applied and environmental microbiology - biotechlab

APPLIED AND ENVIRONMENTAL MICROBIOLOGY

2007 INSTRUCTIONS TO AUTHORS*

SCOPE

Applied and Environmental Microbiology (AEM) pub-lishes descriptions of all aspects of applied microbialresearch, basic research on microbial ecology, and re-search of a genetic and molecular nature that focuses onmicrobial topics of practical value. Research must addresssalient microbiological principles, fundamental microbialprocesses, or basic questions in applied or environmentalmicrobiology. Topics that are considered include microbi-ology in relation to foods, agriculture, industry, biotechnol-ogy, public health, plants, and invertebrates and basic bio-logical properties of bacteria, fungi, algae, protozoa, andother simple eukaryotic organisms as related to micro-bial ecology. Manuscripts should report new and signif-icant findings that advance the understanding of micro-biology and upon which other scientists may build.

The microbial ecology section covers a wide range oftopics on the ecology of microorganisms, including cul-ture-independent molecular assessments that providenew insights into (i) the structure-function relationshipsof microorganisms, (ii) the impact of in situ conditionson community structure, and (iii) the effect of changes inmicrobial community composition on ecosystem func-tion. Archival phylogenetic snapshots that do not providesuch insights are not acceptable for publication in AEM.

The plant microbiology section covers manuscriptsdealing with all aspects of plant-microorganism interac-tions, including symbiotic and rhizosphere bacteria andphytopathogenic microorganisms.

New microbiological methods must provide novel av-enues to address fundamental biological questions andwill be considered for publication in AEM when accom-panied by a demonstrated application. Descriptions ofthe application of previously described technologies, in-cluding the cloning, amplification, and expression of“foreign” genes, to a new genus or species of microbewill generally not be considered for independent publi-cation. Manuscripts that describe the construction ofengineered strains for innovative process application,development, or enhancement must present results toauthenticate the utility, superiority, and uniqueness ofsuch strains.

Manuscripts submitted to the mycology section shouldbe clearly of a microbiological nature and may deal withbasic biology, biochemistry, genetics, or physiology offungi, molds, yeasts, or algae. Papers dealing purely withtaxonomy or phylogeny, with fungal or algal structure, orwith metabolism/alteration of metabolites/toxins by ani-mal, plant, or insect cells, tissues, or organisms are notsuitable. Documentation of the distribution/occurrenceof toxins or metabolites in natural samples (foods, cere-

als, grains, soils, etc.) is suitable if the work includesstudies involving the isolation, occurrence, or enumera-tion of the responsible microbes in these samples. Thechemical or biochemical elucidation of metabolite ortoxin structures is suitable if the work includes aspects ofthe enzymology or biosynthesis of these compounds.

Invertebrate microbiology manuscripts should addressinteractions between invertebrates and microorganisms,ranging from commensalism and mutualism to parasit-ism and pathogenicity. Manuscripts describing work deal-ing with the metabolites or toxins from animal, plant, orinsect cells or the physiology of such cells are not suit-able for AEM unless it affects a microbial community orindividual microorganisms.

ASM publishes a number of different journals cover-ing various aspects of the field of microbiology. Eachjournal has a prescribed scope which must be consideredin determining the most appropriate journal for eachmanuscript. The following guidelines may be of assistance.

(i) AEM will consider manuscripts describing propertiesof enzymes and proteins that are produced by either wild-type or genetically engineered microorganisms and that aresignificant or have potential significance in industrial orenvironmental settings. Studies dealing with basic biologi-cal phenomena of enzymes or proteins or in which enzymeshave been used in investigations of basic biological func-tions are more appropriate for the Journal of Bacteriology.

(ii) AEM will consider papers which describe the useof antimicrobial agents as tools for elucidating aspectsof applied and environmental microbiology. Other pa-pers dealing with antimicrobial agents, including manu-scripts dealing with the biosynthesis and metabolism ofsuch agents, are more appropriate for AntimicrobialAgents and Chemotherapy.

(iii) Papers on the biology of bacteriophages and otherviruses are more appropriate for the Journal of Virologyor the Journal of Bacteriology. AEM does, however, con-sider manuscripts dealing with viruses in relation to en-vironmental, public health, or industrial microbiology.

(iv) Manuscripts dealing with the immune system orwith topics of basic medical interest or oral microbiologyare more appropriate for Infection and Immunity. Re-ports of clinical investigations and environmental biol-ogy applied to hospitals should be submitted to the Jour-nal of Clinical Microbiology.

(v) AEM and Eukaryotic Cell (EC) accept manuscriptson population dynamics and the ecology of eukaryoticmicrobes. Studies of microbial communities and of mi-crobial populations with identified economic or ecolog-ical significance, e.g., plant pathogens or symbionts, areusually more appropriate for AEM. Studies of singlespecies of eukaryotes, especially “model” organisms orthose without identified economic or ecological impor-tance, are usually more appropriate for EC.

(vi) Manuscripts dealing with the purification and char-* Shading indicates material that has been added or significantly

updated.

1

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Jan. 2007, p. 1–21 Vol. 73, No. 10099-2240/07/$08.00�0 doi:10.1128/AEM.02732-06Copyright © 2007, American Society for Microbiology. All Rights Reserved.

acterization of enzymes or cloning of genes that havealready been extensively described for other organismswill be considered for publication only if they offer ex-perimentally supported new insights into the biologi-cal role, properties, or applications of these enzymes.Descriptions of genes or enzymes that differ only inminor ways from the prototypes are not suitable for AEM.

To best serve its readership, the journal must accept onlythose papers that are most significant to the field of appliedand environmental microbiology. Thus, the editors will re-ject manuscripts that, while scientifically sound, representonly incremental extensions of other studies, are mainlyconfirmatory, or do not pursue a question in sufficientdepth.

Questions about these guidelines may be directed tothe editor in chief of the journal being considered.

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

Note that a manuscript rejected by one ASM journalon scientific grounds or on the basis of its general suit-ability for publication is considered rejected by all otherASM journals.

EDITORIAL POLICY

Use of Microbiological InformationThe Council Policy Committee (CPC) of the Ameri-

can Society for Microbiology affirms the long-standingposition of the Society that microbiologists will work forthe proper and beneficent application of science and willcall to the attention of the public or the appropriateauthorities misuses of microbiology or of informationderived from microbiology. ASM members are obligatedto discourage any use of microbiology contrary to thewelfare of humankind, including the use of microbes asbiological weapons. Bioterrorism violates the fundamen-tal principles expressed in the Code of Ethics of theSociety and is abhorrent to ASM and its members.

ASM recognizes that there are valid concerns regard-ing the publication of information in scientific journalsthat could be put to inappropriate use as described in theCPC resolution mentioned above. Members of the ASMPublications Board will evaluate the rare manuscriptthat might raise such issues during the review process.However, as indicated elsewhere in these Instructions,research articles must contain sufficient detail, and ma-terial/information must be made available, to permit thework to be repeated by others. Supply of materialsshould be in accordance with laws and regulations gov-erning the shipment, transfer, possession, and use ofbiological materials and must be for legitimate, bona fideresearch needs. Links to, and information regarding,these laws and regulations can be found at http://www.asm.org/Policy/index.asp.

General Requirements

Manuscripts submitted to the journal must representreports of original research, and the original data must be

available for review by the editor if necessary. When pre-paring a manuscript, authors are encouraged to pay at-tention to guidelines for reviewers (http://aem.asm.org/misc/reviewguide.shtml).

All authors of a manuscript must have agreed to itssubmission and are responsible for its content (initialsubmission and any subsequent versions), including ap-propriate citations and acknowledgments, and must alsohave agreed that the corresponding author has theauthority to act on their behalf in all matters pertain-ing to publication of the manuscript. The correspondingauthor is responsible for obtaining such agreements andfor informing the coauthors of the manuscript’s statusthroughout the submission, review, and publication pro-cess. For Authors’ Corrections and Retractions, signedletters of agreement from all of the authors must besubmitted (see p. 13).

By submission of a manuscript to the journal, theauthors guarantee that they have the authority topublish the work and that the manuscript, or one withsubstantially the same content, was not publishedpreviously, is not being considered or published else-where, and was not rejected on scientific grounds byanother ASM journal.

It is expected that the authors will provide writtenassurance that permission to cite unpublished data orpersonal communications has been granted.

By publishing in the journal, the authors agree that,subject to requirements or limitations imposed by laws orgovernmental regulations of the United States, any DNAs,viruses, microbial strains, mutant animal strains, celllines, antibodies, and similar materials newly described inthe article are available from a national collection or willbe made available in a timely fashion, at reasonable cost,and in limited quantities to members of the scientific com-munity for noncommercial purposes. The authors guaran-tee that they have the authority to comply with this policyeither directly or by means of material transfer agree-ments through the owner.

Similarly, the authors agree to make available computerprograms, originating in the authors’ laboratory, that arethe only means of confirming the conclusions reported inthe article but that are not available commercially. Theprogram(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 anInternet server-based tool, or (iii) as a compiled or assem-bled form on a suitable medium (e.g., magnetic or optical).It is expected that the material will be provided in a timelyfashion and at reasonable cost to members of the scientificcommunity for noncommercial purposes. The authorsguarantee that they have the authority to comply with thispolicy either directly or by means of material transferagreements through the owner.

Primary Publication

A scientific paper or its substance published in a serial,periodical, book, conference report, symposium pro-

2 2007 AEM INSTRUCTIONS TO AUTHORS APPL. ENVIRON. MICROBIOL.

ceeding, or technical bulletin, posted on a nonpersonalwebsite, or made available through any other retrievablesource, including CD-ROM and other electronic forms,is unacceptable for submission to an ASM journal ongrounds of prior publication. Work, or its substance,presented as a meeting poster and subsequently repro-duced or distributed as a “company white paper” is alsounacceptable for submission on grounds of prior publi-cation.

Posting of a method/protocol on a nonpersonal web-site should not interfere with the author’s ability to havea manuscript utilizing that technique considered for pub-lication in an ASM journal; however, ultimately, it is aneditorial decision whether the method constitutes thesubstance of a paper.

Posting of a limited amount of original data on apersonal/university/company website or websites ofsmall collaborative groups working on a problem doesnot preclude subsequent submission to, and publicationby, an ASM journal. The posted data, however, maynot constitute the substance of the submission. Specificquestions about this policy may be referred to the Pub-lications Board chairman on a case-by-case basis.

Posting of theses and dissertations on a personal/uni-versity-hosted website does not preclude subsequentsubmission to, and publication by, an ASM journal. Sim-ilarly, posting and sale, on a commercial or similar web-site, of an original, unmodified thesis or dissertation (i.e.,as submitted to, and accepted by, the thesis/dissertationcommittee) does not preclude subsequent submission to,and publication by, an ASM journal.

Posting of unpublished sequence data on the Internetis usually not considered prior publication; however, theaddress (URL) of the source of the sequence should beincluded in the text.

Preliminary disclosures of research findings webcastas meeting presentations or published in abstract formas adjuncts to a meeting, e.g., part of a program, are notconsidered prior publication.

It is incumbent upon the author to acknowledge anyprior publication, including his own articles, of the datacontained in a manuscript submitted to an ASM journal.A copy of the relevant work should be submitted withthe paper as supplemental material.

