Application of representational difference analysis to genomic fragments of Marek's disease virus

Differential gene expression analysis in ageing muscle and drug discovery perspectives

Identifying therapeutic target genes represents the key step in functional genomics-based therapies. Within this context, the disease heterogeneity, the exogenous factors and the complexity of genomic structure and function represent important challenges. The functional genomics aims to overcome such obstacles via identifying the gene functions and therefore highlight disease-causing genes as therapeutic targets. Genomic technologies promise to reshape the research on ageing muscle, exercise response and drug discovery. Herein, we describe the functional genomics strategies, mainly differential gene expression methods microarray, serial analysis of gene expression (SAGE), massively parallel signature sequence (MPSS), RNA sequencing (RNA seq), representational difference analysis (RDA), and suppression subtractive hybridization (SSH). Furthermore, we review these illustrative approaches that have been used to discover new therapeutic targets for some complex diseases along with the application of these tools to study the modulation of the skeletal muscle transcriptome.

Effective detection of highly divergent viral genomes in infected cell lines using a new subtraction strategy (primer extension enrichment reaction—PEER)

The development of new molecular approaches for identification or discovery of known and unknown pathogens is essential. The purpose of this study was to evaluate the utility of a new method designated primer extension enrichment reaction (PEER) in detecting viral genomes from highly divergent viral families (ssDNA, dsDNA, ssRNA, dsRNA) in infected cell lines. Findings indicate that the PEER methodology is a powerful tool since it permitted successful ex vivo detection of infectious agents from the Circoviridae, Herpesviridae, Paramyxoviridae, Picornaviridae and Reoviridae families. The great potential of PEER was further confirmed in tests using serial dilutions of West Nile virus (Flaviviridae) and in a "blind" test in which a member of the Poxviridae family was successfully identified. The technique was shown to be useful for identifying causative viral pathogens, following inoculation of susceptible cell lines with clinical biological samples.

Applying a highly specific and reproducible cDNA RDA method to clone garlic up-regulated genes in human gastric cancer cells

AIM: To develop and optimize cDNA representational difference analysis (cDNA RDA) method and to identify and clone garlic up-regulated genes in human gastric cancer (HGC) cells.

METHODS: We performed cDNA RDA method by using abundant double-stranded cDNA messages provided by two self-constructed cDNA libraries (Allitridi-treated and paternal HGC cell line BGC823 cells cDNA libraries respectively). BamH I and Xho I restriction sites harbored in the library vector were used to select representations. Northern and Slot blots analyses were employed to identify the obtained difference products.

RESULTS: Fragments released from the cDNA library vector after restriction endonuclease digestion acted as good marker indicating the appropriate digestion degree for library DNA. Two novel expressed sequence tags (ESTs) and a recombinant gene were obtained. Slot blots result showed a 8-fold increase of glia-derived nexin/protease nexin 1 (GDN/PN1) gene expression level and 4-fold increase of hepatitis B virus x-interacting protein (XIP) mRNA level in BGC823 cells after Allitridi treatment for 72 h.

CONCLUSION: Elevated levels of GDN/PN1 and XIP mRNAs induced by Allitridi provide valuable molecular evidence for elucidating the garlic's efficacies against neurodegenerative and inflammatory diseases. Isolation of a recombinant gene and two novel ESTs further show cDNA RDA based on cDNA libraries to be a powerful method with high specificity and reproducibility in cloning differentially expressed genes.