key: cord-0789959-2ojxucuo authors: nan title: Chapter 12 Style and Usage for Life Science date: 2009-12-31 journal: The Manual of Scientific Style DOI: 10.1016/b978-012373980-3.50016-2 sha: 5fc600260250201e9cfb2d40e6f5b3bc95d24c8d doc_id: 789959 cord_uid: 2ojxucuo Publisher Summary This chapter provides guidelines for manuscript preparation of life science journals. The rules for writing in life science are consistent with those in earth and environmental sciences and medical science. As with all scientific writing, it is important to research the specific needs and preferences of the journal to which the manuscript is being sent. This will not only ease the writing process, but will also increase the chances of publication. This chapter explains biochemical nomenclature and abbreviations used in life science. In addition, it includes a list of preferred units in the life sciences. In scientific writing, especially in the United States, articles dealing with life science issues are appearing much less frequently than those in other scientific disciplines. Chapter 12. Style and Usage for Life Science he rules for writing in life science are consistent with those in earth and environmental sciences and medical science (see Chapters 11 and 13, respectively, as well as Chapter 2 for basic information on manuscript preparation). As with all scientific writing, it is important to research the specific needs and preferences of the journal to which the manuscript is being sent. This will not only ease the writing process, but will also increase the chances of publication. In scientific writing, especially in the United States, articles dealing with life science issues are appearing much less frequently than those in other scientific disciplines. Because of this, it is important that writing in this field should be as concise and readable as possible. Articles written in this way, will not only have a higher chance of publication, but will also be more accessible and understandable to readers based in other scientific fields of study. Life science journal articles will usually contain a summary (in addition to an abstract) or a basic introduction to the piece, separate from the actual text, Summaries, along with the actual title of the article, are scanned for keywords for the purposing of indexing. Many articles (even in professional journals) are made available to the general public. Therefore, titles and summaries should be free of any abbreviations, acronyms, and measures with which those not within the field would be unfamiliar. A section describing research methods is usually included in a separate section at the end of the manuscript; in life science, however, if this section is brief, it may be omitted and described within the actual text. Descriptions of methods that have already been published may also be omitted and, a reference may be cited in its place. In life science writing, it is important to use the correct taxonomic terms and nomenclature within a document. This is especially true, when these terms are used within the title and the abstract of the manuscript. As previously stated, keywords in the title and abstract are weighed more heavily than those in the rest of the text. These keywords are then used to index the article for its journal. If incorrect terms or unfamiliar or improper abbreviations are used in the title or abstract the article may not be properly indexed, or it may not be indexed at all. This will cause serious obstacles in your audience obtaining, reading, and learning from your document. If papers contain taxonomy and nomenclature of newly discovered species, authors should be aware that it is possible for third parties to exploit the prior publication of nomenclature at any time between an online posting and the print publication date within a journal. Journals will not take responsibility for assertions of priorities in the cases of manuscripts it publishes, if they have previously appeared in the public domain as online posts or preprints. It is therefore particularly important in this field that the first publication of original research is in a peerreviewed journal. When creating any new nomenclatures or taxonomic ranks, one must adhere to the rules and principles established by the governing code in their specific field. For example, when naming plant life and fungi, authors should follow the International Code of Botanical Nomenclature (ICBN); for animals, authors should follow the International Commission on Zoological Nomenclature (ICZN); for bacteria, follow the International Code of Nomenclature of Bacteria (ICNB); and for viruses, the International Committee on Taxonomy for Viruses (ICTV). These codes are set forth in order to promote uniformity, accuracy, and stability in the nomenclature