Ultimately, it is an editorial decision whether the ma-terial constitutes the substance of a paper.

Permissions

The corresponding author is responsible for obtainingpermission from both the original author and the origi-nal publisher (i.e., the copyright owner) to reproduceor modify figures (including maps) and tables and toreproduce text (in whole or in part) from previous pub-lications.

The original signed permission(s) must be submitteddirectly to the editor, outside the Rapid Review system,no later than the modification stage and should be iden-tified as to the relevant item in the ASM manuscript

(e.g., “permissions for Fig. 1 in AEM00123-07”). In ad-dition, a statement indicating that the material is beingreprinted with permission must be included in the rele-vant figure legend or table footnote of the manuscript.Reprinted text must be enclosed in quotation marks, andthe permission statement must be included as runningtext or indicated parenthetically.

For supplemental material intended for posting byASM (see p. 5), if the authors of the AEM manuscriptare not also the owners of the supplemental material,the corresponding author must send to ASM signedpermission from the copyright owner that allows postingof the material, as a supplement to the article, by ASM.The corresponding author is also responsible for incor-porating in the supplemental material any copyright no-tices required by the owner.

Authorship

An author is one who made a substantial contributionto the overall design and execution of the experiments;therefore, ASM considers all authors responsible forthe 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 inthe Acknowledgments section.

A study group, surveillance team, working group, con-sortium, or the like (e.g., the Active Bacterial Core Sur-veillance Team) may be listed as a coauthor in the bylineif its contributing members satisfy the requirements forauthorship and accountability as described in these In-structions. The names (and institutional affiliations ifdesired) of the contributing members only may be givenin a footnote keyed to the study group name in the bylineor as a separate paragraph in the Acknowledgmentssection.

If the contributing members of the group associatedwith the work do not fulfill the criteria of substantialcontribution to and responsibility for the paper, thegroup may not be listed in the author byline. Instead, itand the names of its contributing members may be listedin the Acknowledgments section.

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

A change in authorship (order of listing, addition ordeletion of a name, or corresponding author designa-tion) after submission of the manuscript will be imple-mented only after receipt of signed statements of agree-ment from all parties involved.

Disputes about authorship may delay or prevent re-view and/or publication of the manuscript. Should theindividuals involved be unable to reach an accord, re-view and/or publication of the manuscript can proceedonly after the matter is investigated and resolved by the

VOL. 73, 2007 2007 AEM INSTRUCTIONS TO AUTHORS 3

authors’ institution(s) and an official report of such andsigned statements of agreement are provided to ASM.

Conflict of Interest

All authors are expected to disclose, in the manuscriptsubmittal letter, any commercial affiliations as well asconsultancies, stock or equity interests, and patent-licens-ing arrangements that could be considered to pose aconflict of interest regarding the submitted manuscript.(Inclusion of a company name in the author addresslines of the manuscript does not constitute disclosure.)Details of the disclosure to the editor will remain con-fidential. However, it is the responsibility of authors toprovide, in the Acknowledgments section, a generalstatement disclosing financial or other relationships thatare relevant to the study. Examples of potentially con-flicting interests that should be disclosed include rela-tionships that might detract from an author’s objectivityin presentation of study results, and interests whosevalue would be enhanced by the results presented. Allfunding sources for the project, institutional and corpo-rate, should be credited in the Acknowledgments sec-tion, as described below. In addition, if a manuscript con-cerns a commercial product, the manufacturer’s namemust be indicated in the Materials and Methods sectionor elsewhere in the text, as appropriate, in an obviousmanner.

Copyright

To maintain and protect the Society’s ownership andrights and to continue to afford scientists the opportunityto publish in high-quality journals, ASM requires thecorresponding author to sign a copyright transfer agree-ment on behalf of all the authors. This agreement is sentto the corresponding author when the manuscript is ac-cepted and scheduled for publication. Unless this agree-ment is executed (without changes and/or addenda), ASMwill not publish the article.

In the copyright transfer agreement signed by an au-thor, ASM grants to that author (and coauthors) theright to republish discrete portions of his (their) article inany other publication (print, CD-ROM, and other elec-tronic forms) of which he is (they are) the author(s) oreditor(s), on the condition that appropriate credit is givento the original ASM publication. This republication rightalso extends to posting on a host computer to whichthere is access via the Internet. Except as indicated be-low, significant portions of the article may not be reprint-ed/posted without ASM’s prior written permission, how-ever, as this would constitute duplicate publication.

Authors may post their own published articles on theirpersonal or university-hosted (but not corporate, govern-ment, or similar) websites without ASM’s prior writtenpermission provided that appropriate credit is given (i.e.,either the copyright lines shown on the top of the firstpage of the PDF version or “Copyright © American So-ciety for Microbiology, [insert journal name, volume num-ber, page numbers, and year]” for the HTML version).

The copyright transfer agreement asks that authorswho were U.S. Government employees and who wrotethe article as part of their employment duties be identi-fied. This is because works authored solely by such U.S.Government employees are not subject to copyright pro-tection, so there is no copyright to be transferred. Theother provisions of the copyright transfer agreement,such as author representations of originality and author-ity to enter into the agreement, apply to U.S. Govern-ment employee-authors as well as to other authors.

Copyright for supplemental material (see p. 5) re-mains with the author, but a license permitting the post-ing by ASM will be sent, along with the article copyrighttransfer agreement, to the corresponding author forsigning at the acceptance stage. (If the author of thearticle is not also the copyright owner of the supplemen-tal material, the corresponding author must send toASM signed permission from the owner that allows post-ing of the material, as a supplement to the article, byASM. The corresponding author is also responsible forincorporating into the supplemental material any copy-right notices required by the owner.)

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

Funding Agency Repositories

The National Institutes of Health (NIH) requests thatits grantee and intramural authors provide copies oftheir accepted manuscripts to PubMed Central (PMC)for posting in the PMC Public Access Repository. ASMallows such AEM authors to do so. ASM also allowsAEM authors whose work was supported by similarfunding agencies that have public access requirementslike those of NIH (e.g., the Wellcome Trust) to posttheir accepted manuscripts in publicly accessible elec-tronic repositories maintained by those funding agen-cies. If a funding agency does not itself maintain such asite, then ASM allows the author to fulfill that require-ment by depositing the manuscript (not the typeset ar-ticle) in an appropriate institutional or subject-basedopen repository established by a government or non-commercial entity.

Since ASM makes the final, typeset articles from itsprimary-research journals available free of charge on theASM Journals and PMC websites 4 months after finalpublication, ASM recommends that when submitting theaccepted manuscript to PMC or a similar public accesssite, the author specify that the posting release date forthe manuscript be no earlier than 4 months after pub-lication of the typeset article by ASM.

Use of Human Subjects or Animals in Research

The use of human subjects or other animals for re-search purposes is regulated by the federal governmentand individual institutions. Manuscripts containing in-formation related to human or animal use should clearlystate that the research has complied with all relevantfederal guidelines and institutional policies. Copies of


these guidelines and policy statements must be availablefor review by the editor if necessary.

Nucleotide and Amino Acid Sequences

It is expected that newly determined nucleotide and/or amino acid sequence data will be deposited and Gen-Bank/EMBL/DDBJ accession numbers will be includedin the manuscript no later than the modification stage ofthe review process. It is also expected that the sequencedata will be released to the public no later than thepublication date of the article. The accession numbersshould be included in a separate paragraph at the end ofthe Materials and Methods section for long-form papersor at the end of the text for short-form papers. If con-clusions in a manuscript are based on the analysis ofsequences and a GenBank/EMBL/DDBJ accession num-ber is not provided at the time of the review, authorsshould provide the sequence data as supplemental ma-terial.

It is expected that, when previously published se-quence accession numbers are cited in a manuscript,the original citations (e.g., journal articles) will be in-cluded in the References section when possible or rea-sonable.

Authors are also expected to do elementary searchesand comparisons of nucleotide and amino acid sequencesagainst the sequences in standard databases (e.g., Gen-Bank) immediately before manuscripts are submittedand again at the proof stage.

Analyses should specify the database, and the date ofeach analysis should be indicated in the format MM/YY.If relevant, the version of the software used should bespecified.

See p. 15 for nucleic acid sequence formatting instruc-tions.

The URLs of the databases mentioned above are asfollows: 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, Na-tional Center for Biotechnology Information (Gen-Bank), http://www.ncbi.nlm.nih.gov.

Structural Determinations

It is expected that coordinates for new structures ofmacromolecules will be deposited in the Protein DataBank and that assigned identification codes will be in-cluded in the manuscript no later than the modificationstage of the review process. It is also expected that thecoordinates will be released to the public no later thanthe publication date of the article. Authors are encour-aged to send coordinates with their original submission,however, so that reviewers can examine them along withthe manuscript. The accession number(s) should belisted in a separate paragraph at the end of the Materialsand Methods section for full-length papers or at the endof the text for short-form papers.

The URLs for coordinate deposition are http://rcsb

-deposit.rutgers.edu and http://pdbdep.protein.osaka-u.ac.jp.

Microarray Data

It is expected that the entire set of supporting mi-croarray data will be deposited in the appropriate publicdatabase (e.g., GEO, ArrayExpress, or CIBEX) and thatthe assigned accession number(s) will be included in themanuscript no later than the modification stage of thereview process. It is also expected that the data will bereleased to the public no later than 4 months after pub-lication of the typeset article. Authors are encouraged tosend the relevant data with their original submission,however, so that reviewers can examine them along withthe manuscript. The accession number(s) should belisted in a separate paragraph at the end of the Materialsand Methods section for full-length papers or at the endof the text for short-form papers.

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

Culture Deposition

AEM expects authors to deposit important strains inpublicly accessible culture collections and to refer to thecollections and strain numbers in the text. Since theauthenticity of subcultures of culture collection speci-mens that are distributed by individuals cannot be en-sured, authors should indicate laboratory strain des-ignations and donor sources as well as original culturecollection identification numbers.

Supplemental Material

Supplemental material intended for posting by ASMmay not include additional figures or tables that simplysupport the authors’ conclusions. It must be restricted tolarge or complex data sets or results that cannot bereadily displayed in printed form because of space ortechnical limitations. Such material may include datafrom microarray, structural, biochemical, or video imag-ing analyses. In such cases, the manuscript submitted forreview should include a distillation of the results so thatthe principal conclusions are fully supported withoutreferral to the supplemental material.

Supplemental material intended for posting by ASMmust be uploaded in Rapid Review and will be reviewedalong with the manuscript. The maximum size permittedfor an individual file is 25 MB. If your file exceeds thissize, you must use a file compression utility (e.g., WIN-ZIP or Stuffit) to reduce the size below 25 MB. Thedecision to publish (i.e., post online only) the materialwith the article if it is accepted will be made by the editorand conveyed to the corresponding author in the accep-


tance e-mail. Therefore, it is possible that a manuscriptwill be accepted but that the supplemental material willnot be.

If the software required for users to view/use the sup-plemental material is not embedded in the file, you areurged to use shareware or generally available/easily ac-cessible programs.

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

Supplemental material will always remain associatedwith its article and is not subject to any modificationsafter publication.

Material that has been published previously (print oronline) is not acceptable for posting as supplementalmaterial. Instead, the appropriate reference(s) to theoriginal publication should be made in the manuscripttext.

