The DNA sequence quality machine at IFOM: a simple Web-based tool for quantitative assessment of sequencing reactions.

DNA sequence quality is a factor of paramount importance in the world of modern genetic and genomics. Both the sequencing of Human Genome in the "post-draft" era [NHGRI Standard for quality of Human Genomic Sequences, Rev. 7 July (2002) where http://www.nhgri.nih.gov/Grant_info/Funding/ Statements/RFA/quality_standard.html is the HTTP address] and recent "high-throughput" approaches to genetic investigation such as SAGE [Velculescu, V.E., Zhang, L., Vogelstein, B. et al. (1995) "Serial analysis of gene expression", Science 270, 484-487] need a reliable, standardized measure of the quality of a sequencing reaction. The increasing importance of SNP studies also requires a stronger quality control on sequencing reactions by the final user. We propose here a simple, web-based tool for integrated sequence quality evaluation, high quality region quantitative value calculation and chromatogram display. This software is aimed at the small to medium DNA sequence laboratory or to the single researcher, interested in getting a quantitative measure of the sequence quality, browsing the chromatogram and checking the quality values base by base. The program is freely available from the IFOM bioinformatics web Server at http://bio.ifom-firc.it/Phred20/index.html.

Enterotoxins of Staphylococcus aureus induce a cytopathic effect in cell lines.

We describe the use of cell cultures for the detection of Staphylococcus aureus enterotoxins. Madin Darby Bovine Kidney (MDBK), Bovine Embryo lung cells (PEB) and Dog Carcinoma Cell line (A-72) cell monolayers were tested. MDBK, A-72 and PEB cell lines proved to be susceptible to the cytotoxic effect induced by staphylococcal enterotoxins. A cytopathic effect was observed in some cases after 2 hours of incubation. The PEB cell line was the most susceptible and may be used as a useful and cheap method for screening enterotoxigenic S. aureus strains.