A Cancer Recognition Method Based on DNA Microarray

The accurate cancer classification is of great importance in clinical treatment. Recently, the DNA microarray technology provides a promising approach to the diagnosis and prognosis of cancer types. However, it has no perfect method for the multiclass classification problem. The difficulty lies in the fact that the data are of high dimensionality with small sample size. This paper proposed an automatic classification method of multiclass cancers based on Biomimetic pattern recognition (BPR). To the public GCM data set, the average correct classification rate reaches 80% under the condition that the correct rejection rate is 81%.

Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

Background: The model eukaryote, Tetrahymena thermophila, is the first ciliated protozoan whose genome has been sequenced, enabling genome-wide analysis of gene expression. Methodology/Principal Findings: A genome-wide microarray platform containing the predicted coding sequences (putative genes) for T. thermophila is described, validated and used to study gene expression during the three major stages of the organism's life cycle: growth, starvation and conjugation. Conclusions/Significance: Of the,27,000 predicted open reading frames, transcripts homologous to only,5900 are not detectable in any of these life cycle stages, indicating that this single-celled organism does indeed contain a large number of functional genes. Transcripts from over 5000 predicted genes are expressed at levels >5x corrected background and 95 genes are expressed at >250x corrected background in all stages. Transcripts homologous to 91 predicted genes are specifically expressed and 155 more are highly up-regulated in growing cells, while 90 are specifically expressed and 616 are up-regulated during starvation. Strikingly, transcripts homologous to 1068 predicted genes are specifically expressed and 1753 are significantly up-regulated during conjugation. The patterns of gene expression during conjugation correlate well with the developmental stages of meiosis, nuclear differentiation and DNA elimination. The relationship between gene expression and chromosome fragmentation is analyzed. Genes encoding proteins known to interact or to function in complexes show similar expression patterns, indicating that co-ordinate expression with putative genes of known function can identify genes with related functions. New candidate genes associated with the RNAi-like process of DNA elimination and with meiosis are identified and the late stages of conjugation are shown to be characterized by specific expression of an unexpectedly large and diverse number of genes not involved in nuclear functions.

Microarray-Based Study of Carbohydrate-Protein Binding by Gold Nanoparticle Probes

In order to develop a novel high-throughput tool for monitoring carbohydrate-protein interactions, we prepared carbohydrate or glycoprotein microarrays by immobilizing amino modified carbohydrates on aldehyde-derivatized glass slides or glycoprotein on epoxide-derivatized glass slides and carried out lectin binding experiments by using these microarrays, respectively. The interaction events are marked by attachment of gold nanoparticles followed by silver deposition for signal enhancement. The attachment of the gold nanoparticles is achieved by standard avidin-biotin chemistry.

Microarray based Raman spectroscopic detection with gold nanoparticle probes

microarray approach based on surface-enhanced Raman spectroscopic (SERS) was developed for detection of spotted peptide, peptide-protein or protein-antibody interaction. The procedure involves the attachment of peptide-capped gold nanoparticles followed by silver deposition for signal enhancement. The attachment of the gold nanoparticles is achieved by standard avidin-biotin chemistry. The well-known biomolecular recognition pairs, IgG/protein A and biotin/avidin, were used to demonstrate proof-of-concept of the SERS assay.

Microarray-based Raman spectroscopic assay for kinase inhibition by gold nanoparticle probes

In this paper, a microarray-based surface-enhanced Raman spectroscopic (SERS) assay for detection of kinase functionality and inhibition has been reported. Biotinylated anti-phosphoserinen antibodies mark the phosphorylation and inhibition events and gold nanoparticles are attached to the antibodies by standard avidin-biotin chemistry, followed by silver deposition for SERS signal enhancement. The avidin conjugated fluorescein is used as SERS probe. The alpha-catalytic subunit of cyclic adenosine 5'-monophosphate (cAMP) dependent protein kinase (PKA), its well known substrate, kemptide, and three inhibitors, H89, HA1077, and KN62 have been chosen here to establish the SERS assay. As expected, highly selective inhibition of PKA is demonstrated with the inhibitor H89 and the inhibition assay enable to detect kinase inhibition as well as derive IC50 (half maximal inhibitory concentration) plots.

