2010 Instructions to Authors*

2010 INSTRUCTIONS TO AUTHORS*

SCOPE work for the Oversight of Dual Use Life Sciences Research: Strategies for Minimizing the Potential Misuse of Research mBio is a broad-scope open access journal edited by active Information” on the Office of Biotechnology Activities web- research scientists. It strives to publish the best research in site http://oba.od.nih.gov/biosecurity/ (pages 17–22). microbiology and allied fields. mBio publishes outstanding papers in all disciplines that address microbiological problems, including, but not limited to, biochemistry and molec- Ethical Guidelines ular biology, genetics and genomics, environmental science, evolution, immunology, infectious disease, and physiology. Authors are expected to adhere to the highest ethical stan- Topics covered include bacteria, viruses, parasites, fungi, and dards. The following sections of these Instructions include simple eukaryotic organisms, as well as all types of host- detailed information about ASM’s ethical standards. Failure microbe interactions. to comply with the policies described in these Instructions We understand that there may be overlap in the scope may result in a letter of reprimand, a suspension of publish- statements of the ASM journals. Questions about these ing privileges in ASM journals, and/or notification of the au- guidelines may be directed to the editor in chief of the journal thors’ institutions. Authors employed by companies whose being considered. policies do not permit them to comply with ASM policies may be sanctioned as individuals and/or ASM may refuse to consider manuscripts having authors from such companies. The ASM Publications Board wishes to clarify the following EDITORIAL POLICY in particular. Use of Microbiological Information The Council Policy Committee (CPC) of the American Plagiarism. Misappropriating another person’s intellec- Society for Microbiology affirms the long-standing position tual property constitutes plagiarism. This includes copying of the Society that microbiologists will work for the proper sentences or paragraphs verbatim (or almost verbatim) from and beneficent application of science and will call to the at- someone else’s work, even if the original work is cited in the tention of the public or the appropriate authorities misuses of references. The NIH ORI publication “Avoiding Plagiarism, microbiology or of information derived from microbiology. Self-Plagiarism, and Other Questionable Writing Practices: a ASM members are obligated to discourage any use of micro- Guide to Ethical Writing” http://ori.dhhs.gov/education/ biology contrary to the welfare of humankind, including the products/plagiarism/ can help authors identify questionable use of microbes as biological weapons. Bioterrorism violates writing practices. the fundamental principles expressed in the Code of Ethics of Plagiarism is not limited to the text; it can involve any part the Society and is abhorrent to ASM and its members. of the manuscript, including figures and tables, in which ma- ASM recognizes that there are valid concerns regarding the terial is copied from another publication without permission publication of information in scientific journals that could be and attribution. An author may not reuse his or her own put to inappropriate use as described in the CPC resolution previously published work without attribution; this is con- mentioned above. Members of the ASM Publications Board sidered self-plagiarism. will evaluate the rare manuscript that might raise such issues during the review process. However, as indicated elsewhere Primary publication. Manuscripts submitted to the jour- in these Instructions, research articles must contain sufficient nal must represent reports of original research, and the orig- detail, and material/information must be made available, to inal data must be available for review by the editor if neces- permit the work to be repeated by others. Supply of materials sary. should be in accordance with laws and regulations governing By submission of a manuscript to the journal, the authors the shipment, transfer, possession, and use of biological ma- guarantee that they have the authority to publish the work terials and must be for legitimate, bona fide research needs. and that the manuscript, or one with substantially the same Links to, and information regarding, these laws and regula- content, was not published previously, is not being consid- tions can be found at http://www.asm.org/index.php?optionϭ ered or published elsewhere, and was not rejected on scien- com_content&viewϭarticle&idϭ10101&Itemidϭ342.We tific grounds by another ASM journal. It is incumbent upon ask that authors pay particular attention to the NSAR Select the author to acknowledge any prior publication, including Agent/Toxin list on the CDC website http://www.select his/her own articles, of the data contained in a manuscript agents.gov/index.html and the NSABB criteria for identifying submitted to an ASM journal. A copy of the relevant work dual use research of concern in the report “Proposed Frame- should be submitted with the paper as supplemental material. Whether the material constitutes the substance of a pa- *Instructions to Authors are updated throughout the year. A separate per and therefore renders the manuscript unacceptable for HTML version is maintained at the mBio website (http://mbio.asm.org/). publication is an editorial decision. 1 2 2010 mBio INSTRUCTIONS TO AUTHORS mBio

In brief, a paper is not acceptable for submission to an Permission(s) must be obtained no later than the modifi- ASM journal if it, or its substance, has been published/posted cation stage. The original signed permission(s) must be iden- in: tified as to the relevant item in the ASM manuscript (e.g., “permissions for Fig. 1 in mBio00001-10”) and submitted to • A serial, periodical, or book the mBio managing editor on request. In addition, a state- • A conference report or symposium proceedings ment indicating that the material is being reprinted with per- • A technical bulletin or company white paper • A nonpersonal website mission must be included in the relevant figure legend or • Any other retrievable source table footnote of the manuscript. Any reprinted text must be enclosed in quotation marks, and the permission statement The following do not preclude submission to, or publica- must be included as running text or indicated parentheti- tion by, an ASM journal, as long as the posted data do not cally. constitute the substance of a submission: It is expected that the authors will provide written assur- • Posting of a method/protocol on a nonpersonal website ance that permission to cite unpublished data or personal • Posting of a limited amount of original data on a person- communications has been granted. For supplemental mate- al/university/corporate website or websites of small col- rial intended for posting by ASM (see “Supplemental Mate- laborative groups working on a problem rial”), if the authors of the mBio manuscript are not also the • Posting of unpublished sequence data on the Internet owners of the supplemental material, the corresponding au- (the URL where the sequence is posted should be in- thor must send to ASM signed permission from the copyright cluded in the text) owner that allows posting of the material, as a supplement to • Preliminary disclosures of research findings as meeting the article, by ASM. The corresponding author is also respon- posters, webcast as meeting presentations, or published sible for incorporating in the supplemental material any in abstract form as adjuncts to a meeting, e.g., part of a copyright notices required by the owner. program • Posting of theses and dissertations on a personal/ university-hosted website Authorship. All authors of a manuscript must have agreed to its submission and are responsible for its content (initial Availability of materials. By publishing in the journal, the submission and any subsequent versions), including appro- authors agree that, subject to requirements or limitations im- priate citations and acknowledgments, and must also have posed by laws or governmental regulations of the United agreed that the corresponding author has the authority to act States, any DNAs, viruses, microbial strains, mutant animal on their behalf in all matters pertaining to publication of the strains, cell lines, antibodies, and similar materials newly de- manuscript. The corresponding author is responsible for ob- scribed in the article are available from a national collection taining such agreements and for informing the coauthors of or will be made available in a timely fashion, at reasonable the manuscript’s status throughout the submission, review, cost, and in limited quantities to members of the scientific and publication process. Submitting a paper before all coau- community for noncommercial purposes. The authors guar- thors have read and approved it is considered an ethical vio- antee that they have the authority to comply with this policy lation, as is failure to credit someone who qualifies as a coau- either directly or by means of material transfer agreements thor; however, ASM does not itself investigate or attempt to through the owner. resolve authorship disputes. Similarly, the authors agree to make available computer An author is one who made a substantial contribution to programs, originating in the authors’ laboratory, that are the the overall design and execution of the experiments; there- only means of confirming the conclusions reported in the fore, ASM considers all authors responsible for the entire article but that are not available commercially. The pro- paper. Individuals who provided assistance, e.g., supplied gram(s) and suitable documentation regarding its (their) use strains or reagents or critiqued the paper, need not be listed as may be provided by any of the following means: (i) as a pro- authors but may be recognized in the Acknowledgments sec- gram transmitted via the Internet, (ii) as an Internet server- tion. based tool, or (iii) as a compiled or assembled form on a A study group, surveillance team, working group, consor- suitable medium (e.g., magnetic or optical). It is expected tium, or the like (e.g., the Active Bacterial Core Surveillance that the material will be provided in a timely fashion and at Team) may be listed as a coauthor in the byline if its contrib- reasonable cost to members of the scientific community for uting members satisfy the requirements for authorship and noncommercial purposes. The authors guarantee that they accountability as described in these Instructions. The names have the authority to comply with this policy either directly and institutional affiliations of the contributing members or by means of material transfer agreements through the only may be given in a separate paragraph in the Acknowl- owner. edgments section. If the contributing members of the group associated with Permissions. The corresponding author is responsible for the work do not fulfill the criteria of substantial contribution obtaining permission from both the original author and the to and responsibility for the paper, the group may not be original publisher (i.e., the copyright owner) to reproduce or listed in the author byline. Instead, it and the names of its modify figures and tables and to reproduce text (in whole or contributing members may be listed in the Acknowledg- in part) from previous publications. ments section. mBio 2010 mBio INSTRUCTIONS TO AUTHORS 3

