Instructions for Authors of Research Articles

(Initial Submission)

Scope

Science Signaling publishes articles containing original research that report major advances in the understanding of cellular, physiological, or pathophysiological regulation in model organisms and man. Papers from a wide variety of disciplines are welcome; interdisciplinary studies are especially suitable for this journal. Included within the scope are a broad array of traditional medical specialties including (but not limited to) cancer, immunology, cardiovascular biology, neuroscience, cellular and organismal metabolism physiology, computational and systems biology, microbiology, host-microbe interactions, and plant biology.

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Criteria and Evaluation Process

Research Articles should substantially advance our understanding of cellular or physiological responses to external or internal cues and refine our views of these processes, or test cellular signaling pathways previously defined in vitro under both normal and pathological conditions in vivo. Research Resources should present new validated tools or techniques or validated databases or data sets relevant to the regulation of cell biological or physiological processes that are of broad interdisciplinary interest or of exceptional unusual interest within a specialty. Papers will be evaluated for their  importance, technical rigor and novelty. All papers will undergo an initial screening by staff editors and the Advisory Board. Only those most likely to be ultimately published will be sent out for in depth peer review. The Science Signaling editors are committed to a rapid, thorough and fair peer-review process.

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Editorial Policies

Authors of Research Articles should familiarize themselves with the Submission Requirements and Conditions of Acceptance for Science Signaling before submitting their paper. These policies spell out the rights and responsibilities that authors agree to when submitting and publishing their papers. Access this information here.

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Format and Style

All Research Articles should include an Abstract and the following sections: Introduction, Results, Discussion, Materials and Methods, References and Notes. Supplementary Material is permitted (see the section on Supplementary Materials below) but should be limited to information that is not essential for the general understanding of the research presented in the main text paper.

Use double spacing throughout the text, tables, figure legends, and References and Notes.  Technical terms should be defined. Symbols, abbreviations, and acronyms should be defined the first time they are used. All tables and figures must be cited in numerical order. For best results use Times and Symbol fonts only.

The manuscript should be assembled in the following order:

Titles: The titles should be no more than 135 characters (including spaces).

One-sentence summary: The one-sentence summary should capture the most important point of the paper.

Authors: Authors and their affiliated institutions, linked by superscript numbers, should be listed beneath the title on the opening page of the manuscript.

Abstract: The Abstract should not exceed 250 words and should explain to the general reader why the research was done and why the results are important. The Abstract should present background information to convey the context of the research, give a general idea of the methodology used, describe the results, and draw general conclusions. The Abstract is distinct from the main body of the text, and thus should not be the only source of background information critical to understanding the manuscript. Please do not include citations or undefined abbreviations in the Abstract.

Introduction: The manuscript should start with a brief Introduction describing the paper's significance. The Introduction should provide sufficient background information to make the article intelligible to readers in other disciplines, and sufficient context that the significance of the experimental findings is clear..

Results: The Results should describe the experiments performed and the findings observed. The Results section should be divided into subheadings to delineate different experimental themes. Subheadings should either be all phrases or all complete sentences. All data must be shown either in the main text or in the Supplementary Materials, and references to unpublished materials are not permitted. All tables and figures should be cited in numerical order. Do not include extensive descriptions of the experimental methods (such as the concentrations, incubation periods, or protocols). Do not provide N and P values in the Results; these should be in the appropriate figure legends.

Each panel of the main figures and each table in the main manuscript must be called out in the text in order; no exceptions can be made. Each panel of the figures in the Supplementary Materials must be called out at least once in the main text. The editors strongly prefer that the panels of the figures in the Supplementary Materials be called out in order, but it is not strictly required. For main figures and figures in the Supplementary Materials with multiple panels, it is not sufficient to use a generic callout. For example, if Fig. 1 contains panels A to J, it is necessary to refer to the specific figure panel or panels in Fig. 1 that contains the data to which the reader should refer. Items in the Supplementary Materials that are not figures must also be called out at least once in the main text. The editors strongly prefer that that the non-figure items in the Supplementary Materials be called out in order, but it is not strictly required. All figure panels containing data, whether they are in a main or Supplementary Materials figure or table, must be mentioned in the Results before being mentioned in the Discussion.