Copyright for the supplemental material remains withthe author, but a license permitting the posting by ASMwill be sent, along with the article copyright transferagreement, to the corresponding author for signing. Ifyou are not the copyright owner, you must provide toASM signed permission from the owner that allows post-ing of the material, as a supplement to your article, byASM. You are responsible for including in the supple-mental material any copyright notices required by theowner.

A one-time charge (amount not yet determined) maybe levied for posting of supplemental material. Wheninstituted, the charge will be indicated in the ASM ac-ceptance letter.

Compliance

Failure to comply with the policies described in theseInstructions may result in a letter of reprimand, a sus-pension of publishing privileges in ASM journals, and/ornotification of the authors’ institutions.

Warranties and Exclusions

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

Page Charges

Authors whose research was supported by grants, spe-cial funds (including departmental and institutional), orcontracts (including governmental) or whose researchwas done as part of their official duties (government,

corporate, etc.) are required to pay page charges (basedon 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 firsteight pages and $200 per page for each page in excess ofeight (subject to change without notice). To obtain themember rate, the corresponding author must be an ASMmember.

For a nonmember corresponding author, page chargesare currently $75 per page for the first eight pages and$250 for each page in excess of eight (subject to changewithout notice). A corresponding author who is not anASM member may join ASM to obtain the member rate.

If the research was not supported by any of the meansdescribed above, a request to waive the charges may bemailed (Journals Department, ASM, 1752 N St., N.W.,Washington, DC 20036-2904, USA) or faxed (202-942-9355) to the Journals Department. This request mustindicate how the work was supported and should beaccompanied by copies of the title page and Acknowl-edgments section.

Minireviews, Meeting Reviews, Guest Commentaries,and Comment Letters to the Editor are not subject to pagecharges.

Editorial Style

The editorial style of ASM journals conforms to theASM Style Manual for Journals (American Society forMicrobiology, 2007, in-house document) and How ToWrite and Publish a Scientific Paper, 6th ed. (GreenwoodPress, Westport, CT, 2006), as interpreted and modifiedby the editors and the ASM Journals Department.

The editors and the Journals Department reserve theprivilege of editing manuscripts to conform with thestylistic conventions set forth in the aforesaid publica-tions and in these Instructions.

Review Process

All manuscripts are considered to be confidential andare reviewed by the editors, members of the editorialboard, or qualified ad hoc reviewers. To expedite thereview process, authors must recommend as reviewers atleast three editorial board members who are not mem-bers of their institution(s) and have never been associ-ated with them or their laboratory(ies).

Copies of in-press and submitted manuscripts that areimportant for judgment of the present manuscript shouldbe included as supplemental material to facilitate the re-view.

When a manuscript is submitted to the journal, it isgiven a number (e.g., AEM00047-07 version 1) and as-signed to one of the editors. (Always refer to this num-ber in communications with the editor and the JournalsDepartment.) It is the responsibility of the correspondingauthor to inform the coauthors of the manuscript’s statusthroughout the submission, review, and publication pro-cesses. The reviewers operate under strict guidelines set


forth in “Guidelines for Reviewers” (http://www.journals.asm.org/misc/reviewguide.shtml) and are expected tocomplete their reviews expeditiously.

The corresponding author is notified, generally within4 to 6 weeks after submission, of the editor’s decision toaccept, reject, or require modification. When modificationis requested, the corresponding author must either submitthe modified version within 2 months or withdraw themanuscript. A point-by-point response to the reviews mustbe provided in the designated section of the Rapid Reviewsubmission form for the revised manuscript, and a comparecopy of the manuscript (without figures) should be in-cluded as supplemental material if the editor requestedone.

Manuscripts that have been rejected, or withdrawnafter being returned for modification, may be resubmit-ted if the major criticisms have been addressed. (Note: Amanuscript rejected by one ASM journal on scientificgrounds or on the basis of its general suitability forpublication is considered rejected by all other ASMjournals.) The cover letter must state that the manu-script is a resubmission, and the former manuscript num-ber should be provided in the appropriate field on thesubmission form. A point-by-point response to the re-views and a compare copy of the revised manuscript show-ing the changes must be included as supplemental material(the Response to Reviews section appears in the submis-sion form only if the manuscript is a modification). Resub-mitted manuscripts are normally handled by the originaleditor.

Rejected manuscripts may be resubmitted only onceunless permission has been obtained from the originaleditor or from the editor in chief.

Notification of Acceptance

When an editor has decided that a manuscript is ac-ceptable for publication on the basis of scientific merit,the author and the Journals Department are notified. APDF version of the accepted manuscript is posted onlineas 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 beenprepared according to the criteria set forth in theseInstructions and those in Rapid Review, the acceptanceprocedure will be completed successfully. If there areproblems that would cause extensive corrections to bemade at the copyediting stage or if the files are notacceptable for production, ASM Journals staff will con-tact the corresponding author. Once all the materialintended for publication has been determined to be ad-equate, the manuscript is scheduled for the next avail-able issue and an acceptance letter indicating the monthof publication, approximate page proof dates, and tableof contents section is mailed to the corresponding au-thor; a copyright transfer agreement is also included, asis a license to permit posting of supplemental material(if applicable). The editorial staff of the ASM Journals

Department completes the editing of the manuscript tobring it into conformity with prescribed standards.

Publish ahead of Print

For its primary-research journals, ASM posts onlinePDF versions of manuscripts that have been peer re-viewed and accepted but not yet copyedited. This featureis called “[journal acronym] Accepts” (e.g., AEM Ac-cepts) and is accessible from the Journals website. Themanuscripts are published online as soon as possibleafter acceptance, on a weekly basis, before the copy-edited, typeset articles are published. They are posted“as is” (i.e., as submitted by the authors at the modifi-cation stage) and do not reflect ASM editorial changes.No corrections/changes to the PDF manuscripts are ac-cepted. Accordingly, there likely will be differences be-tween the AEM Accepts manuscripts and the final, type-set articles. The manuscripts remain listed on the AEMAccepts page until the final, typeset articles are posted.At that point, the manuscripts are removed from theAEM Accepts page and become available only throughlinks from the final, typeset articles. The manuscripts areunder subscription access control until 4 months afterthe typeset articles are posted, when free access is pro-vided to everyone (subject to the applicable ASM licenseterms and conditions). Supplemental material intended,and accepted, for publication is not posted until publi-cation of the final, typeset article.

Instructions on how to cite such manuscripts may befound in the References section below (p. 10).

Page Proofs

Page proofs, together with a query sheet and instruc-tions for handling proofs, will be made available to thecorresponding author electronically via a PDF file thatcan be accessed through a unique password. Since cor-responding authors will be notified of the availability oftheir PDF proofs, instructed how to access informationabout page charges, reprints, and color figure charges (ifapplicable), and assigned their unique password via e-mail, an e-mail address must be supplied in the corre-spondent footnote. Failure to do so may result in a delayin publication. The PDF page proofs must be printedout, and corrections must be written on the hard copy.Queries must be answered on the query page or on aseparate sheet of paper, and any changes related to thequeries must be indicated on the proofs. Note that thecopy editor does not query at every instance where achange has been made. Queries are written only to re-quest necessary information or clarification of an un-clear passage or to draw attention to edits that may havealtered the sense. It is the author’s responsibility to readthe entire text, tables, and figure legends, not just itemsqueried. As soon as the page proofs are corrected andsigned by the person who proofread them (within 48 h),they should be mailed or sent by a courier service suchas FedEx, not faxed or sent as an e-mail attachment, tothe ASM Journals Department.


The proof stage is not the time to make extensivecorrections, additions, or deletions. Important new in-formation that has become available between accep-tance of the manuscript and receipt of the proofs may beinserted as an addendum in proof with the permission ofthe editor. If references to unpublished data or personalcommunications are added, it is expected that writtenassurance granting permission for the citation will beincluded. Limit changes to correction of spelling errors,incorrect data, and grammatical errors and updated in-formation for references to articles that have been sub-mitted or are in press. If URLs have been provided inthe article, recheck the sites to ensure that the addressesare still accurate and the material that you expect thereader to find is indeed there.

Questions about late proofs and problems in the proofsshould be directed to the ASM Journals Department(telephone, 202-942-9219). Questions about accessing orviewing your PDF proofs should be directed to Katie Gayof Cadmus Professional Communications at 804-261-3155 or [email protected].

Reprints

Reprints (in multiples of 100) may be purchased by allcoauthors. In the proof notification e-mail, the corre-sponding author will be instructed how to access infor-mation about reprints.

The corresponding authors of Minireviews, MeetingReviews, and Guest Commentaries may receive 100 freereprints of their contribution; additional reprints (inmultiples of 100) may be purchased if desired. As forregular articles, the corresponding author will be in-structed, in the proof notification e-mail, how to accessinformation about reprints.

PDF Files

A corresponding author who has included an e-mailaddress in his “corresponding author” footnote will havelimited access (10 downloads, total) to the PDF file ofhis published article. An e-mail alert will automaticallybe sent to him on the day the issue is posted. It willprovide a URL, which will be required to obtain access,and instructions. An article may be viewed, printed, orstored, provided that it is for the author’s own use.

Should coauthors or colleagues be interested in view-ing the paper for their own use, the corresponding au-thor may provide them with the URL; a copy of thearticle may not be forwarded electronically. However,they must be made aware of the terms and conditions ofthe ASM copyright. (For details, go to http://www.journals.asm.org/misc/terms.shtml.) Note that each such down-load will count toward the corresponding author’s totalof 10. After 10 downloads, access will be denied and canbe obtained only through a subscription to the journal(either individual or institutional) or after the standardaccess control has been lifted (i.e., 4 months after pub-lication).

HOW TO SUBMIT MANUSCRIPTS

All submissions to AEM must be made electronicallyvia the Rapid Review online submission and peer reviewsystem at the following URL: www.rapidreview.com/ASM2/author.html. (E-mailed submissions will not beaccepted.) First-time users must create an Author ac-count, which may be used for submitting to all ASMjournals. Instructions for creating an Author accountare available at the above URL under the CreateAccount button. Step-by-step instructions for submit-ting a manuscript via Rapid Review are available fromthe account holder’s My Manuscripts page. Informa-tion on file types acceptable for electronic submissioncan be found under the More About File Formatsbutton.

PDFs of submitted manuscripts are retained in RapidReview for 1 to 2 years, after which they are deleted.

ORGANIZATION AND FORMAT

On receipt at ASM, an accepted manuscript under-goes an automated preediting, cleanup, and tagging pro-cess specific to the particular article type. To optimizethis process, manuscripts must be supplied in the correctformat and with the appropriate sections and headings.

Type every portion of the manuscript double spaced(a minimum of 6 mm between lines), including figurelegends, table footnotes, and References, and numberall pages in sequence, including the abstract, figure leg-ends, and tables. Place the last two items after the Ref-erences section. Manuscript pages should have linenumbers; manuscripts without line numbers may beeditorially rejected by the editor, with a suggestion ofresubmission after line numbers are added. The fontsize should be no smaller than 12 points. It is recom-mended that the following sets of characters be easilydistinguishable in the manuscript: the numeral zero (0)and the letter “oh” (O); the numeral one (1), the letter“el” (l), and the letter “eye” (I); and a multiplication sign(�) and the letter “ex” (x). Do not create symbols asgraphics or use special fonts that are external to yourword processing program; use the “insert symbol” func-tion. Set the page size to 81⁄2 by 11 inches (ca. 21.6 by 28cm). Italicize or underline any words that should appearin italics, and indicate paragraph lead-ins in bold type.

