The Biochemical Journal publishes papers in English in all fields of biochemistry and cellular and molecular biology as conveyed by the nine Knowledge Environments (Biomolecules, Cell, ChemBio, Disease, Energy, Gene, Metabolism, Plant, Signal). The Knowledge Environments and the Deputy Chairs associated with them can be accessed via links on the top right of the journal home page. The primary consideration will be whether papers make a sufficient contribution to knowledge in these fields. Papers may include new results obtained experimentally, descriptions of new experimental methods of biochemical importance, or new interpretations of existing results. Novel theoretical contributions will be considered, although these papers should also contain some experimental testing of the theory. All work presented should have as its aim the development of biochemical concepts rather than the mere recording of facts. Preliminary, confirmatory or inconclusive work will not be published. The Biochemical Journal will not publish material that has been wholly or largely published elsewhere in any language, even as a preliminary communication or in unrefereed symposium proceedings or on the World Wide Web (WWW); equally, fragmentation of research into `least publishable units' is discouraged. The Journal places emphasis on the provision of quantitative data, with appropriate statistical analysis wherever possible.
The Biochemical Journal will not tolerate plagiarism in submitted manuscripts. Passages quoted or closely paraphrased from other authors (or from the submitting authors' own published work) must be identified as quotations or paraphrases, and the sources of the quoted or paraphrased material must be acknowledged. Use of unacknowledged sources will be construed as plagiarism. If any manuscript is found to contain plagiarized material the review process will be halted immediately.
Images will be checked for manipulation when a paper is accepted (see Image manipulation). 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 If authors are unable to comply with such a request, the acceptance of the paper may be withdrawn.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 interpretation of this policy is in the hands of the Editorial Board, who judge whether each paper submitted is acceptable in terms of science and presentation.
Submission of a paper to the Biochemical Journal implies that it has been approved by all the named authors, that all persons entitled to authorship have been so named, that it reports unpublished work that is not under consideration for publication elsewhere in any language, that conflicts of interest are declared and that if the paper is accepted for publication the authors will grant the Biochemical Society an exclusive licence to publish the paper (see section on Copyright policy). The Biochemical Journal endorses the Vancouver Guidelines on authorship as defined in the International Committee of Medical Journal Editors' (ICMJE) Recommendations for the Conduct, Reporting, Editing and Publication of Scholarly Work in Medical Journals, namely that entitlement to authorship should be based on all of the following criteria: (1) substantial contributions to conception and design, or acquisition of data, or analysis and interpretation of data; (2) drafting the article or revising it for important intellectual content;(3) final approval of the version to be published; (4) agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. Acquisition of funding, collection of data, or general supervision of the research group, alone, does not justify authorship. All contributors who do not meet the criteria for authorship should be listed in the Acknowledgements. On acceptance, a paragraph outlining the contribution of each author to the study will be requested and published as part of the paper.
"Painless Publishing" strategy
The Biochemical Journal operates a "Painless Publishing strategy" to ease the burden on authors where their work has been identified by the reviewers as novel and interesting by only requesting extra experimental work if this is absolutely necessary to justify the conclusions in the paper. In addition, authors whose papers are declined by the Biochemical Journal, but whose work is considered by the reviewers to be scientifically sound, will be offered the opportunity to publish their work in the Journal's sister Open Access journal Bioscience Reports.
The Biochemical Journal Knowledge Environments are currently:
BJ Biomolecules welcomes papers on the structure and function of biologically important molecules, encompassing scientific fields such as glycobiology, enzymology, single-molecule analysis and biophysics. Papers submitted to this knowledge environment generally should report a molecular structure of major biological interest, or require detail of a molecular structure in order to address a significant biological problem. Note that papers that represent only an incremental advance in knowledge are unlikely to be considered suitable for publication.
BJ Cell welcomes papers encompassing all aspects of cell biology, including, but not confined to, topics such as membrane biology, endo/exocytosis, trafficking, cell cycle, cellular migration, apoptosis, proteolysis, cell matrix analysis, organelle biogenesis and the cytoskeleton.
BJ ChemBio welcomes research whereby chemistry and chemical tools in their broadest sense are used to study and manipulate biological systems. The development of new tools, compounds and reagents to probe biological questions in innovative ways are welcomed. Please note that papers should provide an element of new biological and/or mechanistic insight in order to be considered for this Knowledge Environment.
BJ Disease welcomes papers concerned with the molecular and cellular mechanisms of disease and developmental processes, infection and immunity, including newer avenues of scientific investigation such as cell reprogramming, regenerative and translational medicine. Note that papers submitted to this Knowledge Environment should present results that offer novel and significant insights into biochemical and mechanistic processes of disease or should provide insights into molecular mechanisms of cellular disease, in vivo systems or other experimental models.
BJ Energy welcomes papers in all aspects of free radical biology, including redox signalling, oxidative stress and hypoxia, sulfhydryls/thiols, mitochondria and bioenergetics.