All authors must agree to the order in which their names ican Society for Microbiology, 1752 N St. NW, Washington, are listed in the byline. Statements regarding equal contribu- DC 20036. tions by two or more authors (e.g., X.J. and Y.S. contributed equally to...)maybeincluded as a footnote to the byline or Supplemental material is also covered by the mBio License to in the Acknowledgments section. Other statements of spe- Publish (see “Supplemental Material”). cific attribution may also be included in the Acknowledg- ments section. Funding Agency Repositories A change in authorship (order of listing, addition or dele- The National Institutes of Health (NIH) requests that its tion of a name, or corresponding author designation) after grantee and intramural authors provide copies of their ac- submission of the manuscript will be implemented only after cepted manuscripts to PubMed Central (PMC) for posting in receipt of signed statements of agreement from all parties the PMC Public Access Repository. However, mBio authors involved. are automatically in compliance with this policy and need Disputes about authorship may delay or prevent review take no action themselves. For the past several years, ASM has and/or publication of the manuscript. Should the individuals deposited in PMC all publications from all ASM journals. involved be unable to reach an accord, review and/or publi- Since mBio articles are open access and are made available cation of the manuscript can proceed only after the matter is through PMC and international PMC-like repositories im- investigated and resolved by the authors’ institution(s) and mediately after publication, ASM is in full compliance with an official report of such and signed statements of agreement NIH policy. For more information, see http://publicaccess are provided to ASM. .nih.gov/. ASM also allows mBio authors whose work was supported by similar funding agencies that have public access Conflict of interest. All authors are expected to disclose, in requirements like those of the NIH (e.g., the Wellcome the cover letter and in the appropriate field on the submission Trust) to post their accepted manuscripts in publicly accessi- form, any commercial affiliations as well as consultancies, ble electronic repositories maintained by those funding agen- stock or equity interests, and patent-licensing arrangements cies. If a funding agency does not itself maintain such a site, that could be considered to pose a conflict of interest regard- then ASM allows the author to fulfill that requirement by ing the submitted manuscript. (Inclusion of a company name depositing the article in an appropriate institutional or in the author address lines of the manuscript does not con- subject-based open repository established by a government stitute disclosure.) Details of the disclosure to the editor will or noncommercial entity. remain confidential. However, it is the responsibility of au- ASM recommends that when submitting an accepted thors to provide, in the Acknowledgments section, a general manuscript to PMC or a similar public access site, the author statement disclosing financial or other relationships that are specify that the posting release date for the manuscript be relevant to the study. Examples of potentially conflicting in- no earlier than the date of publication on the mBio website. terests that should be disclosed include relationships that Articles are published on the website as soon as they are pro- might detract from an author’s objectivity in presentation of cessed, so delays should be minimal. study results and interests whose value would be enhanced by the results presented. All funding sources for the project, in- Use of Human Subjects or Animals in Research stitutional and corporate, should be credited in the Acknowl- edgments section. In addition, if a manuscript concerns a The use of human subjects or animals for research pur- commercial product, the manufacturer’s name must be indi- poses is regulated by the federal government and individual cated in the Materials and Methods section or elsewhere in institutions. Manuscripts containing information related to the text, as appropriate, in an obvious manner. human or animal use should clearly state that the research has complied with all relevant federal guidelines and institutional Copyright policies. Copies of these guidelines and policy statements must be available for review by the editor if necessary. Copyright of all material published in mBio remains with the authors. The authors grant the American Society Patient Identification for Microbiology a nonexclusive license to publish their work if it is accepted. Upon publication, the work becomes When isolates are derived from patients in clinical studies, available to the public to copy, distribute, or display under do not identify them by using the patients’ initials, even as a Creative Commons Attribution-Noncommercial-Share part of a strain designation. Change the initials to numerals Alike 3.0 Unported license (for details, see http://creative or use randomly chosen letters. Do not give hospital unit commons.org/licenses/by-nc-sa/3.0/ and http://creative numbers; if a designation is needed, use only the last two commons.org/licenses/by-nc-sa/3.0/legalcode). The corre- digits of the unit. (Note: established designations of some sponding author must sign the Author Warranty and viruses and cell lines, although they consist of initials, are Provisional License to Publish on behalf of all coauthors. acceptable [e.g., JC virus, BK virus, and HeLa cells].) Authors should return the signed license agreement promptly to avoid publication delays. A scanned PDF file of Nucleotide and Amino Acid Sequences the signed form may be emailed to [email protected]. Alter- natively, the signed form may be faxed to 202-942-9355 or Newly determined nucleotide and/or amino acid sequence mailed to the following address: mBio Editorial Office, Amer- data must be deposited and GenBank/EMBL/DDBJ accession 4 2010 mBio INSTRUCTIONS TO AUTHORS mBio numbers must be included in the manuscript no later than must be deposited in the Protein Data Bank and assigned the modification stage of the review process. It is expected identification codes must be included in the manuscript no that the sequence data will be released to the public no later later than the modification stage of the review process. It is than the publication (online posting) date of the accepted expected that the coordinates will be released to the public no manuscript. As part of the publication process, accession later than the publication (online posting) date of the ac- numbers will be linked from the article to GenBank, which cepted manuscript. will prompt the release of any previously unreleased se- Authors are encouraged to send coordinates with their quences. original submission, so that reviewers can examine them The accession numbers should be included in a separate along with the manuscript. The accession number(s) should paragraph at the end of the Materials and Methods section for be listed in a separate paragraph at the end of the Materials Research Articles or at the end of the text for other formats. If and Methods section for Research Articles or at the end of the conclusions in a manuscript are based on the analysis of se- text for other formats. quences and a GenBank/EMBL/DDBJ accession number is The URLs for coordinate deposition are http://rcsb- not provided at the time of the review, authors should pro- deposit.rutgers.edu/ and http://pdbdep.protein.osaka-u.ac vide the sequence data as supplemental material. .jp/top.html.en. 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 Refer- Microarray Data ences section when possible or reasonable. Authors are also expected to do elementary searches and The entire set of supporting microarray data must be de- comparisons of nucleotide and amino acid sequences against posited in the appropriate public database (e.g., GEO, Ar- the sequences in standard databases (e.g., GenBank) imme- rayExpress, or CIBEX) and the assigned accession number(s) diately before manuscripts are submitted and again at the must be included in the manuscript no later than the modi- proof stage. fication stage of the review process. It is expected that the data Analyses should specify the database, and the date of each will be released to the public no later than the publication analysis should be indicated as, e.g., January 2010. If relevant, (online posting) date of the accepted manuscript. the version of the software used should be specified. Authors are encouraged to send the relevant data with See “Presentation of Nucleic Acid Sequences” for nucleic their original submission, so that reviewers can examine acid sequence formatting instructions. them along with the manuscript. The accession number(s) The URLs of the databases mentioned above are as follows: should be listed in a separate paragraph at the end of the DNA Data Bank of Japan (DDBJ), http://www.ddbj.nig.ac Materials and Methods section for Research Articles or at the .jp/; EMBL Nucleotide Sequence Database (EMBL), http:// end of the text for other formats. www.ebi.ac.uk/embl/; and GenBank, National Center for The URLs of the databases mentioned above are as follows: BiotechnologyInformation(GenBank),http://www.ncbi.nlm Gene Expression Omnibus (GEO), http://www.ncbi.nlm.nih .nih.gov/. .gov/projects/geo/; ArrayExpress, http://www.ebi.ac.uk /microarray-as/ae/; and Center for Information Biology Gene Expression Database (CIBEX), http://cibex.nig.ac.jp /index.jsp. Proper Use of Locus Tags as Systematic Identifiers for Genes To comply with recommendations from the International MycoBank Nucleotide Sequence Database (INSD) Collaborators and to New scientific names of fungi along with key nomencla- avoid conflicts in gene identification, researchers should im- tural and descriptive material must be deposited in Myco- plement the following two fundamental guidelines as stan- Bank (http://www.MycoBank.org) and the assigned acces- dards for utilization of locus tags in genome analysis, anno- sion number(s) must be included in the manuscript no later tation, submission, reporting, and publication. (i) Locus tag than the modification stage of the review process. It is ex- prefixes are systematic gene identifiers for all of the replicons pected that the data will be released to the public no later than of a genome and as such should be associated with a single the publication (online posting) date of the accepted manu- genome project submission. (ii) New genome projects must script. Authors are encouraged to send the relevant data with be registered with INSD, and new locus tag prefixes must be their original submission, however, so that reviewers can ex- assigned in cooperation with INSD to ensure that they con- amine them along with the manuscript. The accession num- form to the agreed-upon criteria. Locus tag prefixes that are ber(s) should be listed in a separate paragraph at the end of currently in use may be searched at the NCBI locus tag data- the Materials and Methods section for Research Articles and base ( http://www.ncbi.nlm.nih.gov/genomes/lltp.cgi ). at the end of the text for other formats.

