Showing papers by "Yi Chen published in 1999"

Expression profiling using cdna microarrays

Abstract: cDNA microarrays are capable of profiling gene expression patterns of tens of thousands of genes in a single experiment. DNA targets, in the form of 3' expressed sequence tags (ESTs), are arrayed onto glass slides (or membranes) and probed with fluorescent- or radioactively-labelled cDNAs. Here, we review technical aspects of cDNA microarrays, including the general principles, fabrication of the arrays, target labelling, image analysis and data extraction, management and mining.

Ratio-based decisions and the quantitative analysis of cDNA micro-array images

Abstract: Gene expression can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA micro-array. Comparison of gene expression levels arising from co-hybridized samples is achieved by taking ratios of average expression levels for individual genes. In an image-processing phase, a method of image segmentation identifies cDNA target sites in a cDNA micro-array image. The resulting cDNA target sites are analyzed based on a hypothesis test and confidence interval to quantify the significance of observed differences in expression ratios. In particular, the probability density of the ratio and the maximum-likelihood estimator for the distribution are derived, and an iterative procedure for signal calibration is developed.

Hormone Therapy Failure in Human Prostate Cancer: Analysis by Complementary DNA and Tissue Microarrays

Abstract: Background: The molecular mechanisms underlying the progression of prostate cancer during hormonal therapy have remained poorly understood. In this study, we developed a new strategy for the identification of differentially expressed genes in hormone-refractory human prostate cancer by use of a combination of complementary DNA (cDNA) and tissue microarray technologies. Methods: Differences in gene expression between hormone-refractory CWR22R prostate cancer xenografts (human prostate cancer transplanted into nude mice) and a xenograft of the parental, hormone-sensitive CWR22 strain were analyzed by use of cDNA microarray technology. To validate the data from cDNA microarrays on clinical prostate cancer specimens, a tissue microarray of specimens from 26 prostates with benign prostatic hyperplasia, 208 primary prostate cancers, and 30 hormone-refractory local recurrences was constructed and used for immunohistochemical detection of protein expression. Results: Among 5184 genes surveyed with cDNA microarray technology, expression of 37 (0.7%) was increased more than twofold in the hormone-refractory CWR22R xenografts compared with the CWR22 xenograft ; expression of 135 (2.6%) genes was reduced by more than 50%. The genes encoding insulin-like growth factor-binding protein 2 (IGFBP2) and 27-kd heat-shock protein (HSP27) were among the most consistently over-expressed genes in the CWR22R tumors. Immunohistochemical analysis of tissue microarrays demonstrated high expression of IGFBP2 protein in 100% of the hormone-refractory clinical tumors, in 36% of the primary tumors, and in 0% of the benign prostatic specimens (two-sided P = .0001). Overexpression of HSP27 protein was demonstrated in 31% of the hormone-refractory tumors, in 5% of the primary tumors, and in 0% of the benign prostatic specimens (two-sided P = .0001). Conclusions: The combination of cDNA and tissue microarray technologies enables rapid identification of genes associated with progression of prostate cancer to the hormone-refractory state and may facilitate analysis of the role of the encoded gene products in the pathogenesis of human prostate cancer.

Fluorescent cDNA microarray hybridization reveals complexity and heterogeneity of cellular genotoxic stress responses

Abstract: The fate of cells exposed to ionizing radiation (IR) may depend greatly on changes in gene expression, so that an improved view of gene induction profiles is important for understanding mechanisms of checkpoint control, repair and cell death following such exposures. We have used a quantitative fluorescent cDNA microarray hybridization approach to identify genes regulated in response to 7-irradiation in the p53 wild-type ML-1 human myeloid cell line. Hybridization of the array to fluorescently-labeled RNA from treated and untreated cells was followed by computer analysis to derive relative changes in expression levels of the genes present in the array, which agreed well with actual quantitative changes in expression. Forty-eight sequences, 30 not previously identified as IR-responsive, were significantly regulated by IR. Induction by IR and other stresses of a subset of these genes, including the previously characterized CIP1/ WAF1, MDM2 and BAX genes, as well as nine genes not previously reported to be IR-responsive, was examined in a panel of 12 human cell lines. Responses varied widely in cell lines with different tissues of origin and different genetic backgrounds, highlighting the importance of cellular context to genotoxic stress responses. Two of the newly identified IR-responsive genes, FRA-1 and ATF3, showed a p53-associated component to their IR-induction, and this was confirmed both in isogenic human cell lines and in mouse thymus. The majority of the IR-responsive genes, however, showed no indication of p53-dependent regulation, representing a potentially important class of stress-responsive genes in leukemic cells.

