Abbreviations and symbols

The abbreviations listed in Table 1 are 'accepted', may be used without definition, and may be used in the title or the page-heading title. Other abbreviations, the use of which should be kept to a minimum compatible with clarity and conciseness, should not be used in the title or page-heading title and should be defined together in a footnote on the title page. In devising such abbreviations and symbols, the recommendations of the Nomenclature Committee of IUBMB and the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (see http://www.chem.qmul.ac.uk/iubmb/) should be followed as far as practicable. The sections following summarize a number of these recommendations; all of the symbols listed may be used without definition.

Amino acids

The full residue names or the three-letter symbols are preferred to the one-letter symbols in the text (e.g. a phenylalanine residue at position 231 should be symbolized Phe-231 or Phe²³¹ rather than F231). Either system may be used in sequences.

Alanine	Ala	A
Arginine	Arg	R
Asparagine	Asn	N
Aspartic acid	Asp	D
Aspartic acid or asparagine (undefined)	Asx	B
Cysteine	Cys	C
	|
Cystine (half)	Cys or Cys	—
	|
Glutamine	Gln	Q
Glutamic acid	Glu	E
Glutamic acid or glutamine (undefined)	Glx	Z
Glycine	Gly	G
Histidine	His	H
Hydroxylysine	Hyl	—
Hydroxyproline	Hyp	—
Isoleucine	Ile	I
Leucine	Leu	L
Lysine	Lys	K
Methionine	Met	M
Ornithine	Orn	—
Phenylalanine	Phe	F
Proline	Pro	P
Serine	Ser	S
Threonine	Thr	T
Tryptophan	Trp	W
Tyrosine	Tyr	Y
Unknown or 'other'	Xaa	X
Valine	Val	V

In polymers or sequences the three-letter symbols should be joined by hyphens if the sequence is known, or by commas if it is not; e.g.:

Gly-Ile-Gly-Phe(Gly,Tyr,Val,Ser)Leu-Val-Ala

represents an undecapeptide composed of four amino acids whose sequence has been established, four for which the sequence is unknown and then three in known sequence. The glycine on the left carries the free amino group and the alanine on the right the free carboxyl group. The prefix poly or the suffix subscript n may accompany these symbols to indicate polymers [see Biochem. J. (1972) 127, 753–756].

Special considerations apply to the spacing and punctuation of the one-letter symbols [see Biochem. J. (1984) 219, 366–368].

Nucleosides, nucleotides and polynucleotides

The symbols for ribonucleosides are as follows (the prefix r should be used if there is possible ambiguity):

A	Adenosine	C	Cytidine
G	Guanosine	T	Ribosylthymine
I	Inosine	U	Uridine
X	Xanthosine
5-Ribosyluracil (pseudouridine)

The 2´-deoxyribonucleosides are designated by the same symbols preceded by d, e.g.:

dA 2´-Deoxyribosyladenine
dT 2´-Deoxyribosylthymine (thymidine)

The letter p (for terminal phosphate only) or a hyphen (for phosphodiester group only) to the left of a nucleoside symbol indicates a 5´-phosphate; to the right it indicates a 3´-phosphate, e.g.:

pA-G	5´-Phosphoadenylyl(3´-5´)guanosine or guanylyl(5´-3´)adenosine 5´-phosphate
A-Gp	Adenylyl(3´-5´)guanosine 3´-phosphate
d(A-T)	Deoxyadenylyl(3´-5´)thymidine
A-G-cyclic-p or A-G > p	Adenylyl(3´-5´)guanosine 2´,3´-phosphate

Other points of attachment may be indicated by numerals, e.g.:

A2´-5´G2´p	Adenylyl(2´-5´)guanosine 2´-phosphate
A-G-(mixed 2´,3´)-p	A mixture of A-Gp and A-G2´p

In sequences, oligonucleotides or polynucleotides the phosphate between nucleoside symbols is shown by a hyphen if the sequence is known, or by a comma if it is not, e.g.:

G-A-U(C₂,U)Gp

indicates a heptanucleotide composed of three nucleotides of known sequence but with a trinucleotide of unknown sequence before the final Gp. The hyphens may be omitted.

For sequences that are repetitive or obscure, shorter forms may be used [see Biochem. J. (1972) 127, 753–756], e.g.:

poly(A)	a simple homopolymer of A
poly(A3,C2)	random co-polymer of A and C in 3:2 proportions
poly[d(A-T)] or poly(dA-dT)	alternating co-polymer of dA and dT
poly(A,G,C,U)	random co-polymer of A, G, C and U, proportions unspecified

The prefix co-poly or oligo may replace poly, if desired. An alternative form is, e.g., A_n for poly(A), where the subscript n may be replaced by numerals indicating actual size. Similarly, d(A-T)_n etc. may be used for poly(dA-dT) etc. It should be noted that no space follows the prefix 'poly'.

Associated (e.g. hydrogen-bonded) chains, or bases within chains, are indicated by a centre dot (not a hyphen or a plus sign) separating the complete names or symbols; non-associated chains are separated by a plus sign, and unspecified or unknown association is indicated by a comma, e.g.:

poly(A)·poly(U)	associated poly(A) and poly(U)
poly(G)·2poly(C) or Gn·2Cn	triple-stranded complex of poly(G) and poly(C) in the proportions 1:2
poly(dA-dC)·poly(dG-dT) or (dA-dC)n·(dG-dT)n	associated poly(dA-dC) and poly(dG-dT)
poly(A)+poly(U)	non-associated poly(A) and poly(U)
poly(A),poly(U)	poly(A) and poly(U), no definite information on association

The abbreviations kb (kilobases), nt [nucleotide(s)] and bp [base-pair(s)] may be used in discussions of nucleic acid sequences without definition.

