NOMENCLATURE
Chemical and Biochemical Nomenclature
The recognized authority for the names of chemical compounds is Chemical Abstracts (CAS) and its indexes. The Merck Index Online (https://www.rsc.org/merck-index) is also an excellent source. For guidelines on the use of biochemical terminology, consult Biochemical Nomenclature and Related Documents (Portland Press, London, United Kingdom, 1992) and the Instructions to Authors of the Journal of Biological Chemistry and the Archives of Biochemistry and Biophysics.
For enzymes, use the recommended (trivial) name assigned by the Nomenclature Committee of the International Union of Biochemistry (IUB) as described in Enzyme Nomenclature (Academic Press, Inc., New York, NY, 1992) and its supplements and at https://www.qmul.ac.uk/sbcs/iubmb/enzyme/. If a nonrecommended name is used, place the proper (trivial) name in parentheses at first use in the abstract and text. Use the EC number when one has been assigned. Authors of papers describing enzymological studies should review the standards of the STRENDA Commission for information required for adequate description of experimental conditions and for reporting enzyme activity data.
Nomenclature of Prokaryotes, Eukaryotes, and Viruses
When the announcement describes the genome of a recognized bacterial species, binary names, consisting of a generic name and a specific epithet (e.g., Saccharomyces cerevisiae), must be used. For resources describing genome data from a species that is unculturable and cannot be maintained in a culture collection, the nomenclature "Candidatus" preceding the genus name is recommended. Names of categories at or above the genus level may be used alone, but specific and subspecific epithets may not. A specific epithet must be preceded by a generic name, written out in full the first time it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital letter (e.g., S. cerevisiae), provided there can be no confusion with other genera used in the paper. Names of all bacterial taxa (kingdoms, phyla, classes, orders, families, genera, species, and subspecies) are printed in italics and should be italicized in the manuscript; strain designations and numbers are not. The spelling of bacterial names should follow the Approved List of Bacterial Names (Amended) & Index of the Bacterial and Yeast Nomenclatural Changes (V. B. D. Skerman et al., ed., American Society for Microbiology, Washington, DC, 1989) and the validation lists and notification lists published in the International Journal of Systemic 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: Prokaryotic Nomenclature Up-to-Date and List of Prokaryotic Names with Standing in Nomenclature.
Since the classification of fungi is far from complete, it is the responsibility of the author to determine the accepted binomial for a given organism. Sources for these names include The Yeasts: a Taxonomic Study, 5th ed. (C. P. Kurtzman, J. W. Fell, and T. Boekhout, ed., Elsevier Science, Amsterdam, Netherlands, 2011), and Dictionary of the Fungi, 10th ed. (P. M. Kirk, P. F. Cannon, D. W. Minter, and J. A. Stalpers, ed., CABI International, Wallingford, Oxfordshire, United Kingdom, 2008); see also http://www.speciesfungorum.org/Names/Fundic.asp. Names used for viruses should be those approved by the International Committee on Taxonomy of Viruses (ICTV) and reported on the ICTV Virus Taxonomy website (https://talk.ictvonline.org/). 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, as with 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.
Microbial strains, viruses, and plasmids should be given individual designations consisting of letters and serial numbers.
It is generally advisable to include a worker's initials or a descriptive symbol of locale or laboratory, etc., in the designation. Each new strain, mutant, isolate, or derivative should be given a new (serial) designation. This designation should be distinct from those of the genotype and phenotype, and genotypic and phenotypic symbols should not be included.
Genetic Nomenclature
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® (for prokaryotes), Molecular and Cellular Biology® (for eukaryotes), and the Journal of Virology® (for viruses). 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. 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.