NOMENCLATURE
Chemical and Biochemical Nomenclature
The recognized authority for the names of chemical compounds is Chemical Abstracts (CAS; http://www.cas.org/) and its indexes. The Merck Index Online (https://www.rsc.org/merck-index) is also an excellent source. For biochemical terminology, including abbreviations and symbols, consult Biochemical Nomenclature and Related Documents (Portland Press, London, United Kingdom, 1992), available at http://www.sbcs.qmul.ac.uk/iupac/bibliog/white.html, 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 http://www.sbcs.qmul.ac.uk/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 (http://www.beilstein-institut.de/en/projects/strenda/guidelines).
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).
Drugs
Whenever possible, use generic names of drugs; the use of trade names is not permitted.
Nomenclature of Microorganisms
Binary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), must be used for all microorganisms. 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., E. coli), provided there can be no confusion with other genera used in the paper. Names of all 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. Vernacular (common) names should be in lowercase roman type (e.g., streptococcus, brucella). For Salmonella, genus, species, and subspecies names should be rendered in standard form: Salmonella enterica at first use, S. enterica thereafter; Salmonella enterica subsp. arizonae at first use, S. enterica subsp. arizonae thereafter. Names of serovars should be in roman type with the first letter capitalized: Salmonella enterica serovar Typhimurium. After the first use, the serovar may also be given without a species name: Salmonella Typhimurium, S. Typhimurium, or Salmonella serovar Typhimurium. For other information regarding serovar designations, see Antigenic Formulae of the Salmonella Serovars, 9th ed. (P. A. D. Grimont and F.-X. Weill, WHO Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur, Paris, France, 2007); see http://www.scacm.org/free/Antigenic%20Formulae%20of%20the%20Salmonella%20Serovars%202007%209th%20edition.pdf. For a summary of the current standards for Salmonella nomenclature and the Kaufmann-White criteria, see the article by Brenner et al. (J Clin Microbiol 38:2465-2467, 2000), the opinion of the Judicial Commission of the International Committee on Systematics of Prokaryotes (Int J Syst Evol Microbiol 55:519-520, 2005), and the article by Tindall et al. (Int J Syst Evol Microbiol 55:521-524, 2005).
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., American Society for Microbiology, 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: Prokaryotic Nomenclature Up-to-Date (https://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html) and List of Prokaryotic Names with Standing in Nomenclature (http://www.bacterio.net/). 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.
For guidelines regarding new names and descriptions of new genera and species, see the articles by Tindall (Int J Syst Bacteriol 49:1309-1312, 1999) and Stackebrandt et al. (Int J Syst Evol Microbiol 52:1043-1047, 2002). To validate new names and/or combinations, authors must submit three copies of their published article to the International Journal of Systematic and Evolutionary Microbiology.
It is recommended that a strain be deposited in at least two recognized culture collections in different countries when that strain is necessary for the description of a new taxon (Int J Syst Evol Microbiol 50:2239-2244, 2000).
Since the classification of fungi is not 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.
Microorganisms, viruses, and plasmids should be given 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 italicized genotypic and phenotypic symbols should not be included. Plasmids are named with a lowercase "p" followed by the designation in uppercase letters and numbers. To avoid the use of the same designation as that of a widely used strain or plasmid, check the designation against a publication database such as Medline.
Genetic Nomenclature
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.
Bacteria. The genetic properties of bacteria are described in terms of phenotypes and genotypes. The phenotype describes the observable properties of an organism. The genotype refers to the genetic constitution of an organism, usually in reference to some standard wild type. Use the recommendations of Demerec et al. (Genetics 54:61-76, 1966) as a guide to the use of these terms. If your manuscript contains information including genetic nomenclature, please refer to the Instructions to Authors of the Journal of Bacteriology.
“Mutant” versus “mutation.” Keep in mind the distinction between a mutation (an alteration of the primary sequence of the genetic material) and a mutant (a strain carrying one or more mutations). One may speak about the mapping of a mutation, but one cannot map a mutant. Likewise, a mutant has no genetic locus, only a phenotype.
“Homology” versus “similarity.” For use of terms that describe relationships between genes, consult the articles by Theissen (Nature 415:741, 2002) and Fitch (Trends Genet 16:227-231, 2000). “Homology” implies a relationship between genes that have a common evolutionary origin; partial homology is not recognized. When sequence comparisons are discussed, it is more appropriate to use the term "percent sequence similarity" or “percent sequence identity,” as appropriate.
Tetracycline resistance determinants. The nomenclature for tetracycline resistance determinants is based on the proposal of Levy et al. (Antimicrob Agents Chemother 43:1523-1524, 1999). The style for such determinants is, e.g., Tet B; the space helps distinguish the determinant designation from that for phenotypes and proteins (TetB). The above-referenced article also gives the correct format for genes, proteins, and determinants in this family.
Locus tags. Locus tags are systematic, unique identifiers that are assigned to each gene in GenBank. All genes mentioned in a manuscript should be traceable to their sequences by the reader, and locus tags may be used for this purpose in manuscripts to identify uncharacterized genes. In addition, authors should check GenBank to make sure that they are using the correct, up-to-date format for locus tags (e.g., uppercase versus lowercase letters and the presence or absence of an underscore, etc.). Locus tag formats vary between different organisms and also may be updated for a given organism, so it is important to check GenBank at the time of manuscript preparation.
Viruses. The genetic nomenclature for viruses differs from that for bacteria. In most instances, viruses have no phenotype, since they have no metabolism outside host cells. Therefore, distinctions between phenotype and genotype cannot be made. Superscripts are used to indicate hybrid genomes. Genetic symbols may be one, two, or three letters.
Eukaryotes. FlyBase (http://flybase.org/) is the genetic nomenclature authority for Drosophila melanogaster. WormBase (http://www.wormbase.org/#01-23-6) is the genetic nomenclature authority for Caenorhabditis elegans. When naming genes for Aspergillus species, the nomenclature guidelines posted at http://www.aspergillusgenome.org/Nomenclature.shtml should be followed, and the Aspergillus Genome Database (http://www.aspgd.org/) should be searched to ensure that any new name is not already in use. The Saccharomyces Genome Database (https://www.yeastgenome.org/) and the Candida Genome Database (http://www.candidagenome.org/) are authorities for Saccharomyces cerevisiae and Candida albicans genetic nomenclature, respectively. For more information about the genetic nomenclature of eukaryotes, see the Instructions to Authors for Molecular and Cellular Biology.