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Journal of Bacteriology, January 2008, p. 1-20, Vol. 190, No. 1
0021-9193/08/$08.00+0     doi:10.1128/JB.01712-07
Copyright © 2008 </misc/terms.shtml>, American Society for Microbiology
<http://www.asm.org>. All Rights Reserved.

*INSTRUCTIONS TO AUTHORS*


    JOURNAL OF BACTERIOLOGY


      2008 INSTRUCTIONS TO AUTHORS

    *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>*
    *    Patient Identification <#Patient_Identification>*
    *    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>*
    *    Full-Length Papers <#Full-Length_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.>*
    *    Notes <#Notes>*
    *    Minireviews <#Minireviews>*
    *    Guest Commentaries <#Guest_Commentaries>*
    *    Errata <#Errata>*
    *    Authors? Corrections <#Authors?_Corrections>*
    *    Retractions <#Retractions>*
    *ILLUSTRATIONS AND TABLES <#ILLUSTRATIONS_AND_TABLES>*
    *    Image Manipulation <#Image_Manipulation>*
    *    Illustrations <#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>*
    *ABBREVIATIONS AND CONVENTIONS <#ABBREVIATIONS_AND_CONVENTIONS>*
    *    Verb Tense <#Verb_Tense>*
    *    Abbreviations <#Abbreviations>*
    *    Reporting Numerical Data <#Reporting_Numerical_Data>*
    *    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>

 
The /Journal of Bacteriology/ (JB) publishes descriptions of basic^
research on bacteria and other microorganisms. Topics that are^
considered include structure and function, biochemistry, enzymology,^
metabolism and its regulation, molecular biology, genetics,^ plasmids
and transposons, general microbiology, plant microbiology,^ chemical or
physical characterization of microbial structures^ or products, and
basic biological properties of organisms.^

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

(i) JB will consider papers that describe the use of antibiotics^ and
antimicrobial agents as tools for elucidating the basic^ biological
processes of microorganisms. However, papers dealing^ with antimicrobial
agents, including manuscripts dealing with^ the susceptibility to,
resistance to, bio syn thesis of, and^ metabolism of such agents, are
more appropriate for /Antimicrobial^ Agents and Chemotherapy/.^

(ii) JB will consider manuscripts that emphasize the interrelationship^
of a bacteriophage and a host cell, manuscripts about work in^ which
viruses were used as tools for elucidating the structures^ or biological
processes of microorganisms, and manuscripts that^ concern phages that
are related to transposable elements or^ plasmids.^

(iii) Manuscripts describing new or novel methods or improvements^ in
media and culture conditions will not be considered by JB^ unless they
are applied to the study of basic problems in microbiology.^ Such
manuscripts are more appropriate for /Applied and Environmental^
Microbiology/ or for the /Journal of Clinical Microbiology/.^

(iv) Manuscripts dealing with ecology or environmental studies^ or with
the application of microorganisms to agricultural or^ industrial
processes are more appropriate for /Applied and Environmental^
Microbiology/.^

(v) Manuscripts dealing with the immune system or with topics^ of
medical interest are more appropriate for /Infection and Immunity/.^

(vi) In most cases, reports that emphasize methods and nucleotide^
sequence data alone (without experimental documentation of the^
functional and evolutionary significance of the sequence) will^ not be
considered by JB.^

(vii) Manuscripts describing work, with a new organism, that^ largely
repeats published research done with a different organism^ will be
considered if they significantly increase the understanding^ of the
original property, if they provide an extensive basis^ for evolutionary
comparison, or if the work is of unusual importance^ because of its
relationship to other properties of the new organism.^ Manuscripts that
describe genes or enzymes, for example, that^ differ only in minor ways
from the prototypes are not suitable^ for JB.^

(viii) The criteria described in section vii above also apply^ to genome
maps. Manuscripts describing a genome map should provide^ an extensive
basis for evolutionary comparisons or significantly^ increase our
fundamental understanding of the organism or system.^

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.^

*All authors of a manuscript must have agreed to its submission^ and are
responsible for its content* (initial submission and^ any subsequent
versions), including appropriate citations and^ acknowledgments, and
must also have agreed that the corresponding^ author has the authority
to act on their behalf in all matters^ pertaining to publication of the
manuscript. The corresponding^ author is responsible for obtaining such
agreements and for^ informing the coauthors of the manuscript's status
throughout^ the submission, review, and publication process. For
Authors?^ Corrections and Retractions, signed letters of agreement from^
all of the authors must be submitted (see p. 12).^

