MOLECULAR AND CELLULAR BIOLOGY

SCOPE

Molecular and Cellular Biology (MCB) is devoted to the advancement and dissemination of fundamental knowledge concerning the molecular biology of eukaryotic cells, of both microbial and higher organisms. Significant papers on cellular morphology and function, genome organization, regulation of genetic expression, morphogenesis, and somatic cell genetics (not simple linkage analyses) are invited for submission. In most cases, reports that emphasize methods and nucleotide sequence data alone (without experimental documentation of the functional significance of the sequence) will not be considered.

ASM publishes a number of different journals covering various aspects of microbiology. Each journal has a prescribed scope that must be considered in determining the most appropriate journal for each manuscript. The following guidelines may be of assistance.

Most manuscripts concerning virus-infected cells should be submitted to the Journal of Virology. Those in which emphasis is clearly on the cell, with the virus being incidental, are appropriate for MCB.

Questions about these guidelines may be directed to the editor in chief.

If transfer to another ASM journal is recommended by an editor, the corresponding author will be contacted.

Note that a manuscript rejected by one ASM journal on scientific grounds or on the basis of its general suitability for publication is considered rejected by all other ASM journals.

EDITORIAL POLICY

Use of Microbiological Information

The Council Policy Committee (CPC) of the American Society for Microbiology affirms the long-standing position of the Society that microbiologists will work for the proper and beneficent application of science and will call to the attention of the public or the appropriate authorities misuses of microbiology or of information derived from microbiology. ASM members are obligated to discourage any use of microbiology contrary to the welfare of humankind, including the use of microbes as biological weapons. Bioterrorism violates the fundamental principles expressed in the Code of Ethics of the Society and is abhorrent to ASM and its members.

ASM recognizes that there are valid concerns regarding the publication of information in scientific journals that could be put to inappropriate use as described in the CPC resolution mentioned above. Members of the ASM Publications Board will evaluate the rare manuscript that might raise such issues during the review process. However, as indicated elsewhere in these Instructions, research articles must contain sufficient detail, and material/information must be made available, to permit the work to be repeated by others. Supply of materials should be in accordance with laws and regulations governing the shipment, transfer, possession, and use of biological materials and must be for legitimate, bona fide research needs. Links to, and information regarding, these laws and regulations can be found at http://www.asm.org/ under the Public Policy tab. We ask that authors pay particular attention to the NSAR Select Agent/Toxin list on the CDC website http://www.selectagents.gov/index.html and the NSABB criteria for identifying dual use research of concern in the report “Proposed Framework for the Oversight of Dual Use Life Sciences Research: Strategies for Minimizing the Potential Misuse of Research Information” on the Office of Biotechnology Activities website http://oba.od.nih.gov/biosecurity/pdf/Framework%20for%20transmittal%200807_Sept07.pdf (p. 17-22).

Ethical Guidelines

ASM requirements for submitted manuscripts are consistent with the Uniform Requirements for Manuscripts Submitted to Biomedical Journals, as last updated by the International Committee of Medical Journal Editors in April 2010 (http://www.icmje.org).

Authors are expected to adhere to the highest ethical standards. The following sections of these Instructions include detailed information about ASM's ethical standards. Failure to comply with the policies described in these Instructions may result in a letter of reprimand, a suspension of publishing privileges in ASM journals, and/or notification of the authors’ institutions. Authors employed by companies whose policies do not permit them to comply with ASM policies may be sanctioned as individuals and/or ASM may refuse to consider manuscripts having authors from such companies. The ASM Publications Board wishes to clarify the following in particular.

Plagiarism.

Misappropriating another person's intellectual property constitutes plagiarism. This includes copying sentences or paragraphs verbatim (or almost verbatim) from someone else's work, even if the original work is cited in the references. The NIH ORI publication “Avoiding Plagiarism, Self-Plagiarism, and Other Questionable Writing Practices: a Guide to Ethical Writing” (http://ori.dhhs.gov/education/products/plagiarism/) can help authors identify questionable writing practices.

Plagiarism is not limited to the text; it can involve any part of the manuscript, including figures and tables, in which material is copied from another publication without permission and attribution. An author may not reuse his or her own previously published work without attribution; this is considered self-plagiarism.

Fabrication, manipulation, and falsification of data.

As a member of the Committee on Publication Ethics (COPE), ASM encourages authors to consult COPE's “Guidelines on Good Publication Practice” (http://publicationethics.org/static/1999/1999pdf13.pdf). Fabrication, manipulation, and falsification of data constitute misconduct. As defined by the U.S. Department of Health and Human Services, fabrication is “making up data or results and recording or reporting them,” and falsification is “manipulating research materials, equipment, or processes, or changing or omitting data or results such that the research is not accurately represented in the research record” (42 Code of Federal Regulations, §93.103). All sources and methods used to obtain and analyze data, including any electronic preprocessing, should be fully disclosed; detailed explanations should be provided for any exclusions.

Primary publication.

Manuscripts submitted to the journal must represent reports of original research, and the original data must be available for review by the editor if necessary.

By submission of a manuscript to the journal, the authors guarantee that they have the authority to publish the work and that the manuscript, or one with substantially the same content, was not published previously, is not being considered or published elsewhere, and was not rejected on scientific grounds by another ASM journal. It is incumbent upon the author to acknowledge any prior publication, including his/her own articles, of the data contained in a manuscript submitted to an ASM journal. A copy of the relevant work should be submitted with the paper as supplemental material. Whether the material constitutes the substance of a paper and therefore renders the manuscript unacceptable for publication is an editorial decision.

In brief, a paper is not acceptable for submission to an ASM journal if it, or its substance, has been published/posted in:

• A serial, periodical, or book

• A conference report or symposium proceedings

• A technical bulletin or company white paper

• A nonpersonal website

• Any other retrievable source

The following do not preclude submission to, or publication by, an ASM journal, as long as the posted data do not constitute the substance of a submission:

• Posting of a method/protocol on a nonpersonal website

• Posting of a limited amount of original data on a personal/university/corporate website or websites of small collaborative groups working on a problem

• Posting of unpublished sequence data on the Internet (the URL where the sequence is posted should be included in the text)

• Preliminary disclosures of research findings as meeting posters, webcast as meeting presentations, or published in abstract form as adjuncts to a meeting, e.g., part of a program

• Posting of theses and dissertations on a personal/university-hosted website

Availability of materials.

By publishing in the journal, the authors agree that, subject to requirements or limitations imposed by laws or governmental regulations of the United States, any DNAs, viruses, microbial strains, mutant animal strains, cell lines, antibodies, and similar materials described in the article are available from a national collection or will be made available in a timely fashion, at reasonable cost, and in limited quantities to members of the scientific community for noncommercial purposes. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner.

Similarly, the authors agree to make available computer programs, originating in the authors’ laboratory, that are the only means of confirming the conclusions reported in the article but that are not available commercially. The program(s) and suitable documentation regarding its (their) use may be provided by any of the following means: (i) as a program transmitted via the Internet, (ii) as an Internet server-based tool, or (iii) as a compiled or assembled form on a suitable medium (e.g., magnetic or optical). It is expected that the material will be provided in a timely fashion and at reasonable cost to members of the scientific community for noncommercial purposes. The authors guarantee that they have the authority to comply with this policy either directly or by means of material transfer agreements through the owner.

Permissions.

The corresponding author is responsible for obtaining permission from both the original author and the original publisher (i.e., the copyright owner) to reproduce or modify figures and tables and to reproduce text (in whole or in part) from previous publications.

Permission(s) must be obtained no later than the modification stage. The original signed permission(s) must be identified as to the relevant item in the ASM manuscript (e.g., “permissions for Fig. 1 in MCB00123-11”) and submitted to the ASM production editor on request. In addition, a statement indicating that the material is being reprinted with permission must be included in the relevant figure legend or table footnote of the manuscript. Reprinted text must be enclosed in quotation marks, and the permission statement must be included as running text or indicated parenthetically.

It is expected that the authors will provide written assurance that permission to cite unpublished data or personal communications has been granted. For supplemental material intended for posting by ASM (see “Supplemental Material”), if the authors of the MCB manuscript are not also the owners of the supplemental material, the corresponding author must send to ASM signed permission from the copyright owner that allows posting of the material, as a supplement to the article, by ASM. The corresponding author is also responsible for incorporating in the supplemental material any copyright notices required by the owner.

Authorship.

All authors of a manuscript must have agreed to its submission and are responsible for its content (initial submission and any subsequent versions), including appropriate citations and acknowledgments, and must also have agreed that the corresponding author has the authority to act on their behalf in all matters pertaining to publication of the manuscript. The corresponding author is responsible for obtaining such agreements and for informing the coauthors of the manuscript's status throughout the submission, review, and publication process. Submitting a paper before all coauthors have read and approved it is considered an ethical violation, as is failure to credit someone who qualifies as a coauthor; however, ASM does not itself investigate or attempt to resolve authorship disputes.

An author is one who made a substantial contribution to the overall design and execution of the experiments; therefore, ASM considers all authors responsible for the entire paper. Individuals who provided assistance, e.g., supplied strains or reagents or critiqued the paper, need not be listed as authors but may be recognized in the Acknowledgments section.

A study group, surveillance team, working group, consortium, or the like (e.g., the Active Bacterial Core Surveillance Team) may be listed as a coauthor in the byline if its contributing members satisfy the requirements for authorship and accountability as described in these Instructions. The names (and institutional affiliations if desired) of the contributing members only may be given in a footnote linked to the study group name in the byline or as a separate paragraph in the Acknowledgments section.

If the contributing members of the group associated with the work do not fulfill the criteria of substantial contribution to and responsibility for the paper, the group may not be listed in the author byline. Instead, it and the names of its contributing members may be listed in the Acknowledgments section.

All authors must agree to the order in which their names are listed in the byline. Statements regarding equal contributions by two or more authors (e.g., X.J. and Y.S. contributed equally to …) are permitted as footnotes to bylines and must be agreed to by all of the authors. Other statements of attribution may be included in the Acknowledgments section.

A change in authorship (order of listing, addition or deletion of a name, or corresponding author designation) after submission of the manuscript will be implemented only after receipt of signed statements of agreement from all parties involved.

Disputes about authorship may delay or prevent review and/or publication of the manuscript. Should the individuals involved be unable to reach an accord, review and/or publication of the manuscript can proceed only after the matter is investigated and resolved by the authors’ institution(s) and an official report of such and signed statements of agreement are provided to ASM.

Conflict of interest.

