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SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities.

Martínez-García E, Aparicio T, Goñi-Moreno A, Fraile S, de Lorenzo V - Nucleic Acids Res. (2014)

Bottom Line: By adopting simple compositional rules, the SEVA standard facilitates combinations of functional DNA segments that ease both the analysis and the engineering of diverse Gram-negative bacteria for fundamental or biotechnological purposes.The large number of users of the SEVA-DB during its first two years of existence has resulted in a valuable feedback that we have exploited for fixing DNA sequence errors, improving the nomenclature of the SEVA plasmids, expanding the vector collection, adding new features to the web interface and encouraging contributions of materials from the community of users.The SEVA platform is also adopting the Synthetic Biology Open Language (SBOL) for electronic-like description of the constructs available in the collection and their interfacing with genetic devices developed by other Synthetic Biology communities.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain.

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The formatted structure of SEVA plasmids. SEVA vectors are shaped by three basic modules: a cargo (blue), a plasmid replication origin (green) and an antibiotic marker (magenta). Restriction sites that punctuate the boundaries between modules in all constructs are indicated. Note the numbering position +1 of the DNA sequence is the first T of the unique PacI site. The directionality of the stronger transcription flow in the genetic device engineered in the cargo and the preferred site for inserting functional gadgets are indicated. See http://seva.cnb.csic.es for details.
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Figure 1: The formatted structure of SEVA plasmids. SEVA vectors are shaped by three basic modules: a cargo (blue), a plasmid replication origin (green) and an antibiotic marker (magenta). Restriction sites that punctuate the boundaries between modules in all constructs are indicated. Note the numbering position +1 of the DNA sequence is the first T of the unique PacI site. The directionality of the stronger transcription flow in the genetic device engineered in the cargo and the preferred site for inserting functional gadgets are indicated. See http://seva.cnb.csic.es for details.

Mentions: Once faced with the general structure of the SEVA vectors (Figure 1), users can easily decide what is the best configuration of replication origin, antibiotic resistance and business segment (cargo) that serves better their specific purposes. The visual web interface has been reshaped to make it more intuitive and user-friendly, and it also contains more entries/tabs, the contents of which are explained below. The most salient changes or improvements of the SEVA-DB 2.0 in respect to its earlier form are examined in the following paragraphs. Any other features of the platform not explicitly indicated as a change can be safely considered to be identical to the first complete description of the system as published in (1). The web curators regularly update new acquisitions and information and, to the best of their abilities, aim at maintaining an interactive and dynamic platform in real time. Most clones are readily constructed and ready for release upon request.


SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities.

Martínez-García E, Aparicio T, Goñi-Moreno A, Fraile S, de Lorenzo V - Nucleic Acids Res. (2014)

The formatted structure of SEVA plasmids. SEVA vectors are shaped by three basic modules: a cargo (blue), a plasmid replication origin (green) and an antibiotic marker (magenta). Restriction sites that punctuate the boundaries between modules in all constructs are indicated. Note the numbering position +1 of the DNA sequence is the first T of the unique PacI site. The directionality of the stronger transcription flow in the genetic device engineered in the cargo and the preferred site for inserting functional gadgets are indicated. See http://seva.cnb.csic.es for details.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383931&req=5

Figure 1: The formatted structure of SEVA plasmids. SEVA vectors are shaped by three basic modules: a cargo (blue), a plasmid replication origin (green) and an antibiotic marker (magenta). Restriction sites that punctuate the boundaries between modules in all constructs are indicated. Note the numbering position +1 of the DNA sequence is the first T of the unique PacI site. The directionality of the stronger transcription flow in the genetic device engineered in the cargo and the preferred site for inserting functional gadgets are indicated. See http://seva.cnb.csic.es for details.
Mentions: Once faced with the general structure of the SEVA vectors (Figure 1), users can easily decide what is the best configuration of replication origin, antibiotic resistance and business segment (cargo) that serves better their specific purposes. The visual web interface has been reshaped to make it more intuitive and user-friendly, and it also contains more entries/tabs, the contents of which are explained below. The most salient changes or improvements of the SEVA-DB 2.0 in respect to its earlier form are examined in the following paragraphs. Any other features of the platform not explicitly indicated as a change can be safely considered to be identical to the first complete description of the system as published in (1). The web curators regularly update new acquisitions and information and, to the best of their abilities, aim at maintaining an interactive and dynamic platform in real time. Most clones are readily constructed and ready for release upon request.

Bottom Line: By adopting simple compositional rules, the SEVA standard facilitates combinations of functional DNA segments that ease both the analysis and the engineering of diverse Gram-negative bacteria for fundamental or biotechnological purposes.The large number of users of the SEVA-DB during its first two years of existence has resulted in a valuable feedback that we have exploited for fixing DNA sequence errors, improving the nomenclature of the SEVA plasmids, expanding the vector collection, adding new features to the web interface and encouraging contributions of materials from the community of users.The SEVA platform is also adopting the Synthetic Biology Open Language (SBOL) for electronic-like description of the constructs available in the collection and their interfacing with genetic devices developed by other Synthetic Biology communities.

View Article: PubMed Central - PubMed

Affiliation: Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain.

Show MeSH