Biophysical Journal - Style Guide

Please note that this guide may change periodically. This was originally written for the use of copy editors, not authors, so some of the entries may be confusing. This guide is not "complete," in the sense that many points of grammar and general technical style are not included. As stated in the Information to Authors, the CBE Style Manual should be used for material not covered here. Please feel free to email suggestions about this guide to bj{at}biophysics.org

A

Abbreviations:

• no period (cpm)
• Usage in text:

  Minimum usage for allowance in text? 3x
  

  Minimum usage for allowance in Abstract? 3x

• Define in text OR use authors' supplied abbreviations list. Make sure author lists first in the footnote the first abbreviation used in the text. Example: High-performance liquid chromatography (HPLC)...
• Standard abbreviations (do not spell out): Hepes or HEPES, EGTA, EDTA, Tris, NMR
• Abbreviations for buffers: spell out first time used except as above; all caps or cap and lc ok; be consistent within article (Mes or MES; Pipes or PIPES

• Supported by information follows acknowledgments.

• To authors of paper (usually in parens): D.J. Jones (note initials closed up)
• To other parts of Text: see Results

B

baseline (not "base-line" or "base line")
basepair
before not prior to
blots: Western blot, Northern blot, Southern blot (but "dot blot")
brackets: Use brackets for labeling and other typical math functions.
Brownian motion
buffers: buffers should be written in text by abbreviated form first with ingredients listed in parens with first mention.

• Examples:
  
• TEM buffer (0.2 M Tris, 0.54 M EDTA, 1.5 M methylhydroxy)
  
• buffer A (0.2 M Tris, 0.54 M EDTA, 1.5 M methylhydroxy)

C

10°C (no space); 10° angle
ca. change to approximately or symbol, follow copy
Ca²⁺ not Ca⁺⁺
cells: B cells, blood cell, Caco-2 cells, carrier cells, egg cell, fat cell, ganglion cell, germ cell, ghost cell, HeLa cell, killer or K cells, Kupffer cells, Langerhans' cells, Leydig's cells, natural killer or NK cells, Purkinje's cells, Schwann cells, sickle cell, T cell, target cell
centrifugation: 100 × g
cf.
cis and trans (italicize)
classic vs. classical: leave as classical; this has a special meaning
cm³
co-linear
Company names:

• Company,   Co,   Co.: follow Guide to Scientific Instruments
  
• Add city and state.

	crossability
	crossbar
	crossbite
	crossbreeding
	crossbred
	cross-bridge
	cross-check
	cross-cylinder
	cross-examination
	cross-eye(d)
	cross-fertilize
	cross-grained
	cross-hair
	crosshybridization
	cross-index
	crossing-over of genes
	cross-link
	crossmatching
	cross multiply
	crossover
	crosspeak
	cross-pollinate
	cross product
	cross-reaction
 	cross-reference
	crossroad
	cross section
	cross-sterile
	cross talk
	crossway

cutoff
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D

Da daltons
DC (not D.C.)
10°C (closed up for temp.) 10° angle
dpm
day do not abbreviate
Designative terms:

day 1

week 3

experiment 1

model 15

E

e.g., Roman with following comma
en bloc (Roman)
end plate
enzymes: consult "Enzyme Nomenclature."
et al., Roman (e.g., Jones et al., 1987)
Epstein-Barr virus
Equations:

• "Eq. 1" in text. use "(1)" for numbers for displayed equations. Appendix equations: numbers can be either continuation of text numbers or "(A1)" or "(1a)" if author prefers.
  
• Use either "...in the following:" or "...as follows." or "...in the equation," be consistent.
  
• Use "Equation 1" at start of sentence.
  
• possessive ('s) with equations: change to "values":
  
• Never: "the a's were used..."   Always: "the a values were used..."
  

F

Figures:

For digital art information, please visit http://www.dartmouthjournals.com/digart.html

• Fig. (Fig.) (use Fig. at start of sentence. Use cap or lowercase letters according to figure.
  

  Fig. 1 A
  

  Fig. 1, A and B
  

  Fig. 1, A--C
  

• Use (see Fig. 2) if reference to figure appears before actual callout
  
• Figure legends: parts of figures and references to items on figures italic (e.g., Fig. 2, B and C, show; Concentrations of 1 (squares), 5 (triangles) . . .). Only use italics when elements of figure are used within parentheses. Otherwise use Roman:
  

  The arrow points toward the DNA..."
  

  ...found in the DNA (arrow)."
  

  Preferred style: (A) The cell membrane...; (B) The DNA...
  

severalfold, manyfold

a two- to fourfold increase, but a 2- to 4.5-fold increase

an 8- to 12-fold increase

G

G-protein
g for centrifugation (100 × g)
G gauss
Gaussian capital "G"
genus and species: write out upon first usage, thereafter use abbreviation: E. coli
Germany - do not use "FRG"
Greek: characters (rather than spelled out)
Giemsa stain
Golgi's stain
Gram's stain
Grants:

• ...supported by grant 12345 from the National...
  
