Seeking punctuation clarity—that is, the proper use of the hyphen and dashes—for publishing in Autophagy

Keywords:

• autophagy
• em-dash
• en-dash
• grammar
• punctuation

As an editor, and in this case I mean as a person who, along with the assistant editor, proofreads the final text of submitted manuscripts to help ensure uniformity, clarity and adherence to a standard set of rules, I think it is worthwhile spending one editor's corner considering the use of dashes and the hyphen.

There are 2 types of dashes, “em” and “en”. The em-dash (—) is theoretically as wide as the capital letter “M” (although this depends on the font used), hence the name, whereas the en-dash (–) is half the width of the em-dash (Fig. 1A). Furthermore, these are both distinct from a hyphen (-). This distinction obviously corresponds to length, but also to use. In particular, a hyphen is used to connect words that have a particular meaning when combined, such as “self-eating.”

Figure 1. The evolution of the autophagy conjugation denotation. (A) An illustration of the different widths of the em-dash (approximately the width of the letter “M”), the en-dash (half the width of the em-dash) and the hyphen. (B) The original denotation (initially using the “Apg” nomenclature) used an interpunct to differentiate between the covalent bond (Atg12–Atg5) and noncovalent bond (Atg5·Atg16; referring to the yeast proteins). (C) A brief intermediate form used an em-dash to denote the covalent bond, eliminating the need for the interpunct. (D) The current nomenclature utilizes an en-dash to mark the ubiquitin-like conjugation-derived covalent bond between Atg12 and Atg5, and a hyphen to indicate the noncovalent bond.

You may wonder why I bring this up in the first place. One reason for discussing this issue is to save the editors some time during proofreading (and the authors some time in responding to the editors' requests for corrections). For people working in the autophagy field, the issue of the en- and em-dash comes up at least in part because of the novel conjugation systems in macroautophagy, which result in the formation of Atg8–PE and Atg12–Atg5 (obviously you can tell that I am referring to the yeast proteins here, for simplicity). The first paper describing the latter referred to the “Apg5/Apg12” conjugate.¹ The subsequent discovery of Apg16/Atg16 led to the need for a means to distinguish between the covalent bond between Atg12 and Atg5 (that is, conjugation) and the noncovalent interaction between Atg5 and Atg16. This necessity resulted in the use of the elevated period (middle dot, centered dot, etc.), properly called an interpunct, in the notation “Atg12-Atg5·Atg16” (Fig. 1B).² Note also that it is important to present the proteins in the correct order to indicate for example that Atg12 is conjugated to Atg5, similar to Atg8 being conjugated to phosphatidylethanolamine (that is, you would never write “PE–Atg8”, and similarly it is not correct to write “Atg5–Atg12”).

Certainly the intention with the interpunct was good; however, I think that there were 2 problems with this approach. First, the hyphen—which appeared using this notation between Atg12 and Atg5—is typically used to denote noncovalent protein-protein interactions (note the use of the hyphen in the very term “protein-protein interactions”). Second, the interpunct is not a common key on most keyboards (for example, using Microsoft Word on a Macintosh computer it is necessary to click on Insert:Symbol:Advanced Symbol… and then choose the appropriate mark), making it awkward to use. Accordingly, an agreement was made to use the easily distinguished em-dash to mark the covalent bond between Atg12 and Atg5 (Fig. 1C). The Autophagy copyeditor subsequently suggested (and I think correctly so) that this notation (i.e., Atg12—Atg5-Atg16) was too extreme, resulting in a shift to the en-dash rather than the em-dash (Fig. 1D). Thus, the proper way to denote this complex is “Atg12–Atg5-Atg16”, or “ATG12–ATG5-ATG16L1” for mammals. Note that the width of the first dash—that is, the en-dash—is substantially longer than that of the subsequent hyphen (more than twice the length). The same rule applies to “Atg8–PE” because this is also a covalent bond that is formed posttranslationally (another conjugation event). I added the last term—posttranslationally—to dispel any thoughts of using the en-dash for chimeric proteins such as GFP-Atg8. Also, note that LC3-II is an abbreviation or alternate denotation for LC3–PE; the latter, but not the former, uses an en-dash because the “II” is used to distinguish between LC3-I (the cleaved, but nonlipidated form) from LC3-II, but the “II” is not equivalent to “PE” (i.e., “I” and “II” refer primarily to “nonlipidated” and “lipidated” with regard to the stage of modification). On a Macintosh computer holding down the option key and typing the dash key generates an en-dash.

What about the em-dash? According to Garner's Modern American Usage³ “The em-dash…is used to mark an interruption in the structure of a sentence…” The em-dash can be used to replace commas, making the sentence easier to read (for example, see the title of this article). Note that there should not be any open spaces on either side of the em-dash; I often see people use an en-dash with spaces as in “to clarify – if that is possible,” when an em-dash is in order. Also, a double hyphen “--” is frequently used in place of an em-dash. One problem with the latter is that the double hyphen in not always retained when copying and pasting, especially when pasting into a window on a computer screen, resulting in a single hyphen—and obviously that is not a mistake we want to contemplate. On a Macintosh computer holding down the option and shift keys and typing the dash key generates the em-dash.

While we are on the topic of dashes, let's attempt to clarify the use of the dash/hyphen. In general, the term “dash” is not used in this context by itself. That is, we can refer to an en-dash or an em-dash, but otherwise we are referring to a hyphen. As noted in Garner's Modern American Usage,³ it is important to use a hyphen to avoid ambiguity as in “re-signing” a document versus “resigning” from a position. For our purposes (that is, in the journal Autophagy), some examples of the proper use versus avoidance of a hyphen include “… as seen with a gain-of-function mutation…”, as opposed to “…resulted in a gain of function”, or “…using a long-term assay…” versus “…in the long term.” Hyphens are not needed, and should be avoided, in words such as anticancer, nonselective, and nonadherent.

Finally, straying a moment from the dashes and hyphen—but sticking with the topic—we can consider one additional type of punctuation, the virgule, which is more commonly referred to as the “slash” (/). I find that many authors attempt to use the virgule/slash to mean “and/or” as in the “PtdIns3K complex consisting of ULK1/Vps34/Vps15/Beclin 1/ATG101”. First, the nomenclature is not correct in this list,⁴ and, second, the virgule/slash is used by Autophagy to indicate equivalency (as in “Vps30/Atg6”). Thus, the proper way to write this would be the “PtdIns3K complex consisting of ULK1-PIK3C3/VPS34-PIK3R4/VPS15-BECN1/Beclin 1-ATG101” where the hyphen denotes a noncovalent interaction. Thus, returning to our original example of the Atg12–Atg5 conjugate, it is not appropriate to refer to the “ATG12-ATG5/ATG16L1” complex, which I see appear on occasion in less discriminating journals, because ATG5 is not equivalent to ATG16L1 (and ATG12 is covalently linked to ATG5). Finally, do not insert spaces on either side of the slash, which is the custom in some countries. Thus, “Vps30/Atg6” is correct as opposed to “Vps30 / Atg6”. In addition, the virgule/slash should not be used when referring to ratios; in this case, a colon is appropriate as in calculating the ratio of “LC3-II:LC3-I” or using a “1:10,000 dilution.”

Keeping these simple rules in mind can save all of us—meaning both authors and editors—a lot of time and trouble.

Daniel J. Klionsky

Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA

[email protected]

Funding

This work was supported by NIH grant GM053396 to DJK.