Microbiology and Molecular Biology Reviews, March 2006, p. 1-11, Vol. 70, No. 1
1092-2172/06/$08.00+0 doi:10.1128/MMBR.70.1.1-11.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
| INSTRUCTIONS TO AUTHORS |
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
2006 INSTRUCTIONS TO AUTHORS*
SCOPE
SCOPE EDITORIAL POLICY Use of Microbiological Information General Requirements Supplemental Material Primary Publication Permissions Copyright Authorship Conflict of Interest Warranties and Exclusions Correspondent Footnote Errata Authors' Corrections Compliance Review Process Notification of Acceptance Page Proofs Reprints PDF Files Editorial Style HOW TO SUBMIT MANUSCRIPTS ORGANIZATION AND FORMAT References (i) Works listed in References. (ii) Items cited in the text. Abbreviations General. Not requiring introduction. Reporting Numerical Data Nomenclature ILLUSTRATIONS AND TABLES Illustrations File types and formats. Minimum resolution. Size. Contrast. Labeling and assembly. Fonts. Compression. Color illustrations. Drawings Tables Presentation of Nucleic Acid Sequences
Microbiology and Molecular Biology Reviews (MMBR) publishes reviews dealing with all aspects of microbiology and other fields of concern to microbiologists, such as immunology. Authoritative and critical reviews of the current state of knowledge are preferred, although historical analyses will be accepted if the importance of the subject justifies this approach. Unevaluated compilations of the literature and annotated bibliographies do not fall within the scope of MMBR. Manuscripts of lectures delivered at symposia and roundtables are likewise unacceptable; however, their authors are encouraged to discuss with the editor the possibility of using such material as the basis for preparation of a review when publication in this form seems appropriate. Because a distinct goal of the journal is to appeal to the interests of its diverse group of subscribers, authors are asked to address themselves to both specialists and generalists; this demands conscious concern for this goal in writing.
Manuscripts reach MMBR by one of two mechanisms. First, reviews are solicited by the editors from leading investigators around the world. Second, suggestions for reviews of subjects that have not been reviewed recently may be e-mailed to the MMBR editorial office (mmbr{at}bact.wisc.edu). Such suggestions should be accompanied by a summary; an annotated topical outline; a one- or two-paragraph statement describing the aim, scope, and relevance of the review; a list of key references showing the author's contributions to the field, as well as other investigators' findings; and a curriculum vitae and bibliography for each proposed author. Such outlines will be evaluated by the editors, and if the material is satisfactory, the authors will be invited to write the review and submit it via Rapid Review.
A review, whether invited or not, cannot be finally accepted until the finished product has been reviewed and found to be satisfactory.
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/Policy/index.asp.
By submission of a manuscript to the journal, the authors guarantee that the manuscript, or one with substantially the same content, was not published previously and is not being considered or published elsewhere.
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 processes. For Authors' Corrections, signed letters of agreement from all of the authors must be submitted (see p. 4).
It is expected that the authors will provide written assurance that permission to cite unpublished data or personal communications has been granted.
Supplemental material intended for posting by ASM may not include additional figures or tables that simply support the authors' conclusions. It must be restricted to large or complex data sets or results that cannot be readily 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 in Rapid Review and will be reviewed along with the manuscript. The decision to publish (i.e., post online only) the material with the article if it is accepted will be made by the editor in chief and conveyed to the corresponding author in the acceptance e-mail. Note, therefore, it is possible that an article will be accepted but that the supplemental material will not be.
If the software required for users to view/use the supplemental material is not embedded in the file, you are urged to use shareware or generally available/easily accessible programs.
Unlike the article, supplemental material will not be edited by the ASM Journals staff and proofs will not be made available.
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 data. Instead, the appropriate reference(s) to the original publication should be made in the article text.
Copyright for the 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. If you are not the copyright owner, you must provide directly to the editor, outside the Rapid Review system and no later than the modification stage, 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.
A scientific paper or its substance published in a serial, periodical, book, conference report, symposium proceeding, or technical bulletin, posted on a nonpersonal website, or made available through any other retrievable source, including CD-ROM and other electronic forms, is unacceptable for submission to an ASM journal on grounds of prior publication.
