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*Instructions for Authors
Last Updated November 16, 2007*

PLEASE NOTE: Significant changes have been made to the MANUSCRIPT
PREPARATION AND ORGANIZATION section. Please review this section
carefully prior to submitting your manuscript.

*TABLE OF CONTENTS*
STATEMENT OF SCOPE <#STATEMENT OF SCOPE>
     Ethics <#Ethics>
FEATURE ARTICLES <#FEATURE ARTICLES>
MANUSCRIPT SUBMISSION <#MANUSCRIPT SUBMISSION>
     Authorship <#Authorship>
     Cover Letter <#Cover Letter>
     Availability of Materials <#Availability of Materials>
     Language-Editing Services <#Language-Editing Services>
MANUSCRIPT PREPARATION AND ORGANIZATION <#MANUSCRIPT PREPARATION AND
ORGANIZATION>
     Title Page <#Title Page>
     Manuscript Title <#Manuscript Title>
     Abstract <#Abstract>
     Introduction, Results, and Discussion <#Introduction Results and
Discussion>
     Nomenclature and Terminology <#Nomenclature and Terminology>
     Methods <#Methods>
          Large-scale experiments
          Quantification of molecules, including DNA, RNA, and proteins
          Molecular phylogenetic analyses
     Tables <#Tables>
     References <#References>
     Figures <#Figures>
          Figure legends
          Figure manipulation
          Figure size
          Black and white figures
          Color figures
          Figure format
          Figure resolution
          Figure file size
          Help with digital art
     Supplemental Data <#Supplemental Data>
          Supplemental data presentation
          Large-scale data sets
          Movies
     Cover Submissions <#Cover Submissions>
PEER REVIEW <#PEER REVIEW>
MANUSCRIPT ACCEPTANCE <#MANUSCRIPT ACCEPTANCE>
PROOFS <#PROOFS>
FEES AND CHARGES <#FEES AND CHARGES>
POLICIES <#POLICIES>
     Electronic Posting of Articles <#Electronic Posting of Articles>
     Materials Distribution Policy <#Materials Distribution Policy>
     Corrections and Retractions <#Corrections and Retractions>

*STATEMENT OF SCOPE *
/The Plant Cell/ publishes novel research of special significance in
plant biology, especially in the areas of cellular biology, molecular
biology, genetics, development, and evolution. The primary criterion for
publication is new insight that is of broad interest to plant
biologists, not only specialists. The presentation of results must be
appropriate for a wide audience of plant biologists. Research on the
biology of plant pathogens falls within our scope if it is /directly/
relevant to the plant's response to the pathogen. (Back to top) <#TABLE
OF CONTENTS>

*Ethics. *Please see http://www.aspb.org/publications/ethics.cfm for
expectations for authors and ASPB procedures for handling allegations of
scientific misconduct in journals. (Back to top) <#TABLE OF CONTENTS>

*FEATURE ARTICLES *
The front section of the journal features occasional Editorials, Letters
to the Editor, In This Issue articles, Current Perspective Essays,
Historical Perspective Essays, Reviews, and Commentaries. Prospective
authors may inquire about contributing to an article to one of these
feature sections by contacting Dr. Nancy Eckardt, News and Reviews
Editor (neckardt@aspb.org <mailto:neckardt@aspb.org>), or Dr. Richard
Jorgensen, Editor in Chief (raj@ag.arizona.edu
<mailto:raj@ag.arizona.edu>). (Back to top) <#TABLE OF CONTENTS>

*MANUSCRIPT SUBMISSION*
Before initiating the submission process, these Instructions for Authors
should be reviewed in full to ensure that the article is in compliance
with Plant Cell standards. Even if authors have previously read them, it
is strongly recommended that these pages be reread in their entirety, as
they are updated periodically.

If an author does not have access to the Internet, contact Annette
Kessler, Manuscript Manager, at 301/251-0560, ext. 120; e-mail:
akessler@aspb.org <mailto:akessler@aspb.org>

Authors should submit manuscripts online at
http://submit.plantcell.org/. The Bench>Press submission system will
prompt authors through the process. Help is also available from
http://submit.plantcell.org/submission/submissionhelp and from Annette
Kessler in the ASPB manuscript tracking office (301/251-0560, ext. 120;
akessler@aspb.org <mailto:akessler@aspb.org> ). A manuscript file in
Microsoft Word (or some other word processing format) is required and
will be automatically converted to a PDF. If using Microsoft Word, you
must submit a .doc file. Please do not submit .docx files as they
cannnot be processed by the Bench>Press submission system. If conversion
is not satisfactory, authors may submit their own PDF, which will not be
subjected to any conversion. Although there are no file size
limitations, note that large files will take longer to upload and
convert to PDF depending on the Internet connection. Please try to keep
the maximum combined PDF file size to less than 5 MB. If you are not
satisfied with the final conversion results when the submission is
proofed, the complete manuscript can be reloaded as a PDF file. (Back to
top) <#TABLE OF CONTENTS>

*Authorship*. Contribution to a manuscript must be substantive in order
to justify authorship. An author is responsible for major aspects of the
research that is presented. All other contributors should instead be
acknowledged appropriately in the Acknowledgments section. The
corresponding author is responsible for ensuring that all authors have
made bona fide, substantive contributions to the research and have seen
and approved the manuscript in final form prior to submission. For more
information on corresponding authors, see "Title Page" below. An e-mail
acknowledging submission of the manuscript will be sent automatically to
every author (a valid, unique e-mail address must be provided for each
author). If any author has not approved this submission or has any
concern about the nature of this submission, the author should first
contact the corresponding author about their concern and contact /The
Plant Cell/ directly only if the concern cannot be resolved to the
satisfaction of all coauthors. Some concerns may be resolvable by
reviewing ASPB's Ethics in Publishing
<http://www.aspb.org/publications/ethics.cfm> policy. In the case of an
unresolved concern, the corresponding author is obligated to notify /The
Plant Cell/ and explain the nature of the disagreement. After
submission, any requested change in authorship will require the
agreement of all coauthors. (Back to top) <#TABLE OF CONTENTS>

