Author Archives: Dorothy Clyde

Meeting report: 4th Single Molecule Localisation Microscopy Symposium

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In the shadow of The Shard at the end of August, I joined about ~120 scientists at KCL for the 4th Single Molecule Localisation Microscopy Symposium. This 3-day meeting preceded the announcement in October that the Nobel Prize in Chemistry had been awarded to Eric Betzig, Stefan Hell and William E. Moerner for their contributions to the field of super-resolution (SR) microscopy (which includes SMLM approaches), but it was already very clear from the content and calibre of the programme that the field was having an important impact on several key areas of biological research.

The Symposium was superbly organized by Helge Ewers, Mike Heilemann, Aleksandra Radenovic, and Jean-Baptiste Sibarita; the only real disappointment being the cancellation of Stefan Hell’s keynote lecture due to illness. The 25 talks were divided into 5 broad topics: technical developments; biological systems; quantitative localization microscopy; labelling; and data analysis. It was particularly pleasing from my perspective that women researchers were well-represented, with at least 1 female speaker in all but 1 of the high quality sessions. Nature Protocols authors were also among the speakers1, 2. The full schedule of talks can be found here.

I found most of the talks to be surprisingly accessible and, as someone very interested in techniques and methods, there was a lot to hold my attention. Much effort is being expended on improving SMLM with respect to: the achievable resolution, especially axially; its live imaging capabilities; and quantitative applications. Progress in all these areas largely relies on a combination of new microscope setups, improved labels, and advanced data analysis methods. Biological applications discussed included nanoscale clustering of membrane proteins (particularly during synaptic and T cell signalling in mammalian cells), molecular assembly/organisation of protein complexes, and single particle tracking. The talks were complemented by ~60 posters, which covered additional applications such as imaging the cytoskeleton, chromatin structure, and plant tissues.

But it wasn’t all hard work – attendees were treated to an evening boat trip along the Thames, which provided the opportunity for less formal discussions over dinner, whilst enjoying the beautiful views on offer. I spent a very enjoyable evening in the company of a lovely group of PhD students and young post-docs discussing life the universe and everything – and trying not to feel my age!

At the close of my 3-day crash course in SMLM, I certainly felt much better-informed and very much inspired by the amazing work being done by this small but enthusiastic community. It is certainly an area of research I will continue to follow closely – perhaps a trip to Bordeaux is on the cards for next year!

 

1. Quantitative imaging of membrane lipid order in cells and organisms Dylan M Owen,    Carles Rentero, Astrid Magenau, Ahmed Abu-Siniyeh & Katharina Gaus Nature Protocols 7, 24–35 (2012) doi:10.1038/nprot.2011.419

2. Direct stochastic optical reconstruction microscopy with standard fluorescent probes Sebastian van de Linde, Anna Löschberger, Teresa Klein, Meike Heidbreder, Steve Wolter, Mike Heilemann & Markus Sauer Nature Protocols 6, 991–1009 (2011) doi:10.1038/nprot.2011.336

 

 

 

Nobel success

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We are a little late to the party (it has been a busy month at Protocols HQ!), but Nature Protocols would like to extend their warmest congratulations to all this year’s winners of the Nobel Prize for Chemistry: Eric Betzig, Stefan Hell and William E. Moerner for their contributions to the development of super-resolution microscopy.

We are very pleased to have published a Nature Protocol from the Betzig lab earlier this year on Bessel beam plane illumination microscopy.  And we are equally pleased that the Protocol Exchange can claim a Nobel Laureate amongst its authors; the Moerner lab has published a guide to using Easy-DHPSF to measure the precise localisations of molecules in images acquired using a wide-field DH epifluorescence microscope. I would also encourage you to visit Moerner’s very informative lab website, if only to find out about the guacamole!

Microscopy Madness in Bangalore

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Editorial note: Welcome (and a big thank you) to our first ever guest bloggers – Professor Hari Shroff and Dr Abhishek Kumar! Their post perfectly illustrates why we at Nature Protocols are so passionate about helping to ensure detailed technical knowledge and experience is transferred from one lab bench to another, from senior to junior researchers, across the globe. Enjoy their story – and be inspired by the achievements of the students!

 

A guest blog post by Hari Shroff and Abhishek Kumar

Optical imaging is experiencing an explosion, and not a month goes by without the publication of some new microscopy method. This can make it difficult to keep up, even for a lab like ours1, whose business is to create new imaging tools for use in biology. Even more challenging is the lag between the development or prototype of a new technology, and deployment of the tool in a form that biologist can easily use. Technology translation can take years and commercial adoption of a new method even longer- if it happens at all.

