Preprints: Trying Something New in Publishing

As a trainee, having my papers reviewed by experts in the field has been both a frustrating and positive experience.  It has been positive, in that in nearly every case my publications have been improved by the process.  The enhancements from little embarrassing typos to new ways of conceptualizing our data, and certainly these papers are better for it.

On the other hand, some times it takes forever.  One paper went through 18 rounds of submission/resubmission, lasting over 3 years.  Another took almost 3 years and 10 submissions.  Some of these delays were certainly self-inflicted but in general it takes a really long time for papers to work through their pipeline.  Steven Royle recently looked at this more rigorously for the papers his group has published here.  In his experience, the average has been about 9 months

This can be bad for the careers of those involved, and for those for whom the data might help.  To get around this, we are trying something new with our next paper.  We submitted it to bioRxiv as a preprint.  The paper can be found here, so go ahead and take a look, I'll wait.  The posted version is identical to the submitted version, which was sent to a normal peer-reviewed journal.

What do I hope to gain?

This has been covered really well over the internet including in science, at Haldane's Sieve, and in PLOS Biology.  I hope that this will give people in my field a chance to read our work earlier.  I also hope that the people who may be interested in reading it will provide some feedback.  This paper, like all of our papers gets informally reviewed by colleagues and lab members before it goes out.  By putting it out online, I would like a broader audience to be empowered to take a look and give us their thoughts, before the 'final' version is done.

What are the downsides?

There are a couple, we could be scooped, or it could affect our ability to publish it in another journal.  For the latter, we used SHERPA/ROMEO to pick a journal that has an established policy that pre-prints are acceptable.  As far as getting scooped, I am even less concerned about that.  The data is freely available for this paper on GitHub for anyone to use and I think the risk of scooping is dramatically overstated in science.

So take a look, and let us know here or at the paper what you think.

Rab5 Knockdown In Vivo

This paper from the Zerial Laboratory describes a study in which the three mammalian isoforms of Rab5 are reduced in whole livers or cultured hepatocytes by a lipid nanoparticle mediated knockdown treatment. They then analyse images from these cells and liver sections and determine that there are reduced early endosomes, late endosomes and lysosomes in cells depleted of Rab5.

They also identify two functional defects in these tissues; reduced LDL uptake and impaired apical polarity of the hepatocytes. They also generate a simplified model of Rab5/early endosomal dynamics and suggest a role for Rab5 in vesicle fission as well as fusion. Although this model fits the available data quite well, it ignores several other key components of endosomal formation and maturation.

The authors also present the curious finding that while Rab5 depletion reduces both LDL uptake and endosome numbers, dynamin depletion only affects LDL uptake but not the number of endosomes. One possible explanation for this defect is that they quantify the presence of endosomes in this assay largely by EEA1 puncta. Since EEA1 is a Rab5 effector, it is possible that in the Rab5 depleted cells there is still a population of early endosomes, but that these are not detected by EEA1 staining.

Together this study presents a convincing picture for the role of Rab5 in endosomal dynamics, and highlight the important role of Rab5 in both endocytic pathways and in the establishment of polarity in vivo.

Citation

Zeigerer A, Gilleron J, Bogorad RL, Marsico G, Nonaka H, Seifert S, Epstein-Barash H, Kuchimanchi S, Peng CG, Ruda VM, Del Conte-Zerial P, Hengstler JG, Kalaidzidis Y, Koteliansky V, & Zerial M (2012). Rab5 is necessary for the biogenesis of the endolysosomal system in vivo. Nature, 485 (7399), 465-70 PMID: 22622570

Disclosure: I have received constructs and yeast strains from the Zerial laboratory in the past.



Rab5 Knockdown In Vivo by Dave Bridges is licensed under a Creative Commons Attribution 3.0 Unported License.

Why Isn't There Anonymous Post-Publication Peer Review

If pre-publication review is anonymous, and it almost always is why isnt there anonymous post-publication peer review? If there is a benefit to anonymous review, then isn't it odd that the Faculty of 1000 and most journals commenting/letter to editor mechanisms require the submitter to provide a real name and appointment. Would post-publication review of articles suck less if it were anonymous?