*Cover Letter*. A cover letter must be submitted along with the
manuscript, stating that the manuscript has not been submitted for
publication elsewhere. Any closely related papers that are in press or
that have been submitted elsewhere should be noted in the cover letter,
cited in the submitted manuscript as is appropriate, and uploaded as
additional supplemental files in the Bench>Press manuscript submission
system. If any new gene symbols are introduced, the authors should state
that they have conducted a search of the literature and of community
databases and whether each new symbol has been registered in the
appropriate community database (see Nomenclature and Terminology). If
authors wish to request exclusion of any reviewers, specific reasons
must be provided (for journal policy, see Peer Review). Authors should
list the supplemental data they are submitting with the manuscript and
state why it should be supplemental rather than integral to the article
(aside from movies, large-scale data tables, unusual imaging software,
etc). Also in the cover letter, we recommend that authors also explain
the importance of their work and how and why their major findings relate
to the scope of the journal. (Back to top) <#TABLE OF CONTENTS>

*Availability of Materials. *Publication in /The Plant Cell/ implies
that the authors agree to provide materials that are integral to the
results presented in the article, including whatever would be necessary
for a skilled investigator to verify or replicate the claims. Authors
are generally expected to take advantage of public repositories or
commercial vendors to the extent possible. Authors should refer to the
Materials Distribution Policy in these instructions for explanation of
the journal's expectations of authors and requestors. (Back to top)
<#TABLE OF CONTENTS>

*Language-Editing Services*. Authors who believe their manuscripts would
benefit from professional editing are encouraged to use language-editing
services, such as the ones described at the following web sites, prior
to submission.
http://www.prof-editing.com/ <http://www.prof-editing.com>
http://www.bostonbioedit.com/ <http://www.bostonbioedit.com>
http://www.internationalscienceediting.com/
<http://www.internationalscienceediting.com>
http://www.asiascienceediting.com/ <http://www.asiascienceediting.com>
http://www.biosciencewriters.com/ <http://www.biosciencewriters.com>
http://www.biomeditor.com/ <http://www.biomeditor.com>
http://www.oleng.com.au/ <http://www.oleng.com.au>
http://davidherron.tripod.com/index-6.html
http://www.scientific-editor.com
http://www.bluepencilscience.com/ <http://www.bluepencilscience.com>
http://www.journalexperts.com/ <http://www.journalexperts.com>
http://www.writescienceright.com/ <http://www.writescienceright.com>
http://documentclinic.com

*NOTE:* ASPB provides these links as a service to our author community.
The Society does not take responsibility for or endorse the services
these companies offer and cannot attest to the quality of their work.
*Use of such services in no way guarantees acceptance of a manuscript
for publication. *If you have questions, or if you do use one of these
services and would like to send ASPB feedback on your experience, please
contact Nancy Winchester, ASPB Director of Publications, at
nancyw@aspb.org <mailto:nancyw@aspb.org>. (Back to top) <#TABLE OF CONTENTS>

*MANUSCRIPT PREPARATION AND ORGANIZATION*
Manuscripts should follow /The Plant Cell/ style, be written in concise
and grammatically correct English, and be presented in a manner and at a
level that will be accessible to the broad readership of the journal.
Papers that do not meet these standards will be returned to the authors
without further review. Consult a current issue of /The Plant Cell/ for
guidance on format, organization, and preparation of figures, legends,
tables, and references. While there are no limits to the length of
manuscripts published in /The Plant Cell/, papers of more than 10
journal pages will be published only if the coeditor judges that the
content is sufficiently novel to warrant a long paper. Ten published
pages in /The Plant Cell/ correspond to approximately 30 manuscript
pages, including tables and figure legends and an average of six
one-column figures.

Original manuscripts must be prepared using a standard word processing
program (such as Microsoft Word) and should be prepared with 1.5 line
spacing and in 12 point type using one of the following fonts: Times
Roman, Courier, Helvetica, or Arial for text and Symbol font for Greek
characters to avoid inadvertent character substitutions. Please do not
use Chinese, Japanese or Korean fonts. Use settings for standard 8.5 x
11-inch paper. Figures should be digitally prepared (see below).

Organize manuscripts in the following order: Title Page, Abstract,
Introduction, Results, Discussion, Methods, Acknowledgments, Figure
Legends, Tables, and References. Note that when submitting your
manuscript the References must be placed at the end of your document
file. Tables should be included as part of your manuscript file. Figures
and regular Supplemental data (Supplemental text, figures and small
tables) should be included in separate files and not as part of the
manuscript. These will be converted, along with the manuscript, into a
single PDF on upload. See the sections on Figures and Supplemental Data
below for more details. (Back to top) <#TABLE OF CONTENTS>

*Title Page*. The title page should include the authors' full names and
affiliations, a running title of 40 characters or less (in addition to
the full paper title), and the e-mail address of the corresponding
author. A second corresponding author may be listed but only in cases in
which the authors are from different collaborating labs. Both
corresponding authors will assume full and equal responsibility for the
manuscript, including compliance with journal policies. One of the
corresponding authors will be designated in the online submission system
to be the primary contact with the journal office. In the manuscript,
please provide each author's institutional affiliation at the time the
research was done. If an author has since moved to a different
institution, the new location can be indicated in a footnote. In the
online submission system, the most current contact information for each
author should be provided. The title page also must include the
following statement as an unnumbered footnote: "The author(s)
responsible for distribution of materials integral to the findings
presented in this article in accordance with the policy described in the
Instructions for Authors (www.plantcell.org) is (are): John D. Author
(author@college.edu)." Contact information for the author(s) responsible
for distribution of material(s) should be provided. (See Materials
Distribution Policy for journal expectations in this regard.) (Back to
top) <#TABLE OF CONTENTS>

*Manuscript Title*. The full manuscript title should be succinct
(approximately 120 characters) and informative. The title should include
sufficient detail for indexing but be general enough to be clear to the
broad readership of the journal. Abbreviations and acronyms, including
those for gene and protein names, should be avoided in titles or the
general nature of the abbreviated entity should be clear. The journal
encourages active titles over merely descriptive ones. The title must
mention the subject organism (or general group in the case of
comparative works). Common names are allowed for major model systems
(maize, rice, yeast); Latin names should be used for all organisms that
have no widely accepted common name. (Back to top) <#TABLE OF CONTENTS>

*Abstract*. The abstract should summarize for a broad audience the
question being addressed, the approach taken, and the major findings and
their significance. It should also be concise (approximately 200 words)
and stand on its own with no reference to the text. General background
should be reserved for the introduction. Literature references should
not be included. (Back to top) <#TABLE OF CONTENTS>