Authors who are unsure of proper English usageshould have their manuscripts checked by someone pro-ficient in the English language.

Manuscripts may be editorially rejected, without re-view, on the basis of poor English or lack of conformityto the standards set forth in these Instructions.

Manuscript Submission Checklist:

• Double space all text, including references and fig-ure legends

• Number pages


• Number lines• Present statistical treatment of data where appro-

priate• Format references in ASM style• Indicate journal section for manuscript publication• Provide accession numbers for all sequences or se-

quence alignments important for evaluation of themanuscript as supplemental material or make thematerial available on a website for access by theeditor and reviewers

• Confirm that genetic and chemical nomenclatureconforms to instructions

• Include as supporting material in-press and submit-ted manuscripts that are important for judgment ofthe present manuscript

Long-Form Papers

Long-form papers should include the elements de-scribed in this section.

Title, running title, and byline. Each manuscriptshould present the results of an independent, cohesivestudy; thus, numbered series titles are not permitted.Exercise care in composing a main title. Avoid the maintitle/subtitle arrangement, complete sentences, and un-necessary 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) atwhich the work was performed, each author’s affiliation,and a footnote indicating the present address of anyauthor no longer at the institution where the work wasperformed. Place an asterisk after the name of the au-thor to whom inquiries regarding the paper should bedirected (see “Correspondent footnote” below).

Study group in byline. A study group, surveillanceteam, working group, consortium, or the like (e.g., theActive Bacterial Core Surveillance Team) may be listedas a coauthor in the byline if its contributing memberssatisfy the requirements for authorship and accountabil-ity as described in these Instructions. The names (andinstitutional affiliations if desired) of the contributingmembers may be given in a footnote keyed to the studygroup name in the byline or as a separate paragraph inAcknowledgments.

If the contributing members of the group associatedwith the work do not fulfill the criteria of substantialcontribution to and responsibility for the paper, thegroup may not be listed in the author byline. Instead, itand the names of its contributing members may be listedin the Acknowledgments section.

Correspondent footnote. The complete mailing address,a single telephone number, a single fax number, and asingle e-mail address for the corresponding authorshould be included on the title page of the manuscript.This information will be published in the article as afootnote to facilitate communication, and the e-mail ad-

dress will be used to notify the corresponding author ofthe availability of proofs and, later, of the PDF file of thepublished article.

Abstract. Limit the abstract to 250 words or fewer andconcisely summarize the basic content of the paper with-out presenting extensive experimental details. Avoid ab-breviations and references, and do not include diagrams.When it is essential to include a reference, use the sameformat as shown for the References section but omit thearticle title. Because the abstract will be published sep-arately by abstracting services, it must be complete andunderstandable without reference to the text.

Introduction. The introduction should supply suffi-cient background information to allow the reader tounderstand and evaluate the results of the present studywithout referring to previous publications on the topic.The introduction should also provide the hypothesis thatwas addressed or the rationale for the present study. Useonly those references required to provide the most sa-lient background rather than an exhaustive review of thetopic.

Materials and Methods. The Materials and Methodssection should include sufficient technical information toallow the experiments to be repeated. When centrifuga-tion conditions are critical, give enough information toenable another investigator to repeat the procedure:make of centrifuge, model of rotor, temperature, time atmaximum speed, and centrifugal force (� g rather thanrevolutions per minute). For commonly used materialsand methods (e.g., media and protein concentration de-terminations), a simple reference is sufficient. If severalalternative methods are commonly used, it is helpful toidentify the method briefly as well as to cite the refer-ence. For example, it is preferable to state “cells werebroken by ultrasonic treatment as previously described(9)” rather than to state “cells were broken as previouslydescribed (9).” This allows the reader to assess themethod without constant reference to previous publica-tions. Describe new methods completely, and givesources of unusual chemicals, equipment, or microbialstrains. When large numbers of microbial strains or mu-tants are used in a study, include tables identifying theimmediate sources (i.e., sources from whom the strainswere obtained) and properties of the strains, mutants,bacteriophages, plasmids, etc.

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

Results. In the Results section, include only the re-sults of the experiments; reserve extensive interpretationof the results for the Discussion section. Present theresults as concisely as possible in one of the following:


text, table(s), or figure(s). Avoid extensive use of graphsto present data that might be more concisely presentedin the text or tables. For example, except in unusualcases, double-reciprocal plots used to determine appar-ent Km values should not be presented as graphs; in-stead, the values should be stated in the text. Similarly,graphs illustrating other methods commonly used to de-rive kinetic or physical constants (e.g., reduced-viscosityplots and plots used to determine sedimentation veloc-ity) need not be shown except in unusual circumstances.Limit photographs (particularly photomicrographs andelectron micrographs) to those that are absolutely nec-essary to show the experimental findings. Number fig-ures and tables in the order in which they are cited in thetext, and be sure to cite all figures and tables.

Discussion. The Discussion should provide an inter-pretation of the results in relation to previously pub-lished work and to the experimental system at hand andshould not contain extensive repetition of the Resultssection or reiteration of the introduction. In short pa-pers, the Results and Discussion sections may be com-bined.

Acknowledgments. The source of any financial sup-port received for the work being published must be in-dicated in the Acknowledgments section. (It will be as-sumed that the absence of such an acknowledgment is astatement by the authors that no support was received.)The usual format is as follows: ‘‘This work was supportedby Public Health Service grant CA-01234 from the Na-tional Cancer Institute.’’

Recognition of personal assistance should be given asa separate paragraph, as should any statements disclaim-ing endorsement or approval of the views reflected in thepaper or of a product mentioned therein.

Appendixes. Appendixes, which contain additionalmaterial to aid the reader, are permitted. Titles, authors,and References sections that are distinct from those ofthe primary article are not allowed. If it is not feasible tolist the author(s) of the appendix in the byline or theAcknowledgments section of the primary article, rewritethe appendix so that it can be considered for publicationas an independent article, either long-form or short-form style. Equations, tables, and figures should be la-beled with the letter ‘‘A’’ preceding the numeral to dis-tinguish them from those cited in the main body of thetext.

References. (i) References listed in the Referencessection. The References section must include all journalarticles (both print and online), books and book chapters(both print and online), patents, theses and disserta-tions, published conference proceedings, meeting ab-stracts from published abstract books or journal supple-ments, letters (to the editor), and company publications,as well as in-press journal articles, book chapters, andbooks (publication title must be given). Arrange the

citations in alphabetical order (letter by letter, ignoringspaces and punctuation) by first author and numberconsecutively. Provide the names of all the authors foreach reference. All listed references must be cited par-enthetically by number in the text. Since title and bylineinformation that is downloaded from PubMed does notshow accents, italics, or special characters, authorsshould refer to the PDF files or hard-copy versions ofthe articles and incorporate the necessary corrections inthe submitted manuscript. Abbreviate journal names ac-cording to BIOSIS Serial Sources (The Thomson Corpo-ration, Philadelphia, PA, 2006).

Follow the styles shown in the examples below forprint references.

1. Arendsen, A. F., M. Q. Solimar, and S. W. Ragsdale.1999. Nitrate-dependent regulation of acetate bio-synthesis and nitrate respiration by Clostridium ther-moaceticum. 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 titleis 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, Truper and da Costa 1996b,605, p. 404–414. In D. R. Boone, R. W. Castenholz,and G. M. Garrity (ed.), Bergey’s manual of system-atic bacteriology, 2nd ed., vol. 1. Springer, NewYork, 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, Washing-ton, DC.

5. Falagas, M. E., and S. K. Kasiakou. 2006. Use ofinternational units when dosing colistin will helpdecrease confusion related to various formulationsof the drug around the world. Antimicrob. AgentsChemother. 50:2274–2275. (Letter.) {“Letter” or“Letter to the editor” is allowed but not required at theend 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. Specimencollection, 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 salmonellaDNA in synovial membrane and synovial fluid fromLatin American patients. Arthritis Rheum. 39(Suppl.):S185. {Meeting abstract published in journal supple-ment.}

9. Green, P. N., D. Hood, and C. S. Dow. 1984. Taxo-nomic status of some methylotrophic bacteria, p.251–254. In R. L. Crawford and R. S. Hanson (ed.),


Microbial growth on C1 compounds. Proceedings ofthe 4th International Symposium. American Societyfor Microbiology, Washington, DC.

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

11. O’Malley, D. R. 1998. Ph.D. thesis. University ofCalifornia, Los Angeles. {Title is optional.}

12. Rotimi, V. O., N. O. Salako, E. M. Mohaddas, andL. P. Philip. 2005. Abstr. 45th Intersci. Conf. Anti-microb. Agents Chemother., abstr. D-1658. {Ab-stract title is optional.}

13. Smith, D., C. Johnson, M. Maier, and J. J. Maurer.2005. Distribution of fimbrial, phage and plasmidassociated virulence genes among poultry Salmo-nella enterica serovars, abstr. P-038, p. 445. Abstr.105th Gen. Meet. Am. Soc. Microbiol. AmericanSociety for Microbiology, Washington, DC. {Ab-stract title is optional.}

14. Stratagene. 2006. Yeast DNA isolation system: in-struction manual. Stratagene, La Jolla, CA. {Use thecompany name as the author if none is provided for acompany publication.}

*A reference to an in-press ASM publication shouldstate the control number (e.g., AEM00577-07) if it is ajournal article or the name of the publication if it is abook.

Online references must provide the same informationthat print references do, but some variation is allowed.For online journal articles, posting or revision dates mayreplace the year of publication, and a DOI or URL maybe provided in addition to or in lieu of volume and pagenumbers. Some examples follow.

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

2. Dionne, M. S., and D. S. Schneider. 2002. Screen-ing 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, andD. M. Engelman. 2001. Polar residues drive associ-ation 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? Pedi-atrics 115:e718–e724.

NOTE: A posting or accession date is required for anyonline reference that is periodically updated or changed.

(ii) References cited in the text. References to unpub-lished data, manuscripts submitted for publication, un-published conference presentations (e.g., a report orposter that has not appeared in published conferenceproceedings), personal communications, patent applica-tions and patents pending, computer software, data-bases, and websites (home pages) should be made par-enthetically 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, andP. N. Brighton, submitted for publication).

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

. . . this new process (V. R. Smoll, 20 June 1999, Austra-lian 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 Mi-crobiology, State University [http://www.stu.micro]).

URLs for companies that produce any of the productsmentioned in your study or for products being sold mayNOT be included in the article. However, companyURLs that permit access to scientific data related to thestudy or to shareware used in the study are permitted.

(iii) References related to supplemental material.References that are related only to supplemental mate-rial hosted by ASM or posted on a personal/institutionalwebsite should not be listed in the References section ofan article; include them with the supplemental materialitself.

(iv) Referencing publish-ahead-of-print manuscripts.Citations of ASM Accepts manuscripts should look likethe following example.

