving phylogenetic relationships between seven species of Enterococcus with accuracies of 100% (n=100 probes) and 95% (n=46 probes); more probes are required for intraspecific differentiation. Compared to multilocus sequence methods and whole-genome microarrays, MGMs provide additional discrimination between closely related strains and offer the possibility of identifying unique strain or lineage markers. Representational bias can have mixed effects. Microarrays composed of probes from a single genome can be used to derive phylogenetic relationships, although branch length can be exaggerated for the reference strain. We describe a case where disproportional representation of different strains used to construct an MGM can result in inaccurate phylogenetic inferences, and we illustrate an algorithm that is capable of correcting this type of bias. The bias correction algorithm automatically provides bootstrap confidence values and can provide multiple bias-corrected trees with high confidence values.

Algorithms↗

PubMed2005

Detection of hepatitis B virus DNA by real-time PCR using TaqMan-MGB probe technology.

AIM: To develop a real-time PCR for detecting hepatitis B virus (HBV) DNA based on TaqMan technology using a new MGB probe. METHODS: Plasmid containing the sequence of X gene (1414-1744 nt) was constructed as HBV-DNA standard for quantitative analysis. A TaqMan-MGB probe between primers for amplification was designed to detect PCR products. The interested sequence contained in the plasmid and in clinical specimens was quantitatively measured. RESULTS: The detection limit of the assay for HBV DNA was 1 genome equivalent per reaction. A linear standard curve was obtained between 10(0) and 10(9) DNA copies/reaction (r>0.990). None of the negative control samples showed false-positive reactions in duplicate. HBV DNA was detected in 100% (50/50) of HBV patients with HbeAg, and in 72.0% (36/50) with HBsAg, HBeAb and HBcAb. The coefficient of variation for both intra- and inter-experimental variability demonstrated high reproducibility and accuracy. CONCLUSION: Real-time PCR based on TaqMan-MGB probe technology is an excellent method for detection of HBV DNA.

Base Sequence↗

PubMed2004

An effective method for extracting DNA from contaminated soil due to industrial waste.

Recently, labor accidents caused by toxic gas production such as H2S and CH4 have happened at some waste disposal sites and illegal dumping sites in Japan. The gas production has been known to be end products of bacterial respiration. In order to investigate a microbial flora in industrial waste contaminated soil by a DNA-based detection method, we developed a simple DNA extraction method. The method is based on lysis with sodium dodecyl sulfate (SDS) and a high concentration (4.0 mg/ml) of lysozyme at room temperature. DNA yields increased according to the concentration of lysozyme (0-2 mg/ml), although the cell lysis occurred at comparable efficiency independent of the lysozyme concentration. Interestingly, bovine serum albumin and insulin (4 mg/ml) also contributed high DNA yields. This suggests proteins play an important role at high concentration on a DNA extraction process, presumably by suppressing DNA degradation or adsorption. DNA yields from three contaminated soil samples at 0.3, 1.5 and 3 m in depth by using our method were significantly higher than those extracted by using a widely-used conventional method which did not contain lysozyme. A novel and simple DNA extraction method using high concentration of protein was established for a DNA-based detection method of microbial flora in soil.

Air Pollution↗

PubMed2003

Virtual microscopy as a tool for proficiency testing in cytopathology: a model using multiple digital images of Papanicolaou tests.

BACKGROUND: Modern digital cameras can acquire images from cytologic slides at sufficient resolution to allow for digital enlargement and scrolling on a video monitor, allowing for the simulation of microscopy using a computer. OBJECTIVE: The purpose of this study was to develop a tool for proficiency testing in cytopathology using multiple digital images of Papanicolaou tests. METHODS: Nine images were photographed from each of 10 Papanicolaou tests at x100 optical magnification, 3400 x 2300-pixel resolution, using a light microscope and a digital camera. All images from each case were tiled in a single canvas with Photoshop 4.0 software. Two cytopathologists and 3 cytotechnologists interpreted these "virtual slides" using a computer and graded diagnostic codes (PAP program, College of American Pathologists). Subjects were retested a year later using the glass slides from the same cases and routine microscopy. Both test results, by diagnostic code, were compared with the McNemar test of symmetry. RESULTS: The 5 test subjects provided 42 and 50 correct diagnostic codes by "virtual microscopy" and light microscopy, respectively. No significant asymmetry in results obtained by virtual microscopy and light microscopy was encountered with the McNemar test of symmetry. All test answers were correctly classified by selection series, using both virtual microscopy and light microscopy, and the responses would have been graded as 100% by current PAP program scoring guidelines. This suggests that virtual microscopy could be used for proficiency testing purposes. CONCLUSIONS: A simple virtual microscopy method designed to challenge participants to locate and diagnose cells of interest was effective for the administration of standardized proficiency tests. Virtual microscopy methods that rely on single-plane images to locate and diagnose cells of interest could provide effective proficiency testing tools prior to the development of more computationally intensive systems that represent an entire Papanicolaou test at multiple focal planes.

Computer Simulation↗