• ...supported by National Institutes of Health (12344 and 12567) and American Heart Association grants...
  
• Change initialized agencies to full name form.
  

 ACS     American Chemical Society
 AHA     American Heart Association
 BMFT    Bundeministerium für Forschung und Technologie
 CDC     Center for Disease Control
 CNRS    Centre National de la Recherche Scientifique
 EMBL    European Molecular Biology Laboratory
 INSERM  Institut National de la Sante et de la Recherche Medicale
 MRC     Medical Research Council
 MRCC    Medical Research Council of Canada
 NCI     National Cancer Institute
 NFWO    National Fund for Scientific Research
 NHMRC   National Health and Medical Research Council
 NIH     National Institutes of Health
 NIADDK  National Institute of Arthritis, Diabetes, and Digestive and Kidney Diseases
 NIAID   National Institute of Allergy and Infectious Diseases
 NICHHD  National Institute of Child Health and Human Development
 NINCDS  National Institute of Neurological and Communicative Disorders and Stroke
 NSERCC  National Science and Engineering Research Council of Canada
 NSF     National Science Foundation
 ONR     Office of Naval Research
 UNDF    United Nations Development Fund
 USPHS   U.S. Public Health Service
 WHO     World Health Organization

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H

h for hours
headgroup (one word)
herpesvirus
herpes simplex virus
homolog
Hill number (nH) No definition needed.
Hyphenation:

• Unit modifiers: 20-ms pulse
  
• Combination modifiers: conductance-concentration relation
  

I

ical (biological)
i.e., Roman, with following comma; in vivo, in vitro, en bloc, per se, vice versa, in situ (all Roman)
intraarterial
isotopes: [¹⁴C]hexane; but ²H-NMR, ³H-labeled
Italics: Italicize elements of figure when they are used inside parentheses. Use Roman in text:

"The arrow points to DNA..."

"The DNA (arrow) represents the..."

J-K

kHz kiloHertz
kDa kilodaltons (see also daltons)
kbar
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L

labeled
Latin word/phrases: Roman: per se ad libitum in vitro cf. viz
lipid
-log (analog)
Lorentzian (cap)
LUV large unilamellar vesicle
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M

magnification: use ×: "40× magnification."
mid (midline incision)
model (lowercase)
Molar concentration: M (not small cap!)
molecular mass versus weight: According to the CBE Style Manual, "It is correct to say the molecular weight of protein X is 30,000 or the molecular mass of protein X is 30,000 daltons. However, it is incorrect to say that the molecular weight of protein X is 30,000 daltons."
mol for moles
mol wt (molecular weight; use with numbers preceding it, write out otherwise): A 60,000-mol wt protein. The protein had a molecular weight of 60,000.
mol %
molecular size and apparent molecular weight are both acceptable terms
min for minutes
mixed nomenclature: Change "Na-acetate" to "sodium acetate"
month do not abbreviate except in tables
multiplication dot: always change to times sign.

change "3 · 4 = 12" to "3 × 4 = 12"

change "20 mg·ml" to "20 mg/ml"

N

n italic before a chemical name (means 'normal')
nH (Hill number, no definition needed)
non (closed up)
Normal concentration: N (not small cap!)
Note added in proof: This should appear immediately before ack. Code as ack and flush actual ack's, i.e.,
Number: N n (follow copy for cap or lowercase)
Numbers:

• Use numerals for all units of measure except months.
  
• Use words for numbers one through nine and numerals for larger numbers, except within a context in which some numbers are 10 or more and some are less than 10.
  
• Do not add comma to 4-digit numbers; add them to 5-digit and over numbers.
  

O

overall
OD outside diameter
"of" in quantities: do not use e.g., 3 g/ml salmon sperm
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P-Q

p probability
p-value
P_i, inorganic phosphate
/ (shilling) for per
%
per se (Roman)
Personal communications:

R. Smith, University of Iowa, personal communication, 1992)

( name , affiliation , personal/written commun, yr)

Never: "the a's were used..."
a values were used..."

R

Ranges: 7-9 (but, "from 7 to 9 days")
received information line: Received for publication 15 December 1992 and in final form 20 March 1993."
red shift (n) red-shift (adj)
Reference citations: Numbered
Reference list:
Numbered

