Mike Bunce, Murdoch University
Mike Bunce, from Murdoch University, is using the science of DNA to unlock the secrets of the past, present and future.
Chris Smith caught up with him to find out more.
Mike - In a nutshell, what our lab is good at is getting DNA out of really crappy substrates sometimes literally because we work a lot both on fossilised faecal material, but also modern faecal material.
Chris - Why should that be difficult?
Mike - In the post mortem environment, after you die, your DNA starts to decay and also, when you eat, material of the DNA starts to decay as you start digesting it. Why it’s difficult is that during that decay process, the DNA starts to break into small little pieces. So, it’s technically challenging because we’ve got to try and get all these small bits of the jigsaw puzzle and try and piece them all together again.
Chris - So, how are you using this technique?
Mike - We’ve got research programmes, looking at fossil bone material. We use it to look at the faecal material of penguins that live off the coast here to figure out what they're eating. We use it in the airport environment to look at birds and what's in their gastrointestinal tract after they’ve had a bad encounter with an aeroplane. So, there's lots of applications of how we can use degraded material and try, and figure out what's actually in it.
Chris - Tell me about the bird example; I've not come across that before.
Mike - We were contacted by Perth Airport here in Western Australia. When birds come into contact with airplanes either literally, by hitting them or they go through the jet wash, they cost the industry over a billion dollars a year. We first got involved with the airport, mainly through the idea of swabbing airplane engines and wings, to try and figure out what species is actually in that blood smear that you might swab off an engine cowling for example. But the question quickly became more subtle than that and we were saying, “What was the bird doing at the aerodrome in the first place?” And so, when we had carcases like that, rather than them being discarded, we were actually trying to extract as much as scientific information as we could from them, which involved dissecting them open,taking out gut contents, and then figuring out what brought them to the aerodrome in the first place. Were they eating grasshoppers? Were they eating grass or trees that were planted in and around the airport?
Chris - Have you found out what was attracting the birds?
Mike - Yeah, well we looked at about 80 odd birds, things like galahs, cockatoos, water birds and of course, they all have different diets because they're different species – things like galahs which are flocking birds- they ate a lot of this invasive weed called erodium. And so, we know right from the outset that this is not a good thing to have around your airport especially not on a high risk bird species that flocks. Of course, if we end up with flocking birds and an airplane hits a flock of birds, the implications are of course much more damming than they are, just a single small species. So, we are actually providing information on grass and weed species where better control measures could actually reduce the incidences of aircraft interactions with the wildlife.
Chris - What about way back time because this area is particularly rich? If I just go southwest out of Perth a couple of hours, I'm along Caves Road in the Margaret River region, and having been there, it is beautiful, but there's a very rich archaeological scene running through there. Are you working there?
Mike - Yes, we’re doing a lot of work in the southwest corner of Australia. It’s one of the 34 biodiversity hotspots in the world. There's huge numbers of endemic taxa are only found here by going down some of the caves and looking at some of the archaeological sites and paleontological sites down there. We’re asking questions like, “How many species used to be there? How biodiverse were they? What plants and animals used to live in the Sydney areas?”
Chris - So, someone will excavate one of these sites and they’ll get what, bone? Is that what you're using to get the DNA?
Mike - We use both bone excavated from the material as well as sediment. So, to give you an example, Devil’s Lair is one of the most famous archaeological sites in Australia. It’s a sequence that goes back 50,000 years. Actually, the oldest campfire dated to Australia today at about 42,000 years was found there. So, Australia’s first barbecue if you like.
Chris - Where is it exactly?
Mike - So, Devil’s Lair is located right down the southwest corner close to the Margaret River area. So, when we excavate material down there, we take all the very small bits of scraps of bones that the archaeologists and palaeontologists aren't that interested in and we collectively grind them all up into a soup and then we ask the question, “What's in that soup of bone? How many species are in there? What's the biodiversity of say, kangaroos located in that soup of material?”
Chris - And I suppose because archaeology is in a series of levels or layers, if you take different bits from different layers, you’ve got a timeline there, haven't you, so you can map your biodiversity onto time.
Mike - And that’s the key thing that we’re trying to find. It’s really how the biodiversity has changed over time.
Chris - What sort of quality of DNA comes out of that and how far back in time can you go?
Mike - The quality of DNA is highly variable. Some caves preserve DNA really nicely. Other caves do not. In the southwest caves in the southwest WA, we are getting DNA back to 45,000 to 50,000 years.
Chris - Are any surprises coming up as you unlock this amazing sort of molecular fossil that we’ve got in these bones?
Mike - There's always surprises especially when we’re starting doing these bulk bone sampling really where we just collectively look at all the material. We’re accessing things like swans that could only have ever got onto the site because people were hunting them and taking them in there. We’ve got these unknown sequences of kangaroos. The closest match that we’ve got to something is a tree kangaroo that now lives in Papua New Guinea. Clearly, that’s not the species that used to be there, but something a bit like that was there. All we’ve now is a DNA signature. We’ve got no fossil to actually match up with that.
Chris - What about more contemporary studies because one other thing that I know you’ve been working on, because I saw you give a talk on this, was analysing what are in traditional Chinese herbal remedies-you can subject this to DNA analysis too?
Mike - Yes. It’s really no different what it boils down to, whether we start off with a herbal medicine tablet, a 40,000-year old sediment sample, or gut contents out of a bird at an airport. They're all just degraded DNA. So, the herbal medicines, Australian Customs here was asking us, what is in this material? In a wildlife forensic context, it’s illegal to trade in certain endangered species and so, we start off saying, “What are all the animals in the sample? What are all the plants in the sample?” So last year, we published our first paper in PLoS Genetics that looked at extracting DNA from herbal medicines and asking us, “What’s in the mix?”
Chris - Dare I ask, what is in the mix?
Mike - It is a lot of undeclared plants and animal constituents in there and some of them are probably of quite worrying concern for human safety.
Chris - What sorts of things were you discovering?
Mike - One of the medicines that were seized by customs here has the species of Asarum in it. That’s a genus of plant. Asarum has a chemical in it called aristolochic acid. This is a potent carcinogen that binds to your DNA and causes a bulge in your DNA, and when it copies it, and it will mutate that DNA strand and potentially cause cancer. That sounds quite extreme, but in actual fact, the highest rate of urinary tract cancer in the world in Taiwan where they have a lot of herbal medicines that contain Asarum in them. It’s the species that really shouldn’t be in any herbal medicines that we have because we know it’s bad for us.