Discussion: The Discussion describes the conclusions that can be drawn from the results, as well as the significance and implications of the research. If subheadings are present, they should either be all phrases or all complete sentences. Be concise as possible in the Discussion. Excessively long Discussions are not allowed.

Materials and Methods: The Materials and Methods should provide sufficient information to allow replication of the results (standard methods may be referenced without a detailed description) or cite previous publications that adequately describe the experimental procedures used. There must be a single Materials and Methods for the entire manuscript. The only exception for Materials and Methods in the Supplementary Materials is generally detailed computational methodology.

Supplementary Materials: List your Supplementary Material items, including titles for each of the supplementary figures, tables, videos, audio files, or other files.

References and Note: References are numbered in the order in which they are cited, first through the text, then through the figure and table legends, and finally through the Supplementary Materials. Each reference should have a unique number; do not combine references or embed references in notes. There must be a single reference list for the entire manuscript. Journal article references should be complete, including the complete list of authors, the full titles, and the inclusive pagination. See Citation Style below for details of citation style.

In a paragraph after the last reference, include the following sections. Acknowledgments: In addition to thanking individuals who provided technical and conceptual support, “Acknowledgments” should thank individuals who provided reagents. Funding: This section should include funding sources for all authors. Author contributions: Describe the contributions of each author (use initials) to the paper. Competing interests: Include any financial interests of the authors that could be perceived as being a conflict of interest and any awarded or filed patents pertaining to the results presented in the paper.  Data and materials availability: A statement is necessary for manuscripts for which data has been deposited or when reagents used in the manuscript require an MTA. Indicate the repository where the data has been deposited and the dataset identifier or accession number. Indicate the reagents and institutes that require an MTA.

Tables should be included after the references and should supplement, not duplicate, the text. They should be called out within the text and numbered in the order of their citation in the text. The first sentence of the table legend should be a brief descriptive title.

Figure legends should be double-spaced in numerical order and included in the text file immediately after any tables. A short figure title should be given as the first line of the legend. Legends should describe the figure, specifically the parameter being measured in the figure and the different treatment or experimental groups. Legends should not recapitulate the Materials and Methods or include interpretation that belongs in the Results. Excessively long figure legends are not permitted. Nomenclature, abbreviations, symbols, and units used in a figure should match those used in the text.

Figures should be called out within the text. Figures should be numbered in the order of their citation in the text. See below for detailed instructions on preparing your figures.

Supplementary Materials can accommodate various types of auxiliary information of use to the reader, including material not presentable in a text format. We encourage authors to provide original data in the Supplementary Materials. We can host supplementary figures and legends, complex materials and methods, video files, original data files, and large data sets. Each item in the Supplementary Materials should be accompanied by a brief text description. The first sentence of this caption should be a title, and the titles of the Supplementary Materials items should be listed immediately before the References section. The Supplementary Materials should not be essential to the general understanding of the research presented in the main text of the paper.

A Microsoft Word template for this format can be downloaded here.

Standards for Analysis and Presentation of Data

All data must be shown; references to unpublished results or data not shown are not permitted. Units of measure should be given in SI units. If measurements were made in English units, give metric equivalents.

N values

N values must be provided in the figure legends for every data panel (including those in the Supplementary Figures). What N represents - cells, blots, mice, or experiments - must be indicated. For data requiring quantification and statistical analysis, N must represent at least 3 independent biological replicates. For data that does not require quantification and statistical analysis, Presenting data from a single experiment is not acceptable except under very limited circumstances, and N of at least 3 is preferable. Representative data may be shown.

