Tuesday, January 26, 2010

This blog post is intended to distract you from the fact that I haven't updated my blog in ages

I think this (including the accompanying comments) is what all blog posts should be like.

Wednesday, January 20, 2010

Extraordinary Embryo of the Week

What a beauty! This is a mouse embryo, and you can tell that it has been stained for the expression of a gene. But this is not just any gene! This mouse has actually been genetically modified to contain some DNA from the extinct Tasmanian Tiger, Thylacinus cynocephalus.

Now, the point of this genetic modification wasn't to create a half-mouse-half-Tassie-tiger (that would just be absurd. Not to mention impossible...), but rather just to study the function of a particular gene. Because it would be damn near impossible to bring the Tasmanian tiger back from extinction, this approach is the best way to study its genetics.

The Tasmanian tiger

What the scientists did was very carefully extract DNA from four 100-year-old Tasmanian tiger specimens that had been preserved in alcohol, and amplify the DNA of interest (not an easy task if you're working with old DNA!). The DNA they amplified was from a region that controls the expression of a gene called Col2A1. You can think of this DNA as the 'switch' that turns Col2A1 on or off.

They attached the switch to an additional piece of DNA, a 'reporter' gene. Then, they inserted the whole DNA construct into a mouse genome. The reporter gene produces the blue pigment you can see. This method tells us where and when in the embryo the 'switch' is turning on. If the switch is turned on, the reporter gene is active and produces a blue pigment.

Basically, this was a really neat method for studying the function of a gene from an extinct animal! The blue pigment allows us to see where the gene is switched on, and then we can compare that to the mouse version of Col2A1. Turns out, Col2A1 seems to perform the same function whether it's from the Tasmanian tiger or the mouse (its function is in cartilage formation, which is why it is expressed in the forming bones).

This may not be a particularly thrilling conclusion, but the applications of the technique are pretty awesome. For example, maybe one day we could examine what dinosaurs looked like, if we could extract the relevant genes from dinosaurs and insert them into another animal!

And actually, geneticists use this technique for non-extinct animals as well. It's a really good way to figure out if a similar gene performs the same function in different animals. These kinds of studies tell us about the evolutionary history of individual genes, which is bloody interesting, if you ask me.

Reference: Pask, A.J., Behringer, R.R., Renfree, M.B., 2008. Resurrection of DNA Function In Vivo From an Extinct Genome. PLoS ONE, 3(5), e2240.

Thursday, January 7, 2010

Movie Review - The China Cup

I went to see this kiwi film at Matakana Cinema a couple of days ago. Having not heard anything about it, I wasn't sure what to expect.

First of all, it was a seriously low budget production. That alone is not a problem, but it was very clear that it was made by people who were totally inexperienced in making film. The quality was poor, and the acting was stilted and distracting. But I was still willing to forgive that if it was a good story...

SPOILER ALERT: I'm going to outline the essentials of the plot here... Stop reading if you don't want to know what happens.

Charlie is an alcoholic, and is well known for drinking Jack Daniel's from a china cup (his late wife's favourite china cup, to be specific). His daughter, Sam, shows up out of nowhere, there's some friction between them. He thinks she ran off after Mum died. She thinks he was never around when Mum was dying. She tries to talk to him about his drinking, and tries several times to speak to him about it. He's not interested in hearing it.

Sam's 'serious' talks with Charlie usually wind up as "come to church with me, Dad, it would mean a lot to me". Charlie's not interested in having religion shoved down his throat, so understandably he kicks up a big fuss and (maybe a bit more unreasonably) he storms out. This happens several times. At one point he even goes to church, but leaves before the service is finished.

By this stage I was getting a bit ticked off, and starting to suspect that it was a religious production dressed up as a secular kiwi film. In the meantime there were a lot of humourous moments involving other characters, and they were pretty entertaining. But then...

Sam finally admits to her dad that she lost her husband and son the previous year, in a car crash. They were killed by a drunk driver. Jesus helped her get through it.

