NOMENCLATURE

Bacteria, Viruses, Enzymes

The spelling of bacterial names should follow the Approved Lists of Bacterial Names (Amended) & Index of the Bacterial and Yeast Nomenclatural Changes (V. B. D. Skerman et al., ed., ASM Press, Washington, DC, 1989) and the validation lists and notification lists published in the International Journal of Systematic and Evolutionary Microbiology (formerly the International Journal of Systematic Bacteriology) since January 1989. In addition, two sites on the World Wide Web list current approved bacterial names: Bacterial Nomenclature Up-to-Date (http://www.dsmz.de/microorganisms/main.php?contentleft_id=14) and List of Prokaryotic Names with Standing in Nomenclature (http://www.bacterio.cict.fr/). If there is reason to use a name that does not have standing in nomenclature, the name should be enclosed in quotation marks in the title and at its first use in the abstract and the text and an appropriate statement concerning the nomenclatural status of the name should be made in the text. "Candidatus" species should always be set in quotation marks.

Names used for viruses should be those approved by the International Committee on Taxonomy of Viruses (ICTV) and published in Virus Taxonomy: Classification and Nomenclature of Viruses, Seventh Report of the International Committee on Taxonomy of Viruses (M. H. V. van Regenmortel et al., ed., Academic Press, San Diego, CA, 2000). In addition, the recommendations of the ICTV regarding the use of species names should generally be followed: when the entire species is discussed as a taxonomic entity, the species name, like other taxa, is italic and has the first letter and any proper nouns capitalized (e.g., Tobacco mosaic virus, Murray Valley encephalitis virus). When the behavior or manipulation of individual viruses is discussed, the vernacular (e.g., tobacco mosaic virus, Murray Valley encephalitis virus) should be used. If desired, synonyms may be added parenthetically when the name is first mentioned. Approved generic (or group) and family names may also be used.

For enzymes, use the recommended (trivial) name assigned by the Nomenclature Committee of the IUB as described in Enzyme Nomenclature (Academic Press, Inc., New York, NY, 1992) and at http://www.chem.qmul.ac.uk/iubmb/enzyme/.

For nomenclature of restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes, refer to the article by Roberts et al. (Nucleic Acids Res. 31:1805-1812, 2003).

Genetic nomenclature should essentially follow the recommendations of Demerec et al. (Genetics 54:61-76, 1966) and those given in the instructions to authors of the Journal of Bacteriology, Molecular and Cellular Biology, and Eukaryotic Cell (January issues). To facilitate accurate communication, it is important that standard genetic nomenclature be used whenever possible and that deviations or proposals for new naming systems be endorsed by an appropriate authoritative body. Review and/or publication of submitted manuscripts that contain new or nonstandard nomenclature may be delayed by the editor or the Journals Department so that they may be reviewed by the Genetics and Genomics Committee of the ASM Publications Board.

Before submission of manuscripts, authors may direct questions on genetic nomenclature to the committee's chairman: Maria Costanzo (maria{at}genome.stanford.edu). Such a consultation should be mentioned in the manuscript submission letter.

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