The use of a single symbol to designate a variety of possible nucleotides at a single position has become widespread. The following set of symbols, applicable to both DNA and RNA, has been recommended. These symbols do not discriminate between DNA and RNA, and the symbol T is used at all positions where U might appear in the RNA. Sequences may be assumed to have a deoxyribose phosphate (DNA) backbone unless otherwise specified; in circumstances where confusion between DNA and RNA is possible, the sequence may be prefixed with the lower-case letter d or r.

G	guanine		S	G or C
A	adenine		W	A or T
T	thymine		H	A or C or T
C	cytosine		B	G or T or C
R	G or A		V	G or C or A
Y	T or C		D	G or A or T
M	A or C		N	G or A or T or C
K	G or T

Sugars

These symbols are for use only in representing polymers or sequences and in Tables and Figures:

Ara	Arabinose	Glc	Glucose
dRib	2-Deoxyribose	Man	Mannose
Fru	Fructose	Neu	Neuraminic acid
Fuc	Fucose	Rib	Ribose
Gal	Galactose	Xyl	Xylose

When it is necessary to indicate furanose or pyranose, the letter f or p after the saccharide symbol may be used: e.g. Ribf for ribofuranose.

The following suffixes may be used, also without definition, to indicate derivatives:

NeuAc or AcNeu suffices for N-acetylneuraminate.

Two systems (the extended and the condensed) exist for the representation of oligosaccharide chains. Either may be used.

In the extended system the configurational symbol ( or ) is included before the symbol for the monosaccharide, and is separated therefrom by a hyphen. The anomeric symbol ( or ) is included before the configurational symbol and separated therefrom by a hyphen. Between the symbol (abbreviated name) of one monosaccharide group or residue and the next are placed two locants that indicate the respective positions involved in this glycosidic union. These locants are separated by an arrow (directed from the locant corresponding to the glycosyl carbon atom to the locant corresponding to the carbon atom carrying the hydroxy group involved) and are enclosed in parentheses. The position of a branch is indicated above or below the main chain, with the numerals and an arrow indicating the glycosidic linkage:

The hyphens, except that separating the configurational symbol and the symbol for the monosaccharide, may be omitted.

In the condensed system the common configuration and ring size are implied in the symbol. Thus, Glc means -glucopyranose; Fru, -fructofuranose; and Fuc, -fucopyranose. Whenever the configuration or ring size is found to differ from the common one, or is to be emphasized, this may be indicated by using the appropriate symbols from the extended system. The anomeric descriptor indicates the configuration of the glycoside linkage, and is therefore placed before the locant if the direction of the bond is to the right, or after the locant if the direction of the bond is to the left. The two locants are separated by a hyphen. No hyphens are used between the symbol for the sugar and the parentheses indicating the glycosidic bond; such parentheses may be omitted in representing branched oligosaccharides, when parentheses are used to indicate the branches:

Glc1-4(Xyl1-2)Glc1-4Man

The condensed form may be shortened further by (i) omitting locants of anomeric carbon atoms, (ii) omitting the parentheses around the specifications of linkage, and (iii) omitting hyphens if desired:

Glc4(Xyl2)Glc4Man

(Poly)phosphoinositides and their hydrolysis products

The following, and their various combinations with appropriate locants, need not be defined:

Ptd	phosphatidyl
Ins	1-myo-inositol
P	phosphate

Multiple locants should be placed in parentheses, e.g. PtdIns(4,5)P₂ symbolizes phosphatidylinositol 4,5-bisphosphate and Ins(1,4,5)P₃ symbolizes myo-inositol 1,4,5-trisphosphate (but note Ins4P etc. for the monophosphate).

The alternative ('Chilton') forms (e.g. PIP₂ and IP₃) may be used if defined; one or the other form should be used consistently throughout a paper.

Table 1 Accepted abbreviations (may be used without definition in the title, page-heading title and text; see also Table 3)

Animals

The full binominal Latin names should be included for all experimental animals other than common laboratory animals. The strain, and if possible the source, of laboratory animals should be stated. The source, and if possible the composition, of the diet of laboratory animals should be specified; this is particularly important in papers reporting the effects of dietary manipulation.

Array data

The Biochemical Journal recommends that authors adhere to the MIAME guidelines for the submission of gene chip array data (see http://www.mged.org/Workgroups/MIAME/miame.html)

Studies looking at large-scale gene expression across a range of different tissues that do not provide insights into mechanisms are unlikely to be accepted.

Biochemical nomenclature

As far as possible authors should follow the recommendations of the Nomenclature Committee of IUBMB and the IUPAC–IUBMB Joint Commission on Biochemical Nomenclature (see http://www.chem.qmul.ac.uk/iubmb/)

Centrifugation

When conditions for centrifuging are critical, sufficient information should be given for the procedure to be repeated. The centrifugal field should be stated in multiples of g (9.81 m·s^–2), based on the average radius of rotation of the liquid, not rev./min. The quantitative composition of the suspension medium should be stated. The centrifuge rotor should be unambiguously identified and the temperature of operation stated. The time of operation of the rotor at sustained plateau speed (ignoring initial rotor acceleration and deceleration periods) should be stated. For example: 'The rotor was operated for 15 min at 2 °C and 10000 g'.

Density-gradient centrifugation

The make of centrifuge and rotor used, the temperature of the run and the composition of the gradients should be stated. Results should preferably be plotted against distance from rotor centre rather than against fraction numbers; it is then unnecessary to indicate top and bottom of the gradient. If fraction numbers are used, the top and bottom of the gradient should be indicated.