Expression profiling in cancer using cDNA microarrays.

Abstract: Currently there are over 1,000,000 human expressed sequence tag (EST) sequences available on the public database, representing perhaps 50-90% of all human genes The cDNA microarray technique is a recently developed tool that exploits this wealth of information for the analysis of gene expression In this method, DNA probes representing cDNA clones are arrayed onto a glass slide and interrogated with fluorescently labeled cDNA targets The power of the technology is the ability to perform a genome-wide expression profile of thousands of genes in one experiment In our review we describe the principles of the microarray technology as applied to cancer research, summarize the literature on its use so far, and speculate on the future application of this powerful technique

Plastic Microchip Electrophoresis for Analysis of PCR Products of Hepatitis C Virus

Abstract: Background: Electrophoresis on polymeric rather than glass microstructures is a promising separation method for analytical chemistry. Assays on such devices need to be explored to allow assessment of their utility for the clinical laboratory. Methods: We compared capillary and plastic microchip electrophoresis for clinical post-PCR analysis of hepatitis C virus (HCV). For capillary electrophoresis (CE), we used a separation medium composed of 10 g/L hydroxypropyl methyl cellulose in Tris-borate-EDTA buffer and 10 μmol/L intercalating dye. For microchip electrophoresis, the HCV assay established on the fused silica tubing was transferred to the untreated polymethylmethacrylate microchip with minimum modifications. Results: CE resolved the 145-bp amplicon of HCV in 15 min. The confidence interval of the migration time was <3.2%. The same HCV amplicon was resolved by microchip electrophoresis in <1.5 min with the confidence interval of the migration time <1.3%. Conclusion: The polymer microchip, with advantages that include fast processing time, simple operation, and disposable use, holds great potential for clinical analysis.

Diffuse Reflectance Infrared Fourier Transform and Raman Spectroscopic Studies of MoO3 Dispersed on CeO2 Support

Abstract: The MoO3/CeO2 system has been studied by diffuse reflectance infrared Fourier transform and Raman spectroscopies. CeO2 surface is usually terminated with the surface hydroxyl groups, carbonate spec...

Cluster model study on the surface interactions of γ-alumina-supported metal oxides

Abstract: Cluster models embodying the periodicity and symmetry of atomic arrangement on the surface of γ -Al 2 O 3 , as a support, have been applied to discuss the dispersion state of metal oxide (i.e., MoO 3 , NiO, or CuO) on the basis of the incorporation model from the theoretical chemistry's point of view. The preference occupation of the tetrahedral or octahedral vacant sites available on the surface of γ -Al 2 O 3 by the dispersed metal cations is related to the intrinsic properties and the amount of the dispersed metal oxide as well as the calcination temperature used for sample preparation. The results are in good agreement with the experimental facts.

Microarray ratio analysis under noisy background

Abstract: 37 the extent of their roles in vivo is not yet understood. These complexes are also of interest because they share five subunits and possess histone acetylase activities, raising the possibility that they are functionally redundant. The results of genomewide analysis on individual components of TFIID and SAGA reveal that expression of most genes requires the function of one or more of the shared subunits, demonstrating that SAGA and TFIID are together required for expression of most genes. Most striking was evidence that the different histone acetylase components of SAGA and TFIID are functionally redundant, revealing that half of the genome can be expressed through the function of either complex.