Quantification

Statements about changes or lack of change should be supported by quantification of at least 3 independent assays and statistical analysis performed on amalgamated data from at least 3 independent experiments, not on the results of a single experiment. Statements about increases or decreases cannot be made if differences are not statistically significant.

For Western blot data, key statements about increases, decreases, or lack of changes in protein abundance, phosphorylation, posttranslational modification, association, and activation must be supported by quantification of data amalgamated from at least 3 Western blots (that represent independent biological replicates) and statistical analysis where appropriate. Showing the densitometry from a single Western blot is not acceptable. When quantifying signals from lysates, the signal for the protein of interest must be normalized to that of a loading control. The signal for a phosphorylated form of a protein must be normalized to that for the total abundance of that protein, a requirement that also applies to other posttranslational modifications. When quantifying changes in protein-protein interactions, the signal for the immunoprecipitated protein must be normalized to that in the total lysate. See additional information about Western blot standards below.

Statistical Analysis

Provide statistical analysis in graphs to support statements about increases, decreases, or lack of change in the variable being measured. Statistical tests used must be stated in the figure legends. Note that t-tests and ANOVAs may not be appropriate for data with a non-normal distribution (such as percentages or qRT-PCR data). t-tests may not be appropriate for multiple overlapping comparisons in an experiment. For multiple comparison tests, such as ANOVAs, please specify the post-test used to derive P values.

For guidance on selecting an appropriate statistical test, please consult a statistician. A statement from a statistician confirming the appropriateness of the statistical tests used to analyze the data will be required if revisions in response to the reviewers’ comments are requested.

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Western blotting

Western blots for phosphorylated forms of a protein of interest must be accompanied by Western blots for the total protein, to show that changes or lack of changes in the phosphorylation of the protein of interest are not due to changes in the overall abundance of the protein. This requirement also applies to other posttranslational modifications.

Each set of Western blotting data must include an input blot, such as for actin or tubulin.

Input blots (not actin or tubulin) must be shown for all coimmunoprecipitation blots for both the protein being pulled down and the protein(s) of interest that coprecipitated.

Non-contiguous lanes within or between blots should be made obvious (delineated with borders, if necessary) and stated as such in the legend.

Knockdown by RNA interference or morpholino oligonucleotides

To control for off-target effects, knockdown experiments should be performed with more than one siRNA or shRNA OR rescue experiments should be performed in knockdown cells. Alternatively, data obtained through the use of RNA interference can be supported by complementary data obtained through an alternative experimental approach. Knockdown efficiency must be shown by Western blotting.

In zebrafish models, data obtained through the use of morpholino oligonucleotides must be supported by complementary data obtained in vivo through an alternative experimental approach and should follow the latest community standards (http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007000).

Genotypes, genes and mRNAs

The names of genotypes, genes, and mRNAs must be italicized in the main text, figure labels, and Supplementary Materials. For genotypes, -/-, -/+, and +/+ must be superscripted in the main text, figure labels, and Supplementary Materials.

Use gene names for genotypes or when referring to genes or mRNAs. Primary and precursor forms of miRNAs are italicized  while the functional, mature form is not.

Scale bars

All microscopy images must have scale bars and the length of the scale bar must be noted in the legend, not the figure itself. This requirement applies to histology, light microscopy, and immunofluorescence images. A single bar is sufficient for a group of images in a panel if they are all the same scale; if not, please include the appropriate scale bar within each image.

Data and materials availability

Per the Science journals’ policy on data availability, all RNAi screens, microarray, mass spectrometry, or structure data must be deposited in a publicly accessible repository prior to publication. Please provide the accession number in the paragraph after the last reference in the section called “Data and materials availability.” If your paper passes peer review, we will not prepare the paper for publication until we have this deposition information.