Ultracentrifuge data

Sedimentation coefficient (not constant), s; sedimentation coefficient corrected at 20 °C in water, s_20,w; sedimentation coefficient at zero concentration, s⁰, s; Svedberg unit (10^–13 s), S; partial specific volume, ; diffusion coefficient, D, D⁰, D_20,w etc. as for sedimentation coefficient. The temperature at which the sedimentation and diffusion measurements are made should be stated.

Chemical nomenclature

The IUPAC recommendations on chemical nomenclature should be followed (see http://www.chem.qmul.ac.uk/iupac/index.html).

Formulae

Chemical symbols may be used for elements, groups and simple compounds, but authors are advised that the excessive use of chemical symbols may reduce the readability of a paper.

R, R´, R´´ (or R¹, R², R³, R⁴ if more than three) should be used to denote variable substituents in formulae.

C₂₀ acid is used to denote an acid containing 20 carbon atoms, and C-3 or C₍₃₎ to denote the carbon atom numbered 3. C_18:0, C_18:1 etc. are used similarly to denote the number of double bonds in an unsaturated fatty acid.

Ions

These should be represented thus: Na⁺, Zn²⁺, Cl^–, PO₄^3–.

Naming compounds

All chemical names are run together, except for those of acids, acetals, esters, ethers, glycosides, ketones and salts, which are printed as separate words; hyphens are used to separate numbers, Greek letters or some configurational and italic prefixes from words, e.g. m-dinitrobenzene, ,-dimethyl--cysteine, 2-p-isopropylphenylheptane, ethyl methyl ketone (butan-2-one).

Optically active isomers

Names of chiral compounds whose absolute configuration is known may be differentiated by the prefixes R- and S- [see Pure Appl. Chem. (1976) 45, 11–30]. When the compounds can be correlated sterically with glyceraldehyde, serine or other standard accepted for a specialized class of compound, small capital letters -, - and ,- may be used for chiral compounds and their racemates. Where the direction of optical rotation is all that can be specified, (+)-, (-)- and (±)-, or dextro, laevo and 'optically inactive', are used.

Prefixes

Italics are used for certain prefixes, e.g. cis-, trans-, o-, m-, p-, dextro, laevo, meso, and also for O-, N- etc. to indicate an element carrying a substituent, e.g. N⁴- acetylsulphanilamide. Italics are not used for allo, bis, cyclo, epi, iso, n, neo, nor, s, t, tris.

An alphabetical order will be followed for prefixes denoting substituents. Syllables indicating multiple substituents, e.g. di-, tri-, do not count in deciding the order.

Locants (both numerical and alphabetical) should be separated by commas, e.g. p-nitroso-N,N-dimethylaniline.

Chromatography

The rate of movement of a substance relative to the solvent front in paper or thin-layer chromatography is best expressed as its R_F value, or, if relative to a reference compound, by its R_compound value. Solvents should be described in the form butan-l-ol/acetic acid/water (4:4:1, by vol.) or butan-l-ol/acetic acid (4:1, v/v).

Elution diagrams for chromatographic columns should be shown with the effluent volume increasing from left to right. Units of concentration and volume must be shown clearly. Column (i.e. bed) dimensions should always be quoted, and where possible column void volumes (V₀) should be given. Elution zone maxima may be characterized by elution volumes (V_e) or preferably by partition coefficients ( or K_D). The course of any eluent gradients used should be indicated clearly. Column calibration curves (e.g. plots of molecular mass against V_e or K_D) will not be published.

Computer programs

If the use of a computer program forms a significant and essential part of the work described in a paper, the program must be adequately documented, if not in the paper itself, then by reference to a previously published original source, or by deposition of the program listing with a suitable depository (it should be noted, however, that the Editorial Board cannot accept the responsibility of checking the accuracy of such deposited programs).

Electrophoresis

Electrophoretic mobilities (m) and the composition of the electrophoretic medium, pH and temperature should be quoted. The operative voltage should be specified where possible.

The symbol pI should be used for isoelectric point.

English style

The Biochemical Journal uses as a standard for spelling the Concise Oxford Dictionary of Current English (Clarendon Press, Oxford). Papers must be concise and should conform to normal English usage.

Enzymes

Enzyme nomenclature

The recommendations of the latest edition of Enzyme Nomenclature (1992, ISBN 0 12 227 165 3, Academic Press, San Diego; and its supplements) should be followed as far as possible (see http://www.chem.qmul.ac.uk/iubmb/enzyme). This includes the quoting of EC numbers.

The Biochemical Journal recommends that authors use the new nomenclature for restriction enzymes, DNA, methyltransterases, homing endonucleases (and their genes) that has been proposed by Roberts et al. [(2003) Nucleic Acids Research 31 1805 - 1812].

Enzyme units

Units of the amount of enzyme should be defined in each paper, and this may be done in terms of the rate of reaction catalysed under conditions specified. The SI unit for the rate is 1 mol of substrate transformed/s (or, if necessary, 1 mol of measured product formed/s), and this gives the unit of the amount of enzyme that has been given the name of katal (symbol: kat). Units of the amount of enzyme may, however, be expressed in terms of the amount that can catalyse other rates, e.g. 1 mol of substrate transformed/min (the 'EC unit').

Kinetic constants

Velocity constants for the forward and the backward reactions in the nth step of an enzymic reaction should be represented by k_n and k_–n respectively. The Michaelis constant is defined as K_m = [S] when = V/2, where is the velocity of appearance of product or disappearance of substrate at a given substrate concentration [S] and V (or V_max) is the velocity when the enzyme is saturated with the substrate. When reactions with two substrates A and B are being considered, K = [A] when = V/2 and [B] has been extrapolated to infinity; a value for [A] when = V/2 at a finite concentration (which must be specified) of B should be referred to as the apparent K_m for A. K_s is the equilibrium constant of the dissociation of the substrate–enzyme complex. Catalytic-centre activity (not 'turnover number') is defined as the number of molecules of substrate transformed/s per catalytic centre.

