Tag Archives: personal experience

Random thoughts on peer-review

The New-York Times published an article about the weaknesses of the scientific peer-review process. The article also provides a few ideas for improvements. I will not discuss this article, but please read it if you are unfamiliar with the current peer-review “crisis”.

Here are a few random thoughts i had about peer-review, which I do not remember reading about in articles or posts.

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My tenure-track faculty position search

My career goal is to get a tenure-track faculty position at an academic institution. My career took several twists & turns (see this eLife “Scientist and Parent” article). Once my main postdoc paper was accepted, I thought that I am finally ready to begin this search. I guess I was wrong.

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Intercellular mRNA transfer through membrane nanotubes – behind the scenes.

My paper was recently published. I suggest that you read it before reading this post (it is an open access paper). In this paper we show that full-length mRNA molecules can be transferred between mammalian cells through membrane nanotube-like extensions that connect the cells.

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MS2 mRNA imaging in yeast: more evidence for artefacts

Previously, on the story of MS2 in yeast: Last year, Roy Parker published a short article, in which he claimed that using the MS2 system in yeast causes the accumulation of 3′ RNA fragments, probably due to inhibition of mRNA degradation by the 5′ to 3′ exoribonuclease Xrn1. He argued that these findings put in question all the work on mRNA localization in yeast using the MS2 system. About a year later, we wrote a response to that article. We argued that, yes, such fragments exist, but 1. most of it stems from over-expression of the labeled mRNA. Parker agreed with that. 2. That these fragments accumulate in P-bodies, and are distinguishable from single mRNAs and we can discard cells which show these structures. 3. We argued that this might not be the case for every mRNA and should be tested on a case by case basis.  4. We and Parker agreed that the best way to determine if such fragments exist is by performing single-molecule FISH (smFISH) with double labeling – a set of probes for the length of the mRNA and a set of probes for the MS2 stem-loops. Now, a new paper from Karsten Weis’ lab shows more evidence, by doing smFISH, for the existence of these fragments.

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The Bio-protocol experience

A few months ago, I joined Bio-protocol as an associate editor. The first  protocol I edited is now published, so I thought I’ll write about this experience.

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Bio-protocol is an open access, peer-reviewed e-journal which specializes, you guessed it, in publishing life-science protocols. Submission is almost exclusively by formal invitation and it is free of charge (i.e. no submission or publishing fees).

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Does bound MS2 coat protein inhibit mRNA decay?

Roy Parker recently sent a  “Letter to the Editor“, published in RNA journal, in which he suggested that the MS2 system might not be best suited for live imaging of mRNA in budding yeast. According to Parker, the MS2 system inhibits the function of Xrn1, the major cytoplasmic  5′ to 3′ RNA exonuclease in budding yeast, causing us to image mostly the remaining 3’UTR fragments. Thus, he claims, it is possible that interpertation of mRNA localization data using this system in yeast can be faulty. We wrote a response to his letter which just opened the debate even further.

But lets start with his Letter:

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Corrigendum

It takes a lot of work to publish a paper. There’s the research itself, of course. Then there’s the writing and preparation of the figures for the paper, that are submitted to the journal for publication. Typically, most of the people who contributed to the research are involved in that, so the draft is circulated between at least 2 people, usually many more. There is one author (typically the 1st author, or the PI who is leading the research) who also needs to combine all the comments & changes into one coherent text.

The paper then goes through several rounds of  changes, following reviewers’ comments, editor’s comments, final proof-reading etc…

The accepted manuscript (MS) should be “perfect”. But mistakes can happen. Mistakes did happen for three of my recent papers.

For my Cell paper, I have prepared a nice schematic model to summarize the main highlights. It was nice, but we decided it is worth spending money on a professional artist to make a nicer one. Somehow, my scheme was uploaded for the accepted MS, instead of the more artistic one, and this is the one that was eventually  published  (you can see the artistic version in the blog post about the paper). I found that out after the fact, but since it was just a model, and the only difference was the art, we decided that publishing a correction just wasn’t worth the trouble.

Then, we published a paper in PLOS One. Only after it was published, I noticed that something happened to figure 4. Here it is:

Can you find the error?

Can you find the error?

Here, we had no choice but to publish a correction.

Recently we published a review paper, in Nature Reviews Molecular Cell biology. We worked very hard with lots of proof-reading and integrating each other’s changes to make sure it is perfect. Then, a few weeks ago, I was looking for some papers which I knew we referenced in that review. Strangely enough, those papers were mis-quoted in our review. Maybe its silly to publish a corrigendum just for a tiny mistake in references. But I think that it is important to keep science as mistake-free as possible, even with those tiny seemingly unimportant mistakes. So we published a corrigendum.

Here is also the place to thank the editors for handling these corrections pleasantly and efficiently.

I’m looking forward for my next corrigendum. What will that be?