Wait, what? She lost the two most important people in her life, a year ago, and she's like totally pretty much over it? Because of Jesus? Reality-check FAIL.

OK, so she has a bit of a cry, but she's talking about it as though it's all in the past and she's moved on. Totally unbelievable. AND THEN, she asks Charlie to come to church and he storms off again.

The next day she's driving round (with some bird who went on like two dates with Charlie) looking for him, coz he's been gone all night, and they have a car crash.

Guess what happens. Seriously. Guess.

Charlie feels crap for essentially being the reason that Sam had a car crash, and when she gets better he apologizes. Sam asks him to come to church again, Charlie calmly outlines that he's just not interested in religion, and Sam respects his decision.

JUST kidding. That was just my wishful thinking.

When he finds out she's had an accident, he's devastated. Next, he's sitting on the porch, waiting for news, and a friend of Sam's from church comes over and sits down next to him and starts singing "Amazing Grace". Charlie bursts into tears. When Sam gets better, Charlie apologizes and says "I guess I'll be coming to that church of yours".

That's it. That's the film's resolution. Presumably Charlie is a changed man and no longer goes near the sauce.

It's just so superficial! There are no alcoholics in church, right? Alcoholics don't need proper treatment, they just need to find Jesus, and he'll sort it all out, right? Un-be-lievable. Utter nonsense.

If people want to make these superficial films they can go right ahead, but I'd prefer a bit of a warning before forking out $15 to see it in an actual movie theatre. I googled the film afterwards, and still found no indication that it was secretly a piece of churchy woo.

When I pay to see a movie, I'm not just paying for the entertainment. I'm paying for a solid quality piece of film by people who know what they're doing. I don't want to pay for a movie ticket to endure some poorly disguised preaching.

Tuesday, January 5, 2010

Extraordinary Embryo of the Week

Oops, a day late again. I was shopping yesterday. I'm sure all 2 of my readers understand that me getting a bargain price on some beautiful black patent leather pumps is worth a slightly late blog post :D


This little guy is a Xenopus laevis embryo that I stained for the expression of a gene called FGF-8 (fibroblast growth factor 8).

FGF-8 is important for the development of many different tissues throughout the body - you can see at this stage that FGF-8 is turned on in the tail bud (to the right of the picture), the somites (the stripy bits along its middle), the midbrain-hindbrain boundary (the stripe at the top of its head) and a couple of the branchial/pharyngeal arches (other stripy bits on its head).

So what?

This gene is being turned on in a bunch of different places. And in each different tissue, it is doing a slightly different job. How can the same gene have different functions in different places?

It all depends on context. The environment that the cells are in, and the complement of genes that are turned on in each cell, all affect how FGF-8 functions. It's kind of a space-saver in the genome; instead of having a different set of genes for every conceivable developmental job, we find that some genes are re-used all over the body to control the development of different organs and tissues, and FGF-8 is just one of these multifunctional genes.

FGF-8 does even more work during development at different developmental stages. For example, later on in development, FGF-8 will be used to control the growth of the developing limbs.

So, our Xenopus embryo above illustrates a couple of really fundamental ideas in developmental biology:

1. The same gene can perform different functions in various tissues (AND at different time-points).

2. The environment and genetic context affect how a gene will function.

I'd really like to pause here, and I'll pick up later this week to explore what these points mean for the evolution of developmental systems.

Saturday, January 2, 2010

Spelling and Grammar

I must admit that I'm one of those people who gets incredibly agitated by people who mis-spell simple words. I found this excellent comic on Stumble this afternoon (click through for the rest):

Although, I've found that the problem is some people don't actually realise that Lose and Loose are two different words. Another similar case is Then and Than: some folk are entirely unaware of the presence of one of these words (than) in the English dictionary. It really baffles me.

Unfortunately, people also hate to be corrected. There's no point in telling people when they get it wrong, because not only will they not listen, I'll just end up with no friends (except the grammatically correct ones, of course...).

And don't even get me started on "would of" instead of "would have".