Microarray-based kinase inhibition assay by gold nanoparticle probes

We report on the development of a new class of kinase microarray for the detection of kinase inhibition based on marking peptide phosphorylation/biotinylation events by attachment of gold nanoparticles followed by silver deposition for signal enhancement. The alpha-catalytic subunit of cyclic adenosine 5'-monophosphate-dependent protein kinase (PKA), and its well-known substrate, kemptide, were used for the purpose of monitoring phosphorylation and inhibition. As expected, highly selective inhibition of PKA is demonstrated with the four inhibitors: H89, HA1077, mallotoxin, and KN62. Furthermore, an inhibition assay demonstrates the ability to detect kinase inhibition as well as derive IC50 (half-maximal inhibitory concentration) plots.

In situ FTIR spectroelectrochemistry of a microarray electrode

A thin-layer microdisk array electrode (TLMDAE) was designed for in situ reflectance FTIR spectroelectrochemical studies. A theoretical estimation, cyclic voltammetry, chronoamperometry and in situ IR measurements demonstrate that this novel design of array electrode results in advantages such as reduced ohmic potential drop, small cell constant and facility for diffusional exchange between thin layer and bulk solution. It has been suggested that the enhanced edge diffusion on the TLMDAE leads to a reduced accumulation of species in the thin layer. (C) 1997 Elsevier Science S.A.

COBALT PORPHYRIN NAFION FILM ON CARBON MICROARRAY ELECTRODE TO MONITOR OXYGEN FOR ENZYME ANALYSIS OF GLUCOSE

A microcarbon array electrode was modified by the placement of a Nafion film containing cobalt tetramethylpyridyl phorphyrin on its surface. This electrode was applied to the analysis of solution glucose when it was further modified by the immobilization of glucose oxidase on the outermost surface of the Nafion by the cross-linking of serum albumin with glutaraldehyde. The concomitant decrease in the concentration of oxygen, as it was consumed in the enzymatic reaction of glucose with glucose oxidase, was determined by either cyclic voltammetry or a double potential step method at the porphyrin-Nafion catalytic electrode. Glucose could be determined in the range of 0.01-4 mM rapidly, without interference from substances such as ascorbate or other saccharides.

Discovery of the genes in response to white spot syndrome virus (WSSV) infection in Fenneropenaeus chinensis through cDNA microarray

We used microarray technology to study differentially expressed genes in white spot syndrome virus (WSSV)-infected shrimp. A total of 3136 cDNA targets, including 1578 unique genes from a cephalothorax cDNA library and 1536 cDNA clones from reverse and forward suppression subtractive hybridization (SSH) libraries of Fenneropenaeus chinensis, plus 14 negative and 8 blank control clones, were spotted onto a 18 x 18 mm area of NH2-modified glass slides. Gene expression patterns in the cephalothorax of shrimp at 6 h after WSSV injection and moribund shrimp naturally infected by WSSV were analyzed. A total of 105 elements on the arrays showed a similar regulation pattern in artificially infected shrimp and naturally infected moribund shrimp; parts of the results were confirmed by semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR). The up-regulated expression of immune-related genes, including heat shock proteins (HSP70 and HSP90), trehalose-phosphate synthase (TPS), ubiquitin C, and so forth, were observed when shrimp were challenged with WSSV. Genes including myosin LC2, ATP synthase A chain, and arginine kinase were found to be down-regulated after WSSV infection. The expression of housekeeping genes such as actin, elongation factor, and tubulin is not stable, and so these genes are not suitable as internal standards for semiquantitative RT-PCR when shrimp are challenged by WSSV. As a substitute, we found that triosephosphate isomerase (TPI) was an ideal candidate of interstandards in this situation.

