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Applied and Environmental Microbiology, January 2008, p. 1-22, Vol. 74,
No. 1
0099-2240/08/$08.00+0     doi:10.1128/AEM.02454-07
Copyright © 2008 </misc/terms.shtml>, American Society for Microbiology
<http://www.asm.org>. All Rights Reserved.

*INSTRUCTIONS TO AUTHORS*


    APPLIED AND ENVIRONMENTAL MICROBIOLOGY


      2008 INSTRUCTIONS TO AUTHORS^* <#FN1>

    *SCOPE <#SCOPE>*
    *EDITORIAL POLICY <#EDITORIAL_POLICY>*
    *    Use of Microbiological Information
    <#Use_of_Microbiological_Information>*
    *    General Requirements <#General_Requirements>*
    *    Primary Publication <#Primary_Publication>*
    *    Permissions <#Permissions>*
    *    Authorship <#Authorship>*
    *    Conflict of Interest <#Conflict_of_Interest>*
    *    Copyright <#Copyright>*
    *    Funding Agency Repositories <#Funding_Agency_Repositories>*
    *    Use of Human Subjects or Animals in Research
    <#Use_of_Human_Subjects_or_Animals_in_Research>*
    *    Nucleotide and Amino Acid Sequences
    <#Nucleotide_and_Amino_Acid_Sequences>*
    *    Structural Determinations <#Structural_Determinations>*
    *    Microarray Data <#Microarray_Data>*
    *    Culture Deposition <#Culture_Deposition>*
    *    Supplemental Material <#Supplemental_Material>*
    *    Compliance <#Compliance>*
    *    Warranties and Exclusions <#Warranties_and_Exclusions>*
    *    Page Charges <#Page_Charges>*
    *    Editorial Style <#Editorial_Style>*
    *    Review Process <#Review_Process>*
    *    Notification of Acceptance <#Notification_of_Acceptance>*
    *    Publish ahead of Print <#Publish_ahead_of_Print>*
    *    Page Proofs <#Page_Proofs>*
    *    Reprints <#Reprints>*
    *    PDF Files <#PDF_Files>*
    *HOW TO SUBMIT MANUSCRIPTS <#HOW_TO_SUBMIT_MANUSCRIPTS>*
    *ORGANIZATION AND FORMAT <#ORGANIZATION_AND_FORMAT>*
    *    Manuscript Submission Checklist:
    <#Manuscript_Submission_Checklist:>*
    *    Long-Form Papers <#Long-Form_Papers>*
    *        Title, running title, and byline.
    <#Title,_running_title,_and_byline.>*
    *        Study group in byline. <#Study_group_in_byline.>*
    *        Correspondent footnote. <#Correspondent_footnote.>*
    *        Abstract. <#Abstract.>*
    *        Introduction. <#Introduction.>*
    *        Materials and Methods. <#Materials_and_Methods.>*
    *        Results. <#Results.>*
    *        Discussion. <#Discussion.>*
    *        Acknowledgments. <#Acknowledgments.>*
    *        Appendixes. <#Appendixes.>*
    *        References. <#References.>*
    *            (i) References listed in the References section.
    <#(i)_References_listed_in_the_References_section.>*
    *            (ii) References cited in the text.
    <#(ii)_References_cited_in_the_text.>*
    *            (iii) References related to supplemental material.
    <#(iii)_References_related_to_supplemental_material.>*
    *            (iv) Referencing publish-ahead-of-print manuscripts.
    <#(iv)_Referencing_publish-ahead-of-print_manuscripts.>*
    *    Short-Form Papers <#Short-Form_Papers>*
    *    Minireviews <#Minireviews>*
    *    Meeting Reviews <#Meeting_Reviews>*
    *    Guest Commentaries <#Guest_Commentaries>*
    *    Letters to the Editor <#Letters_to_the_Editor>*
    *    Errata <#Errata>*
    *    Authors' Corrections <#Authors'_Corrections>*
    *    Retractions <#Retractions>*
    *ILLUSTRATIONS AND TABLES <#ILLUSTRATIONS_AND_TABLES>*
    *    Image Manipulation <#Image_Manipulation>*
    *    Illustrations <#Illustrations>*
    *        Minimum resolution. <#Minimum_resolution.>*
    *        Size. <#Size.>*
    *        Contrast. <#Contrast.>*
    *        Labeling and assembly. <#Labeling_and_assembly.>*
    *        Fonts. <#Fonts.>*
    *        Compression. <#Compression.>*
    *        Color illustrations. <#Color_illustrations.>*
    *    Drawings <#Drawings>*
    *    Presentation of Nucleic Acid Sequences
    <#Presentation_of_Nucleic_Acid_Sequences>*
    *    Figure Legends <#Figure_Legends>*
    *    Tables <#Tables>*
    *    Cover Photographs and Drawings <#Cover_Photographs_and_Drawings>*
    *NOMENCLATURE <#NOMENCLATURE>*
    *    Chemical and Biochemical Nomenclature
    <#Chemical_and_Biochemical_Nomenclature>*
    *    Nomenclature of Microorganisms <#Nomenclature_of_Microorganisms>*
    *    Genetic Nomenclature <#Genetic_Nomenclature>*
    *        Bacteria. <#Bacteria.>*
    *        Conventions for naming genes. <#Conventions_for_naming_genes.>*
    *        Locus tags. <#Locus_tags.>*
    *        ''Mutant'' versus ''mutation.''
    <#''Mutant''_versus_''mutation.''>*
    *        ''Homology'' versus ''similarity.''
    <#''Homology''_versus_''similarity.''>*
    *        Strain designations. <#Strain_designations.>*
    *        ''Natural'' versus ''artificial'' transformation.
    <#''Natural''_versus_''artificial''_transformation.>*
    *        Viruses. <#Viruses.>*
    *        Eukaryotes. <#Eukaryotes.>*
    *        Transposable elements, plasmids, and restriction enzymes.
    <#Transposable_elements,_plasmids,_and_restriction_enzymes.>*
    *        Tetracycline resistance determinants.
    <#Tetracycline_resistance_determinants.>*
    *ABBREVIATIONS AND CONVENTIONS <#ABBREVIATIONS_AND_CONVENTIONS>*
    *    Verb Tense <#Verb_Tense>*
    *    Abbreviations <#Abbreviations>*
    *        General. <#General.>*
    *        Not requiring introduction. <#Not_requiring_introduction.>*
    *    Reporting Numerical Data <#Reporting_Numerical_Data>*
    *    Statistics <#Statistics>*
    *    Equations <#Equations>*
    *    Isotopically Labeled Compounds <#Isotopically_Labeled_Compounds>*


	   SCOPE

Top
<#top> SCOPE
EDITORIAL POLICY
<#EDITORIAL_POLICY> HOW TO SUBMIT MANUSCRIPTS
<#HOW_TO_SUBMIT_MANUSCRIPTS> ORGANIZATION AND FORMAT
<#ORGANIZATION_AND_FORMAT> ILLUSTRATIONS AND TABLES
<#ILLUSTRATIONS_AND_TABLES> NOMENCLATURE
<#NOMENCLATURE> ABBREVIATIONS AND CONVENTIONS
<#ABBREVIATIONS_AND_CONVENTIONS>

 
/Applied and Environmental Microbiology/ (AEM) publishes descriptions^
of all aspects of applied microbial research, basic research^ on
microbial ecology, and research of a genetic and molecular^ nature that
focuses on microbial topics of practical value.^ Research must address
salient microbiological principles, fundamental^ microbial processes, or
basic questions in applied or environmental^ microbiology. Topics that
are considered include microbiology^ in relation to foods, agriculture,
industry, biotechnology,^ public health, plants, and invertebrates and
basic biological^ properties of bacteria, fungi, algae, protozoa, and
other simple^ eukaryotic organisms as related to microbial ecology.
Manuscripts^ should report new and significant findings that advance
the^ understanding of microbiology and upon which other scientists^ may
build.^

The *microbial ecology* section covers a wide range of topics^ on the
ecology of microorganisms, including culture-independent^ molecular
assessments that provide new insights into (i) the^ structure-function
relationships of microorganisms, (ii) the^ impact of in situ conditions
on community structure, and (iii)^ the effect of changes in microbial
community composition on^ ecosystem function. Archival phylogenetic
snapshots that do^ not provide such insights are not acceptable for
publication^ in AEM.^

The *plant microbiology* section covers manuscripts dealing with^ all
aspects of plant-microorganism interactions, including symbiotic^ and
rhizosphere bacteria and phytopathogenic microorganisms.^

New microbiological *methods* must provide novel avenues to address^
fundamental biological questions and will be considered for^ publication
in AEM when accompanied by a demonstrated application.^ Descriptions of
the application of previously described technologies,^ including the
cloning, amplification, and expression of "foreign"^ genes, to a new
genus or species of microbe will generally not^ be considered for
independent publication. Manuscripts that^ describe the construction of
engineered strains for innovative^ process application, development, or
enhancement must present^ results to authenticate the utility,
superiority, and uniqueness^ of such strains.^