We are thus grateful for the opportunity to publish a do-it-yourself, easier-to-use implementation of our dual-view selective plane illumination microscope (diSPIM)2, a high-resolution light-sheet system, in Nature Protocols3. Apart from employing fiber-coupled excitation (making it easier to use a variety of commercial laser sources, and improving the flexibility and alignment of our device) and describing the use of GPU-ready processing software (speeding up image processing tremendously compared to our earlier efforts2), the protocol provides step-by-step instructions on construction, alignment, and imaging at a level of detail impossible to provide in our previous publication.

Of course, there’s no better test of a method than trying to put it into practice – which we were lucky to do recently at the 6th annual microscopy course in Bangalore, India at the National Center for Biological Sciences (NCBS). The course runs for one week, and students alternate between lectures and labs. Working days are long, with most days 12-14 hours. At the end of the course, students pick up a short independent project, putting what they learned at the course into practice.

When we arrived in Bangalore, NCBS staff had pieced together much of a diSPIM, based on an earlier version of the Protocol that we had sent them. We spent most of the week checking various components and fixing small issues. By the time the final weekend rolled around, we decided to rip it up and build it again from scratch – a great student project. In about 6 hours, course participants were able to assemble and align a functional microscope (well, almost functional as we had some trouble with the piezos…) by following our Protocol – perhaps the first light-sheet system in India but certainly the first diSPIM.

The results of their labors (a total time of ~6 hours) are entertaining (sped up ~65x and condensed to ~4 minutes), and can be viewed here.  We hope you enjoy it – for maximizing the audio-visual experience, we recommend turning your speakers up!

 

  1. https://www.nibib.nih.gov/about-nibib/staff/hari-shroff
  2. Wu, Y. et al. Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Nat Biotechnol. 31, 1032-1038 (2013). DOI: 10.1038/nbt.2713
  3. Kumar, A. et al. Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. Nature Protocols 9(11), 2555 – 2573 (2014). DOI: 10.1038/nprot.2014.172

 

March’s SoNYC: On setting the research record straight – Sound familiar?

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Dorothy Clyde (Dot), is a Senior Editor at Nature Protocols and has been with the journal since its inception in January 2006. In her previous life as a research scientist, she spent close to a decade studying various aspects of fruit fly development and genetics. In her guest post she explains the role an editor plays in avoiding plagiarism, giving advice to all parties. 

Imitation may be the highest form of flattery, but I doubt if anyone feels particularly flattered when they come across their own work – copied verbatim and unattributed – in someone else’s publication.  Unfortunately, instances of plagiarism are becoming more commonplace. As a result, tackling plagiarism has now become part of an editor’s job, and at Nature Protocols we work closely with our authors to avoid it. Once upon a time plagiarism was difficult to detect, but now that so much of the scientific literature is online there are a number of services that help us spot when parts of a submitted manuscript have already appeared elsewhere.

Thankfully, plagiarism of the classic kind is rare; when we do come across plagiarism, it usually takes the form of self-plagiarism (where an author reproduces uncited sections of text from one of their previous publications), or duplicate submissions (where the same manuscript is submitted to more than one journal, often simultaneously). Self-plagiarism, if detected early enough, is usually relatively straightforward to resolve. Duplicate submissions, on the other hand, are one of the more frustrating aspects of an editor’s job, as the problem often does not become apparent until the later stages of the editorial process – or worse, until both versions have been accepted and published in different journals!

Why is self-plagiarism a particular problem for Nature Protocols?

In order to ensure that our protocols are reproducible, Nature Protocols has a policy that all our protocols are based on a previous primary research paper from the author’s lab, in which the technique was used to generate data. If this supporting paper is very methodological, there may be some degree of overlap with the Nature Protocols manuscript. Alternatively, the authors may have published a protocol-type paper on a similar topic in another journal. In these circumstances, it is easy for sections of duplicated text to creep in, especially if the authors are unaware of the problems associated with self-plagiarism.

With respect to duplicate submission, we hope that all authors realise that it is unacceptable to submit identical manuscripts to more than one journal at the same time. However, duplicate submission (and self-plagiarism) problems can arise when manuscripts that were seemingly unrelated at initial submission, progressively become more similar as they pass through the editorial process, for example, when additional material is added in response to referee or editorial comments. In addition, some authors view protocols differently to other publication types and do not see a potential conflict in publishing the same protocol in more than one journal.

The role of editors in avoiding plagiarism

It is our job as editors to ensure our authors are fully informed about our plagiarism policies and to detect potential problems early in the editorial process. So how do we set out to achieve this at Nature Protocols?