Estrutura básica do MicroArray Gene Expression Markup Language - MAGE-ML.

Um dos objetivos da Rede Genômica Animal é a identificação de genes que contribuam para o melhoramento de características de interesse econômico em animais de produção. Uma das ferramentas para prospecção e análise desses genes é o Microarranjo de DNA, uma técnica que permite avaliar a expressão gênica em condições específicas. Apesar de seu uso amplamente difundido na comunidade científica, os procedimentos e as informações de experimentos nem sempre são padronizados, a despeito dos esforços na criação de uma linguagem padrão como o MAGE-ML. Este documento visa apresentar o padrão MAGE-ML para aqueles que ainda não se utilizam desse recurso e gostariam de aprender um pouco a respeito.

How well do we understand the clusters found in microarray data?

Clare, A. and King R.D. (2002) How well do we understand the clusters found in microarray data? In In Silico Biol. 2, 0046

In situ synthesis of DNA microarray on functionalized cyclic olefin copolymer substrate.

Thermoplastic materials such as cyclic-olefin copolymers (COC) provide a versatile and cost-effective alternative to the traditional glass or silicon substrate for rapid prototyping and industrial scale fabrication of microdevices. To extend the utility of COC as an effective microarray substrate, we developed a new method that enabled for the first time in situ synthesis of DNA oligonucleotide microarrays on the COC substrate. To achieve high-quality DNA synthesis, a SiO(2) thin film array was prepatterned on the inert and hydrophobic COC surface using RF sputtering technique. The subsequent in situ DNA synthesis was confined to the surface of the prepatterned hydrophilic SiO(2) thin film features by precision delivery of the phosphoramidite chemistry using an inkjet DNA synthesizer. The in situ SiO(2)-COC DNA microarray demonstrated superior quality and stability in hybridization assays and thermal cycling reactions. Furthermore, we demonstrate that pools of high-quality mixed-oligos could be cleaved off the SiO(2)-COC microarrays and used directly for construction of DNA origami nanostructures. It is believed that this method will not only enable synthesis of high-quality and low-cost COC DNA microarrays but also provide a basis for further development of integrated microfluidics microarrays for a broad range of bioanalytical and biofabrication applications.

SplicerAV: a tool for mining microarray expression data for changes in RNA processing.

BACKGROUND: Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but has not been previously mined en masse for changes in mRNA processing. We explored the possibility of using HG-U133 microarray data to identify changes in alternative mRNA processing in several available archival datasets. RESULTS: Data from these and other gene expression microarrays can now be mined for changes in transcript isoform abundance using a program described here, SplicerAV. Using in vivo and in vitro breast cancer microarray datasets, SplicerAV was able to perform both gene and isoform specific expression profiling within the same microarray dataset. Our reanalysis of Affymetrix U133 plus 2.0 data generated by in vitro over-expression of HRAS, E2F3, beta-catenin (CTNNB1), SRC, and MYC identified several hundred oncogene-induced mRNA isoform changes, one of which recognized a previously unknown mechanism of EGFR family activation. Using clinical data, SplicerAV predicted 241 isoform changes between low and high grade breast tumors; with changes enriched among genes coding for guanyl-nucleotide exchange factors, metalloprotease inhibitors, and mRNA processing factors. Isoform changes in 15 genes were associated with aggressive cancer across the three breast cancer datasets. CONCLUSIONS: Using SplicerAV, we identified several hundred previously uncharacterized isoform changes induced by in vitro oncogene over-expression and revealed a previously unknown mechanism of EGFR activation in human mammary epithelial cells. We analyzed Affymetrix GeneChip data from over 400 human breast tumors in three independent studies, making this the largest clinical dataset analyzed for en masse changes in alternative mRNA processing. The capacity to detect RNA isoform changes in archival microarray data using SplicerAV allowed us to carry out the first analysis of isoform specific mRNA changes directly associated with cancer survival.