Syntheses and magnetic properties of Rm+nCo5m+3nB2n compounds

Abstract: New compounds Pr3Co13B2 and Nd5Co19B6 have been synthesized successfully. They belong to the Rm+nCo5m+3nB2n family with m = 2, n = 1 and m = 2 and n = 3, respectively. Pr3Co13B2 adopts the hexagonal La3Ni13B2-type structure with lattice parameters a = 5.0672(3) Angstrom and c = 10.6850(6) Angstrom, while Nd5Co19B6 is isostructural to Lu5Ni19B6 With a = 5.1328(3) Angstrom and c = 16.6519(5) Angstrom. Magnetic measurements indicate that Pr3Co13B2 is ferromagnetic with a Curie temperature of 360 K. Its saturation magnetic moment at 5 K is 20.0 mu(B) fu(-1). Based on the results of the saturation magnetization, two kinds of Co sites with different magnetic moments are proposed. Pr3Co13B2 exhibits large uniaxial anisotropy with an anisotropy field of 90 A m(-1) at 5 K. The Nd5Co19B6 compound is ferromagnetic with a Curie temperature of 380 K. Its saturation magnetic moment and anisotropy field are 21.5 mu(B) fu(-1) and 340 A m(-1) at 5 K, respectively. No spin reorientation was detected from the temperature dependence of the magnetization of these compounds from 5 K to their Curie temperatures, and the behaviour of magnetocrystalline anisotropy was analysed using the single-ion model.

Pharmacokinetic applications of capillary electrophoresis.

Abstract: This review briefly discusses the use of capillary electrophoretic (CE) methods for the investigations of different aspects of pharmacokinetics. In most investigations, CE was the method of choice because of its unique features, including high resolving power for chiral or metabolite separation, small sample volume for pediatric pharmacokinetics or for cell-based investigations, in situ microdialysis sampling for rapid eliminations, low UV wavelength detection for nonderivatized analytes, fast and simplified sample processing for existing methods that require tedious sample preparation, or as a second method for verifications. Moreover, instrumental aspects of CE-based assays for pharmacokinetic studies, such as different modes of CE methods for analyzing biological samples, sample stacking for increasing detection sensitivity, and coupling techniques with microdialysis and mass spectrometry, are also discussed in this review. Furthermore, the advantages and limitations of CE methods as well as the future outlook for pharmacokinetic studies are summarized.

Crystallographic and magnetic properties of intermetallic compound Nd3Co13B2

Abstract: The crystal structure and magnetic properties of the intermediate compound Nd3Co13B2 have been investigated by x-ray diffraction and magnetic measurement. Nd3Co13B2 is a member of homologous series Rm+1Co5m+3B2 with m=2. It adopts the hexagonal La3Ni13B2-type structure with lattice parameters a=5.0722(4) A and c=10.7840(5) A. The Nd3Co13B2 compound is ferromagnetic with a Curie temperature of 420 K. Its saturation magnetic moment and anisotropy field are 20.8 μB/f.u. and 163 kOe at 1.5 K, respectively.

Clustering analysis for gene expression data

Abstract: The recent development of cDNA microarray allows ready access to large amount gene expression patterns for many genetic materials. Gene expression of tissue samples can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA microarray. Ratios of average expression level arising from co-hybridized normal and pathological samples are extracted via image segmentation, thus the gene expression pattern are obtained. The gene expression in a given biological process may provide a fingerprint of the sample development, or response to certain treatment. We propose a K-mean based algorithm in which gene expression levels fluctuate in parallel will be clustered together. The resulting cluster suggests some functional relationships between genes, and some known genes belongs to a unique functional classes shall provide indication for unknown genes in the same clusters.© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Microcalorimetric Studies of Zn—Al Mixed Oxides Obtained From Hydrotalcite-type Precursors

Abstract: A series of Zn–Al hydrotalcites with Zn/Al molar ratios of 1, 2, 3 and 6 were prepared by co-precipitation method. TG-DTG results showed that the hydrotalcites decompose in two stages, corresponding to the two endothermic peaks around 180 and 220°C. After calcination at 400°C, the samples were converted into Zn–Al mixed oxides with the only XRD pattern of ZnO, except for the sample with the ratio of 6. The Zn–Al mixed oxides possess similar surface acidity revealed by microcalorimetric adsorption of NH3. The basicity of the samples increases with the order: ZnO>6Zn/Al>1Zn/Al>Al2O3.