Ethics

Animal experimentation

Experiments with animals should be performed in accordance with the legal requirements of the relevant local or national authority and a statement to this effect must be included in the Materials and Methods section. Procedures should be such that experimental animals do not suffer unnecessarily. The text of papers should include experimental details of the procedures and of anaesthetics used.

Information and advice about experiments involving animals are to be found in the Handbook for the Animal Licence Holder (1991), ISBN 0 900 490 276, obtainable from the Institute of Biology, 20 Queensberry Place, London SW7 2DZ, U.K., price £10.60, post free.

Human experimentation

Papers describing any experimental work with humans should include a statement that the research has been carried out in accordance with the Declaration of Helsinki (2000) of the World Medical Association, that the Ethical Committee of the Institution in which the work was performed has approved it, and that the subjects have given informed consent to the work.

Scientific publication

The Biochemical Journal is a member of COPE (Committee on Publication Ethics) and endorses its guidelines, including the Code of Conduct for Editors, which are available at http://www.publicationethics.org.uk. Complaints against the Journal must be submitted in writing to the Chairman of the Editorial Board; if a complaint is not resolved to the satisfaction of the complainant they have the option of referring the matter to COPE.

Authors may like to refer to the Ethical Guidelines to Publication of Chemical Research formulated by the American Chemical Society [see Biochemistry (1986) 25, 9A–10A].

Notwithstanding, the Editorial Board will not accept papers where the ethical aspects are, in the Board's opinion, open to doubt.

The Biochemical Journal will always investigate fully any matters of apparent misconduct that it becomes aware of.

Footnotes

These must not be used, except in Tables and in footnotes to the title page concerning abbreviations, the address for offprint requests, an author's current address or a sequence database accession number (in that order). Reference is made by the superscript numerals ^{1, 2, 3} etc. on the title page, and by the symbols * † ‡ § ¶ in that order in Tables.

Gene nomenclature and symbols

The Biochemical Journal encourages authors to use the symbols and nomenclature recommended by the HUGO Gene Nomenclature Committee which is responsible for approving and implementing unique human gene symbols and names, and works closely with the Mouse Genome Database and other organism databases. Considerable efforts are made to approve symbols acceptable to workers in the field, but sometimes it is not possible to use exactly what has previously appeared in the literature. In such cases the previously used symbols are listed as aliases for the approved nomenclature in the Human Genome Nomenclature Database (http://www.genenames.org/cgi-bin/hgnc_search.pl) and Entrez Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene) to allow retrieval of all the information available for each gene.

Approved mouse nomenclature may be obtained before submission from Lois Maltais, The Jackson Laboratory, Bar Harbor, Maine 04609-0800, U.S.A.; tel: +1 207 288 6429; fax: +1 207 288 6132; e-mail: nomen@informatics.jax.org; http://www.informatics.jax.org/mgihome/nomen/

`Homology'

The term 'homologous' has a precise meaning in biology of 'having a common evolutionary origin', but it has often been used in work on protein and nucleic acid sequences to mean simply 'similar'. A group of experts has urged that the interests of clarity are best served by restricting use to the more precise definition [Reeck, G.R. et al. (1987) Cell 50, 667; Lewin, R. (1987) Science 237, 1570]. The Biochemical Journal agrees with these arguments and seeks to preserve the distinction between 'homologous' and 'similar' in its pages.

Illustrations

Illustrations constitute an expensive item of publication; their number should be kept to a minimum.

Titles and legends

Each illustration should be supplied with an informative title and an explanatory legend, starting on a new line. The title and legend should make the general meaning comprehensible without reference to the text. Conditions specific to a particular experiment should be stated. Reference to the text for general experimental details is permissible provided there is no ambiguity. All Figure legends should be grouped in a section at the end of the text.

Lettering

Figures are not routinely relettered. Authors should ensure that nomenclature, abbreviations, etc. used in lettering of Figures correspond to those used in the text. Separate panels within Figures should be clearly marked (a), (b), (c) etc. so that they can be referred to easily in the legend and text.

Care is needed when using powers in axes labels to avoid numbers with too many digits (see the section Powers in Tables and Figures).

Line diagrams

Figures will usually be reduced in size to occupy a single column (width 8.5 cm) or less unless a larger format is necessary for clarity. All lettering and symbols should be produced to be at least 1.5 mm, but not more than 3 mm, after reduction. All curves and lines should be drawn clearly, and of a line thickness that allows for the reduction in size on final printing. Axes should not extend appreciably beyond the curves, and it is often unnecessary for an axis scale to start at 0; only the part of the scale relevant to the curves should be given. The use of tints should be avoided; however, if tints are necessary, please ensure that a dot fill of 100 lines per inch or lower is used.

The preferred symbols for experimental points are , , , , , . Symbols should not be generated by using tints or a graphics program. The same symbols must not be used on two curves where the points might be confused; subject to that limitation, however, the same symbols should, if possible, be used for the same entities throughout a paper. Individual curves may also be distinguished by distinctive line forms (e.g. —— and ----) or by single-letter labels or by brief explanatory labels (see below).

Authors are encouraged to use brief explanatory labels within a figure if it is thereby more readily understood and if the labels can be inserted without requiring a larger Figure.

Chemical structures must be clearly and accurately drawn.

Histograms

Simple histograms recording only a few values will not be published. The information can be given more accurately, usefully and concisely as a Table or as a sentence or two in the text. However, histograms will be acceptable when the visual complexity of the Figure overrides other considerations. Three-dimensional histograms are not acceptable.

