ABSTRACT
MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbas e.pl. The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme.
Subject(s)
DNA, Mitochondrial/genetics , Databases, Factual , Animals , DNA, Fungal/genetics , DNA, Plant/genetics , Eukaryota/genetics , Humans , Internet , Invertebrates/genetics , Plants/genetics , Vertebrates/geneticsABSTRACT
KEYnet is a database where gene and protein names are hierarchically structured. Particular care has been devoted to the search and organisation of synonyms. The structuring is based on biological criteria in order to assist the user in data search and to minimise the risk of information loss. Links to the EMBL data library by the entry name and the accession number are implemented. KEYnet is available through the WWW at the following site: http://www.ba.cnr.it/keynet.html
Subject(s)
Databases, Factual , Proteins/genetics , Information Storage and Retrieval , Internet , Proteins/chemistryABSTRACT
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.
Subject(s)
DNA, Mitochondrial/genetics , Databases, Factual , Animals , Cell Nucleus/genetics , Classification , DNA, Mitochondrial/classification , Eukaryota/genetics , Europe , Fungi/genetics , Genetic Code , Genetic Diseases, Inborn/genetics , Genetic Variation , Humans , Information Storage and Retrieval , Internet , Invertebrates/genetics , Mutation , Plants/genetics , User-Computer Interface , Vertebrates/geneticsABSTRACT
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.
Subject(s)
DNA, Mitochondrial/genetics , Databases, Factual , Animals , Databases, Factual/standards , Evolution, Molecular , Genetic Diseases, Inborn/genetics , Genetic Diseases, Inborn/pathology , Genetic Variation/genetics , Humans , Information Storage and Retrieval , Internet , Polymorphism, Genetic/geneticsABSTRACT
KEYnet is a database where gene and protein names are hierarchically structured. Particular care has been devoted to the search and organisation of synonyms. The structuring is based on biological criteria in order to assist the user in the data search and to minimise the risk of loss of information. Links to the EMBL data library by the entry name and the accession number have been implemented. KEYnet is available through the World Wide Web at the following site: http://www.ba.cnr.it/keynet.html. Recently KEYnet has incorporated specific gene name classifications, which can be browsed starting from the above-mentioned KEYnet home page: the Mitochondrial Gene Names classification and the Rat Gene Names classification. KEYnet database has also been structured in a flatfile format and can be queried through SRS (http://bio-www.ba.cnr.t:8000/srs).
Subject(s)
Databases, Factual , Genes , Proteins/classification , Terminology as Topic , Animals , DNA, Mitochondrial/classification , Information Storage and Retrieval , Internet , Rats , Software , Vocabulary, ControlledABSTRACT
An in organello footprinting approach has been used to probe a protein-DNA interaction of a nuclear coded 25 kDa protein, previously isolated in our laboratory, that binds "in vitro" a region within the ND2 gene, located upstream of the Ori-L. Footprinting studies with the purine-modifying reagent dimethyl sulfate and the pirimidine-modifying reagent potassium permanganate were carried out in isolated mitochondria from rat liver. Dimethyl sulfate footprinting has allowed the detection of a protein-DNA interaction within the curved ND2 region with contact sites located in both the strands. Potassium permanganate footprinting allowed detection of an adjacent permanganate-reactive region. We hypothesize that the permanganate-reactive region is a single stranded DNA due to a profound helix distortion induced by a 25 kDa protein binding to the nearest region.
Subject(s)
DNA Footprinting , DNA, Mitochondrial/metabolism , DNA-Binding Proteins/chemistry , Mitochondria, Liver/ultrastructure , Animals , Base Sequence , DNA Replication , DNA, Mitochondrial/ultrastructure , DNA-Binding Proteins/metabolism , Deoxyribonucleoproteins/chemistry , Mitochondria, Liver/chemistry , Molecular Weight , Nucleic Acid Conformation , Potassium Permanganate/chemistry , Protein Binding , Rats , Sulfuric Acid Esters/chemistryABSTRACT
The presence of a curved DNA sequence in the gene for the NADH-dehydrogenase subunit 2 of rat mitochondrial genome, upstream from the origin of the light strand replication have been demonstrated through theoretical analysis and experimental approaches. Gel retardation assays showed that this structure makes a complex with a protein component extracted from the mitochondrial matrix. The isolation and purification of this protein is reported. With a Sepharose CL-6B and magnetic DNA affinity chromatography a polypeptide was purified to homogeneity having 25-kDa mass as shown by gel electrophoresis. To functionally characterize this protein, its capability to bind to other sequences of the homologous or heterologous DNA and to specific riboprobes was also investigated. A role for this protein as a trans-acting agent required for the expression of the mammalian mitochondrial genome is suggested.
Subject(s)
DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , DNA-Binding Proteins/isolation & purification , DNA-Binding Proteins/metabolism , Mitochondria/metabolism , Animals , Base Sequence , Chromatography, Affinity , DNA Replication , DNA, Mitochondrial/chemistry , DNA-Binding Proteins/chemistry , Genome , In Vitro Techniques , Molecular Sequence Data , Molecular Weight , NADH Dehydrogenase/chemistry , NADH Dehydrogenase/genetics , Nucleic Acid Conformation , Protein Conformation , Rats , Replication OriginABSTRACT
We have purified, by sequence-specific affinity chromatography, a mitochondrial (mt) matrix protein which binds to the curved DNA located between the replication origin (ori) of the leading strand (ori-H) and the two transcription promoters in the rat mt genome. The protein was characterized by gel electrophoresis as a 67-kDa polypeptide and seems to be involved in the DNA contact on the mt light strand. This protein differs (in the size and location of its DNA-binding site) from other DNA-binding proteins studied so far in animal mt systems. We suggest a role for the 67-kDa protein, assisted by other proteins, in regulating the initiation of leading-strand replication.
Subject(s)
DNA, Mitochondrial/metabolism , DNA-Binding Proteins/isolation & purification , Mitochondria, Liver/metabolism , Rats/metabolism , Regulatory Sequences, Nucleic Acid , Transcription Factors/isolation & purification , Animals , Base Sequence , DNA, Mitochondrial/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/physiology , Molecular Sequence Data , Nucleic Acid Conformation , Protein Binding , Rats/genetics , Rats, Wistar , Transcription Factors/metabolism , Transcription Factors/physiologySubject(s)
Hepatitis C/transmission , Renal Dialysis/adverse effects , Adult , Aged , Female , Humans , Male , Middle Aged , Sexual PartnersABSTRACT
The case of a 1 year and five month-old male infant with craniometaphyseal dysplasia is reported. Several clinical examinations showed weight and height greater than 97%.
