Well Matias and I have been spotting these for a while so I thought this could be an online wall of fame/shame for the worst puns ever to appear in titles of papers in otherwise respectable journals. This was prompted by my discovery today of this - the culprit/genius punster being my supervisor in this case!

http://www.ncbi.nlm.nih.gov/pubmed/9843198

Groan! I also feel that this deserves a special mention.

http://www.ncbi.nlm.nih.gov/pubmed/12509281

Getting a joke like that past the editors is basically the goal of my life.

Anyone else have any favourites?

Following on from Matias' post, here's an example of an annoying problem faced by lab people, and a cool way to fix it.

The process of stitching together various bits of DNA to make plasmids for use in experiments occupies a large amount of time for many molecular biologists, especially in the early stages of a project. The most established way to do this is to use restriction enzymes and ligases in vitro to chop DNA up and stick it back together, and then stuff it into bacteria to select intact plasmids and amplify them. The fidelity of the process is generally good, but mutations do arise sometimes. I just found one such mutation in my plasmid - four base pairs of a critical recombinase recognition sequence deleted. Worse, this mutation is also present in the lab stock of the parent plasmid. Now here's the big difficulty in using restriction enzymes - they cut at a defined sequence, and if you need to modify part of the plasmid without convenient restriction sites (like this one), you're stuffed.

Or perhaps not. Recently (at least more recently than restriction enzymes) a new set of methods dubbed 'recombineering' have been developed. These take advantage of the fact that homologous recombination can occur in bacteria. So if you make a construct with some homology either side of the region you need to fix, and with a correct version in the middle, you can introduce this into the bacteria carrying the mutant plasmid and get replacement of the broken bit. I took advantage of the fact I was fixing a Cre recombinase site (lox site) and replaced the broken site with an antibiotic resistance gene (bsd) flanked by two working lox sites - meaning I can select for the replacement first, then use Cre to delete the marker and restore a single, functional site. Amazingly it actually worked - yay for small victories.

Most lab bacterial strains are recombination defective (recA mutation), to give better plasmid stability, so to use this technique you need to reintroduce the recombination function to the bacteria. Of course this carries the risk of causing other random plasmid mutations (due to recombination between small bits of homologous sequence) - so let's hope I didn't just make things worse :)

Highly technical diagram below - the lox site represented by a triangle. There are a lot of other uses for this technique, more info here http://www.nature.com/nrg/journal/v2/n10/abs/nrg1001-769a.html

SJP

You spend years waiting for someone to invent a jetpack and then this comes along!

http://news.bbc.co.uk/1/hi/world/7402016.stm

In other news, this is an awesome paper in the current issue of Nature. An enzyme to catalyse a non-biological reaction designed computationally, synthesised and then fine tuned by directed evolution. I'm not actually sure if this is the first example, but it's the first I've heard of. These guys must have some big brains, and some serious computers.

Reactions in synthetic organic chemistry such as the one in this paper (removal of a proton from a carbon atom and its effective transfer to another part of the molecule) are generally pretty tricky - in my hands at least! This is reflected by the fact that a lot of reaction schemes are named after the guy who worked it out, presumably in recognition of their creativity; the one in the paper is called the Kemp elimination. Considering how to accelerate a reaction (or make it possible at all) involves thinking about the transition state(s) - a transient state (TS) somewhere between products and reactants. This will often have a different shape or charge distribution. Enzymes contain active sites which fit, bind and stabilise the TS, which favours progress of the reaction.

Unfortunately, nature is only really interested in making things like amino acids, nucleotides and lipids rather than oil, plastic, cars, money etc., so it hasn't designed (via evolution) any enzymes to do these things. It should be possible to design enzymes to do a wider range of reactions by considering the shape of the TS for the relevant reaction and the properties of an active site that would fit it, but this requires big computers to do the search, as well as a good understanding of the possible shapes proteins can take.

I guess we're getting there, which to me is astonishing. These guys designed their active site taking into account shape, charge, and even positioning a side chain to change the pKa of one of the other bases in the active site. Once they worked out protein backbone sequences (in 3D) that would support this site, they synthesised corresponding genes, whacked them into bacteria and got functional enzymes out. Then they randomly mutagenise their initial genes and look for increased activity to get an even better enzyme, with activity similar to conventional organic catalysis. Ideally enzymes should outperform organic catalysts and I'd hope to see that in future, but it's early days - very exciting. It even involves computers ;) But not jetpacks.

Paper: Röthlisberger et al (2008) Kemp elimination catalysis by computational enzyme design. Nature 453:190-5
http://www.nature.com/nature/journal/v453/n7192/full/nature06879.html

Time for some biology! I just saw this paper which deals with a subject I enjoy reading about:

DOI (still in advance publication): 10.1126/science.1154520

The process of dividing a cell involves generation of various forces - the chromosomes have to be positioned correctly so that they segregate evenly, as well as be pulled towards the daughter cells later on. The membrane also has to contract and separate down the middle to complete the division.

Experiments that investigate these forces are some of the most elegant in molecular biology. A good example is the proof that chromosomes must be under tension via microtubules binding at the kinetochores before they separate - this was shown by taking cells arrested due to one unattached kinetochore, sticking a tiny needle in and 'tugging' the chromosome in the right direction - the cells then undergo mitosis! (http://www.nature.com/nature/journal/v373/n6515/abs/373630a0.html)

This paper isn't in the same league technically, but it's still nice. They add one of the proteins involved in the actual division of the cell to some artificial lipid membrane tubes, and show that it spontaneously forms rings around the tube which contract when given GTP. I wonder how far they can take this system - I think it would be cool if they can get all the way to fission by adding a few more components. As they note at the end of the paper, this is probably how the earliest forms of life looked.

SJP