*Introduction, Results, and Discussion*. Manuscripts should be written
to be understood by a wide audience of plant biologists. The use of
abbreviations and jargon should be avoided, and terms that are not
widely known should be explained clearly at first use. The Introduction
should provide the necessary background information for the average
reader; it should be both complete and concise. Previous publications
that form a basis for the work presented must be cited. Citation of
reviews is not a substitute for citing primary research articles.
Citation of recent research articles is not a substitute for citing
original discoveries. An author's own work should not be cited
preferentially over equally relevant work of others. Authors' previously
published data that are presented along with new data must be identified
clearly and cited appropriately; duplicate publication of data
(including data previously published as supplemental material) is not
allowed without citation. Use of phrases such as "data not shown" or
"unpublished results" is discouraged in the print article; instead,
authors are encouraged to present such data as supplemental material.
The Results and Discussion can be subdivided if subheadings give the
manuscript more clarity. The Discussion should not repeat the Results;
instead, the Discussion should explore the implications of the Results,
citing relevant published research, and should also be as concise as
possible. A Conclusions section is generally not permitted. Statements
of priority or first finding are generally not permitted in /The Plant
Cell/. (Back to top) <#TABLE OF CONTENTS>

*Nomenclature and Terminology*. /The Plant Cell/ requires that all
nomenclature, including gene names and symbols, conform to nomenclature
conventions adopted by the scientific community and that all genetic
terminology be used in a scientifically accurate manner.

*     */Organisms/. In the Abstract, text, and Methods, organisms should
be referred to by their common name at first use (if a standard common
name applies), and the Latin name should be given in parentheses.
Subsequent references to organisms can be either Latin or common names
but should be consistent throughout the manuscript.

*     */Gene and protein symbols/. Prior to submission, authors should
determine that all gene and protein symbols used in a manuscript have
priority in the literature. When introducing new symbols, the manuscript
cover letter must state that the authors have conducted a search of the
literature and of relevant community databases and that the new symbol
has priority and has been registered in the appropriate community
database (if one is available for the species in question). New gene
symbols should be compliant with the naming conventions of the relevant
research community. Priority may be established for a gene symbol either
by publication in the literature or formal registration in a community
gene symbol database. Possible conflicts and/or confusion regarding
nomenclature should be resolved prior to submission, if possible, and/or
addressed in the cover letter. The full name for a gene should be stated
where first used in the manuscript. Full gene names, not symbols, should
generally be used in the title of the manuscript.

Authors are responsible for determining that all nomenclature conforms
to accepted community standards prior to submission. Some helpful
resources follow.

http://www.arabidopsis.org/portals/nomenclature/guidelines.jsp
<http://www.arabidopsis.org/portals/nomenclature/guidelines.jsp>
(/Arabidopsis/)
http://www.maizegdb.org/maize_nomenclature.php (Maize)
http://www.gramene.org/newsletters/rice_genetics/rgn3/v3C.html (Rice)
Nomenclature rules are being revised by the rice community at this time.
When a new link is available, it will appear here.
http://wheat.pw.usda.gov/ggpages/wgc/98/ (Wheat)
http://tgrc.ucdavis.edu (Tomato)
http://www.chlamy.org/nomenclature.html (/Chlamydomonas/)
VandenBosch, A., and Frugoli, J. 2001. Guidelines for genetic
nomenclature and community governance for the model legume /Medicago
trunculata/. MPMI *14,* 1364-1367.
http://www.chem.qmw.ac.uk/iupac/ (protein nomenclature)
http://www.expasy.org/cgi-bin/lists?nomlist.txt (list of
nomenclature-related references for proteins)

Nomenclature conventions differ among species and so, for instance,
/Arabidopsis/ nomenclature should not be used for other species, or vice
versa. Note also the requirements for case: nearly all plant species use
uppercase for the first letter and lowercase for subsequent letters,
whereas all letters are uppercase in /Arabiodopsis/ and /Petunia/ genes
and proteins. Maize genes are referred to with only lowercase letters,
except when referring to dominant alleles. Prefixes indicating species
(e.g., At, Zm, Os) are not generally allowed as part of a gene symbol,
except to avoid confusion in cross-species comparisons. Where used, a
two-letter prefix (e.g., At for /Arabidopsis thaliana/) should not be
italicized as it is not part of the gene symbol and should be separated
from the gene name by a space or hyphen. Although a lowercase "p" is
used to indicate the protein product of a gene in /Saccharomyces
cerevisiae/ nomenclature (e.g., SNF2p), this is not used in most plant
nomenclature systems; please use the accepted protein nomenclature
system for the species in question.

Symbols for putative orthologs often differ between species. However, if
probable orthology has not been established, genes should not be named
or renamed for homologs in other species because this may create
confusion in the future when more gene sequences are known in the
species and true orthologs can be predicted with greater confidence.
Authors may propose a revised nomenclature for a given clade of
orthologs using a shared symbol (e.g., /Xyz/1), accompanied by
two-letter prefixes (e.g., Zm, At, Hv, etc.; defined in the Methods and
not italicized) to indicate species: e.g., Zm/ Xyz/1 and Os/ Xyz/1. All
such proposals must be based on good phylogenetic information
demonstrating probable orthology (see definition below).

*     */Relationships between homologous genes/. The Plant Cell follows
the recommendations of Theissen (/Nature/ 415:741, 2002) and Fitch
(/Trends in Genetics/ 16:227-231, 2000) for usage of terms that describe
relationships between genes. / *Homology*/ is a relationship between
features or genes that share a common evolutionary origin. DNA sequences
may be homologous or not, but they may not be "partially" or "highly
homologous"; */percent sequence similarity/* may be used, but not
"percent homology." /*Paralogy*/ is a relationship between genes that
have originated by gene duplication, whereas /*orthology*/ is a
relationship between genes that originated by speciation. If orthology
or paralogy have not been established by a proper phylogenetic analysis,
"homolog(ue)" or modified terms such as "putative ortholog(ue)" or
"likely paralog(ue)" should be used. Homeolog(ue) is preferred over
paralog when gene pairs have arisen via polyploidy as opposed to gene or
segmental duplication.