Manuscripts submitted to the *mycology* section should be clearly^ of a
microbiological nature and may deal with basic biology,^ biochemistry,
genetics, or physiology of fungi, molds, yeasts,^ or algae. Papers
dealing purely with taxonomy or phylogeny,^ with fungal or algal
structure, or with metabolism/alteration^ of metabolites/toxins by
animal, plant, or insect cells, tissues,^ or organisms are not suitable.
Documentation of the distribution/occurrence^ of toxins or metabolites
in natural samples (foods, cereals,^ grains, soils, etc.) is suitable if
the work includes studies^ involving the isolation, occurrence, or
enumeration of the responsible^ microbes in these samples. The chemical
or biochemical elucidation^ of metabolite or toxin structures is
suitable if the work includes^ aspects of the enzymology or biosynthesis
of these compounds.^

*Invertebrate microbiology* manuscripts should address interactions^
between invertebrates and microorganisms, ranging from commensalism^ and
mutualism to parasitism and pathogenicity. Manuscripts describing^ work
dealing with the metabolites or toxins from animal, plant,^ or insect
cells or the physiology of such cells are not suitable^ for AEM unless
it affects a microbial community or individual^ microorganisms.^

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

(i) AEM will consider manuscripts describing properties of enzymes^ and
proteins that are produced by either wild-type or genetically^
engineered microorganisms and that are significant or have potential^
significance in industrial or environmental settings. Studies^ dealing
with basic biological phenomena of enzymes or proteins^ or in which
enzymes have been used in investigations of basic^ biological functions
are more appropriate for the /Journal of^ Bacteriology/.^

(ii) AEM will consider papers which describe the use of antimicrobial^
agents as tools for elucidating aspects of applied and environmental^
microbiology. Other papers dealing with antimicrobial agents,^ including
manuscripts dealing with the biosynthesis and metabolism^ of such
agents, are more appropriate for /Antimicrobial Agents^ and Chemotherapy/.^

(iii) Papers on the biology of bacteriophages and other viruses^ are
more appropriate for the /Journal of Virology/ or the /Journal^ of
Bacteriology/. AEM does, however, consider manuscripts dealing^ with
viruses in relation to environmental, public health, or^ industrial
microbiology.^

(iv) Manuscripts dealing with the immune system or with topics^ of basic
medical interest or oral microbiology are more appropriate^ for
/Infection and Immunity/. Reports of clinical investigations^ and
environmental biology applied to hospitals should be submitted^ to the
/Journal of Clinical Microbiology/.^

(v) AEM and /Eukaryotic Cell/ (EC) accept manuscripts on population^
dynamics and the ecology of eukaryotic microbes. Studies of^ microbial
communities and of microbial populations with identified^ economic or
ecological significance, e.g., plant pathogens or^ symbionts, are
usually more appropriate for AEM. Studies of^ single species of
eukaryotes, especially "model" organisms or^ those without identified
economic or ecological importance,^ are usually more appropriate for EC.^

(vi) Manuscripts dealing with the purification and characterization^ of
enzymes or cloning of genes that have already been extensively^
described for other organisms will be considered for publication^ only
if they offer experimentally supported new insights into^ the biological
role, properties, or applications of these enzymes.^ Descriptions of
genes or enzymes that differ only in minor ways^ from the prototypes are
not suitable for AEM.^

To best serve its readership, the journal must accept only those^ papers
that are most significant to the field of applied and^ environmental
microbiology. Thus, the editors will reject manuscripts^ that, while
scientifically sound, represent only incremental^ extensions of other
studies, are mainly confirmatory, or do^ not pursue a question in
sufficient depth.^

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

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

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


	   EDITORIAL POLICY

Top
<#top> SCOPE
<#SCOPE> EDITORIAL POLICY
HOW TO SUBMIT MANUSCRIPTS
<#HOW_TO_SUBMIT_MANUSCRIPTS> ORGANIZATION AND FORMAT
<#ORGANIZATION_AND_FORMAT> ILLUSTRATIONS AND TABLES
<#ILLUSTRATIONS_AND_TABLES> NOMENCLATURE
<#NOMENCLATURE> ABBREVIATIONS AND CONVENTIONS
<#ABBREVIATIONS_AND_CONVENTIONS>

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

ASM recognizes that there are valid concerns regarding the publication^
of information in scientific journals that could be put to
inappropriate^ use as described in the CPC resolution mentioned above.
Members^ of the ASM Publications Board will evaluate the rare
manuscript^ that might raise such issues during the review process.
However,^ as indicated elsewhere in these Instructions, research
articles^ must contain sufficient detail, and material/information must^
be made available, to permit the work to be repeated by others.^ Supply
of materials should be in accordance with laws and regulations^
governing the shipment, transfer, possession, and use of biological^
materials and must be for legitimate, bona fide research needs.^ Links
to, and information regarding, these laws and regulations^ can be found
at http://www.asm.org/Policy/index.asp.^

*General Requirements*
Manuscripts submitted to the journal must represent reports^ of original
research, and the /original data must be available^ for review by the
editor/ if necessary. When preparing a manuscript,^ authors are
encouraged to pay attention to guidelines for reviewers^
(http://aem.asm.org/misc/reviewguide.shtml).^

*All authors of a manuscript must have agreed to its submission^ and are
responsible for its content* (initial submission and^ any subsequent
versions), including appropriate citations and^ acknowledgments, and
must also have agreed that the corresponding^ author has the authority
to act on their behalf in all matters^ pertaining to publication of the
manuscript. The corresponding^ author is responsible for obtaining such
agreements and for^ informing the coauthors of the manuscript's status
throughout^ the submission, review, and publication process. For
Authors?^ Corrections and Retractions, signed letters of agreement from^
all of the authors must be submitted (see p. 13).^

By submission of a manuscript to the journal, *the authors guarantee^
that they have the authority to publish the work and that the^
manuscript, or one with substantially the same content, was^ not
published previously, is not being considered or published^ elsewhere,
and was not rejected on scientific grounds by another^ ASM journal*.^

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

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

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

*Primary Publication*
A scientific paper /or its substance/ published in a serial,
periodical,^ book, conference report, symposium proceeding, or
technical^ bulletin, posted on a nonpersonal website, or made available^
through any other retrievable source, including CD-ROM and other^
electronic forms, is unacceptable for submission to an ASM journal^ on
grounds of prior publication. Work, or its substance, presented^ as a
meeting poster and subsequently reproduced or distributed^ as a "company
white paper" is also unacceptable for submission^ on grounds of prior
publication.^

Posting of a method/protocol on a nonpersonal website should^ not
interfere with the author's ability to have a manuscript^ utilizing that
technique considered for publication in an ASM^ journal; however,
ultimately, it is an editorial decision whether^ the method constitutes
the substance of a paper.^

Posting of a limited amount of original data on a
personal/university/company^ website or websites of small collaborative
groups working on^ a problem does not preclude subsequent submission to,
and publication^ by, an ASM journal. The posted data, however, may not
constitute^ the substance of the submission. Specific questions about
this^ policy may be referred to the Publications Board chairman on^ a
case-by-case basis.^

Posting of theses and dissertations on a personal/university-hosted^
website does not preclude subsequent submission to, and publication^ by,
an ASM journal. Similarly, posting for sale on a commercial^ or similar
website of an /original, unmodified/ thesis or dissertation^ (i.e., as
submitted to, and accepted by, the thesis/dissertation^ committee) does
not preclude subsequent submission to, and publication^ by, an ASM
journal.^

Posting of unpublished sequence data on the Internet is usually^ not
considered prior publication; however, the address (URL)^ of the source
of the sequence should be included in the text.^

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

It is incumbent upon the author to acknowledge any prior publication,^
including his own articles, of the data contained in a manuscript^
submitted to an ASM journal. A copy of the relevant work should^ be
submitted with the paper as supplemental material.^

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

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

The original *signed* permission(s) must be submitted directly^ to the
editor, outside the Rapid Review system, no later than^ the modification
stage and should be identified as to the relevant^ item in the ASM
manuscript (e.g., "permissions for Fig. 1 in^ AEM00123-08"). In
addition, a statement indicating that the^ material is being reprinted
with permission must be included^ in the relevant figure legend or table
footnote of the manuscript.^ Reprinted text must be enclosed in
quotation marks, and the^ permission statement must be included as
running text or indicated^ parenthetically.^

For supplemental material intended for posting by ASM (see p.^ 5), if
the authors of the AEM manuscript are not also the owners^ of the
supplemental material, the corresponding author *must*^ send to ASM
*signed* permission from the copyright owner that^ allows posting of the
material, as a supplement to the article,^ by ASM. The corresponding
author is also responsible for incorporating^ in the supplemental
material any copyright notices required^ by the owner.^

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

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

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

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

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

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

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

*Copyright*
To maintain and protect the Society's ownership and rights and^ to
continue to afford scientists the opportunityto publish in^ high-quality
journals, ASM requires the corresponding author^ to sign a copyright
transfer agreement on behalf of all the^ authors. This agreement is sent
to the corresponding author^ when the manuscript is accepted and
scheduled for publication.^ Unless this agreement is executed (/without
changes and/or addenda/),^ ASM will not publish the article.^

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

Authors may post their own published articles on their /personal^ or
university-hosted/ (but not corporate, government, or similar)^ websites
without ASM's prior written permission provided that^ appropriate credit
is given (i.e., either the copyright lines^ shown on the top of the
first page of the PDF version or "Copyright^ © American Society for
Microbiology, [insert journal name,^ volume number, page numbers, and
year]" for the HTML version).^