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

If an author of an article cites an ASM Accepts manu-script in his paper but wishes at the proof stage tochange the reference entry to that for the publishedarticle, the following style should be used:

Wang, G. G., M. P. Pasillas, and M. P. Kamps. 15May 2006. Persistent transactivation by Meis1 re-places Hox function in myeloid leukemogenesis mod-


els: evidence for co-occupancy of Meis1-Pbx and Hox-Pbx complexes on promoters of leukemia-associatedgenes. 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 pub-lish-ahead-of-print manuscripts, but citation entriesmust include the following information: author name(s),posting date, title, journal title, and volume and pagenumbers 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 res-idues drive association of polyleucine transmembranehelices. Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.041593698.

Short-Form Papers

The short-form format is intended for the presenta-tion of brief observations that do not warrant full-lengthpapers. Submit short-form papers in the same way asfull-length papers. They receive the same review, they arenot published more rapidly than full-length papers, andthey are not considered preliminary communications.

The title, running title (not to exceed 54 charactersand spaces), byline, and correspondent footnote shouldbe prepared as for the long-form paper. Each short-formpaper must have an abstract of no more than 50 words.Do not use section headings in the body of the paper;combine methods, results, and discussion in a singlesection. Paragraph lead-ins are permissible. The textshould be kept to a minimum and, if possible, should notexceed 1,000 words; the number of figures and tablesshould also be kept to a minimum. Materials and meth-ods should be described in the text, not in figure legendsor table footnotes. Present acknowledgments as in long-form papers, but do not use a heading. The Referencessection is identical to that of long-form papers.

Minireviews

Minireviews are brief (limit of 6 printed pages exclu-sive of references) biographical profiles, historical per-spectives, or summaries of developments in fast-movingareas. They must be based on published articles; theymay address any subject within the scope of AEM.

Minireviews may be either solicited or proffered byauthors responding to a recognized need. Irrespective oforigin, Minireviews are subject to review and should besubmitted via Rapid Review. The cover letter shouldstate whether the article was solicited and by whom.

Minireviews do not have abstracts. In the Abstract sec-tion of the submission form, put “Not Applicable.” Thebody of the Minireview may either have section headingsor be set up like a short-form paper (see above).

Meeting Reviews

Meeting Reviews are brief summaries of recent scien-tific meetings that cover topics within the scope of AEM.Reviews should be timely and focus on major themes,new developments, emerging trends, and significant un-answered questions presented and discussed at themeeting. Sufficient background should be provided tomake the report useful to the general reader. The authormust provide written assurance from the relevant indi-viduals that permission to cite their presented materialhas been granted.

Meeting Reviews, which may be solicited or profferedby authors, are subject to editorial review and should besubmitted via Rapid Review.

Guest Commentaries

Guest Commentaries are communications written inresponse to invitations issued by the editors and concernrelevant topics in microbiology that are not necessarilycovered by Minireviews. They should raise issues of in-terest to the scholarly community, initiate or focus dis-cussion, and propose needed position or consensusstatements by the Academy of Microbiology, the Na-tional Academy of Sciences, and other leadership groupsin research and education. Reviews of the literature,methods and other how-to papers, and responses tar-geted at a specific published paper are not appropriate.Guest Commentaries are subject to review.

The length may not exceed 4 printed pages, and theformat is like that of a Minireview (see above). Com-mentaries should be submitted via Rapid Review.

Letters to the Editor

Letters to the Editor are intended only for commentson articles published previously in the journal and mustcite published references to support the writer’s argu-ment.

Letters may be no more than 500 words long and mustbe typed double spaced. Refer to a recently publishedLetter for correct formatting. Note that authors andaffiliations are listed at the foot of the Letter. Provideonly the primary affiliation for each author.

All Letters to the Editor must be submitted electron-ically, and the manuscript type (Comment Letter) mustbe selected from the drop-down list in the submissionform. The cover letter should state the volume and issuein which the article commented on was published, thetitle of the article, and the last name of the first author.In the Abstract section of the submission form, put “Notapplicable.” Letters to the Editor do not have abstracts.The Letter must have a title, which must appear on themanuscript and on the submission form. Figures andtables should be kept to a minimum.

The Letter will be sent to the editor who handled thearticle in question. If the editor believes that publicationis warranted, he will solicit a reply from the correspond-ing author of the article and make a recommendation tothe editor in chief. Final approval for publication restswith the editor in chief.


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

Errata

The Erratum section provides a means of correctingerrors 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. SubmitErrata via Rapid Review (see “How To Submit Manu-scripts,” above). In the Abstract section of the submis-sion form (a required field), put “Not Applicable.” Up-load the text of your Erratum as an MS Word file. Pleasesee a recent issue for correct formatting.

Authors’ Corrections

The Author’s Correction section provides a means ofcorrecting errors of omission (e.g., author names or cita-tions) and errors of a scientific nature that do not alter theoverall basic results or conclusions of a published article(e.g., an incorrect unit of measurement or order of magni-tude used throughout, contamination of one of numerouscultures, or misidentification of a mutant strain, causingerroneous data for only a portion [noncritical] of thestudy). Note that the addition of new data is not permitted.

For corrections of a scientific nature or issues involv-ing authorship, including contributions and use or own-ership of data and/or materials, all disputing partiesmust agree, in writing, to publication of the Correction.For omission of an author’s name, letters must be signedby the authors of the article and the author whose namewas omitted. The editor who handled the article will beconsulted if necessary.

Submit an Author’s Correction via Rapid Review (see“How To Submit Manuscripts,” above). In the submis-sion form, select Erratum as the manuscript type; thereis no separate selection in Rapid Review for Authors’Corrections, but your Correction will be published assuch if appropriate. In the Abstract section of the sub-mission form (a required field), put “Not Applicable.”Upload the text of your Author’s Correction as an MSWord file. Please see a recent issue for correct format-ting. Signed letters of agreement must be supplied assupplemental material (scanned PDF files).

Retractions

Retractions are reserved for major errors or breachesof ethics that, for example, may call into question thesource of the data or the validity of the results and con-clusions of an article. Submit Retractions via Rapid Re-view (see “How To Submit Manuscripts,” above). In theAbstract section of the submission form (a requiredfield), put “Not Applicable.” Upload the text of yourRetraction as an MS Word file. Letters of agreementsigned by all of the authors must be supplied as supple-mental material (scanned PDF files). The Retractionwill be assigned to the editor in chief of the journal, andthe editor who handled the paper and the chairman ofthe ASM Publication Board will be consulted. If all

parties agree to the publication and content of the Re-traction, it will be sent to the Journals Department forpublication.

We strongly recommend that before returning theirmodified manuscripts, authors check the acceptability oftheir digital images for production by running their filesthrough Rapid Inspector, a tool provided at the followingURL: http://rapidinspector.cadmus.com/mw/. Rapid In-

ILLUSTRATIONS AND TABLES

Digital files that are acceptable for production (seebelow) must be provided for all illustrations on returnof the modified manuscript. (On initial submission, theentire paper may be submitted in PDF format.)

Macintosh

ApplicationFile type

Black and white Color (CMYK)a

Adobe Illustrator 6.0, 7.0, 8.0,9.0, 10.0, 11.0 CS

EPS EPS

Adobe InDesign 1.0 EPS EPSAdobe PageMaker 6.5 EPS EPSAdobe Photoshop 4.0, 5.0, 5.5,

6.0, 7.0, 8.0 CSTIFF TIFF

Adobe Photoshop 5.0 LE TIFF N/Ab

ChemDraw Pro 5.0 EPS/TIFF EPS/TIFFCorel Photo-Paint 8.0 TIFF EPSCorelDRAW 6.0, 8.0 EPS/TIFF EPSDeneba Canvas 6.0, 7.0, 8.0 EPS/TIFF EPSMacromedia FreeHand 7.0, 8.0,

9.0EPS EPS

PowerPoint 98, 2001 PPTc N/Ab

Prism 3 by GraphPad TIFF N/Ab

Synergy Kaleidagraph 3.08, 3.51 EPS N/Ab

a Color graphics must be saved and printed in the CMYK mode, not RGB.b ASM accepts only black-and-white, not color, graphics created with Kalei-

dagraph, Adobe Photoshop 5.0 LE, Prism 3 by GraphPad, and PowerPoint.c For instructions on saving PowerPoint files, refer to the Cadmus digital art

website at http://cjs.cadmus.com/da/index.jsp.

Windows

ApplicationFile type

Black and white Color (CMYK)a

Adobe Illustrator 7.0, 8.0, 9.0,10.0, 11.0 CS

EPS EPS

Adobe InDesign 1.0 EPS EPSAdobe PageMaker 6.5 EPS EPSAdobe Photoshop 4.0, 5.0, 5.5,

6.0, 7.0, 8.0 CSTIFF TIFF

Adobe Photoshop 5.0 LE TIFF N/Ab

ChemDraw Pro 5.0 EPS/TIFF EPS/TIFFCorel Photo-Paint 8.0, 9.0 TIFF EPSCorelDRAW 7.0, 8.0, 9.0 EPS/TIFF EPSDeneba Canvas 6.0, 7.0 EPS/TIFF EPSMacromedia FreeHand 7.0, 8.0,

9.0EPS EPS

PowerPoint 97, 2000, XP PPTc N/Ab

Prism 3 by GraphPad TIFF N/Ab

SigmaPlot 8.01 EPS EPS

a Color graphics must be saved and printed in the CMYK mode, not RGB.b ASM accepts only black-and-white, not color, graphics created with Adobe

Photoshop 5.0 LE, Prism 3 by GraphPad, and PowerPoint.c For instructions on saving PowerPoint files, refer to the Cadmus digital art

website at http://cjs.cadmus.com/da/index.jsp.


spector is an easy-to-use Web-based application that iden-tifies file characteristics that may render the image unus-able for production.

Illustrations may be continuous-tone images, linedrawings, or composites. Color graphics may be submit-ted, but the cost of printing in color must be borne by theauthor. Suggestions about how to reduce costs and en-sure accurate color reproduction are given below.

The preferred format for tables is MS Word; however,WordPerfect and Acrobat PDF are also acceptable (seethe section on Tables below).

Image Manipulation

Computer-generated images may be processed onlyminimally. Processing (e.g., changing contrast, bright-ness, or color balance) is acceptable only if applied to allparts of the image, as well as to the controls, equally, anddescriptions of all such adjustments and the tools used(both hardware and software) must be provided in themanuscript. Unprocessed data and files must be retainedby the authors and be provided to the editor on request.

Illustrations

File types and formats. As mentioned above, illus-trations may be supplied as PDF files for reviewingpurposes only on initial submission; in fact, we recom-mend this option to minimize file upload time. At themodification stage, production quality digital files mustbe submitted: TIFF or EPS files from supported appli-cations or PowerPoint files (black and white only). Ex-cept for figures produced in PowerPoint, all graphicssubmitted with modified manuscripts must be bitmap,grayscale, or CMYK (not RGB). Halftone images (thosewith various densities or shades) must be grayscale, notbitmap.

Color PowerPoint files are not accepted because theapplication, designed for developing on-screen com-puter presentations, uses the RGB color mode whereasthe printing process uses the CMYK color mode. Colorsthat are represented in a PowerPoint image may not bereproducible on a printing press. Although black-and-white Microsoft PowerPoint files are accepted, we do notrecommend the use of PowerPoint. PowerPoint requiresusers to pay close attention to the fonts used in theirimages (see the section on Fonts below). If instructionsfor fonts are not followed exactly, images prepared forpublication are subject to missing characters, improperlyconverted characters, or shifting/obscuring of elementsor text in the figure. Use of PowerPoint is therefore notrecommended for either color or black-and-white illustra-tions. Acceptable file types and formats for productionare given in the charts above. More-detailed instructionsfor preparing illustrations are available at http://cjs.cadmus.com/da. Please review this information beforepreparing your files. If you require additional information,please send an e-mail inquiry to [email protected].