After publication, all data and materials necessary to understand, assess, and extend the conclusions of the manuscript must be made available. All computer codes involved in the creation or analysis of data must also be made available. After publication, all reasonable requests for data or materials must be fulfilled. Any restrictions on the availability of data, codes, or materials, including fees and restrictions on original data obtained from other sources must be disclosed to the editors as must any Material Transfer Agreements (MTAs) pertaining to data or materials used or produced in this research, that place constraints on providing these data or materials. Patents (whether applications or awards to the authors or home institutions) related to the work should also be declared. Unreasonable restrictions on data or material availability may preclude publication.

Ethics compliance

For investigations on humans, a statement indicating that informed consent was obtained after the nature and possible consequences of the studies were explained. For studies using experimental animals, a statement that the animals' care was in accordance with institutional guidelines is required.

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Preparation of Figures

Creating your figures

We strongly recommend using Adobe Illustrator or a program that can generate vector-based images to prepare your figures. We prefer that figures be provided as PDFs with editable text.

Prepare your main figures at high resolution (300-600 dpi for gray scale and color; 1200 for line art), at 3.5, 5.0, 6.125, or 7.3 inches wide. Use the smallest of these sizes that retains legibility. Size your figures, minimize unnecessary white space in figures, and split up figures if necessary so that each page with a main figure can fit not only the figure, but also the legend and some main text. Multi-page figures are not allowed.

  • The figure's title should be at the beginning of the figure legend, not in the figure itself.

  • Include the figure's identifying number (e.g., "Fig. 1") on the same manuscript page that includes the figure.

  • For figure labels, use Helvetica between within a font size range that does not span more than 4 sizes, with the smallest font size used for superscript or subscript. Acceptable examples: figure labels at font sizes between 6 and 9 point, with 6 point for superscript and subscript OR figure labels at font sizes between 13 and 16 point, with 13 point for superscript and subscript. Unacceptable example: figure labels at font sizes between from 5 to 12 point. Do not use bold for any labels within the figures. Do not use italics for any labels within the figures unless referring to genes, mRNAs, genotypes, or species.

  • Keys to symbols, if needed, should be kept as simple as possible and be positioned so they do not needlessly enlarge the figure. Details can be put into the legends.

  • Use solid symbols for plotting data if possible. Size symbols and line widths should be distinguishable when the figure is reduced.

  • Panels should be set close to each other, and common axis labels should not be repeated.

  • Column scatter plots with the mean or median ± standard error or deviation overlaid are preferred over means ± standard error or deviation bar graphs.

  • Scales or axes should not extend beyond the range of the data plotted.

  • Avoid using red and green together out of consideration for color-blind readers.

  • Avoid using grayscale.

  • Use simple solid or open symbols when possible.

  • Label graphs on the ordinate and abscissa with the parameter or variable being measured, the units of measurement, and the scale. Scales with large or small numbers should be presented as powers of 10.

  • All microscopy images must have scale bars and the length of the scale bar must be noted in the legend, not the image itself. This requirement applies to histology, light microscopy, and immunofluorescence images. A single bar is sufficient for a group of images in a panel if they are all the same scale; if not, include the appropriate scale bar within each image.

  • Units should be included in parentheses. Use SI notation.

  • Use leading zeros on all decimals -- e.g., 0.3, 0.55 -- and only report significant digits.

  • Use capital letters for part labels in multipart figures -- A, B, C, etc. Each element should have a unique letter. Do not use A, A′, A"; A, a, b, c; A(i), A(ii), A(iii); or A, 1, 2, 3.

Modification of figures

Science Signaling does not allow certain electronic enhancements or manipulations of micrographs, gels, or other digital images. Figures assembled from multiple photographs or images must indicate the separate parts with lines between them. Linear adjustment of contrast, brightness, or color must be applied to an entire image or plate equally. Nonlinear adjustments must be specified in the figure legend. Selective enhancement or alteration of one part of an image is not acceptable. In addition, Science Signaling may ask authors of papers returned for revision to provide additional documentation of their primary data.

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Language and stylistic guidelines

  • Use the past tense to describe the results in your manuscript and the present tense to describe previously published results. Avoid the use of "recent" and similar words. Do not present previously published results as a historical perspective.

