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, 14th ed. (Merck & Co., Inc., Whitehouse Station, NJ, 2006), is also an excellent source. For guidelines to the use of biochemical terminology, 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 (first issues of each year).

Do not express molecular weight in daltons; molecular weight is a unitless ratio. Molecular mass is expressed in daltons.

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 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, and express enzyme activity either in katals (preferred) or in the older system of micromoles per minute.

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 Database 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 Microorganisms

Binary names, consisting of a generic name and a specific epithet (e.g., Saccharomyces cerevisiae), 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., S. cerevisiae), 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 (or underlined) in the manuscript; strain designations and numbers are not.

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/).

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, 4th ed. (C. P. Kurtzman and J. W. Fell, ed., Elsevier Science Publishers B.V., Amsterdam, The Netherlands, 1998) and Ainsworth and Bisby's Dictionary of the Fungi, 9th ed. (P. M. Kirk, P. F. Cannon, J. C. David, and J. A. Stalpers, ed., CABI Publishing, Wallingford, Oxfordshire, United Kingdom, 2001); 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 published in Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses (C. M. Fauquet et al., ed., Elsevier Academic Press, San Diego, CA, 2005). 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 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

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.

Eukaryotes. The nomenclature used for the genetics of lower eukaryotic microorganisms has not been as well formalized as that for bacteria and bacteriophages. Generally, authors should conform to current practices in identifying mutants and their genotypes. For organisms not mentioned below, it is advisable to consult the Handbook of Microbiology, 2nd ed. (A. I. Laskin and H. A. Lechevalier, ed., CRC Press, Boca Raton, FL, 1988) or the Handbook of Genetics, vol. 1, Bacteria, Bacteriophages, and Fungi (R. C. King, ed., Plenum Publishing Corp., New York, NY, 1974).

Gene names may begin with prefixes to indicate the genus and species from which the gene is derived only when needed 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.

The genetic nomenclature of Dictyostelium is summarized in the Trends in Genetics "Genetic Nomenclature Guide" (p. S.5-S.6; Elsevier Science Ltd., Cambridge, United Kingdom, 1998; out of print). The most recent modifications can be found at http://dictybase.org/GeneNames.html.

For Saccharomyces cerevisiae, a gene name should always be indicated in italics and, for the wild-type locus (or dominant alleles), capital letters (e.g., URA3). Loss-of-function (hypomorphic) or altered-function (neomorphic) alleles of the same locus should always be indicated in italics and lowercase letters (e.g., ura3). The product of a gene (i.e., a protein) should be indicated in roman type with an initial capital letter (e.g., Ura3). There is generally no need to add the suffix "p" to the symbol for a protein; however, in rare instances where it may be deemed necessary to indicate unambiguously that the symbol refers to a protein, the "p" suffix may be added (e.g., Ura3p). For the most recent information on S. cerevisiae gene names, consult the Saccharomyces Genome Database (SGD) at http://www.yeastgenome.org/. Details on the format of S. cerevisiae locus and allele designations are provided in the SGD and are also described by Cherry (Trends Genet. March:11-12, 1995) (available for download as a PDF file at SGD, http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf). Authors should use standard S. cerevisiae gene names, as listed in the SGD, in their submitted manuscripts and register new gene names with the SGD no later than the modification stage.

The most recent information for Neurospora crassa can be found in The Neurospora Compendium: Chromosomal Loci (D. R. Perkins et al., Academic Press, San Diego, CA, 2001), and that for Aspergillus spp. can be found at http://www.fgsc.net/nomenclature.htm. The 1998 Trends in Genetics "Genetic Nomenclature Guide" (Elsevier Science Ltd., Cambridge, United Kingdom; out of print) contains nomenclature guidelines for several eukaryotic microbes: Schizosaccharomyces pombe (p. S.7-S.9), Chlamydomonas reinhardtii (p. S.18-S.19), Neurospora crassa (p. S.14-S.15), and Aspergillus nidulans (p. S.12-S.13). In addition, for S. pombe, the websites http://www.sanger.ac.uk/Projects/S_pombe/SP_Name_FAQ.shtml and http://www-rcf.usc.edu/forsburg/plasmids.html#nomenclature may be helpful, and for C. reinhardtii, use http://www.chlamy.org/chlamydb.html.

For Trypanosoma and Leishmania, consult the article by Clayton et al. (Mol. Biochem. Parasitol. 97:221-224, 1998).

For the most recent information on Candida albicans, consult the Candida Genome Database (CGD) at http://www.candidagenome.org. Details on the format of C. albicans gene nomenclature are described at http://www.candidagenome.org/Nomenclature.shtml. Authors should use standard C. albicans gene names, as listed in the CGD, in their submitted manuscripts and should register new gene names with the CGD no later than the modification stage.

Prokaryotes. The genetic properties of prokaryotes 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 genetic nomenclature, please refer to the Instructions to Authors in the January issue of the Journal of Bacteriology.

Viruses. In most cases, viruses have no phenotype, since they have no metabolism outside host cells. Therefore, distinctions between phenotype and genotype are not made. Superscripts are used to indicate hybrid genomes. Genetic symbols may be one, two, or three letters. For example, a mutant strain of lambda may be designated cI857 int2 red114 Aam11; this strain carries mutations in genes cI, int, and red and an amber-suppressible (am) mutation in gene A. 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 used for the host genome.

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 organism 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, the GenBank locus tag may be used to designate the gene; it should not be 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. However, since locus tags are not genetic names, they should appear in roman type rather than in italics. 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 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.

"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.

"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.

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 referred to in the Instructions to Authors in the Journal of Bacteriology.

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). 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 endonucleases, 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.

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