Sequence diagrams

Amino acid and nucleotide sequences are often printed in a form that requires careful vertical alignment and are best supplied as a figure rather than as a table, thereby avoiding the misalignments that can be introduced by typesetting and obviating the need for proof-reading of large arrays of complex information. Tints should not be used to highlight parts of sequences.

Half-tone illustrations

For half-tone figures where the magnification is to be indicated (e.g. on electron micrographs), this should be done by adding a bar representing a stated length. The Biochemical Journal does not charge authors for half-tone reproduction.

Colour figures

These are accepted when, in the opinion of the Editorial Board, they are essential to illustrate a particular scientific point. The use of colour confocal images is only necessary for structures that image differentially. Authors will normally be required to pay the cost of colour reproduction (£550 for the first Figure and £300 for each subsequent Figure in a paper). For papers accepted from January 2007 onwards, all colour figures will be published free of charge provided that the corresponding author on the published paper has been a member of the Biochemical Society for at least two years.

If authors are unable to meet the costs of colour reproduction, they should appeal in writing to the Chairman of the Editorial Board, who may in certain circumstances recommend that the charges to authors be reduced.

Image manipulation

Images will be checked for manipulation when a paper is accepted. The Editorial Board may request that authors supply the original data for comparison against the prepared figures. If authors are unable to comply with such a request, the acceptance of the paper may be withdrawn.

The Biochemical Journal endorses the guidelines given in the Instructions for Authors of the Journal of Cell Biology, from where the following is reproduced by kind permission of Rockefeller University Press:

No specific feature within an image may be enhanced, obscured, moved, removed or introduced. The grouping of images from different parts of the same gel, or from different gels, fields or exposures must be made explicit by the arrangement of the figure (i.e. using dividing lines) and in the text of the figure legend. Adjustments of brightness, contrast or colour balance are acceptable if they are applied to the whole image and as long as they do not obscure, eliminate or misrepresent any information present in the original, including backgrounds. Without any background information, it is not possible to see exactly how much of the original gel is actually shown. Non-linear adjustments (e.g. changes to gamma settings) must be disclosed in the figure legend

Authors are encouraged to read the paper by M. Rossner and K. M. Yamada (2004) J. Cell Biol. 166, 11-15

Isotopes

Units of measurement

Where possible radioactivity should be expressed in absolute terms; the SI unit for radioactivity is the becquerel (symbol Bq), defined as 1 disintegration/s, but the curie (symbol Ci; 1 Ci = 3.7×10¹⁰ Bq) may also be used. Alternatively, radioactivity may be expressed as disintegrations (or counts) per unit of time, e.g. disintegrations/s (d.p.s.) or counts/min (c.p.m.).

Isotopically labelled compounds

The symbol for the isotope introduced is placed in square brackets directly attached to the front of the name (word), as in [¹⁴C]urea. When more than one position in a substance is labelled by means of the same isotope and the positions are not indicated (as below), the number of labelled positions is added as a right-hand subscript, as in [¹⁴C₂]glycollic acid. The symbol 'U' indicates uniform and 'G' general labelling, e.g. [U-¹⁴C]glucose (where the ¹⁴C is uniformly distributed among all six positions) and [G-¹⁴C]glucose (where the ¹⁴C is distributed among all six positions, but not necessarily uniformly); in the latter case it is often sufficient to write simply '[¹⁴C]glucose'.

The isotopic prefix precedes that part of the name to which it refers, as in sodium [¹⁴C]formate, iodo[¹⁴C₂]acetic acid, 1-amino[¹⁴C]methylcyclopentanol (H₂N-¹⁴CH₂-C₅H₈-OH), -naphth[¹⁴C]oic acid (C₁₀H₇-¹⁴CO₂H), 2-acetamido-7-[¹³¹I]iodofluorene, fructose 1,6-[1-³²P]bisphosphate, -[¹⁴C]glucose, 2H-[2-²H]pyran, S-[8-¹⁴C]adenosyl[³⁵S]methionine. Terms such as '¹³¹I-labelled albumin' should not be contracted to '[¹³¹I]albumin' [since native albumin does not contain iodine (but ¹³¹I-albumin can be used)], and '¹⁴C-labelled amino acids' should similarly not be written as '[¹⁴C]amino acids' (since there is no carbon in the amino group).

When isotopes of more than one element are introduced, their symbols are arranged in alphabetical order, including ²H and ³H for deuterium and tritium respectively.

When not sufficiently distinguished by the foregoing means, the positions of isotopic labelling are indicated by Arabic numerals, Greek letters or prefixes (as appropriate), placed within the square brackets and before the symbol of the element concerned, to which they are attached by a hyphen; examples are [1-²H]ethanol (CH₃-C²H₂-OH), [1-¹⁴C]aniline, -[2-¹⁴C]leucine (or -[-¹⁴C]leucine), [carboxyl-¹⁴C]leucine, [Me-¹⁴C]isoleucine, [2,3-¹⁴C]maleic anhydride, [6,7-¹⁴C]xanthopterin, [3,4-¹³C,³⁵S]methionine, [2-¹³C,1-¹⁴C]acetaldehyde, [3-¹⁴C,2,3-²H,¹⁵N]serine.

The same rules apply when the labelled compound is designated by a standard abbreviation or symbol, other than the atomic symbol, e.g. [-³²P]ATP.

For simple molecules, however, it is often sufficient to indicate the labelling by writing the chemical formulae, e.g. ¹⁴CO₂, H₂¹⁸O, ²H₂O (not D₂O), H₂³⁵SO₄, with the prefix superscripts attached to the proper atomic symbols in the formulae. The square brackets are not to be used in these circumstances, nor when the isotopic symbol is attached to a word that is not a chemical name, abbreviation or symbol (e.g. '¹³¹I-labelled').

