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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Quantum dots for smFISH

Single molecule FISH is currently the best method to get accurate measurements of mRNA levels at single molecule, single cell level in cell culture or tissue slices with a spatial resolution of ~200 nanometer (or less). One of the drawbacks of this method is the deterioration of the fluorescent signal (bleaching) of the organic dyes that are used to label the probes. Andrew Smith’s lab from University of Illinois now show how FISH can work with quantum dots instead of organic dyes. This provides better fluorophore stability and also the possibility to have more colors with less overlap of the emission spectra.

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Single molecule peptide sequencing

One of the greatest breakthroughs of the past decade was the development of the next generation sequencing. Sequencing of DNA of course. It is relatively easy to sequence DNA  – the polymerase is doing it for you – simply add fluorescently labeled nucleotides. For RNA sequencing, we simply convert it into DNA. We now even have a method for in situ sequencing of RNA. But proteins pose a challenge. Now, maybe, this challenge can be overcome with a new-old method to sequence peptides.

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Re-Evaluating the Spherical-Nucleic-Acid (SmartFlare) Technology

I co-authored a Correspondence pre-print article that puts into question the Smartflare technology. SmartFlares (the commercial name of NanoFlares) are gold nanoparticles covered in  oligos specific to a certain mRNA of interest (aka spherical nucleic acids). Supposedly, cells internalize these particles and, once the mRNA hybridize to the oligo, a complementary fluorecently labeled oligo is being unquenched and “flares”, indicating the presence of said mRNA. In this post I want to briefly mention the main topics of our pre-print, and expand on some points. I encourage readers to comment here or on Pubpeer on our article.

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Fluorescent protein databases

Two new awesome databases for fluorescent proteins are now available: FPbase and Fluorescent Biosensor database.

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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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A molecular ribosome counting mechanism – where’s the data?

A recent paper in Nature from the lab of Pavel Baranov and collaborators suggests a new type of mechanism of translation regulation. However, After discussing this paper in a journal club today – I’m not convinced about their model. Continue reading