All authors are expected to disclose, in the manuscript submittal letter, any commercial affiliations as well as consultancies, stock or equity interests, and patent-licensing arrangements that could be considered to pose a conflict of interest regarding the submitted manuscript. (Inclusion of a company name in the author address lines of the manuscript does not constitute disclosure.) Details of the disclosure to the editor will remain confidential. However, it is the responsibility of authors to provide, in the Acknowledgments section, a general statement disclosing financial or other relationships that are relevant to the study. Examples of potentially conflicting interests that should be disclosed include relationships that might detract from an author's objectivity in presentation of study results, and interests whose value would be enhanced by the results presented. All funding sources for the project, institutional and corporate, should be credited in the Acknowledgments section, as described below. In addition, if a manuscript concerns a commercial product, the manufacturer's name must be indicated in the Materials and Methods section or elsewhere in the text, as appropriate, in an obvious manner.

Copyright

To maintain and protect the Society's ownership and rights and to continue to afford scientists the opportunity to publish in high-quality journals, ASM requires the corresponding author to sign a copyright transfer agreement on behalf of all the authors on acceptance. Unless this agreement is executed (without changes and/or addenda), ASM will not publish the article.

In the copyright transfer agreement signed by an author, ASM grants to that author (and coauthors) the right to republish discrete portions of his/her (their) article in any other publication (print, CD-ROM, and other electronic forms) of which he/she is (they are) the author(s) or editor(s), on the condition that appropriate credit is given to the original ASM publication. This republication right also extends to posting on a host computer to which there is access via the Internet. Except as indicated below, significant portions of the article may not be reprinted/posted without ASM's prior written permission, however, as this would constitute duplicate publication.

Authors may post their own published articles on their personal or university-hosted (but not corporate, government, or similar) websites without ASM's prior written permission provided that appropriate credit is given (i.e., the copyright lines shown at the top of the first page).

The copyright transfer agreement asks that authors who were U.S. government employees and who wrote the article as part of their employment duties be identified. This is because works authored solely by such U.S. government employees are not subject to copyright protection, so there is no copyright to be transferred. The other provisions of the copyright transfer agreement, such as author representations of originality and authority to enter into the agreement, apply to U.S. government employee-authors as well as to other authors.

ASM also requires that copyright transfer agreements be signed for cover artwork/photographs.

Copyright for supplemental material (see “Supplemental Material”) remains with the author, but a license permitting the posting by ASM will be sent, along with the article copyright transfer agreement, to the corresponding author for signing at the acceptance stage. If the author of the article is not also the copyright owner of the supplemental material, the corresponding author must send to ASM signed permission from the owner that allows posting of the material, as a supplement to the article, by ASM. The corresponding author is also responsible for incorporating into the supplemental material any copyright notices required by the owner.

Funding Agency Repositories

The National Institutes of Health (NIH) requests that its grantee and intramural authors provide copies of their accepted manuscripts to PubMed Central (PMC) for posting in the PMC Public Access Repository. However, MCB authors are automatically in compliance with this policy and need take no action themselves. For the past several years, ASM has deposited in PubMed Central all publications from all ASM journals. Further, ASM policy is that all primary research articles are made available to everyone, free, 6 months after publication through PubMed Central, HighWire, and international PubMed Central-like repositories. By having initiated these policies, ASM is in full compliance with NIH policy. For more information, see http://publicaccess.nih.gov/. ASM also allows MCB authors whose work was supported by similar funding agencies that have public access requirements like those of the NIH (e.g., the Wellcome Trust) to post their accepted manuscripts in publicly accessible electronic repositories maintained by those funding agencies. If a funding agency does not itself maintain such a site, then ASM allows the author to fulfill that requirement by depositing the manuscript (not the typeset article) in an appropriate institutional or subject-based open repository established by a government or noncommercial entity.

Since ASM makes the final, typeset articles from its primary-research journals available free of charge on the ASM Journals and PMC websites 6 months after final publication, ASM recommends that when submitting the accepted manuscript to PMC or a similar public access site, the author specify that the posting release date for the manuscript be no earlier than 6 months after publication of the typeset article by ASM.

Use of Human Subjects or Animals in Research

The use of human subjects or other animals for research purposes is regulated by the federal government and individual institutions. Manuscripts containing information related to human or animal use should clearly state that the research has complied with all relevant federal guidelines and institutional policies. Copies of these guidelines and policy statements must be available for review by the editor if necessary.

Patient Identification

When isolates are derived from patients in clinical studies, do not identify them by using the patients’ initials, even as part of a strain designation. Change the initials to numerals or use randomly chosen letters. Do not give hospital unit numbers; if a designation is needed, use only the last two digits of the unit. (Note: established designations of some viruses and cell lines, although they consist of initials, are acceptable [e.g., JC virus, BK virus, and HeLa cells].)

Nucleotide and Amino Acid Sequences

Newly determined nucleotide and/or amino acid sequence data must be deposited and GenBank/EMBL/DDBJ accession numbers must be included in the manuscript no later than the modification stage of the review process. It is expected that the sequence data will be released to the public no later than the publication (online posting) date of the accepted manuscript. The accession numbers should be included in a separate paragraph at the end of the Materials and Methods section. If conclusions in a manuscript are based on the analysis of sequences and a GenBank/EMBL/DDBJ accession number is not provided at the time of the review, authors should provide the sequence data as supplemental material.

It is expected that, when previously published sequence accession numbers are cited in a manuscript, the original citations (e.g., journal articles) will be included in the References section when possible and reasonable.

Authors are also expected to do elementary searches and comparisons of nucleotide and amino acid sequences against the sequences in standard databases (e.g., GenBank) immediately before manuscripts are submitted and again at the proof stage.

Analyses should specify the database, and the date of each analysis should be indicated as, e.g., January 2011. If relevant, the version of the software used should be specified.

See “Presentation of Nucleic Acid Sequences” for nucleic acid sequence formatting instructions.

The URLs of the databases mentioned above are as follows: DNA Data Bank of Japan (DDBJ), http://www.ddbj.nig.ac.jp/; EMBL Nucleotide Sequence Database, http://www.ebi.ac.uk/embl/; and GenBank, National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/.

Proper Use of Locus Tags as Systematic Identifiers for Genes

To comply with recommendations from the International Nucleotide Sequence Database (INSD) Collaborators and to avoid conflicts in gene identification, researchers should implement the following two fundamental guidelines as standards for utilization of locus tags in genome analysis, annotation, submission, reporting, and publication. (i) Locus tag prefixes are systematic gene identifiers for all of the replicons of a genome and as such should be associated with a single genome project submission. (ii) New genome projects must be registered with INSD, and new locus tag prefixes must be assigned in cooperation with INSD to ensure that they conform to the agreed-upon criteria. Locus tag prefixes that are currently in use may be searched at the NCBI locus tag database (http://www.ncbi.nlm.nih.gov/genomes/lltp.cgi).

Structural Determinations

Coordinates for new structures of macromolecules determined by X-ray crystallography or cryo-electron microscopy must be deposited in the Protein Data Bank and assigned identification codes must be included in the manuscript no later than the modification stage of the review process. It is expected that the coordinates will be released to the public no later than the publication (online posting) date of the accepted manuscript. Authors are encouraged to send coordinates with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph at the end of the Materials and Methods section.

The URLs for coordinate deposition are http://rcsb-deposit.rutgers.edu/ and http://pdbdep.protein.osaka-u.ac.jp/en/.

Microarray Data

The entire set of supporting microarray data must be deposited in the appropriate public database (e.g., GEO, ArrayExpress, or CIBEX) and the assigned accession number(s) must be included in the manuscript no later than the modification stage of the review process. It is expected that the data will be released to the public no later than the publication (online posting) date of the accepted manuscript. Authors are encouraged to send the relevant data with their original submission, however, so that reviewers can examine them along with the manuscript. The accession number(s) should be listed in a separate paragraph at the end of the Materials and Methods section.

The URLs of the databases mentioned above are as follows: Gene Expression Omnibus (GEO), http://www.ncbi.nlm.nih.gov/projects/geo/; ArrayExpress, http://www.ebi.ac.uk/microarray-as/ae/; and Center for Information Biology Gene Expression Database (CIBEX), http://cibex.nig.ac.jp/index.jsp.

Culture Deposition

MCB expects authors to deposit important microbial strains in publicly accessible culture collections and to refer to the collections and strain numbers in the text. Since the authenticity of subcultures of culture collection specimens that are distributed by individuals cannot be ensured, authors should indicate laboratory strain designations and donor sources as well as original culture collection identification numbers.

Supplemental Material

Supplemental material intended for posting by ASM should be restricted primarily to large or complex data sets or results that cannot readily be displayed in printed form because of space or technical limitations. Such material may include data from microarray, structural, biochemical, or video imaging analyses. In such cases, the manuscript submitted for review should include a distillation of the results so that the principal conclusions are fully supported without referral to the supplemental material.

Supplemental material intended for posting by ASM must be uploaded as a separate Supplemental Material file(s) in the manuscript submission and peer review system and will be reviewed along with the manuscript. The maximum size permitted for an individual file is 8 MB (20 MB for movie files). If your file exceeds this size, you must use the file compression utility WinZip to reduce the file size. The decision to publish (i.e., post online only) the material with the article if it is accepted will be made by the editor. ASM will post no more than 10 individual supplemental files with an individual article. It is possible that a manuscript will be accepted but that the supplemental material will not be.

To ensure broad access, supplemental files should be submitted in the following standard formats:

(i) Text. Word, RTF, or PDF files.

(ii) Figures. TIFF, EPS, high-resolution PDF, JPEG, or GIF format. Supplemental figures should not be embedded in the manuscript text.

(iii) Tables. Word, RTF, or PDF files.

(iv) Data sets. Excel (.xls), RTF, TXT, or PDF files.

(v) Movies. Audio Video Interleave (.avi), QuickTime (.mov), or MPEG files. All movies should be submitted at the desired reproduction size and length.

Unlike the manuscript, supplemental material will not be edited by the ASM Journals staff and proofs will not be made available. References related to supplemental material only should not be listed in the References section of an article; instead, include them with the supplemental material hosted by ASM or posted on a personal/institutional website.

Supplemental material will always remain associated with its article and is not subject to any modifications after publication.

Material that has been published previously (print or online) is not acceptable for posting as supplemental material. Instead, the appropriate reference(s) to the original publication should be made in the manuscript text.

Copyright for the supplemental material remains with the author, but a license permitting the posting by ASM must be signed by the corresponding author. If you are not the copyright owner, you must provide to ASM signed permission from the owner that allows posting of the material, as a supplement to your article, by ASM. You are responsible for including in the supplemental material any copyright notices required by the owner.

See also “Publication Fees.”

Warranties and Exclusions

Articles published in this journal represent the opinions of the authors and do not necessarily represent the opinions of ASM. ASM does not warrant the fitness or suitability, for any purpose, of any methodology, kit, product, or device described or identified in an article. The use of trade names is for identification purposes only and does not constitute endorsement by ASM.