Structural Determinations Culture Deposition Coordinates for new structures of macromolecules deter- mBio expects authors to deposit strains used in therapeutic mined by X-ray crystallography or cryo-electron microscopy activity assessments and studies of mechanisms of action, re- mBio 2010 mBio INSTRUCTIONS TO AUTHORS 5 sistance, and cross-resistance in publicly accessible culture • Text: Word, RTF, or PDF files. collections and to refer to the collections and strain numbers • Figures: TIFF, EPS, high-resolution PDF, JPEG, or GIF in the text. Since the authenticity of subcultures of culture format. Figures may not be embedded in the manuscript collection specimens that are distributed by individuals can- text. Do not save figure numbers, legends, or author not be ensured, authors should indicate laboratory strain names as part of the image. Composite figures must be designations and donor sources as well as original culture preassembled. Images should not exceed 500 pixels per collection identification numbers. inch in width or height. • Tables: Word, RTF, or PDF files. Include only 1 table per file. Do not use tabs or spaces to separate columns in Supplemental Material Word tables. • Data sets: Excel (.xls), RTF, TXT, or PDF files. Supplemental material intended for posting by ASM • Movies: Audio Video Interleave (.avi), Quicktime should be restricted primarily to large or complex data sets or (.mov), or MPEG files. All movies should be submitted results that cannot readily be displayed in the article. This at the desired reproduction size and length. material may include data from microarray, structural, biochemical, or video imaging analyses. In such cases, the manu- For information about supplemental material posting fees, script submitted for review should include a distillation of the see “Publication Fees.” results such that the principal conclusions are fully supported without referral to the supplemental material. Warranties and Exclusions Supplemental material will be reviewed along with the manuscript. The decision to post the supplemental material Articles published in this journal represent the opinions of with the article will be made by the editor. It is possible that a the authors and do not necessarily represent the opinions of manuscript will be accepted but that the supplemental mate- ASM. ASM does not warrant the fitness or suitability, for any rial will not. Unlike the manuscript, supplemental material purpose, of any methodology, kit, product, or device de- will not be edited by the ASM Journals staff, and proofs will scribed or identified in an article. The use of trade names is not be made available. Supplemental material will always re- for identification purposes only and does not constitute en- main associated with the article and is not subject to any dorsement by ASM. modifications after publication. Material that has been published previously (in print or online) is not acceptable for posting as supplemental material. Instead, the appropriate reference(s) to the original pub- SUBMISSION, REVIEW, AND PUBLICATION lication should be made in the manuscript text. PROCESSES Supplemental material is covered by the mBio Author Submission Process Warranty and Provisional License to Publish; copyright for supplemental material remains with the author. If you are All submissions to mBio must be made electronically via not the copyright owner, you must provide to ASM signed the mBio online submission and peer review system at http:// permission from the owner that allows ASM to post the ma- mbio.msubmit.net/. First-time users must create an Author terial as a supplement to your article. You are responsible for account. including in the supplemental material any copyright notices required by the owner. Review Process Supplemental material intended for posting by ASM must be uploaded as a separate Supplemental Material file(s) in the All manuscripts are considered to be confidential and are manuscript submission system. The maximum size permit- reviewed by members of the mBio Board of Editors, invited ted for an individual file is 3 MB (20 MB for movie files). If editors, or invited reviewers. your file exceeds this size, you must use a file compression To expedite the review process, authors must recommend utility (e.g., WinZip or Stuffit) to reduce the size. three (3) members of the mBio Board of Editors (available at ASM will post no more than 10 individual supplemental http://mbio.asm.org/site/misc/edboard.xhtml) who would items. Each item in the supplemental material should be sub- be able to handle the review of their manuscript. Authors also mitted as a separate file, e.g., multiple figures should not be must suggest at least three (3) reviewers (five are recom- zipped together or combined in a single PDF. At the end of mended) who have expertise in the field, who are not mem- the manuscript text file, include a legend for each item of bers of their institution(s), who have not been recently asso- supplemental material, clearly labeled as such. If it is neces- ciated with their laboratory(ies), and who could not sary to cite references that are relevant only to these supple- otherwise be considered to have a conflict of interest regard- mental legends, use the style described for “ Citations in ab- ing the submitted manuscript. stracts ”; do not include these references in the References Copies of in-press and submitted manuscripts that are section of the manuscript. Supplemental material should be important for judgment of the present manuscript should numbered with an “S” (e.g., Movie S1, Fig. S2, etc.), and each be included as supplemental material to facilitate the re- item should be cited at least once in the text. view. To ensure broad access, we ask that supplemental files be When a manuscript is submitted to the journal, it is given submitted in the following standard formats. a manuscript control number (e.g., mBio00001-10) and as- 6 2010 mBio INSTRUCTIONS TO AUTHORS mBio signed to a member of the Board of Editors. (Always refer to completed successfully. If there are problems that would this control number in communications with the editor cause extensive corrections to be made at the copyediting and the Journals Department.) It is the responsibility of the stage or if the files are not acceptable for production, ASM corresponding author to inform the coauthors of the manu- Journals staff will contact the corresponding author. Once all script’s status throughout the submission, review, and publi- the material intended for publication has been determined to cation processes. The reviewers operate under strict guide- be adequate, the editorial staff of the ASM Journals Depart- lines set forth in “Guidelines for Reviewers” (http://mbio ment completes the editing of the manuscript to bring it into .asm.org/site/misc/guidelines.xhtml) and are expected to conformity with prescribed standards. complete their reviews expeditiously. The corresponding author is notified, generally within 4 mBio Publication Schedule weeks after submission, of the decision to accept, reject, or require modification. When modification is requested, the mBio articles are released in an article-based workflow. Ar- corresponding author must either submit the modified ver- ticles are not held until an issue is released. Instead, at the end sion within 30 days or withdraw the manuscript. A point-by- of each month, the articles published over the preceding point response to the reviews must be provided in a separate weeks are collected into an issue and moved into the mBio file, and a compare copy of the manuscript (without figures) archive. should be included as supplemental material if the editor requested one. Page Proofs