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

Copyright for supplemental material (see p. 5) remains with^ the author,
but a license permitting the posting by ASM will^ be sent, along with
the article copyright transfer agreement,^ to the corresponding author
for signing at the acceptance stage.^ (If the author of the article is
not also the copyright owner^ of the supplemental material, the
corresponding author *must*^ send to ASM *signed* permission from the
owner that allows posting^ of the material, as a supplement to the
article, by ASM. The^ corresponding author is also responsible for
incorporating into^ the supplemental material any copyright notices
required by^ the owner.)^

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

*Funding Agency Repositories*
The National Institutes of Health (NIH) requests that its grantee^ and
intramural authors provide copies of their accepted manuscripts^ to
PubMed Central (PMC) for posting in the PMC Public Access^ Repository.
ASM allows such AEM authors to do so. ASM also allows^ AEM authors whose
work was supported by similar funding agencies^ that have public access
requirements like those of the NIH (e.g.,^ the Wellcome Trust) to post
their *accepted manuscripts* in publicly^ accessible electronic
repositories maintained by those funding^ agencies. If a funding agency
does not itself maintain such^ a site, then ASM allows the author to
fulfill that requirement^ by depositing the manuscript (*not* the
typeset article) in an^ appropriate institutional or subject-based open
repository established^ by a government or noncommercial entity.^

Since ASM makes the final, typeset articles from its primary-research^
journals available free of charge on the ASM Journals and PMC^ websites
4 months after final publication, ASM recommends that^ when submitting
the accepted manuscript to PMC or a similar^ public access site, the
author specify that the *posting release^ date for the manuscript be no
earlier than 4 months after publication^ of the typeset article by ASM.*^

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

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

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

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

Analyses should specify the database, and the date of each analysis^
should be indicated as, e.g., January 2008. If relevant, the^ version of
the software used should be specified.^

See p. 16 for nucleic acid sequence formatting instructions.^

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

*Structural Determinations*
It is expected that coordinates for new structures of macromolecules^
will be deposited in the Protein Data Bank and that assigned^
identification codes will be included in the manuscript no later^ than
the modification stage of the review process. It is also^ expected that
the coordinates will be released to the public^ no later than the
publication (online posting) date of the accepted^ manuscript. Authors
are encouraged to send coordinates with^ their original submission,
however, so that reviewers can examine^ them along with the manuscript.
The accession number(s) should^ be listed in a separate paragraph at the
end of the Materials^ and Methods section for full-length papers or at
the end of^ 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 microarray^ data will
be deposited in the appropriate public database (e.g.,^ GEO,
ArrayExpress, or CIBEX) and that the assigned accession^ number(s) will
be included in the manuscript no later than the^ modification stage of
the review process. It is also expected^ that the data will be released
to the public no later than the^ publication (online posting) date of
the accepted manuscript.^ Authors are encouraged to send the relevant
data with their^ original submission, however, so that reviewers can
examine^ them along with the manuscript. The accession number(s) should^
be listed in a separate paragraph at the end of the Materials^ and
Methods section for full-length papers or at the end of^ the text for
short-form papers.^

The URLs of the databases mentioned above are as follows: Gene^
Expression Omnibus (GEO), http://www.ncbi.nlm.nih.gov/projects/geo/;^
ArrayExpress, http://www.ebi.ac.uk/arrayexpress/?#ae=main[0];^ and
Center for Information Biology Gene Expression Database^ (CIBEX),
http://cibex.nig.ac.jp/index.jsp.^

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

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

Supplemental material intended for posting by ASM must be uploaded^ in
Rapid Review and will be reviewed along with the manuscript.^ The
maximum size permitted for an individual file is 25 MB.^ If your file
exceeds this size, you must use a file compression^ utility (e.g.,
WinZip or Stuffit) to reduce the size below 25^ MB. The decision to
publish (i.e., post online only) the material^ with the article if it is
accepted will be made by the editor^ and conveyed to the corresponding
author in the acceptance e-mail.^ Therefore, it is possible that a
manuscript will be accepted^ but that the supplemental material will not.^

If the software required for users to view/use the supplemental^
material is not embedded in the file, you are urged to use shareware^ or
generally available/easily accessible programs.^

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

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

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

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

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

*Compliance*
Failure to comply with the policies described in these Instructions^ may
result in a letter of reprimand, a suspension of publishing^ privileges
in ASM journals, and/or notification of the authors?^ institutions.^

Authors employed by companies whose policies do not permit them^ to
comply with the ASM policies may be sanctioned as individuals^ and/or
ASM may refuse to consider manuscripts having authors^ from such
companies.^

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

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

For a *corresponding author who is an ASM member*, page charges^ are
currently $65 per page for the first eight pages and $200^ per page for
each page in excess of eight (subject to change^ without notice). To
obtain the member rate, the /corresponding^ author/ must be an ASM member.^

For a *nonmember corresponding author*, page charges are currently^ $75
per page for the first eight pages and $250 for each page^ in excess of
eight (subject to change without notice). A corresponding^ author who is
not an ASM member may join ASM to obtain the member^ rate.^

If the research was not supported by any of the means described^ above,
a request to waive the charges may be mailed (Journals^ Department, ASM,
1752 N St., N.W., Washington, DC 20036-2904,^ USA) or faxed
(202-942-9355) to the Journals Department. This^ request must indicate
how the work was supported and should^ be accompanied by copies of the
title page and Acknowledgments^ section.^

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

*Editorial Style*
The editorial style of ASM journals conforms to the /ASM Style^ Manual
for Journals/ (American Society for Microbiology, 2008,^ in-house
document) and /How To Write and Publish a Scientific^ Paper/, 6th ed.
(Greenwood Press, Westport, CT, 2006), as interpreted^ and modified by
the editors and the ASM Journals Department.^

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

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

To expedite the review process, authors *must* recommend at least^ three
reviewers who have expertise in the field, who are not^ members of their
institution(s), who have not recently been^ associated with their
laboratory(ies), and who could not otherwise^ be considered to pose a
conflict of interest regarding the submitted^ manuscript. Please
provide, where indicated on the submission^ form, contact information
for suggested reviewers who are not^ editorial board members.^

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

When a manuscript is submitted to the journal, it is given a^ number
(e.g., AEM00047-08 version 1) and assigned to one of^ the editors.
*(Always refer to this number in communications^ with the editor and the
Journals Department.)* /It is the responsibility^ of the corresponding
author to inform the coauthors of the manuscript's^ status throughout
the submission, review, and publication processes/.^ The reviewers
operate under strict guidelines set forth in "Guidelines^ for Reviewers"
(http://www.journals.asm.org/misc/reviewguide.shtml)^ and are expected
to complete their reviews expeditiously.^

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

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

For *all* resubmissions (to the same or a different journal, and^
irrespective of the extent of the revisions and irrespective^ of the
amount of time between rejection and resubmission), the^ cover letter
*must* state that the manuscript is a resubmission,^ and the former
manuscript number *must* be provided in the appropriate^ field on the
submission form. A point-by-point response to the^ review(s) and a
compare copy of the revised manuscript showing^ all changes *must* be
included as supplemental material (the Rebuttal^ section appears in the
submission form only if the manuscript^ is a modification). Manuscripts
resubmitted to the same journal^ are normally handled by the original
editor.^

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

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

The text files undergo an automated preediting, cleanup, and^ tagging
process specific to the particular article type, and^ the illustrations
are examined. If all files have been prepared^ according to the criteria
set forth in these Instructions and^ those in Rapid Review, the
acceptance procedure will be completed^ successfully. If there are
problems that would cause extensive^ corrections to be made at the
copyediting stage or if the files^ are not acceptable for production,
ASM Journals staff will contact^ the corresponding author. Once all the
material intended for^ publication has been determined to be adequate,
the manuscript^ is scheduled for the next available issue and an
acceptance^ letter indicating the month of publication, approximate
page^ proof dates, and table of contents section is mailed to the^
corresponding author; a copyright transfer agreement is also^ included,
as is a license to permit posting of supplemental^ material (if
applicable). The editorial staff of the ASM Journals^ Department
completes the editing of the manuscript to bring^ it into conformity
with prescribed standards.^

*Publish ahead of Print*
For its primary-research journals, ASM posts online PDF versions^ of
manuscripts that have been peer reviewed and accepted but^ not yet
copyedited. This feature is called "[journal acronym]^ Accepts" (e.g.,
AEM Accepts) and is accessible from the Journals^ website. The
manuscripts are published online as soon as possible^ after acceptance,
on a weekly basis, before the copy- edited,^ typeset articles are
published. They are posted "*as is*" (i.e.,^ as submitted by the authors
at the modification stage) and do^ not reflect ASM editorial changes.
*No corrections/changes to^ the PDF manuscripts are accepted*.
Accordingly, there likely^ will be differences between the AEM Accepts
manuscripts and^ the final, typeset articles. The manuscripts remain
listed on^ the AEM Accepts page until the final, typeset articles are
posted.^ At that point, the manuscripts are removed from the AEM
Accepts^ page and become available only through links from the final,^
typeset articles. The manuscripts are under subscription access^ control
until 4 months after the typeset articles are posted,^ when free access
is provided to everyone (subject to the applicable^ ASM license terms
and conditions). Supplemental material intended,^ and accepted, for
publication is not posted until publication^ of the final, typeset
article.^

Instructions on how to cite such manuscripts may be found in^ the
"References" section below (p. 10).^