SUBMISSION, REVIEW, AND PUBLICATION PROCESSES

Submission Process

All submissions to MCB must be made electronically. In 2011, the ASM journals are switching from Rapid Review to the eJournalPress manuscript submission and peer review system. Journals will be transitioned one by one over the course of several months, and the exact timing for MCB has not been determined. When the transition occurs, only new manuscript submissions will be through the eJP system. If you are returning a modified manuscript and made the original submission in Rapid Review, please use Rapid Review. For up-to-date information about where to submit your manuscript, please refer to the separate html version of Instructions to Authors, http://mcb.asm.org/misc/ifora.dtl, which is updated throughout the year.

Review Process

All manuscripts are considered to be confidential and are reviewed by the editors, members of the editorial board, or qualified ad hoc reviewers.

To expedite the review process, authors must recommend at least three possible reviewers, including one editorial board member, who have expertise in the field, who are not members of their institution(s), who have not recently been associated with their laboratory(ies), and who could not otherwise be considered to pose a conflict of interest regarding the submitted manuscript.

Copies of in-press and submitted manuscripts that are important for judgment of the present manuscript should be included as supplemental material to facilitate the review.

When a manuscript is submitted to the journal, it is given a control number (e.g., MCB00047-11 version 1) and assigned to one of the editors. (Always refer to this control number in communications with the editor and the Journals Department.) It is the responsibility of the corresponding author to inform the coauthors of the manuscript's status throughout the submission, review, and publication processes. The reviewers operate under strict guidelines set forth in “Guidelines for Reviewers” (http://www.journals.asm.org/misc/reviewguide.dtl) and are expected to complete their reviews expeditiously.

The corresponding author is notified, generally within 4 to 6 weeks after submission, of the editor's decision to accept, reject, or require modification. When modification is requested, the corresponding author must either submit the modified version within 2 months or withdraw the manuscript. A point-by-point response to the reviews must be provided with the revised manuscript, and a compare copy of the manuscript (without figures) should be included as supplemental material if the editor requested one.

Manuscripts that have been rejected, or withdrawn after being returned for modification, may be resubmitted to the same ASM journal if the major criticisms have been addressed. A manuscript rejected by one ASM journal on scientific grounds or on the basis of its general suitability for publication is considered rejected by all other ASM journals; however, a manuscript rejected solely on the basis of scope may be “resubmitted” to a more appropriate ASM journal. A manuscript is considered a resubmission no matter how much (or little) it differs from the rejected or withdrawn manuscript and regardless of how much time has passed.

For all resubmissions (to the same or a different journal, irrespective of the extent of the revisions, and irrespective of the amount of time between rejection and resubmission), the cover letter must state that the manuscript is a resubmission, and the former manuscript control number must be provided. A point-by-point response to the review(s) and a compare copy of the revised manuscript showing all changes must be included as supplemental material. Manuscripts resubmitted to the same journal are normally handled by the original editor.

Rejected manuscripts may be resubmitted only once unless permission has been obtained from the original editor or from the editor in chief.

Notification of Acceptance

When an editor has decided that a manuscript is acceptable for publication on the basis of scientific merit, the author and the Journals Department are notified. A PDF version of the accepted manuscript is posted online as soon as possible (see “MCB Accepts”).

The text files undergo an automated preediting, cleanup, and tagging process specific to the particular article type, and the illustrations are examined. If all files have been prepared according to the criteria set forth in these Instructions and those in the online manuscript submission system, the acceptance procedure will be completed successfully. If there are problems that would cause extensive corrections to be made at the copyediting stage or if the files are not acceptable for production, ASM Journals staff will contact the corresponding author. Once all the material intended for publication has been determined to be adequate, the manuscript is scheduled for the next available issue. The editorial staff of the ASM Journals Department completes the editing of the manuscript to bring it into conformity with prescribed standards.

MCB Accepts

For its primary-research journals, ASM posts online PDF versions of manuscripts that have been peer reviewed and accepted but not yet copyedited. This feature is called “[journal acronym] Accepts” (e.g., MCB Accepts) and is accessible from the Journals website. The manuscripts are published online as soon as possible after acceptance, on a weekly basis, before the copyedited, typeset articles are published. They are posted “as is” (i.e., as submitted by the authors at the modification stage) and do not reflect ASM editorial changes. No corrections/changes to the PDF manuscripts are accepted. Accordingly, there likely will be differences between the MCB Accepts manuscripts and the final, typeset articles. The manuscripts remain listed on the MCB Accepts page until the final, typeset articles are posted. At that point, the manuscripts are removed from the MCB Accepts page. The manuscripts are under subscription access control until 6 months after the typeset articles are posted, when free access is provided to everyone (subject to the applicable ASM license terms and conditions). Supplemental material intended, and accepted, for publication is not posted until publication of the final, typeset article.

Instructions on how to cite such manuscripts may be found in “References.”

Page Proofs

Page proofs, together with a query sheet and instructions for handling proofs, will be made available to the corresponding author electronically via a PDF file that can be accessed through a unique password. Since corresponding authors will be notified of the availability of their PDF proofs, instructed how to access information about page charges, reprints, and color figure charges (if applicable), and assigned their unique password via e-mail, an e-mail address must be supplied in the correspondent footnote. Failure to do so may result in a delay in publication. The PDF page proofs must be printed out, and corrections must be written on the hard copy. Queries must be answered on the query page or on a separate sheet of paper, and any changes related to the queries must be indicated on the proofs. Note that the copy editor does not query at every instance where a change has been made. Queries are written only to request necessary information or clarification of an unclear passage or to draw attention to edits that may have altered the sense. It is the author's responsibility to read the entire text, tables, and figure legends, not just items queried. As soon as the page proofs are corrected and signed by the person who proofread them (within 48 h), they should be mailed or sent by a courier service such as FedEx, not faxed or sent as an e-mail attachment, to the ASM Journals Department, 1752 N St., N.W., Washington, DC 20036-2904.

The proof stage is not the time to make extensive corrections, additions, or deletions. Figures as they appear in the proofs are for validation of content and placement, not quality of reproduction or color accuracy. Print output of figures in the PDF page proofs will be of lower quality than the same figures viewed on a monitor. Please avoid making changes to figures based on quality of color or reproduction in proof.

Important new information that has become available between acceptance of the manuscript and receipt of the proofs may be inserted as an addendum in proof with the permission of the editor. If references to unpublished data or personal communications are added, it is expected that written assurance granting permission for the citation will be included. Limit changes to correction of spelling errors, incorrect data, and grammatical errors and updated information for references to articles that have been submitted or are in press. If URLs have been provided in the article, recheck the sites to ensure that the addresses are still accurate and the material that you expect the reader to find is indeed there.

Questions about late proofs and problems in the proofs should be directed to the ASM Journals Department (e-mail, bzwadyk@asmusa.org; telephone, 202-942-9214). Questions about accessing or viewing your PDF proofs should be directed to Katie Gay of Cadmus Communications at 804-261-3155 or gayk@cadmus.com.

PDF Files

A corresponding author who has included an e-mail address in his/her “corresponding author” footnote will have limited access (10 downloads, total) to the PDF file of his/her published article. An e-mail alert will automatically be sent to him/her on the day the issue is posted. It will provide a URL, which will be required to obtain access, and instructions. An article may be viewed, printed, or stored, provided that it is for the author's own use.

Should coauthors or colleagues be interested in viewing the paper for their own use, the corresponding author may provide them with the URL; a copy of the article may not be forwarded electronically. However, they must be made aware of the terms and conditions of the ASM copyright. (For details, go to http://www.journals.asm.org/misc/terms.dtl.) Note that each such download will count toward the corresponding author's total of 10. After 10 downloads, access will be denied and can be obtained only through a subscription to the journal (either individual or institutional) or after the standard access control has been lifted (i.e., 6 months after publication).

Publication Fees

Page charges.

Authors whose research was supported by grants, special funds (including departmental and institutional), or contracts (including governmental) or whose research was done as part of their official duties (government or corporate, etc.) are required to pay page charges (based on the number of typeset pages, including illustrations, in the article).

For a corresponding author who is an ASM member, page charges are currently $67 per page for the first eight pages and $125 per page for each page in excess of eight (subject to change without notice). To obtain the member rate, the corresponding author must be an ASM member.

For a nonmember corresponding author, page charges are currently $80 per page for the first eight pages and $250 for each page in excess of eight (subject to change without notice). A corresponding author who is not an ASM member may join ASM to obtain the member rate.

If the research was not supported by any of the means described above, a request to waive the charges may be sent to the Journals Department, ASM, 1752 N St., N.W., Washington, DC 20036-2904, USA (fax, 202-942-9355; e-mail, aluckey@asmusa.org). The request must include the manuscript control number assigned by ASM and indicate how the work was supported. Waivers apply only to page charges; responsibility for color charges and other publication fees remains with the author.

Minireviews, Commentaries, and Letters to the Editor are not subject to page charges.

Color charges.

The cost of publishing in color must be borne by the author.

For a corresponding author who is an ASM member, color charges are currently $170 per color figure (subject to change without notice).

For a nonmember corresponding author, color charges are currently $375 per color figure (subject to change without notice). A corresponding author who is not an ASM member may join ASM to obtain the member rate.

Minireviews, Commentaries, and Letters to the Editor are not subject to color charges.

Reprints.

Reprints (in multiples of 100) may be purchased by all coauthors. In the proof notification e-mail, the corresponding author will be instructed how to access information about reprints.

The corresponding authors of Minireviews and Commentaries may receive 100 free reprints of their contribution; additional reprints (in multiples of 100) may be purchased if desired. As for regular articles, the corresponding author will be instructed, in the proof notification e-mail, how to access information about reprints.

Supplemental material fee.

Authors are charged a flat fee for posting supplemental material as an adjunct to their published article. For 2011, the fee is $190. (Exceptions: no fee is charged for supplemental material associated with Minireviews or Commentaries.)

Optional open access fee.

Author-paid optional open access (OOA) is now available for all article types. The 2011 fee is $2,000. This fee is in addition to any page charges, color charges, or supplemental material charges and permits immediate public access to both the preliminary “Accepts” version and the copyedited, typeset version published in the online journal. This option is in addition to the open access already provided through NIH's PubMed Central repository; all primary research published in ASM journals is freely available through PubMed Central 6 months after publication.

ORGANIZATION AND FORMAT

Editorial Style

The editorial style of ASM journals conforms to the ASM Style Manual for Journals (American Society for Microbiology, 2011, in-house document) and How To Write and Publish a Scientific Paper, 6th ed. (Greenwood Press, Westport, CT, 2006), as interpreted and modified by the editors and the ASM Journals Department.

