INFECTION AND IMMUNITY

Use of Microbiological InformationThe 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 .

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

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. For Authors’ Corrections and Retractions, signed letters of agreement from all of the authors must be submitted (see p. 12).

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 expected that the authors will provide written assurance that permission to cite unpublished data or personal communications has been granted.

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 newly 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.

Primary PublicationA 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. Work, or its substance, presented as a meeting poster and subsequently reproduced or distributed as a “company white paper” is also unacceptable for submission 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. Similarly, posting for sale on a commercial or similar website of an original, unmodified thesis or dissertation (i.e., as submitted to, and accepted by, the thesis/dissertation committee) 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.

Preliminary disclosures of research findings webcast as meeting presentations or published in abstract form as adjuncts to a meeting, e.g., part of a program, are not considered prior publication.

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 supplemental material.

Ultimately, it is an editorial decision whether the material constitutes the substance of a paper.

PermissionsThe corresponding author is responsible for obtaining permission from both the original author and the origi-nal 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 directly 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 IAI00123-08”). 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 p. 5), if the authors of the IAI 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.

AuthorshipAn 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 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.

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 InterestAll 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.

CopyrightTo 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. This agreement is sent to the corresponding author when the manuscript is accepted and scheduled for publication. 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 (their) article in any other publication (print, CD-ROM, and other electronic forms) of which he is (they are) the author(s) or editor(s), on the condition that appropriate credit is given to the original ASM publication. This republication rightalso 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., 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).

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. Theother 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.

Copyright for supplemental material (see p. 5) 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.)

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

Funding Agency RepositoriesThe 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. ASM allows such IAI authors to do so. ASM also allows IAI 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 4 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 4 months after publication of the typeset article by ASM.

Use of Human Subjects or Animals in ResearchThe use of human subjects or other animals for research purposes is regulated by the federal government and individual institutions. Manuscripts containing in-formation 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 IdentificationWhen 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 SequencesIt is expected that newly determined nucleotide and/or amino acid sequence data will be deposited and GenBank/EMBL/DDBJ accession numbers will be included in the manuscript no later than the modification stage of the review process. It is also 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 2008. If relevant, the version of the software used should be specified.

See p. 14 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 (EMBL), http://www.ebi.ac.uk/embl/ ; and GenBank, National Center for Biotechnology Information (GenBank), http://www.ncbi.nlm.nih.gov/ .

Structural DeterminationsIt is expected that coordinates for new structures of macromolecules will be deposited in the Protein Data Bank and that assigned identification codes will be included in the manuscript no later than the modification stage of the review process. It is also 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/ .

Microarray DataIt is expected that the entire set of supporting microarray data will be deposited in the appropriate public database (e.g., GEO, ArrayExpress, or CIBEX) and that the assigned accession number(s) will be included in the manuscript no later than the modification stage of the review process. It is also 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/arrayexpress/?#ae=main[0] ; and Center for Information Biology Gene Expression Database (CIBEX), http://cibex.nig.ac.jp/index.jsp .

Culture DepositionIAI expects authors to deposit important 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 MaterialSupplemental 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 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 in Rapid Review and will be reviewed along with the manuscript. The maximum size permitted for an individual file is 25 MB. If your file exceeds this size, you must use a file compression utility (e.g., WinZip or Stuffit) to reduce the size below 25 MB. The decision to publish (i.e., post online only) the material with the article if it is accepted will be made by the editor and conveyed to the corresponding author in the acceptance e-mail. Therefore, it is possible that a manuscript 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 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 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 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.

A one-time charge (amount not yet determined) may be levied for posting of supplemental material. When instituted, the charge will be indicated in the ASM acceptance letter.

ComplianceFailure 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 the ASM policies may be sanctioned as individuals and/or ASM may refuse to consider manuscripts having authors from such companies.

Warranties and ExclusionsArticles 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.

Page ChargesAuthors 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, 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 $65 per page for the first eight pages and $200 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 $75 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 mailed (Journals Department, ASM, 1752 N St., N.W., Washington, DC 20036-2904, USA) or faxed (202-942-9355) to the Journals Department. This request must indicate how the work was supported and should be accompanied by copies of the title page and Acknowledgments section.

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

Editorial StyleThe editorial style of ASM journals conforms to the ASM Style Manual for Journals (American Society for Microbiology, 2008, 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.