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

The proof stage is not the time to make extensive corrections,^
additions, or deletions. Important new information that has^ become
available between acceptance of the manuscript and receipt^ of the
proofs may be inserted as an addendum in proof with the^ permission of
the editor. If references to unpublished data^ or personal
communications are added, it is expected that written^ assurance
granting permission for the citation will be included.^ Limit changes to
correction of spelling errors, incorrect data,^ and grammatical errors
and updated information for references^ to articles that have been
submitted or are in press. If URLs^ have been provided in the article,
recheck the sites to ensure^ that the addresses are still accurate and
the material that^ you expect the reader to find is indeed there.^

Questions about /late proofs and problems in the proofs/ should^ be
directed to the ASM Journals Department (telephone, 202-942-9219).^
Questions about /accessing or viewing your PDF proofs/ should^ be
directed to Katie Gay of Cadmus Communications at 804-261-3155^ or
gayk@cadmus.com <mailto:gayk@cadmus.com>.^

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

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

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

Should coauthors or colleagues be interested in viewing the^ paper for
their own use, the corresponding author may provide^ them with the URL;
a copy of the article may not be forwarded^ electronically. However,
they must be made aware of the terms^ and conditions of the ASM
copyright. (For details, go to
http://www.journals.asm.org/misc/terms.shtml.)^ Note that each such
download will count toward the corresponding^ author's total of 10.
After 10 downloads, access will be denied^ and can be obtained only
through a subscription to the journal^ (either individual or
institutional) or after the standard access^ control has been lifted
(i.e., 4 months after publication).^


	   HOW TO SUBMIT MANUSCRIPTS

Top
<#top> SCOPE
<#SCOPE> EDITORIAL POLICY
<#EDITORIAL_POLICY> HOW TO SUBMIT MANUSCRIPTS
ORGANIZATION AND FORMAT
<#ORGANIZATION_AND_FORMAT> ILLUSTRATIONS AND TABLES
<#ILLUSTRATIONS_AND_TABLES> NOMENCLATURE
<#NOMENCLATURE> ABBREVIATIONS AND CONVENTIONS
<#ABBREVIATIONS_AND_CONVENTIONS>

 
All submissions to AEM must be made electronically via the Rapid^ Review
online submission and peer review system at the following^ URL:
https://www.rapidreview.com/ASM2/CALogon.jsp. (E-mailed^ submissions
will not be accepted.) First-time users must create^ an Author account,
which may be used for submitting to all ASM^ journals. Instructions for
creating an Author account are available^ at the above URL under the
Create Account button. Step-by-step^ instructions for submitting a
manuscript via Rapid Review are^ available from the account holder's My
Manuscripts page. Information^ on file types acceptable for electronic
submission can be found^ under the More About File Formats button.^

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


	   ORGANIZATION AND FORMAT

Top
<#top> SCOPE
<#SCOPE> EDITORIAL POLICY
<#EDITORIAL_POLICY> HOW TO SUBMIT MANUSCRIPTS
<#HOW_TO_SUBMIT_MANUSCRIPTS> ORGANIZATION AND FORMAT
ILLUSTRATIONS AND TABLES
<#ILLUSTRATIONS_AND_TABLES> NOMENCLATURE
<#NOMENCLATURE> ABBREVIATIONS AND CONVENTIONS
<#ABBREVIATIONS_AND_CONVENTIONS>

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

Type every portion of the manuscript double spaced (a minimum^ of 6 mm
between lines), including figure legends, table footnotes,^ and
References, and number all pages in sequence, including^ the abstract,
figure legends, and tables. Place the last two^ items after the
References section. *Manuscript pages should^ have line numbers;
manuscripts without line numbers may be editorially^ rejected by the
editor, with a suggestion of resubmission after^ line numbers are
added*. The font size should be no smaller than^ 12 points. It is
recommended that the following sets of characters^ be easily
distinguishable in the manuscript: the numeral zero^ (0) and the letter
"oh" (O); the numeral one (1), the letter^ "el" (l), and the letter
"eye" (I); and a multiplication sign^ (x) and the letter "ex" (x). Do
not create symbols as graphics^ or use special fonts that are external
to your word processing^ program; use the "insert symbol" function. Set
the page size^ to 81/2 by 11 inches (ca. 21.6 by 28 cm). Italicize or
underline^ any words that should appear in italics, and indicate
paragraph^ lead-ins in bold type.^

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

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

*Manuscript Submission Checklist:*

    * Double space all text, including references and figure legends^
    * Number pages^
    * Number lines^
    * Present statistical treatment^ of data where appropriate^
    * Format references in ASM style^
    * Indicate^ journal section for manuscript publication^
    * Provide accession^ numbers for all sequences or sequence
      alignments^ important for^ evaluation of the manuscript as
      supplemental material^ or make^ the material available on a
      website for access by the^ editor^ and reviewers^
    * Confirm that genetic and chemical nomenclature^ conforms to
      instructions^
    * Include as supporting material in-press^ and submitted
      manuscripts^ that are important for judgment of^ the present
      manuscript^

^

*Long-Form Papers*
Long-form papers should include the elements described in this^ section.^

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

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

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

*Correspondent footnote.*
The complete mailing address, a single telephone number, a single^ fax
number, and a single e-mail address for the corresponding^ author should
be included on the title page of the manuscript.^ This information will
be published in the article as a footnote^ to facilitate communication,
and the e-mail address will be^ used to notify the corresponding author
of the availability^ of proofs and, later, of the PDF file of the
published article.^

*Abstract.*
Limit the abstract to *250 words or fewer* and concisely summarize^ the
basic content of the paper without presenting extensive^ experimental
details. Avoid abbreviations and references, and^ do not include
diagrams. When it is essential to include a reference,^ use the same
format as shown for the References section but^ omit the article title.
Because the abstract will be published^ separately by abstracting
services, it must be complete and^ understandable without reference to
the text.^

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

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

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

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

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

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

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

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

*References.*
/(i) References listed in the References section./
The References section must include all journal articles (both^ print
and online), books and book chapters (both print and online),^ patents,
theses and dissertations, published conference proceedings,^ meeting
abstracts from published abstract books or journal supplements,^ letters
(to the editor), and company publications, as well as^ in-press journal
articles, book chapters, and books (publication^ title must be given).
Arrange the citations in *alphabetical^ order* (letter by letter,
ignoring spaces and punctuation) by^ first author and *number
consecutively*. Provide the names of^ *all* the authors for each
reference. All listed references *must*^ be cited parenthetically by
number in the text. Since title^ and byline information that is
downloaded from PubMed does not^ always show accents, italics, or
special characters, authors^ should refer to the PDF files or hard-copy
versions of the articles^ and incorporate the necessary corrections in
the submitted manuscript.^ Abbreviate journal names according to the
/List of Journals Indexed^ for Medline/ (National Library of Medicine,
National Institutes^ of Health, 2007; available at
ftp://nlmpubs.nlm.nih.gov/online/journals/ljiweb.pdf),^ the primary
source for ASM style.^

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

   1. *Arendsen, A. F., M. Q. Solimar, and S. W. Ragsdale*. 1999.
      Nitrate-dependent^ regulation of acetate biosynthesis and nitrate
      respiration by^ /Clostridium thermoaceticum/. J. Bacteriol.
      *181*:1489-1495.^
   2. *Cox,^ C. S., B. R. Brown, and J. C. Smith*. J. Gen. Genet., in^
      press.*^ {/Article title is optional; journal title is mandatory/.}^
   3. *da^ Costa, M. S., M. F. Nobre, and F. A. Rainey*. 2001. Genus^
      I.^ Thermus Brock and Freeze 1969, 295,^AL emend. Nobre, Trüper^
      and da Costa 1996b, 605, p. 404-414. /In/ D. R. Boone, R. W.
      Castenholz,^ and G. M. Garrity (ed.), Bergey's manual of
      systematic bacteriology,^ 2nd ed., vol. 1. Springer, New York, NY.^
   4. *Elder, B. L., and^ S. E. Sharp*. 2003. Cumitech 39, Competency^
      assessment in the^ clinical laboratory. Coordinating ed., S.^ E.
      Sharp. ASM Press,^ Washington, DC.^
   5. *Falagas, M. E., and S. K. Kasiakou*. 2006.^ Use of international^
      units when dosing colistin will help decrease^ confusion related^
      to various formulations of the drug around^ the world.
      Antimicrob.^ Agents Chemother. *50*:2274-2275. (Letter.)^
      {/"Letter" or "Letter^ to the editor" is allowed but not required^
      at the end of such^ an entry/.}^
   6. *Fitzgerald, G., and D. Shaw*.^ /In/ A. E. Waters (ed.), Clinical^
      microbiology, in press. EFH^ Publishing Co., Boston, MA.*
      {/Chapter^ title is optional/.}^
   7. *Forman,^ M. S., and A. Valsamakis*. 2003. Specimen collection,^
      transport,^ and processing: virology, p. 1227-1241. /In/ P. R.^
      Murray, E.^ J. Baron, M. A. Pfaller, J. H. Jorgensen, and R.^ H.
      Yolken (ed.),^ Manual of clinical microbiology, 8th ed. ASM^
      Press, Washington,^ DC.^
   8. *Garcia, C. O., S. Paira, R. Burgos, J. Molina, J. F. Molina,^ and
      C. Calvo*. 1996. Detection of salmonella DNA in synovial^ membrane
      and synovial fluid from Latin American patients. Arthritis^ Rheum.
      *39*(Suppl.)*:*S185. {/Meeting abstract published in journal^
      supplement/.}^
   9. *Green, P. N., D. Hood, and C. S. Dow*. 1984. Taxonomic^ status^
      of some methylotrophic bacteria, p. 251-254. /In/ R. L.^ Crawford^
      and R. S. Hanson (ed.), Microbial growth on C_1 compounds.^
      Proceedings^ of the 4th International Symposium. American Society^
      for Microbiology,^ Washington, DC.^
  10. *Odell, J. C*. April 1970.^ Process for batch culturing. U.S.
      patent^ 484,363,770. {/Include^ the name of the patented
      item/process^ if possible; the patent^ number is mandatory/.}^
  11. *O'Malley, D. R*. 1998. Ph.D. thesis.^ University of California,^
      Los Angeles. {/Title is optional/.}^
  12. *Rotimi, V. O., N. O. Salako, E. M. Mohaddas, and L. P. Philip*.^
      2005. Abstr. 45th Intersci. Conf. Antimicrob. Agents Chemother.,^
      abstr. D-1658. {/Abstract title is optional/.}^
  13. *Smith, D., C.^ Johnson, M. Maier, and J. J. Maurer*. 2005.
      Distribution^ of fimbrial,^ phage and plasmid associated virulence
      genes among^ poultry /Salmonella^ enterica/ serovars, abstr.
      P-038, p. 445.^ Abstr. 105th Gen. Meet.^ Am. Soc. Microbiol.
      American Society^ for Microbiology, Washington,^ DC. {/Abstract
      title is optional/.}^
  14. *Stratagene*. 2006. Yeast^ DNA isolation system: instruction
      manual.^ Stratagene, La Jolla,^ CA. {/Use the company name as the
      author^ if none is provided^ for a company publication/.}^