BJ Gene welcomes papers in all aspects of transcription, RNA processing, translation, chromatin structure and nucleic acids. Note that 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. Neither would papers that go no further than simply identifying methylation sites in a gene or promoter be generally considered acceptable, unless they provide novel insights into the functional significance of the control of methylation or how methylation influences gene expression.
BJ Metabolism welcomes papers on all aspects of metabolic processes and their regulation from the cellular to the organismal level, including manuscripts with relevance to diabetes, obesity, nutrition, the cardiovascular system and cancer.
BJ Plant welcomes papers in all aspects of the biochemistry, biophysics, molecular and cellular biology of plants. Examples of topical areas include circadian rhythms, hormones, photosynthesis, nitrogen fixation, the cell wall, plant diseases/pathogens, plastids, membrane trafficking and transport processes and signalling.
BJ Signal welcomes papers in all aspects of intra- and intercellular signalling, including (but not confined to) such topics as second messengers, lipid mediators, reversible protein phosphorylation and ubiquitination, G-proteins, GTPases, receptors, integrins and growth factors.
Biochemical Journal Immediate Publications
PDFs of manuscripts are mounted on the Journal's website as Biochemical Journal Immediate Publications as soon as they are accepted, unless on submission the author has requested that this not be done. Biochemical Journal Immediate Publications are listed in and accessible through MEDLINE.
Biochemical Journal Online (http://www.BiochemJ.org)
Access to the previous 12 months content in Biochemical Journal online is restricted to current subscribers. To ensure that you have access, ask your subscribing librarian to contact firstname.lastname@example.org. An electronic back archive is freely available to all users.
Authors are encouraged to set up a hot-link from their home page to the abstract of their paper published in the online journal.
The Biochemical Journal Online offers authors the opportunity to enhance their papers with the multimedia adjuncts (e.g. time-lapse movies, three-dimensional structures). These will be submitted to peer review alongside the manuscript. To submit a paper with a multimedia adjunct, attach the file when you submit your manuscript online. Preferred formats are QuickTime for time-lapse movies, PDB for structures and Flash for animated schemes. There is no extra charge associated with the publication of a multimedia adjunct online.
Declaration of financial interests
Authors are strongly encouraged to disclose all relevant financial interests and sources of research funding that could be perceived to compromise the integrity of their article published in the Biochemical Journal.
The Biochemical Journal is published by Portland Press Ltd on behalf of the Biochemical Society, the sole owner of the journal. In order allow your article to be distributed as widely as possible in the Journal we ask that you grant Portland Press Ltd an exclusive licence to publish your article if it is accepted for publication. There are also a number of other reasons for this: (i) you authorize Portland Press Ltd and the Biochemical Society to act to defend your copyright, although we are under no obligation to act in this way; (ii) it will enable us to deal efficiently with requests from third parties to reproduce or reprint the article, or part of it.
Ownership of copyright remains with you as the author (or with your employer if they own the copyright in the work) and you retain non-exclusive rights to do the following (provided that the Journal is acknowledged in standard bibliographic citation form):
You need not seek permission from Portland Press Ltd and the Biochemical Society to apply the above rights.
Please note: you are NOT permitted to post the Portland Press Ltd version of your article (the Version of Record, VoR) online. For definitions of journal article versions, see the Recommended Practice of the National Information Standards Organization in Partnership with the Association of Learned and Professional Society Publishers.
Full details will be provided on the Licence to Publish that you will be asked to sign after you submit your article.
|Open Access option - Opt2Pay|
On acceptance authors may choose to pay a fee to make the Version of Record (VoR) of their paper freely available under the Creative Commons Attribution Licence (CC-BY). Portland Press will post all pre-paid articles on PubMed Central (PMC) on receipt of payment as a service to authors and permit their inclusion on PMC mirror sites. The Opt2Pay scheme allows authors to post the PDF version of the Version of Record (VoR), for non-commercial purposes, on their own or institutional website or to free public servers in the relevant subject area, in whole or in part according to the terms of the licence, provided they include a link to the published article on the Journal's website and that the Journal, the Biochemical Society and Portland Press are given the correct attributions. For more information, see Opt2Pay FAQs.
Portland Press books
Authors, Editors and all contributors to Portland Press journals may order books published by Portland Press, for their personal use, at 25% discount. A complete list of books can be found at http://www.portlandpress.com
The editorial offices are part of Portland Press Ltd., the publishing division of the Biochemical Society, and administers all aspects of the processing, subediting and printing of the Biochemical Journal. The Chairman of the Editorial Board, on behalf of the Editorial Board, takes responsibility for the journal's content.