Review ProcessAll 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 as reviewers at least three editorial board members 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 number (e.g., IAI00047-08 version 1) and assigned to one of the editors. (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, generally within 6 to 8 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 in the designated section of the Rapid Review submission form for 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, and 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 number must be provided in the appropriate field on the submission form. 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 (the Rebuttal section appears in the submission form only if the manuscript is a modification). 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 AcceptanceWhen 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 below).

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, approximate page proof dates, and table of contents section 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.

Publish ahead of PrintFor 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., IAI 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 IAI Accepts manuscripts and the final, typeset articles. The manuscripts remain listed on the IAI Accepts page until the final, typeset articles are posted. At that point, the manuscripts are removed from the IAI Accepts page and become available only through links from the final, typeset articles. The manuscripts are under subscription access control until 4 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 the “References” section (p. 9).

Page ProofsPage 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.

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. 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 (telephone, 202-942-9288). Questions about accessing or viewing your PDF proofs should be directed to Katie Gay of Cadmus Communications at 804-261-3155 or gayk{at}cadmus.com .

ReprintsReprints (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 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.

PDF FilesA 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., 4 months after publication).

Title, running title, and byline.Each manuscript should present the results of an independent, cohesive study; thus, numbered series titles are not permitted. Exercise care in composing a title. Avoid the main title/subtitle arrangement, complete sentences, and unnecessary articles. On the title page, include the title, running title (not to exceed 54 characters and spaces), name of each author, address(es) of the institution(s) at which the work was performed, each author's affiliation, and a footnote indicating the present address(es) of any author(s) 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).

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.

Abstract.Limit the abstract to 250 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. Include a succinct description of the microbe and its associated disease. 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 or the rationale for the present study and include a succinct description of the microbe and its associated disease. Choose references carefully 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 “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, plasmids, etc.

A method, 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.In the Results section, include the rationale or design of the experiments as well as the results; 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 graphic 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. All tabular data must be accompanied by either standard deviation values or standard errors of the means. The number of replicate determinations (or animals) used for making such calculations must also be included. All statements concerning the significance of the differences observed should be accompanied by probability values given in parentheses. The statistical procedure used should be stated in Materials and Methods. 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 sup-port 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 re-ceived.) 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.

Appendixes.Appendixes, which contain additional material to aid the reader, are permitted. Titles, authors, and References 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.

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). 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 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 List of Journals Indexed for Medline (National Library of Medicine, National Institutes of Health, 2007; available at ftp://nlmpubs.nlm.nih.gov/online/journals/ljiweb.pdf ), the primary source for ASM style.

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

1. 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.

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., S. Paira, R. Burgos, J. Molina, J. F. Molina, and C. Calvo. 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. {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., IAI00577-08) if it is a journal article or the name of the publication if it is a book.

Online references must provide the same information that print references do, but some variation is allowed. 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/ecosal/index.jsp . {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. USA 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 (home pages) 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, 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.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.

(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 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.

If an author of an article cites an ASM Accepts manuscript in his paper but wishes at the proof stage to change the reference entry to that for the published article, the following style should be used:

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. (Subsequently published, Mol. Cell. Biol. 26:3902-3916, 2006.)

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. USA doi:10.1073/pnas.041593698.

NotesIAI no longer publishes Notes.

MinireviewsMinireviews are brief (limit of 6 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 IAI.

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 Rapid Review. The cover letter should state whether the article was solicited and by whom.

Minireviews do not have abstracts. In the Abstract section of the submission form, put “Not Applicable.” The body of the Minireview may have section headings, paragraph lead-ins, or both.

Letters to the EditorLetters 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 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.

ErrataThe 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, or mislabeling in a figure) of a published article. Submit Errata via Rapid Review (see “How To Submit Manuscripts,” above). In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Erratum as an MS Word file. Please see a recent issue for correct formatting.

Authors’ CorrectionsThe 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 portion [noncritical] 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 Rapid Review (see “How To Submit Manuscripts,” above). In the submission form, select Erratum as the manuscript type; there is no separate selection in Rapid Review for Authors’ Corrections, 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 an MS Word file. Please see a recent issue for correct formatting. Signed letters of agreement must be supplied as supplemental material (scanned PDF files).

RetractionsRetractions 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 Rapid Review (see “How To Submit Manuscripts,” above). In the Abstract section of the submission form (a required field), put “Not Applicable.” Upload the text of your Retraction as an MS 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 chairman 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.

Image ManipulationComputer-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.

Illustrations 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). Halftone images (those with various densities or shades) must be grayscale, not bitmap.