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

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

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

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

*Primary 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 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^ JB00123-08"). 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 JB 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 opportunity to publish^ in
high-quality journals, ASM requires the corresponding author^ to sign a
copyright transfer agreement on behalf of all the^ authors. This
agreement is sent to the corresponding author^ when the manuscript is
accepted and scheduled for publication.^ Unless this agreement is
executed (/without changes and/or addenda/),^ ASM will not publish the
article.^

In the copyright transfer agreement signed by an author, ASM^ grants to
that author (and coauthors) the right to republish^ /discrete portions/
of his (their) article in any other publication^ (print, CD-ROM, and
other electronic forms) of which he is (they^ are) the author(s) or
editor(s), /on the condition that appropriate^ credit is given to the
original ASM publication/. This republication^ 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.^

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

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.)^

*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 JB authors to do so. ASM also allows^ JB 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.^

*Patient Identification*

When isolates are derived from patients in clinical studies,^ do not
identify them by using the patients? initials,^ even as part of a strain
designation. Change the initials to^ numerals or use randomly chosen
letters. Do not give hospital^ unit numbers; if a designation is needed,
use only the last^ two digits of the unit. (Note: Established
designations of some^ viruses and cell lines, although they consist of
initials, are^ acceptable [e.g., JC virus, BK virus, and HeLa cells].)^

*Nucleotide and Amino Acid 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 full-length^ papers or at the end of the text for
Notes. 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. 15 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 publication (online posting) date of the accepted manuscript.^ It is
also expected that the coordinates will be released to^ the public no
later than the publication date of the article.^ 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^ Notes.^

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
Notes.^

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*

JB 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
be.^

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

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

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

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

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

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

*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, Dialogs, and Guest Commentaries^ 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
their contact information where indicated^ on the submission form.^

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

When a manuscript is submitted to the journal, it is given a^ number
(e.g., JB00047-08 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 modifica-tion 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^ the 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.,
JB Accepts) and is accessible from the Journals^ website. The
manuscripts are published online as soon as possible^ after acceptance,
on a weekly basis, before the copyedited,^ typeset articles are
published. They are posted "*as is*" (i.e.,^ as submitted by the authors
at the modification stage) and do^ not reflect ASM editorial changes.
*No corrections/changes to^ the PDF manuscripts are accepted.*
Accordingly, there likely^ will be differences between the JB Accepts
manuscripts and the^ final, typeset articles. The manuscripts remain
listed on the^ JB Accepts page until the final, typeset articles are
posted.^ At that point, the manuscripts are removed from the JB 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, 202-942-9243).^
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 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 JB 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.*^

*Full-Length Papers*

Full-length 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 allowed.^ 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.^

Enzyme purifications should be described in this section, but^ the
results of such procedures should be described in the Results^ section.^

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.*

The Results section should include 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 (e.g., calibration
plots for molecular^ weight by gel filtration or electrophoresis) 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 full-length or^ Note 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., JB00577-08) 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.^

*Notes*

The Note format is intended for the presentation of brief observations^
that do not warrant full-length papers. Submit Notes 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/.^

Each Note must have an *abstract of no more than 50 words.* Do^ not use
section headings in the body of the Note; 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
full-length papers,^ but do not use a heading. The References section is
identical^ to that of full-length 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
the journal.^

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 Note (see^ above).^

*Guest Commentaries*

Guest Commentaries are communications written in response to^
invitations issued by the editors and concern relevant topics^ in
bacteriology 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.^

*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:*
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  	Macintosh

 

*View this table:*
[in this window] </cgi/content/full/190/1/1/TU2>
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  	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://art.cadmus.com/da/index.jsp. Please^ review this
information before preparing your files. If you^ require additional
information, please send an e-mail inquiry^ to digitalart@cadmus.com
<mailto:digitalart@cadmus.com>.^

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

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

^

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

    Maximum width^ for a 1-column figure: 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 sending a^ separate file for each panel in a figure,
assemble all panels^ in one piece and supply them as one file.^

*Fonts.* To avoid font problems, set all type in one of the following^
fonts: Helvetica, Times Roman, European PI, Mathematical PI,^ or Symbol.
All fonts other than these five must be converted^ to paths (or
outlines) in the application with which they were^ created. For 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 appropriate 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. 19)
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/190/1/1/T1>
[in a new window] </cgi/content-nw/full/190/1/1/T1>