Isotopically substituted compounds

The attention of authors is drawn to the distinction between 'isotopically labelled' and 'isotopically substituted' compounds [see Eur. J. Biochem. (1978) 86, 9–25].

Mathematical modelling papers

The Biochemical Journal welcomes modelling papers where they advance our knowledge of biochemistry and cellular and molecular biology. However, such manuscripts will only be considered for publication if they also contain experimental testing of the mathematical model,i.e. by biochemical experimentation.

Micro-organisms

In the title, in the synopsis and at the first mention in the text, micro-organisms must be given their full binominal Latin name, which will be printed in italics (e.g. Escherichia coli). Each organism should preferably have been obtained from or deposited with a recognized collection of micro-organisms, and the collection number must be given. Alternatively, a strain number or name should be quoted; this should not be italicized. Names of ranks higher than genus (e.g. Eubacteriales, Lactobacilleae), generic names used adjectivally (e.g. 'staphylococcal') and names of micro-organisms used colloquially (e.g. as in 'most lactobacilli behave thus') are not italicized. The first (i.e. generic) name should be spelt with a capital letter. Elsewhere in the text, single-letter abbreviations may be given for the generic name; if two genera with the same initial letter are studied, abbreviations such as Strep. and Staph. should be used.

Great care is needed in verifying the identities of micro-organisms, and authors should bear in mind that the value of their work may be limited if material is wrongly named. Many major culture collections of micro-organisms are able to verify identifications. Authors are urged to deposit new organisms in pertinent culture collections so that they may be readily available to other workers.

Recommendations on nomenclature in bacterial genetics have been proposed by M. Demerec, E. A. Adelberg, A. J. Clark and P. E. Hartman [(1966) Genetics 54, 61–76]. Authors should follow these guidelines wherever appropriate. Genetic designations for various micro-organisms are listed in Genetic Maps (edited by S. J. O'Brien), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, U.S.A.

Molecular mass and the dalton

There are two preferred ways of specifying the mass of a biochemical entity. 'Relative molecular mass' (M_r; not 'molecular weight') is the ratio of the mass of a molecule to of the mass of the nuclide ¹²C; it is thus dimensionless. 'Molecular mass' is the mass of one molecule of a substance expressed in daltons (symbol Da) or atomic mass units; the dalton is defined as of the mass of one atom of ¹²C.

Thus a protein may be said to have a relative molecular mass of 50000 (M_r = 50000) or a molecular mass of 50000 Da (more conveniently, 50 kDa), and may be referred to as the 50000-M_r protein or the 50 kDa protein. It is not correct to express M_r in daltons or to use K to represent M_r 1000 or 1 kDa. Either 'M_r' or 'molecular mass (kDa)' should be used consistently throughout a single paper.

Nucleotide and protein sequences

Authors should note that nucleotide sequences should be fully determined on both strands of the DNA. An explicit statement to this effect and a supporting diagram summarizing the sequence data are normally sufficient evidence.

Papers reporting nucleotide sequences only are not acceptable as Accelerated Publications.

Before their paper can be published, authors of papers containing primary sequence data are required to have deposited their data with one of the major collaborative databases that comprise the Nucleotide Sequence Database Collaboration (INSDC): DNA Data Bank of Japan (DDBJ), EMBL Nucleotide Sequence Database and GenBank (see below for addresses). It is only necessary to submit to one database, as data are exchanged between DDBJ, EMBL and GenBank on a daily basis. The accession number provided by the Database must be included on the title page of the paper as a footnote. When depositing data please include a specific statement within the database record indicating how readers can obtain a sample of the DNA from which the sequence was reported; this could be simply a culture collection identifier for an organism or a specific individual, with contact details, who could deal with requests. For further information see the INSDC website (http://insdc.org).

Database addresses:

DNA Data Bank of Japan
Center for Information Biology
National Institute of Genetics
Mishima
Shizuoka 411
Japan
telephone: +81 559 81 6853
fax: +81 559 81 6849
e-mail: ddbjsub@ddbj.nig.ac.jp (for data submissions)
http://www.ddbj.nig.ac.jp

EMBL Nucleotide Sequence Submissions
European Bioinformatics Institute
Hinxton Hall
Cambridge CB10 1SD
U.K.
telephone: +44 1223 494401
fax: +44 1223 494472
e-mail: datasubs@ebi.ac.uk
http://www.ebi.ac.uk

GenBank Submissions
National Center for Biotechnology Information
Bldg. 38A, Rm 8N-803
Bethesda
MD 20894
U.S.A.
telephone: +1 301 496 2475
fax: +1 301 480 9241
e-mail: gb-sub@ncbi.nlm.nih.gov
http://www.ncbi.nlm.nih.gov

Pharmacological inhibitors

Papers that are restricted exclusively to the use of pharmacological inhibitors will generally not be accepted. Such studies should be complemented by alternative strategies (e.g. the use of siRNA) that substantiate the conclusions.

Physical quantities and units

The recommended SI symbols should be used for all physical quantities and units (see Quantities, Units and Symbols in Physical Chemistry, 3rd edn., 2007, RSC Publishing, Cambridge, U.K.). A list of the most commonly used quantities and units appears in Table 2. Where a quantity is given in terms of non-SI units, the SI equivalent should generally also be stated, e.g. either '42 kJ/mol' or '42 kJ/mol (10 kcal/mol)', but not '10 kcal/mol' alone. However, distance measurements at the molecular scale may be given in terms of the ångström (Å) only.