Color PowerPoint files are not accepted because the application, designed for developing on-screen computer presentations, uses the RGB color mode whereas the printing process uses the CMYK color mode. Colors that are represented in a PowerPoint image may not be reproducible on a printing press. Although black-and-white Microsoft PowerPoint files are accepted, we do not recommend the use of PowerPoint. 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. Use of PowerPoint is therefore not recommended for either color or black-and-white illustrations.

Acceptable file types and formats for production are given in the charts above. More-detailed instructions for preparing illustrations are available at http://art.cadmus.com/da/index.jsp . Please review this information before preparing your files. If you require additional information, please send an e-mail inquiry to digitalart{at}cadmus.com .

Minimum resolution. It is extremely important that a high enough resolution is used. Any imported images must be at the correct resolution before they are placed. 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 lettering

• 1,200 dpi for line art

• 600 dpi for combination art (lettering and images)

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$$mathtex$$\({5}/{16}\)$$mathtex$$ inches (ca. 8.4 cm)

• Maximum width for a 2-column figure: 6⅞ inches (ca. 17.4 cm)

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

• Maximum height: 9$$mathtex$$\({1}/{16}\)$$mathtex$$ inches (23.0 cm)

Contrast. Illustrations must contain sufficient contrast to withstand the inevitable loss of contrast and detail inherent in the printing process. See also “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 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: 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 proper font use in PowerPoint images, refer to the Cadmus digital art website, http://art.cadmus.com/da/instructions/ppt_disclaimer.jsp .

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. The cost of printing in color must be borne by the author. The current color cost per figure may be accessed from the submission form in Rapid Review. For accepted manuscripts, the total cost of the color will be included in the acceptance letter sent out by ASM. Adherence to the following guidelines, in addition to the general ones below, will help to minimize costs and to ensure color reproduction that is as accurate as possible.

Because of the requirements of print production, color illustrations must be in the CMYK (cyan, magenta, yellow, black) color space. The “normal” color mode for most computer software is RGB (red, green, blue), which is also the color space of your computer monitor. Since CMYK is a smaller color space (meaning it can define fewer colors), colors often shift when an RGB file is converted to CMYK. In particular, figures showing red or green fluorescence and those with a significant range of colors may be difficult or impossible to reproduce during the printing process.

Color illustrations must be supplied in the CMYK color mode, as either (i) CMYK TIFF images with a resolution of at least 300 pixels per inch (raster files, consisting of pixels) or (ii) Illustrator-compatible EPS files with CMYK color elements (vector files, consisting of lines, fonts, fills, and images). See the charts above for a list of supported applications.

We cannot accept any Microsoft Office files (PowerPoint, Word, Excel) for color illustrations because they are restricted to the RGB color space.

DrawingsSubmit 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:

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 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.

3. Use thick, solid lines that are no finer than 1 point in thickness.

4. No type should be smaller than 6 points at the final publication size.

5. Avoid layering type directly over shaded or textured areas.

6. Avoid the use of reversed type (white lettering on a black background).

7. Avoid heavy letters, which tend to close up, and unusual symbols, which the printer may not be able to reproduce in the legend.

8. 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 in 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) publication Quantities, Units and Symbols in Physical Chemistry (Blackwell Science, Oxford, United Kingdom, 1993); an abbreviated list is available at http://www.iupac.org/reports/1993/homann/index.html . 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 × 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).

Presentation of Nucleic Acid SequencesNucleic 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.

Figure LegendsLegends 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.

TablesTables 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. 18) 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.

Cover Photographs and DrawingsIAI publishes photographs and drawings on the front cover. Invitations are issued to authors whose manuscripts are returned for modification or whose manuscripts have been accepted for publication in IAI; material should be related to the work presented in the IAI 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 for submission are available from the cover editor, Victor J. DiRita (e-mail: heiditho{at}umich.edu ).

Chemical and Biochemical NomenclatureThe recognized authority for the names of chemical compounds is Chemical Abstracts (CAS, Columbus, OH) and its indexes. The Merck Index, 14th ed. (Merck & Co., Inc., Whitehouse Station, NJ, 2006), is also an excellent source. For biochemical terminology, including abbreviations and symbols, 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, and express enzyme activity either in katals (preferred) or in the older system of micromoles per minute.

Amino Acid SequencesSingle-letter designations, rather than three-letter designations, should be used for sequences of amino acids.

DrugsChemical or generic names of drugs should be used; the use of code numbers or trade names is generally not permitted.