Rejected Manuscripts Page proofs will be made available to the corresponding author electronically via a PDF file that can be accessed Authors who believe that their manuscript has been un- through a unique password. Included in the proofs will be the fairly rejected because an important aspect was misunder- typeset pages of the article, a page showing the legends for any stood or overlooked by the reviewers may submit an appeal. supplemental material (since these legends will appear in the The appeal will be processed by the editor in chief, who may HTML view of the published article), and an author query consult with the Editor and/or Invited Editor of the manu- sheet. script. Please note that while we are willing to entertain ap- Since corresponding authors will be notified of the avail- peals, it is uncommon for editorial decisions to be reversed. ability of their PDF proofs and assigned their unique pass- Manuscripts that have been rejected, or withdrawn after word via e-mail, a valid e-mail address must be supplied in being returned for modification, may be resubmitted to mBio the correspondent footnote. Failure to do so may result in a (once; see below) if the major criticisms have been addressed. delay in publication. Manuscripts rejected by mBio may be resubmitted to a more All author queries must be answered, and any changes re- appropriate ASM journal without penalty. lated to the queries must also be marked on the proofs. Note For all resubmissions (to the same or a different ASM jour- that the copy editor does not query at every instance where a nal, irrespective of the extent of the revisions, and irrespective change has been made. Queries are written only to request of the amount of time between rejection and resubmission), necessary information or clarification of an unclear passage the cover letter must state that the manuscript is a resubmis- or to draw attention to edits that may have altered the sense. sion, and the former manuscript control number must be It is the author’s responsibility to read the entire text, tables, provided in the appropriate field on the submission form. A and figure legends, not just items queried. As soon as the page point-by-point response to the review(s) must be included proofs are corrected (within 48 h), the annotated PDF file (the Response to Reviewer Comments section appears in the should be e-mailed to [email protected], or alternatively, a submission form only if the manuscript is a modification), marked-up printout of the proof should be scanned and sent and a compare copy of the revised manuscript showing the via e-mail to [email protected] or sent via an express courier changes (as supplemental material) should be included as service such as FedEx to the ASM Journals Department, 1752 well. Manuscripts resubmitted to the same journal are nor- N St. NW, Washington, DC 20036-2904. mally handled by the original editor. The proof stage is not the time to make extensive correc- Rejected manuscripts may be resubmitted only once un- tions, additions, or deletions. Figures as they appear in the less permission has been obtained from the original editor or proofs are for validation of content and placement, not qual- from the editor in chief. ity of reproduction or color accuracy. Print output of figures in the PDF page proofs will be of lower quality than the same Notification of Acceptance figures viewed on a monitor. Please avoid making changes to figures based on quality of color or reproduction in proof. When an editor has decided that a manuscript is acceptable Important new information that has become available be- for publication on the basis of scientific merit, the author and tween acceptance of the manuscript and receipt of the proofs the Journals Department are notified. The text files undergo may be inserted as an addendum in proof with the approval an automated preediting, cleanup, and tagging process spe- of the editor. If references to unpublished data or personal cific to the particular article type, and the illustrations are communications are added, it is expected that written assur- examined. If all files have been prepared according to the ance granting permission for the citation will be included. criteria set forth in these Instructions and those in the manu- Limit changes to correction of spelling errors, incorrect data, script submission system, the acceptance procedure will be and grammatical errors and updated information for refer- mBio 2010 mBio INSTRUCTIONS TO AUTHORS 7 ences to manuscripts that have been submitted or are in automated preediting, cleanup, and tagging process specific press. If URLs have been provided in the article, recheck the to the particular article type. To optimize this process, manu- sites to ensure that the addresses are still accurate and the scripts must be supplied in the correct format and with the material that you expect the reader to find is indeed there. appropriate sections and headings. Questions about late proofs and problems in the proofs Type every portion of the manuscript double-spaced (a should be directed to the ASM Journals Department (e-mail, minimum of 6 mm between lines), including figure legends, [email protected]; telephone, 202-737-3600). Questions table footnotes, and References, and number all pages in se- about accessing or viewing your PDF proofs should be di- quence, including the abstract, figure legends, and tables. rected to Katie Gay of Cadmus Communications at 804-261- Place the last two items after the References section. Manu- 3155 or [email protected]. script pages should have line numbers; manuscripts without line numbers may be editorially rejected by the editor, with a Publication Fees suggestion of resubmission after line numbers are added. The font size should be no smaller than 12 points. It is recom- Authors whose research was supported by grants, special mended that the following sets of characters be easily distin- funds (including departmental and institutional), or con- guishable in the manuscript: the numeral zero (0) and the tracts (including governmental) or whose research was done letter “oh” (O); the numeral one (1), the letter “el” (l), and the as part of their official duties (government or corporate, etc.) letter “eye” (I); and a multiplication sign (ϫ) and the letter are required to pay a publication fee. “ex” (x). Do not create symbols as graphics or use special The publication fee (maximum of 8 journal pages) is fonts that are external to your word processing program; use $2,000 for ASM members ($3,000 for nonmembers) and in- the “insert symbol” function. Set the page size to 81⁄2 by 11 cludes immediate open access and unlimited color figures. inches (ca. 21.6 by 28 cm). Italicize any words that should The fee for publishing the short “Observations” and “Opin- appear in italics, and indicate paragraph lead-ins in boldface ions and hypotheses” (2 journal pages) articles is $1,000 for type. ASM members ($1,500 for nonmembers). To obtain the Authors who are unsure of proper English usage should member rate, the corresponding author must be an ASM have their manuscripts checked by someone proficient in the member. A corresponding author who is not an ASM mem- English language. ber may join ASM to obtain the member rate. Manuscripts may be editorially rejected, without review, If the research was not supported by any of the means on the basis of poor English or lack of conformity to the described above, a request to waive the fee may be made standards set forth in these Instructions. through the online submission form or submitted via e-mail to [email protected]. The request must include the manuscript control number assigned by ASM and indicate how the Research Articles work was supported. Minireviews, Commentaries, Perspectives, Editorials, and Research Articles are limited to 8 journal pages and should Letters to the Editor are not subject to publication fees. report a major advance in any area of microbiology or allied fields. These articles should include the elements described in this section. Supplemental material fee. Authors are charged a flat fee for posting supplemental material as an adjunct to their pub- Title, running title, and byline. Each manuscript should lished article. For 2010, the fee is $190. present the results of an independent, cohesive study; thus, numbered series titles are not allowed. Avoid the main title/ Reprints. Authors of accepted manuscripts will be di- subtitle arrangement, complete sentences, and unnecessary rected to the Author Billing System, where they (or any of articles. Indicate the specific organisms under study in the their coauthors) can purchase reprints (in multiples of 100). title or abstract as appropriate. On the title page, include the title, the running title (not to exceed 54 characters and spaces), the name of each author, the address(es) of the insti- ORGANIZATION AND FORMAT tution(s) at which the work was performed, each author’s Editorial Style affiliation, and a footnote indicating the present address of any author no longer at the institution where the work was The editorial style of ASM journals conforms to the ASM performed. Place an asterisk after the name of the author to Style Manual for Journals (American Society for Microbiol- whom inquiries regarding the paper should be addressed (see ogy, 2010, in-house document) and How To Write and Pub- “Correspondent footnote”). lish a Scientific Paper, 6th ed. (Greenwood Press, Westport, Also include on the title page the word count for the ab- CT, 2006), as interpreted and modified by the editors and the stract and the word count for the text (excluding the refer- ASM Journals Department. ences, table footnotes, and figure legends). The editors and the Journals Department reserve the priv- ilege of editing manuscripts to conform with the stylistic con- Correspondent footnote. A single e-mail address for the ventions set forth in the aforesaid publications and in these corresponding author should be included on the title page of Instructions. the manuscript. This information will be published with the On receipt at ASM, an accepted manuscript undergoes an article to facilitate communication, and the e-mail address 8 2010 mBio INSTRUCTIONS TO AUTHORS mBio will be used to notify the corresponding author of the avail- centrifugal force (ϫ g rather than revolutions per minute). ability of proofs and, later, of the PDF file of the published For commonly used materials and methods (e.g., media and article. protein concentration determinations), a simple reference is sufficient. If several alternative methods are commonly used, Structured abstract. mBio Research Articles have struc- it is helpful to identify the method briefly as well as to cite the tured abstracts with two sections: “Abstract” and “Impor- reference. For example, it is preferable to state “cells were tance.” The Abstract section should be 250 words or fewer broken by ultrasonic treatment as previously described (9)” and should concisely summarize the basic content of the pa- rather than to state “cells were broken as previously described per without presenting extensive experimental details. The (9).” This allows the reader to assess the method without Importance section should be 150 words or fewer and should constant reference to previous publications. Describe new provide a nontechnical explanation of why the work was un- methods completely and give sources of unusual chemicals, dertaken. For a discussion of how to evaluate the importance equipment, or microbial strains. When large numbers of mi- of a piece of research, see the essay by A. Casadevall and F. C. crobial strains or mutants are used in a study, include tables Fang, Important Science—It’s All About the SPIN, Infect. identifying the immediate sources (i.e., sources from whom Immun. 77:4177-4180 (http://iai.asm.org/cgi/content the strains were obtained) and properties of the strains, mu- /abstract/77/10/4177). Avoid abbreviations and references, tants, bacteriophages, and plasmids, etc. and do not include diagrams. When it is essential to include a A method or strain, etc., used in only one of several exper- reference, use the same format as shown for the References iments reported in the paper may be described in the Results section but omit the article title. Because the abstract will be section or very briefly (one or two sentences) in a table foot- published separately by abstracting services, it must be com- note or figure legend. It is expected that the sources from plete and understandable without reference to the text. Au- whom the strains were obtained will be identified. thors should indicate the specific organisms under study in the title or abstract as appropriate. Acknowledgments. The source of any financial support received for the work being published must be indicated in Introduction. The introduction should supply sufficient the Acknowledgments section. (It will be assumed that the background information to allow the reader to understand absence of such an acknowledgment is a statement by the and evaluate the results of the present study without referring authors that no support was received.) The usual format is as to previous publications on the topic. The introduction follows: “This work was supported by Public Health Service should also provide the hypothesis that was addressed or the grant CA-01234 from the National Cancer Institute.” rationale for the present study. Choose references carefully to Recognition of personal assistance should be given as a provide the most salient background rather than an exhaus- separate paragraph, as should any statements disclaiming en- tive review of the topic. dorsement or approval of the views reflected in the paper or of a product mentioned therein. 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. References. (i) References listed in the References sec- Present the results as concisely as possible in one of the fol- tion. The following types of references must be listed in the lowing: text, table(s), or figure(s). Data in tables (e.g., cpm of References section: radioactivity) should not contain more significant figures than the precision of the measurement allows. Illustrations • Journal articles (both print and online) (particularly photomicrographs and electron micrographs) • Books (both print and online) should be limited to those that are absolutely necessary to • Book chapters (publication title is required) show the experimental findings. Number figures and tables in • Patents the order in which they are cited in the text, and be sure to cite • Theses and dissertations all figures and tables. • Published conference proceedings • Meeting abstracts (from published abstract books or Discussion. The Discussion should provide an interpre- journal supplements) tation of the results in relation to previously published work • Letters (to the editor) and to the experimental system at hand and should not con- • Company publications tain extensive repetition of the Results section or reiteration • In-press journal articles, books, and book chapters of the introduction. In short papers, the Results and Discus- mBio uses the numbered citation (citation-sequence) sion sections may be combined. reference method. List and number references in the Refer- ences section in the order in which they are cited in the text. Materials and Methods. The Materials and Methods sec- Citations in the text should be indicated by the reference tion should include sufficient technical information to allow number(s) in parentheses. When practical, provide the the experiments to be repeated. When centrifugation condi- names of all the authors for each reference; long bylines may tions are critical, give enough information to enable another be abbreviated with “et al.” All listed references must be cited investigator to repeat the procedure: make of centrifuge, in the text. Abbreviate journal names according to the model of rotor, temperature, time at maximum speed, and PubMed Journals Database (National Library of Medicine, mBio 2010 mBio INSTRUCTIONS TO AUTHORS 9