Posting of a method/protocol on a nonpersonal website should not interfere with the author's ability to have a manuscript utilizing that technique considered for publication in an ASM journal; however, ultimately, it is an editorial decision whether the method constitutes the substance of a paper.
Posting of a limited amount of original data on a personal/university/company website or websites of small collaborative groups working on a problem does not preclude subsequent submission to, and publication by, an ASM journal. The posted data, however, may not constitute the substance of the submission. Specific questions about this policy may be referred to the Publications Board chairman on a case-by-case basis. Posting of theses and dissertations on a personal/university-hosted website does not preclude subsequent submission to, and publication by, an ASM journal.
Posting of unpublished sequence data on the Internet is usually not considered prior publication; however, the address (URL) of the source of the sequence should be included in the text.
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It is incumbent upon the author to acknowledge any prior publication, including his 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 supporting material.
Ultimately, it is an editorial decision whether the material constitutes the substance of a paper.
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.
The original signed permission(s) must be submitted to the editor, outside the Rapid Review system, no later than the modification stage and should be identified as to the relevant item in the ASM manuscript (e.g., "permissions for Fig. 1 in submitted manuscript"). 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.
For supplemental material intended for posting by ASM (see above), if the authors of the MMBR manuscript are not also the owner of the supplemental material, the corresponding author must send directly to the editor, outside the Rapid Review system and no later than the modification stage, 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.
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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., either the copyright lines shown on the top of the first page of the PDF version or "Copyright © American Society for Microbiology, [insert journal name, volume number, page numbers, and year]" for the HTML version).
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Copyright for supplemental material (see p. 1) 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 directly to the editor, outside the Rapid Review system and no later than the modification stage, 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.)
An author is one who made a substantial contribution to the article; therefore, ASM considers all authors responsible for the entire paper. Individuals who provided assistance, e.g., supplied strains 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 keyed 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.
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The Erratum section provides a means of correcting errors that occurred during the writing, typing, editing, or printing (e.g., a misspelling, a dropped word or line, mislabeling in a figure) of a published article. Send Errata directly to the ASM Journals Department (1752 N St., N.W., Washington, DC 20036-2904, USA), both on disk and in hard copy (only one hard copy is necessary). Please see a recent issue for correct formatting.
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.
For omission of an author's name, the authors of the article and the author whose name was inadvertently omitted must agree, in writing, to publication of the Correction. For other 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. Copies of the agreement letters must accompany the Correction and be sent directly to the Journals Department. Send the Correction both on disk and in hard copy (only one hard copy is necessary). Please see a recent issue for correct formatting.
Corrections of a scientific nature (e.g., an incorrect unit of measurement or order of magnitude used throughout; contamination of one of numerous cultures; misidentification of a mutant strain, causing erroneous data for only a portion [noncritical] of the study) must be sent, both on disk and in hard copy, directly to the editor in chief and must be accompanied by signed letters of agreement from all of the authors of the article. If the editor in chief believes that publication is warranted, he will send the Correction to the Journals Department for publication. Note that the addition of new data is not permitted.
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.
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 should recommend at least two reviewers who are not members of their institution(s) and have never been associated with them or their laboratory(ies); please provide their contact information where indicated on the submission form.
Copies of in-press and submitted manuscripts that are important for judgment of the present manuscript should be included as supporting material to facilitate the review.
When a manuscript is submitted to the journal, it is given a number (e.g., MMBR00047-06 version 1) and assigned to the editor in chief. (Always refer to this 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.shtml) and are expected to complete their reviews expeditiously.
The corresponding author is notified by the editor in chief of her decision to accept, reject, or require modification. When modification is requested, the corresponding author must either submit the modified version within 2 to 3 months or withdraw the manuscript. A point-by-point response to the reviews must be provided in the Rebuttal section of the Rapid Review submission form for the revised manuscript, and a compare copy of the manuscript (without figures) should be included as supporting material if the editor in chief requested one.