Table 2 Physical quantities and their units

Physical quantity	Name of unit	Symbol for unit	Definition of unit
Activity (of radioactive source)	becquerel	Bq	s-1
Amount of substance	mole*	mol
Dose absorbed (of radiation)	gray	Gy	J·kg-1
Electric capacitance	farad	F	A·s·V-1
Electric charge	coulomb	C	s·A
Electric conductance	siemens	S	A·V-1
Electric current	ampere*	A
Electric potential difference	volt	V	J·A-1·s-1
Electric resistance	ohm		V·A-1
Energy	joule	J	m2·kg·s-2
Force	newton	N	J·m-1
Frequency	hertz	Hz	s-1
Illuminance	lux	lx	m-2·cd·sr
Length	metre*	m
	ångström†	Å	10-10 m
Luminous flux	lumen	lm	cd·sr
Luminous intensity	candela*	cd
Magnetic flux	weber	Wb	V·s
Magnetic flux density	tesla	T	V·s·m-2
Mass	kilogram*	kg
Plane angle	radian	rad
Power	watt	W	J·s-1
Pressure	pascal	Pa	N·m-2
	bar†	bar	105 Pa
Solid angle	steradian	sr
Temperature (Celsius)	degree Celsius	°C	°C = K‡
Temperature (thermodynamic)	kelvin*	K
Time	second*	s
Volume	litre (cubic decimetre)	l (dm3)	10-3 m3

* SI base unit.

† These units do not belong to the International System of units, but may be used if defined.

‡ The Celsius temperature, t, is defined by t = T–T₀, where T is thermodynamic temperature and T₀ = 273.15 K.

Plants

The full binominal Latin names should be included for all plant species. Where appropriate, the variety and the source should be specified.

Powers in Tables and Figures

Care is needed where powers are used in Table headings and in Figures in order to avoid numbers with too many digits. The quantity expressed is to be preceded by the power of 10 by which its value has been multiplied. The units in which the quantity is expressed may not be multiplied by a power of 10; the unit may be changed by the use of prefixes, e.g. m, , n or p. For example: (i) an entry '2' under heading 10³ k means that the value of k is 0.002; an entry '2' under heading 10^-3 k means that the value of k is 2000; (ii) a concentration 0.00015 M may be expressed as 0.15 under heading 'concn. (mM)' or as 150 under heading 'concn. (M)' or as 15 under heading '10⁵×concn. (M)', but not as 15 under heading 'concn. (M×10^-5); (iii) complex quantities are treated similarly; a value for 1/[S] of 200 M^-1 would appear as '2' under the heading 10^-2/[S] (M^-1) or as '0.2' under the heading 1/[S] (mM^-1). Square brackets may conventionally be used to indicate concentration.

Prefixes for multiples and submultiples of units

These should be as follows:

Multiple	Prefix	Symbol	Multiple	Prefix	Symbol
1012	tera	T	10-2	centi	c*
109	giga	G	10-3	milli	m
106	mega	M	10-6	micro
103	kilo	k	10-9	nano	n
102	hecto	h*	10-12	pico	p
10	deka	da*	10-15	femto	f
10-1	deci	d*	10-18	atto	a

* To be avoided where possible (except for cm).

Promoter mapping studies

Simple promoter mapping studies are not acceptable unless they show novel and significant cis-acting elements and the factors they bind, and these extend our knowledge of the function of the gene in question.

Propagatable biological materials

Authors are encouraged to make samples of propagatable biological materials (including cell lines, DNA clones and antibodies) available to academic workers who request them. Authors are urged to deposit cell lines of more than local interest with appropriate collections at national centres (e.g. in Europe at the European Collection of Cell Cultures, Centre for Applied Microbiology and Research, Porton Down, Salisbury, Wilts. SP4 0J6, U.K., and in the U.S.A. at the American Type Culture Collection, 12301 Parklawn Drive, Rockville, MD 20852, U.S.A.).

Quantification of data

The Biochemical Journal places emphasis on provision of quantitative data. Experiments which involve comparison of data from gels, blots, autoradiograms or similar techniques should, wherever possible, be quantified in order to permit pooling and statistical analysis of data from independent experiments, although it may in addition be useful to illustrate representative experiments in pictorial form.

Figure legends should define what was actually measured, e.g. terms such as "percentage apoptosis" or "percentage necrosis" should be replaced by terms that exactly describe the experimental results such as "fraction of cells with DNA fragmentation", etc.

References and citations

The number of references should not normally exceed 50, and 20–30 references are frequently adequate.

The Numbering System must be used. References should be cited in the text by sequential numbers in square brackets, e.g. `[1]', `[2–6]', `[4,5,7–10]', etc. At the end of the paper references should be listed in numerical order, in the style shown in the following examples, preceded by the number. Thus:

1Igarashi, K. and Kashiwagi, K. (1999) Polyamine transport in bacteria and yeast. Biochem. J. 344, 633-642

Names and initials of all authors, the paper or chapter title, and first and last page numbers, should be provided for all references. Titles of journals should be abbreviated in accordance with the Chemical Abstracts Service Source Index (2004) and subsequent Quarterly Supplements (American Chemical Society; http://www.cas.org/).

References to books and monographs should be in accordance with the following example:

2Jackson, A. A. and Moran, B. J. (1995) Intestinal flora in the conservation of body nitrogen. In Role of Gut Bacteria in Human Toxicology and Pharmacology (Hill, M. J., ed.), pp. 39-58, Taylor and Francis, London

References to a paper 'in the press' are permissible provided that it has been accepted for publication (the name of the journal and documentary evidence of acceptance must be provided):

3Smith, A. (2001) Another paper. Biochem. J., in the press

Alternatively, for papers 'in the press', if the doi (digital object identifier) is known, then this should be cited instead:

4Flashman, E., Watkins, H. and Redwood, C. (2006) Localization of the binding site of the C-terminal domain of cardiac myosin-binding protein on the myosin rod. Biochem. J. doi:10.1042/BJ20060500

References to 'personal communication' and 'unpublished work' are permitted in the text only, not in the list of references; for the former citation, documentary evidence from the person quoted showing agreement with the quotation must be provided. A reference to `unpublished work' must be supported by the names and initials of all involved. The use of `in preparation', 'private communication' and 'submitted for publication' is not allowed.