*     */Gene fusions and constructs/. Gene fusions may be indicated by
either a single colon or a hyphen, but not by a double colon. For
example, /35S:GFP/, /35S-GFP/, /CRY2:GFP/, and /CRY2-GFP/ are acceptable
to refer to promoter-coding sequence fusions and fusions of coding
sequences. A double colon should be used only for insertions (such as
insertions by transposable elements), as in /An1::dTph1/, /Bz1::Ac/, or
/LFY::TAG1/. Lowercase "p" should be used to refer to plasmids (e.g.,
pBR322), and to avoid confusion it should not be used to refer to
promoters. Authors should designate promoters as, e.g., P35S, Pro35S, or
35S_pro and promoter/coding sequence fusions as P35S:LFY, Pro35S:LFY or
35S_pro :LFY. Transactivations should be written, e.g., P_FIL >> or
FIL_pro >>.

     /Genes and mutations/. The standard definition of the term gene in
molecular terms is the complete segment of chromosome that is required
for expression of a gene product (i.e., including promoters, enhancers,
introns, exons, untranslated regions, etc.) Thus, a coding sequence or
transcription unit should not be referred to as a gene, but rather as a
component of a gene. To avoid confusion, double or triple mutations
should contain the names of the mutated genes separated by a space,
e.g., /sad1 sad2/, or /cad4 cad5 cad6/, and should not be given entirely
new names.

Authors should note that insertional mutations are not necessarily
"knockout" mutations and should not be referred to as such unless they
have been shown experimentally to be null alleles. Also, putative
insertional mutations should generally be characterized at both ends of
an insertion prior to manuscript submission; otherwise, the possibility
cannot be ruled out that the observed sequence fusion represents a
translocation rather than an insertion.

Generally, characterization of multiple, independent alleles is
necessary to establish that a mutation (such as a T-DNA insertion or
chemically induced mutation) is responsible for an observed phenotype,
as opposed to an undetected, linked mutation. Complementation tests via
transformation can be valuable, although their interpretation may be
limited by the possibility of redundancy, and so statements of proof
should be limited to cases in which multiple independent alleles have
been characterized. (Back to top) <#TABLE OF CONTENTS>

*Methods*. Methods must be described completely enough that other
laboratories can replicate results and verify claims. Generally,
standard procedures should be referenced, though significant variations
should be described. Appropriate experimental design and statistical
methods should be applied and described wherever necessary for proper
interpretation of data and verification of claims. All novel materials
and the procedures to prepare them should be described in sufficient
detail to allow their reproduction (e.g., DNA constructs, genetic
stocks, enzyme preparations, and analytical software). The penultimate
section of Methods should be the section entitled "Accession Number,"
and the last section should be "Supplemental Data," containing the
titles only of all supplemental materials that will be posted online.

*     */Accession numbers/. Accession numbers should be provided as the
last paragraph of Methods (just before Acknowledgements) with the
heading ?Accession Numbers? for any genes or new sequence data discussed
in the article. Insert the following statement and provide accession
numbers: ?Sequence data from this article can be found in the
EMBL/GenBank data libraries under accession number(s) XX000000.? In the
case of Arabidopsis, the AGI locus identifier (?At number?) must be
provided for each gene described (see http://www.arabidopsis.org). If a
list of accession numbers is provided in a table or figure, that can be
stated in this section, rather than listing all of the numbers. If an
accession number has not been assigned at the time of submission, please
use Xs as placeholders to be updated later. In general, accession
numbers should be provided only in the Methods, not elsewhere in the
manuscript, unless needed for clarity. Accession numbers for genes must
be specific for each gene; accession numbers for BAC clones or
chromosomes are not acceptable substitutes. Accession numbers must also
be provided for any supplemental data that is placed in a permanent
public repository (e.g., GEO http://www.ncbi.nlm.nih.gov/geo,
Array-Expresshttp://www.ebi.ac.uk/arrayexpress, or Protein Data Bank
(http://www.rcsb.org/pdb).

     Novel nucleotide and amino acid sequences must be deposited in a
public repository such as the GenBank database
(http://www.ncbi.nlm.nih.gov <http://www.ncbi.nlm.nih.gov/>). If a new
function or mutation is found to be associated with a previously known
DNA sequence (i.e., an existing GenBank entry), authors are encouraged
to create a new GenBank entry in order to link the sequence and the gene
symbol/function in the database. In the case of (partially or
completely) sequenced vectors and constructs, accession numbers should
be provided. All data necessary to validate protein structure
determinations, including x-ray amplitudes and phases and the derived
atomic coordinates, should be submitted to the Protein Data Bank
(http://www.rcsb.org/pdb).

*     Large-scale experiments*. In evaluating large-scale experiments
such as transcript profiling, we will consider whether there is a clear
and complete description of each experiment; whether biological and/or
technical replicates should have been used; what statistical analysis
has been performed; whether a multiple comparison correction has been
used to control for Type I family-wise error, where necessary; and/or
whether the need for statistical analysis to support the claims has been
obviated through validation of claims by independent experiments.
Authors are encouraged to involve statisticians in both the design and
analysis of experiments, to whatever extent is necessary, to properly
interpret results. Large-scale data sets must be made available for
review at the time of submission and must be deposited in an accepted
format to a permanent public repository with open access (e.g., GEO
http://www.ncbi.nlm.nih.gov/geo or Array-Express
http://www.ebi.ac.uk/arrayexpress). The purpose of this policy is to
ensure that conclusions are scientifically sound, i.e., based on an
appropriate experimental design and statistical analysis of the data. If
conclusions are not drawn and such experiments are used simply as a
screen, then the preceding does not apply, as long as the manuscript
explicitly indicates that the experiment should be regarded only as a
screen, that results were used only to identify candidates which were
then validated independently, and that no conclusions have been or
should be drawn from the data (such as what number or fraction of genes
respond in a given manner). Provision of datasets used only as screens
as supplemental information is encouraged, but not necessarily required.

*     Quantification of molecules, including DNA, RNA, and proteins.
*Methods for quantification of levels or differences in levels of
molecules in biological samples must be described fully and shown to be
quantitative and reproducible, using true biological replicates. Any
conclusion that levels differ between samples must be supported by
presentation of methods and data shown to be reliable; supporting
information demonstrating reliability of an assay may sometimes be
provided as Supplemental Information rather than in the body of the
manuscript, subject to the approval of the handling editor. Use of the
term ?semi-quantitative? is not acceptable in /The Plant Cell/; instead,
assays must be shown to be sufficiently quantitative to support a
conclusion of changes in levels.