Manuscripts that have been rejected, or withdrawn after being returned for modification, may be resubmitted if the major criticisms have been addressed. The cover letter must state that the manuscript is a resubmission. The former manuscript number should be provided in the appropriate field on the submission form. A point-for-point response to the reviews and a compare copy of the revised manuscript showing the changes must be included as supporting material (the Rebuttal section appears in the submission form only if the manuscript is a modification). Rejected manuscripts may be resubmitted only once unless permission has been obtained from the editor in chief.
When a manuscript has been found acceptable for publication on the basis of scientific merit, the author and the Journals Department are notified by the editor in chief. 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 Rapid Review, 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 and an acceptance letter indicating the month of publication and approximate page proof dates is mailed to the corresponding author; a copyright transfer agreement is also included, as is a license to permit posting of supplemental material (if applicable). The editorial staff of the ASM Journals Department completes the editing of the manuscript to bring it into conformity with prescribed standards.
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 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. 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 in chief. If references to unpublished data or personal communications are added, it is expected that written assurance granting permission for the citation will be provided. 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 (telephone, 202-942-9231). Questions about accessing or viewing your PDF proofs should be directed to Katie Gay of Cadmus Professional Communications at 804-261-3155 or gayk{at}cadmus.com.
The corresponding author will receive up to 300 free reprints of his contribution; additional reprints (in multiples of 100) may be purchased if desired. In the proof notification e-mail, the corresponding author will be instructed how to access information about reprints.
A corresponding author who has included an e-mail address in his "corresponding author" footnote will have limited access (10 downloads, total) to the PDF file of his published article. An e-mail alert will automatically be sent to him 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.shtml.) 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., 1 year after publication).
The editorial style of ASM journals conforms to the ASM Style Manual for Journals (American Society for Microbiology, 2006, in-house document) and How To Write and Publish a Scientific Paper, 5th ed. (Oryx Press, 1998), as interpreted and modified by the editors and the ASM Journals Department.
The editors and the Journals Department reserve the privilege of editing manuscripts, whether invited or not, to conform with the stylistic conventions set forth in the aforesaid publications and in these Instructions. Any deviations from this style must be approved by the Journals Department.
All submissions to MMBR must be made electronically via the Rapid Review online submission and peer review system at the following URL: www.rapidreview.com/ASM2/author.html. (E-mailed submissions will not be accepted.) For solicited reviews, the name of the editor who invited the submission must be specified in the cover letter. First-time users must create an Author account, which may be used for submitting to all ASM journals. Instructions for creating an Author account are available at the above URL under the Create Account button. The person from whose account a submission is made will be recorded as the corresponding author, and any correspondence will be sent to the e-mail address in that account. Step-by-step instructions for submitting a manuscript via Rapid Review are available from the account holder's My Manuscripts page. Information on file types acceptable for electronic submission can be found under the More About File Formats button.
On receipt at ASM, the electronic file of 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 section headings. Consult a recent issue of MMBR for format and style. The title page must include the title, the running title (not to exceed 54 characters and spaces), the name and affiliation of each author, and a footnote indicating the complete mailing address, telephone number, fax number and e-mail address of the corresponding author. A table of contents showing the major headings and subheadings of the text should follow the title page. Headings and subheadings have the following format:
LEVEL 1 HEAD
Level 2 Head
Level 3 head. (i) Level 4 head. (a) Level 5 head.
The summary, which will be included in the issue table of contents and must be no longer than 250 words, should be placed at the end of the electronic file, after the References section and the figure legends (but before any tables).
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 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 (x) 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 8
by 11 inches (ca. 21.6 by 28 cm). Italicize or underline any words that should appear in italics, and indicate paragraph lead-ins in bold 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.
(i) Works listed in References. The References section must include all journal articles (both print and online), books and book chapters (both print and online), patents, theses and dissertations, and published conference proceedings (not abstracts; see below), as well as in-press journal articles, book chapters, and books (publication title must be given). Arrange the citations in alphabetical order (letter by letter, ignoring spaces and punctuation) by first author and number consecutively. Provide the names of all the 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 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 BIOSIS Serial Sources (BIOSIS, Philadelphia, Pa., 2005).
Follow the styles shown in the examples below.
Print references:
- Arendsen, A. F., M. Q. Solimar, and S. W. Ragsdale. 1999. Nitrate-dependent regulation of acetate biosynthesis and nitrate respiration by Clostridium thermoaceticum. J. Bacteriol. 181:1489-1495.