Dr Clare Curtis, Executive Editor
Charles Darwin House
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telephone (UK) 020 7685 2410
(from overseas) +44 20 7685 2410
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(from overseas) +44 20 7685 2469
Charles Darwin House
12 Roger Street
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telephone (UK) 020 7685 2410
(from overseas) +44 20 7685 2410
fax (UK) 020 7685 2469
(from overseas) +44 20 7685 2469
Portland Customer Services
Charles Darwin House
12 Roger Street
London WC1N 2JU
telephone (UK) 020 7685 2410
(from overseas) +44 20 7685 2410
fax (UK) 020 7685 2469
(from overseas) +44 20 7685 2469
The Editorial Board and the Editorial Advisory Panel
Members of the Editorial Board, which is international, are appointed by the Executive Committee of the Biochemical Society on the recommendation of the Editorial Board. The composition of the Board is such that there is a wide range of expert opinion covering most areas of research in biochemistry and cellular and molecular biology.
The Editors are supported by an international panel of some 400 Editorial Advisers. These are independent reviewers, who are expert each in their own specific field of biochemistry, and who review up to ten papers a year for the journal. The close association of the Advisers with the journal means that a high standard of reviewing can be maintained.
Editors normally serve for a period of 3 years, although this may be extended for a further 4 years in some cases. The composition of the Advisory Panel is reviewed each year. The names of the members of the Editorial Board are published on the Journal's website and in each issue of the print journal; those of the members of the Advisory Panel appear on the website and in part 2 of each print volume.
Authors may suggest potential reviewers for their paper in the letter of submission, but the journal will usually regard such suggestions as a guide only and is under no obligation to follow them. Authors may also specify the names of those they wish to be excluded from the review process for a particular paper; in such cases their wishes are usually respected, unless, of course, in the opinion of the journal such a request unreasonably excludes all the expertise available to it in that scientific area.
Handling of papers
Copies of submitted papers are sent simultaneously to a selected Adviser (or, occasionally, to another independent reviewer) and to a relevant Editor. The Adviser (or other reviewer) assesses the paper and sends a report directly to the Editor by a date stipulated by the editorial office. The Editor will, in the meantime, have reached an independent judgement and, on receipt of the report, compiles a combined editorial report based on both opinions. In some cases, Editors will seek further advice from other scientists, and the report then reflects the views of all consulted. If the Editor and Adviser disagree, even after direct discussion, a second Editor is asked for an opinion and, if need be, a further Adviser. This may also be done when review of a paper demands expertise in more than one field of biochemistry. All papers are therefore seen by at least two independent scientists, and sometimes by more. The time taken for review is monitored by the editorial office, so that the policy of the journal to give authors rapid decisions is sustained.
When a paper is judged to have scientific merit and thus to be basically acceptable, a Deputy Chairman will send an appropriate letter to the authors together with an editorial report containing comments for the authors' consideration. After revision by the author the paper is checked by an Editor before being finally prepared for press by the subeditors. After typesetting, proofs are supplied to authors (except for Accelerated Publications) for correction of printer's errors only. Information regarding the purchase of offprints will be provided on a form supplied with the proofs; no free offprints are available.
If a paper is to be declined, the reports and correspondence are seen by the Chairman or one of the Deputy Chairmen, who then writes an explanatory letter to the authors. Papers may be declined for several reasons. They may, in the opinion of the reviewers, be unsatisfactory scientifically in that the methodology is open to criticism or that the conclusions are not sufficiently supported by the evidence presented. They may contain material that is, in principle, of interest but which is not clearly expounded; many papers suffer from being overlong, with the result that the salient points are not as clear to the reader(s) as to the author(s). They may be sound but only of peripheral biochemical interest and thus of more relevance to another discipline. Finally, and often most contentiously, they may represent an insufficient advance in knowledge. It cannot be overemphasized that, because of pressure for space in the journal, scientific soundness alone is not sufficient reason for publication of a paper: it must represent a definite and significant contribution to the field of study. Thus, in general, preliminary or confirmatory papers, or those reporting the existence of well-known biochemical processes in sources not previously studied, will not be accepted.
The Chairman's, or Deputy Chairman's, letter will set out the reasons why a paper has been declined and will indicate whether this decision is a final one or whether suitable revision might improve the paper sufficiently for it to be reconsidered. In this latter instance, encouragement for resubmission does not imply that a revised version will necessarily be accepted. In all cases the decision of the Chairman of the Editorial Board will be final.
If a paper that is returned to the authors for amendment, for whatever reason, is not resubmitted within 3 months (1 month for Accelerated Publications) it will be treated as a new paper and the date of receipt will be altered to the date of resubmission.
It is accepted that the reviewers may from time to time come to decisions that are not easily accepted by authors. This may be because of a conflict of opinion or, for example, and as frequently happens, because the authors' point is felt by the reviewers to be obscured by the presentation. The journal is always willing to hear from authors and to consider their views sympathetically. Appeals against decisions will always be considered by the Editorial Board. In rare cases, and if the reviewers and the Chairman agree, the usual anonymity of the reviewers may be set aside to allow discussion between all parties concerned. In all cases the decision of the Chairman of the Editorial Board will be final.