Minimum resolution. It is extremely important that ahigh enough resolution is used. Any imported imagesmust be at the correct resolution before they are placed.Note, however, that the higher the resolution, the largerthe file and the longer the upload time. Publication qual-ity will not be improved by using a resolution higher thanthe minimum. Minimum resolutions are as follows:

300 dpi for grayscale and color600 dpi for lettering1,200 dpi for line art600 dpi for combination art (lettering and images)

Size. All graphics MUST be submitted at their in-tended publication size; that is, the image uploadedshould be 100% of its print dimensions so that no re-duction or enlargement is necessary. Resolution must beat the required level at the submitted size. Include onlythe significant portion of an illustration. White spacemust be cropped from the image, and excess space be-tween panel labels and the image must be eliminated.

Maximum width for a 1-column figure: 35⁄16 inches(ca. 8.4 cm)

Maximum width for a 2-column figure: 67⁄8 inches(ca. 17.4 cm)

Minimum width for a 2-column figure: 41⁄4 inches(10.8 cm)

Maximum height: 91⁄16 inches (23.0 cm)

Contrast. Illustrations must contain sufficient contrastto withstand the inevitable loss of contrast and detailinherent in the printing process. See also the section oncolor illustrations below.

Labeling and assembly. All final lettering, labeling,tooling, etc., MUST be incorporated into the figures. Itcannot be added at a later date. If a figure number isincluded, it must appear well outside the boundaries ofthe image itself. (Numbering may need to be changed atthe copyediting stage.) Each figure must be uploaded asa separate file, and any multipanel figures must be as-sembled into one file; i.e., rather than uploading a sep-arate file for each panel in a figure, assemble all panelsin one piece and supply them as one file.

Fonts. To avoid font problems, set all type in one ofthe following fonts: Helvetica, Times Roman, EuropeanPI, Mathematical PI, or Symbol. All fonts other thanthese five must be converted to paths (or outlines) in theapplication with which they were created. For properfont use in PowerPoint images, refer to the Cadmusdigital art website, http://cjs.cadmus.com/da/instructions/ppt_disclaimer.jsp.

Compression. Images created with Macintosh appli-cations may be compressed with Stuffit. Images createdwith Windows applications may be compressed withWINZIP or PKZIP.


Color illustrations. The cost of printing in color must beborne by the author. The current color cost per figuremay be accessed from the submission form in RapidReview. For accepted manuscripts, the total cost of thecolor will be included in the acceptance letter sent out byASM. Adherence to the following guidelines, in additionto the general ones below, will help to minimize costsand to ensure color reproduction that is as accurate aspossible.

Because of the requirements of print production,color illustrations must be in the CMYK (cyan, magenta,yellow, black) color space. The “normal” color mode formost 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 candefine fewer colors), colors often shift when an RGB fileis converted to CMYK. In particular, figures showing redor green fluorescence and those with a significant rangeof colors may be difficult or impossible to reproduceduring the printing process.

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

We cannot accept any Microsoft Office files (Power-Point, Word, Excel) for color illustrations because theyare restricted to the RGB color space.

Drawings

Submit graphs, charts, complicated chemical or mathe-matical formulas, diagrams, and other drawings as finishedproducts not requiring additional artwork or typesetting.No part of the graph or drawing may be handwritten. Allelements, including letters, numbers, and symbols, must beeasily readable, and both axes of a graph must be labeled.Keep in mind that the journal is published both in print andonline and that the same electronic files submitted by theauthors are used to produce both.

When creating line art, please use the following guide-lines:

1. All art MUST be submitted at its intended publica-tion size. For acceptable dimensions, see the Sizesection on p. 14.

2. Avoid using screens (i.e., shading) in line art. It canbe difficult and time-consuming to reproduce theseimages without moire patterns. Various pattern back-grounds are preferable to screens as long as the pat-terns are not imported from another application. Ifyou must use images containing screens,

• Generate the image at line screens of 85 lines perinch or lower.

• When applying multiple shades of gray, differenti-ate 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 uponscanning and reduction.

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

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

5. Avoid layering type directly over shaded or texturedareas.

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

7. Avoid heavy letters, which tend to close up, and un-usual symbols, which the printer may not be able toreproduce in the legend.

8. If colors are used, avoid using similar shades of thesame color and avoid very light colors.

In figure ordinate and abscissa scales (as well astable column headings), avoid the ambiguous use ofnumbers with exponents. Usually, it is preferable touse the Systeme International d’Unites (SI) symbols(� for 10�6, m for 10�3, k for 103, M for 106, etc.). Acomplete listing of SI symbols can be found in theInternational Union of Pure and Applied Chemistry(IUPAC) publication Quantities, Units and Symbols inPhysical Chemistry (Blackwell Science, Oxford, UnitedKingdom, 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 tobe made by the number 20 accompanied by the label kcpm.

When powers of 10 must be used, the journal re-quires that the exponent power be associated with thenumber shown. In representing 20,000 cells per ml,the numeral on the ordinate would be ‘‘2’’ and thelabel would be ‘‘104 cells per ml’’ (not ‘‘cells per ml �10�4’’). Likewise, an enzyme activity of 0.06 U/mlwould 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 Sequences

Nucleic acid sequences of limited length which are theprimary subject of a study may be presented freestyle in themost effective format. Longer nucleic acid sequences mustbe presented as figures in the following format to conservespace. Print the sequence in lines of approximately 100 to120 nucleotides in a nonproportional (monospace) fontthat is easily legible when published with a line length of 6inches (ca. 15.2 cm). If possible, lines of nucleic acid se-quence should be further subdivided into blocks of 10 or 20nucleotides by spaces within the sequence or by marksabove it. Uppercase and lowercase letters may be used todesignate 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, tothe left of the lines. Minimize spacing between lines of


sequence, leaving room only for annotation of the se-quence. Annotation may include boldface, underlining,brackets, boxes, etc. Encoded amino acid sequences maybe presented, if necessary, immediately above or below thefirst nucleotide of each codon, by using the single-letteramino acid symbols. Comparisons of multiple nucleic acidsequences should conform as nearly as possible to the sameformat.

Figure Legends

Legends should provide enough information so thatthe figure is understandable without frequent referenceto the text. However, detailed experimental methodsmust be described in the Materials and Methods section,not in a figure legend. A method that is unique to one ofseveral experiments may be reported in a legend only ifthe discussion is very brief (one or two sentences). De-fine all symbols used in the figure and define all abbre-viations that are not used in the text.

Tables

Tables that contain artwork, chemical structures, orshading must be submitted as illustrations in an acceptableformat at the modification stage. The preferred format forregular tables is MS Word; however, WordPerfect andAcrobat PDF are also acceptable. Note that a straightExcel file is not currently an acceptable format. Excel filesmust be either embedded in a Word or WordPerfect doc-ument or converted to PDF before being uploaded. If yourmodified manuscript contains PDF tables, select “for re-viewing purposes only” at the beginning of the file uploadprocess.

Tables should be formatted as follows. Arrange thedata so that columns of like material read down, notacross. The headings should be sufficiently clear so thatthe meaning of the data is understandable without ref-erence to the text. See the Abbreviations section (p. 20)of these Instructions for those that should be used intables. Explanatory footnotes are acceptable, but moreextensive table “legends” are not. Footnotes should notinclude detailed descriptions of the experiment. Tablesmust include enough information to warrant table for-mat; those with fewer than six pieces of data will beincorporated into the text by the copy editor. Table 1 isan example of a well-constructed table.

Cover Photographs and Drawings

AEM publishes photographs and drawings on thefront cover. Invitations are issued to authors whosemanuscripts are returned for modification or whosemanuscripts have been accepted for publication inAEM; material should be related to the work presentedin the AEM manuscript. Unsolicited photos will be con-sidered in hard-copy format (two copies) only; if anunsolicited photo is chosen for the cover, the author maybe asked to submit digital files. No material submittedfor consideration will be returned to the author. Authorswill be notified only if their cover art is selected. Copy-right for the chosen material must be transferred toASM. A short description of the cover material will beincluded at the end of the table of contents or the authorindex of the issue. Technical specifications for submis-sion are available from the cover editor, Matthew R.Parsek (e-mail: [email protected]).

NOMENCLATURE

Chemical and Biochemical Nomenclature

The recognized authority for the names of chemicalcompounds is Chemical Abstracts (CAS, Columbus, OH)and its indexes. The Merck Index, 14th ed. (Merck & Co.,Inc., Whitehouse Station, NJ, 2006), is also an excellentsource. For biochemical terminology, including abbrevia-tions and symbols, consult Biochemical Nomenclature andRelated Documents (Portland Press, London, UnitedKingdom, 1992), available at http://www.chem.qmul.ac.uk/iupac/bibliog/white.html, and the instructions to au-thors of the Journal of Biological Chemistry and the Archivesof Biochemistry and Biophysics (first issues of each year).

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

For enzymes, use the recommended (trivial) name as-signed by the Nomenclature Committee of the Interna-tional Union of Biochemistry (IUB) as described in En-zyme 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 (triv-ial) name in parentheses at first use in the abstract and text.Use the EC number when one has been assigned, andexpress enzyme activity either in katals (preferred) or in theolder system of micromoles per minute.

Nomenclature of Microorganisms

Binary names, consisting of a generic name and aspecific epithet (e.g., Escherichia coli), must be used forall microorganisms. Names of categories at or above thegenus level may be used alone, but specific and subspe-cific epithets may not. A specific epithet must be pre-ceded by a generic name, written out in full the first timeit is used in a paper. Thereafter, the generic name shouldbe abbreviated to the initial capital letter (e.g., E. coli),

TABLE 1. Distribution of protein and ATPase infractions of dialyzed membranesa

Membrane Fraction

ATPase

U/mg ofprotein Total U

Control Depleted membrane 0.036 2.3Concentrated supernatant 0.134 4.82

E1 treated Depleted membrane 0.034 1.98Concentrated supernatant 0.11 4.6

a Specific activities of ATPase of nondepleted membranes from control andtreated bacteria were 0.21 and 0.20, respectively.


provided there can be no confusion with other generaused 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 under-lined) in the manuscript; strain designations and num-bers are not. Vernacular (common) names should be inlowercase roman type (e.g., streptococcus, brucella). ForSalmonella, genus, species, and subspecies names shouldbe rendered in standard form: Salmonella enterica at firstuse, S. enterica thereafter; Salmonella enterica subsp. ari-zonae at first use, S. enterica subsp. arizonae thereafter.Names of serovars should be in roman type with the firstletter capitalized: Salmonella enterica serovar Typhi-murium. After the first use, the serovar may also begiven without a species name: Salmonella serovar Typhi-murium. For other information regarding serovar desig-nations, see Antigenic Formulas of the Salmonella Sero-vars, 8th ed. (M. Y. Popoff, WHO Collaborating Centrefor Reference and Research on Salmonella, Institut Pas-teur, Paris, France, 2001). For a summary of the currentstandards for Salmonella nomenclature and the Kauf-mann-White criteria, see the article by Brenner et al. (J.Clin. Microbiol. 38:2465-2467, 2000), the opinion of theJudicial Commission of the International Committee onSystematics 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 theApproved Lists of Bacterial Names (Amended) & Indexof the Bacterial and Yeast Nomenclatural Changes(V. B. D. Skerman et al. ed., ASM Press, Washington,DC, 1989) and the validation lists and notification listspublished in the International Journal of Systematicand Evolutionary Microbiology (formerly the Interna-tional Journal of Systematic Bacteriology) since Jan-uary 1989. In addition, two sites on the World WideWeb list current approved bacterial names: Bac-terial Nomenclature Up-to-Date (http://www.dsmz.de/microorganisms/main.php?contentleft_id�14) and List ofProkaryotic Names with Standing in Nomenclature (http://www.bacterio.cict.fr). If there is reason to use a namethat does not have standing in nomenclature, the nameshould be enclosed in quotation marks in the title and atits first use in the abstract and the text and an appropri-ate statement concerning the nomenclatural status ofthe name should be made in the text. “Candidatus” spe-cies should always be set in quotation marks.