National Institutes of Health; available at http://www.ncbi 13. Odell, J. C. April 1970. Process for batch culturing. U.S. .nlm.nih.gov/sites/entrez?dbϭjournals), the primary source patent 484,363,770. {Include the name of the patented for ASM style. item/process if possible; the patent number is mandatory.} mBio follows ASM style for reference entries: 14. Elder, B. L., and S. E. Sharp. 2003. Cumitech 39, Com- petency assessment in the clinical laboratory. Coordinat- 1. Alexander, T. W., L. J. Yanke, E. Topp, M. E. Olson, ing ed., S. E. Sharp. ASM Press, Washington, DC. R. R. Read, D. W. Morck, and T. A. McAllister. 2008. Effect of subtherapeutic administration of antibiotics on *A reference to an in-press ASM publication should state the the prevalence of antibiotic-resistant Escherichia coli bac- control number (e.g., mBio00001-10) if it is a journal article teria in feedlot cattle. Appl. Environ. Microbiol. or the name of the publication if it is a book. 74:4405–4416. 2. Falagas, M. E., and S. K. Kasiakou. 2006. Use of interna- Online references must provide essentially the same infor- tional units when dosing colistin will help decrease con- mation that print references do. For online journal articles, fusion related to various formulations of the drug posting or revision dates may replace the year of publication, around the world. Antimicrob. Agents Chemother. 50: and a DOI or URL may be provided in addition to or in lieu of 2274–2275. (Letter.) {“Letter” or “Letter to the editor” is volume and page numbers. Some examples follow. allowed but not required at the end of such an entry.} 3. Cox, C. S., B. R. Brown, and J. C. Smith. J. Gen. Genet., in 1. Johnson, J., and V. R. Robinson. 2010. Cleavage of JPS-1 press.* {Article title is optional; journal title is mandatory.} in cells infected with human rhinovirus. mBio 1:e00001- 4. Forman, M. S., and A. Valsamakis. 2003. Specimen col- 10. doi:10.1128/mBio.00001-10. lection, transport, and processing: virology, p. 2. Dionne, M. S., and D. S. Schneider. 2002. Screening the 1227–1241. In P. R. Murray, E. J. Baron, M. A. Pfaller, fruitfly immune system. Genome Biol. 3:REVIEWS1010. J. H. Jorgensen, and R. H. Yolken (ed.), Manual of clin- http://genomebiology.com/2002/3/4/reviews/1010. ical microbiology, 8th ed. ASM Press, Washington, DC. 3. Smith, F. X., H. J. Merianos, A. T. Brunger, and D. M. 5. da Costa, M. S., M. F. Nobre, and F. A. Rainey. 2001. Engelman. 2001. Polar residues drive association of Genus I. Thermus Brock and Freeze 1969, 295,AL emend. polyleucine transmembrane helices. Proc. Natl. Acad. Sci. Nobre, Tru¨per and da Costa 1996b, 605, p. 404–414. In U. S. A. 98:2250-2255. doi:10.1073/pnas.041593698. D. R. Boone, R. W. Castenholz, and G. M. Garrity (ed.), 4. Charlier, D., and N. Glansdorff. September 2004, posting Bergey’s manual of systematic bacteriology, 2nd ed., vol. date. Chapter 3.6.1.10, Biosynthesis of arginine and poly- 1. Springer, New York, NY. amines. In R. Curtiss III et al. (ed.), EcoSal—Escherichia 6. Fitzgerald, G., and D. Shaw. In A. E. Waters (ed.), Clin- coli and Salmonella: cellular and molecular biology. ASM ical microbiology, in press. EFH Publishing Co., Boston, Press, Washington, DC. http://www.ecosal.org/.{Note MA.* {Chapter title is optional.} that each chapter has its own posting date.} 7. Green, P. N., D. Hood, and C. S. Dow. 1984. Taxonomic 5. Winnick, S., D. O. Lucas, A. L. Hartman, and D. Toll. status of some methylotrophic bacteria, p. 251–254. In 2005. How do you improve compliance? Pediatrics 115: R. L. Crawford and R. S. Hanson (ed.), Microbial growth e718–e724. on C1 compounds. Proceedings of the 4th International Symposium. American Society for Microbiology, Wash- Note: a posting or accession date is required for any online ington, DC. reference that is periodically updated or changed. 8. Rotimi, V. O., N. O. Salako, E. M. Mohaddas, and L. P. Philip. 2005. Abstr. 45th Intersci. Conf. Antimicrob. (ii) References cited in the text. References that should be Agents Chemother., abstr. D-1658. {Abstract title is op- cited in the text include: tional.} 9. Smith, D., C. Johnson, M. Maier, and J. J. Maurer. 2005. • Unpublished data Distribution of fimbrial, phage and plasmid associated • Manuscripts submitted for publication virulence genes among poultry Salmonella enterica sero- • Unpublished conference presentations (e.g., a report or poster that has not appeared in published conference vars, abstr. P-038, p. 445. Abstr. 105th Gen. Meet. Am. proceedings) Soc. Microbiol. American Society for Microbiology, • Personal communications Washington, DC. {Abstract title is optional.} • Patent applications and patents pending 10. Garcia, C. O., S. Paira, R. Burgos, J. Molina, J. F. Molina, • Computer software, databases, and websites (home and C. Calvo. 1996. Detection of salmonella DNA in sy- pages) novial membrane and synovial fluid from Latin Ameri- can patients. Arthritis Rheum. 39(Suppl.):S185. {Meet- These references should be cited parenthetically in the text as ing abstract published in journal supplement.} follows: 11. O’Malley, D. R. 1998. Ph.D. thesis. University of Califor- nia, Los Angeles, CA. {Title is optional.} . . . similar results (R. B. Layton and C. C. Weathers, 12. Stratagene. 2006. Yeast DNA isolation system: instruc- unpublished data). tion manual. Stratagene, La Jolla, CA. {Use the company name as the author if none is provided for a company pub- . . . system was used (J. L. McInerney, A. F. Holden, and lication.} P. N. Brighton, submitted for publication). 10 2010 mBio INSTRUCTIONS TO AUTHORS mBio

...asdescribed previously (M. G. Gordon and F. L. Rat- When necessary, this style should also be used for references tner, presented at the Fourth Symposium on Food Mi- cited in legends for supplemental material and in Addenda in crobiology, Overton, IL, 13 to 15 June 1989). {For non- Proof. published abstracts and posters, etc.} . . . this new process (V. R. Smoll, 20 June 1999, Austra- Observations lian Patent Office). {For non-U.S. patent applications, give the date of publication of the application.} Observations are short descriptions (4 journal pages with a maximum of 2 figures and 25 references) of research results . . . available in the GenBank database (http://www of exceptional importance and unusual interest to the broad .ncbi.nlm.nih.gov/Genbank/index.html). microbiology community, e.g., reports of a new type of or- . . . using ABC software (version 2.2; Department of Mi- ganism, a new organelle, a new association of microbes and crobiology, State University [http://www.state.micro disease, etc. .edu]). The body of an Observation may have paragraph lead-ins. As with Research Articles, authors should include an abstract URLs for companies that produce any of the products of 250 words or fewer as well as an Importance section of 150 mentioned in your study or for products being sold may not words or fewer, providing a nontechnical explanation of why be included in the article. However, company URLs that per- the work was undertaken. mit access to scientific data related to the study or to share- ware used in the study are permitted. Minireviews