of new species. Since codes are updated every few years, authors should be aware of any new or revised guidelines before publishing new nomenclature. In order for new nomenclature or taxonomic ranks to be valid, they must be approved and published with their specific code. Concentration of uridine in plasma was elevated. iii. Designating nucleotide sequences. Nitrogenous bases and nucleosides can be designated by one-letter abbreviations when indicating the sequences of bases. The telomere DNA sequence in humans is GGGTTA. By convention, nucleotide sequences start (on the left) at the 5 end and finish (on the right) at the 3 end. Codon triplets can be indicated by placing a space every 3 base pairs. GCA TTA ACC GGT AGA TAC GCA iv. Designations for nucleotide length. DNA sequence length is designated in base pairs, which can be abbreviated as bp when used as a unit in written text. Abbreviate kilobases as kb and megabases as Mb. The enzyme recognizes a 6 bp sequence. The plasmid is 3.4 kb in length. C. elegans has a genome of 97 Mb. Nucleotide length can be indicated by using the suffix -mer. The primer consisting of 22 nucleotides is a 22mer. v. Designating nucleotide mutations. iii. Designating protein sequences. When presenting protein sequences, use either the three-letter or the one-letter abbreviations for amino acids. When three-letter symbols are used to represent polypeptides, a hyphen between amino acids indicates a peptide bond. When one-letter symbols are used, a hyphen between amino acids is not necessary. Met-Glu-Ala-Thr-Arg-Arg-Arg-Gln-His-Leu-Gly-Ala-Thr MEATRRRQHLGAT iv. Naming proteins. The word protein, as well as names of proteins, should be written as common nouns in lowercase. Abbreviations for proteins must be defined when used. multidrug resistance protein (MDR) Krüppel-like factor 6 (KLF6) v. Amino acid mutations. Amino acid sequence mutations may be represented in shorthand form in either 3-letter or 1-letter notation. A histidine to glutamine amino acid mutation would be designated as follows: His527Gln H527Q vi. Transfer RNAs. The type of transfer RNA (tRNA) may be specified based on its amino acid attachment. Abbreviations are often used when naming sugars and carbohydrates, especially those that are lengthy with substituted carbons. An example of three-letter abbreviations for parent aldoses is given below. Fatty acids can be designated in shorthand by their number of carbons and their number of double bonds, separated by a colon. If the number of carbons and double bonds is the same between two or more different fatty acids, the positions of the double bonds is added in parentheses. 20:4(8,11,14,17) eicosatetraenoic acid 20:4(5,8,11,14) arachidonic acid A fatty acid radical is indicated by adding "acyl" in parentheses. 18:2(acyl) acyl radical of linoleic acid 480 (1) Human chromosomes are autosomal chromosomes numbered 1 through 22, or sex chromosomes designated X or Y. (2) The chromosome number is followed by the arm designation: p for the short arm of the chromosome, or q for the long arm. (3) The arm designation is followed by the region number (1 to 4), which specifies a region on the chromosomal arm. (4) The region number is followed by the band number, a period, the subband number, and, when applicable, the sub-subband number. 7q32.31 7 = chromosome number q = long arm 32 = region 3, band 2 31 = subband 3, sub-subband 1 ii. Dimensional units for chromosomes. The unit for distances between genetic loci on a chromosome is the centimorgan (cM). iii. Designations for anonymous DNA sequences. Anonymous DNA sequences are designated by D-number nomenclature and are named according to their chromosomal location, the sequence type, and the site. D4S7E DXF12S1 . D = anonymous DNA sequence D = anonymous DNA sequence 4 = chromosome 4 X = X chromosome S = unique sequence* F = family sequence* 7 = sequence number 12 = sequence number E = expressed sequence* S1 = site number 481 When describing chromosomal abnormalities, abnormal sex chromosomes are designated first, followed by abnormal autosomal chromosomes listed in numerical order. Karyotype designations may also indicate structural alterations in chromosomes. A single chromosomal rearrangement is indicated in the karyotype using a symbol that identifies the type of chromosomal alteration, followed by the chromosome number in parenthesis. If there has been a rearrangement of more than one chromosome, a semicolon separates the designations. For abbreviations used to indicate chromosomal rearrangements, see Section 12. Gene names most commonly describe the mutant phenotype or the protein encoded. Gene symbols are usually derived by shortening the original name or by using the initials of a multiword name. They are almost always italicized. Gene symbols