  	TABLE 1. Induction of creatinine deiminase in /Clostridium/ sp.
strains XP32 and XP56

 
*Cover Photographs and Drawings*

JB 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 JB;^ material
should be related to the work presented in the manuscript.^ Unsolicited
photos will also be considered. 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^ are available from the cover editor,
Roberto Kolter (e-mail:^ rkolter@hms.harvard.edu
<mailto:rkolter@hms.harvard.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 guidelines to the^ use of biochemical
terminology, 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.^

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.^

*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, 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 only
a single such locus exists or 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 the /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., /galT236/::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 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/, and Piggot and Hoch
(Microbiol.^ Rev. *49:*158-179, 1985) for /Bacillus subtilis/.^

*Conventions for naming genes.* It is recommended that (entirely)^ new
genes be given names that are mnemonics 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 differ-ent organisms^ receive the same name. When
homology is not apparent or the^ function of a new gene has not been
established, a provisional^ name may be given by one of the following
methods. (i) The gene^ may be named on the basis of its map location in
the style /yaaA/,^ analogous to the style used for recording transposon
insertions^ (/zef/) as discussed below. A list of such names in use for
/E.^ coli/ has been published by Rudd (Microbiol. Mol. Biol. Rev.^
*62:*985-1019, 1998). (ii) A provisional name may be given in^ the style
described by Demerec et al. (e.g., /usg/, gene upstream^ of /folC/).
Such names should be unique, and names such as /orf/^ or /genX/ should
not be used. For reference, the /E. coli/ Genetic^ Stock Center's
database includes an updated listing of /E. coli/^ gene names and gene
products. It is accessible on the Internet^
(http://cgsc.biology.yale.edu/cgsc.html). The Center's re-lational^
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 bacte-ria, consult the
references given^ above.^

For prokaryotes, gene names should not begin with prefixes indicating^
the genus and species from which the gene is derived (for example,^ do
not use Ec/mecA/ for the /mecA/ gene from /E. coli/). However,^
subscripts may be used where necessary to distinguish between^ genes
from different organisms or strains as described in section^ v of
"Bacteria" above.^

*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 the 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").^

*Bacteriophages.* The genetic nomenclature for phages differs^ from that
for bacteria and tends to have separate conventions^ for each phage.
Genetic symbols may be one, two, or three letters^ and are italicized.
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/. Phenotypic symbols and designations of gene products^ are not
italicized (e.g., "the Spi phenotype" or "Int protein"),^ and
superscript plus and minus symbols can be used to indicate^ wild-type
and mutant phenotypes, respectively. Host DNA insertions^ into phages
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. Lists of gene symbols^ for several phages can be found in
/Genetic Maps/, 6th ed. (S.^ J. O'Brien, ed., Cold Spring Harbor
Laboratory, Cold Spring^ Harbor, NY, 1993). Relevant references for some
of the more^ widely studied phages are as follows: for phage {lambda},
Daniels et^ al. (p. 469-515, /in/ R. W. Hendrix, J. W. Roberts, F. W.
Stahl,^ and R. A. Weisberg, ed., /Lambda II/, Cold Spring Harbor
Laboratory,^ Cold Spring Harbor, NY, 1983); for phage T4, Kutter et al.
(p.^ 491-519, /in/ J. D. Karam, ed., /Molecular Biology of
Bacteriophage^ T4/, American Society for Microbiology, Washington, DC,
1994);^ and for phage T7, Dunn and Studier (J. Mol. Biol.
*166:*477-535,^ 1983).^

*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. 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^ also gives the correct format for genes,
proteins, and determinants^ in this family.^


	   ABBREVIATIONS AND CONVENTIONS

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
<#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^ ad-enine 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.^ Use
µg/ml or µg/g in place of the ambiguous ppm.^ Units of temperature are
presented as follows: 37°C or 324^ K.^

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

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

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

*Isotopically Labeled Compounds*

For simple molecules, isotopic labeling is indicated in the^ chemical
formula (e.g., ^14 CO_2 , ^3 H_2 O, and H_2 ^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 square brackets directly preceding the part of^ the name that
describes the labeled entity. Note that configuration^ symbols and
modifiers precede the isotopic symbol. The following^ examples
illustrate correct usage:

    [^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]bisphosphate^

^

JB 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).^

^

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Journal of Bacteriology, January 2008, p. 1-20, Vol. 190, No. 1
0021-9193/08/$08.00+0     doi:10.1128/JB.01712-07
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