Conventions in Biology

 

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Using Latin Binomial Name Conventions

Biologists often refer to organisms by a formal naming system called binomial nomenclature, in which the Latin genus name and species name are given. For example, in binomial nomenclature, baker’s yeast is called Saccharomyces cerevisiae.

 

Rules for using binomial nomenclature in formal writing
  • Always capitalize the genus name.
  • Never capitalize the species name.
  • Always italicize the whole name.
  • The first time an organism is referred to in the body of a paper, write the name in full (e.g. Saccharomyces cerevisiae). Any time it is used later in the text, the genus name can be abbreviated using its capitalized first letter followed by its species name (e.g. S. cerevisiae).
  • In the title of a paper, always write the name, genus and species, in full.

Exception: If the paper exclusively studies modern humans, do not use Homo sapiens. (Instead, indicate the group studied, such as “Middlebury College students” or “Ethiopian adult males.”)

 

 

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Test yourself

Which of the following is formatted correctly for use in the title of a paper?

  1. Danaus plexippus
  2. Homo sapiens
  3. Nephrolepis exaltata
  4. M. domestica
  5. Escherichia Coli

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Solutions

  1. No
  2. Yes
  3. Yes
  4. No
  5. No

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Formatting Citations and References

 

To help you cite and reference material in your papers, we are providing some of the most common citation styles used in biology. More important than following any one style, however, is being consistent within a paper or poster. Make sure all of your citations and references are formatted the same way so that readers can  easily find information about the sources of your information.

 

In-text citation styles

  1. Author-date format
    • Separate the citation from the text using parentheses ( ).
    • Separate author last names from the year of publication by a comma.
    • Separate the names of two authors by “and;” for papers with more than two authors, list the first author followed by “et al.”
    • List multiple citations in the order of their year of publication, then in alphabetical order, separated by a semicolon.

    Example: “Because increased hyperplasia and apoptosis have been reported in hepatocytes of diabetic rats (Herrman et al., 1999; Ahmed, 2005), it has been hypothesized that hyperglycemic animals might suffer from early aging (Blazer et al., 2009; Mello et al., 2009).” (Adapted from Ghiraldini, Crispim, and Mello 2013)

  2. Numbers in parentheses
    • Place citations in parentheses before commas or periods
    • Place a space between the text and the brackets or parentheses
    • Use commas (with spaces) between numbers

Example: “High concentrations of molecular gas have been identified in ultraluminous galaxies (4, 6-8, 12).”

 

Reference styles

Remember that if a numbered citation style is used, references must be listed in the order that they appear in the text. If the author-date format is used, references should be listed in alphabetical order. If The following are some common reference styles used in biological journals.

  1. Author 1, Author 2, etc. (Year). Title of article with only proper nouns capitalized. Journal Abbreviation Volume, Inclusive Pagination.
  2. Author 1, Author 2, etc., Title of article with only proper nouns capitalized. Journal Abbreviation Volume, Inclusive Pagination (Year).

In almost all cases, authors’ names should be composed of their first and possibly second initials as well as their full last names. In some journals, the authors’ initials should precede their last names, while in others, the initials should follow the last names with separation by a comma.

Furthermore, how many authors’ names are listed before use of “et al.” varies by journal. Some acceptable systems are:

    • to name all authors, regardless of number,
    • to name up to 10 authors, then follow with “et al.,”
    • or to use “et al.” after the first author’s name if there are more than 5 authors.

 

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Designing Figures

Most of the information about designing figures and tables found on the “Using Visuals” page of this website applies directly to the construction of figures in biology. Schemes are less common in biology than they are in chemistry, but figures and tables are both critical parts of most experimental biology papers. But one notable difference is that figures and tables published in biological journals often have much more detailed legends than those in other types of journals.

Below is an adaptation of some of the instructions for constructing figure legends in biology from Middlebury’s Cellular and Molecular Biology lab manual:

  • If the figure includes regression analysis, include the type of regression and the R2 value for the line(s) in the legend. If the equation is important for your results and/or discussion include it in the legend, otherwise don’t show it.
  • Indicate what type of error has been calculated.
  • Include information about the sample size using the format n=#.
  • Include information about the statistics.
  • If you have a multi-part figure (i.e. three different images of cells, each in a different condition) you should begin with legend information that is common to all three parts. This is followed by information for panels A, B, C etc.

 

The 3 major goals of a figure and legend (from the BIO 145 lab manual)
Used together, a figure and legend should accomplish 3 things:

  1. Allow the reader to know the question you are trying to answer with the experiment. This is most easily accomplished in the title.
  2. Allow the reader to know the experimental method used to answer the question.
  3. Allow the reader to extract the important trends in your data.

 

 

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Writing RNA/DNA/Protein names

 

Like with all abbreviations and acronyms, remember that gene, protein, and other symbols should often be defined at first use in the abstract and text so that non-expert readers can still understand your paper.

The abbreviated names for genes and their corresponding proteins, RNA, and cDNA are usually identical in structure–so we rely on the formatting of the name to help us distinguish among them. It is important to stay consistent with the following conventions to prevent your readers from being too confused–but remember, if the conventions in a journal you want to emulate or publish in are different, you may choose to adopt those instead! It is most critical to be consistent within your paper.

 

Structure Case Style Example
Gene Upper Italicized ZLT5
Protein Upper Plain ZLT5
RNA/cDNA Upper Italicized ZLT5

 

Notice that RNA follows the same formatting conventions as DNA. So how do we differentiate between them? You should word your sentences carefully to indicate distinctions, such as:

MET3 gene expression was used to predict MET3 RNA levels.

 

This strategy can also be used with proteins and other similar-looking structure names in order to keep your language especially clear.

 

There are also more specific conventions for particular species or groups of species, which we outline below. Unless otherwise noted, gene symbols are always italicized while protein symbols are not.

 

Species/Group Convention For more information:
Human Gene symbols contain 3-6 characters, all upper-case; may be a combination of letters and Arabic numerals, but must begin with a letter. Protein symbols are identical to gene but are not italicized. HUGO Gene Nomenclature Committee (HGNC)
Mouse Gene symbols have only the first letter capitalized. Protein symbols are all upper-case. Mouse Genome Nomenclature Committee (MGNC)
Rat Gene symbols have only the first letter capitalized. Protein symbols are all upper-case. Rat Genome and Nomenclature Committee (RGNC)
Bovine (Follows human convention) Bovine Genome Database (BGD)
Fish Full genome names are also italicized. Gene names are all lower-case. Protein names have only the first letter capitalized. The Zebrafish Model Organism Database (ZFIN)
Fly Gene names and symbols begin with an upper-case letter if: (1) the gene is named for a protein or (2) the gene was initially named for a mutant phenotype that is dominant to the wild-type phenotype. Gene names and symbols begin with a lower-case letter if the gene was first named for a mutant phenotype that is recessive. Symbols for proteins that were named for genes begin with an upper-case letter (otherwise there are no accepted conventions for proteins). FlyBase
Worm Gene and protein symbols generally contain 3-4 letters and an Arabic numeral connected by a hyphen.
Bacteria Gene symbols are composed of 3 lower-case letters that describe the encoded pathway. Different alleles are distinguished by a subsequent upper-case letter. Protein symbols begin with an upper-case letter. Journal of Bacteriology Instructions for Authors

 

 

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