The main way in which authors can contribute to shortening the time between receipt and publication of a paper is to follow the requirements and suggestions in these Instructions to Authors, and to write in a concise style, although sufficient information must always be included to permit repetition of the experimental work and to support the conclusions that are drawn. Papers containing over-lengthy or repetitive text or unnecessary Figures or Tables will always be returned for revision, with consequent delay in publication. Fragmentation of research into the 'least publishable unit' should be avoided, and authors considering the submission of a series of papers on the same topic, which usually involves some degree of repetition, should consider whether appropriate combination of two or more papers could be achieved without loss of clarity of presentation.
The Biochemical Journal publishes papers in all fields of biochemistry and cellular and molecular biology; therefore it is important that papers on specialized subjects should be written in such a way that their approach and conclusions are intelligible to the informed, but non-specialist, reader of the journal.
The Editorial Board reserves the right to reject papers that cannot adequately be assessed because of a poor standard of English.
Preferred format of papers
Our preferred format for papers is described below:
Before preparing papers, authors should consult a current issue of the journal to make themselves familiar with the general format, such as the use of cross-headings, layout of Tables and citation of references.
The full title should be concise (no more than 25 words) but informative to the general reader. Papers should also be headed by the authors' names (with one forename in full for each author, other forenames being given as initials) and by the name and full postal address (including postal code) of the establishment(s) where the work was done. The e-mail address of the corresponding author will be published, unless requested otherwise. If there is more than one institution involved in the work, authors' names should be linked to the appropriate insititution by the use of symbols *, , , §, and ¶ in that order. A short (page heading) title of up to 75 characters should also be provided.
Separate papers in a series should not be numbered, but subtitles may be used.
The abstract should have a maximum of 250 words. It should summarize the main findings of the paper in a clear manner for readers. Unnecessary details or material not described in the body of the paper should not be included. References quoted in the abstract must be given in full (surnames of all authors, year of publication, name of journal, volume number, inclusive pagination), and must not form part of the numbered reference system. Up to six keywords, of which at least three do not appear in the title, should be provided.
Important: the title and the abstract should clearly express the key points of your paper.
Please provide a summary statement for publication: this should highlight the key finding of your study. The statement should not exceed 40 words and should be written for a broad audience without the use of abbreviations and acronyms that are not widely known.
The main body of the paper should be divided into: (a) introduction; (b) experimental, including materials and methods; (c) results, with appropriate quantification and statistical treatment of data; (d) discussion; (e) acknowledgements, including declarations of interest (if any); (f) author contribution, outlining the contribution of each author to the study; (g) funding, in the form of a sentence with the funding agency written out in full followed by the grant number in square brackets, (h) numbered references; (i) Tables and Figures. It is often an advantage to combine (c) and (d) with gains of conciseness and clarity. The discussion section should not repeat the results, but only discuss their implications. Authors may cite as many papers as are realistically necessary to properly reference the manuscript. We encourage authors to attribute the original source of findings through the citation of primary research papers wherever possible.
Authors may find it helpful to know that a full page of text in the Biochemical Journal contains approximately 1100 words. When calculating the length of papers, allowance must be made for the space taken up by insertions such as Figures, Tables and Schemes, and this is best assessed by looking at a recent issue of the Journal. The Journal provides for authors to publish supplementary data provided it is not integral to the understanding of the paper (see Supplementary data).
Procedure for submission
Types of paper
1. Research Papers are the normal form of publication, and authors are strongly encouraged to keep the length to between six and eight printed pages. Authors should note that no paper, whatever its scientific merits, will be accepted if it exceeds the minimum length required for precision in describing the experiments and clarity in interpreting them. A concise well-written paper tends to be published more quickly. To allow the reviewers to assess possible overlap with previous work, all papers must be accompanied by duplicate copies of the author's relevant published work, including that on the WWW, and of all related papers that are in press or under editorial consideration in this or other journals. Failure to do so may seriously delay evaluation of the paper.
2. Accelerated Publications (APs) are short papers (normally no more than four printed pages) bringing particularly novel and significant findings to the attention of the research community. It is intended that a decision on acceptance or rejection will be made within 10 working days of receipt, and publication of accepted APs in an issue will follow within ~ 7 weeks. The criteria of 'novelty and significance' are strictly enforced; APs may be rejected solely on the grounds of lack of novelty and significance or, if a Deputy Chair considers it appropriate, reviewed as full Research Papers. APs are not a path to accelerated publication of sound but non-urgent material. Papers reporting nucleotide sequences only are not acceptable as APs.
