Category Archives: Journal policy

Journal policy

Our reporting standards for fluorescent proteins – Feedback wanted

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Several years ago, based on informal input from various members of the community, Nature Methods established some internal minimum reporting standards for manuscripts describing new or improved fluorescent proteins. These were never formally reported but were often communicated to authors of submitted manuscripts when the characterization data provided didn’t meet these standards.

Recently we were fortunate enough to be able to meet with a substantial number of fluorescent protein developers to informally endorse and revise these standards. Our revised reporting requirements for fluorescent proteins are listed below.

Minimum reporting requirements for fluorescent proteins

  1. Full absorption and excitation (250nm to 750nm) and emission curves (350nm to 950nm) under single-photon excitation and at least some data under 2-photon excitation
  2. Values for quantum yield, extinction coefficient, brightness and pKa
  3. Gel filtration data to show that the protein is monomeric or acknowledgement that it isn’t monomeric
  4. Data on fluorophore maturation time including the final maturation percentage. Detailed protocol must be provided
  5. Image data on several representative protein fusions to show that it does not disrupt protein function. This should include tubulin since it is pretty universally used for this purpose
  6. In vitro photostability data compared to other representative proteins. At a minimum this should be decay curves under widefield and confocal illumination to test two different irradiation intensity regimes. Ideally, graphs of the decay time constant versus power should be provided
  7. Cytotoxicity measured in mammalian cells by flow cytometry and compared to EGFP and at least one established fluorescent protein in the spectral range of the reported protein

We also used this opportunity to set some standards for photoswitchable fluorescent proteins. These proteins display quite complicated behaviors and the desired characteristics can vary depending on the application. An example of this is the different characteristics desired for (f)PALM/STORM vs RESOLFT or SSIM super-resolution imaging. These new reporting standards are listed below and supplement the ones above which would also apply to photoswitchable fluorescent proteins.

Additional minimum reporting requirements for photoswitchable FPs

  1. Graphs of 20+ cycles at different powers to observe decay with full details on power and methods
  2. Absorption spectra before and after photoconversion
  3. Optimal parameters for the best power and also for another power
  4. Measurement of how complete the switching is

We encourage developers and users of fluorescent proteins to comment on these minimal reporting standards. But more than that… we’d like your help in moving forward from here.

Are additional standards needed due to new developments?

Do we need standards similar to these in other areas?

We have found that enforcing common standards on highly related tools can greatly improve the efficiency and objectivity of the peer review process and help avoid holding similar developments to different standards. Of course, this requires flexibility in enforcement and we will always allow editor’s some discretion in enforcing these requirements when there is a legitimate reason for doing so.

The potential and perils of trying new methods

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The remit of Nature Methods has always been to publish new or improved methods that will have an immediate practical impact on researchers working at the bench. But unfortunately, even though ‘new’ methods can provide substantial advantages to the first labs to adopt them, they aren’t always ready for primetime. And the more novel the method the more likely it is that all the kinks aren’t yet worked out.

Although we strive to ensure that methods we publish have been as well validated as necessary for people to begin trying to use them, early adopters can find unanticipated problems or other deficiencies that they must first solve. This vital work is often under-appreciated. We discuss this situation in our March Editorial and invite researchers who have identified such problems with methods we have published to alert the community through a Correspondence to Nature Methods.

This provides the potential for high-profile recognition of the contribution that early adopters make to methodological development. We welcome feedback on the need and value of this opportunity.

We would also like to know if a less formal online commenting capability would be a valuable alternative. We have noted that such commenting has so far not been embraced by the community but we believe it could form an important adjunct to formal publication. Especially in cases when the issues raised aren’t substantial enough to justify a Correspondence but would still benefit the community by wide dissemination and tight association with the original manuscript.

What’s in an acronym?

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Many scientists (and editors) lament the proliferation of acronyms in the literature, especially for describing methods. As editors of a methods journal, we have some definite opinions about when acronyms are useful, when a new acronym is unnecessary, and what makes a good (or bad) acronym. We discuss this in depth in our July issue Editorial.