     /RNA and DNA. /In the case of quantification of nucleic acids,
?real time? PCR assays are preferred, when feasible. In ?standard? PCR
assays, including ChIP (chromatin immunoprecipitation) assays, ethidium
bromide staining should be not be used unless it is demonstrated to be
quantitative in the range of DNA concentrations being investigated.
Ethidium bromide staining is not quantitative above very low levels of
DNA because fluorescence saturates rapidly, leading to under-estimation
of fold-changes in DNA or transcript levels or the equality of
expression of controls. Thus, use of more quantitative methods of
staining DNA, including SYBR green/ SYBR gold which gives linear
responses over much broader ranges of DNA concentration, is generally
preferred for publication in /The Plant Cell. /Alternatively,
radioactive detection followed by appropriately short time exposures is
also acceptable if shown to be quantitative. Methods must include
details showing that amplification was in the logarithmic phase for each
DNA molecule being analyzed. Data from low-cycle RT-PCR amplifications
stained with SYBR green or gold/radio-actively detected should be
referred to as 'quantitative' rather than 'semi-quantitative' RT-PCR.

     *Molecular phylogenetic analyses*. Methods used for sequence
analysis must be reported in full with citations and software and
parameter values (even if only default values were used) in a separate
section of Methods entitled "Phylogenetic Analysis". Please note that
CLUSTAL does not produce an acceptable phylogeny; use a true
phylogenetic analysis program (e.g., PHYLIP, MEGA, MR. BAYES).
Alignments used to produce phylogenies should be produced with an
appropriate alignment program (e.g., CLUSTAL), then manually adjusted to
optimize alignments. Alignments must be provided as a Supplemental Table
or Figure (preferably as a .doc file). Statistical support for nodes in
phylogenetic tree figures must be reported (e.g., posterior
probabilities or bootstrap values from a minimum of 1000 trials). If
phylogenetic trees are depicted or interpreted as rooted, the criterion
used for rooting (e.g., midpoint, outgroup) must be provided and, if
outgroup rooting is used, the basis for the choice of outgroup should be
explained. Authors are encouraged to consult with an expert in molecular
phylogenetics if they do not have such expertise themselves. (Back to
top) <#TABLE OF CONTENTS>

*Tables*. Tables should be submitted embedded within the text file just
before the references. Prepare tables using Word's table feature. If not
using Word's table feature, tables can be prepared using a single tab
between columns. Number tables consecutively as they are first mentioned
in the text. Provide a concise title for each table, and label each
column with an unambiguous heading. If footnotes are needed for clarity,
designate them with lowercase letters in the order in which they are
referenced in the table. Table titles and footnotes should be placed as
regular text outside the table body. Each table may include a short
general description before the footnotes. (Back to top) <#TABLE OF CONTENTS>

*References*. Cite references in the text by name and date of
publication and not by number. List only articles that are published or
in press. References should contain complete titles and inclusive page
numbers. Authors are expected to proofread every citation in their
reference list against the PDF or photocopy of the cited work so that
the reference list is accurate with respect to spellings, symbols,
italics, subscripts/superscripts, and accents. Cite in the text all
unpublished results, including personal communications and submitted
manuscripts (for example, R. Goldberg and K. Jofuku, unpublished
results). A permission letter from each person cited as a personal
communication will be required upon acceptance. Permission is also
required from the authors of unpublished information cited in the text
if those authors are different from the article's authors. Citations for
web sites (other than for primary literature) should be handled
parenthetically in the text and not included in the reference list.
Authors should test all URLs and links.

If you are citing an article that only exists as an early online
version, include the PubMed ID (PMID) number to allow reviewers to link
directly to the article. At the bottom of the PubMed record for the
article, you will find the PMID number which you should include in the
reference as follows:

    *Author, A.B., and Author, B.B.* (2006). Title of article. PMID:
    16723506.

It is expected that all cited publications have been read and determined
to be appropriate by the authors, not merely identified by database
searches. Reference to specific results should be to original research
articles, not to more recent articles or reviews. (Back to top) <#TABLE
OF CONTENTS>

*Figures*. Number figures consecutively according to the order in which
they are called out in the text. Figures should be unambiguous and as
conceptual as possible and should provide enough information so that the
reader can understand them without significant input from the text. For
the best possible reproduction of gel blots, submit combination figures
in which the labels and photographs or autoradiographs are composite
images. Format sequence data preferably to one-column width for shorter
sequences and two- column width for longer sequences. Make sure that the
fonts in sequences are easily readable, especially if sections are
highlighted to display conserved or structural features. Use the same
fonts for all figures. For those figures that contain more than one
panel, designate the panels with capital letters (no parentheses and no
periods following letters) in the upper left-hand corner of each panel,
if possible. Wording in figures must match the rest of the manuscript
for capitalization, italics, and use of symbols. If labels contain
typographic errors or inconsistencies, the author will be asked to
upload corrected figures.

*     Figure legends*. Provide a short title for each figure. Figure
legends should be concise and should not repeat information presented in
the text. Figure panels that are designated with capital letters should
have specific subtitles in the legend and should be described separately
and completely. Do not describe methods in figure legends unless they
are necessary to interpret the results conveyed by the figure. Define in
the legend all symbols and abbreviations that are used in the figure.
Accession numbers should not be included in figure legends. For bar
graphs, error bars should be defined in the legend, along with sample
sizes. Each figure legend should appear at the end of the manuscript
text file.(Back to top) <#TABLE OF CONTENTS>

*     Figure manipulation*. /The Plant Cell/ does not allow certain
electronic enhancements or manipulations of micrographs, gels, or other
digital images using Photoshop or any other software. If multiple images
are collected into a single figure, be sure to separate them clearly
with lines. If a digital tool is used to adjust contrast, brightness, or
color, it must be applied uniformly to an entire image; targeted
alteration of only part of an image is prohibited. /The Plant Cell/
reserves the right to ask authors to provide supporting data on which
figures were based. Please refer to J Cell Biol (2002) 158: 1151
(http://www.jcb.org/cgi/content/full/158/7/1151) for guidance on
acceptable and unacceptable digital image manipulation.