(iii) Referencing publish-ahead-of-print manuscripts. Minireviews are brief (maximum of 6 journal pages) sum- Citations of ASM Accepts manuscripts (articles from other, maries of important developments in microbiology research. issue-based ASM journals that are published ahead of the They must be based on published articles and may address issue) should look like the following example. any subject within the scope of the journal. Minireviews must have abstracts. Limit the abstract to Wang, G. G., M. P. Pasillas, and M. P. Kamps. 15 May 250 words or fewer. The body of the Minireview may have 2006. Persistent transactivation by Meis1 replaces Hox section headings and/or paragraph lead-ins. function in myeloid leukemogenesis models: evidence for co-occupancy of Meis1-Pbx and Hox-Pbx com- Opinions and Hypotheses plexes on promoters of leukemia-associated genes. Mol. Cell. Biol. doi:10.1128/MCB.00586-06. Opinions and Hypotheses are short articles (4 journal pages with a maximum of 25 references) that present original Other journals may use different styles for their publish- and well-developed insights without complete supporting ahead-of-print manuscripts, but citation entries must in- data. Although microbiology and allied fields are primarily clude the following information: author name(s), posting experimental sciences, this article type places equal impor- date, title, journal title, and volume and page numbers and/or tance on new thought that is formulated in a manner that DOI. The following is an example: summarizes a problem, provides a new synthesis, and/or is suitable for subsequent experimental testing. Zhou, F. X., H. J. Merianos, A. T. Brunger, and D. M. In this category, the journal provides a highly visible venue Engelman. 13 February 2001, posting date. Polar resi- for the publication of ideas that have the potential to move dues drive association of polyleucine transmembrane fields and to challenge the status quo. helices. Proc. Natl. Acad. Sci. U. S. A. doi:10.1073/ Authors should provide an abstract of 150 words or fewer. pnas.041593698. The body of an Opinions and Hypotheses article may have section headings and/or paragraph lead-ins. (iv) Citations in abstracts. Since the abstract must be able to stand apart from the article, references cited in it should be Commentaries clear without recourse to the References section. Use an abbreviated form of citation, omitting the article title, as fol- Commentaries are short invited articles (1 to 2 journal lows. pages) that discuss mBio papers of special interest. These are solicited by editors from reviewers or experts in the field. (M. J. Fraser, G. E. Smith, and M. D. Summers, J. Virol. Authors should provide an abstract of 150 words or fewer. 47:287–300, 1983) The body of a Commentary may have section headings and/or paragraph lead-ins. (J. Scholefield, R. Manson, R. J. Johnston, R. Scott, and M. Spinell, p. 179–183, in R. C. Tilton, ed., Rapid Meth- Perspectives ods and Automation in Microbiology, 1981) Perspectives are brief reviews (limited to 4 journal pages) “. . . the recent report of A. K. Datta and J. S. Pagano that offer a succinct overview of a specific topic with an em- (Antimicrob. Agents Chemother. 24:10–14, 1983)....” phasis on opinion and synthesis. mBio 2010 mBio INSTRUCTIONS TO AUTHORS 11

Authors should provide an abstract of 150 words or fewer. For corrections of a scientific nature or issues involving The body of a Perspectives article may have section headings authorship, including contributions and use or ownership of and/or paragraph lead-ins. data and/or materials, all disputing parties must agree, in writing, to publication of the Correction. For omission of an Editorials author’s name, letters must be signed by the authors of the article and the author whose name was omitted. The editor Editorials communicated by members of the mBio Board who handled the article will be consulted if necessary. of Editors address issues of science, politics, or policy. Submit an Author’s Correction via the mBio online sub- Editorials should include an abstract of 150 words or mission and peer review system at http://mbio.msubmit.net/. fewer. In the submission form, select Erratum as the manuscript type; there is no separate selection in the submission system Letters to the Editor for an Author’s Correction, but your Correction will be published as such if appropriate. In the Abstract section of the Letters to the Editor are intended for comments on articles submission form (a required field), put “Not Applicable.” published in the journal and must cite published references Upload the text of your Author’s Correction as a Microsoft to support the writer’s argument. Word file. Signed letters of agreement from all authors must Letters may be no more than 500 words long and must be be included as supplemental material (scanned and submit- typed double-spaced. Note that authors and affiliations are ted as PDF files). listed at the foot of the Letter. Provide only the primary affiliation for each author. All Letters to the Editor must be submitted electronically. Retractions The cover letter should refer to the article in question by its Retractions are reserved for major errors or breaches of title and the last name of the first author. In addition, the ethics that, for example, may call into question the source of volume and issue and/or DOI should be indicated. In the the data or the validity of the results and conclusions of an Abstract section of the submission form, put “Not Applica- article. If you feel that a Retraction may be necessary for an ble.” Letters to the Editor do not have abstracts. The Letter article that you have authored, you should contact the mBio must have a distinct title, which must appear on the manu- staff at [email protected]. The mBio staff will submit a Re- script and on the submission form. Figures and tables should traction on your behalf. The Retraction will be assigned to the be kept to a minimum. editor in chief of the journal, and the editor who handled the The Letter will be sent to the editor who handled the article paper and the chairman of the ASM Publications Board will in question. If the editor believes that publication is war- be consulted. If the Retraction is approved, all authors will be ranted, he/she will solicit a reply from the corresponding au- asked to sign a letter of agreement before the Retraction is thor of the article and make a recommendation to the editor processed for publication. 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. ILLUSTRATIONS AND TABLES Errata Illustrations The Erratum section provides a means of correcting errors Image manipulation. Computer-generated images may that occurred during the writing, typing, editing, or publica- be processed only minimally. Processing (e.g., changing con- tion (e.g., a misspelling, a dropped word or line, or mislabel- trast, brightness, or color balance) is acceptable only if ap- ing in a figure) of a published article. Submit Errata via the plied to all parts of the image, as well as to the controls, mBio online submission and peer review system at http:// equally, and descriptions of all such adjustments and the mbio.msubmit.net/. In the Abstract section of the submis- tools used (both hardware and software) must be provided in sion form (a required field), put “Not Applicable.” Upload the manuscript. Unprocessed data and files must be retained the text of your Erratum as a Microsoft Word file. by the authors and be provided to the editor on request.

Authors’ Corrections File types and formats. Illustrations may be continuous- tone images, line drawings, or composites. On initial submis- The Author’s Correction section provides a means of cor- sion, illustrations may be supplied as PDF files, with the leg- recting errors of omission (e.g., author names or citations) end on the same page, to assist review. At the modification and errors of a scientific nature that do not alter the overall stage, production quality digital files must be provided, along basic results or conclusions of a published article (e.g., an with text files for the legends. The legends are copyedited and incorrect unit of measurement or order of magnitude used typeset for final publication, not included as part of the figure throughout, contamination of one of numerous cultures, or itself. All graphics submitted with modified manuscripts misidentification of a mutant strain, causing erroneous data should be grayscale or in the RGB color mode. See “Color for only a [noncritical] portion of the study). Note that the illustrations.” Halftone images (those with various densities addition of new data is not permitted. or shades) must be grayscale, not bitmap. mBio accepts only 12 2010 mBio INSTRUCTIONS TO AUTHORS mBio

TIFF or EPS files; PowerPoint files will not be accepted. In- nonproportional (monospace) font is required. All fonts structions for converting PowerPoint files may be found at other than these must be converted to paths (or outlines) in http://art.cadmus.com/da/howto/creating_ai_eps_excell.jsp. the application with which they were created. General instructions for creating acceptable EPS and TIFF files may be found at http://art.cadmus.com/da/index.jsp. Compression. Images created with Macintosh applica- We strongly recommend that before returning their modi- tions may be compressed with Stuffit. Images created with fied manuscripts, authors check the acceptability of their Windows applications may be compressed with WinZip or digital images for production by running their files PKZIP. through Rapid Inspector, a tool provided at the following URL: http://rapidinspector.cadmus.com/RapidInspector/ Color illustrations. All figures submitted in color will be zmw/index.jsp. Rapid Inspector is an easy-to-use, Web- processed as color. Adherence to the following guidelines will based application that identifies file characteristics that may help to ensure color reproduction that is as accurate as pos- render the image unusable for production. If you require sible. additional information, please send an e-mail inquiry to Color illustrations should be supplied in the RGB color [email protected]. mode, as either (i) RGB TIFF images with a resolution of at least 300 pixels per inch (raster files, consisting of pixels) or Minimum resolution. Minimum resolution is 300 dpi (ii) Illustrator-compatible EPS files with RGB color elements for all file types. All images imported into a figure file must be (vector files, consisting of lines, fonts, fills, and images). For at the correct resolution before they are placed in the file. (For reprints, ASM’s print provider will automatically create instance, placing a 72-dpi image in a 300-dpi EPS file will not CMYK versions of color illustrations from the supplied RGB result in the placed image meeting the minimum require- versions. Color in the reprints may not exactly match that in ments for file resolution.) Note that publication quality will the online journal of record because of the smaller range of not be improved by using a resolution higher than the mini- colors capable of being reproduced by CMYK inks on a print- mum. ing press. Size. All graphics should be submitted at their intended publication size; that is, the image uploaded should be 100% of its final dimensions so that no reduction or enlargement is Drawings necessary. Resolution must be at the required level at the Submit graphs, charts, complicated chemical or mathe- submitted size. Include only the significant portion of an il- matical formulas, diagrams, and other drawings as finished lustration. White space must be cropped from the image, and products not requiring additional artwork or typesetting. excess space between panel labels and the image must be All elements, including letters, numbers, and symbols, eliminated. must be easily readable, and both axes of a graph must be labeled. Maximum width for a 1-column figure: 35⁄16 inches (ca. 8.4 When creating line art, please use the following guidelines: cm) Maximum width for a 2-column figure: 67⁄8 inches (ca. (i) All art must be submitted at its intended publication 17.4 cm) size. For acceptable dimensions, see “Size.” Minimum width for a 2-column figure: 41⁄4 inches (10.8 cm) (ii) Avoid using screens (i.e., shading) in line art. It can be Maximum height: 91⁄16 inches (23.0 cm) difficult and time-consuming to reproduce these images without moire´ patterns. Various pattern backgrounds are Contrast. Illustrations should contain sufficient contrast preferable to screens as long as the patterns are not imported to be viewed easily on a monitor or on the printed page (for from another application. If you must use images containing reprints). screens,