- Cox, C. S., B. R. Brown, and J. C. Smith. J. Gen. Genet., in press.* {Article title is optional; journal title is mandatory.}
- 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, N.Y.
- Elder, B. L., and S. E. Sharp. 2003. Cumitech 39, Competency assessment in the clinical laboratory. Coordinating ed., S. E. Sharp. ASM Press, Washington, D.C.
- Fitzgerald, G., and D. Shaw. In A. E. Waters (ed.), Clinical microbiology, in press. EFH Publishing Co., Boston, Mass.* {Chapter title is optional.}
- 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, D.C.
- 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, D.C.
- 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.}
- O'Malley, D. R. 1998. Ph.D. thesis. University of California, Los Angeles. {Title is optional.}
*A reference to an in-press ASM publication should state the control number (e.g., JB00577-06) if it is a journal article or the name of the publication if it is a book.
Online references:
- Charlier, D., and N. Glansdorff. September 2004, posting date. Biosynthesis of arginine and polyamines. In R. Curtiss III et al. (ed.), EcoSal-Escherichia coli and Salmonella: cellular and molecular biology, chapter 3.6.1.10
. [Online.] http://www.ecosal.org. ASM Press, Washington, D.C. {For online-only books or continually updated Web resources [for the latter, posting or accession date is required, but publisher's name and location are optional].}
- Dimick, J. B., H. G. Welch, and J. D. Birkmeyer. 18 August 2004, posting {or revision} date. Surgical mortality as an indicator of hospital quality. JAMA 292. [Online.] http://jama.ama-assn.org/cgi/content/short/292/7/847. {For online journals; page numbers may not be available.}
- Sullivan, C. J. (ed.). 1999-2001. Fungi: an evolving electronic resource for the microbiological commu- nity. ASM Press. [Online.] http://link.asmusa.de/link/service/books/91090. Accessed 7 September 2001. {For online-only books.}
- Zellnitz, F., and P. M. Foley. 2 October 1998, posting {or revision} date. History of virology. Am. Virol. J. 1:30-50. [Online.] http://www.avj.html. {For online-only journals; page numbers may not be available.}
- Zheng, Z., and J. Zou. 5 September 2001. The initial step of the glycerolipid pathway: identification of glycerol-3-phosphate/dihydroxyacetone phosphate dual substrate acyltransferases in Saccharomyces cerevisiae. J. Biol. Chem. doi:10.1074/jbc.M104749200. {For papers published online in manuscript form.}
NOTE: A URL or DOI is necessary for each online-only reference; a posting or accession date is required for any online reference that is periodically updated or changed.
(ii) Items cited in the text. References to meeting abstracts (including those published in journal supplements), letters (irrespective of type) and authors' replies to letters, company publications, 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).
... in mitochondria (S. De Wit, C. Thioux, and N. Clumeck, Abstr. 34th Intersci. Conf. Antimicrob. Agents Chemother., abstr. 114, 1994).
... for other bacteria (A. X. Jones, personal communication.
... discussed previously (L. B. Jensen, A. M. Hammerum, R. L. Poulsen, and H. Westh, Letter, Antimicrob. Agents Chemother. 43:724-725, 1999).
... discussed previously (S. L. W. On and P. A. R. Vandamme, Authors' Reply to Letter, J. Clin. Microbiol. 39:2751-2752, 2001).
... the manufacturer (Sigma manual, Sigma Chemical Co., St. Louis, Mo.).
... this process (V. R. Smoll, 20 June 1999, Australian Patent Office). {For non-U.S. patent applications, give the date of publication of the application.}
... information found at the XYZ website (http://cbx_iou.pgr).
... the ABC program (version 2.2; Department of Microbiology, State University [http://www.stu.micro]).
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.
If any reference(s) must be moved from the References section to the text to conform to ASM style, the numbered reference (byline, title, etc.) will be replaced with the words "Reference deleted" in order to preserve the author's original numbering sequence and to avoid excessive renumbering.
