The inestimable Dr Rohn has, on more than one occasion, sung the praises of the engineering prowess of her lab-mates. But in this week’s Nature music and ingenuity were combined to produce a new high note of technical wonderment. A fascinating News and Views piece directed my attention to a recent paper* by Hua-Zhong Yu and colleagues at Simon Fraser University in Canada.
The Yu group have created a ‘home-made’ micro-array on a music CD that just needs an ordinary CD player to scan the disk for the results of the binding assay.
They did what!?!
You heard right – and their system is impressively flexible since interactions involving DNA and protein can both be analysed. First, the CD is treated so that spots at defined positions on the surface will allow covalent attachment of DNA or proteins. Biotinylated DNA or protein samples are then added to perform the binding assay and in the final step the bound material captures strepavidin-labeled gold nanoparticles. A simple chemical treatment deposits silver on these gold seeds, so the tiny spots containing bound DNA or protein end up coated with silver clusters.
Then comes the devilishly clever bit.
The disk can be inserted into a standard CD player to analyse the results! Because music CDs have been designed to play back smoothly even when they get scratched or dirty, the music is encoded in a way that allows error detection and correction. The software analyzing the readout from the disk knows precisely where the errors on the disk lie. Now, normally you don’t care about the errors; you’re only interested in hearing a faithful rendition the toe-tapping tunes of your favourite combo (‘Hold on Tight’ by The Electric Light Orchestra anyone?), but with freely-available software tools, you can access the error information and that is exactly what the Yu group have done.
Since the silver clusters scatter the laser light just like a defect, each spot of bound proteins can be found on the treated disk. And not only that: the software also reports the size of the defect, which in this case is proportional to the amount of material bound, so the interaction can be analysed quantitatively. Yu and co showed they could measure DNA hybridisation, detect SNPs and determine antibody-antigen affinities.
How cool is that? As Ian Dury put it, “There ain’t half been some clever bastards!”
*Yunchao Li, Lily M. L. Ou, Hua-Zhong Yu (2008). Digitized Molecular Diagnostics: Reading Disk-Based Bioassays with Standard Computer Drives Analytical Chemistry, 80 (21), 8216-8223 DOI: 10.1021/ac8012434
Incredible!
I love engineers. Both generally and specifically. This just confirms it.
@Heather – I love engineers. Both generally and specifically
Intriguing. Do tell!
But only if it involves bodice-ripping.
Wow, what a collection of Barry Manilow CDs will drive some people to do. That’s just, well, wow.
In principle, Bob, the CDs should still be playable so you can listen while you work and don’t necessarily have to sacrifice your more erratic purchases for science…!
‘playable’ and ‘Barry Manilow’ in the same breath?
Well, admittedly he’s not as good as Ian Dury and the Blockheads…
I love engineers specifically, too. Well, my Dad was one. In fact, he was one of the very first computer engineers, and I was almost born on the Mark One computer, but that is another story, perhaps one to pitch to the Cold Spring Harbor Laboratory Press (see RPG’s comment).
My dear Maxine, that is a glorious image.
This reminds me of the engineers around our place who are subverting standard laser-printers to print silicon elastomer micropatterns for the purposes of
torturingstudying single cells.Aargh! How did we get onto the release of calcium from intracellular stores!
My Dad was an engineer of sorts – he was a dentist. One of his favourite aspects of the jobs was orthodontics, so he would often be found of an evening bending and shaping wires to make braces that fit perfectly to plaster-cast models of his patients’ teeth. It was fascinating to watch.
I have just informed my friend Norman of that, Stephen. I know Norman as a fellow-enthusiast for crime fiction as well as a history expert, but he also is a retired dentist.
In one of those blogging weirdnesses, I first met Norman on the Internet, but as a result of a post I once wrote about our local fish and chip shop going upmarket, it transpired that Norman’s practice was in walking distance of my house, and that he lived a couple of stops down the train line. (He sensibly left London when he retired and now lives near Exeter.)
I confess I’m not a massive devotee of crime fiction, Maxine. I quite liked Miss Smilla’s Feeling for Snow. A friend recommended my fellow Northern Irelander, Colin Bateman, and I read The Horse with My Name which was OK but didn’t really inspire me to read any more of his work, though I enjoy Murphy’s Law (also by Bateman) on the TV.
But, thinking of that, I do love crime fiction on screen (currently working my way through Season 1 of The Wire – absolutely brilliant!) but when it comes to reading I think I may be a bit snooty about the genre. What would you recommend as a corrective?
If you like crime fiction on screen, Stephen, watch out for Kenneth Branagh as “Wallander” – 3 TV films (BBC I think) starting Sunday 23 November in the UK (next year on PBS in the USA). If you enjoy these, I can highly recommend the books, by Henning Mankell. If you like these, you will be able to read them in order, unlike me – I’ve read them over the years as translated (from the Swedish) – in what seemed to be random order.