Labeling and assembly. All final lettering and labeling (a) Generate the image at line screens of 85 lines per inch must be incorporated into the figures. Put the figure number or lower. well outside the boundaries of the image itself. (Numbering may need to be changed at the copyediting stage.) Each figure (b) When applying multiple shades of gray, differentiate must be supplied as a separate file, and any multipanel figures the gray levels by at least 20%. must be assembled into one file; i.e., rather than uploading a separate file for each panel in a figure, assemble all panels in (c) Never use levels of gray below 5% or above 95%, as one piece and supply them as one file. they are likely to fade out or become totally black when output. Fonts. To avoid font problems, set all type in one of the following fonts: Arial, Helvetica, Times Roman, European PI, Mathematical PI, or Symbol. Courier may be used but should (iii) Use thick, solid lines that are no finer than 1 point in be limited to nucleotide or amino acid sequences, where a thickness. mBio 2010 mBio INSTRUCTIONS TO AUTHORS 13

(iv) No type should be smaller than 6 points at the final Figure Legends publication size. On initial submission, to assist review, figure legends may (v) Avoid layering type directly over shaded or textured be incorporated in the image files and appear beneath the areas. figures. At the modification stage, figure legends must be provided as text files separate from the image file. (vi) Avoid the use of reversed type (white lettering on a Legends should provide enough information so that the black background). figure is understandable without frequent reference to the text. However, detailed experimental methods must be de- (vii) Avoid heavy letters, which tend to close up, and un- scribed in the Materials and Methods section, not in a figure usual symbols, which the printer may not be able to repro- legend. A method that is unique to one of several experiments duce in the legend. may be reported in a legend only if the discussion is very brief (one or two sentences). Define all symbols used in the figure (viii) If colors are used, avoid using similar shades of the and define all abbreviations that are not used in the text. same color and avoid very light colors. The main text file should also contain a legend for each item in the supplemental material (see “Supplemental In figure ordinate and abscissa scales (as well as table col- Material”). umn headings), avoid the ambiguous use of numbers with exponents. Usually, it is preferable to use the Syste`me Inter- national d’Unite´s (SI) symbols (␮ for 10Ϫ6, m for 10Ϫ3, k for Tables 103, and M for 106, etc.). A complete listing of SI symbols can be found in the International Union of Pure and Applied Tables that contain artwork, chemical structures, or shad- Chemistry (IUPAC) publication Quantities, Units and Sym- ing must be submitted as illustrations in an acceptable format bols in Physical Chemistry (RSC Publishing, Cambridge, at the modification stage. The preferred format for regular United Kingdom, 2007); an abbreviated list is available at tables is Microsoft Word; however, WordPerfect and Acrobat http://old.iupac.org/reports/1993/homann/index.html. Thus, a PDF are also acceptable. Note that a straight Excel file is not representation of 20,000 cpm on a figure ordinate is to be currently an acceptable format. Excel files must be either em- made by the number 20 accompanied by the label kcpm. bedded in a Word or WordPerfect document or converted to When powers of 10 must be used, the journal requires that PDF before being uploaded. the exponent power be associated with the number shown. In Tables should be formatted as follows. Arrange the data so representing 20,000 cells per ml, the numeral on the ordinate that columns of like material read down, not across. The should be “2” and the label should be “104 cells per ml” (not headings should be sufficiently clear so that the meaning of “cells per ml ϫ 10Ϫ4”). Likewise, an enzyme activity of 0.06 the data is understandable without reference to the text. See U/ml might be shown as 6 accompanied by the label 10Ϫ2 the “Abbreviations” section of these Instructions for those U/ml. The preferred designation is 60 mU/ml (milliunits per that should be used in tables. Explanatory footnotes are ac- milliliter). ceptable, but more-extensive table “legends” are not. Foot- notes should not include detailed descriptions of the experi- Presentation of Nucleic Acid Sequences ment. Tables must include enough information to warrant table format; those with fewer than four pieces of data will be Long nucleic acid sequences must be presented as figures incorporated into the text by the copy editor. Table 1 is an in the following format to conserve space. Print the sequence example of a well-constructed table. in lines of approximately 100 to 120 nucleotides in a nonproportional (monospace) font (e.g., Courier) that is easily legible when published with a line length of 6 inches (ca. 15.2 Featured Image cm). If possible, lines of nucleic acid sequence should be fur- ther subdivided into blocks of 10 or 20 nucleotides by spaces Each collected monthly issue of mBio is represented by a within the sequence or by marks above it. Uppercase and featured image, derived from an article in the issue. These lowercase letters may be used to designate the exon-intron featured images are used to represent the issues in the online structure or transcribed regions, etc., if the lowercase letters archives. remain legible at a 6-inch (ca. 15.2-cm) line length. Number Invitations to submit a featured image are issued to au- the sequence line by line; place numerals representing the thors whose manuscripts are returned for modification or first base of each line to the left of the lines. Minimize spacing whose manuscripts have been accepted for publication in between lines of sequence, leaving room only for annotation mBio; material should be related to the work presented in the of the sequence. Annotation may include boldface, underlin- manuscript. Unsolicited art will also be considered. No ma- ing, brackets, and boxes, etc. Encoded amino acid sequences terial submitted for consideration will be returned to the au- may be presented, if necessary, immediately above or below thor. Authors will be notified only if their image is selected. A the first nucleotide of each codon, by using the single-letter license for the chosen material must be granted to ASM. amino acid symbols. Comparisons of multiple nucleic acid Questions or suggestions regarding the featured image sequences should conform as nearly as possible to the same can be sent to the editor in chief, Arturo Casadevall format. ([email protected]). 14 2010 mBio INSTRUCTIONS TO AUTHORS mBio

NOMENCLATURE Viruses. Names used for viruses should be those approved by the International Committee on Taxonomy of Viruses Chemical and Biochemical Nomenclature (ICTV) and reported on the ICTV Virus Taxonomy website The recognized authority for the names of chemical com- (http://www.ictvonline.org/index.asp). In addition, the rec- pounds is Chemical Abstracts (CAS; http://www.cas.org/) and ommendations of the ICTV regarding the use of species its indexes. The Merck Index, 14th ed. (Merck & Co., Inc., names should generally be followed: when the entire species Whitehouse Station, NJ, 2006), is also an excellent source. is discussed as a taxonomic entity, the species name, as with For biochemical terminology, including abbreviations and other taxa, is italic and has the first letter and any proper symbols, consult Biochemical Nomenclature and Related Doc- nouns capitalized (e.g., Tobacco mosaic virus, Murray Valley uments (Portland Press, London, United Kingdom, 1992), encephalitis virus). When the behavior or manipulation of available at http://www.chem.qmul.ac.uk/iupac/bibliog/ individual viruses is discussed, the vernacular (e.g., tobacco white.html, and the instructions to authors of the Journal of mosaic virus, Murray Valley encephalitis virus) should be Biological Chemistry and the Archives of Biochemistry and Bio- used. If desired, synonyms may be added parenthetically physics (first issues of each year). when the name is first mentioned. Approved generic (or Do not express molecular weight in daltons; molecular group) and family names may also be used. weight is a unitless ratio. Molecular mass is expressed in daltons. Bacteria. Binary names, consisting of a generic name and For enzymes, use the recommended (trivial) name as- a specific epithet (e.g., Escherichia coli), should be used for all signed by the Nomenclature Committee of the International bacteria. Names of categories at or above the genus level may Union of Biochemistry (IUB) as described in Enzyme No- be used alone, but specific and subspecific epithets may not. A menclature (Academic Press, Inc., New York, NY, 1992) and specific epithet must be preceded by a generic name, written its supplements and at http://www.chem.qmul.ac.uk/iubmb/ out in full the first time it is used in a paper. Thereafter, the enzyme/. If a nonrecommended name is used, place the generic name should be abbreviated to the initial capital letter proper (trivial) name in parentheses at first use in the abstract (e.g., E. coli), provided there can be no confusion with other and text. Use the EC number when one has been assigned. genera used in the paper. Names of all taxa (kingdoms, phyla, Authors of papers describing enzymological studies should classes, orders, families, genera, species, and subspecies) are review the standards of the STRENDA Commission for in- printed in italics; strain designations and numbers are not. formation required for adequate description of experimental Two sites on the World Wide Web list current approved bac- conditions and for reporting enzyme activity data (http:// terial names: Bacterial Nomenclature Up-to-Date (http:// www.strenda.org/documents.html). www.dsmz.de/microorganisms/main.php?contentleft_idϭ14) For nomenclature of restriction enzymes, DNA methyl- and List of Prokaryotic Names with Standing in Nomencla- transferases, homing endonucleases, and their genes, refer to ture (http://www.bacterio.cict.fr/). For guidelines regarding the article by Roberts et al. (Nucleic Acids Res. 31:1805–1812, new names and descriptions of new genera and species, see 2003). the articles by Tindall (Int. J. Syst. Bacteriol. 49:1309–1312, 1999) and Stackebrandt et al. (Int. J. Syst. Evol. Microbiol. 52:1043–1047, 2002). Drug Nomenclature Chemical or generic names of drugs should be used; the Fungi. Since the classification of fungi is not complete, it is use of code numbers or trade names is generally not permit- the responsibility of the author to determine the accepted ted. When code names or corporate proprietary numbers are binomial for a given organism. Sources for these names in- to be used, either the chemical structure of the compound or clude The Yeasts: a Taxonomic Study, 4th ed. (C. P. Kurtzman a published literature reference illustrating the chemical and J. W. Fell, ed., Elsevier Science Publishers B.V., Amster- structure, if known, must be provided at the first occurrence dam, the Netherlands, 1998), and Ainsworth and Bisby’s Dic- of the code name or number. For compounds not identified tionary of the Fungi, 9th ed. (P. M. Kirk, P. F. Cannon, J. C. by generic nomenclature, all previous or concurrent identifi- David, and J. A. Stalpers, ed., CABI Publishing, Wallingford, cation numbers or appellations should be listed in the manu- Oxfordshire, United Kingdom, 2001); see also http://www script. .speciesfungorum.org/Names/Fundic.asp.