The editors and the Journals Department reserve the privilege of editing manuscripts to conform with the stylistic conventions set forth in the aforesaid publications and in these Instructions.

The length of the text of a research article is limited to 40,000 characters (excluding spaces) for the abstract, introduction, Results, Discussion, and figure legends. The abstract is also limited to 200 words or fewer. Authors should note in the cover letter to the editor that the length of these text elements conforms to these limitations. There is no limit on the Materials and Methods section, the References section, or the number of figures if these are directly relevant to the study described.

On receipt at ASM, an accepted manuscript undergoes an automated preediting, cleanup, and tagging process specific to the particular article type. To optimize this process, manuscripts must be supplied in the correct format and with the appropriate sections and headings.

Type every portion of the manuscript double-spaced (a minimum of 6 mm between lines), including figure legends, table footnotes, and References, and number all pages in sequence, including the abstract, figure legends, and tables. Place the last two items after the References section. Manuscript pages should have line numbers; manuscripts without line numbers may be editorially rejected by the editor, with a suggestion of resubmission after line numbers are added. The font size should be no smaller than 12 points. It is recommended that the following sets of characters be easily distinguishable in the manuscript: the numeral zero (0) and the letter “oh” (O); the numeral one (1), the letter “el” (l), and the letter “eye” (I); and a multiplication sign (×) and the letter “ex” (x). Do not create symbols as graphics or use special fonts that are external to your word processing program; use the “insert symbol” function. Set the page size to 8½ by 11 inches (ca. 21.6 by 28 cm). Italicize any words that should appear in italics, and indicate paragraph lead-ins in boldface type.

Authors who are unsure of proper English usage should have their manuscripts checked by someone proficient in the English language.

Manuscripts may be editorially rejected, without review, on the basis of poor English or lack of conformity to the standards set forth in these Instructions.

Title, running title, and byline.

Each manuscript should present the results of an independent, cohesive study; thus, numbered series titles are not allowed. Avoid the main title/subtitle arrangement, complete sentences, and unnecessary articles. On the title page, include the title, the running title (not to exceed 54 characters and spaces), the name of each author, the address(es) of the institution(s) at which the work was performed, each author's affiliation, and a footnote indicating the present address of any author no longer at the institution where the work was performed. Place an asterisk after the name of the author to whom inquiries regarding the paper should be directed (see “Correspondent footnote,” below).

Also include on the title page the word count for the Materials and Methods section and the combined word count for the introduction, Results, and Discussion sections.

Study group in byline.

A study group, surveillance team, working group, consortium, or the like (e.g., the Active Bacterial Core Surveillance Team) may be listed as a coauthor in the byline if its contributing members satisfy the requirements for authorship and accountability as described in these Instructions. The names (and institutional affiliations if desired) of the contributing members may be given in a footnote keyed to the study group name in the byline or as a separate paragraph in Acknowledgments.

If the contributing members of the group associated with the work do not fulfill the criteria of substantial contribution to and responsibility for the paper, the group may not be listed in the author byline. Instead, it and the names of its contributing members may be listed in the Acknowledgments section.

Correspondent footnote.

The complete mailing address, a single telephone number, a single fax number, and a single e-mail address for the corresponding author should be included on the title page of the manuscript. This information will be published in the article as a footnote to facilitate communication, and the e-mail address will be used to notify the corresponding author of the availability of proofs and, later, of the PDF file of the published article. No more than two authors may be designated corresponding authors.

Abstract.

Limit the abstract to 200 words or fewer and concisely summarize the basic content of the paper without presenting extensive experimental details. Avoid abbreviations and references, and do not include diagrams. When it is essential to include a reference, use the same format as shown for the References section but omit the article title. Because the abstract will be published separately by abstracting services, it must be complete and understandable without reference to the text.

Introduction.

The introduction should supply sufficient background information to allow the reader to understand and evaluate the results of the present study without referring to previous publications on the topic. The introduction should also provide the hypothesis that was addressed and the rationale for the present study. Use only those references required to provide the most salient background rather than an exhaustive review of the topic.

Materials and Methods.

The Materials and Methods section should include sufficient technical information to allow the experiments to be repeated. When centrifugation conditions are critical, give enough information to enable another investigator to repeat the procedure: make of centrifuge, model of rotor, temperature, time at maximum speed, and centrifugal force (× g rather than revolutions per minute). For commonly used materials and methods (e.g., media and protein concentration determinations), a simple reference is sufficient. If several alternative methods are commonly used, it is helpful to identify the method briefly as well as to cite the reference. For example, it is preferable to state “cells were broken by ultrasonic treatment as previously described (9)” rather than to state “cells were broken as previously described (9).” This allows the reader to assess the method without constant reference to previous publications. Describe new methods completely and give sources of unusual chemicals, equipment, or microbial strains. When large numbers of microbial strains or mutants are used in a study, include tables identifying the immediate sources (i.e., sources from whom the strains were obtained) and properties of the strains, mutants, bacteriophages, and plasmids, etc.

A method or strain, etc., used in only one of several experiments reported in the paper may be described in the Results section or very briefly (one or two sentences) in a table footnote or figure legend. It is expected that the sources from whom the strains were obtained will be identified.

Results.

The Results section should include the results of the experiments. Reserve extensive interpretation of the results for the Discussion section. Present the results as concisely as possible in one of the following: text, table(s), or figure(s). Avoid extensive use of graphs to present data that might be more concisely presented in the text or tables. For example, except in unusual cases, double-reciprocal plots used to determine apparent K_m values should not be presented as graphs; instead, the values should be stated in the text. Similarly, graphs illustrating other methods commonly used to derive kinetic or physical constants (e.g., reduced-viscosity plots and plots used to determine sedimentation velocity) need not be shown except in unusual circumstances. Limit photographs (particularly photomicrographs and electron micrographs) to those that are absolutely necessary to show the experimental findings. Number figures and tables in the order in which they are cited in the text, and be sure to cite all figures and tables.

Discussion.

The Discussion should provide an interpretation of the results in relation to previously published work and to the experimental system at hand and should not contain extensive repetition of the Results section or reiteration of the introduction. In short papers, the Results and Discussion sections may be combined.

Acknowledgments.

The source of any financial support received for the work being published must be indicated in the Acknowledgments section. (It will be assumed that the absence of such an acknowledgment is a statement by the authors that no support was received.) The usual format is as follows: “This work was supported by Public Health Service grant CA-01234 from the National Cancer Institute.”

Recognition of personal assistance should be given as a separate paragraph, as should any statements disclaiming endorsement or approval of the views reflected in the paper or of a product mentioned therein.

References.

(i) References listed in the References section.

The References section must include all journal articles (both print and online), books and book chapters (both print and online), patents, theses and dissertations, published conference proceedings, meeting abstracts from published abstract books or journal supplements, letters (to the editor), and company publications, as well as in-press journal articles, book chapters, and books (publication title must be given). As we use the citation-name reference style, arrange the citations in alphabetical order (letter by letter, ignoring spaces and punctuation) by first-author surname and number consecutively. Provide the names of all authors for each reference. All listed references must be cited parenthetically by number in the text. Since title and byline information that is downloaded from PubMed does not always show accents, italics, or special characters, authors should refer to the PDF files or hard-copy versions of the articles and incorporate the necessary corrections in the submitted manuscript. Abbreviate journal names according to the PubMed Journals Database (National Library of Medicine, National Institutes of Health; available at http://www.ncbi.nlm.nih.gov/sites/entrez?db=journals), the primary source for ASM style.

Follow the styles shown in the examples below for print references.

1. Alexander, T. W., et al. 2008. Effect of subtherapeutic administration of antibiotics on the prevalence of antibiotic-resistant Escherichia coli bacteria in feedlot cattle. Appl. Environ. Microbiol. 74:4405-4416.

2. Cox, C. S., B. R. Brown, and J. C. Smith. J. Gen. Genet., in press.* {Article title is optional; journal title is mandatory.}

3. da Costa, M. S., M. F. Nobre, and F. A. Rainey. 2001. Genus I. Thermus Brock and Freeze 1969, 295,^AL emend. Nobre, Trüper and da Costa 1996b, 605, p. 404-414. In D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Springer, New York, NY.

4. Elder, B. L., and S. E. Sharp. 2003. Cumitech 39, Competency assessment in the clinical laboratory. Coordinating ed., S. E. Sharp. ASM Press, Washington, DC.

5. Falagas, M. E., and S. K. Kasiakou. 2006. Use of international units when dosing colistin will help decrease confusion related to various formulations of the drug around the world. Antimicrob. Agents Chemother. 50:2274-2275. (Letter.) {“Letter” or “Letter to the editor” is allowed but not required at the end of such an entry.}

6. Fitzgerald, G., and D. Shaw. In A. E. Waters (ed.), Clinical microbiology, in press. EFH Publishing Co., Boston, MA.* {Chapter title is optional.}

7. Forman, M. S., and A. Valsamakis. 2003. Specimen collection, transport, and processing: virology, p. 1227-1241. In P. R. Murray, E. J. Baron, M. A. Pfaller, J. H. Jorgensen, and R. H. Yolken (ed.), Manual of clinical microbiology, 8th ed. ASM Press, Washington, DC.

8. Garcia, C. O., et al. 1996. Detection of salmonella DNA in synovial membrane and synovial fluid from Latin American patients. Arthritis Rheum. 39(Suppl.):S185. {Meeting abstract published in journal supplement.}

9. Green, P. N., D. Hood, and C. S. Dow. 1984. Taxonomic status of some methylotrophic bacteria, p. 251-254. In R. L. Crawford and R. S. Hanson (ed.), Microbial growth on C₁ compounds. Proceedings of the 4th International Symposium. American Society for Microbiology, Washington, DC.

10. Odell, J. C. April 1970. Process for batch culturing. U.S. patent 484,363,770. {Include the name of the patented item/process if possible; the patent number is mandatory.}

11. O'Malley, D. R. 1998. Ph.D. thesis. University of California, Los Angeles, CA. {Title is optional.}

12. Rotimi, V. O., N. O. Salako, E. M. Mohaddas, and L. P. Philip. 2005. Abstr. 45th Intersci. Conf. Antimicrob. Agents Chemother., abstr. D-1658. {Abstract title is optional.}

13. Smith, D., C. Johnson, M. Maier, and J. J. Maurer. 2005. Distribution of fimbrial, phage and plasmid associated virulence genes among poultry Salmonella enterica serovars, abstr. P-038, p. 445. Abstr. 105th Gen. Meet. Am. Soc. Microbiol. American Society for Microbiology, Washington, DC. {Abstract title is optional.}

14. Stratagene. 2006. Yeast DNA isolation system: instruction manual. Stratagene, La Jolla, CA. {Use the company name as the author if none is provided for a company publication.}

*A reference to an in-press ASM publication should state the control number (e.g., MCB00577-11) if it is a journal article or the name of the publication if it is a book.

