Author Guidlines

Manuscript Format for HPBS

Protocols

Title

The title should succinctly describe the method and, if appropriate, its application. It should be no longer than 30 words.

Authors

Include those who have contributed intellectually and practically to the development of the technique. For all authors please include first name, middle initial (if appropriate), last names, postal address (Department, Institution, City and Country) and e-mail address. Also include the telephone number and fax number for the corresponding author. A link to a lab home page or staff information page may also be included for appropriate authors.

Abstract/Summary

Include a summary of the protocol (maximum 150 words), briefly describing the protocol and its applications. The suggested format is to include one or two sentences summarizing the protocol; then to explain more specifically the stages of the protocol, and if appropriate, how these compare with other protocols; and then to include one or two sentences describing the results that can be expected. If possible, include a final sentence indicating how long the whole protocol takes. We would prefer that the abstract contained information about the procedure rather than a summary of the results that have been obtained previously using the method.

Introduction (use heading ‘INTRODUCTION’)

The purpose of the introduction is to enable readers to make a decision as to the suitability of the protocol to their experimental problem. Initially you should introduce the technique. Include references to key papers where the protocol has been used previously, including those published by your own group or to reviews that discuss applications of the protocol (see below for how to cite references). You are actively encouraged, where appropriate, to reference other protocols in HPBS. Use subheadings where appropriate; these could include:

Materials (use heading ‘MATERIALS’)

REAGENTS, EQUIPMENT, REAGENT SETUP and EQUIPMENT SETUP are the only subheadings that are allowed. You must include at least one of these headings. Within REAGENT SETUP and EQUIPMENT SETUP the title of the reagent or equipment being discussed forms a second level of subheading.

Include a list of the essential materials, split into reagents (use heading ‘REAGENTS’) and equipment (use heading ‘EQUIPMENT’). This should include information about the suppliers used for reagents (e.g., Company, web address and catalog number). If you have found that deviations from a particular reagent, or its source, have adverse effects on the outcome of the protocol this should be made clear by the word ‘CRITICAL’ followed by a brief explanation. Toxic or harmful agents should be made clear by the word ‘CAUTION’ followed by a brief explanation of the hazard and the precautions that should be taken when handling the agent. Please also highlight any specialist equipment required. The information you provide about the sources of reagents and equipment will enable us to link your protocol to Nature Product Finder to help users obtain the equipment and materials they need. Please provide as much information as you can to help us successfully identify the product, e.g. company name, company website, product code. If you need to include detailed information about specific reagents or equipment, please list in additional optional sections, called ‘REAGENT SETUP’ and ‘EQUIPMENT SETUP’. These sections are suitable for details of composition of buffers or the setup of equipment.

REAGENT SETUP is the appropriate section to include details regarding e.g. the required sample specification (in terms of minimum protein quantity and allowed buffer components) for a mass spectrometry experiment; a way to prepare a complicated buffer; and the pre-treatment of solvents and/or reagents to make sure they are moisture-free and/or air-free. For each item listed in the REAGENT SETUP section please indicate whether it should be made up fresh or can be stored and if so under which conditions (e.g temperature) and for how long. In addition please state whether % solutions are wt/vol or vol/vol. EQUIPMENT SETUP is the appropriate section to include details regarding e.g. the setup of HPLC separation methods.

For protocols that use live vertebrates or higher invertebrates, authors must state that all experiments should be performed in accordance with relevant guidelines and regulations. For manuscripts reporting experiments on human subjects, authors must also include a statement confirming that informed consent must be obtained from all subjects. These statements should appear as CAUTIONS. These must be placed in the reagents section, procedure and in the legend of any tables and figures that show data collected using human or animal subjects. Referees may be asked to comment specifically on any cases in which concerns arise.

Step by step methodology (use heading ‘PROCEDURE’)

This is the major part of the protocol and must be a numbered list, ideally with numbers in bold; do not follow the numbers with a period (full stop). Use the active tense rather than the passive tense, for example, “Pipette 20ml of buffer A into the flask”, instead of “20ml of buffer A are/were pipetted into the flask”. If the protocol naturally breaks into separate stages, then include subheadings and resume the numbered list. Include a TIMING callout with each subheading and state how long the section will take to complete. Subheadings are particularly appropriate after steps in the protocol where the procedure can be stopped (pause point), i.e. when the experiment can be stopped and resumed at a later date. Any pause points should be indicated with the heading ‘PAUSE POINT’, followed by a brief description of the options available, for example “Can be left overnight at 4°C or frozen for up to a month at -20°C”.

