Archive for April, 2009

Bio-Rad’s PCR Songs

Saturday, April 18th, 2009

On the subject of the PCR Reaction: PCR is extremely widely used, and is a highly variable technique. There are dozens of different slight variations on the DNA polymerase, lots of ways of designing primers to get them to stick just right, dozens of different machines (called thermal cyclers) that heat and cool the DNA to keep the enzyme, DNA strands and primers happy (and everyone has their own settings for the machines). Entire cultures build up around the PCR reaction. Someone I work with told me a story about their previous lab having a little statue to a PCR God, to bless the thermal cycling machines.

Anyway, as a result the image that a PCR company projects is pretty damn important for tapping into these cultural norms (polymerases are described as High Fidelity or Lightening Fast, and have names like UltraFusion and Pfx Platinum). The master of this game is the lab technology company Bio-Rad. They sponsor the Nature Podcast, and their adverts always seem to stick in my head with worrying efficiency (from memory: ‘The Nature Podcast is brought to you by Bio-Rad’s 1000-series thermal cycling platform: when you rethink PCR, you think about how easy it can be’).

However, the most, er, interesting viral advertising they attempted came about last year. They produced a song, with a music video, with scientists singing the praises of PCR. I kid you not…
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Basics: Sequencing DNA, Part 1

Friday, April 17th, 2009

For an embarrassingly long time, I had very little idea how we read people’s DNA. We deal with DNA sequence so often, and use it for such a plethora of things, that if I thought about it at all, my thoughts would have been something along the lines of “er, well, you just, you know, sequence it, right? Run it out on a gel, or, er, something”. I remember years ago admitting this ignorance to a friend, who said “Oh, they have machines that do it”; this response is both reassuring and terrifying. Anyway, I finally rectified my ignorance (about the time I read the book Genomes 3, which filled in a lot of the blanks on the molecular side of my subject); it is actually a pretty fascinating topic, and also a pretty important one, since progress in sequencing technology drives progress in much of genetics generally. So, I thought I’d dedicate a series of posts to sequencing.

While it seems so simple, sequencing DNA is a pretty major challenge. If you ever hold DNA in your hands, it basically takes the form of a long-chained acid dissolved in water. If you want to know something about it you can dye it and run it out on a gel, to see how large the molecules are (large molecules run more slowly through a gel, so you can tell how big the molecule is by how far it moves), but doing much beyond that requires quite a bit of thinking.
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An Ammonite Tree

Monday, April 13th, 2009

I was clearing out my photos this weekend, and I found a number of pictures that I had taken on my trip to Amsterdam Zoo a few months ago. One exhibit consisted of a long tree/time-line of Ammonite evolution, stretching from the Devonian up to the KT Boundary, showing which groups were descended from which. I found it wonderfully presented, with different colouring representing the different suborders, and fossils attached at various times, so you could see how the different forms changed over time. I really am a sucker for phylogenetic trees, especially those that manage to integrate other visual information.

The exhibit was slightly sad, however. It was up a relatively hidden away staircase in an already pretty out-of-the-way building. I stood there looking at it and taking pictures for a good half an hour, and nobody even came into the room, let alone spent any time looking at the exhibition. I found it a little tragic that someone had put so much effort into presenting so much information in a way that could be easily understood, and now it sits where not many people will see it. Added to this, I expect (though don’t know) that not many people will be interested in following ammonite evolution, especially when there are dinosaur bones around.

My hope is that the University of Amsterdam makes us of these sorts of resources in their classes: I remember loving the undergrad classes which involved wondering around the Cambridge museums, especially those that went through different groups, describing how they fit together in a classification system, and what that can tell us about how they evolved.

Anyway, I stuck the pictures I took together to reconstruct part of the exhibit. Click the (rather large) thumbnail below to see low quality .gif of it; when I get back I’ll upload a higher quality one.

UPDATE 17/04/09: Uploaded higher quality version, click thumbnail to view.

amniotes.gif

On Stuffed Venereal Diseases

Sunday, April 12th, 2009

I’m currently visiting my parents, and my female spawner, always keen to spoil me, presented me with a couple of biology-related presents (including this novelty t-shirt). One particularly cool thing, picked up in CyberDog in Camden Market, is this stuffed toy:

hiv

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