APs should be arranged in the usual style for a Biochemical Journal paper (synopsis, introduction, methods, results and discussion, with sufficient experimental detail to permit repetition of the work) and should not normally be longer than four printed pages of the journal [about 4000 words (24000 characters) of uninterrupted text, including references, but this number should be decreased to allow for the space taken up by Figures and Tables]. Papers submitted as APs that clearly exceed this length will be treated as Research Papers and the authors informed. The online submission procedures outlined above for Research Papers should be followed. The covering letter must contain a brief statement of why it is believed that the paper merits accelerated treatment.
3. Reviews will usually be solicited, although unsolicited reviews will be considered for publication. Prospective authors should first consult the Reviews Editor, via the US editorial office (email@example.com), and should enclose a short (one page) summary of the area they propose to cover. As well as full-length state of the art reviews, shorter more focused reviews in emerging areas will also be considered.
Covering letter (including justification for Accelerated Publications)
Master electronic copy of typescript, as a single-line-spaced PDF
complete text in appropriate style, pages numbered
names (including forenames) and addresses of authors
name, address, telephone and fax numbers and e-mail address of corresponding author (all correspondence and proofs will be sent to this author)
short (page heading) title
acknowledgements and declarations of interest (if any)
checked references in the Numbering System
Tables, with titles and legends
Figure legends, with titles
Related papers in press or under editorial consideration
Evidence of approval of personal communications
Evidence of submission of nucleic acid or protein sequences to an appropriate data bank
PDB Validation Report (annotated by the wwPDB) for papers reporting the structure of a biological macromolecule
On acceptance authors will be requested to supply a Word file of their paper to the editorial office. Authors must ensure that the file has been updated to incorporate all revisions, and hence that the file matches the final version of the manuscript seen by the reviewers. Our preferred word-processing format is Word for Windows version 6.
Tables should be prepared using the Microsoft Word table editor.
No artwork should be incorporated into the text files. Figures should be supplied as electronic files. Full instructions will be provided on acceptance and guidance notes for the preparation of figures are available here.
In-line equations should be typed as text. Displayed equations (unless prepared by the 'MathType Equation Editor') are re-keyed by our typesetter.
NOMENCLATURE, STYLE AND CONVENTIONS
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.
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.
|Aspartic acid or asparagine (undefined)||Asx||B|
|Cystine (half)||Cys or Cys|||
|Glutamic acid or glutamine (undefined)||Glx||Z|
|Unknown or 'other'||Xaa||X|
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.:
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, 753756].
Special considerations apply to the spacing and punctuation of the one-letter symbols [see Biochem. J. (1984) 219, 366368].
The symbols for ribonucleosides are as follows (the prefix r should be used if there is possible ambiguity):
The 2´-deoxyribonucleosides are designated by the same symbols preceded by d, e.g.:
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-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.:
|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.:
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, 753756], 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., An 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|
These symbols are for use only in representing polymers or sequences and in Tables and Figures:
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:
|A||for uronic acid (e.g. GlcA for glucuronic acid, GalA for galacturonic acid)|
|N and NAc||for 2-amino-2-deoxysaccharides and their N-acetyl derivatives (e.g. GlcN for glucosamine and GalNAc for N-acetylgalactosamine)|
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:
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:
The following, and their various combinations with appropriate locants, need not be defined:
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)
|ADP (CDP, GDP, IDP, UDP, XDP, dTDP)||adenosine 5'-diphosphate (and similarly for cytidine, guanosine, inosine, uridine, xanthosine, thymidine)|
|AFM||atomic force microscopy|
|AIDS||acquired immunodeficiency syndrome|
|AMP etc.||adenosine 5'-phosphate etc.|
|ANOVA||analysis of variance|
|ATP etc.||adenosine 5'-triphosphate etc.|
|ATPase etc.||adenosine 5'-triphosphatase etc.|
|BSA||bovine serum albumin|
|cAMP etc.||cyclic AMP (adenosine 3':5'-cyclic monophosphate) etc.|
|CFP, ECFP||cyan fluorescent protein, enhanced cyan fluorescent protein|
|CoA and acyl-CoA||coenzyme A and its acyl derivatives|
|EC50||concentration giving half-maximal response|
|EMSA||electrophoretic mobility-shift assay|
|EPR||electron paramagnetic resonance|
|ELISA||enzyme-linked immunosorbent assay|
|ESR||electron spin resonance|
|EST||expressed sequence tag|
|EXAFS||extended X-ray absorption fine structure|
|FACS||fluorescence-activated cell sorting|
|FBS||fetal bovine serum|
|FPLC||fast protein liquid chromatography|
|FRAP||fluorescence recovery after photobleaching|
|FRET||fluorescence/Förster resonance energy transfer|
|GFP, EGFP||green fluorescent protein, enhanced green fluorescent protein|