Online references must provide essentially the same information that print references do. For online journal articles, posting or revision dates may replace the year of publication, and a DOI or URL may be provided in addition to or in lieu of volume and page numbers. Some examples follow.

1. Charlier, D., and N. Glansdorff. September 2004, posting date. Chapter 3.6.1.10, Biosynthesis of arginine and polyamines. In R. Curtiss III et al. (ed.), EcoSal—Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, DC. http://www.ecosal.org/. {Note that each chapter has its own posting date.}

2. Dionne, M. S., and D. S. Schneider. 2002. Screening the fruitfly immune system. Genome Biol. 3:REVIEWS1010. http://genomebiology.com/2002/3/4/reviews/1010.

3. Smith, F. X., H. J. Merianos, A. T. Brunger, and D. M. Engelman. 2001. Polar residues drive association of polyleucine transmembrane helices. Proc. Natl. Acad. Sci. U. S. A. 98:2250-2255. doi:10.1073/pnas.041593698.

4. Winnick, S., D. O. Lucas, A. L. Hartman, and D. Toll. 2005. How do you improve compliance? Pediatrics 115:e718-e724.

Note: a posting or accession date is required for any online reference that is periodically updated or changed.

(ii) References cited in the text.

References to unpublished data, manuscripts submitted for publication, unpublished conference presentations (e.g., a report or poster that has not appeared in published conference proceedings), personal communications, patent applications and patents pending, computer software, databases, and websites should be made parenthetically in the text as follows.

… similar results (R. B. Layton and C. C. Weathers, unpublished data).

… system was used (J. L. McInerney, A. F. Holden, and P. N. Brighton, submitted for publication).

… as described previously (M. G. Gordon and F. L. Rattner, presented at the Fourth Symposium on Food Microbiology, Overton, IL, 13 to 15 June 1989). {For nonpublished abstracts and posters, etc.}

… this new process (V. R. Smoll, 20 June 1999, Australian Patent Office). {For non-U.S. patent applications, give the date of publication of the application.}

… available in the GenBank database (http://www.ncbi.nlm.nih.gov/genbank/index.html).

… using ABC software (version 2.2; Department of Microbiology, State University [http://www.state.micro.edu]).

URLs for companies that produce any of the products mentioned in your study or for products being sold may not be included in the article. However, company URLs that permit access to scientific data related to the study or to shareware used in the study are permitted.

(iii) References related to supplemental material.

References that are related only to supplemental material hosted by ASM or posted on a personal/institutional website should not be listed in the References section of an article; include them with the supplemental material itself.

(iv) Referencing ASM Accepts (publish-ahead-of-print) manuscripts.

Citations of ASM Accepts manuscripts should look like the following example.

Wang, G. G., M. P. Pasillas, and M. P. Kamps. 15 May 2006. Persistent transactivation by Meis1 replaces Hox function in myeloid leukemogenesis models: evidence for co-occupancy of Meis1-Pbx and Hox-Pbx complexes on promoters of leukemia-associated genes. Mol. Cell. Biol. doi:10.1128/MCB.00586-06.

Other journals may use different styles for their publish-ahead-of-print manuscripts, but citation entries must include the following information: author name(s), posting date, title, journal title, and volume and page numbers and/or DOI. The following is an example:

Zhou, F. X., H. J. Merianos, A. T. Brunger, and D. M. Engelman. 13 February 2001, posting date. Polar residues drive association of polyleucine transmembrane helices. Proc. Natl. Acad. Sci. U. S. A. doi:10.1073/pnas.041593698.

Minireviews

Minireviews are brief (limit of six printed pages exclusive of references) biographical profiles, historical perspectives, or summaries of developments in fast-moving areas. They must be based on published articles; they may address any subject within the scope of MCB.

Minireviews may be either solicited or proffered by authors responding to a recognized need. Irrespective of origin, Minireviews are subject to review and should be submitted via the online manuscript submission and peer review system. The cover letter should state whether the article was solicited and by whom.

Minireviews must have abstracts. Limit the abstract to 200 words or fewer. The body of the Minireview may have section headings and/or paragraph lead-ins.

Author biographies.

At the editor's invitation, corresponding authors of Minireviews may submit brief biographical sketches (limit, 150 words) of each contributing author, to be published at the end of the article. If the editor asks you to submit a modified manuscript, you should submit biographical text and photos with your modification.

Commentaries

Commentaries are communications written in response to invitations issued by the editors and concern topics of interest to the broad readership of MCB that are not necessarily covered by Minireviews. They should raise issues of interest to the scholarly community, initiate or focus discussion, or propose position or consensus statements for leadership groups in research and education. Reviews of the literature, methods and other how-to papers, and responses targeted at a specific published paper are not appropriate. Commentaries are subject to review.

The length may not exceed four printed pages, and the format is like that of a Minireview (see above) except that Commentaries do not have abstracts. (In the submission form, use “NA” or “Not applicable” in the space provided for the abstract.)

Letters to the Editor

Letters to the Editor are intended only for comments on final, typeset articles published in the journal (not on publish-ahead-of-print manuscripts) and must cite published references to support the writer's argument.

Letters may be no more than 500 words long and must be typed double-spaced. Refer to a recently published Letter for correct formatting. Note that authors and affiliations are listed at the foot of the Letter. Provide only the primary affiliation for each author.

All Letters to the Editor must be submitted electronically, and the manuscript type (Comment Letter) must be selected from the drop-down list in the submission form. The cover letter should state the volume and issue in which the article was published, the title of the article, and the last name of the first author. In the Abstract section of the submission form, put “Not Applicable.” Letters to the Editor do not have abstracts. The Letter must have a title, which must appear on the manuscript and on the submission form. Figures and tables should be kept to a minimum.

The Letter will be sent to the editor who handled the article in question. If the editor believes that publication is warranted, he/she will solicit a reply from the corresponding author of the article and make a recommendation to the editor in chief. Final approval for publication rests with the editor in chief.

Please note that some indexing/abstracting services do not include Letters to the Editor in their databases.

Errata

The Erratum section provides a means of correcting errors that occurred during the writing, typing, editing, or publication (e.g., a misspelling, a dropped word or line, or mislabeling in a figure) of a published article. Submit Errata via the online manuscript submission and peer review system (see “Submission, Review, and Publication Processes”). In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Erratum as a Microsoft Word file. Please see a recent issue for correct formatting.

Authors’ Corrections

The Author's Correction section provides a means of correcting errors of omission (e.g., author names or citations) and errors of a scientific nature that do not alter the overall basic results or conclusions of a published article (e.g., an incorrect unit of measurement or order of magnitude used throughout, contamination of one of numerous cultures, or misidentification of a mutant strain, causing erroneous data for only a [noncritical] portion of the study). Note that the addition of new data is not permitted.

For corrections of a scientific nature or issues involving authorship, including contributions and use or ownership of data and/or materials, all disputing parties must agree, in writing, to publication of the Correction. For omission of an author's name, letters must be signed by the authors of the article and the author whose name was omitted. The editor who handled the article will be consulted if necessary.

Submit an Author's Correction via the online manuscript submission and peer review system (see “Submission, Review, and Publication Processes”). Select Erratum as the manuscript type; there is no separate selection for an Author's Correction, but your Correction will be published as such if appropriate. In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Author's Correction as a Microsoft Word file. Please see a recent issue for correct formatting. Signed letters of agreement must be supplied as supplemental material (scanned PDF files).

Retractions

Retractions are reserved for major errors or breaches of ethics that, for example, may call into question the source of the data or the validity of the results and conclusions of an article. Submit Retractions via the online manuscript submission and peer review system (see “Submission, Review, and Publication Processes”). In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Retraction as a Microsoft Word file. Letters of agreement signed by all of the authors must be supplied as supplemental material (scanned PDF files). The Retraction will be assigned to the editor in chief of the journal, and the editor who handled the paper and the chairperson of the ASM Publications Board will be consulted. If all parties agree to the publication and content of the Retraction, it will be sent to the Journals Department for publication.

ILLUSTRATIONS AND TABLES

Illustrations

Image manipulation.

Computer-generated images may be processed only minimally. Processing (e.g., changing contrast, brightness, or color balance) is acceptable only if applied to all parts of the image, as well as to the controls, equally, and descriptions of all such adjustments and the tools used (both hardware and software) must be provided in the manuscript. Unprocessed data and files must be retained by the authors and be provided to the editor on request.

File types and formats.

Illustrations may be continuous-tone images, line drawings, or composites. Color graphics may be submitted, but the cost of printing in color must be borne by the author. Suggestions about how to reduce costs and ensure accurate color reproduction are given below.

On initial submission, illustrations should be supplied as PDF files, with the legend on the same page, to assist review. At the modification stage, production quality digital files must be provided, along with text files for the legends. The legends are copyedited and typeset for final publication, not included as part of the figure itself. All graphics submitted with modified manuscripts must be bitmap, grayscale, or in the RGB (preferred) or CMYK color mode. See “Color illustrations.” Halftone images (those with various densities or shades) must be grayscale, not bitmap. MCB accepts TIFF or EPS files but discourages PowerPoint for either black-and-white or color images.

For instructions on creating acceptable EPS and TIFF files, refer to the Cadmus digital art website, http://art.cadmus.com/da/index.jsp. PowerPoint requires users to pay close attention to the fonts used in their images (see the section on fonts below). If instructions for fonts are not followed exactly, images prepared for publication are subject to missing characters, improperly converted characters, or shifting/obscuring of elements or text in the figure. For proper font use in PowerPoint images, refer to the Cadmus digital art website, http://art.cadmus.com/da/instructions/ppt_disclaimer.jsp.

We strongly recommend that before returning their modified manuscripts, authors check the acceptability of their digital images for production by running their files through Rapid Inspector, a tool provided at the following URL: http://rapidinspector.cadmus.com/RapidInspector/zmw/index.jsp. Rapid Inspector is an easy-to-use, Web-based application that identifies file characteristics that may render the image unusable for production.

If you require additional information, please send an e-mail inquiry to digitalart@cadmus.com.

Minimum resolution.

It is extremely important that a high enough file resolution is used. All separate images that you import into a figure file must be at the correct resolution before they are placed. (For instance, placing a 72-dpi image in a 300-dpi EPS file will not result in the placed image meeting the minimum requirements for file resolution.) Note, however, that the higher the resolution, the larger the file and the longer the upload time. Publication quality will not be improved by using a resolution higher than the minimum. Minimum resolutions are as follows:

• 300 dpi for grayscale and color

• 600 dpi for combination art (lettering and images)

• 1,200 dpi for line art

Size.