*     Figure size*. All parts of a figure must fit on a single printed
page in portrait, not landscape, format and each figure should be sent
in its own file. Please format figures to fit into one column whenever
appropriate. In general, smaller gel images look neater than larger
ones. Format figures for full-page size when a figure contains multiple
panels or when important morphological, microscopic, or other
experimental data could not be distinguished at one-column width. Place
panels as close together as possible and eliminate or reduce black or
white backgrounds as much as possible. For panels that are side-by-side
or stacked vertically, repeated identical ordinate or abscissa labels
can be deleted, unless needed for clarity. Include the figure number at
the top or bottom of the page.

*     Black and white figures.* Do not save black and white or grayscale
images in color mode such as RGB or CMYK, as this will result in huge
file sizes.

*     Color figures*. Color figures must be submitted in RGB mode only.
"Adobe (1998)" should be selected as the ICC profile to ensure that we
can reproduce the color accurately. One in twelve males, on average, is
colorblind. In preparing your figures, please observe the following
guidelines to ensure that all readers, reviewers, and editors will be
able to comprehend your data. In fluorescent double-staining micrographs
and DNA chips, do not use the combination of red and green; use magenta
and green instead. For micrographs with triple or more channels,
additionally show either a grayscale image of each channel, or the
combination of the two most important channels in magenta and green. For
graphs and line drawings, label elements on the graph itself rather than
making a separate color-coded key. Do not try to convey information in
color only, but use BOTH color and shape (solid and dotted lines,
different symbols, various hatchings, etc.; however, avoid pattern fills
if creating PowerPoint files). For more information, see the following
website: http://jfly.iam.u-tokyo.ac.jp/color/.

*     Figure format. *Figures may be created using PDF, Photoshop,
Powerpoint, Illustrator or other Windows Office software. If you use
Photoshop or similar software, send .tif files or lzw compression .tif
files at full size and delete any blank space around the edges of each
figure. If you use Illustrator or similar software, send .eps files.
Type should be set to "create outlines" or "convert to paths," or fonts
should be embedded when saving the file. If you use PowerPoint, send the
original .ppt files. Use only basic PowerPoint fonts, do not draw lines
that are less than .25 pts thick, and use shaded or colored fills
instead of ?pattern? fills. PDF files are acceptable if they are of high
quality and should have fonts embedded.

*     Figure resolution. *Resolution of most figures should be 600 dpi
at the actual size the figure is to print. For all-black line art, 1000
dpi is needed. Images imported into PowerPoint should have 600 dpi
resolution. Please be sure that figures are at the size you expect them
to be published in the journal. The width of one column is about 3.25
inches (85 mm) and a two-column width is about 7 inches (175mm).

*     Figure file size. *Please keep file size as small as possible.
Large file sizes (30 MB or greater) may occasionally be needed, but
should be avoided if possible. Please do not use any compression such as
WinZip or STF. For .tif image files, use lzw lossless compression, which
has no quality loss due to compression.

*     Help with digital art*. Helpful information on technical aspects
of creating figures is available at
http://submit.plantcell.org/journals/plantcell/forms/TPCdigital_art.pdf.
Questions may be directed to Susan Entwistle at /The Plant Cell/
editorial office (301/251-0560, ext. 118; susan@aspb.org
<mailto:susan@aspb.org>). (Back to top) <#TABLE OF CONTENTS>

*Supplemental Data*. Data that are integral to the manuscript but
impractical to include in the printed journal (for instance, large-scale
data sets and videos) may be presented in /The Plant Cell/ Online. Data
and information that are peripheral to the conclusions may be provided
as supplemental data if the coeditor agrees that these data would be
valuable to specialist readers and are not necessary for other readers
to understand the experimental support for important claims and
conclusions. All data that are directly relevant to, and necessary for
support of the central claims and conclusions of the article must be
presented in the manuscript itself. Authors should note that the
function of /The Plant Cell/ Online is to provide an opportunity to
present data and information that would not normally be published in the
print journal, rather than to reduce article length. Important control
experiments should always be presented in the manuscript, whereas assays
that merely demonstrate that a reagent is suitable for use in an
experiment (for instance) may be presented as supplemental material with
the permission of the coeditor. Detailed experimental protocols that
would be of interest only to specialists and are not necessary to
support the central claims and conclusions are also permissible in
Supplemental Data. Use of phrases such as "data not shown" or
"unpublished results" is discouraged in the print article; instead,
authors are encouraged to present such data as supplemental material.
All supplemental materials will be reviewed as part of the normal
manuscript review process.

     *Supplemental data presentation. *Supplemental materials presented
at /The Plant Cell /Online are subject to the same copyright
restrictions as published manuscripts and cannot be presented elsewhere
without proper citation.

      Supplemental materials must be briefly described in the manuscript
(in the Results or Methods section, as appropriate) with direct
reference to each item, such as "Supplemental Figure 1 online,"
"Supplemental Table 1 online," etc. The titles (only) of each
Supplemental Figure, Table, Movie, etc. should be listed at the end of
the Methods section under the heading ?Supplemental Data? in the
following order: Supplemental Figures, Supplemental Tables, Supplemental
Methods, Supplemental Movies.

     Multiple supplemental files should be combined and submitted as a
single .pdf file, no larger than 5 MB, entitled ?Supplemental Data?.
(Please note: high resolution files are not necessary for online
viewing.) Files to be merged into a single Supplemental file include
figures, tables and supplemental methods. Titles and complete legends to
Supplemental Figures should be placed above or below each figure and
should follow the same guidelines as for article figure legends (see
above). Supplemental Tables should include any relevant footnotes and
information necessary to understand the material in the table.
References associated with supplemental materials may be placed
immediately below the corresponding figure or table, or in a separate
section entitled ?Supplemental References? at the end of the
Supplemental Data file.

     Large-scale data sets (i.e., large tables) should be presented as
separate files in .xls or other appropriate format (e.g., .dat, .hmm),
and not as pdf files. Individual file sizes of large tables should be no
larger than 5 MB.

     Supplemental Movies should be presented as separate files no larger
than 10 MB. Any legends associated with Supplemental Movies should be
presented in a separate Microsoft Word file entitled ?Supplemental Movie
Legends?. (Please do not include this file in the combined .pdf file).