^

*A reference to an in-press ASM publication should state the^ control
number (e.g., AEM00577-08) if it is a journal article^ or the name of
the publication if it is a book.^

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

   1. *Charlier, D., and N. Glansdorff*. September 2004, posting date.^
      Chapter 3.6.1.10, Biosynthesis of arginine and polyamines. /In/^
      R. Curtiss III et al. (ed.), EcoSal?/Escherichia coli/ and^
      /Salmonella/: cellular and molecular biology. ASM Press,
      Washington,^ DC. http://www.ecosal.org/ecosal/index.jsp. {/Note
      that each^ chapter has its own posting date/.}^
   2. *Dionne, M. S., and D. S.^ Schneider*. 2002. Screening the
      fruitfly^ immune system. Genome^ Biol. *3:*REVIEWS1010.
      http://genomebiology.com/2002/3/4/reviews/1010.^
   3. *Smith, F. X., H. J. Merianos, A. T. Brunger, and D. M.
      Engelman*.^ 2001. Polar residues drive association of polyleucine
      transmembrane^ helices. Proc. Natl. Acad. Sci. USA *98*:2250-2255.
      doi:10.1073/pnas.041593698.^
   4. *Winnick, S., D. O. Lucas, A. L. Hartman, and D. Toll*. 2005.^ How
      do you improve compliance? Pediatrics *115:*e718-e724.^

^

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

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

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

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

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

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

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

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

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

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

/(iv) Referencing publish-ahead-of-print manuscripts./
Citations of ASM Accepts manuscripts should look like the following^
example.

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

^

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

    *Wang, G. G., M. P. Pasillas, and M. P. Kamps.*^ 15 May 2006.
    Persistent^ transactivation by Meis1 replaces Hox^ function in
    myeloid leukemogenesis^ models: evidence for co-occupancy^ of
    Meis1-Pbx and Hox-Pbx complexes^ on promoters of
    leukemia-associated^ genes. Mol. Cell. Biol.^
    doi:10.1128/MCB.00586-06. (Subsequently^ published, Mol. Cell.^
    Biol. *26*:3902-3916, 2006.)^

^

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

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

^

*Short-Form Papers*
The short-form format is intended for the presentation of brief^
observations that do not warrant full-length papers. Submit^ short-form
papers in the same way as full-length papers. /They^ receive the same
review, they are not published more rapidly^ than full-length papers,
and they are not considered preliminary^ communications/.^

The title, running title (not to exceed 54 characters and spaces),^
byline, and correspondent footnote should be prepared as for^ the
long-form paper. Each short-form paper 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 single section.
Paragraph lead-ins are permissible. The^ text should be kept to a
minimum and, if possible, *should not^ exceed 1,000 words*; the number
of figures and tables should^ also be kept to a minimum. *Materials and
methods should be described^ in the text, not in figure legends or table
footnotes*. Present^ acknowledgments as in long-form papers, but do not
use a heading.^ The References section is identical to that of long-form
papers.^

*Minireviews*
Minireviews are brief (*limit of 6 printed pages exclusive of^
references*) biographical profiles, historical perspectives,^ or
summaries of developments in fast-moving areas. They must^ be based on
published articles; they may address any subject^ within the scope of AEM.^

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

Minireviews do not have abstracts. In the Abstract section of^ the
submission form, put "Not Applicable." The body of the Minireview^ may
either have section headings or be set up like a short-form^ paper (see
above).^

*Meeting Reviews*
Meeting Reviews are brief summaries of recent scientific meetings^ that
cover topics within the scope of AEM. Reviews should be^ timely and
focus on major themes, new developments, emerging^ trends, and
significant unanswered questions presented and discussed^ at the
meeting. Sufficient background should be provided to^ make the report
useful to the general reader. The author must^ provide written assurance
from the relevant individuals that^ permission to cite their presented
material has been granted.^

Meeting Reviews, which may be solicited or proffered by authors,^ are
subject to editorial review and should be submitted via^ Rapid Review.^

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

The length may not exceed 4 printed pages, and the format is^ like that
of a Minireview (see above). Commentaries should be^ submitted via Rapid
Review.^

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

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

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

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

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

*Errata*
The Erratum section provides a means of correcting errors that^ occurred
during the writing, typing, editing, or printing (e.g.,^ a misspelling,
a dropped word or line, or mislabeling in a figure)^ of a published
article. Submit Errata via Rapid Review (see^ "How To Submit
Manuscripts," above). In the Abstract section^ of the submission form (a
required field), put "Not Applicable."^ Upload the text of your Erratum
as an MS Word file. Please see^ a recent issue for correct formatting.^

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

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

Submit an Author's Correction via Rapid Review (see "How To^ Submit
Manuscripts," above). In the submission form, select^ Erratum as the
manuscript type; there is no separate selection^ in Rapid Review for
Authors? Corrections, but your Correction^ will be published as such if
appropriate. In the Abstract section^ of the submission form (a required
field), put "Not Applicable."^ Upload the text of your Author's
Correction as an MS Word file.^ Please see a recent issue for correct
formatting. Signed letters^ of agreement must be supplied as
supplemental material (scanned^ PDF files).^

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


	   ILLUSTRATIONS AND TABLES

Top
<#top> SCOPE
<#SCOPE> EDITORIAL POLICY
<#EDITORIAL_POLICY> HOW TO SUBMIT MANUSCRIPTS
<#HOW_TO_SUBMIT_MANUSCRIPTS> ORGANIZATION AND FORMAT
<#ORGANIZATION_AND_FORMAT> ILLUSTRATIONS AND TABLES
NOMENCLATURE
<#NOMENCLATURE> ABBREVIATIONS AND CONVENTIONS
<#ABBREVIATIONS_AND_CONVENTIONS>

 
*Digital files that are acceptable for production (see below)^ must be
provided for all illustrations on return of the modified^ manuscript.
(On initial submission, the entire paper may be^ submitted in PDF
format.)*^

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

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

The preferred format for tables is MS Word; however, WordPerfect^ and
Acrobat PDF are also acceptable (see the section on tablesGo <#TU1>Go
<#TU2>^ below).^


*View this table:*
[in this window] </cgi/content/full/74/1/1/TU1>
[in a new window] </cgi/content-nw/full/74/1/1/TU1>

  	Macintosh

 

*View this table:*
[in this window] </cgi/content/full/74/1/1/TU2>
[in a new window] </cgi/content-nw/full/74/1/1/TU2>

  	Windows

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

*Illustrations*
*File types and formats*. As mentioned above, *illustrations may^ be
supplied as PDF files for reviewing purposes only on initial^
submission; in fact, we recommend this option to minimize file^ upload
time. At the modification stage, production quality digital^ files must
be submitted:* TIFF or EPS files from supported applications^ or
PowerPoint files (black and white only). Except for figures^ produced in
PowerPoint, all graphics submitted with modified^ manuscripts must be
bitmap, grayscale, or CMYK (/not/ RGB). Halftone^ images (those with
various densities or shades) must be grayscale,^ /not/ bitmap.^

Color PowerPoint files are /not/ accepted because the application,^
designed for developing on-screen computer presentations, uses^ the RGB
color mode whereas the printing process uses the CMYK^ color mode.
Colors that are represented in a PowerPoint image^ may not be
reproducible on a printing press. Although black-and-white^ Microsoft
PowerPoint files are accepted, we do /not/ recommend^ the use of
PowerPoint. PowerPoint requires users to pay close^ attention to the
fonts used in their images (see the section^ on fonts below). If
instructions for fonts are not followed^ /exactly/, images prepared for
publication are subject to missing^ characters, improperly converted
characters, or shifting/obscuring^ of elements or text in the figure.
*Use of PowerPoint is therefore^ not recommended for either color or
black-and-white illustrations*.^