All graphics should be submitted at their intended publication size; that is, the image uploaded should be 100% of its print dimensions so that no reduction or enlargement is necessary. Resolution must be at the required level at the submitted size. Include only the significant portion of an illustration. White space must be cropped from the image, and excess space between panel labels and the image must be eliminated.

• Maximum width for a 1-column figure: 3 inches (ca. 8.4 cm)

• Maximum width for a 2-column figure: 6 inches (ca. 17.4 cm)

• Minimum width for a 2-column figure: 4¼ inches (10.8 cm)

• Maximum height: 9 inches (23.0 cm)

Contrast.

Illustrations must contain sufficient contrast to be viewed easily on a monitor or on the printed page.

Labeling and assembly.

All final lettering and labeling must be incorporated into the figures. On initial submission, illustrations should be provided as PDF files, with the legend beneath each image, to assist review. At the modification stage, production quality digital figure files must be provided, along with text files for the legends. Put the figure number well outside the boundaries of the image itself. (Numbering may need to be changed at the copyediting stage.) Each figure must be uploaded as a separate file, and any multipanel figures must be assembled into one file; i.e., rather than uploading a separate file for each panel in a figure, assemble all panels in one piece and supply them as one file.

Fonts.

To avoid font problems, set all type in one of the following fonts: Arial, Helvetica, Times Roman, European PI, Mathematical PI, or Symbol. Courier may be used but should be limited to nucleotide or amino acid sequences, where a nonproportional (monospace) font is required. All fonts other than these must be converted to paths (or outlines) in the application with which they were created.

Compression.

When figure files are uploaded to the manuscript submission and peer review system, they may be compressed with WinZip.

Color illustrations.

Color costs must be borne by the author. See “Publication Fees.” All figures submitted in color will be processed as color. Adherence to the following guidelines will help to minimize costs and to ensure color reproduction that is as accurate as possible.

The online version is considered the version of record for MCB and all other ASM journals. To maximize online reproduction, color illustrations should be supplied in the RGB color mode, as either (i) RGB TIFF images with a resolution of at least 300 pixels per inch (raster files, consisting of pixels) or (ii) Illustrator-compatible EPS files with RGB color elements (vector files, consisting of lines, fonts, fills, and images). CMYK files are also accepted. Other than in color space, CMYK files must meet the same production criteria as RGB files. The RGB color space is the native color space of computer monitors and of most of the equipment and software used to capture scientific data, and it can display a wider range of colors (especially bright fluorescent hues) than the CMYK (cyan, magenta, yellow, black) color space used by print devices that put ink (or toner) on paper. For the print version (and reprints), ASM's print provider will automatically create CMYK versions of color illustrations from the supplied RGB versions. Color in the print journal may not match that in the online journal of record because of the smaller range of colors capable of being reproduced by CMYK inks on a printing press. For additional information on RGB versus CMYK color, refer to the Cadmus digital art site, http://art.cadmus.com/da/guidelines_rgb.jsp.

Drawings

Submit graphs, charts, complicated chemical or mathematical formulas, diagrams, and other drawings as finished products not requiring additional artwork or typesetting. All elements, including letters, numbers, and symbols, must be easily readable, and both axes of a graph must be labeled. Keep in mind that the journal is published both in print and online and that the same electronic files submitted by the authors are used to produce both.

When creating line art, please use the following guidelines:

1. All art must be submitted at its intended publication size. For acceptable dimensions, see “Size” above.

2. Avoid using screens (i.e., shading) in line art. It can be difficult and time-consuming to reproduce these images without moiré patterns. Various pattern backgrounds are preferable to screens, as long as the fill patterns are not imported from another application. If you must use images containing screens,

   1. Generate the image at line screens of 85 lines per inch or less.
   2. When applying multiple shades of gray, differentiate the gray levels by at least 20%.
   3. Never use levels of gray below 5% or above 95% as they are likely to fade out or become totally black when output.
   4. Use thick, solid lines that are no finer than 1 point in thickness.
   5. No type should be smaller than 6 points at the final publication size.
   6. Avoid layering type directly over shaded or textured areas.
   7. Avoid the use of reversed type (white lettering on a black background).
   8. Avoid heavy letters, which tend to close up, and unusual symbols, which the printer may not be able to reproduce in the legend.
   9. If colors are used, avoid using similar shades of the same color and avoid very light colors.

In figure ordinate and abscissa scales (as well as table column headings), avoid the ambiguous use of numbers with exponents. Usually, it is preferable to use the appropriate Système International d'Unités (SI) symbols (μ for 10⁻⁶, m for 10⁻³, k for 10³, and M for 10⁶, etc.). A complete listing of SI symbols can be found in the International Union of Pure and Applied Chemistry (IUPAC) publication Quantities, Units and Symbols in Physical Chemistry (RSC Publishing, Cambridge, United Kingdom, 2007); an abbreviated list is available at http://old.iupac.org/reports/1993/homann/index.html. Thus, representation of 20,000 cpm on a figure ordinate should be made by the number 20 accompanied by the label kcpm.

Where powers of 10 must be used, the journal requires that the exponent power be associated with the number shown. In representing 20,000 cells per ml, the numeral on the ordinate should be “2” and the label should be “10⁴ cells per ml” (not “cells per ml × 10⁻⁴”). Likewise, an enzyme activity of 0.06 U/ml might be shown as 6 accompanied by the label 10⁻² U/ml. The preferred designation is 60 mU/ml (milliunits per milliliter).

Presentation of Nucleic Acid Sequences

Long nucleic acid sequences must be presented as figures in the following format to conserve space. Print the sequence in lines of approximately 100 to 120 nucleotides in a nonproportional (monospace) font that is easily legible when published with a line length of 6 inches (ca. 15.2 cm). If possible, lines of nucleic acid sequence should be further subdivided into blocks of 10 or 20 nucleotides by spaces within the sequence or by marks above it. Uppercase and lowercase letters may be used to designate the exon-intron structure or transcribed regions, etc., if the lowercase letters remain legible at a 6-inch (ca. 15.2-cm) line length. Number the sequence line by line; place numerals representing the first base of each line to the left of the lines. Minimize spacing between lines of sequence, leaving room only for annotation of the sequence. Annotation may include boldface, underlining, brackets, and boxes, etc. Encoded amino acid sequences may be presented, if necessary, immediately above or below the first nucleotide of each codon, by using the single-letter amino acid symbols. Comparisons of multiple nucleic acid sequences should conform as nearly as possible to the same format.

Figure Legends

On initial submission, to assist review, the legend should be incorporated in the image file and appear beneath the figure. At the modification stage, figure legends must be provided as text files separate from the image file.

Legends should provide enough information so that the figure is understandable without frequent reference to the text. However, detailed experimental methods must be described in the Materials and Methods section, not in a figure legend. A method that is unique to one of several experiments may be reported in a legend only if the discussion is very brief (one or two sentences). Define all symbols used in the figure and define all abbreviations that are not used in the text.

Tables

Tables that contain artwork, chemical structures, or shading must be submitted as illustrations in an acceptable format at the modification stage. The preferred format for regular tables is Microsoft Word; however, WordPerfect and Acrobat PDF are also acceptable. Note that a straight Excel file is not currently an acceptable format. Excel files must be either embedded in a Word or WordPerfect document or converted to PDF before being uploaded. If your modified manuscript contains PDF tables and is being submitted in Rapid Review, select “for reviewing purposes only” at the beginning of the file upload process.

Tables should be formatted as follows. Arrange the data so that columns of like material read down, not across. The headings should be sufficiently clear so that the meaning of the data is understandable without reference to the text. See the “Abbreviations” section (below) of these Instructions for those that should be used in tables. Explanatory footnotes are acceptable, but more-extensive table “legends” are not. Footnotes should not include detailed descriptions of the experiment. Tables must include enough information to warrant table format; those with fewer than six pieces of data will be incorporated into the text by the copy editor. Table 1 is an example of a well-constructed table.

TABLE 1.

Yeast strains used in this study

Strain	Genotype	Reference or source
BY263	MATatrp1Δ63 GAL2+ura3-52 lys2-801 ade2-107 his3Δ200 leu2-Δ1	14
BY107a	MATα swi6Δ HIS3	This study
L40	MATahis3 leu2 trp1 URA3::lexA-lacZ LYS2::lexA-HIS3 gal80 ade	20

^aIsogenic relative to BY263.

Cover Photographs and Drawings

MCB publishes photographs and drawings on the front cover. Since we still want to optimize print presentation for covers even though the online journal is the journal of record (see above), color cover art must be prepared in the CMYK color space. Invitations are issued to authors whose manuscripts are returned for modification or whose manuscripts have been accepted for publication in MCB; material should be related to the work presented in the manuscript. Unsolicited photos will be considered in hard-copy format (two copies) only; if an unsolicited photo is chosen for the cover, the author may be asked to submit digital files. No material submitted for consideration will be returned to the author. Authors will be notified only if their cover art is selected. Copyright for the chosen material must be transferred to ASM. A short description of the cover material will be included at the end of the table of contents or the author index of the issue. Technical specifications are available from the cover editor, Roger J. Davis (mcbdavis@umassmed.edu).

NOMENCLATURE

Chemical and Biochemical Nomenclature

The recognized authority for the names of chemical compounds is Chemical Abstracts (CAS; http://www.cas.org/) and its indexes. The Merck Index, 14th ed. (Merck & Co., Inc., Whitehouse Station, NJ, 2006), is also an excellent source. For guidelines to the use of biochemical terminology, consult Biochemical Nomenclature and Related Documents (Portland Press, London, United Kingdom, 1992), available at http://www.chem.qmul.ac.uk/iupac/bibliog/white.html, and the instructions to authors of the Journal of Biological Chemistry and the Archives of Biochemistry and Biophysics (first issues of each year).

Do not express molecular weight in daltons; molecular weight is a unitless ratio. Molecular mass is expressed in daltons.

For enzymes, use the recommended (trivial) name assigned by the Nomenclature Committee of the International Union of Biochemistry (IUB) as described in Enzyme Nomenclature (Academic Press, Inc., New York, NY, 1992) and at http://www.chem.qmul.ac.uk/iubmb/enzyme/. If a nonrecommended name is used, place the proper (trivial) name in parentheses at first use in the abstract and text. Use the EC number when one has been assigned. Authors of papers describing enzymological studies should review the standards of the STRENDA Commission for information required for adequate description of experimental conditions and for reporting enzyme activity data (http://www.beilstein-institut.de/en/projekte/strenda/guidelines/).