  • To refer to single amino acid residues, use the 3-letter abbreviation and superscript the residue number (for example, Ser25). This must be done in the main text, figures, and Supplementary Materials. Single letter abbreviations book-ending a normal-scripted residue are used when describing amino acid mutants (for example, S25A).

  • Do not use imprecise terms, such as "up-regulated", "down-regulated", "controlled", "regulated", and "modulated" where possible. Change "up-regulated" to "increased abundance", "increased activity", or whatever is appropriate and use similar language for "down-regulated". Change "regulates" to "inhibits", "attenuates", or "reduces" or "stimulates", "enhances", or "promotes", as appropriate.

  • Define all acronyms the first time that they are used in the main text. Define even very commonly used acronyms, including those in the Materials and Methods.

  • Do not italicize "in vivo", "in vitro", "ex vivo", "de novo", "in silico", or "in situ". Italicize "et al."

  • Avoid claims of novelty or being first.

  • Do not start sentences with "Importantly" or "Interestingly". Avoid hyperbole and delete "dramatically" wherever you have used it.

  • "significant" should be used only to describe the results of statistical analysis. Do not use it as a replacement for "important" or "substantial".

  • Do not start sentences with "As shown in Fig. 1B…".

  • Make sure that URLs resolve correctly.

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File formats for initial submission

Initial submissions must be uploaded to our electronic submission website as a Microsoft Word .docx file that contains all components of the paper, including the figures. Create one Word .docx file consisting of the text (title through materials and methods; see above for correct order), references, tables and table legends, figure legends, and embedded figures. Supplementary Materials are not required but if they are needed they should be prepared as a separate Word .docx file that includes embedded supplementary figures and captions, as well as supplementary tables. Other Supplementary Materials with file types that cannot be incorporated into a Word .docx document can be uploaded separately to a designated section of the submission site.

Figures

See the above instructions for creating your original figures. For initial submission, the figure files must be incorporated into the main text .docx file, with the legend below the figure.

Supplementary Materials

Text and figures. Supplementary Materials (supplementary tables and figures plus captions) should be prepared as a separate .docx file. Figures should be embedded in the file, with the legend below each figure.

Video files. Acceptable formats for videos are Quicktime, MPEG and Flash. Keep videos short and the display window small to minimize the file size of the video. Supply caption information with the videos in the Supplementary Materials .docx file. Upload these file types as Auxiliary Supplementary Materials on our submission site. Our system can handle files up to 25 MB.

Other files types. All other file types can be uploaded as Auxiliary Supplementary Materials on our submission site. Our system can handle files up to 25 MB.

Submission of your Research Article

All Research Articles should be submitted through the Manuscript Submission and Information Portal.

Submission Checklist

In addition to the manuscript files, the following items are required for submission:

  • Cover letter, containing:
    • The title of the paper and a statement of its main point;
    • Any information needed to ensure a fair review process;
    • Names of colleagues who have reviewed the paper;
    • A statement that none of the material has been published or is under consideration elsewhere;
  • Names and contact information for all authors, including selection of at least one to be corresponding author.
  • Names, affiliations, and e-mail addresses of five potential referees.
  • Copies of any paper by you or your coauthors that is in press or under consideration elsewhere that relates to the work submitted to Science Signaling, or of any paper that is cited in your paper as in press.

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Citation style

Science Signaling uses a complete citation format that includes all authors, full titles of journal articles, the journal abbreviation, the volume, the first and last page, and the year of publication. References are cited by number within the text. An example of the citation style is below:

  1. J. J. Tesmer, R. K. Sunahara, A. G. Gilman, S. R. Sprang, Crystal structure of the catalytic domains of adenylyl cyclase in a complex with Gs·GTP-γ-S. Science 278, 1907-1916 (1997).

 

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Article Publication Fees

Figure processing fees for both color and black and white illustrations will be assessed for Research Articles and Resources. There is no cost to have a manuscript evaluated.

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