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

*Minimum resolution.*
It is extremely important that a high enough resolution is used.^ Any
imported images must be at the correct resolution before^ they are
placed. Note, however, that the higher the resolution,^ the larger the
file and the longer the upload time. Publication^ quality will /not/ be
improved by using a resolution higher than^ the minimum. Minimum
resolutions are as follows:

    300 dpi for^ grayscale and color^
    600 dpi for lettering^
    1,200 dpi for^ line art^
    600 dpi for combination art (lettering and images)^

^

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

    Maximum width^ for a 1-column figure: 3Formula 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: 9Formula inches (23.0 cm)^

^

*Contrast.*
Illustrations must contain sufficient contrast to withstand^ the
inevitable loss of contrast and detail inherent in the printing^
process. See also "Color illustrations" below.^

*Labeling and assembly.*
All final lettering, labeling, tooling, etc., *must* be incorporated^
into the figures. It cannot be added at a later date. If a figure^
number is included, it *must* appear well outside the boundaries^ of the
image itself. (Numbering may need to be changed at the^ copyediting
stage.) Each figure must be uploaded as a separate^ file, and any
multipanel figures must be assembled into one^ file; i.e., rather than
uploading a separate file for each panel^ in a figure, assemble all
panels in one piece and supply them^ as one file.^

*Fonts.*
To avoid font problems, set all type in one of the following^ fonts:
Helvetica, Times Roman, European PI, Mathematical PI,^ or Symbol. All
fonts other than these five must be converted^ to paths (or outlines) in
the application with which they were^ created. For proper font use in
PowerPoint images, refer to^ the Cadmus digital art website,
http://art.cadmus.com/da/instructions/ppt_disclaimer.jsp.^

*Compression.*
Images created with Macintosh applications may be compressed^ with
Stuffit. Images created with Windows applications may be^ compressed
with WinZip or PKZIP.^

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

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

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

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

*Drawings*
Submit graphs, charts, complicated chemical or mathematical^ formulas,
diagrams, and other drawings as finished products^ not requiring
additional artwork or typesetting. No part of^ the graph or drawing may
be handwritten. /All/ elements, including^ letters, numbers, and
symbols, /must/ be easily readable, and^ both axes of a graph must be
labeled. Keep in mind that the^ journal is published both in print and
online and that the same^ electronic files submitted by the authors are
used to produce^ both.^

When creating line art, please use the following guidelines:^

   1. *All art MUST be submitted at its intended publication size.*^ For
      acceptable dimensions, see "Size" above.^
   2. *Avoid using screens^ (i.e., shading)* in line art. It can be
      difficult^ and time-consuming^ to reproduce these images without
      moiré^ patterns. Various^ pattern backgrounds are preferable to
      screens^ as long as the^ patterns are not imported from another
      application.^ If you must^ use images containing screens,
          * Generate the image^ at line screens^ of 85 lines per inch or
            lower.^
          * When applying^ multiple shades^ of gray, differentiate the
            gray^ levels by at^ least 20%.^
          * Never^ use levels of gray below 20% or above 70%^ as they
            will^ fade^ out or become totally black upon scanning^ and
            reduction.^
      ^
   3. Use thick, solid lines that are no finer than 1 point in thickness.^
   4. No type should be smaller than 6 points at the final publication^
      size.^
   5. Avoid layering type directly over shaded or textured^ areas.^
   6. Avoid the use of reversed type (white lettering on^ a black
      background).^
   7. Avoid heavy letters, which tend to close^ up, and unusual
      symbols,^ which the printer may not be able to^ reproduce in the
      legend.^
   8. If colors are used, avoid using similar^ shades of the same color^
      and avoid very light colors.^

^

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

When powers of 10 must be used, the journal requires that the^ exponent
power be associated with the number shown. In representing^ 20,000 cells
per ml, the numeral on the ordinate would be "2"^ and the label would be
"10^4 cells per ml" (not "cells per ml^ x 10^?4 "). Likewise, an enzyme
activity of 0.06 U/ml would^ be shown as 6 accompanied by the label
10^?2 U/ml. The^ preferred designation would be 60 mU/ml (milliunits per
milliliter).^

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

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

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

Tables should be formatted as follows. Arrange the data so that^
*columns of like material read down, not across*. The headings^ should
be sufficiently clear so that the meaning of the data^ is understandable
without reference to the text. See the "Abbreviations"^ section (p. 20)
of these Instructions for those that should^ be used in tables.
Explanatory footnotes are acceptable, but^ more extensive table
"legends" are not. Footnotes should not^ include detailed descriptions
of the experiment. Tables must^ include enough information to warrant
table format; those with^ fewer than six pieces of data will be
incorporated into the^ text by the copy editor. Table 1 <#T1> is an
example of a well-constructed^ table.^


*View this table:*
[in this window] </cgi/content/full/74/1/1/T1>
[in a new window] </cgi/content-nw/full/74/1/1/T1>

  	TABLE 1. Distribution of protein and ATPase in fractions of dialyzed
membranes^/a/

 
*Cover Photographs and Drawings*
AEM publishes photographs and drawings on the front cover. Invitations^
are issued to authors whose manuscripts are returned for modification^
or whose manuscripts have been accepted for publication in AEM;^
material should be related to the work presented in the AEM^ manuscript.
Unsolicited photos will be considered in hard-copy^ format (two copies)
only; if an unsolicited photo is chosen^ for the cover, the author may
be asked to submit digital files.^ No material submitted for
consideration will be returned to^ the author. Authors will be notified
only if their cover art^ is selected. Copyright for the chosen material
must be transferred^ to ASM. A short description of the cover material
will be included^ at the end of the table of contents or the author
index of the^ issue. Technical specifications for submission are
available^ from the cover editor, Matthew R. Parsek (e-mail:
parsem@u.washington.edu <mailto:parsem@u.washington.edu>).^


	   NOMENCLATURE

Top
<#top> SCOPE
<#SCOPE> EDITORIAL POLICY
<#EDITORIAL_POLICY> HOW TO SUBMIT MANUSCRIPTS
<#HOW_TO_SUBMIT_MANUSCRIPTS> ORGANIZATION AND FORMAT
<#ORGANIZATION_AND_FORMAT> ILLUSTRATIONS AND TABLES
<#ILLUSTRATIONS_AND_TABLES> NOMENCLATURE
ABBREVIATIONS AND CONVENTIONS
<#ABBREVIATIONS_AND_CONVENTIONS>

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

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

For enzymes, use the recommended (trivial) name assigned by^ the
Nomenclature Committee of the International Union of Biochemistry^ (IUB)
as described in /Enzyme Nomenclature/ (Academic Press, Inc.,^ New York,
NY, 1992) and at http://www.chem.qmul.ac.uk/iubmb/enzyme/.^ If a
nonrecommended name is used, place the proper (trivial)^ name in
parentheses at first use in the abstract and text. Use^ the EC number
when one has been assigned, and express enzyme^ activity either in
katals (preferred) or in the older system^ of micromoles per minute.^

*Nomenclature of Microorganisms*
Binary names, consisting of a generic name and a specific epithet^
(e.g., /Escherichia coli/), must be used for all microorganisms.^ Names
of categories at or above the genus level may be used^ alone, but
specific and subspecific epithets may not. A specific^ epithet must be
preceded by a generic name, written out in full^ the first time it is
used in a paper. Thereafter, the generic^ name should be abbreviated to
the initial capital letter (e.g.,^ /E. coli/), provided there can be no
confusion with other genera^ used in the paper. Names of all taxa
(kingdoms, phyla, classes,^ orders, families, genera, species, and
subspecies) are printed^ in italics and should be italicized (or
underlined) in the manuscript;^ strain designations and numbers are not.
Vernacular (common)^ names should be in lowercase roman type (e.g.,
streptococcus,^ brucella). For /Salmonella/, genus, species, and
subspecies names^ should be rendered in standard form: /Salmonella
enterica/ at^ first use, /S. enterica/ thereafter; /Salmonella enterica/
subsp.^ /arizonae/ at first use, /S. enterica/ subsp. /arizonae/
thereafter.^ Names of serovars should be in roman type with the first
letter^ capitalized: /Salmonella enterica/ serovar Typhimurium. After^
the first use, the serovar may also be given without a species^ name:
/Salmonella/ serovar Typhimurium. For other information^ regarding
serovar designations, see /Antigenic Formulas of the^ Salmonella
Serovars/, 8th ed. (M. Y. Popoff, WHO Collaborating^ Centre for
Reference and Research on Salmonella, Institut Pasteur,^ Paris, France,
2001). For a summary of the current standards^ for /Salmonella/
nomenclature and the Kaufmann-White criteria,^ see the article by
Brenner et al. (J. Clin. Microbiol. *38*:2465-2467,^ 2000), the opinion
of the Judicial Commission of the International^ Committee on
Systematics of Prokaryotes (Int. J. Syst. Evol.^ Microbiol.
*55:*519-520, 2005), and the article by Tindall et^ al. (Int. J. Syst.
Evol. Microbiol. *55:*521-524, 2005).^

The spelling of bacterial names should follow the /Approved Lists^ of
Bacterial Names (Amended) & Index of the Bacterial and^ Yeast
Nomenclatural Changes/ (V. B. D. Skerman et al., ed., ASM^ Press,
Washington, DC, 1989) and the validation lists and notification^ lists
published in the /International Journal of Systematic and^ Evolutionary
Microbiology/ (formerly the /International Journal^ of Systematic
Bacteriology/) since January 1989. In addition,^ two sites on the World
Wide Web list current approved bacterial^ names: Bacterial Nomenclature
Up-to-Date
(http://www.dsmz.de/microorganisms/main.php?contentleft_id=14)^ and List
of Prokaryotic Names with Standing in Nomenclature^
(http://www.bacterio.cict.fr/). If there is reason to use a^ name that
does not have standing in nomenclature, the name should^ be enclosed in
quotation marks in the title and at its first^ use in the abstract and
the text and an appropriate statement^ concerning the nomenclatural
status of the name should be made^ in the text. "/Candidatus/" species
should always be set in quotation^ marks.^

