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.chem.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.chem.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).
Amino Acid Sequences
Single-letter designations, rather than three-letter designations, should be used for sequences of amino acids.
Drugs
Chemical or generic names of drugs should be used; the use of code numbers or trade names is generally not permitted.
Nomenclature of Microorganisms
Binary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), should 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 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. 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 (http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html) and the 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.
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.
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 genotypic and phenotypic symbols should not be included.
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.
Mice. For mouse strain and genetic nomenclature, ASM encourages authors to refer to the guidelines set forth by the International Committee on Standardized Genetic Nomenclature for Mice, available on the Mouse Genome Informatics home page at http://www.informatics.jax.org/ and in Genetic Variants and Strains of the Laboratory Mouse, 3rd ed. (M. F. Lyon et al., ed., Oxford University Press, Oxford, England, 1996).
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.
Conventions for naming genes. It is recommended that (entirely) new genes be given names that are mnemonics of their function, avoiding names that are already assigned and earlier or alternative gene names, irrespective of the bacterium for which such assignments have been made. Similarly, it is recommended that, whenever possible, orthologous genes present in different organisms receive the same name. When homology is not apparent or the function of a new gene has not been established, a provisional name may be given by one of the following methods. (i) The gene may be named on the basis of its map location in the style yaaA, analogous to the style used for recording transposon insertions (zef) as discussed below. A list of such names in use for E. coli has been published by Rudd (Microbiol Mol Biol Rev 62:985-1019, 1998). (ii) A provisional name may be given in the style described by Demerec et al. (e.g., usg, gene upstream of folC). Such names should be unique, and names such as orf or genX should not be used. For reference, the Coli Genetic Stock Center's database includes an updated listing of E. coli gene names and gene products. It is accessible on the Internet (http://cgsc.biology.yale.edu/index.php). A list can also be found in the work of Riley (Microbiol Rev 57:862-952, 1993). For the genes of other bacteria, consult the references given above. For prokaryotes, gene names should not begin with prefixes indicating the genus and species from which the gene is derived. However, subscripts may be used where necessary to distinguish between genes from different organisms or strains. For eukaryotes, such prefixes may be used for clarity when discussing genes with the same name from two different organisms (e.g., ScURA3 versus CaURA3); the prefixes are not considered part of the gene name proper and are not italicized.
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. 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.
"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.
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 (http://www.yeastgenome.org/) and the Candida Genome Database (http://www.candidagenome.org/) are authorities for Saccharomyces cerevisiae and Candida albicans genetic nomenclature, respectively. For information about the genetic nomenclature of other eukaryotes, see the Instructions to Authors for Molecular and Cellular Biology.
Transposable elements, plasmids, and restriction enzymes. Nomenclature of transposable elements (insertion sequences, transposons, and phage Mu, etc.) should follow the recommendations of Campbell et al. (Gene 5:197-206, 1979), with the modifications given in the Instructions to Authors of the Journal of Bacteriology. The Internet site where insertion sequences of eubacteria and archaea are described and new sequences can be recorded is http://www-is.biotoul.fr//.
The system of designating transposon insertions at sites where there are no known loci, e.g., zef-123::Tn5, has been described by Chumley et al. (Genetics 91:639-655, 1979). Whenever possible, use the nomenclature recommendations of Novick et al. (Bacteriol Rev 40:168-189, 1976) for plasmids and plasmid-specified activities, of Low (Bacteriol Rev 36:587-607, 1972) for F' factors, and of Roberts et al. (Nucleic Acids Res 31:1805-1812, 2003) for restriction enzymes, DNA methyltransferases, homing nucleases, and their genes. The nomenclature for recombinant DNA molecules constructed in vitro follows the nomenclature for insertions in general. DNA inserted into recombinant DNA molecules should be described by using the gene symbols and conventions for the organism from which the DNA was obtained.
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). Table 2 of the above-referenced article shows the correct format for genes, proteins, and determinants in this family.