Nomenclature of Mice

For mouse strain and genetic nomenclature, ASM encourages authors to refer to the guidelines set forth by the International Committee on Standardized Genetic Nomenclature for Mice, available on the Mouse Genome Database home page at http://www.informatics.jax.org/ and in Genetic Variants and Strains of the Laboratory Mouse, 3rd ed. (M. F. Lyon et al., ed., Oxford University Press, Oxford, England, 1996).

Nomenclature of Microorganisms

Binary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), must be used for all microorganisms. Names of categories at or above the genus level may be used alone, but specific and subspecific epithets may not. A specific epithet must be preceded by a generic name, written out in full the first time it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital letter (e.g., E. coli), provided there can be no confusion with other genera used in the paper. Names of all taxa (kingdoms, phyla, classes, orders, families, genera, species, and subspecies) are printed in italics and should be italicized in the manuscript; strain designations and numbers are not.

The spelling of bacterial names should follow the Approved Lists of Bacterial Names (Amended) & Index of the Bacterial and Yeast Nomenclatural Changes (V. B. D. Skerman et al., ed., American Society for Microbiology, Washington, DC, 1989) and the validation lists and notification lists published in the International Journal of Systematic and Evolutionary Microbiology (formerly the International Journal of Systematic Bacteriology) since January 1989. In addition, two sites on the World Wide Web list current approved bacterial names: Bacterial Nomenclature Up-to-Date (http://www.dsmz.de/microorganisms/main.php?contentleft_id=14) and List of Prokaryotic Names with Standing in Nomenclature (http://www.bacterio.cict.fr/).

Since the classification of fungi is far from complete, it is the responsibility of the author to determine the accepted binomial for a given organism. Sources for these names include The Yeasts: a Taxonomic Study, 5th ed. (C. P. Kurtzman, J. W. Fell, and T. Boekhout, ed., Elsevier Science, Amsterdam, Netherlands, 2010), and Dictionary of the Fungi, 10th ed. (P. M. Kirk, P. F. Cannon, and J. A. Stalpers, ed., CABI Publishing, Wallingford, Oxfordshire, United Kingdom, 2008); see also http://www.speciesfungorum.org/Names/Fundic.asp.

Names used for viruses should be those approved by the International Committee on Taxonomy of Viruses (ICTV) and reported on the ICTV Virus Taxonomy website (http://www.ictvonline.org/index.asp). In addition, the recommendations of the ICTV regarding the use of species names should generally be followed: when the entire species is discussed as a taxonomic entity, the species name, as with other taxa, is italic and has the first letter and any proper nouns capitalized (e.g., Tobacco mosaic virus, Murray Valley encephalitis virus). When the behavior or manipulation of individual viruses is discussed, the vernacular (e.g., tobacco mosaic virus, Murray Valley encephalitis virus) should be used. If desired, synonyms may be added parenthetically when the name is first mentioned. Approved generic (or group) and family names may also be used.

Microorganisms, viruses, and plasmids should be given designations consisting of letters and serial numbers. It is generally advisable to include a worker's initials or a descriptive symbol of locale or laboratory, etc., in the designation. Each new strain, mutant, isolate, or derivative should be given a new (serial) designation. This designation should be distinct from those of the genotype and phenotype, and genotypic and phenotypic symbols should not be included.

Genetic Nomenclature

To facilitate accurate communication, it is important that standard genetic nomenclature be used whenever possible and that deviations or proposals for new naming systems be endorsed by an appropriate authoritative body. Review and/or publication of submitted manuscripts that contain new or nonstandard nomenclature may be delayed by the editor or the Journals Department so that they may be reviewed by the Genetics and Genomics Committee of the ASM Publications Board.

Before submission of manuscripts, authors may direct questions on genetic nomenclature to the committee's chairperson: Maria Costanzo (maria@genome.stanford.edu). Such a consultation should be mentioned in the manuscript submission letter.

Prokaryotes.

The genetic properties of prokaryotes are described in terms of phenotypes and genotypes. The phenotype describes the observable properties of an organism. The genotype refers to the genetic constitution of an organism, usually in reference to some standard wild type. In preparing a manuscript, follow the recommendations of Demerec et al. (Genetics 54:61-76, 1966) and the practices currently in use in the Journal of Bacteriology and described in its Instructions to Authors. A brief description follows.

(i) Phenotype designations must be employed when mutant loci have not been identified or mapped. They can also be used to identify the protein product of a gene, e.g., the OmpA protein. Phenotype designations generally consist of three-letter symbols; these are not italicized, and the first letter of the symbol is capitalized (e.g., Pol). Wild-type characteristics can be designated with a superscript plus (Pol⁺), and, when necessary for clarity, negative superscripts (Pol⁻) can be used to designate mutant characteristics. Lowercase superscript letters may be used to further delineate phenotypes (e.g., Str^r for streptomycin resistance). Phenotype designations should be defined.

(ii) Genotype designations are also indicated by a three-letter symbol. In contrast to phenotype designations, genotype designations are lowercase italic (e.g., ara his rps). If several loci govern related functions, these are distinguished by an italicized capital letter following the locus symbol (e.g., araA araB). Mutation sites are distinguished by placing serial isolation numbers (allele numbers) after the locus symbol (e.g., ara-1 hisB5). Promoter, terminator, and operator sites should be indicated as described by Bachmann and Low (Microbiol. Rev. 44:1-56, 1980): e.g., lacZp, lacAt, and lacZo. It is essential in papers reporting the isolation of new mutants that allele numbers be given to the mutations. For Escherichia coli, there is a registry of such numbers: E. coli Genetic Stock Center (http://cgsc.biology.yale.edu/). For the genus Salmonella, the registry is Salmonella Genetic Stock Center (http://people.ucalgary.ca/∼kesander/).

(iii) Wild-type alleles are indicated with a superscript plus (ara⁺ his⁺). A superscript minus is not used to indicate a mutant locus; thus, one refers to an ara mutant rather than an ara⁻ strain.

(iv) The use of superscripts with genotypes (other than + to indicate wild-type alleles) should be avoided. Designations indicating amber mutations (Am), temperature-sensitive mutations (Ts), constitutive mutations (Con), cold-sensitive mutations (Cs), and production of a hybrid protein (Hyb) should follow the allele number [e.g., araA230(Am) hisD21(Ts)]. All other such designations of phenotype must be defined at the first occurrence. If superscripts must be used, they must be approved by the editor and defined at the first occurrence in the text.

Subscripts may be used in two situations. Subscripts may be used to distinguish between genes (having the same name) from different organisms or strains; e.g., his_{E. coli} or his_K-12 for the his gene of E. coli or strain K-12, respectively, may be used to distinguish this gene from the his gene in another species or strain. An abbreviation may also be used if it is explained. Similarly, a subscript can also be used to distinguish between genetic elements that have the same name. For example, the promoters of the gln operon can be designated glnAp₁ and glnAp₂.

(v) Avoid the use of a genotype as a name (e.g., “subsequent use of leuC6 for transduction”). If a strain designation has not been chosen, select an appropriate word combination (e.g., “either strain PA3092 or another strain containing the leuC6 mutation”).

Locus tags.

Locus tags are systematic, unique identifiers that are assigned to each gene in GenBank. All genes mentioned in a manuscript should be traceable to their sequences by the reader, and locus tags may be used for this purpose in manuscripts to identify uncharacterized genes. In addition, authors should check GenBank to make sure that they are using the correct, up-to-date format for locus tags (e.g., uppercase versus lowercase letters and the presence or absence of an underscore, etc.). Locus tag formats vary between different organisms and also may be updated for a given organism, so it is important to check GenBank at the time of manuscript preparation.

Viruses.

In most cases, viruses have no phenotype, since they have no metabolism outside host cells. Therefore, distinctions between phenotype and genotype are not made. Superscripts are used to indicate hybrid genomes. Genetic symbols may be one, two, or three letters. For example, a mutant strain of lambda may be designated λ cI857 int2 red114 Aam11; this strain carries mutations in genes cI, int, and red and an amber-suppressible (am) mutation in gene A. Host DNA insertions into viruses should be delineated by square brackets, and the genetic symbols and designations for such inserted DNA should conform to those used for the host genome.

Eukaryotes.

The nomenclature used for the genetics of lower eukaryotic microorganisms has not been as well formalized as that for bacteria and bacteriophages. Generally, authors should conform to current practices in identifying mutants and their genotypes. For organisms not mentioned below, it is advisable to consult the Handbook of Microbiology, 2nd ed. (A. I. Laskin and H. A. Lechevalier, ed., CRC Press, Boca Raton, FL, 1988) or the Handbook of Genetics, vol. 1, Bacteria, Bacteriophages, and Fungi (R. C. King, ed., Plenum Publishing Corp., New York, NY, 1974).

Gene names may begin with prefixes to indicate the genus and species from which the gene is derived only when needed for clarity when discussing genes with the same name from two different organisms (e.g., ScURA3 versus CaURA3); the prefixes are not considered part of the gene name proper and are not italicized.

The genetic nomenclature of Dictyostelium is summarized in the Trends in Genetics “Genetic Nomenclature Guide” (p. S.5-S.6; Elsevier Science Ltd., Cambridge, United Kingdom, 1998; out of print). The most recent modifications can be found at http://dictybase.org/.

For Saccharomyces cerevisiae, a gene name should always be indicated in italics and, for the wild-type locus (or dominant alleles), capital letters (e.g., URA3). Loss-of-function (hypomorphic) or altered-function (neomorphic) alleles of the same locus should always be indicated in italics and lowercase letters (e.g., ura3Δ). The product of a gene (i.e., a protein) should be indicated in roman type with an initial capital letter (e.g., Ura3). There is generally no need to add the suffix “p” to the symbol for a protein; however, in rare instances where it may be deemed necessary to indicate unambiguously that the symbol refers to a protein, the “p” suffix may be added (e.g., Ura3p). For the most recent information on S. cerevisiae gene names, consult the Saccharomyces Genome Database (SGD) at http://www.yeastgenome.org/. Details on the format of S. cerevisiae locus and allele designations are provided in the SGD and are also described by Cherry (Trends Genet. March:11-12, 1995) (available for download as a PDF file at SGD, http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf). Authors should use standard S. cerevisiae gene names, as listed in the SGD, in their submitted manuscripts and register new gene names with the SGD no later than the modification stage.