|G-protein||guanine-nucleotide-binding regulatory protein|
|GSH, GSSG||reduced and oxidized glutathione|
|HIV||human immunodeficiency virus|
|HLA||histocompatibility locus antigen|
|HMQC||heteronuclear multiple-quantum coherence|
|HPLC||high-performance liquid chromatography|
|HSQC||heteronuclear single-quantum coherence|
|IC50||concentration giving half-maximal inhibition|
|IgG etc.||immunoglobulin G etc.|
|MALDI||matrix-assisted laser-desorption ionization|
|MHC||major histocompatibility complex|
|MRI||magnetic resonance imaging|
|NAD+, NADH||oxidized and reduced nicotinamide-adenine dinucleotide|
|NADP+, NADPH||oxidized and reduced nicotinamide-adenine dinucleotide phosphate|
|NMR||nuclear magnetic resonance|
|NOE||nuclear Overhauser effect|
|NOESY||nuclear Overhauser enhancement spectroscopy|
|ORF||open reading frame|
|p||phosphorylated/phospho- (e.g. pTyr for phosphotyrosine)|
|PAGE||polyacrylamide gel electrophoresis|
|PCR||polymerase chain reaction|
|Pi, PPi||orthophosphate, pyrophosphate|
|PMA||phorbol 12-myristate 13-acetate|
|RACE||rapid amplification of cDNA ends|
|RFP, ERFP||red fluorescent protein, enhanced red fluorescent protein|
|RMSD||root mean square deviation|
|shRNA||short/small hairpin RNA|
|siRNA||short/small interfering RNA|
|SAXS||small-angle X-ray scattering|
|SDS||sodium dodecyl sulfate|
|SEM||scanning electron microscopy|
|SV40||simian virus 40|
|TEM||transmission electron microscopy|
|TOCSY||total correlation spectroscopy|
|TROSY||transverse relaxation optimized spectroscopy|
|YFP, EYFP||yellow fluorescent protein, enhanced yellow fluorescent protein|
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.
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.
As far as possible authors should follow the recommendations of the Nomenclature Committee of IUBMB and the IUPACIUBMB Joint Commission on Biochemical Nomenclature (see http://www.chem.qmul.ac.uk/iubmb/)
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·s2), 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'.
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.
Sedimentation coefficient (not constant), s; sedimentation coefficient corrected at 20 °C in water, s20,w; sedimentation coefficient at zero concentration, s0, s; Svedberg unit (1013 s), S; partial specific volume, ; diffusion coefficient, D, D0, D20,w etc. as for sedimentation coefficient. The temperature at which the sedimentation and diffusion measurements are made should be stated.
The IUPAC recommendations on chemical nomenclature should be followed (see http://www.chem.qmul.ac.uk/iupac/index.html).
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. C18:0, C18:1 etc. are used similarly to denote the number of double bonds in an unsaturated fatty acid.
These should be represented thus: Na+, Zn2+, Cl, PO43.
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).
names of chiral compounds whose absolute configuration is known may be differentiated by the prefixes R- and S- [see Pure Appl. Chem. (1976) 45, 1130]. 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.
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.
The rate of movement of a substance relative to the solvent front in paper or thin-layer chromatography is best expressed as its RF value, or, if relative to a reference compound, by its Rcompound 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 (Ve) or preferably by partition coefficients ( or KD). The course of any eluent gradients used should be indicated clearly. Column calibration curves (e.g. plots of molecular mass against Ve or KD) will not be published.
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).
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.
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.
The Biochemical Journal recommends that authors use the new nomenclature for restriction enzymes, DNA, methyltransferases, homing endonucleases (and their genes) that has been proposed by Roberts et al. [(2003) Nucleic Acids Research 31 1805 - 1812].
The Biochemical Journal requires that SI units are used.
Units of the amount of enzyme activity should be defined in each paper, and this may be done in terms of the rate of reaction catalysed under conditions specified. The conditions, such as temperature, pH, buffer composition and pressure (if not atmospheric), as well as the origin of the enzyme (natural purified, recombinant, any known post-translational modifications), must all be specified.
Steady-state, first-order enzyme and nucleic acids activity should be reported in terms of Vmax (nmol or μmol of product formed per amount of enzyme per time) or, when the active enzyme concentration is known, as kcat (Vmax divided by molar enzyme concentration) in units of s-1. Second-order rate constants should be reported as Vmax/Km or, when the active enzyme concentration is known, as kcat/Km in units of M-1 · s-1. Equilibrium binding constants (Km, Ki, Kd) should be reported as dissociation constants with units of concentration (M, mM, μM, or M-1, mM-1, μM-1 etc. as appropriate). Whenever possible, for reversible reactions Ki values should be determined in place of IC50.
All indirect measures of activity (change in absorbance, % change, etc.) should be converted into units of molarity to express kcat or Vmax. The use of linear transformation for Michaelis–Menten parameters is recognized to be inaccurate and therefore values of kcat (Vmax) and Km should be estimated using non-linear fitting and the software system used must be cited. Experimental confidence should include estimates of error (e.g. S.E.M.). In addition, by way of demonstrating data quality, inclusion of examples of some of the raw data is encouraged, at least as part of a Supplemental Data section.