Nomenclature of MicroorganismsBinary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), should 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 (or underlined) in the manuscript; strain designations and numbers are not. Vernacular (common) names should be in lowercase roman type (e.g., streptococcus, brucella). For Salmonella, genus, species, and subspecies names should be rendered in standard form: Salmonella enterica at first use, S. enterica thereafter; Salmonella enterica subsp. arizonae at first use, S. enterica subsp. arizonae thereafter. Names of serovars should be in roman type with the first letter capitalized: Salmonella enterica serovar Typhimurium. After the first use, the serovar may also be given without a species name: Salmonella serovar Typhimurium. For other information regarding serovar designations, see Antigenic Formulas of the Salmonella Serovars, 8th ed. (M. Y. Popoff, WHO Collaborating Centre for Reference and Research on Salmonella, Institut Pasteur, Paris, France, 2001). For a summary of the current standards for Salmonella nomenclature and the Kaufmann-White criteria, see the article by Brenner et al. (J. Clin. Microbiol. 38:2465-2467, 2000), the opinion of the Judicial Commission of the International Committee on Systematics of Prokaryotes (Int. J. Syst. Evol. Microbiol. 55:519-520, 2005), and the article by Tindall et al. (Int. J. Syst. Evol. Microbiol. 55:521-524, 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, 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/ ). 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.

It is recommended that a strain be deposited in a recognized culture collection when that strain is necessary for the description of a new taxon (see Bacteriological Code, 1990 Revision, American Society for Microbiology, 1992).

Since the classification of fungi is not 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, 4th ed. (C. P. Kurtzman and J. W. Fell, ed., Elsevier Science Publishers B.V., Amsterdam, The Netherlands, 1998), and Ainsworth and Bisby's Dictionary of the Fungi, 9th ed. (P. M. Kirk, P. F. Cannon, J. C. David, and J. A. Stalpers, ed., CABI Publishing, Wallingford, Oxfordshire, United Kingdom, 2001); see also http://www.speciesfungorum.org/Names/Fundic.asp .

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, 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 NomenclatureTo 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.

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).

Bacteria. The genetic properties of bacteria 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. Use the recommendations of Demerec et al. (Genetics 54:61-76, 1966) as a guide to the use of these terms. If your manuscript contains information including genetic nomenclature, please refer to the Instructions to Authors in the January issue of the Journal of Bacteriology.

Conventions for naming genes. It is recommended that (entirely) new genes be given names that are mne-monics of their function, avoiding names that are al-ready assigned and earlier or alternative gene names, irrespective of the bacterium for which such assignments have been made. Similarly, it is recommended that, whenever possible, orthologous genes present in differ-ent organisms receive the same name. When homology is not apparent or the function of a new gene has not been established, a provisional name may be given by one of the following methods. (i) The gene may be named on the basis of its map location in the style yaaA, analogous to the style used for recording transposon insertions (zef) as discussed below. A list of such names in use for E. coli has been published by Rudd (Microbiol. Mol. Biol. Rev. 62:985-1019, 1998). (ii) A provisional name may be given in the style described by Demerec et al. (e.g., usg, gene upstream of folC). Such names should be unique, and names such as orf or genX should not be used. For reference, the E. coli Genetic Stock Center's database includes an updated listing of E. coli gene names and gene products. It is accessible on the Internet (http://cgsc.biology.yale.edu/cgsc.html ). The Center's relational database can also be searched via Telnet; for access, send a request to berlyn{at}cgsc.biology.yale.edu . A list can also be found in the work of Riley (Microbiol. Rev. 57:862-952, 1993). For the genes of other bacteria, consult the references given above. For prokaryotes, gene names should not begin with prefixes indicating the genus and species from which the gene is derived. For eukaryotes, such prefixes may be used for clarity when discussing genes with the same name from two different organisms (e.g., ScURA3 vs. CaURA3); the prefixes are not considered part of the gene name proper and are not italicized.

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. However, since locus tags are not genetic names, they should appear in roman type rather than in italics. 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, 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.

“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 share 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.

Eukaryotes. For information about the genetic nomenclature of eukaryotes, see the Instructions to Authors for Eukaryotic Cell and Molecular and Cellular Biology.

Transposable elements, plasmids, and restriction enzymes. Nomenclature of transposable elements (insertion sequences, transposons, phage Mu, etc.) should follow the recommendations of Campbell et al. (Gene 5:197-206, 1979), with the modifications given in the Instructions to Authors of 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). Whenever possible, 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 nucleases, 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.