General. Abbreviations should be used as an aid to the reader, rather than as a convenience to the author, and therefore their use should be limited. Abbreviations other than those recommended by the International Union of Pure and Applied Chemistry-International Union of Biochemistry (IUPAC-IUB) (Biochemical Nomenclature and Related Documents, 1978) 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, 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, summary, 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, GTP, etc. (for the respective 5' phosphates of adenosine and other nucleosides) (add 2'-, 3'-, or 5'- when needed for contrast); ATPase, dGTPase, etc. (adenosine triphosphatase, 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), poly(dT), etc. (polyadenylic acid, 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(ß-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)
- SE (standard error)
- approx (approximately)
- SEM (standard error of the mean
- avg (average)
- concn (concentration)
- sp act (specific activity)
- diam (diameter)
- sp gr (specific gravity)
- exptl (experimental)
- temp (temperature)
- expt (experiment)
- tr (trace)
- ht (height)
- vol (volume)
- mo (month)
- vs (versus)
- mol wt (molecular weight)
- wk (week)
- no. (number)
- wt (weight)
- prepn (preparation)
- yr (year)
- SD (standard deviation)
- SE (standard error)
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 applicable 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).
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., ASM Press, Washington, D.C., 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). If there is reason to use a name that does not have standing in nomenclature, the name should be enclosed in quotation marks in the title and at its first use in the abstract and the text and an appropriate statement concerning the nomenclatural status of the name should be made in the text. "Candidatus" species should always be set in quotation marks.
Names used for viruses should be those approved by the International Committee on Taxonomy of Viruses (ICTV) and published in Virus Taxonomy: Classification and Nomenclature of Viruses, Seventh Report of the International Committee on Taxonomy of Viruses (M. H. V. van Regenmortel et al., ed., Academic Press, San Diego, Calif., 2000). 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, like 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.
For enzymes, use the recommended (trivial) name assigned by the Nomenclature Committee of the IUB as described in Enzyme Nomenclature (Academic Press, Inc., New York, N.Y., 1992) and at http://www.chem.qmul.ac.uk/iubmb/enzyme/.
For nomenclature of restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes, refer to the article by Roberts et al. (Nucleic Acids Res. 31:1805-1812, 2003).
Genetic nomenclature should essentially follow the recommendations of Demerec et al. (Genetics 54:61-76, 1966) and those given in the instructions to authors of the Journal of Bacteriology and Molecular and Cellular Biology (January issues) and Eukaryotic Cell (February issue). 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 chairman: Maria Costanzo (e-mail: maria{at}genome.stanford.edu). Such a consultation should be mentioned in the manuscript submission letter.
Digital files that are acceptable for production (see below) must be provided for all illustrations on return of the modified manuscript. (On initial submission, the entire paper may be submitted in PDF format.)
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/mw/. Rapid Inspector is an easy-to-use Web-based application that identifies file characteristics that may render the image unusable for production.
Illustrations may be continuous-tone images, line drawings, or composites. Suggestions about how to ensure accurate color reproduction are given below.
The preferred format for tables is MS Word; however, WordPerfect and Acrobat PDF are also acceptable (see the section on Tables below).
Since the contents of computer-generated images can be manipulated for better clarity, the Publications Board at its May 1992 meeting mandated that a description of the software/hardware used should be put in the figure legend(s).
File types and formats. As mentioned above, illustrations may be supplied as PDF files for reviewing purposes only on initial submission; in fact, we recommend this option to minimize file upload time. At the modification stage, production quality digital files must be submitted: TIFF or EPS files from supported applications or PowerPoint files (black and white only). Except for figures produced in PowerPoint, all graphics submitted with modified manuscripts must be bitmap, grayscale, or CMYK (not RGB). Acceptable file types and formats for production are given in the charts below.
More-detailed instructions for preparing illustrations are available on the World Wide Web at http://cjs.cadmus.com/da. Please review this information before preparing your files. If you require additional information, please send an e-mail inquiry to digitalart{at}cadmus.com. |
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- 300 dpi for grayscale and color
- 600 dpi for lettering
- 1,200 dpi for line art
- 600 dpi for combination art (lettering and images)
- 600 dpi for lettering
Size. All graphics MUST 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: 4
inches (10.8 cm)
- Maximum height: 9
inches (23.0 cm)
- Maximum width for a 2-column figure: 6
Contrast. Illustrations must contain sufficient contrast to withstand the inevitable loss of contrast and detail inherent in the printing process. See also the section on color illustrations below.