A lack of activity should be defined in terms of a limit of detection taking into account the sensitivity of the assay, not as “not determined” or “not cleaved”.
See the Beilstein Institut/STRENDA (Standards for Reporting Enzymology Data) commission website (http://www.beilstein-institut.de/en/projekte/strenda/guidelines/) for additional suggestions of how to report and interpret kinetic data.
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. For additional information on the reporting of work in animals, please see the ARRIVE Guidelines.
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 (2013) 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.
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/. 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, 9A10A].
Notwithstanding, the Editorial Board will not accept papers where the ethical aspects are, in the Board's opinion, open to doubt.
The Biochemical Journal believes that its Editorial Board has a duty to protect the scientific record. Therefore it will always investigate fully any matter of apparent misconduct that it becomes aware of with respect to both published and unpublished papers, in conjunction with the institution where the work was performed or with funding bodies as appropriate.
The Biochemical Journal follows the guidelines published by COPE in respect of the retraction of articles.
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.
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/) 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 human gene symbols may be obtained before submission from the HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, U.K.; fax: +44 (0)1223 494 468; e-mail: firstname.lastname@example.org; http://www.genenames.org/
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: email@example.com; http://www.informatics.jax.org/mgihome/nomen/
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.
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.
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).
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. 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 , , , , , . 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 (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.
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.
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.
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.
There is no charge for the use of colour in figures. Colour should only be used if it is essential to illustrate a particular scientific point.
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
Please also see our document Best practices for preparing figures showing gel and blot data
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.).
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').
The attention of authors is drawn to the distinction between 'isotopically labelled' and 'isotopically substituted' compounds [see Eur. J. Biochem. (1978) 86, 925].
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.
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, 6176]. 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.
There are two preferred ways of specifying the mass of a biochemical entity. 'Relative molecular mass' (Mr; 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 (Mr = 50000) or a molecular mass of 50000 Da (more conveniently, 50 kDa), and may be referred to as the 50000-Mr protein or the 50 kDa protein. It is not correct to express Mr in daltons or to use K to represent Mr 1000 or 1 kDa. Either 'Mr' or 'molecular mass (kDa)' should be used consistently throughout a single paper.
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).
Authors describing new protein sequences or protein families are encouraged to contact the primary protein sequence and protein family resources UniProtKB (http://www.uniprot.org/help/uniprotkb) and InterPro (http://www.ebi.ac.uk/interpro/).
DNA Data Bank of Japan
Center for Information Biology
National Institute of Genetics
telephone: +81 559 81 6853
fax: +81 559 81 6849
e-mail: firstname.lastname@example.org (for data submissions)
EMBL Nucleotide Sequence Submissions
European Bioinformatics Institute
Cambridge CB10 1SD
telephone: +44 1223 494401
fax: +44 1223 494472
National Center for Biotechnology Information
Bldg. 38A, Rm 8N-803
telephone: +1 301 496 2475
fax: +1 301 480 9241
For studies employing cell-permeable chemical inhibitors to address protein function in cellular regulation, it is recommended that submitting authors consult the guidelines provided in Table 1 in the following review, which sets out useful criteria that should be met before any investigation using such compounds may be accepted for publication:
Cohen, P. (2010) Guidelines for the effective use of chemical inhibitors of protein function to understand their roles in cell regulation. Biochem. J. 425, 53-54
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 potential difference||volt||V||J·A-1·s-1|
|Magnetic flux density||tesla||T||V·s·m-2|
|Temperature (Celsius)||degree Celsius||°C||°C = K|
|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 = TT0, where T is thermodynamic temperature and T0 = 273.15 K.
The full binominal Latin names should be included for all plant species. Where appropriate, the variety and the source should be specified.
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.
These should be as follows:
* To be avoided where possible (except for cm).
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.
If, in their paper, authors describe new chemicals or propagatable biological materials (including cell lines, DNA clones and antibodies), they are strongly encouraged to make these available to academic workers who request them for non-commercial research projects. 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.).
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.
Authors may cite as many papers as are realistically necessary to properly reference the manuscript. We encourage authors to attribute the original source of findings through the citation of primary research papers wherever possible.
The Numbering System must be used. References should be cited in the text by sequential numbers in square brackets, e.g. '', '', '[4,5,710]', 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 PubMed. Full points should be included for each word abbreviated, e.g. Biochem. J.
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.
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.
Papers reporting data acquired by the use of RNAi (RNA interference) must demonstrate appropriate controls [see Nature Cell Biol. (2003), 5, 489-490]. Examples of controls that may be used include:
Note that use of a scrambled sequence is not an appropriate control.
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 KrebsRinger solution, Eagle's medium, Waymouth's medium etc. should be defined by reference.
The symbol for ionic strength (mol/l) is I.