For guidelines regarding new names and descriptionsof new genera and species, see the articles by Tindall(Int. J. Syst. Bacteriol. 49:1309–1312, 1999) and Stack-ebrandt et al. (Int. J. Syst. Evol. Microbiol. 52:1043–1047, 2002). To validate new names and/or combina-tions, authors must submit three copies of theirpublished article to the International Journal of System-atic and Evolutionary Microbiology.

It is recommended that a strain be deposited in at leasttwo recognized culture collections in different countrieswhen that strain is necessary for the description of a newtaxon (Int. J. Syst. Evol. Microbiol. 50:2239–2244, 2000).

Since the classification of fungi is not complete, it isthe responsibility of the author to determine the ac-cepted binomial for a given organism. Sources for thesenames include The Yeasts: a Taxonomic Study, 4th ed.(C. P. Kurtzman and J. W. Fell, ed., Elsevier SciencePublishers 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. Stalp-ers, ed., CABI Publishing, Wallingford, Oxfordshire,United Kingdom, 2001); see also http://www.speciesfungorum.org/Names/Fundic.asp.

Names used for viruses should be those approved bythe International Committee on Taxonomy of Viruses(ICTV) and published in Virus Taxonomy: Eighth Reportof the International Committee on Taxonomy of Viruses(C. M. Fauquet et al., ed., Elsevier Academic Press, SanDiego, CA, 2005). In addition, the recommendations ofthe ICTV regarding the use of species names shouldgenerally be followed: when the entire species is dis-cussed as a taxonomic entity, the species name, likeother taxa, is italic and has the first letter and any propernouns capitalized (e.g., Tobacco mosaic virus, Murray Valleyencephalitis virus). When the behavior or manipulation ofindividual viruses is discussed, the vernacular (e.g., tobaccomosaic virus, Murray Valley encephalitis virus) should beused. If desired, synonyms may be added parentheticallywhen the name is first mentioned. Approved generic (orgroup) and family names may also be used.

Microorganisms, viruses, and plasmids should be giv-en designations consisting of letters and serial numbers.It is generally advisable to include a worker’s initials ora descriptive symbol of locale, laboratory, etc., in the des-ignation. Each new strain, mutant, isolate, or derivativeshould be given a new (serial) designation. This desig-nation should be distinct from those of the genotype andphenotype, and genotypic and phenotypic symbols shouldnot be included. Plasmids are named with a lowercase“p” followed by the designation in uppercase letters andnumbers. To avoid the use of the same designation asthat of a widely used strain or plasmid, check the desig-nation against a publication database such as Medline.

Genetic Nomenclature

To facilitate accurate communication, it is importantthat standard genetic nomenclature be used wheneverpossible and that deviations or proposals for new nam-ing systems be endorsed by an appropriate authoritativebody. Review and/or publication of submitted manu-scripts that contain new or nonstandard nomenclaturemay be delayed by the editor or the Journals Depart-ment so that they may be reviewed by the Genetics andGenomics Committee of the ASM Publications Board.

Before submission of manuscripts, authors may di-rect questions on genetic nomenclature to the commit-tee’s chairman: Maria Costanzo (e-mail: [email protected]). Such a consultation should be mentionedin the manuscript submission letter.

Bacteria. The genetic properties of bacteria are de-


scribed in terms of phenotypes and genotypes. The pheno-type describes the observable properties of an organism.The genotype refers to the genetic constitution of an or-ganism, usually in reference to some standard wild type.The guidelines that follow are based on the recommen-dations of Demerec et al. (Genetics 54:61–76, 1966).

(i) Phenotypic designations must be used when mu-tant loci have not been identified or mapped. They canalso be used to identify the protein product of a gene,e.g., the OmpA protein. Phenotypic designations gener-ally consist of three-letter symbols; these are not itali-cized, and the first letter of the symbol is capitalized. Itis preferable to use Roman or Arabic numerals (insteadof letters) to identify a series of related phenotypes.Thus, a series of nucleic acid polymerase mutants mightbe designated Pol1, Pol2, Pol3, etc. Wild-type character-istics can be designated with a superscript plus (Pol�),and, when necessary for clarity, negative superscripts(Pol�) can be used to designate mutant characteristics.Lowercase superscript letters may be used to furtherdelineate phenotypes (e.g., Strr for streptomycin resis-tance). Phenotypic designations should be defined.

(ii) Genotypic designations are also indicated bythree-letter locus symbols. In contrast to phenotypic des-ignations, these are lowercase italic (e.g., ara his rps). Ifseveral loci govern related functions, these are distin-guished by italicized capital letters following the locussymbol (e.g., araA araB araC). Promoter, terminator, andoperator sites should be indicated as described by Bach-mann and Low (Microbiol. Rev. 44:1–56, 1980), e.g.,lacZp, lacAt, and lacZo.

(iii) Wild-type alleles are indicated with a superscriptplus (ara� his�). A superscript minus is not used toindicate a mutant locus; thus, one refers to an ara mu-tant rather than an ara� strain.

(iv) Mutation sites are designated by placing serialisolation numbers (allele numbers) after the locussymbol (e.g., araA1 araA2). If it is not known in whichof several related loci the mutation has occurred, ahyphen is used instead of the capital letter (e.g., ara-23). It is essential in papers reporting the isolation ofnew mutants that allele numbers be given to the mu-tations. For Escherichia coli, there is a registry of suchnumbers: E. coli Genetic Stock Center, Department ofBiology, Yale University, New Haven, CT 06511-5188.For the genus Salmonella, the registry is Salmonella Ge-netic Stock Center, Department of Biology, Universityof Calgary, Calgary, Alberta T2N 1N4, Canada. For thegenus Bacillus, the registry is Bacillus Genetic Stock Cen-ter, Ohio State University, Columbus, OH 43210.

(v) The use of superscripts with genotypes (other than� to indicate wild-type alleles) should be avoided. Des-ignations indicating amber mutations (Am), temperature-sensitive mutations (Ts), constitutive mutations (Con),cold-sensitive mutations (Cs), production of a hybrid pro-tein (Hyb), and other important phenotypic propertiesshould follow the allele number [e.g., araA230(Am)hisD21(Ts)]. All other such designations of phenotypemust be defined at the first occurrence. If superscripts

must be used, they must be approved by the editor anddefined at the first occurrence in the text.

Subscripts may be used in two situations. Subscriptsmay be used to distinguish between genes (having thesame name) from different organisms or strains, e.g.,hisE. coli or hisK-12 for the his genes of E. coli or strainK-12 in another species or strain, respectively. An abbre-viation may also be used if it is explained. Similarly, asubscript is also used to distinguish between genetic ele-ments that have the same name. For example, the pro-moters of the gln operon can be designated glnAp1 andglnAp2. This form departs slightly from that recom-mended by Bachmann and Low (e.g., desC1p).

(vi) Deletions are indicated by the symbol � placedbefore the deleted gene or region, e.g., �trpA432, �(aroP-aceE)419, or �his(dhuA hisJ hisQ)1256. Similarly, othersymbols can be used (with appropriate definition). Thus,a fusion of the ara and lac operons can be shown as�(ara-lac)95. Likewise, �(araB�-lacZ�)96 indicates thatthe fusion results in a truncated araB gene fused to anintact lacZ gene, and �(malE-lacZ)97(Hyb) shows thata hybrid protein is synthesized. An inversion is shown asIN(rrnD- rrnE)1. An insertion of an E. coli his gene intoplasmid pSC101 at zero kilobases (0 kb) is shown aspSC101 (0kb::K-12hisB)4. An alternative designationof an insertion can be used in simple cases, e.g., galT236::Tn5. The number 236 refers to the locus of the inser-tion, and if the strain carries an additional gal mutation,it is listed separately. Additional examples, which utilizea slightly different format, can be found in the papers byCampbell et al. and Novick et al. cited below. It is im-portant in reporting the construction of strains in whicha mobile element was inserted and subsequently deletedthat this fact be noted in the strain table. This can be doneby listing the genotype of the strain used as an interme-diate in a table footnote or by making a direct or paren-thetical remark in the genotype, e.g., (F�), �Mu cts, ormal::�Mu cts::lac. In setting parenthetical remarks withinthe genotype or dividing the genotype into constituentelements, parentheses and brackets are used without spe-cial meaning; brackets are used outside parentheses. To in-dicate the presence of an episome, parentheses (or brack-ets) are used (, F�). Reference to an integrated episomeis indicated as described above for inserted elements, andan exogenote is shown as, for example, W3110/F�8(gal�).

For information about the symbols in current use,consult Berlyn (Microbiol. Mol. Biol. Rev. 62:814–984,1998) for E. coli K-12, Sanderson and Roth (Microbiol.Rev. 52:485–532, 1988) for Salmonella serovar Typhi-murium, Holloway et al. (Microbiol. Rev. 43:73–102, 1979)for the genus Pseudomonas, Piggot and Hoch (Microbiol.Rev. 49:158–179, 1985) for Bacillus subtilis, Perkins et al.(Microbiol. Rev. 46:426–570, 1982) for Neurospora crassa,and Mortimer and Schild (Microbiol. Rev. 49:181–213,1985) for Saccharomyces cerevisiae. For yeasts, Chlamydo-monas spp., and several fungal species, symbols such asthose given in the Handbook of Microbiology, 2nd ed. (A. I.Laskin and H. A. Lechevalier, ed., CRC Press, Inc., Cleve-land, OH, 1988) should be used.


Conventions for naming genes. It is recommendedthat (entirely) new genes be given names that are mne-monics of their function, avoiding names that are alreadyassigned and earlier or alternative gene names, irrespectiveof the bacterium for which such assignments have beenmade. Similarly, it is recommended that, whenever pos-sible, homologous genes present in different organismsreceive the same name. When homology is not apparentor the function of a new gene has not been established,a provisional name may be given by one of the followingmethods. (i) The gene may be named on the basis of itsmap location in the style yaaA, analogous to the styleused for recording transposon insertions (zef) as dis-cussed below. A list of such names in use for E. coli hasbeen published by Rudd (Microbiol. Mol. Biol. Rev. 62:985–1019, 1998). (ii) A provisional name may be given inthe style described by Demerec et al. (e.g., usg, gene up-stream of folC). Such names should be unique, and namessuch as orf or genX should not be used. For reference, theE. coli Genetic Stock Center’s database includes an up-dated listing of E. coli gene names and gene products. It isaccessible on the Internet (http://cgsc.biology.yale.edu/cgsc.html). The Center’s relational database can also besearched via Telnet; for access, send a request to [email protected]. A list can also be found in thework of Riley (Microbiol. Rev. 57:862–952, 1993). For thegenes of other bacteria, consult the references given above.