Tetracycline resistance determinants. The nomencla-ture for tetracycline resistance determinants is based on the proposal of Levy et al. (Antimicrob. Agents Chemother. 43:1523-1524, 1999). The style for such determinants is, e.g., Tet B; the space helps distinguish the determinant designation from that for phenotypes and proteins (TetB). Table 2 of the above-referenced article shows the correct format for genes, proteins, and deter-minants in this family.

Verb TenseASM 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 to 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, Leu, etc.) may also be used.

It is strongly recommended that all abbreviations except those listed below be introduced in the first paragraph in Materials and Methods. Alternatively, 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, 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(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 DataStandard 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.

Representation of data as accurate to more than two significant figures must be justified by presentation of appropriate statistical analyses.

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).

StatisticsStatistical analysis of data is a crucial component of scientific publication. Authors who are unsure of proper statistical analysis should have their manuscripts checked by a qualified statistician.

The following is a list of important items that must be considered before manuscript submission. Deficiencies in any of these areas may delay review and/or publication.

Statistical analyses were performed on all quantitative data regardless of how significant the differences look in the tables or figures.

Data were appropriately analyzed as parametric (normally distributed) or nonparametric data.

Parametric and nonparametric data are presented appropriately. Means and standard deviations or standard errors are appropriate means of presenting data analyzed by parametric analyses (i.e., t test and analysis of variance [ANOVA]), but only medians and surrounding levels (quartiles, quintiles, 10th and 90th percentiles, etc.) are appropriate for nonparametric statistics (Mann-Whitney test, Kruskal-Wallis test, etc.). Means have no meaning in nonparametric analyses.

For any data in which there are more than two comparisons (i.e., between one control and more than one experimental group), an analysis must be done for multigroup comparisons. Such an analysis would usually be an ANOVA for parametric data or a Kruskal-Wallis test for nonparametric data. t tests cannot be used when more than two groups are being compared (except as indicated below). Failure to use multigroup tests generates type 1 errors: concluding that two data sets within the overall data set being compared are different when in fact they are not. Exception: Some statisticians argue that two-group comparisons can be used on multigroup data if the expected outcomes are appropriately anticipated before the experiment. For example, data generated by individually testing two unrelated factors for their effects on a target with only a single, untreated target as a control could be appropriately analyzed by t tests instead of ANOVA.

For all appropriate multigroup comparisons, two P values must be generated and provided in the manuscript. The main P value applies to the overall data set and indicates that within that data set at least two groups differ from each other. The overall P value does not indicate which two groups are different. The main P value and the overall P value should be computed by using a post hoc test. For ANOVA, these post hoc tests are usually Dunnett's test (used to compare multiple experimental groups to a single control), the Fisher protected least significant difference (PLSD) test, the Tukey-Kramer test, and the Games-Howell test. Others may be used. Note that each post hoc test has certain underlying assumptions that may not be applicable to the data under analysis. For a Kruskal-Wallis nonparametric ANOVA, the Dunn procedure is appropriate to generate P values for two-group comparisons.

Data presented as endpoints (i.e., LD₅₀, ID₅₀, etc.) contain both the calculated value and a confidence interval with a statistical significance associated with it (95%, 99%, or similar confidence interval), calculated by logit or probit analysis. Simple LD₅₀ values such as Reed-Muench calculations may not be used alone.

When samples are taken multiple times from one experimental entity (i.e., multiple serum samples from one animal, gross pathology scores measured for the same animal over time, growth curves, etc.), one cannot use analyses such as t tests, ANOVA, the Mann-Whitney test, etc., because these tests assume that each measure is independent. An entity with a high score on day 1 is more likely to have a high score on day 2 than is an entity with a low score. It is likely that some expert statistical help will be needed for these situations, usually involving regression analysis, survival analysis, etc.

Statistical significance and biological significance are not the same. There is nothing magic about a P value of 0.05. When results from small sample sizes are compared, a P value of <0.05 will often be obtained, but it may be dependent on the outcome of a single experimental value. If sample sizes are small, then more-vigorous (i.e., smaller) P values may be necessary. If sample sizes are large, P values of >0.05 may be important. There should be both statistical and biological significance to the results and conclusions in the manuscript.

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).

Isotopically Labeled CompoundsFor simple molecules, labeling is indicated in the chemical formula (e.g., ¹⁴CO₂, ³H₂O, and H₂³⁵SO₄). 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 which 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 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

• UDP-[U-¹⁴C]glucose

• E. coli [³²P]DNA

• fructose 1,6-[1-³²P]bisphosphate

• [γ-³²P]ATP

IAI 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).