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).
Nomenclature of 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).
Nomenclature of Viruses
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. 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.
Nomenclature of Bacteria
Binary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), should be used for all bacteria. 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; strain designations and numbers are not.
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.
When appropriate for viral genetic systems, use the recommendations of Demerec et al. (Genetics 54:61-76, 1966) as a guide.
(i) Phenotype designations must be employed when mutant loci have not been identified or mapped. They can also be used to identify the protein product of a gene, e.g., the OmpA protein. Phenotype designations generally consist of three-letter symbols; these are not italicized and the first letter of the symbol is capitalized. It is preferable to use Roman or Arabic numerals (instead of letters) to identify a series of related phenotypes. Thus, a series of bacteriocin-tolerant mutants might be designated TolI, TolII, and TolIII, etc., or a series of nucleic acid polymerase mutants might be designated Pol1, Pol2, and Pol3, etc. Wild-type characteristics can be designated Tol+ or Pol+, and, when necessary for clarity, negative superscripts (Tol– Pol–) can be used to designate mutant characteristics. Lowercase superscript letters may be used to further delineate phenotypes (e.g., Strr for streptomycin resistance). Phenotype designations should be defined.
(ii) Genotype designations are also indicated by three-letter locus symbols. These are lowercase italic (e.g., pol src). If several loci govern related functions, these are distinguished by italicized capital letters following the locus symbol.
(iii) Wild-type alleles are indicated with a superscript plus (ara+ his+). A superscript minus is not used to indicate a mutant locus; thus, one refers to an ara mutant rather than an ara– strain.
(iv) The rules for genetic nomenclature of viruses (phages) differ from those of bacteria. As a general rule, the entire description of a virus is italicized, including the designations am or sus (amber suppressible) and ts (temperature sensitive). Superscripts are employed to indicate hybrid genomes. Genetic symbols may be one, two, or three letters. For example, a mutant strain of λ might be designated λ cI857 int2 red114 susA11; this strain carries mutations in genes cI, int, and red and a suppressible (sus) mutation in gene A. A strain designated λ imm21 att434 would represent a hybrid of phage λ that carries the immunity (imm) region of phage 21 and the attachment (att) region of phage 434. Host DNA insertions into viruses should be delineated by square brackets, and the genetic symbols and designations for such inserted DNA should conform to those employed for the host genome. Genetic symbols for phage λ can be found in reports by Echols and Murialdo (Microbiol Rev 42:577-591, 1978) and Szybalski and Szybalski (Gene 7:217-270, 1979).
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." ASM style preserves 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.