Highlight critical steps in the protocol that must be performed in a very precise manner e.g., where the time and temperature of a step is crucial or the use of RNase free solutions is required; thus providing the user with hints to maximize the likelihood of success. Make these clear with the heading ‘CRITICAL STEP’, followed by a brief explanation.

Highlight any toxic or harmful chemicals that are used. Make these clear by preceding them with the wording ‘CAUTION’ prior to their first mention and include brief details of the hazard and the appropriate handling information.

Include diagrams and/or photographs of equipment set-up, where appropriate. If the protocol is complicated you should consider including a flow diagram to demonstrate how the stages fit together. We welcome movies of particularly complicated procedures.

Where there are alternative routes to reach the next stage of the protocol, please give enough background so that the reader will be able to make an informed decision on the route to choose. Letters of the Latin alphabet (A), B), C)…) should be used to identify the different options, and Roman numerals (i), ii), etc.) should be used to break down the appropriate steps. For example:

1.This step can be performed using option A or option B depending on whether…

A.First option

i.First part

ii.Second part, etc.

B.Second option

i.First part

ii.Second part, etc.

Please note that these options cannot have subheadings.

Please state all centrifugation speeds in g and include the length of time and temperature of the centrifugation e.g., centrifuge at 14,000 g for 5 mins, 4°C.

Please include TROUBLESHOOTING callouts after steps where problems are encountered, that are subsequently mentioned in the Troubleshooting section.

Timing (use heading ‘TIMING’)

If possible, please include a timeline indicating the approximate time a step, or set of steps, will take e.g. Steps 1–3, 30 min.; Steps 6+7, 2 h. Provide this information as a summary at the end of the procedure, as a list. If you think it would be more user friendly you could refer to time needed for each section or detail what needs to be performed on each day of the protocol.

Troubleshooting (use heading ‘TROUBLESHOOTING’)

Include information on how to troubleshoot the most likely problems users will encounter with the protocol. Please provide this information in the form of a table with the columns ‘Step’, ‘problem’, ‘possible reason’, ‘solution’. The step number should be given where the problem is first observed (not where it occurred). The appropriate steps should also be flagged in the main text by adding ‘TROUBLESHOOTING’ callouts. If troubleshooting text refers to only one or two steps, it can also be formatted as normal text with subheadings referring to the steps or sections that the information pertains to.

Anticipated results (use heading ‘ANTICIPATED RESULTS’)

Include information about, or examples of, the likely outcome to users, for example, likely yield of protein, typical microscopy images, etc.

If possible, please include one set of data from an experiment that worked very well and a second for an experiment that required troubleshooting to obtain meaningful results. If not described in detail in the introduction, this is a good place to include directions on how to interpret and analyze the raw data including equations if necessary.

This is the appropriate section to include any analytical data for chemical compounds synthesized as part of the procedure. An example of how this should be formatted is shown below:

Supplementary Information

Each piece of Supplementary Information should have a title and a legend and be cited in order in the text. If any references are cited in Supplementary Information, an individually numbered reference list should be created for the Supplementary Information and included with the Supplementary Information legends. References in the Supplementary Information should not be cited directly from main reference list. If any references are cited in both the main text and the SI, they can be repeated in the SI reference list. Please use one of our approved titles for your Supplementary Information.

Author contributions statements

Authors are required to include a statement of responsibility in the manuscript that specifies the contribution of every author. The level of detail varies; some disciplines produce manuscripts that comprise discrete efforts readily articulated in detail, whereas other fields operate as group efforts at all stages.

Acknowledgments

Please note an acknowledgments section can be included.

Competing financial interests

The published protocol will indicate if the authors have competing financial interests. Please include one of these statements in your manuscript:

·The authors declare that they have no competing financial interests.

·The authors declare competing financial interests (see the HTML version of this article for details).

Submission of a signed Competing Financial Interests Statement is required for all content of the journal. This statement will be published at the end of all papers, whether or not a competing financial interest is reported. In cases where the authors declare a competing financial interest, a short statement to that effect is published at the end of article, which is linked to a more detailed version available online.

References (use heading ‘REFERENCES’)

List all references mentioned in the protocol. References are numbered sequentially as they appear in the text, figure legends, tables and boxes. Use superscript numbers to indicate a reference, for example 1. Only one publication is given for each number, and footnotes are not used. Only papers that have been published or accepted by a named publication should be in the numbered list; meeting abstracts and papers in preparation should be mentioned in the text with a list of authors (or initials if any of the authors are co-authors of the present contribution). Patents should be included in the reference list. Published conference abstracts and URLs for web sites should be cited parenthetically in the text, not in the reference list; articles in formal, peer-reviewed online journals should be included in the reference list. Grant details and acknowledgments are not permitted as numbered references.