*     **Large-scale data sets*. Large-scale data sets (e.g., complete or
draft genome sequences, genome annotations, genetic maps, EST data sets,
transcript profiles, proteomic data sets, and metabolic profiles) that
are integral to the manuscript must be provided at time of manuscript
submission. At time of submission, large-scale supplemental data must be
placed in a permanent public repository (e.g., GEO
http://www.ncbi.nlm.nih.gov/geo or Array-Express
http://www.ebi.ac.uk/arrayexpress), as it will not be stored at /The
Plant Cell/ Online site permanently, only during the review process.
Non-permanent URLs may be provided at the option of authors as a means
to enable readers to access or query information more conveniently.
Non-permanent URLs should also be provided if authors want to make
available imaging or other software with unusual file types requiring
special software downloads or those that are not compatible with /The
Plant Cell /Online site. In general, large-scale data sets must be
complete (e.g., must include the complete set of genome sequences
analyzed, ESTs identified, genes queried in transcript profiling,
peptides identified, molecules identified, etc.) and should be provided
in Microsoft Excel format. Data supporting transcript profiling
experiments must include complete sequence information (e.g., accession
numbers, any relevant annotation data, and in the case of /Arabidopsis/,
TAIR locus identifiers [http://www.arabidopsis.org]). Authors are
encouraged to follow the MIAME (Minimal Information for a Microarray
Experiment) standards. See Methods for expectations of experimental
design, analysis, and reporting.

*     **Movies*. Video material that is absolutely required for
interpretation of data may be used to supplement the online journal.
Please upload your video as supplemental data in QuickTime (.mov) 3.0 or
higher format so that reviewers can evaluate the video. (Other
acceptable video formats include .mpeg and .avi.) To avoid excessive
delays in downloading, video files should be no larger than 10 MB and
should run between 30 and 60 seconds. Use QuickTime's "compress" option
when preparing files to help control file size. Cropping frames and
image sizes can also significantly reduce file sizes. Files submitted
can be looped to play more than once, provided the file size does not
become excessive. All videos should be submitted at the desired
reproduction size and length. No editing will be done to the videos at
the editorial office; all changes are the author's responsibility.

IMPORTANT: A set of still images corresponding to each video must be
included as a figure in the article. The figure should include three
frames of the video, indicating the beginning, middle, and end. Please
indicate clearly in your text whether a figure has a video associated
with it as supplemental data. A brief figure legend should also be
provided. The figures should be prepared using the guidelines for
figures indicated above. Stills from more than one video may be included
in the same figure. (Back to top) <#TABLE OF CONTENTS>

*Cover Submissions*. Each cover of /The Plant Cell/ will feature an
image representative of an article published in that issue. Authors who
wish to have an image considered for the cover should upload the image
as an additional supplemental file along with a separate text file that
includes a brief one-paragraph description of the image, and indicate on
the checklist provided at acceptance that a cover candidate has been
submitted. Authors may also email a .jpg file of their cover submission,
along with the brief description to Susan Entwistle at /The Plant Cell/
editorial office: susan@aspb.org <mailto:susan@aspb.org>. If an author
does not hold the copyright for a submitted image, they are responsible
for obtaining the necessary permission to use the image in /The Plant
Cell/. (Back to top) <#TABLE OF CONTENTS>

*PEER REVIEW*
Members of the editorial board will evaluate all manuscripts upon
submission to determine whether they are appropriate for evaluation by
expert outside reviewers. Reviewers are required to follow ASPB?s policy
regarding conflicts of interest
<http://www.aspb.org/publications/coi.cfm> . Authors may suggest
reviewers, but should not suggest persons who have a conflict of
interest as defined by the ASPB policy. Editors are permitted to use any
reviewer reasonably believed to be an appropriate scientific expert,
except reviewers who would be excluded by ASPB?s conflict of interest
policy. If authors wish to request the exclusion of certain reviewers
for other reasons, specific justification must be provided in the cover
letter; such requests may be considered at the discretion of the editor.
Decisions will be made as rapidly as possible, and the journal strives
to return reviewers' comments to authors within 4 weeks whenever
possible. If revision is requested, the editorial board will evaluate
revised manuscripts and determine whether outside review is required.
The board normally will consider only one revised manuscript, and this
manuscript must be submitted within 1 month unless an extension is
granted. In the case that extensive revision including additional
experimentation is required, journal policy is to decline the
manuscript, but editors may choose to encourage resubmission.
Resubmissions are subject to the full review process. It is the goal of
the journal to publish manuscripts within 4 months after submission, but
this can only be achieved if the original submission meets all journal
requirements. (Back to top) <#TABLE OF CONTENTS>

*MANUSCRIPT ACCEPTANCE*
Authors of accepted manuscripts will be provided with a checklist for
preparing their final submission. Accepted manuscripts are copyedited
for grammar and journal style before proof is generated. To facilitate
rapid publication, after authors have reviewed proof and corrections are
made, the article will be posted online as part of the publication
/Plant Cell Preview/. Articles are posted anywhere from a few days to a
few weeks prior to the full online issue of the journal. Any subsequent
final corrections to the paper will appear in the final published
version (and will suppress any earlier version) for both /The Plant
Cell/ Online and /The Plant Cell/ (paper) versions. If an author does
not want to have an article posted online ahead of final publication,
this should be specified on the checklist provided at acceptance. The
official date of publication is the date that the article first appears
online as part of /Plant Cell Preview/. (Back to top) <#TABLE OF CONTENTS>

*PROOFS*
The journal printer will deliver electronic page proofs to the
corresponding author. The printer will notify the author via e-mail to
retrieve page proofs. The author will have access to a PDF file, which
will contain PDF pages (with figures and tables), a high-resolution PDF
file of the images only, and a reprint order form. Page proofs are
considered to be the final version of the manuscript. *With the
exception of typographical or minor clerical errors, no changes will be
made in the manuscript at the proof stage.* Notes added in proof will be
sent to the coeditor assigned to the manuscript prior to publication and
will be reviewed for appropriate content and wording. Authors will
receive proofs approximately 3 to 4 weeks after final acceptance of the
manuscript. Because of the tight publication schedule, authors must
relay all additions and corrections to the printer by e-mail or by
overnight mail within 24 hours of receipt of the proofs. Failure to act
promptly to approve the page proofs may delay publication of the
manuscript. For electronic correction of manuscripts, please use the
free text tool to mark your PDF proof and e-mail your corrections to
tpc@dartmouthjournals.com <mailto:tpc@dartmouthjournals.com>. (Back to
top) <#TABLE OF CONTENTS>

*FEES AND CHARGES*
Corresponding authors will be assessed a per page charge of $75.
Corresponding authors who are ASPB members will receive a $20 per page
discount. There will also be a charge of $350 for each color figure.
Publication of an article in /The Plant Cell /is not contingent upon the
author's ability to pay. Under exceptional circumstances that are
explained in writing to the Managing Editor, authors may request waiver
of the page charges or the color reproduction charges. Authors will need
to justify that the color figure is essential for interpreting the
results presented in the manuscript. Authors are charged for alterations
made in proof that are not due to editor or typesetter errors. Color
figures changed to grayscale in proof will be charged as author alterations.