For guidelines regarding new names and descriptions of new genera^ and
species, see the articles by Tindall (Int. J. Syst. Bacteriol.^
*49*:1309-1312, 1999) and Stackebrandt et al. (Int. J. Syst. Evol.^
Microbiol. *52:*1043-1047, 2002). To validate new names and/or^
combinations, authors must submit three copies of their published^
article to the /International Journal of Systematic and Evolutionary^
Microbiology/.^

It is recommended that a strain be deposited in at least two^ recognized
culture collections in different countries when that^ strain is
necessary for the description of a new taxon (Int.^ J. Syst. Evol.
Microbiol. *50*:2239-2244, 2000).^

Since the classification of fungi is not complete, it is the^
responsibility of the author to determine the accepted binomial^ for a
given organism. Sources for these names include /The Yeasts:^ a
Taxonomic Study/, 4th ed. (C. P. Kurtzman and J. W. Fell, ed.,^ Elsevier
Science Publishers B.V., Amsterdam, The Netherlands,^ 1998), and
/Ainsworth and Bisby's Dictionary of the Fungi/, 9th^ ed. (P. M. Kirk,
P. F. Cannon, J. C. David, and J. A. Stalpers,^ ed., CABI Publishing,
Wallingford, Oxfordshire, United Kingdom,^ 2001); see also
http://www.speciesfungorum.org/Names/Fundic.asp.^

Names used for viruses should be those approved by the International^
Committee on Taxonomy of Viruses (ICTV) and published in /Virus^
Taxonomy: Eighth Report of the International Committee on Taxonomy^ of
Viruses/ (C. M. Fauquet et al., ed., Elsevier Academic Press,^ San
Diego, CA, 2005). In addition, the recommendations of the^ ICTV
regarding the use of species names should generally be^ followed: when
the entire species is discussed as a taxonomic^ entity, the species
name, like other taxa, is italic and has^ the first letter and any
proper nouns capitalized (e.g., /Tobacco^ mosaic virus/, /Murray Valley
encephalitis virus/). When the behavior^ or manipulation of individual
viruses is discussed, the vernacular^ (e.g., tobacco mosaic virus,
Murray Valley encephalitis virus)^ should be used. If desired, synonyms
may be added parenthetically^ when the name is first mentioned. Approved
generic (or group)^ and family names may also be used.^

Microorganisms, viruses, and plasmids should be given designations^
consisting of letters and serial numbers. It is generally advisable^ to
include a worker's initials or a descriptive symbol of locale,^
laboratory, etc., in the designation. Each new strain, mutant,^ isolate,
or derivative should be given a new (serial) designation.^ This
designation should be distinct from those of the genotype^ and
phenotype, and genotypic and phenotypic symbols should not^ be included.
Plasmids are named with a lowercase "p" followed^ by the designation in
uppercase letters and numbers. To avoid^ the use of the same designation
as that of a widely used strain^ or plasmid, check the designation
against a publication database^ such as Medline.^

For submissions on the topic of probiotics, the Food and Agriculture^
Organization and World Health Organization (FAO/WHO) definition^ must be
used: "Live microorganisms, which when administered^ in adequate
amounts, confer a health benefit on the host." To^ avoid any
misrepresentation of how this term should be applied,^ authors are
encouraged to read the FAO/WHO Guidelines published^ in 2002
(ftp://ftp.fao.org/es/esn/food/wgreport2.pdf).^

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

*Before submission of manuscripts, authors may direct questions^ on
genetic nomenclature to the committee's chairman: Maria Costanzo^
(e-mail: maria@genome.stanford.edu <mailto:maria@genome.stanford.edu>)*.
Such a consultation should^ be mentioned in the manuscript submission
letter.^

*Bacteria.*
The genetic properties of bacteria are described in terms of^ phenotypes
and genotypes. The phenotype describes the observable^ properties of an
organism. The genotype refers to the genetic^ constitution of an
organism, usually in reference to some standard^ wild type. The
guidelines that follow are based on the recommendations^ of Demerec et
al. (Genetics *54*:61-76, 1966).^

(i) Phenotypic designations must be used when mutant loci have^ not been
identified or mapped. They can also be used to identify^ the protein
product of a gene, e.g., the OmpA protein. Phenotypic^ designations
generally consist of three-letter symbols; these^ are /not/ italicized,
and the first letter of the symbol is capitalized.^ It is preferable to
use Roman or Arabic numerals (instead of^ letters) to identify a series
of related phenotypes. Thus, a^ series of nucleic acid polymerase
mutants might be designated^ Pol1, Pol2, Pol3, etc. Wild-type
characteristics can be designated^ with a superscript plus (Pol^+ ),
and, when necessary for clarity,^ negative superscripts (Pol^? ) can be
used to designate^ mutant characteristics. Lowercase superscript letters
may be^ used to further delineate phenotypes (e.g., Str^r for
streptomycin^ resistance). Phenotypic designations should be defined.^

(ii) Genotypic designations are also indicated by three-letter^ locus
symbols. In contrast to phenotypic designations, these^ are lowercase
italic (e.g., /ara his rps/). If several loci govern^ related functions,
these are distinguished by italicized capital^ letters following the
locus symbol (e.g., /araA araB araC/). Promoter,^ terminator, and
operator sites should be indicated as described^ by Bachmann and Low
(Microbiol. Rev. *44*:1-56, 1980), e.g., /lacZp/,^ /lacAt/, and /lacZo/.^

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

(iv) Mutation sites are designated by placing serial isolation^ numbers
(allele numbers) after the locus symbol (e.g., /araA1^ araA2/). If it is
not known in which of several related loci^ the mutation has occurred, a
hyphen is used instead of the capital^ letter (e.g., /ara-23/). It is
essential in papers reporting the^ isolation of new mutants that allele
numbers be given to the^ mutations. For /Escherichia coli/, there is a
registry of such^ numbers: /E. coli/ Genetic Stock Center, Department of
Biology,^ Yale University, New Haven, CT 06511-5188. For the genus
/Salmonella/,^ the registry is /Salmonella/ Genetic Stock Center,
Department^ of Biology, University of Calgary, Calgary, Alberta T2N
1N4,^ Canada. For the genus /Bacillus/, the registry is /Bacillus/
Genetic^ Stock Center, Ohio State University, Columbus, OH 43210.^

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

Subscripts may be used in two situations. Subscripts may be^ used to
distinguish between genes (having the same name) from^ different
organisms or strains; e.g., /his_E. coli / or /his/_K-12 ^ for the /his/
gene of /E. coli/ or strain K-12, respectively, may^ be used to
distinguish this gene from the /his/ gene in another^ species or strain.
An abbreviation may also be used if it is^ explained. Similarly, a
subscript is also used to distinguish^ between genetic elements that
have the same name. For example,^ the promoters of the /gln/ operon can
be designated /glnAp/_1 and^ /glnAp/_2 . This form departs slightly from
that recommended by^ Bachmann and Low (e.g., /desC1p/).^

(vi) Deletions are indicated by the symbol {Delta} placed before the^
deleted gene or region, e.g., {Delta}/trpA432/,
{Delta}(/aroP/-/aceE/)/419/, or {Delta}(/hisQ-hisJo/)/1256/.^ Similarly,
other symbols can be used (with appropriate definition).^ Thus, a fusion
of the /ara/ and /lac/ operons can be shown as {Phi}(/ara-lac/)/95/.^
Likewise, {Phi}(/araB/'-/lacZ/^+ )/96/ indicates that the fusion
results^ in a truncated /araB/ gene fused to an intact /lacZ/ gene, and
{Phi}(/malE/-/lacZ/)/97/(Hyb)^ shows that a hybrid protein is
synthesized. An inversion is^ shown as IN(/rrnD/- /rrnE/)/1/. An
insertion of an /E. coli his/ gene^ into plasmid pSC101 at zero
kilobases (0 kb) is shown as pSC101^ {omega}(0kb::K-12/hisB/)/4/. An
alternative designation of an insertion^ can be used in simple cases,
e.g., /galT//236/::Tn/5/. The number^ /236/ refers to the locus of the
insertion, and if the strain^ carries an additional /gal/ mutation, it
is listed separately.^ Additional examples, which utilize a slightly
different format,^ can be found in the papers by Campbell et al. and
Novick et^ al. cited below. It is important in reporting the
construction^ of strains in which a mobile element was inserted and
subsequently^ deleted that this fact be noted in the strain table. This
can^ be done by listing the genotype of the strain used as an
intermediate^ in a table footnote or by making a direct or parenthetical
remark^ in the genotype, e.g., (F^? ), {Delta}Mu /c/ts, or
/mal/::{Delta}Mu /c/ts::/lac/.^ In setting parenthetical remarks within
the genotype or dividing^ the genotype into constituent elements,
parentheses and brackets^ are used without special meaning; brackets are
used outside^ parentheses. To indicate the presence of an episome,
parentheses^ (or brackets) are used ({lambda}, F^+ ). Reference to an
integrated episome^ is indicated as described above for inserted
elements, and an^ 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 Typhimurium, 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, /Chlamydomonas/ spp., and
several fungal^ species, symbols such as those given in the /Handbook of
Microbiology/,^ 2nd ed. (A. I. Laskin and H. A. Lechevalier, ed., CRC
Press,^ Inc., Cleveland, OH, 1988) should be used.^