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.
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.
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.
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 Mr 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×.
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'.
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.
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)'.
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.
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.
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.
This is reported as the specific rotation, , which is numerically equal to the rotation in degrees of a 1 g/ml solution with a pathlength of 1 dm (10 cm) at wavelength and temperature t. The concentration (g/100 ml) and solvent are quoted, e.g. '-27.5° (c 2 in methanol)'.
The corresponding molar expressions for the molar rotation, [M] = ×Mr and [m] = ×Mr/100, should be defined.
For biopolymers, the mean residue Mr is used, and [m]m.r.w. is the mean residue rotation. Where a refractive-index correction is applied, [m´], the reduced mean residue rotation, is reported. Dimensions of [m] and [m´] are degrees·cm2·dmol-1.
Optical rotatory dispersion is reported as the variation of  or [m] with wavelength (or frequency).
The general name for the quantity log(I0/I) is attenuance, and this reduces to absorbance when there is negligible scattering or reflection. The more general term attenuance should be used when scattering is considerable, e.g. when the quantity is measured to estimate the cell density of a culture. Otherwise the term absorbance should be used; neither should be called extinction or optical density. Symbols used are: A, absorbance; D, attenuance; a, specific absorption coefficient (litre·g-1·cm-1) (alternatively used A); , molar absorption coefficient (numerically equal to the absorbance of a 1 mol/litre solution in a 1 cm light-path) (use units of litre·mol-1·cm-1 or M-1·cm-1 and not cm2·mol-1). Wavelengths are given (in nm) as subscripts without units, e.g. A. No equals sign need be given between or A and its value.
Data from a sufficient number of independent experiments should be reported to permit evaluation of the reproducibility and significance of the results. When the object is to determine the value of a quantity or the statistical characteristics of a population, sufficient information is usually conveyed by the following: (i) the number of independent experiments (replicate measurements in an individual animal or preparation and results from pooled tissues etc. represent only one independent estimate); (ii) the mean value; (iii) the standard error of the estimate of mean value (S.E.M.), the standard deviation (S.D.) or the coefficient of variation, as may be appropriate. It should be made clear whether the S.E.M. or S.D. is used. A convenient form for inclusion in a Table is, for example, 263±2.5 (10), where the number in parentheses represents the number of values used in calculating the mean. Where statistical analysis is performed on replicate values within a single experiment, evidence should also be provided for reproducibility of findings between independent experiments (it would normally be expected that an experiment has been performed at least three times). In analysing the statistical significance of differences between data sets, it should be made clear which statistical tests have been applied and the choice of statistical test should be appropriate to the analysis.
For papers describing structures of biological macromolecules, the atomic coordinates and the related experimental data (structure factor amplitudes/intensities and/or NMR restraints) must be deposited at a member site of the Worldwide Protein Data Bank (www.wwpdb.org): RCSB PDB (www.pdb.org), PDBe (www.ebi.ac.uk/pdbe), PDBj (www.pdbj.org) or BMRB (www.bmrb.wisc.edu). The PDB ID should be included in the manuscript. Authors must agree to release the atomic coordinates and experimental data when the associated article is published. Questions relating to depositions should be sent to email@example.com
For papers submitted after 1 December 2012, authors must also provide the PDB Validation Report (after annotation by the wwPDB) for the information of the Biochemical Journal reviewers. The Validation Report should be uploaded as a Supplementary file on submission.
For papers describing structures of biological macromolecules from electron microscopy experiments, the 3D map should be deposited at either the EMBL-EBI (UK) or RCSB (USA) EMDB deposition site (http://www.emdatabank.org/). Once the map has been deposited, any fitted atomic coordinates should be deposited with the PDB by following the link provided from the EMDB deposition session.
As a service to authors, additional data (e.g. large tables or datasets) that may be of interest to readers can be published in the online journal (the journal of record) only where they are made freely available via a link from the abstract and paper. It is essential, however, that these data are not critical to the understanding of the paper and that the paper can stand alone.
Supplementary data should be supplied preferably as a PDF for the review process, must be cited in a relevant place in the text of the paper and be accompanied by a title and a self-explanatory legend. Offprints of papers will not contain Supplementary data.
Each Table should be supplied with an informative heading and an explanatory legend, starting on a new line. The heading and legend should make the general meaning comprehensible without reference to the text. Footnotes should be as few as possible, only being used where it is necessary to draw attention to a feature of a particular row, column or value. Conditions specific to the particular experiment should be stated. Reference to the text for general experimental methods is permissible provided that there is no ambiguity. Parameters being measured, with units if appropriate, should be clearly indicated in the column headings. Care is needed when using powers in Table headings to avoid numbers with too many digits (see the section Powers in Tables and Figures).
Tables should be typed on separate pages and their approximate position in the text indicated. Words or numerals should be repeated on successive lines; `ditto' or `,,' are not to be used.
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