  1. When an author agrees to submit a full manuscript to Nature Protocols, they will be sent an e-mail that reminds them we take plagiarism seriously and it must be avoided, directing them to “NPG’s policy on plagiarism” for further information. This e-mail also requests that authors make the editor aware of any methods/protocol papers they have previously written or have agreed to write on a similar topic – and, if possible, to provide us with a copy of these papers. We also ask authors to provide us with a copy of their supporting primary research paper. Editors will have already carried out extensive literature checks by this stage and may ask authors to upload specific publications that these searches have identified as being potentially overlapping or a source of potential problems. In such cases, the editor will make it clear that we expect the Nature Protocol to add substantial value to the existing literature and request that the author outlines to the editor how the manuscript expands upon previous publications.
  2. Authors are reminded of our policy again when their manuscript is returned to them for revision. It is also made clear in the editorial comments that duplication of text must be avoided and that all our manuscripts are cross-checked against the published literature before being accepted for publication. Thus, all authors are informed at least twice of our position on plagiarism.
  3. Nature Protocols (along with all other NPG journals) participates in the “CrossCheck initiative.” Prior to accepting any manuscript for publication, it is compared to the CrossCheck database using “iThenticate”.  iThenticate will generate an overall similarity score and provide a summary report that highlights instances of duplicated text in the submitted manuscript and links back to the original source(s). The editor then carefully checks each ‘hit’ in the report to determine its significance. Large sections, or multiple smaller sections, of highly similar text are an immediate red flag; if such sections are a clear indication of deliberate plagiarism or if the duplicated text cannot be removed by careful revision by the author (for example, by extensive rewriting or appropriate referencing) the manuscript will be rejected. We understand that paraphrasing sections of the Procedure can be difficult and not always helpful so in these cases it may make most sense to ensure the original source is prominently cited. However, the software will also turn up hits that are not plagiarism, such as isolated occurrences of partially similar sentences. Some standard phrases will be present in most of our manuscripts and can also be excluded, for example text reminding authors to follow institutional and national guidelines when performing experiments on animals. Another example where our editorial requirements make some duplication inevitable is the Materials section and so hits limited to this section can usually be overlooked.

Taking action

If self-plagiarism is detected before a manuscript is accepted for publication, the author is made aware of the offending sections and asked to either cite the original source or to rewrite the duplicated text. Duplicate submissions will be rejected outright as soon as they are detected. No manuscript will be accepted for publication until we are satisfied that all text is original and appropriately referenced.

Once a manuscript has been published, the course of action will depend on a number of factors, including: proof of intent; severity of plagiarism; policies of other journals involved. In cases where it is judged that the plagiarism is relatively minor and unintentional, authors will most likely be given the opportunity to correct the publication record by including additional citations or rewriting sections of text in the form of an official correction. In more serious cases, it is likely that we will retract the Protocol. That is about the limit of what we as editors can do ourselves although an author’s institution may well decide to investigate. In theUS, there is also the US Office of Research Integrity (ORI) which will investigate complaints of plagiarism. We are of course happy to cooperate with Institutions, the ORI or equivalent authorities.

Limitations of our approach

Unfortunately, there will be cases of plagiarism that slip past the Nature Protocols editors unnoticed. Plagiarism detection software, such as iThenticate, is not foolproof; determined individuals will find a way to ensure their manuscripts evade detection. Services such as PubMed, Scopus or CrossCheck do not index content from every journal; neither do they index all content types from participating journals. And by definition, only published papers are included in these databases. Thus, concurrent submission of identical manuscripts to more than one journal is a serious problem with no immediate solution.

A closing plea to authors

Authors – remember, your editor is your friend when it comes to avoiding plagiarism. It is in everyone’s best interests to identify and resolve potential issues early in the publication process. To facilitate this, I would urge all authors to be honest and transparent with your editor. And if you are unsure about how the policies apply to your manuscript –just ask!

Science Online NYC (SoNYC) is a monthly discussion series held in New York City where invited panellists and the in-person and online audiences talk about a particular topic related to how science is carried out and communicated online. For this month’s SoNYC the topic for discussion is:  Setting the research record straight. We’re looking at issues such as retractions and plagiarism and how they relate to real or perceived increases in research misconduct.  More details about this month’s SoNYC can be found here.

To complement the event, we’re running a series of guest posts on Of Schemes and Memes, discussing what steps publications are taking to deal with fraudulent research practices and what is being done to investigate and deter such practices. We’ve already heard from Richard Van Noorden, Assistant News Editor at Nature. He gave us an overview of  what retractions can tell us about setting the research record straight, highlighting some recent high profile cases of retraction, explaining why retraction rates appear to be increasing. We also compiled a Storify from a session at February’s AAAS meeting in Vancouver on Global Challenges to Peer Review which touched on some of the challenges faced by journal editors. More guest posts coming soon.