Thursday, 31 October 2013

The walking viral-microbial-fungal dead

I've just finished watching the first season of "The Walking Dead", yes I know, where have I been, there are already 4 seasons so hey no spoilers everyone. But what a series it is! Exciting stuff and I can't wait to spend another 12 hours today getting through the 2nd season.

The zombies will be amongst us once more for this year's Halloween. Tonight will bring the rise of pasty white faces, fake blood and calls for "braaaaains". Thankfully, not the actual flesh eating, party spoiling type but more the we like to get our drunk on kind. But what is it that makes those guys on The Walking Dead so antisocial?

The last two episodes of the first season gave us a big insight into the science behind the zombification that has plagued the world. The team end up at the Centre for Disease Control (CDC) where Dr Jenner is the last scientist standing. He seems to have a pretty neat set-up with voice activated computers and a top notch lab. So good is his equipment that through a standard bench top microscope he can see DNA. Yes DNA, that stuff in everyone's cells that is only a few billionths of a millimetre thick. Wow, I only wish I had access to that kind of kit. He later shows the other guys a video of Test Subject 19, with the "MRI virtual camera" and we see the brain activity dying out and coming back before he shoots a bullet through the patient's head. He fired a gun in an MRI machine! That could not have done the equipment much good, no wonder they hadn't made much progress.

Despite the cutting edge work that was obviously possible at the CDC, Dr Jenner admitted that they didn't really know anything. "It could microbial, viral, parasitic, fungal ... or the wrath of god!" Well, from the earlier microscope view I'd put my money on viral. Other (real) viral diseases like HIV and influenza are so difficult to treat due to the complicated nature of how they attack cells and mutations constantly altering them. Viruses are of course not treatable with common antibiotics and without proper hospitals available the infection will no doubt kill you fairly quickly. Luckily for us, in a "real" zombie attack, all that rotting flesh would fall prey to Nature's excellent ability to clean up the dead.

These scenes really made me laugh out loud. A nice attempt by the show to bring some actual science to it that was maybe lacking but maybe not needed. Always fun to see them try though and can only be a good thing for making people aware of current (more likely far in the future) technology and that in an apocalypse science is still very important. Also if you want to do research whilst the world is ending, then go to France, apparently those guys can last the longest.

Thursday, 10 October 2013

The PhD that was

After having submitted my thesis last week, I thought it time to retire the PhD page from my blog. So here it is for posterity...

I had the pleasure of working with Dr Bruce Turnbull at Leeds. My project was to develop general strategies towards controlling protein self-assembly into designed nanostructures.

Taking advantage of weak protein-carbohydrate interactions we aim to construct three-dimensional nanoscale virus-like particles and other nanoarchitecture (my new favourite word). Ligands of various lengths, and with different carbohydrate moieties of varying affinity, have been covalently attached to the cholera toxin B‑pentamer (CTB). The carbohydrate units bind into the natural binding pocket of another CTB pentamer, bringing the proteins together to form different aggregates and particles. Analysis of the structures can be performed with AUC, MS, AFM, SEC, ITC, DLS and any other acronym you can think of.

PhD strategy

So what does it all mean?

Well, to simplify things just imagine a brick. Now stick some velcro to that brick. Then get a load of these in a bag, shake them about a bit and hopefully out should pop a discrete spherical object. If this sounds unlikely and a bit crazy then you've grasped the idea perfectly.

If we can build organised, controlled structures on the nanoscale then this opens up possibilities for nanomachines, templated reactions and drug delivery vehicles.

PhD life

Doing a PhD is stressful, hard work and immensely fun. The work differs day to day with massive highs when your reactions unexpectedly work and terrible lows when your proteins commit suicide. There is a lot of self-motivation and commitment needed to complete a successful PhD, and it also helps having a great team around you and a kind word of encouragement every now and then (cheers Bruce). All for the advancement of the human race, and maybe also for the title of Dr before your name.

Turnbull lab group