All authors should be included in reference lists unless there are more than five, in which case only the first author should be given, followed by ‘et al.’. Authors should be listed last name first, followed by a comma and initials of given names. Titles of cited articles are required and should be in Roman text and titles of books in italics; the first word of the title is capitalized, the title written exactly as it appears in the work cited, ending with a period. Journal names are italicized and abbreviated (with periods) according to common usage; refer to the National Library of Medicine for details. Volume numbers appear in bold. For book citations, the publisher and city of publication are required (e.g. John Wiley & Sons, Hoboken, New Jersey, USA, 2003).

List all references mentioned in the protocol. Use the format given in the examples below:

3.Helms, C. et al. A putative RUNX1 binding site variant between SLC9A3R1 and RAT9 is associated with susceptibility to psoriasis. Nat. Genet. 35, 349-356 (2003).

4.Lovett, M. Direct selection of cDNAs with large genomic DNA clones. In Molecular Cloning: A Laboratory Manual Edn. 3 Vol. 2 (eds. Sambrook., J. & Russell, D.W.) 11.98-11.133 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 2001).

5.Petroff, M.D. & Stapelbroek, M.G. Blocked impurity band detectors. US Patent 4,586,960 filed 23 Oct. 1980, and issued 4 Feb. 1986.

Life sciences reporting guidelines

It is a policy of NPG that authors of life sciences papers presenting research results must include in their manuscripts relevant details about several elements of experimental and analytical design. These requirements aim to improve the transparency of reporting and the reproducibility of published results. They focus on elements of methodological information that are frequently poorly reported (see more details on these elements here). If your Protocol contains previously unpublished data you will be asked to confirm that these elements are included in the manuscript by filling out a checklist that will be made available to the editors and reviewers.

Nomenclature

Submission of Figures, Tables, and other additional protocol components

HPBS discourages the use or adaptation of previously published display items (for example—figures, tables, images, videos or text boxes) however we recognize that to illustrate some concepts the use of published data is required and the reuse of previously published display items may be necessary. Please note that in these instances we might not be able to obtain the necessary rights for some images to be re-used (as is, or adapted versions) in our articles. In such cases, we will contact you to discuss the sourcing of alternative material.

Figures, tables, boxes and Supplementary Information must be cited in the text and numbered in the order in which they are cited.

Tables

Please submit tables in Word format at the end of your text document, or as a separate file. Tables should be created using the Microsoft Word table editor, where possible.

Chemical structure display items.

Figures

Image types

Images fall into two basic categories: photographic or scanned images, and graphs and schematic diagrams. Rasterized formats are best for photographs, scans, and composite figures containing photographic or scanned images with minimal or relatively simple labeling, whereas line or vector formats are best for graphs and schematic diagrams, and for composite figures containing a mixture of photographs or scans and detailed text or line artwork. The best format for any particular figure therefore depends partly on what kind of images it contains.

Electronic image formats

A wide variety of software is available to generate and manipulate images, and a huge range of graphics file formats exist. Rasterized (or bitmapped) formats such as TIFF are composed of an array of dots (pixels). The quality is determined by the resolution, usually measured in dots per inch (dpi; also referred to as ‘pixels per inch’). For adequate reproduction we need a minimum of 300 dpi at the size the image is to appear. Size and resolution are linked so that, for example, enlarging an image to twice its original size will halve the resolution. If the resolution is too low, individual pixels become visible to the eye, the edges of lines begin to appear ‘stepped’ and the image may look blurred or pixelated.

Line (or vector) formats such as Postscript, EPS and PDF preserve individual lines and text as separate, editable components. This makes them easier and quicker to reletter or edit as necessary, reducing the chance of errors, and gives sharper results in print and online. Also, because these images have no ‘resolution’ as such, they may be enlarged without any reduction in quality.

Leave all layers intact in TIFF and EPS files.

Preferred formats

Adobe Photoshop (layered .psd file only) or TIFF format (high resolution, minimum 300 dpi) for photographic images.

Adobe Illustrator, Postscript, EPS or PDF format for figures containing line drawings and graphs, including figures combining text and line art with photographs or scans. If these formats are not possible, we can also accept Microsoft Word, Microsoft Excel, Microsoft PowerPoint or JPEG (high-resolution, 300 dpi, as separate files (not embedded in your text file).

Please do not send figures prepared in the following formats, as we cannot use them: Canvas, Freehand, CorelDraw.

Manuscript Media Format

Video format of the protocols is strongly encouraged. With the assistance of our videographers and editors, the authors can deliver their protocols clearly, accurately, and professionally. Manuscripts in PDF format with step-by-step descriptions of the procedures are also welcome.