The EMBL Nucleotide Sequence Database

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes to achieve swift synchrony. Webin is the preferred tool for individual submissions of nucleotide sequences, including Third Party Annotation (TPA) and alignments. Automated procedures are provided for submissions from large-scale sequencing projects and data from the European Patent Office. New and updated data records are distributed daily and the whole EMBL Nucleotide Sequence Database is released four times a year. Access to the sequence data is provided via ftp and several WWW interfaces. With the web-based Sequence Retrieval System (SRS) it is also possible to link nucleotide data to other specialist molecular biology databases maintained at the EBI. Other tools are available for sequence similarity searching (e.g. FASTA and BLAST). Changes over the past year include the removal of the sequence length limit, the launch of the EMBLCDSs dataset, extension of the Sequence Version Archive functionality and the revision of quality rules for TPA data

EMBL Nucleotide Sequence Database: developments in 2005

The EMBL Nucleotide Sequence Database () at the EMBL European Bioinformatics Institute, UK, offers a comprehensive set of publicly available nucleotide sequence and annotation, freely accessible to all. Maintained in collaboration with partners DDBJ and GenBank, coverage includes whole genome sequencing project data, directly submitted sequence, sequence recorded in support of patent applications and much more. The database continues to offer submission tools, data retrieval facilities and user support. In 2005, the volume of data offered has continued to grow exponentially. In addition to the newly presented data, the database encompasses a range of new data types generated by novel technologies, offers enhanced presentation and searchability of the data and has greater integration with other data resources offered at the EBI and elsewhere. In stride with these developing data types, the database has continued to develop submission and retrieval tools to maximise the information content of submitted data and to offer the simplest possible submission routes for data producers. New developments, the submission process, data retrieval and access to support are presented in this paper, along with links to sources of further information

A Possible Mechanism for Evading Temperature Quantum Decoherence in Living Matter by Feshbach Resonance

A new possible scenario for the origin of the molecular collective behaviour associated with the emergence of living matter is presented. We propose that the transition from a non-living to a living cell could be mapped to a quantum transition to a coherent entanglement of condensates, like in a multigap BCS superconductor. Here the decoherence-evading qualities at high temperature are based on the Feshbach resonance that has been recently proposed as the driving mechanism for high Tc superconductors. Finally we discuss how the proximity to a particular critical point is relevant to the emergence of coherence in the living cell

Plasmid-mediated restriction evasion mechanisms

Plasmid ColIb-P9 (Incll) encodes mechanisms which allow it to avoid destruction by type I and type II restriction enzymes during transfer by conjugation between strains of Escherichia coli. A genetic system was developed to analyse these mechanisms. The system relied on measuring Collb-mediated rescue of the restriction-sensitive plasmid R751 (IncPp) from destruction by EcoKI (type I) and EcoRI (type II). One Collb mechanism was known to involve a plasmid-encoded antirestriction gene known as ardA, the product of which is active against type I enzymes. Tests for alleviation of EcoKI restriction of R751, showed strong protection by a co-transferring Collb (Ard+) plasmid, slight protection when Collb was resident in the recipient and no effect when Collb was immobilised in the donor by removal of its nic site. Hence, expression of ardA is activated in the recipient cell following transfer no detectable transfer of the ArdA protein occurs from the donor to the recipient. The ardA gene is found in the leading region of Collb, which is defined as the first segment of the plasmid to enter the recipient cell during conjugation. Nucleotide sequencing of 11.7 kb of this region identified ten open reading frames. Furthermore, the region also contains three dispersed repeat sequences homologous to a novel single-stranded DNA promoter described by Masai and Arai (1997, Cell 89, 897-907). It is proposed that these secondary structures form in the transferring T-strand of Collb and function as promoters for transcription of genes encoded on the unique plasmid strand transferred during conjugation. Another mechanism, which acts independently of ardA, alleviates restriction of both type I and type II enzymes in the recipient in second or subsequent rounds of transfer. Two separate mechanisms appear to be operating since alleviation of type I restriction occurs in trans and is constitutive. In contrast, alleviation of type II restriction is by a czs-acting mechanism. The 'substrate saturation' hypothesis, whereby increasing amounts of transferred DNA saturates the restriction system (Read et al. 1992, Mol Microbiol 6, 1933-1941) is ruled out by data presented

EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res., 35, D16–D20. ...................................................................................................................................................................................

ABSTRACT The EMBL Nucleotid

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<p><b>Copyright information:</b></p><p>Taken from "EMBL Nucleotide Sequence Database in 2006"</p><p>Nucleic Acids Research 2006;35(Database issue):D16-D20.</p><p>Published online 05 Dec 2006</p><p>PMCID:PMC1897316.</p><p>© 2006 The Author(s)</p> Using the same geographical information, SRS views of EMBL entries link data to googlemaps