“Mutant” versus “mutation.” Keep in mind the dis-tinction between a mutation (an alteration of the primarysequence of the genetic material) and a mutant (a straincarrying one or more mutations). One may speak about themapping 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 termsthat describe relationships between genes, consult thearticles by Theissen (Nature 415:741, 2002) and Fitch(Trends Genet. 16:227–231, 2000). “Homology” impliesa relationship between genes that share a common evo-lutionary origin; partial homology is not recognized.When sequence comparisons are discussed, it is moreappropriate to use the term “percent sequence similar-ity” or “percent sequence identity,” as appropriate.

Strain designations. Do not use a genotype as a name(e.g., ‘‘subsequent use of leuC6 for transduction’’). If astrain designation has not been chosen, select an appro-priate word combination (e.g., ‘‘another strain contain-ing the leuC6 mutation’’).

“Natural” versus “artificial” transformation. Naturaltransformation is a process whereby the recipient cellhas the inherent capacity to take up and integrate exog-enous DNA into its genome. As such, natural transfor-mation is part of the biology of the recipient cell line andshould not be confused with processes through whichintegration of DNA is forced upon recipient cells.

Viruses. The genetic nomenclature for viruses dif-fers from that for bacteria. In most instances, viruseshave no phenotype, since they have no metabolismoutside host cells. Therefore, distinctions betweenphenotype and genotype cannot be made. Super-scripts are used to indicate hybrid genomes. Geneticsymbols may be one, two, or three letters. For example, amutant strain of might be designated Aam11 int2red114 cI857; this strain carries mutations in genes cI, int,and red and an amber-suppressible (am) mutation in geneA. A strain designated att434 imm21 would represent ahybrid of phage which carries the immunity region (imm)of phage 21 and the attachment (att) region of phage 434.Host DNA insertions into viruses should be delineated bysquare brackets, and the genetic symbols and designationsfor such inserted DNA should conform to those used forthe host genome. Genetic symbols for phage can befound in reports by Szybalski and Szybalski (Gene 7:217–270, 1979) and Echols and Murialdo (Microbiol. Rev. 42:577–591, 1978).

Eukaryotes. For information about the genetic nomen-clature of eukaryotes, see the Instructions to Authors forEukaryotic Cell and Molecular and Cellular Biology.

Transposable elements, plasmids, and restriction en-zymes. Nomenclature of transposable elements (inser-tion sequences, transposons, phage Mu, etc.) should fol-low the recommendations of Campbell et al. (Gene 5:197–206, 1979), with the modifications given in section viabove. The Internet site where insertion sequences of eu-bacteria and archaea are described and new sequencescan be recorded is http://www-is.biotoul.fr/is.html.

The system of designating transposon insertions at siteswhere there are no known loci, e.g., zef-123::Tn5, has beendescribed by Chumley et al. (Genetics 91:639–655, 1979).The nomenclature recommendations of Novick et al. (Bac-teriol. 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 AcidsRes. 31:1805–1812, 2003) for restriction enzymes, DNAmethyltransferases, homing endonucleases, and their genesshould be used when possible. The nomenclature for re-combinant DNA molecules constructed in vitro follows thenomenclature for insertions in general. DNA inserted intorecombinant DNA molecules should be described by usingthe gene symbols and conventions for the organism fromwhich the DNA was obtained.

Tetracycline resistance determinants. The nomencla-ture for tetracycline resistance determinants is based onthe proposal of Levy et al. (Antimicrob. Agents Chemo-ther. 43:1523–1524, 1999). The style for such determinantsis, e.g., Tet B; the space helps distinguish the determi-nant designation from that for phenotypes and proteins(TetB). The above-referenced article shows the correctformat for genes, proteins, and determinants in thisfamily.


ABBREVIATIONS AND CONVENTIONS

Verb Tense

ASM strongly recommends that for clarity you use thepast tense to narrate particular events in the past, in-cluding the procedures, observations, and data of thestudy that you are reporting. Use the present tense foryour own general conclusions, the conclusions of previ-ous researchers, and generally accepted facts. Thus, mostof the abstract, Materials and Methods, and Results willbe in the past tense, and most of the introduction andsome of the Discussion will be in the present tense.

Be aware that it may be necessary to vary the tense ina single sentence. For example, it is correct to say ‘‘White(30) demonstrated that XYZ cells grow at pH 6.8,’’ ‘‘Fig-ure 2 shows that ABC cells failed to grow at room tem-perature,’’ and ‘‘Air was removed from the chamberand the mice died, which proves that mice require air.’’In reporting statistics and calculations, it is correct tosay ‘‘The values for the ABC cells are statisticallysignificant, indicating that the drug inhibited. . . .’’

For an in-depth discussion of tense in scientific writ-ing, see p. 191–193 in How To Write and Publish a Sci-entific Paper, 6th ed.

Abbreviations

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

It is often possible to use pronouns or to paraphrase along word after its first use (e.g., ‘‘the drug’’ or ‘‘the sub-strate’’). Standard chemical symbols and trivial names ortheir symbols (folate, Ala, Leu, etc.) may also be used.

It is strongly recommended that all abbreviations ex-cept those listed below be introduced in the first para-graph in Materials and Methods. Alternatively, defineeach abbreviation and introduce it in parentheses thefirst time it is used; e.g., ‘‘cultures were grown in Eagleminimal essential medium (MEM).’’ Generally, elimi-nate abbreviations that are not used at least three times inthe text (including tables and figure legends).

Not requiring introduction. In addition to abbrevia-tions for Systeme International d’Unites (SI) units of mea-surement, other common units (e.g., bp, kb, and Da), andchemical symbols for the elements, the following should beused without definition in the title, abstract, text, figurelegends, 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 triphospha-tase, 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 dinucleotidephosphate, oxidized); poly(A), poly(dT), etc. (polyadenylicacid, polydeoxythymidylic acid, etc.); oligo(dT), etc. (oli-godeoxythymidylic acid, etc.); UV (ultraviolet); PFU(plaque-forming units); CFU (colony-forming units); MIC(minimal inhibitory concentration); Tris [tris(hydroxy-methyl)aminomethane]; DEAE (diethylaminoethyl);EDTA (ethylenediaminetetraacetic acid); EGTA [ethyl-ene glycol-bis(�-aminoethyl ether)-N,N,N�,N�-tetraaceticacid]; HEPES (N-2-hydroxyethylpiperazine-N�-2-ethane-sulfonic acid); PCR (polymerase chain reaction); andAIDS (acquired immunodeficiency syndrome). Abbrevia-tions for cell lines (e.g., HeLa) also need not be defined.

The following abbreviations should be used withoutdefinition in tables:

amt (amount) SE (standard error)approx (approximately) SEM (standard error of theavg (average) mean)concn (concentration) sp act (specific activity)diam (diameter) sp gr (specific gravity)expt (experiment) temp (temperature)exptl (experimental) tr (trace)ht (height) vol (volume)mo (month) vs (versus)mol wt (molecular weight) wk (week)no. (number) wt (weight)prepn (preparation) yr (year)SD (standard deviation)

Reporting Numerical Data

Standard metric units are used for reporting length,weight, and volume. For these units and for molarity, usethe prefixes m, �, n, and p for 10�3, 10�6, 10�9, and10�12, respectively. Likewise, use the prefix k for 103.Avoid compound prefixes such as m� or ��. Parts permillion (ppm) may be used when that is the commonmeasure for the science in that field. Units of tempera-ture are presented as follows: 37°C or 324 K.

When fractions are used to express such units as en-zymatic activities, it is preferable to use whole units, suchas g or min, in the denominator instead of fractional ormultiple units, such as �g or 10 min. For example,‘‘pmol/min’’ is preferable to ‘‘nmol/10 min,’’ and ‘‘�mol/g’’ is preferable to ‘‘nmol/�g.’’ It is also preferable thatan unambiguous form, such as exponential notation, beused; for example, ‘‘�mol g�1 min�1’’ is preferable to‘‘�mol/g/min.’’ Always report numerical data in the ap-plicable SI units.

Representation of data as accurate to more than twosignificant figures must be justified by presentation ofappropriate statistical analyses.

For a review of some common errors associated withstatistical analyses and reports, plus guidelines on how to


avoid them, see the article by Olsen (Infect. Immun.71:6689–6692, 2003).

For a review of basic statistical considerations for vi-rology experiments, see the article by Richardson andOverbaugh (J. Virol. 79:669–676, 2005).

Statistics

If biological variation within a treatment (coefficientof variation, the standard deviation divided by the mean)is small (less than 10%) and the difference among treat-ment means is large (greater than 3 standard devia-tions), it is not necessary to report statistics. If the datado not meet these criteria, however, the authors mustinclude an appropriate statistical analysis (e.g., Student’st test, analysis of variance, Tukey’s test, etc.). Statisticsshould represent the variation among biological units(e.g., replicate incubations) and not just the variationdue to method of analysis.

Phylogenetic trees based on nucleotide or amino acidsequence alignments must be supported by appropriatestatistical analyses of tree stability (e.g., bootstrap anal-ysis), and nonsupported branches (e.g., bootstrap coef-ficients below 50%) should be collapsed. A copy of thealignment should be available for examination by theeditor or the reviewers upon request.

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

For a review of basic statistical considerations for vi-rology experiments, see the article by Richardson andOverbaugh (J. Virol. 79:669–676, 2005).

EquationsIn mathematical equations, indicate the order of op-

erations clearly by enclosing operations in parentheses,brackets, and braces, in that order: (a � b) � c or a �(b � c), 100 � {[(a/b) � c] � d} or 100 � {a/[(b � c) �d]}. Italicize (or underline) variables and constants (butnot numerals), and use roman type for designations: E0,Eh, Mr, Km, Ks, a � 2b � 1.2 mM, Ca2� Vmax � exp(1.5x� y), BOD � 2.7x2.

Isotopically Labeled Compounds

For simple molecules, isotopic labeling is indicated inthe chemical formula (e.g., 14CO2, 3H2, and H35SO4).Brackets are not used when the isotopic symbol isattached to the name of a compound that in its natu-ral state does not contain the element (e.g., 32S-ATP) or toa word that is not a specific chemical name (e.g., 131I-labeled protein, 14C-amino acids, and 3H-ligands).

For specific chemicals, the symbol for the isotope intro-duced is placed in brackets directly preceding the part ofthe name that describes the labeled entity. Note that con-figuration symbols and modifiers precede the isotopic sym-bol. The following examples illustrate correct usage.

[14C]urea UDP-[U-14C]glucoseL-[methyl-14C]methionine E. coli [32P]DNA[2,3-3H]serine fructose 1,6-[1-32P]bisphos-[�-14C]lysine phate[ -32P]ATP

AEM follows the same conventions for isotopic label-ing as the Journal of Biological Chemistry, and more-detailed information can be found in the instructions toauthors of that journal (first issue of each year).