ASPB is now offering an Open Access option that allows authors to have
their online articles available for free to all users immediately upon
publication. The fee for Open Access, which is in addition to the usual
author charges, is $1000 (discounted to $500 if the author's institution
subscribes to the journal). For more information, click here.
<http://www.aspb.org/openaccess/> (Back to top) <#TABLE OF CONTENTS>

*POLICIES*

*Electronic Posting of Articles*. /The Plant Cell/ will review
manuscripts that include data that are posted on an author's web site.
If the data are posted in the form of a preprint, it should be clearly
stated beneath the title of the web preprint that it is under review (or
accepted for publication) by /The Plant Cell/. Authors may post only the
version of their manuscript that is under consideration by /The Plant
Cell/ editorial board. Final published manuscripts will reside on the
journal sites. Once the published article has appeared online at the
journal site, a toll-free link providing barrier-free access to the HTML
and PDF versions of the article will be e-mailed to all authors. Authors
should replace their manuscript posting with the toll-free link to their
article. These links also may be deposited in institutional
repositories. (Back to top) <#TABLE OF CONTENTS>

*Materials Distribution Policy*. Publication in /The Plant Cell/
requires that authors make available all materials integral to the
reported results (i.e., necessary to support the major claims and enable
their verification or replication) for non-commercial research purposes.
Such materials include mutants, genetic stocks, transgenic plants, cell
lines, recombinant constructs, vectors, viruses, enzymes, antibodies,
and software. In general, authors are expected to deposit novel
materials in public repositories, to the extent possible and consistent
with the policy stated here. All manuscripts submitted to /The Plant
Cell/ will be reviewed for compliance with journal policy and should
include the following statement as an unnumbered footnote: "The
author(s) responsible for distribution of materials integral to the
findings presented in this article in accordance with the policy
described in the Instructions for Authors (www.plantcell.org) is (are):
John D. Author (author@college.edu)." Contact information for the
author(s) responsible for distribution of materials must be provided.

Authors should expect to comply with requests for materials within 60
days. Requestors should expect to comply with conditions (including via
a signed Materials Transfer Agreement) that do not unreasonably limit
use for non-commercial research purposes. Authors are expected to make
materials available to all qualified investigators in private or public
organizations on similar, if not identical, terms. If authors do not
possess rights to distribute materials, upon request they should supply
contact information for the source of the materials and should make
their best efforts to facilitate the transfer of these materials within
the expected timeframe, preferably by arranging for standard, reasonable
terms in advance of publication or even prior to the initiation of
research with such materials. In the case of unreasonable delay (and
lack of extenuating circumstances, such as travel or illness, or special
circumstances, such as significant and reasonable regulatory or safety
issues), the requestor may contact the managing editor. Non-compliance
with this policy by authors may result in denial of future rights to
publish in /The Plant Cell/ and/or notification of authors' funding
agencies or employers and/or retraction of the publication describing
the materials on the grounds that it is not possible to confirm the
results and conclusions. It is reasonable for authors to require that
requestors obtain a license for research use of patented materials.
Reasonable approaches to protect ownership rights are allowable if they
are described in the Methods. For instance, mutants or alleles that
exist only in proprietary inbred lines may be provided via hybrids if
the inbred line itself is not integral to the findings. In lieu of
providing plasmid constructs, complete DNA sequences necessary to
replicate them could be provided via a public repository or supplemental
data, assuming component elements are readily available and the
construct is not so complex that it could not be replicated in a timely
manner. Authors may reasonably limit amounts of materials (such as
enzymes, antibodies, and natural products) that will be distributed in
the case that substantial effort is required for their isolation.
Sufficiently detailed procedures must be provided to permit production
of such materials; detailed protocols should be provided as supplemental
material via /The Plant Cell/ Online.

To facilitate sharing of materials, authors may choose to use one of the
following services.
Addgene (http://www.addgene.org) <http://www.addgene.org>
Arabidopsis Biological Resource Center
(http://www.biosci.ohio-state.edu/pcmb/Facilities/abrc/abrchrome.htm)
<http://www.biosci.ohio-state.edu/pcmb/Facilities/abrc/abrchrome.htm>
Maize Genetics Cooperation Stock Center
(http://maizecoop.cropsci.uiuc.edu/) <http://maizecoop.cropsci.uiuc.edu/>

*NOTE: *ASPB provides these links as a service to our author community.
The Society does not take responsibility for or endorse the services
these companies offer and cannot attest to the quality of their work. If
you have questions, or if you do use one of these services and would
like to send ASPB feedback on your experience, please contact Nancy
Winchester, ASPB Director of Publications, at nancyw@aspb.org
<mailto:nancyw@aspb.org>. (Back to top) <#TABLE OF CONTENTS>

*Corrections and Retractions*. If necessary, corrections of significant
errors in published articles will be published in a later issue of the
journal. Authors are requested to bring any errors to the attention of
the Production Manager as soon as possible. A correction published in
the print journal will also be published as a correction in the online
journal and will be linked to the original article. Articles may be
retracted by their authors, academic or institutional sponsor, editor,
or publisher because of pervasive error or unsubstantiated or
irreproducible data. A correction or retraction, so labeled, will appear
in a prominent section of the journal, will be listed in the contents
page, and will include the title of the original article. The text of a
retraction will explain why the article is being retracted and will
include a bibliographic reference to it.
(Back to top) <#TABLE OF CONTENTS>

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