References quoted in the synopsis must be given in full (surnames of all authors, year of publication, journal name, volume number, inclusive pagination). Such references should also be cited in the main text by number.

Authors should make their best endeavours to cite all previous publications with particular relevance to their manuscript. Failure to acknowledge properly such 'prior art' may result in the publication of an Erratum.

References are often the cause of many proof corrections, and inaccuracies hamper inter-journal linking and Medline links in the online journal. Please check the list carefully before submission.

URLs

WWW URLs are permitted in the text only, not in the reference list, and should be quoted only when a literature reference(s) will not suffice. Authors quoting URLs of WWW sites other than those maintained by internationally recognized organizations must provide written assurance from the Webmaster that the site will be maintained and the relevant information maintained on it.

Solutions

Description

Solutions should be described in terms of molarity (M); 'normality' (N) is not acceptable. Fractional concentrations should be expressed in the decimal system, e.g. 0.25 M HCl (not M/4 HCl). The term % must be defined as w/w, w/v or v/v, e.g. 5% (w/v) means 5 g/100 ml. For aqueous solutions of concentration less than 1%, w/v need not be inserted if it is clear that the concentration is stated in terms of weight of solute.

Incubation media such as Krebs–Ringer solution, Eagle's medium, Waymouth's medium etc. should be defined by reference.

The symbol for ionic strength (mol/l) is I.

Buffers

These must be specified so that readers can reproduce the conditions used by authors. It is often useful to give the complete composition of each solution, e.g. '0.09 M sodium acetate/ 0.01 M acetic acid, pH 5.6' (which means that a single solution has these concentrations of these substances) at the first mention or in the Experimental section. A short designation, e.g. '0.1 M sodium acetate buffer, pH 5.6', may be used elsewhere throughout the paper.

Table 3 lists accepted abbreviations for buffers; these need not be defined.

Table 3 Abbreviations for common buffers (may be used without definition)

Sources of materials

The commercial sources of chemicals and reagents should be stated, but company addresses need not be given. Addresses must be provided, however, for non-commercial sources of, e.g., antibodies or organism strains.

Spectra and spectroscopic data

Full spectra should be published when important or novel features are demonstrated; however, other spectra or spectral information may be published as Supplementary Data (see the Supplementary data section).

The spectra for UV and visible absorption, fluorescence, circular dichroism and optical rotation should have a wave-length scale (e.g. nm or m) whether or not a wavenumber scale (e.g. cm^-1) is given. Where possible, molar terms should be used in absorption, circular dichroism and optical rotation.

Circular dichroism (CD)

This is reported as the molar circular-dichroism absorption coefficient = _L-_R [or the molar ellipticity, []_M (see below)]. For biopolymers, molar concentrations in terms of the mean residue M_r are generally used. Units of are the same as for , i.e. litre·mol^-1·cm^-1 or M^-1·cm^-1.

Specific ellipticity [], molar ellipticity []_M and mean residue ellipticity []_m.r.w. are directly analogous to the terms used in optical rotation. The units of [] are as for [m]. Note that []_M = 3300×.

Electron spin (paramagnetic) resonance (ESR/EPR)

Derivative spectra are given, unless otherwise stated; a scale of the magnetic-field strength (in mT) and/or g values should be given. Peaks are described as, e.g., 'the g = 2 peak'.

Fluorescence spectroscopy

In reporting fluorescence excitation and emission spectra it should be stated whether intensities, F, are relative, normalized or corrected (and the nature of the correction).

Fluorescence-polarization data and spectra are reported as polarization ratio, P, or preferably anisotropy ratio, A; both are dimensionless.

Infrared spectroscopy (IR)

Spectra are reported as percentage transmittance, T, as a function of wavelength (given in m) or frequency (given in cm^-1). When assigning bands the units need be given for the first value only and the description should be in the style, e.g. '(broad NH band)'.

Mass spectrometry (MS)

Spectra may be described as, e.g. 'm/z 300 [M⁺ (the molecular ion)], 282 (M⁺–H₂O) etc.'. If parenthetic values are quoted for percentage peak heights, it should be stated what these are relative to.

Mössbauer spectroscopy

The absorption (in %, arbitrary units or crude channel counts) is plotted against the Doppler velocity, (in mm/s). The chemical shift, , in units of mm/s should be quoted relative to a specified standard (e.g. metallic iron at 290 K). The temperature should always be given and the applied magnetic field, if any, should be precisely described.

Nuclear magnetic resonance (NMR)

NMR chemical-shift data, , are expressed as parts per million (p.p.m.) and the reference compound must be quoted. The recommended convention is that downfield shifts are positively signed. Coupling constants are expressed in Hz.

For reporting structural NMR data the style suggested is: ' (_H, _C etc.) (solvent) chemical-shift value [integration, peak type, coupling constant (in Hz), designation (relevant proton in italics)]'. E.g. '_H [(²H)chloroform] 0.92 [6 H, d, J 6 Hz, CH(CH₃)], 2.16 (2 H, t, J 7 Hz, CH₂CH₂CO)'. Singlet, doublet etc. are abbreviated to s, d, etc. without definition, but other descriptions, e.g. broad and overlapping, should be in full.

Optical rotation