Thursday, 25 October 2012

Weird and wonderful

In my free minutes, between experiments or when I'm grabbing a breather, I like to click around and explore those bits of the news and science that aren't strictly in my discipline. Today I saw a couple of articles (both via Ed Yong, from one route or another),which have stuck with me, which I thought might be worth sharing.

The weird first, without much preamble; a movie of a duck's penis. This doesn't require any explanation, except maybe from god. Mindbleach, please.

Then on to the wonderful, with this blog post (combined with this article), talking about micro-chimerism in mothers.

This deals with a rather beautiful aspect of mammalian biology, where cells from the developing foetus enter the circulation of the mother, and are even detectable after birth.

The latter paper even reports detecting the DNA of these cells over 27 years after the birth of the child (by looking for Y chromosome DNA from a mother who's borne sons).

I've always known there was so much of my mother in me (about half, genetically speaking), but it's profoundly lovely to think that there's probably a bit of me in her.

Monday, 22 October 2012

UCL Triple-Eye Symposium

I meant to write this post over the weekend, but unfortunately a dinner of all I could eat barbecue meant I spent most of the time sleeping and rubbing my stomach. Now I've recovered somewhat, I just thought I'd share a couple of highlights of Friday's symposium

It was the UCL Infection, Immunology & Inflammation Domain's third annual symposium, celebrating the work of this aggregation of UCL (and partner institution) academics' research.

There were a few highlights for me. The keynote speaker, Stephen Goff, gave an engaging account of his work into embryonic stem cell restriction of retroviral infection.

Another great talk came from one of our BiPR colleagues, Brenden Wren, who studies bacterial glycosylation, but moreover has developed a glyco-toolkit, allowing bacterial production of proteins-of-interest with desired sugar modifications.

However the best bit of the day was a bit more selfish, as two PhDs in our lab (myself and Lucy Bell) won first prize in our respective poster sessions, which was very warmly appreciated!

There had been a lot of interest in our TCR repertoire work throughout the poster sessions, particularly to a figure I'd presented of some of the difficulties inherent in deep-sequencing TCR repertoires. I think I might expand on this for a later blog post, so if that's interesting to you, watch this space.

Saturday, 6 October 2012

Restriction digest with OLD enzyme

I suspect most labs are like mine, with freezers overflowing with old, unused restriction enzmyes, bought for some odd bit of cloning, used once, then kept in the freezer forevermore.

In most labs I've worked in, the general rule of thumb for out of date enzymes was just add a few more units (up to the 10% of total volume permissable to prevent glycerol inhibiting the reaction), and maybe run a bit longer.

However, it's not until my current lab that I've ever found REALLY old enzymes. As in, enzymes older than some of the younger PhDs in the lab.

I've always suspected that the expiration dates on these are largely guesswork, so I thought I'd try out the oldest enzymes I could find.

I wanted to go with an aliquot of AluI I found, dated for September 1989 (although it doesn't say whether this is an expiry date or when it was made). Unfortunately, the lid for AluI is lost to the mists of time; the tube is just full of (likely 20-year old) ice.

However, I did find a tube of BstYI that appears to be of a similar age, perhaps even older; the labelling is fairly similar, but the lack of a date makes me question whether it predates the AluI (and inclusion of estimated expiration dates). Maybe there's someone at NEB who can sort this out - I'll investigate that. At the very earliest, it seems BstYI would have appeared around 1988.

I mixed up a quick 20μl digestion mix, using 2μl enzyme in NEBuffer 4 to digest around a microgram of pUC19 plasmid DNA, incubated at 65°C for two hours.

Lo and behold, it works just fine (presumably - I don't have any in-date BstYI to compare this against). This is an enzyme that is likely somewhere in the region of 25 to 28 years old. I'm not sure if I'll ever pay attention to expiration dates again.

NB: doing a quick search around for this write up showed me this article, which makes me wonder if I shouldn't be surprised; it implies that the companies don't tend to make up many batches of these enzymes, just thaw old ones and assay them for activity!

It's also probably worth noting that this seems to be a fairly robust enzyme, which has been kept at minus twenty for the vast majority of its life (it looks barely used), thus these findings might not apply to other enzymes.

Move to blogspot (and out of inaction?)

With the best of all intentions, last year or I so I set up a Newsgrape account (when it was in beta) to try and spark off a bit of sci-blogging. With the first year of my PhD hogging most of my time, that kind of fell by the way-side.

However, when I then tried to get back into it, I found that the developing Newsgrape hadn't evolved quite as I'd expected; rather than the eclectic blogging community I'd anticipated it had ended up a rather bizarre commercial, uber-syndication service.

I'm sure this is great for some, but it doesn't really push my buttons.

As such, I've dusted off this old blogger account (once I remembered I had it). I plan to port over what few articles I'd put up at Newsgrape*, then start to be ever so slightly more active than I was - which honestly, won't take much.

*I think I might try and back date them so they're roughly in order, which might make this look a bit odd for a first post.