The mitBASE human dataset structure

CC to TT mutation in the mitochondrial DNA of normal skin: relationship to ultraviolet light exposure

We have previously reported that ultraviolet (UV)-specific (CC to TT) mutations in p53 gene can be detected in normal skin. This, however, cannot be used as a cumulative marker of UV exposure, since cells with the p53 mutation acquire a clonal growth advantage. Moreover, a large skin biopsy is necessary for each assay. In order to circumvent these problems, we have measured mitochondrial (Mt) DNA mutations; there are more than 1000 copies of the Mt genome per cell, and Mt genes are not directly involved in cell growth. We have established a sensitive allele-specific polymerase chain reaction (AS-PCR) assay capable of detecting one CC to TT mutation in Mt DNA among 10(7) wild-type genes using a mismatch allele-specific primer. With this assay, we found no mutation-positive samples from internal non-exposed tissue (stomach, colon, and blood) (0/50). In contrast, 17 out of 111 skin samples were positive: the mutation frequency in positive samples was around 10(7)-10(-6) (10-100 copies of mutant in 10(8) wild-type Mt DNA). In normal skin tissue, the prevalence of positive samples was higher in those from exposed sites (13/51) than in those from less-exposed sites (1/26) (p<0.05). However, a quantitative correlation between sunlight exposure and the accumulation of mutations was not found. We conclude that the UV exposure-associated CC to TT mutation in Mt DNA can be detected in normal skin, but that further studies are required to develop this as a quantitative marker for UV exposure.

Update of the Human MitBASE database

Human MitBASE is a database collecting human mtDNA variants. This database is part of a greater mitochondrial genome database (MitBASE) funded within the EU Biotech Program. The present paper reports the recent improvements in data structure, data quality and data quantity. As far as the database structure is concerned it is now fully designed and implemented. Based on the previously described structure some changes have been made to optimise both data input and data quality. Cross-references with other bio-databases (EMBL, OMIM, MEDLINE) have been implemented. Human MitBASE data can be queried with the MitBASE Simple Query System (http://www.ebi.ac.uk/htbin/Mitbase/mit base.pl) and with SRS at the EBI under the 'Mutation' section (http://srs.ebi.ac.uk/srs5/). At present the HumanMitBASE node contains approximately 5000 variants related to studies investigating population polymorphisms and pathologies.

MitBASE: a comprehensive and integrated mitochondrial DNA database

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects all available information from different organisms and from intraspecie variants and mutants. Research institutions from different countries are involved, each in charge of developing, collecting and annotating data for the organisms they are specialised in. The design of the actual structure of the database and its implementation in a user-friendly format are the care of the European Bioinformatics Institute. The database can be accessed on the Web at the following address: http://www.ebi.ac. uk/htbin/Mitbase/mitbase.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecie diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.

Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences

The present paper describes AMmtDB, a database collecting the multi-aligned sequences of vertebrate mitochondrial genes coding for proteins and tRNAs, as well as the multiple alignment of the mammalian mtDNA main regulatory region (D-loop) sequences. The genes coding for proteins are multi-aligned based on the translated sequences and both the nucleotide and amino acid multi-alignments are provided. As far as the genes coding for tRNAs are concerned, the multi-alignments based on the primary and the secondary structures are both provided; for the mammalian D-loop multi-alignments we report the conserved regions of the entire D-loop (CSB1, CSB2, CSB3, the central region, ETAS1 and ETAS2) as defined by Sbisà et al. [ Gene (1997), 205, 125-140). A flatfile format for AMmtDB has been designed allowing its implementation in SRS (http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB ). Data selected through SRS can be managed using GeneDoc or other programs for the management of multi-aligned data depending on the user's operative system. The multiple alignments have been produced with CLUSTALV and PILEUP programs and then carefully optimized manually.