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

For prokaryotes, gene names should not begin with prefixes indicating^
the genus and species from which the gene is derived. (However,^
subscripts may be used where necessary to distinguish between^ genes
from different organisms or strains, as described in section^ v of
"Bacteria" above.) For eukaryotes, such prefixes may be^ used for
clarity when discussing genes with the same name from^ two different
organisms (e.g., Sc/URA3/ vs. Ca/URA3/); the prefixes^ are not
considered part of the gene name proper and are not^ italicized.^

*Locus tags.*
Locus tags are systematic, unique identifiers that are assigned^ to each
gene in GenBank. All genes mentioned in a manuscript^ should be
traceable to their sequences by the reader, and locus^ tags may be used
for this purpose in manuscripts to identify^ uncharacterized genes.
However, since locus tags are not genetic^ names, they should appear in
Roman type rather than in italics.^ In addition, authors should check
GenBank to make sure that^ they are using the correct, up-to-date format
for locus tags^ (e.g., uppercase versus lowercase letters, presence or
absence^ of an underscore, etc.). Locus tag formats vary between
different^ organisms and also may be updated for a given organism, so
it^ is important to check GenBank at the time of manuscript preparation.^

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

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

*Strain designations.*
Do not use a genotype as a name (e.g., "subsequent use of /leuC6/^ for
transduction"). If a strain designation has not been chosen,^ select an
appropriate word combination (e.g., "another strain^ containing the
/leuC6/ mutation").^

*"Natural" versus "artificial" transformation.*
Natural transformation is a process whereby the recipient cell^ has the
inherent capacity to take up and integrate exogenous^ DNA into its
genome. As such, natural transformation is part^ of the biology of the
recipient cell line and should not be^ confused with processes through
which integration of DNA is^ forced upon recipient cells.^

*Viruses.*
The genetic nomenclature for viruses differs from that for bacteria.^ In
most instances, viruses have no phenotype, since they have^ no
metabolism outside host cells. Therefore, distinctions between^
phenotype and genotype cannot be made. Superscripts are used^ to
indicate hybrid genomes. Genetic symbols may be one, two,^ or three
letters. For example, a mutant strain of {lambda} might be^ designated
{lambda} /A/am11 /int/2 /red/114 /c/I857; this strain carries mutations^
in genes /c/I, /int/, and /red/ and an amber-suppressible (am) mutation^
in gene /A/. A strain designated {lambda} /att/^434 /imm/^21 would
represent^ a hybrid of phage {lambda} 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 by square
brackets,^ and the genetic symbols and designations for such inserted
DNA^ should conform to those used for the host genome. Genetic symbols^
for phage {lambda} can be found 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 nomenclature of eukaryotes,^ see the
Instructions to Authors for /Eukaryotic Cell/ and /Molecular^ and
Cellular Biology/.^

*Transposable elements, plasmids, and restriction enzymes.*
Nomenclature of transposable elements (insertion sequences,^
transposons, phage Mu, etc.) should follow the recommendations^ of
Campbell et al. (Gene *5:*197-206, 1979), with the modifications^ given
in section vi above. The Internet site where insertion^ sequences of
eubacteria and archaea are described and new sequences^ can be recorded
is http://www-is.biotoul.fr/is.html.^

The system of designating transposon insertions at sites where^ there
are no known loci, e.g., /zef-123/::Tn/5/, has been described^ by
Chumley et al. (Genetics *91*:639-655, 1979). The nomenclature^
recommendations of Novick et al. (Bacteriol. Rev. *40:*168-189,^ 1976)
for plasmids and plasmid-specified activities, of Low^ (Bacteriol. Rev.
*36:*587-607, 1972) for F' factors, and of Roberts^ et al. (Nucleic
Acids Res. *31:*1805-1812, 2003) for restriction^ enzymes, DNA
methyltransferases, homing endonucleases, and their^ genes should be
used when possible. The nomenclature for recombinant^ DNA molecules
constructed in vitro follows the nomenclature^ for insertions in
general. DNA inserted into recombinant DNA^ molecules should be
described by using the gene symbols and^ conventions for the organism
from which the DNA was obtained.^

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


	   ABBREVIATIONS AND CONVENTIONS

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<#SCOPE> EDITORIAL POLICY
<#EDITORIAL_POLICY> HOW TO SUBMIT MANUSCRIPTS
<#HOW_TO_SUBMIT_MANUSCRIPTS> ORGANIZATION AND FORMAT
<#ORGANIZATION_AND_FORMAT> ILLUSTRATIONS AND TABLES
<#ILLUSTRATIONS_AND_TABLES> NOMENCLATURE
<#NOMENCLATURE> ABBREVIATIONS AND CONVENTIONS

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

Be aware that it may be necessary to vary the tense in a single^
sentence. For example, it is correct to say "White (30) demonstrat/ed/^
that XYZ cells /grow/ at pH 6.8," "Figure 2 show/s/ that ABC cells^
fail/ed/ to grow at room temperature," and "Air /was/ removed from^ the
chamber and the mice /died/, which /proves/ that mice /require/^ air."
In reporting statistics and calculations, it is correct^ to say "The
values for the ABC cells /are/ statistically significant,^ indicating
that the drug inhibit/ed/... ."^

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

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

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

It is strongly recommended that all abbreviations except those^ listed
below be introduced in the first paragraph in Materials^ and Methods.
Alternatively, define each abbreviation and introduce^ it in parentheses
the first time it is used; e.g., "cultures^ were grown in Eagle minimal
essential medium (MEM)." Generally,^ eliminate abbreviations that are
not used at least three times^ in the text (including tables and figure
legends).^

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

The following abbreviations should be used without definition^ in tables:

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

^

*Reporting Numerical Data*
Standard metric units are used for reporting length, weight,^ and
volume. For these units and for molarity, use the prefixes^ m, µ, n, and
p for 10^?3 , 10^?6 , 10^?9 ,^ and 10^?12 , respectively. Likewise, use
the prefix k for^ 10^3 . Avoid compound prefixes such as mµ or µµ.^
Parts per million (ppm) may be used when that is the common^ measure for
the science in that field. Units of temperature^ are presented as
follows: 37°C or 324 K.^

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

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

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

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

*Statistics*
If biological variation within a treatment (coefficient of variation,^
the standard deviation divided by the mean) is small (less than^ 10%)
and the difference among treatment means is large (greater^ than 3
standard deviations), it is not necessary to report statistics.^ If the
data do not meet these criteria, however, the authors^ must include an
appropriate statistical analysis (e.g., Student's^ /t/ test, analysis of
variance, Tukey's test, etc.). Statistics^ should represent the
variation among biological units (e.g.,^ replicate incubations) and not
just the variation due to method^ of analysis.^

Phylogenetic trees based on nucleotide or amino acid sequence^
alignments must be supported by appropriate statistical analyses^ of
tree stability (e.g., bootstrap analysis), and nonsupported^ branches
(e.g., bootstrap coefficients below 50%) should be^ collapsed. A copy of
the alignment should be available for examination^ by the editor or the
reviewers upon request.^

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

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

*Equations*
In mathematical equations, indicate the order of operations^ clearly by
enclosing operations in parentheses, brackets, and^ braces, in that
order: (/a/ + /b/) x /c/ or /a/ + (/b/ x /c/), 100 x {[(/a///b/)^ x /c/]
+ /d/} or 100 x {/a//[(/b/ x /c/) + /d/]}. Italicize (or underline)^
variables and constants (but not numerals), and use Roman type^ for
designations: E_0 , E_h , /M/_r , /K_m /, /K_s /, /a/ + 2/b/ = 1.2 mM,
Ca^2+ ^ /V/_max = exp(1.5/x/ + /y/), BOD = 2.7/x/^2 .^

*Isotopically Labeled Compounds*
For simple molecules, isotopic labeling is indicated in the^ chemical
formula (e.g., ^14 CO_2 , ^3 H_2 , and H^35 SO_4 ). Brackets are^ not
used when the isotopic symbol is attached to the name of^ a compound
that in its natural state does not contain the element^ (e.g., ^32
S-ATP) or to a word that is not a specific chemical^ name (e.g., ^131
I-labeled protein, ^14 C-amino acids, and ^3 H-ligands).^

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

    [^14 C]urea^
    L-[/methyl/-^14 C]methionine^
    [2,3-^3 H]serine^
    [{alpha}-^14 C]lysine^
    [{gamma}-^32 P]ATP^
    UDP-[U-^14 C]glucose^
    /E. coli/ [^32 P]DNA^
    fructose 1,6-[1-^32 P]bisphosphase^

^

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

^


	   FOOTNOTES

 
^* Shading indicates material that has been added or significantly^
updated.^ Back <#RFN1>

------------------------------------------------------------------------
Applied and Environmental Microbiology, January 2008, p. 1-22, Vol. 74,
No. 1
0099-2240/08/$08.00+0     doi:10.1128/AEM.02454-07
Copyright © 2008 </misc/terms.shtml>, American Society for Microbiology
<http://www.asm.org>. All Rights Reserved.




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