Nomenclature of Organisms Genetic Nomenclature Mice. For mouse strain and genetic nomenclature, ASM Genetic nomenclature should essentially follow the rec- encourages authors to refer to the guidelines set forth by the ommendations of Demerec et al. (Genetics 54:61–76, International Committee on Standardized Genetic Nomen- 1966) and those given in the instructions to authors of the clature for Mice, available on the Mouse Genome Database Journal of Bacteriology, Molecular and Cellular Biology, and home page at http://www.informatics.jax.org/ and in Genetic Eukaryotic Cell (January issues). To facilitate accurate Variants and Strains of the Laboratory Mouse, 3rd ed. (M. F. communication, it is important that standard genetic no- Lyon et al., ed., Oxford University Press, Oxford, England, menclature be used whenever possible and that devia- 1996). tions or proposals for new naming systems be endorsed mBio 2010 mBio INSTRUCTIONS TO AUTHORS 15 by an appropriate authoritative body. Review and/or for Syste`me International d’Unite´s (SI) units of measure- publication of submitted manuscripts that contain new or ment, other common units (e.g., bp, kb, and Da), and chemical nonstandard nomenclature may be delayed by the editor symbols for the elements, the following should be used without or the Journals Department so that they may be reviewed definition in the title, abstract, text, figure legends, and tables: by the Genetics and Genomics Committee of the ASM ϩ Publications Board. Before submission of manuscripts, DNA (deoxyribonucleic acid) NADP (nicotinamide adenine cDNA (complementary DNA) dinucleotide phosphate, authors may direct questions on genetic nomenclature RNA (ribonucleic acid) oxidized) to the committee’s chairperson: Maria Costanzo (maria cRNA (complementary RNA) poly(A), poly(dT), etc. @genome.stanford.edu). Such a consultation should be RNase (ribonuclease) (polyadenylic acid and mentioned in the manuscript submission letter. DNase (deoxyribonuclease) polydeoxythymidylic acid, rRNA (ribosomal RNA) etc.) mRNA (messenger RNA) oligo(dT), etc. tRNA (transfer RNA) (oligodeoxythymidylic acid, ABBREVIATIONS AND CONVENTIONS AMP, ADP, ATP, dAMP, ddATP, etc.) GTP, etc. (for the respective 5Ј UV (ultraviolet) Verb Tense phosphates of adenosine and PFU (plaque-forming units) other nucleosides) (add 2Ј-, CFU (colony-forming units) ASM strongly recommends that for clarity you use the past 3Ј-, or 5Ј- when needed for MIC (minimal inhibitory tense to narrate particular events in the past, including the contrast) concentration) procedures, observations, and data of the study that you are ATPase, dGTPase, etc. Tris [tris(hydroxymethyl) reporting. Use the present tense for your own general conclu- (adenosine triphosphatase and aminomethane] sions, the conclusions of previous researchers, and generally deoxyguanosine DEAE (diethylaminoethyl) accepted facts. Thus, most of the abstract, Materials and triphosphatase, etc.) EDTA Methods, and Results will be in the past tense, and most of the NAD (nicotinamide adenine (ethylenediaminetetraacetic introduction and some of the Discussion will be in the dinucleotide) acid) NADϩ (nicotinamide adenine EGTA [ethylene glycol-bis(␤- present tense. Ј Ј Be aware that it may be necessary to vary the tense in a dinucleotide, oxidized) aminoethyl ether)-N,N,N ,N - single sentence. For example, it is correct to say “White (30) NADH (nicotinamide adenine tetraacetic acid] dinucleotide, reduced) HEPES (N-2- demonstrated that XYZ cells grow at pH 6.8,” “Figure 2 shows NADP (nicotinamide adenine hydroxyethylpiperazine-NЈ-2- that ABC cells failed to grow at room temperature,” and “Air dinucleotide phosphate) ethanesulfonic acid) was removed from the chamber and the mice died, which NADPH (nicotinamide adenine PCR (polymerase chain reaction) proves that mice require air.” In reporting statistics and calcu- dinucleotide phosphate, AIDS (acquired lations, it is correct to say “The values for the ABC cells are reduced) immunodeficiency syndrome) statistically significant, indicating that the drug inhib- ited ....” Abbreviations for cell lines (e.g., HeLa) also need not be de- For an in-depth discussion of tense in scientific writing, see p. fined. 191–193 in How To Write and Publish a Scientific Paper, 6th ed. The following abbreviations should be used without definition in tables: Abbreviations amt (amount) SE (standard error) approx (approximately) SEM (standard error of the General. Abbreviations should be used as an aid to the avg (average) mean) concn (concentration) reader, rather than as a convenience to the author, and there- sp act (specific activity) diam (diameter) sp gr (specific gravity) fore their use should be limited. Abbreviations other than expt (experiment) temp (temperature) those recommended by the IUPAC-IUB (Biochemical No- exptl (experimental) tr (trace) menclature and Related Documents, 1992) should be used ht (height) vol (volume) only when a case can be made for necessity, such as in tables mo (month) vs (versus) and figures. mol wt (molecular weight) wk (week) It is often possible to use pronouns or to paraphrase no. (number) wt (weight) a long word after its first use (e.g., “the drug” or “the prepn (preparation) yr (year) substrate”). Standard chemical symbols and trivial names SD (standard deviation) or their symbols (folate, Ala, and Leu, etc.) may also be Reporting Numerical Data used. Define each abbreviation and introduce it in parentheses Standard metric units are used for reporting length, the first time it is used; e.g., “cultures were grown in Eagle weight, and volume. For these units and for molarity, use the minimal essential medium (MEM).” Generally, eliminate ab- prefixes m, ␮, n, and p for 10Ϫ3,10Ϫ6,10Ϫ9, and 10Ϫ12,re- breviations that are not used at least three times in the text spectively. Likewise, use the prefixes c for 10Ϫ2 and k for 103. (including tables and figure legends). Avoid compound prefixes such as m␮ or ␮␮. Use ␮g/ml or ␮g/g in place of the ambiguous ppm. Units of temperature Not requiring introduction. In addition to abbreviations are presented as follows: 37°C or 324 K. 16 2010 mBio INSTRUCTIONS TO AUTHORS mBio

When fractions are used to express units such as enzymatic used when the isotopic symbol is attached to the name of activities, it is preferable to use whole units, such as g or min, a compound that in its natural state does not contain the in the denominator instead of fractional or multiple units, element (e.g., 32S-ATP) or to a word that is not a specific such as ␮g or 10 min. For example, “pmol/min” is preferable chemical name (e.g., 131I-labeled protein, 14C-amino acids, to “nmol/10 min,” and “␮mol/g” is preferable to “nmol/␮g.” and 3H-ligands). It is also preferable that an unambiguous form such as expo- For specific chemicals, the symbol for the isotope intro- nential notation be used; for example, “␮mol gϪ1 minϪ1”is duced is placed in square brackets directly preceding the part preferable to “␮mol/g/min.” Always report numerical data in of the name that describes the labeled entity. Note that con- the appropriate SI units. figuration symbols and modifiers precede the isotopic sym- For a review of some common errors associated with bol. The following examples illustrate correct usage: statistical analyses and reports, plus guidelines on how to [14C]urea [␥-32P]ATP avoid them, see the article by Olsen (Infect. Immun. L-[methyl-14C]methionine UDP-[U-14C]glucose 71:6689–6692, 2003). [2,3-3H]serine SV40 [32P]DNA [␣-14C]lysine fructose 1,6-[1-32P]bisphosphate

Isotopically Labeled Compounds mBio follows the same conventions for isotopic labeling as the Journal of Biological Chemistry, and more-detailed infor- For simple molecules, labeling is indicated in the chemical mation can be found in the instructions to authors of that 14 3 35 formula (e.g., CO2, H2O, and H2 SO4). Brackets are not journal (ﬁrst issue of each year).