We have a new preprint out – it is a cautionary tale about using GFP nanobodies in cells. This short post gives a bit of background to the work. Please read the paper if you are interested in using GFP nanobodies in cells, you can find it here. Paper in a nutshell: Caution is needed when using GFP nanobodies because they can inhibit their target protein in cells.

This week Erick Martins Ratamero and I put up a preprint on vesicle packing. This post is a bit of backstory but please take a look at the paper, it’s very short and simple. The paper started when I wanted to know how many receptors could fit in a clathrin-coated vesicle. Sounds like a simple problem – but it’s actually more complicated.

I really dislike being asked “how big is your lab?”. The question usually arises at scientific meetings when you are chatting to someone during a break. Small talk can lead to some banal questions being asked, and that’s fine, but when this question is asked seriously, the person asking really just wants to compare themselves to you in some way.

Since I have now written several posts on this. I thought I would summarise the computer-based tools that we are using in the lab to automate our work and organise ourselves.

We have a new paper out. It’s not exactly news, because the paper has been up on bioRxiv since December 2016 and hasn’t changed too much. All of the work was done by Nick Clarke when he was a PhD student in the lab. This post is to explain our new paper to a general audience.

This post has been in my drafts folder for a while. With the World Cup here, it’s time to post it! It’s a rule that a 3D assembly of hexagons must have at least twelve pentagons in order to be a closed polyhedral shape. This post takes a look at why this is true. First, some examples from nature. The stinkhorn fungus Clathrus ruber , has a largely hexagonal layout, with pentagons inserted.

A while back, the lab moved to an electronic lab notebook (details here and here). One of the drivers for this move was the huge number of hard copy lab note books that had accumulated in the lab over >10 years. Switching to an ELN solved this problem for the future, but didn’t make the old lab note books disappear. So the next step was to archive them and free up some space.

This wonderful movie has repeatedly popped up into my twitter feed. http://quantixed.org/wp-content/uploads/2018/04/ctenophore.mp4 It was taken by Tessa Montague and is available here (tweet is here). The movie is striking because of the way that cytokinesis starts at one side and moves to the other. Most model systems for cell division have symmetrical division. Rob de Bruin commented that “it makes total sense to segregate this way”.

I read about Antonio Sánchez Chinchón’s clever approach to use the Travelling Salesperson algorithm to generate some math-art in R. The follow up was even nicer in my opinion, Pencil Scribbles. The subject was Boris Karloff as the monster in Frankenstein. I was interested in running the code (available here and here), so I thought I’d run it on a famous scientist.

As with children’s toys and clothes, books aimed at children tend to be targeted in a gender-stereotyped way. This is a bit depressing.