Labeling and assembly. All final lettering, labeling, tooling, etc., MUST be incorporated into the figures. It cannot be added at a later date. If a figure number is included, it must appear 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 sending 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: Helvetica, Times Roman, European PI, Mathematical PI, or Symbol. All fonts other than these five must be converted to paths (or outlines) in the application with which they were created. For font use in PowerPoint images, refer to the Cadmus digital art website, http://cjs.cadmus.com/da.
Compression. Images created with Macintosh applications may be compressed with Stuffit. Images created with Windows applications may be compressed with WINZIP or PKZIP.
Color illustrations. Because the process of placing ink on paper by using printing presses is different from that used to produce a photo print or a laser print and the color rendition on images viewed on a monitor depends to some extent on monitor resolution, some differences in color and contrast between the image you submit and the image printed in the journal or published online will be evident. (Figures showing red or green fluorescence and those with a significant range of colors may be difficult or impossible to reproduce exactly.) Color illustrations must be saved as either TIFF or EPS files, according to the application used (see charts above). The mode of the TIFF or EPS file must be CMYK, not RGB. Graphics in the RGB color space are intended for display on a monitor only and will not separate correctly for printing.
Adherence to the following guidelines, in addition to the general ones above, will help to ensure color reproduction that is as accurate as possible. Include only the significant portions of illustrations so that the number of printed pages containing color figures is minimized. The individual panels of a single figure must be assembled in a single file, including any necessary labels. Optimal color reproduction will be obtained if the composites comprise panels containing similar colors of similar lightness or darkness. If necessary, make unlike panels into separate figures/files; the color rendition will be more accurate since the two panels will be "scanned" separately.
Submit graphs, charts, complicated chemical or mathematical formulas, diagrams, and other drawings as finished products not requiring additional artwork or typesetting. No part of the graph or drawing may be handwritten. 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:
- All art MUST be submitted at its intended publication size. For acceptable dimensions, see the Size section above.
- 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 patterns are not imported from another application. If you must use images containing screens,
- Generate the image at line screens of 85 lines per inch or lower.
- When applying multiple shades of gray, differentiate the gray levels by at least 20%.
- Never use levels of gray below 20% or above 70% as they will fade out or become totally black upon scanning and reduction.
- Generate the image at line screens of 85 lines per inch or lower.
- Use thick, solid lines that are no finer than 1 point in thickness.
- No type should be smaller than 6 points at the final publication size.
- Avoid layering type directly over shaded or textured areas.
- Avoid the use of reversed type (white lettering on a black background).
- Avoid heavy letters, which tend to close up, and unusual symbols, which the printer may not be able to reproduce in the legend.
- 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 Système International d'Unités (SI) symbols (µ for 10–6, m for 10–3, k for 103, M for 106, etc.). A complete listing of SI symbols can be found in the International Union of Pure and Applied Chemistry (IUPAC) "Manual of Symbols and Terminology for Physicochemical Quantities and Units" (Pure Appl. Chem. 21:3-44, 1970). Thus, a representation of 20,000 cpm on a figure ordinate is to be made by the number 20 accompanied by the label kcpm.
When 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 would be "2" and the label would be "104 cells per ml" (not "cells per ml x 10–4"). Likewise, an enzyme activity of 0.06 U/ml would be shown as 6 accompanied by the label 10–2 U/ml. The preferred designation would be 60 mU/ml (milliunits per milliliter).
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 MS 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, 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 (p. 7) 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.
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TABLE 1 Partial restoration of NO production by exogenous TNF- in cytochalasin B-inhibited macrophages treated with GBS and IFN
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Nucleic acid sequences of limited length which are the primary subject of a study may be presented freestyle in the most effective format. Longer 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, 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, 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.
FOOTNOTES
* Shading indicates material that has been added or significantly updated. 
Microbiology and Molecular Biology Reviews, March 2006, p. 1-11, Vol. 70, No. 1
1092-2172/06/$08.00+0 doi:10.1128/MMBR.70.1.1-11.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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