The most recent information for Neurospora crassa can be found in The Neurospora Compendium: Chromosomal Loci (D. R. Perkins et al., Academic Press, San Diego, CA, 2001). When naming genes for Aspergillus species, the nomenclature guidelines posted at http://www.aspergillus.org.uk/indexhome.htm?secure/sequence_info/nomenclature.htm∼main should be followed, and the Aspergillus Genome Database (http://www.aspgd.org) should be searched to ensure that any new name is not already in use. The 1998 Trends in Genetics “Genetic Nomenclature Guide” (Elsevier Science Ltd., Cambridge, United Kingdom; out of print) contains nomenclature guidelines for several eukaryotic microbes: Schizosaccharomyces pombe (p. S.7-S.9), Chlamydomonas reinhardtii (p. S.18-S.19), Neurospora crassa (p. S.14-S.15), and Aspergillus nidulans (p. S.12-S.13). In addition, for S. pombe, the websites http://www.sanger.ac.uk/Projects/S_pombe/SP_Name_FAQ.shtml and http://www-bcf.usc.edu/∼forsburg/plasmids.html may be help ful, and for C. reinhardtii, use http://www.chlamy.org/chlamydb.html.

For Trypanosoma and Leishmania, consult the article by Clayton et al. (Mol. Biochem. Parasitol. 97:221-224, 1998).

For the most recent information on Candida albicans, consult the Candida Genome Database (CGD) at http://www.candidagenome.org. Details on the format of C. albicans gene nomenclature are described at http://www.candidagenome.org/Nomenclature.shtml. Authors should use standard C. albicans gene names, as listed in the CGD, in their submitted manuscripts and should register new gene names with the CGD no later than the modification stage.

Symbols for Drosophila mutations and chromosome aberrations are italicized; they should not contain Greek letters, subscripts, or spaces. The symbol for a mutant type is usually an abbreviation of its name and usually begins with the first letter of that name. Dominant and recessive mutations are indicated by initial capital and lowercase letters, respectively (e.g., R for roughened and r for rudimentary). FlyBase (http://flybase.org/) is the genetic nomenclature authority for Drosophila melanogaster.

WormBase (http://wormbase.org/) is the genetic nomenclature authority for Caenorhabditis elegans.

“Mutant” versus “mutation.”

Keep in mind the distinction between a mutation (an alteration of the primary sequence of the genetic material) and a mutant (a strain carrying one or more mutations). One may speak about the mapping of a mutation, but one cannot map a mutant. Likewise, a mutant has no genetic locus, only a phenotype.

“Homology” versus “similarity.”

For use of terms that describe relationships between genes, consult the articles by Theissen (Nature 415:741, 2002) and Fitch (Trends Genet. 16:227-231, 2000). “Homology” implies a relationship between genes that have a common evolutionary origin; partial homology is not recognized. When sequence comparisons are discussed, it is more appropriate to use the term “percent sequence similarity” or “percent sequence identity,” as appropriate.

Transposable elements, plasmids, and restriction enzymes.

Nomenclature of transposable elements (insertion sequences, transposons, and phage Mu, etc.) should follow the recommendations of Campbell et al. (Gene 5:197-206, 1979), with the modifications referred to in the Instructions to Authors in the Journal of Bacteriology. The Internet site where insertion sequences of eubacteria and archaea are described and new sequences can be recorded is http://www-is.biotoul.fr/is.html.

The system of designating transposon insertions at sites where there are no known loci, e.g., zef-123::Tn5, has been described by Chumley et al. (Genetics 91:639-655, 1979). Use the nomenclature recommendations of Novick et al. (Bacteriol. Rev. 40:168-189, 1976) for plasmids and plasmid-specified activities, of Low (Bacteriol. Rev. 36:587-607, 1972) for F` factors, and of Roberts et al. (Nucleic Acids Res. 31:1805-1812, 2003) for restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes. The nomenclature for recombinant DNA molecules constructed in vitro follows the nomenclature for insertions in general. DNA inserted into recombinant DNA molecules should be described by using the gene symbols and conventions for the organism from which the DNA was obtained.

ABBREVIATIONS AND CONVENTIONS

Verb Tense

ASM strongly recommends that for clarity you use the past tense to narrate particular events in the past, including the procedures, observations, and data of the study that you are reporting. Use the present tense for your own general conclusions, the conclusions of previous researchers, and generally accepted facts. Thus, most of the abstract, Materials and Methods, and Results will be in the past tense, and most of the introduction and some of the Discussion will be in the present tense.

Be aware that it may be necessary to vary the tense in a single sentence. For example, it is correct to say “White (30) demonstrated that XYZ cells grow at pH 6.8,” “Figure 2 shows that ABC cells failed to grow at room temperature,” and “Air was removed from the chamber and the mice died, which proves that mice require air.” In reporting statistics and calculations, it is correct to say “The values for the ABC cells are statistically significant, indicating that the drug inhibited … .”

For an in-depth discussion of tense in scientific writing, see p. 191-193 in How To Write and Publish a Scientific Paper, 6th ed.

Abbreviations

General.

Abbreviations should be used as an aid to the reader, rather than as a convenience for the author, and therefore their use should be limited. Abbreviations other than those recommended by the IUPAC-IUB (Biochemical Nomenclature and Related Documents, 1992) should be used only when a case can be made for necessity, such as in tables and figures.

It is often possible to use pronouns or to paraphrase a long word after its first use (e.g., “the drug” or “the substrate”). Standard chemical symbols and trivial names or their symbols (folate, Ala, and Leu, etc.) may also be used.

Define each abbreviation and introduce it in parentheses the first time it is used; e.g., “cultures were grown in Eagle minimal essential medium (MEM).” Generally, eliminate abbreviations that are not used at least three times in the text (including tables and figure legends).

Not requiring introduction.

In addition to abbreviations for Système International d'Unités (SI) units of measurement, other common units (e.g., bp, kb, and Da), and chemical symbols for the elements, the following should be used without definition in the title, abstract, text, figure legends, and tables: DNA (deoxyribonucleic acid); cDNA (complementary DNA); RNA (ribonucleic acid); cRNA (complementary RNA); RNase (ribonuclease); DNase (deoxyribonuclease); rRNA (ribosomal RNA); mRNA (messenger RNA); tRNA (transfer RNA); AMP, ADP, ATP, dAMP, ddATP, and GTP, etc. (for the respective 5` phosphates of adenosine and other nucleosides) (add 2`-, 3`-, or 5`- when needed for contrast); ATPase and dGTPase, etc. (adenosine triphosphatase and deoxyguanosine triphosphatase, etc.); NAD (nicotinamide adenine dinucleotide); NAD⁺ (nicotinamide adenine dinucleotide, oxidized); NADH (nicotinamide adenine dinucleotide, reduced); NADP (nicotinamide adenine dinucleotide phosphate); NADPH (nicotinamide adenine dinucleotide phosphate, reduced); NADP⁺ (nicotinamide adenine dinucleotide phosphate, oxidized); poly(A) and poly(dT), etc. (polyadenylic acid and polydeoxythymidylic acid, etc.); oligo(dT), etc. (oligodeoxythymidylic acid, etc.); UV (ultraviolet); PFU (plaque-forming units); CFU (colony-forming units); MIC (minimal inhibitory concentration); Tris [tris(hydroxymethyl)aminomethane]; DEAE (diethylaminoethyl); EDTA (ethylenediaminetetraacetic acid); EGTA [ethylene glycol-bis(β-aminoethyl ether)-N,N,N`,N`-tetraacetic acid]; HEPES (N-2-hydroxyethylpiperazine-N`-2-ethanesulfonic acid); PCR (polymerase chain reaction); and AIDS (acquired immunodeficiency syndrome). Abbreviations for cell lines (e.g., HeLa) also need not be defined.

The following abbreviations should be used without definition in tables:

• amt (amount)

• approx (approximately)

• avg (average)

• concn (concentration)

• diam (diameter)

• expt (experiment)

• exptl (experimental)

• ht (height)

• mo (month)

• mol wt (molecular weight)

• no. (number)

• prepn (preparation)

• SD (standard deviation)

• SE (standard error)

• SEM (standard error of the mean)

• sp act (specific activity)

• sp gr (specific gravity)

• temp (temperature)

• tr (trace)

• vol (volume)

• vs (versus)

• wk (week)

• wt (weight)

• yr (year)

Reporting Numerical Data

Standard metric units are used for reporting length, weight, and volume. For these units and for molarity, use the prefixes m, μ, n, and p for 10⁻³, 10⁻⁶, 10⁻⁹, and 10⁻¹², respectively. Likewise, use the prefix k for 10³. Avoid compound prefixes such as mμ or μμ. Use μg/ml or μg/g in place of the ambiguous ppm. Units of temperature are presented as follows: 37°C or 324 K.

When fractions are used to express units such as enzymatic activities, it is preferable to use whole units, such as “g” or “min,” in the denominator instead of fractional or multiple units, such as μg or 10 min. For example, “pmol/min” is preferable to “nmol/10 min,” and “μmol/g” is preferable to “nmol/μg.” It is also preferable that an unambiguous form such as exponential notation be used; for example, “μmol g⁻¹ min⁻¹” is preferable to “μmol/g/min.” Always report numerical data in the appropriate SI units.

For a review of some common errors associated with statistical analyses and reports, plus guidelines on how to avoid them, see the article by Olsen (Infect. Immun. 71:6689-6692, 2003).

For a review of basic statistical considerations for virology experiments, see the article by Richardson and Overbaugh (J. Virol. 79:669-676, 2005).

Isotopically Labeled Compounds

For simple molecules, isotopic labeling is indicated in the chemical formula (e.g., ¹⁴CO₂, ³H₂O, and H_2³⁵SO₄). Brackets are not used when the isotopic symbol is attached to the name of a compound that in its natural state does not contain the element (e.g., ³²S-ATP) or to a word that is not a specific chemical name (e.g., ¹³¹I-labeled protein, ¹⁴C-amino acids, and ³H-ligands).

For specific chemicals, the symbol for the isotope introduced is placed in square brackets directly preceding the part of the name that describes the labeled entity. Note that configuration symbols and modifiers precede the isotopic symbol. The following examples illustrate correct usage:

• [¹⁴C]urea

• l-[methyl-¹⁴C]methionine

• [2,3-³H]serine

• [α-¹⁴C]lysine

• [γ-³²P]ATP

• UDP-[U-¹⁴C]glucose

• E. coli [³²P]DNA

• fructose 1,6-[1-³²P]bisphosphate

MCB follows the same conventions for isotopic labeling as the Journal of Biological Chemistry, and more-detailed information can be found in the instructions to authors of that journal (first issue of each year).

Appendixes.

Appendixes that contain additional material to aid the reader are permitted. Titles, authors, and reference sections that are distinct from those of the primary article are not allowed. If it is not feasible to list the author(s) of the appendix in the byline or the Acknowledgments section of the primary article, rewrite the appendix so that it can be considered for publication as an independent article. Equations, tables, and figures should be labeled with the letter “A” preceding the numeral to distinguish them from those cited in the main body of the text.