Biomedical subjects

Keying Ye

Publications and source records attributed to Keying Ye.

4 recordsLinked to original sources

PubMed2006

Valproic acid-induced fetal malformations are reduced by maternal immune stimulation with granulocyte-macrophage colony-stimulating factor or interferon-gamma.

Valproic acid, a drug commonly used to treat seizures and other psychiatric disorders, causes neural tube defects (NTDs) in exposed fetuses at a rate 20 times higher than in the general population. Failure of the neural tube to close during development results in exencephaly or anencephaly, as well as spina bifida. In mice, nonspecific activation of the maternal immune system can reduce fetal abnormalities caused by diverse etiologies, including diabetes-induced NTDs. We hypothesized that nonspecific activation of the maternal immune system with interferon-gamma (IFN-gamma) and granulocyte-macrophage colony-stimulating factor (GM-CSF) could reduce valproic acid (VA)-induced defects as well. Female CD-1 mice were given immune stimulant prebreeding: either IFN-gamma or GM-CSF. Approximately half of the control and immune-stimulated pregnant females were then exposed to 500 mg/kg VA on the morning of gestational day 8. The incidence of developmental defects was determined on gestational day 17 from at least eight litters in each of the following treatment groups: control, VA only, IFN-gamma only, IFN-gamma+VA, GM-CSF only, and GM-CSF+VA. The incidence of NTDs was 18% in fetuses exposed to VA alone, compared to 3.7% and 2.9% in fetuses exposed to IFN-gamma+VA, or GM-CSF+VA respectively. Ocular defects were also significantly reduced from 28.0% in VA exposed groups to 9.8% in IFN-gamma+VA and 12.5% in GM-CSF+VA groups. The mechanisms by which maternal immune stimulation prevents birth defects remain unclear, but may involve maternal or fetal production of cytokines or growth factors which protect the fetus from the dysregulatory effects of teratogens.

Abnormalities, Drug-Induced↗

PubMed2005

Finite mixture model analysis of microarray expression data on samples of uncertain biological type with application to reproductive efficiency.

Common goals of microarray experiments are the detection of genes that are differentially expressed between several biological types and the construction of classifiers that predict biological type of samples. Here we consider a situation where there is no training data. There is considerable interest in comparing expression profiles associated with successful pregnancies (SP) and unsuccessful pregnancies (UP) in model and farm animals. Successful pregnancy rate is known to be much higher in embryos generated by in vitro fertilization (IVF) than in nuclear transfer (NT) embryos, and higher under induced ovulation for large follicles (LF) than for small follicles (SF). The tasks of identifying genes differentially expressed between SP and UP, and predicting SP for future samples are not well accomplished by comparing IVF and NT, or LF and SF. A suitable method is finite mixture model analysis (FMMA), which models each observed class (IVF and NT, or LF and SF) as a mixture of two distributions, one for SP and one for UP, with different known or unknown proportions (here known to be 0.50 SP for IVF and 0.02 SP for NT). The means of the two distributions differ for the differentially expressed genes, which we identify via a likelihood ratio test. We confirm by simulation that FMMA strongly outperforms hierarchical clustering and linear discriminant analysis using the known class labels (NT, IVF). We apply FMMA to a real data set on IVF and NT embryos, and compute their posterior probabilities of SP, which confirm our prior knowledge of the SP proportions for IVF and NT.

Animals↗

PubMed2004

Comparison of TaqMan and Epoch Dark Quenchers during real-time reverse transcription PCR.

Several biotechnology companies have recently introduced novel quencher fluors for use with dual-labeled fluorogenic hydrolysis probes. The Epoch Dark Quencher trade mark fluorochrome consists of a non-fluorescent moiety capable of absorption at higher wavelengths (400-650 nm). The aim of this study was to: (1) evaluate the feasibility of using Epoch Dark Quencher fluorochromes in real-time PCR pathogen detection assays that were previously optimized with TaqMan (TAMRA) quenching fluors, and (2) compare the sensitivity based on cycle threshold (CT) between probes containing either TaqMan or Epoch Dark Quencher fluors. Our data indicate Epoch Dark Quencher probes can be used in place of TaqMan probes and their performance was not better than traditional TaqMan (TAMRA) quenchers. Marginal differences observed between quenching fluorochromes may arise from concentration differences during probe synthesis.

Fluorescent Dyes↗

PubMed2003

Artificial gene networks for objective comparison of analysis algorithms.

MOTIVATION: Large-scale gene expression profiling generates data sets that are rich in observed features but poor in numbers of observations. The analysis of such data sets is a challenge that has been object of vigorous research. The algorithms in use for this purpose have been poorly documented and rarely compared objectively, posing a problem of uncertainty about the outcomes of the analyses. One way to objectively test such analysis algorithms is to apply them on computational gene network models for which the mechanisms are completely know. RESULTS: We present a system that generates random artificial gene networks according to well-defined topological and kinetic properties. These are used to run in silico experiments simulating real laboratory microarray experiments. Noise with controlled properties is added to the simulation results several times emulating measurement replicates, before expression ratios are calculated. AVAILABILITY: The data sets and kinetic models described here are available from http://www.vbi.vt.edu/~mendes/AGN/as biochemical dynamic models in SBML and Gepasi formats.

Algorithms↗