The ferroelectricity of perovskite-type oxides with alkylamine interlayer

Abstract: The ferroelectricity of layer perovskite-type oxides intermittent with alkylamine, synthesized by hydrothermal method, has been reported. Ferroelectric hysteresis loops were observed in these newly synthesized powder crystals, which were pressed into wafers with platinum electrodes deposited by a pulsed laser. Element analysis shows 69% cations between two layers were exchanged into alkyl ammonium. X-ray powder diffraction pattern, infrared spectra, Raman spectra, and electron microscopy were used to characterize the samples. The results show that perovskite layer contributes to the ferroelectric property. So-synthesized samples may make up a new group of materials with potential use especially in the field of fatigue-free ferroelectricity.

Nonlinear filters in genomic control.

Abstract: The genome is a highly complex nonlinear control system regulating cell function. One of the primary means for regulating cellular activity is the control of protein production. Protein production is controlled by the amount of mRNA expressed by individual genes. This level of gene expression is modulated by protein machinery that senses conditions internal and external to the cell. A set of gene expression levels over time can be modeled as a random time function. The tools required to start building an understanding of genomic regulation of expression are those which allow one to discern the probability characteristics of this random function. Basic to such understanding is the ability to discover how expression levels of various genes predict other expression levels, both at fixed moments in time and through time. Hence, genomic pathway analysis depends on the application of nonlinear signal filters. In the approach here, gene expression levels can have three logical values: −1 (down-regulated), 1 (up-regulated), 0 (invariant). Filters are in terms of ternary logic and are statistically optimized via conditional probabilities. Although recent cDNA microarray technology permits simultaneous measurement of thousands of gene expression levels, current technology severely limits the number of microarrays one can use to acquire data for filter design. Consequently, one is required to constrain optimization by using small numbers of predictor genes or restricting the filter class. The present paper gives an overview of the general paradigm for genomic prediction and provides some early results.

Comparison of cellular gene expression in Ebola-Zaire and Ebola-Reston virus-infected primary human monocytes

Abstract: Comparison of cellular gene expression in Ebola-Zaire and Ebola-Reston virus-infected primary human monocytes

ICARUS. A status report

Abstract: The latest evolutions of the ICARUS project are reviewed. During the present year the collaboration has been heavily involved into the construction of the first full scale prototypes of the 600 ton ICARUS detector. Cryogenic and purification tests as well as mechanical tests on a wires chamber module, are presently under completion. No major problems were found and we foresee to be ready for the commissioning of the major detector components by the end of the present year. Also, the Long Baseline Neutrino Oscillation program has been subject to a rapid acceleration. Following our formal proposal, submitted and approved at the beginning of this year by the CERN SPSLC, a working group has been formed to study the details of the beam and a sensitive program has been formulated by which first neutrinos can be sent to the Gran Sasso at the end of year 2001.

Profiling expression patterns of 2,214 unigenes in mouse craniofacial development by cDNA microarray analysis

Abstract: The recent development of cDNA microarray technology enables parallel expression monitoring of thousands of genes simultaneously, which provides a powerful tool for characterizing transcriptional activities of genes in various developmental stages and pathological states. We initiated the Oral and Craniofacial Genome Anatomy Project (OC-GAP) to identify genes important for craniofacial development and disorders. As part of this genome project, we have examined gene expression patterns during mouse craniofacial development. Fluorescently labelled probes prepared using mRNA from mouse embryonic craniofacial tissues at embryonic day (E) 9.5, E13.5 and E16.5 were hybridized to microarray slides printed with 2,214 mouse unigenes. A microarray quantitative analysis revealed that 10% of these genes were expressed in different levels during craniofacial development, whereas the rest showed no significant differences in expression throughout the different developmental stages. We found that 41 genes, such as those encoding Wnt-1, retinoid receptor and Brca1, showed higher expression levels at E9.5; 54 genes, such as those encoding Bmp-1, IGF II and Sox3, were more highly expressed at E13.5; and another 126 genes, such as those encoding Mash 1, FHF-1 and fibulin-2, were expressed at higher levels at E16.5. The identification of these genes with highly stage-specific expression during craniofacial development is potentially important because they are likely to have key roles in the formation of craniofacial tissues. We are currently studying expression patterns of genes from an E8.5−9.5 mouse craniofacial cDNA library to identify novel craniofacial genes by microarray screening approaches.

Theoretical examination of electroosmosis control with external radial electric field in capillary electrophoresis.