followed by an additional letter or Arabic numeral indicate genes with different loci but similar phenotypes. BRCA1, BRCA2 (breast cancer genes) PFN1, PFN2 (profilin genes) ii. Alleles. Alleles are alternative forms of genes. They are often designated by the gene symbol followed by an asterisk, followed by the italicized allele designation. i. HLA nomenclature. Nomenclature guidelines for the human major histocompatibility complex are established by the World Health Organization Committee for Factors of the HLA System. Human major histocompatibility complex gene names begin with HLA-, followed by a locus symbol and designations for subregions or chains. ii. Symbols representing human retroviral genes. Human retroviral genes are italicized and have a variety of alphanumeric designations. Cell lines are commonly referred to by acronyms and should be defined at first mention. Abbreviations for radioactive isotopes should be defined when used for the first time. To indicate that the nonradioactive isotope is normally part of the compound, use brackets around the isotope symbol. For uniformly labeled compounds, write the abbreviation ul in parenthesis following the compound name. [ 14 C]glucose (ul) See Appendix G.000, for a complete list of taxonomy ranks and endings. i. Standard format for naming taxa. There are seven basic taxa: kingdom, phylum (or division), class, order, family, genus, and species. Any of these taxa can be prefixed by either sub-or super-to further extend the taxonomic categories. The names of taxa at the rank of family and above are written in plain roman type; names of taxa for genus and below are italicized. Names of taxa at the level of genus and above have an initial capital letter. When the taxonomic term precedes the name, the taxonomic term is written in lowercase, as in "kingdom Bacteria." Names of taxa at the rank of family and above are treated as plural, while names of taxa for genus and below are treated as singular. The family Micrococcaceae are… The genus Python is… ii. Standard format for scientific names. Only the names of taxa at the rank of genus and above may stand alone as monomials. Names of taxa at the level of species and below cannot stand alone and must be preceded by the genus name. The first letter of the genus name is capitalized, the species name is written in all lowercase letters, and the entire name is italicized. ii. Standards for scientific names. Using the name of a genus on its own suggests the genus as a whole. Streptococcus is comprised of gram-positive bacteria. Using the term species after the genus name implies that the genus is certain but the species is not. Streptococcus species are part of the normal flora of the mouth. When the vernacular name does not reflect the correct taxonomic position of the plant, join the terms with a hyphen. However, it should be noted that this rule is practiced inconsistently. poison-oak (belongs to a different genus from true oak) white oak (a true oak) Valid scientific names should not be synonyms or homonyms. However, synonyms and homonyms do exist for scientific and vernacular names. Multiple names used for the same species (synonyms) or names that sound the same but represent different species (homonyms) pose problems in consistency and in retrieval of data and should be avoided if possible. b. Cultivar notation. Cultivar notation is defined by the International Code of Nomenclature for Cultivated Plants (ICNCP). Cultivar names are written in roman type with an initial capital letter and are placed within single quotation marks when they come after the scientific name. Single quotation marks are not needed when the cultivar name is used alone. Miscanthus sinesis 'Adagio' Adagio c. Designating hybrids. Hybrids are designated by a formula in which the names of the parents are separated by a multiplication symbol. If no other convention is specified, list the names in alphabetical order. d. Orchid nomenclature. Orchid nomenclature is governed both by the International Code of Botanical Nomenclature and the International Code of Nomenclature for Cultivated Plants. All described orchid species are named using the standard Latin binomial system. e. Construction of common names for plant diseases. Plant disease names are usually based on the major disease symptom or on the pathogen responsible for the disease. A recommended list of common names for plant diseases has been published by the American Phytopathological Society. When the Latin name of the pathogen is part of the disease name, the Latin word should be italicized and its first letter should be capitalized. The same disease name may be used even when the disease is caused by different pathogens in different host species. In order to avoid confusion, include the host name as