There is also an excellent movie, now out on DVD, in French with subtitles, called Tell No One. It is based on the book by Harlen Coben. I watch very few films these days, but this one is excellent.
I could recommend many crime fiction novels – the genre is so broad that it would depend on your area of interest. I am not too keen on thrillers for example, I prefer a bit of character and plot over pyrotechnics. Arnaldur Indridason (Icelandic) might appeal to you, as his first novel (Jar City, recently released in UK cinemas and enjoyed by Lee Turnpenny but I am waiting for DVD), had a scientific theme. (Which I thought flawed, but if you ever read it, we can discuss!)
Peter Temple, an Australian author, is superb. Try The Broken Shore, which won all kinds of awards – it is available in PB.
Sorry to ramble on, but it is Sunday and you touched on a favourite topic of mine! I review quite a few books, if you are really mad and are interested, they are archived here.
Easy response: my Dad and husband are both trained as engineers. Dad kept on with it. I also really enjoy the columns of Brian Hayes and Henry Petroski. I don’t know if the former considers himself an engineer, but he fits my definition – someone who’s ultra-clever and tries out real-world solutions to the questions s/he thinks of.
If I may pre-empt Maxine, I’m quite fond of Henning Mankell, especially the earlier novels featuring Kurt Wallander. One Step Behind , perhaps?
PS I have heard such great reports of The Wire from my crime-fiction blogging circle that I’ve bought the first couple of series on an amazingly cheap deal from Amazon. Goodness knows when I’ll get time to watch them, though – but good to hear you also are enjoying them.
Snap, Heather! (or do I mean, double snap?!)
@Heather and Maxine – sounds like the consensus is for Mankell’s books on Wallander! Thanks for the other tips Maxine – will follow up some of those leads…
I’ll definitely watch out for the TV series. Might well have switched it on anyway since I have enjoyed quite a bit of Branagh’s work. I first came across him in a 1982 Play for Today on the beeb called Too Late to Talk to Billy (that dates me!), but also enjoyed his Henry V (at the Barbican – haven’t seen the film). And he was excellent as Nazi Reinhard Heydrich, in Conspiracy
I’m getting through The Wire by ripping the DVDs (that I bought!) so that I can watch them on my PDA during the evening commute. Takes a little bit of organisation but, like you, I don’t think I’d find the time any other way.
Stephen, brilliant find, thank you! So the CDs are still playable… Jenny, how about the printers – are they still usable?
These people could endlessly subvert ordinary office and home electronics to do clever scientific things… Hang on, sounds like Jimmy Neutron now.
@Steffi – it was a great paper. I thought Brian Derby might have mentioned it since it’s not a million miles from his research interests (I think!) but he must be sleeping this weekend – sensible chap!
I’m old enough to have seen Branagh in his West End debut, Another Country (along with Colin Firth and Rupert Everett, none of whom was then known). I’ve never been a massive fan, mainly because I can’t be doing with someone who writes his autobiography at the age of 23, but I have to say my estimation of him shot up when I saw him on stage the other week as (and in) Ivanov. Superb production. I went with a very good friend I made through blogging, and my eldest daughter, who said she’d be keen to see something featuring Branagh, even though he’s “rathr old” (to me, he is still a young whippersnapper).
I also admit to enjoying his version of Much Ado – one of my favourite Shakespeares – even though the “feelgood” was a bit too “feelgood” in that interpretation, for me.
PS Stephen, your comment about how you are watching The Wire reminds me of Mrs Beeton’s recipe for jugged hare. It begins: “First catch your hare.”
I think I’m stuck with the “not having time to watch it on the TV even if the TV were available” mode. Unfortunately, I lack the skills so admirably demonstrated in this post and in many of the comments.
@Stephen – I am not sleeping, just gardening. I will comment in due course on CDs. it is not the first use of the technology – there was a start up in Portugal that used CDs for analytical chemistry. I will try and find the reference/link – it involved an ex-phD student of mine somewhere along the line.
@Maxine – there’s really not much skill involved. All you’re likely to need is a iPod touch and a nifty little program called Handbrake…
@Brian – I thought you might know something about all this…!
PS late-breaking news from the crime-fic blogs – Wallander now seems to have moved to the 30 November. (1st of 3)
The iPod would be a culture shock indeed, Stephen. But I did buy a CD this afternoon, first one in years. Played it on the CD player in our living room. The other members of the household looked at me as if I was mad. (They all have iPods.)
Don’t let them break you Maxine! I still buy CDs even though I rip them to an iPod since I like to have a hard copy (and there’s still a nostalgic fondling the cover of a vinyl LP vibe going on somewhere in my head). I’m not constitutionally ready to join the download generation…