A 4-gene panel as a marker at chromosome 8q in Asian gastric cancer patients.

A widely held viewpoint is that the use of multiple markers, combined in some type of algorithm, will be necessary to provide high enough discrimination between diseased cases and non-diseased. We applied stepwise logistic regression analysis to identify the best combination of the 32 biomarkers at chromosome 8q on an independent public microarray test set of 80 paired gastric samples. A combination of SULF1, INTS8, ATP6V1C1, and GPR172A was identified with a prediction accuracy of 98.

Detection of rare point mutation via allele-specific amplification in emulsion PCR.

It is essential to analyze rare mutations in many fields of biomedical research. However, the detection of rare mutations is usually failed due to the interference of predominant wild-type DNA surrounded. Herein we describe a sensitive and facile method of detecting rare point mutation on the basis of allele-specific amplification in emulsion PCR.

Impact of the next-generation sequencing data depth on various biological result inferences.

Next-generation sequencing (NGS) technologies have revolutionized the field of genomics and provided unprecedented opportunities for high-throughput analysis at the levels of genomics, transcriptomics and epigenetics. However, the cost of NGS is still prohibitive for many laboratories. It is imperative to address the trade-off between the sequencing depth and cost.

Electrochemiluminescent assay for detection of extremely rare mutations based on ligase reaction and bead enrichment.

The detection of rare mutations is particularly essential in many areas of biomedical research. Here, we report an ultrasensitive method to detect extremely rare point mutations based on electrochemiluminescent assay. The point mutation among large excess wild-type alleles is exclusively amplified through ligase detection reaction.

Genome-wide microRNA profiles identify miR-378 as a serum biomarker for early detection of gastric cancer.

Recent studies demonstrated that in several human malignancies aberrant expression profiles of circulating microRNAs (miRNAs) anticipate great cancer diagnostic potential. Here we showed that serum miR-378 could serve as a novel noninvasive biomarker in gastric cancer (GC) detection. Genome-wide miRNA expression profiles followed with Real-Time quantitative RT-PCR (qRT-PCR) assays revealed that miR-187(*), miR-371-5p and miR-378 were significantly elevated in GC patients.

Different effects of the probe summarization algorithms PLIER and RMA on high-level analysis of Affymetrix exon arrays.

Background: Alternative splicing is an important mechanism that increases protein diversity and functionality in higher eukaryotes. Affymetrix exon arrays are a commercialized platform used to detect alternative splicing on a genome-wide scale. Two probe summarization algorithms, PLIER (Probe Logarithmic Intensity Error) and RMA (Robust Multichip Average), are commonly used to compute gene-level and exon-level expression values.

[A new SNP microarray technology based on single base extension].

Investigation of DNA-protein interactions is fundamental to understand the mechanism underlying a variety of life processes. In this article, various types of biochemical methods in DNA-protein interaction study in vivo and in vitro at the level of DNA, protein, and the complex, respectively were briefly reviewed. Traditional assays including Nitrocellulose filter-binding assay, Footprinting, EMSA, and Southwestern blotting were summarized.

Transcriptome profiling analysis reveals multiple modulatory effects of Ginkgo biloba extract in the liver of rats on a high-fat diet.

Leaf extract of Ginkgo biloba (GBE) is increasingly used as a herbal medicine for the treatment of neurodegenerative, cardiovascular and cerebrovascular diseases. Several studies have demonstrated many protective effects of GBE in neurons, the endothelium and liver. In this study, we investigated the molecular mechanisms underlying the effects of GBE in disorders induced by long-term exposure to a high-fat diet (HFD).

[Protein array technology applied in high throughput monoclonal antibody generation].

Unlabelled: To reduce the huge labor-cost in the screening in traditional monoclonal antibody generation, We established a new system for monoclonal antibody generation integrating with protein array. BALB/c mice were immunized by eight recombinant proteins respectively, and the positive hybridoma cells were obtained by cell fusion and ELISA screening. All the eight kinds of positive hybridoma cells were mixed, cloned, screened by protein array, and definite dilution cloned.

Baclofen, a GABAB receptor agonist, inhibits human hepatocellular carcinoma cell growth in vitro and in vivo.

Gamma aminobutyric acid (GABA) has been reported to affect cancer development, but the activation of its type B receptor (GABABR) has shown contradictory effects on the progress of human carcinoma. In this study, we investigated the antitumor effect of the GABABR agonist baclofen (Bac) on growth of human hepatocellular carcinoma (HCC) in vitro and in vivo. We found Bac induced G(0)/G(1) phase arrest which was associated with down-regulation of intracellular cAMP level, and up-regulation of p21(WAF1) protein expression as well as its phosphorylation level.

REMOVED: SARS Epidemiology From descriptive to mechanistic analyses.

This article has been removed, consistent with Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).

Allelic distributions of CYP2D6 gene copy number variation in the Eastern Han Chinese population.

Aim: The human cytochrome P450 2D6 (CYP2D6) gene copy number variation, involving CYP2D6 gene deletion (CYP2D6*5) and duplication or multiduplication (CYP2D6*xN), can result in reduced or increased metabolism of many clinically used drugs. The identification of CYP2D6*5 and CYP2D6*xN and the investigation of their allelic distributions in ethnic populations can be important in determining the right drug and dosage for each patient.

Methods: The CYP2D6*5 and CYP2D6 genes, and CYP2D6 gene duplication were identified by 2 modified long PCR, respectively.