part of the disease name. Fungal genera are not written in plural form. To refer to a group of species in a genus, write the abbreviation for species after the genus name. The abbreviation for species is either sp. (for a group composed of one species) or spp. (for a group consisting of two or more different species). Pleistosporidium sp. Bacillidium spp. Infrageneric or infraspecific rank names are preceded by an abbreviation indicating the taxonomic rank. This abbreviation is not capitalized or italicized. Banksia subg. Isostylis Erigonum longifolium subsp. Diffusum Below the rank of species, the scientific name may be written in shortened form. E. longifolium var. plantagineum d. Yeasts and slime molds. Rules for naming both yeast and slime molds follow the guidelines set for fungi in the Botanical Code. Yeast is not a taxonomic term, but is usually applied to fungi in the order Saccharomycetales. In a scientific paper, the word yeast can be used if the scientific name is used at first mention. Yeast used for cooking or brewing are not usually identified by genus or species names. Flavoparmelia caperata belongs to the fungal genus Flavoparmelia. Cladonia rangiferina is also known as Reindeer lichen. Cetraria islandica is also known as Iceland moss. iv. Algae. The word algae is not a taxonomic term. The same nomenclature style and format rules set forth for plants in the Botanical Code are also applied to algae. Typical taxonomic endings are shown below. ii. Format for author names. Inclusion of the author's name as part of the genus or species name is optional. When the author's name is included, it should also include the year in which it was named and be written in this format: A document's list of references should include the publication in which the taxonomic name was published. iii. Vernacular names. Common names are not capitalized except in the case of proper names. Lists of scientific names with approved common names have been published for species in a number of phyla, including insects, reptiles, fish, birds, and mammals. Index of Laboratory Animals provides information on inbred animal strains. A system for specifically designating inbred strains of mice has been established by the Committee on Standardized Genetic Nomenclature for Mice (CSGNM) . Preferred units have been established by the International System of Units (SI). SI units are recognized by international agreement, but they are not used exclusively in the United States, which may require dual reporting with metric units. For example, the Celsius scale (°C) is acceptable for reporting temperature rather than the SI unit, the kelvin (K). For SI derived units, multiplying prefixes, and conversion factors, see Appendix B1. Committee on the Common Names of Insects. Common names of insects and related organisms • FINS: the Fish Information Service. Fish index Active Window Productions, Inc.; c1993-2000 The mammals of North America. 2 nd ed Rules for nomenclature of inbred strains • International Commission on Zoological Nomenclature. International code of zoological nomenclature. 4 th ed. London (UK): The Natural History Museum, Intern'l Trust for Zoological Nomenclature • International Committee on Standardized Genetic Nomenclature for Mice; Rat Genome and Nomenclature Committee Official lists and indexes of names and works in zoology. London (UK): International Trust for Zoological Nomenclature Committee on Transgenic Nomenclature. Standardized nomenclature for transgenic animals. ILAR A quarterly of the Society of Systematic Biologists Common names of mammals of the world The Global Bioresource Center American Type Culture Collection; c2005 Recommendations for standardized human pedigree nomenclature. Pedigree Standardization Task Force of the National Society of Genetic Counselors Style Manual Committee. Scientific style and format: the CSE manual for authors The ACS Style Guide: A Manual for Authors and Editors Fishman's manual of pulmonary diseases and disorders • International Anatomical Nomenclature Committee. Nomina anatomica: authorized by the 12 th International Congress of Anatomists in London • The International System of Units (SI) Species plantarum: a facsimile of the first edition A standard nomenclature for structures of the kidney. The Renal Commission of the International Union of Physiological Sciences National Library of Medicine (US) Standardization of definitions and symbols in respiratory physiology Bonehistomorphometry: standardization of nomenclature, symbols, and units. Report of the ASBMR Histomorpho-metry Nomenclature Committee Nomenclature for secreted regulatory proteins of the immune system (interleukins). WHO-IUIS Nomenclature Subcommittee on Interleukin Designation • Proposed standard system of symbols for thermal physiology