A good acronym to describe a novel method gives the research community a simple and effective way to refer to the method. However, optimizations of the method or adaptations for a different application usually do not justify the creation of a new acronym. This trivializes the original advance and the proliferation of similar-sounding acronyms creates confusion in the community. Researchers should be judicious in creating acronyms for methods and think hard about whether a new acronym is truly necessary.

Feel free to share your thoughts about the use—and misuse—of acronyms!

Neuroscience sees the light

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After many years of steady but seemingly slow progress, the development and use of light-based methods for investigating the function of the brain is really accelerating. Part of this is undoubtedly due to the excitement surrounding the use of light-activated channels for neuronal stimulation. This has been highlighted as one of our “”https://www.nature.com/nmeth/focus/moy2008/index.html#mtw">Methods to Watch" for the past two years. But probe development has also overcome some big hurdles recently, from the bolus loading of small calcium dyes to the development of genetically-encoded calcium indicators capable of providing usable signals in living animals.

An editorial in the December issue discusses the advances taking place in optical probes for measuring neuronal function and calls for the use of more standardized procedures for evaluating new probes.

Nature Methods has been requiring a basic set of evaluation tests on new fluorescent proteins that we publish for a few years now and it is possible we could try and do something similar for genetically-encoded sensors but this would obviously be complicated by the greater complexity of sensors and the fact that they respond to different stimuli and have diverse applications.

We encourage the community to tell us what they think about the value and feasibility of standardized tests for new fluorescent probes and sensors.

Author responsibilities

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For those of you who may have missed it, on April 30th Nature and the Nature research journals — including Nature Methods — announced a change in policy regarding the duties of lead authors. The changes are explained in a Nature editorial and have been implemented in our Guide to Authors. A detailed explanation of the Nature journals’ new authorship policy can be found here.

These changes are meant to clarify the responsibilities of our authors to help ensure that the results and conclusions in Nature journal papers accurately reflect the original data, that this data is preserved, and that appropriate actions are taken to ensure the availability of materials — including algorithms — needed to replicate the work.

We will also be requiring that authors provide statements of authors’ contributions in Nature Methods papers submitted after April 30. Since Nature Methods began asking for this in early 2007 the number of authors providing this statement has already increased from 50% in May 2007 to 80% in May 2009 so we hope that making this a requirement won’t be problematic.

We realize that these changes could be seen as an added burden on authors but we don’t believe the expectations exceed what most readers expect of work published in Nature Methods or the other Nature journals and we hope our authors agree.

Methods section remake

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Many of our readers have no doubt noticed a pronounced change in the Methods section of Nature Methods papers published online over the past several weeks. Brief Communications now have a Methods section for the first time ever and in manuscript types that already had a Methods section, the section has been expanded and moved to the end of the paper.

These changes are described in detail in an Editorial accompanying the May issue of the journal. The new design is similar to what Nature implemented in 2007 and we hope our authors and readers appreciate the greatly expanded space this provides for methodological details. We are relieved that we will no longer have to relegate important methodological details to Supplementary Information and we expect our authors will appreciate being able to include more citations in their papers.

A potential downside of this change is that the print and online versions of papers have quite different levels of methodological detail. What do you think? Those of you who are online readers may not have very strong opinions on this, but what about our print readers? If anyone who regularly receives a print copy of the journal is reading this, we would like your feedback as well.

Compare and conquer

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Experimental comparisons of methods, technology platforms or reagents are time-consuming and expensive, but hugely beneficial. An Editorial in the April issue of Nature Methods illustrates how such comparisons have been very useful for scientists in various research disciplines. Nature Methods has now adopted an article format called ‘Analysis’ to accommodate publication of such comparative analyses. Broad guidelines of what the editors will be looking for are provided in the April Editorial.

Social software

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Don’t be mistaken, Nature Methods’ material sharing policy includes the requirement to make custom-developed software available upon publication. But there are several ways of making software available. We examine the various degrees of disclosure and the choice of formats and try to clarify our position. Let us know if we are heading in the right direction!