Abstract: The influence of an external radial electric field (E(R)) on electroosmosis in capillary electrophoresis was studied theoretically. Based on a Stern-like model, three basic equations were deduced, with only two unknown parameters of delta and psi(d) where delta is the distance between the flowing shear interface and the tube wall, while psi(d) is the potential at the starting point of diffuse layer. The new equations reveal that, to effectively regulate the electroosmosis at E(R) <3 x 10(8) V/m, buffer pH should be kept below 5. In a common case of E(R) <10(8) V/m, the buffer pH should be below 4, otherwise the flow direction of the electroosmosis cannot be reversed. A way to increase the working pH range lies in the use of chemically coated rather than bare tubes. As expected, small capillaries and low ionic strength are preferred.

Study on the reactivity of ultrafine cerium-molybdenum oxide particles in the absence of molecular oxygen

Abstract: The state and reactivity of lattice oxygen ions in the ultrafine Ce–Mo oxide particles prepared by the sol–gel method are studied by using X‐ray diffraction, laser Raman spectroscopy, temperature‐programmed reduction, X‐ray photoelectron spectroscopy and pulse microreactor tests. It is found that the lattice oxygen ions in the ultrafine Ce–Mo oxides are the main active species for partial oxidation of toluene to benzaldehyde. By decreasing the size of complex Ce–Mo oxide particles to nanometric scale, the reactivity of lattice oxygen ions can be remarkably improved.

Capillary electrophoresis of FITC labeled amino acids with laser-induced fluorescence detection

Abstract: FITC labeled amino acids have been separated using a home-built capillary electrophoresis with a laser-induced fluorescence detection (CE-LIF) system. Seventeen peaks can now be generated from the twenty common amino acids. The key conditions lie in the optimization of pH, buffer electrolytes and buffer additives.

Molecular pathophysiologic hints into Niemann-Pick Type C disease using cDNA microarray technology

Abstract: Molecular pathophysiologic hints into Niemann-Pick Type C disease using cDNA microarray technology

Simulation and deconvolution of an experimental OCT image

Abstract: Optical coherence tomography (OCT) is a new noninvasive tomographic imaging techniques with resolution of micron scale It has high potential for the application in many fields such as medicine, biology, material and so no In this paper, our OCT system is shown to be successful in the study of both botanic and creatural tissue imaging Furthermore we also use the Monte-Carlo simulation method to analyze 2D OCT image The differences between single scattered light and multiply scattered light and also its influence on the quality of OCT image are discussed To show an example, a conduit immersing in a high scattering medium as the model of blood vessel is simulated and the theoretical result is directly shown in the form of image The conduit immersing in the high scattering medium can be clearly seen in the imags Comparing with the experimental image they are basically accordant Some results helpful for experimental research area draw through the simulation To further enhance the resolution of OCT imaging, computer processing and image deconvolution are introduced The depth resolution is improved by more than one order for the sample image and thus enables intracellular imaging

Markovian Analysis of Adaptive Reconstructive Multiparameter τ-Openings

Abstract: A classical single-parameter τ-opening is a union of openings in which each structuring element is scaled by the same parameter. Multiparameter binary τ-openings generalize the model in two ways: first, parameters for each opening are individually defineds second, a structuring element can be parameterized relative to its overall shape, not merely sized. The reconstructive filter corresponding to an opening is defined by fully passing any grain (connected component) that is not fully eliminated by the opening and deleting all other grains. Adaptive design results from treating the parameter vector of a reconstructive multiparameter τ-opening as the state space of a Markov chain. Signal and noise are modeled as unions of randomly parameterized and randomly translated primary grains, and the parameter vector is transitioned depending on whether an observed grain is correctly or incorrectly passed. Various adaptive models are considered, transition probabilities are discussed, the state-probability increment equations are deduced from the appropriate Chapman-Kolmogorov equations, and convergence of the adaptation is characterized by the steady-state distribution relating to the Markov chain.

Identification of suppressor genes associated with the chromosome 6-mediated suppressed melanoma cell UACC903(+6) by cDNA microarray

Abstract: Identification of suppressor genes associated with the chromosome 6-mediated suppressed melanoma cell UACC903(+6) by cDNA microarray