Unpublished references should not be cited in the References list, but in parentheses in the text.
Reference Style:
Journal:
1. Benditt, E. P., N. Ericksen, and R. H. Hanson. 1979. Amyloid protein SAA is an apoprotein of mouse plasma high density lipoprotein. Proc. Natl. Acad. Sci. USA. 76:4092–4096.
Book:
1. Levinson, S. R., W. B. Thornhill, D. S. Duch, E. Recio-Pinto, and B. W. Urban. 1990. The role of non-protein domains in the function and synthesis of voltage-gated sodium channels. In Ion Channels, 2nd ed, Vol. 2. T. Narahashi and A. S. Jones, editors. Plenum Publishing Corp., New York. 33-64.
Abstract:
1. Fabiato, A. 1986. Inositol (1,4,5)-trisphosphate-induced release of Ca²⁺ from sarcoplasmic reticulum of skinned cardiac cells. Biophys. J. 49:190a. (Abstr.)
Thesis:
1. Bluhm, R. T. Superstrings in four dimensions. Ph.D. thesis. The Rockefeller University, New York. 240 pp.
Supplement:
1. Gall, J. G. 1981. Chromosome structure and the C-value paradox. J. Cell Biol. 91(3, Pt. 2):3s-14s.
Gibbons, I. R. 1985. Cilia and flagella of eukaryotes. Cell. 36(Suppl.):24-38.
Follow BIOSIS: if Suppl. is part of journal title, then it should be printed that way and not in parens after the vol. number.
Proceedings: Cited two ways, with or without article titles:
1. Rozenkranz, N., and L. L. Smith, Jr. 1968. Disposal of nuclear wastes. Proc. Geneva Conf. Peaceful Uses At. Energy, 2nd, Geneva. 15:693-701.
    OR
1. Durelli, N., and V. A. Parks. 1962. Proc. US Natl. Congr. Sppl. Mech., 4th. 938 pp.
 
References (issue numbers): delete issue numbers throughout: change "23(2):244-246" to 23:244-246"
Refs. with subtitles: Use cap after Roman numeral ("I. The end of the gene..."); use lowercase following colon ("...of DNA: the experimental procedures for..."); use cap after a period ("...of DNA. The use of...").
References in press: If author cannot update, use:

1. Smith, A. B. 1993. Title. Biophys. J. In press.

Use Biosis for journal abbreviations.

reprints: use, at end of address, "Tel.: xxx-xxx-xxxx; Fax: xxx-xxx-xxxx; E-mail: ...."
registered marks: delete; capitalize trade names
rpm
restriction enzymes: HindIII,  BamHI,  PstI  (italic and closed up)
Rous sarcoma virus
residues: Author may use 3-letter code, written out form, or single-letter abbreviation in sequences without definition. 3-letter style: "Asp¹⁴" or "Asp-14" are acceptable, but "Asp 14" is NOT o.k. Written out form is "asparaginine 14" NOT "asparaginine-14."

View the Instructions to Authors for further information on references.

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S

sn italic before a chemical name
's (in equations and math terms): change to "values":

Never: "the a's were used..."

Always: "the a values were used..."

s for second; ms for millisecond, etc.
SE: Use for standard error. Change "SEM" to "mean ± SE." "SD" is o.k. also.
semi closed up
Semliki Forest virus
Sendai virus
Series: run in: 1), 2), 3)
Shaker is italic
Shaw is italic (and is often paired with Shaker)
side chain (n) side-chain (adj)
simian virus 40 (or SV40)
Southern blot
Spelling: BJ usually follows first spelling in Webster's.

Single "l" is preferred over double "l." "

Labeled"not "labelled."

prefixes get closed up (coauthor, realign, reinfect, etc.) unless the dictionary suggests otherwise (co-worker, re-try).

Change British spellings to American:

  Change this       to this
  amoeba            ameba
  amoebae           amebas
  anaesthetised     anesthetized
  analyse           analyze
  characterise      characterize
  colour            color
  favour            favor
  fibre             fiber
  grey              gray
  haemocytometer    hemocytometer
  litre             liter
  localise          localize
  neighbouring      neighboring
  polymerisation    polymerization
  tumour            tumor
  whilst            while

standard error/deviation: Use "SE" for standard error. Change "SEM" to "mean ± SE." "SD".
Stains:

Giemsa stain

Golgi's stain

Gram's stain

steady state: space as a noun, hyphenate as modifier
Stokes radius or equation (no apostrophe)
sub closed up
symbols (order): *, ^#, ^§, ^¶, ^||, **,^##, ^§§, ^¶¶, ^{|| ||}, etc. Be sure to make all of these explicitly superscript, except for the asterisk.
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T

Student's t-test
Table 2
Trade names: capitalize; delete TM or registry symbol
trans (cis and trans) (these terms are part of the chemical configuration and thus are not capitalized at the start of a sentence or in titles.
t_1/2
time course
time point
time 0, but zero time
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U-V

U/... (change to "units/...")
Unit modifiers: hyphenate (3-cm tumor)
USAGES (where applicable)

  after       not following
  before      not prior to
  because  /  inasmuch as not since
  although /  whereas not while
  maximal  /  minimal as adj.
  despite     not in spite of
  to...       not   in order to....
  toward      not towards

van der Waals forces
Variables: In general, letters on the line are italic. All superscripts and subscripts are Roman. See printed copy for examples in text and equations.
vice versa (Roman)
Viruses:

Semliki Forest virus

Sendai Virus

simian virus 40 (or SV40)

volume: use v/v even with more than two things. Use colon with numbers (water/air/CO₂, 30:23:3, v/v)
vs. (with numbers) and versus (with text)
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W

W watts
week(s)
Western blot
wt %
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X-Y-Z

x axis
x ray (noun) x-ray (adjective) as in "x-ray therapy." Cap "X" at start of a sentence.
y axis
z-position (Atomic Force Microscope studies, etc.)

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