Posts Tagged ‘DNA’

Notes from the international barcode of life conference #bol4

// December 5th, 2011 // 1 Comment » // Science Communication

Image by .jun, flickr

On Friday I went to day three of the international barcode of life conference, which happened to be in my hometown of Adelaide, actually at the home of my undergrad – The University of Adelaide – how convenient!

DNA barcoding matches a region of DNA to a species, at the moment there’s still plenty of work on building up that barcode database (called BOLD, though GenBank is also used). There are about a million and a half barcodes recorded so far and it’s streaming along.

The database is open access, and people can use it to match a barcode region from an unknown sample to a species.

So far, people have used this to check out the slice of fish in sushi, illegally collected shark fins, and plenty of other stuff.

It’s a powerful technique now in it’s ninth year and with some serious momentum behind it. There were 450-ish delegates at the conference from around the world, and Australia is a fair trek for most of them.

There’s talk that one day DNA sequencing will be so fast and cheap, you could take a sample while walking through the woods and be linked to species information on a handheld device – you would know if it was poisonous, endangered, new to science or what. Still a while away, but sci-fi in its possibilities.

This cool video gives a neat overview. It’s about a project proposal for student/citizen science in barcoding which is unfortunately currently unfunded and basically on ice at the moment. Nonetheless it’s a cute cartoons and great summary.

The region used for barcoding is called CO1 (found in mitochondira) in animals. It’s x base pairs long, and is generally very different between species, but pretty similar within one species. It’s short enough that sequencing is cheap and quick. A different region is used for fungi (called ITS, which was announced as the official fungi barcode at the conference), and plants use two regions, rbcL and matK, (found in chloroplasts).

The session I went to was on education and engagement – how to get people involved in DNA barcoding.

I love open access, power to the people, breaking down barriers stuff, and they’ve got some sweet plans. Already some projects have been successful, like the urban barcode project that gets high school students involved, and one group, who found the ingredients of tea didn’t always match what’s on the label, were even published in a journal (No less than Nature Scientific Reports! Amazing!) One group found a new species of cockroach, which is like my least favourite insect, but still a good effort.

What's in your tea? Image by massdistraction, flickr

BOLD are in the process of adding education and engagement to their online database so students can add to the database and store their results in a quarantined area. So they have a safe space to experiment with barcoding. Plus then they don’t screw it all up, right? Karen James, who moderated the session, actually pointed out that students may be less likely to make mistakes, as they are only working with a small number of samples and there’s less chance of losing track and accidental mislabeling.

Still in development, the BOLD 3.0 interface will look less intimidating than the current version, making it clearer for n00bs like me, and with links for educators at the bottom. They’re beta version is online here. Neat. I played around with BOLD before, taking a look at the barcode regions out of curiousity, and with my amateur skillz found it a bit tricky to navigate. Can’t wait to see the new one up and running so I can play with it.

If you want to read more about DNA barcoding, I recommend the iBOL website. I’ve got some more bits and pieces, but will post them separately once I’ve had a chance to flesh them out properly.

Connecting via common ancestors and Genographics – Interview with Wolfgang Haak

// December 8th, 2010 // Comments Off on Connecting via common ancestors and Genographics – Interview with Wolfgang Haak // Recent Research, Science Communication

At the Genographic Event at the RiAus I also interviewed Dr Wolfgang Haak, who spoke about Y-chromosome markers to determine paternal ancestry. He’s been involved in the Genographic Project for three and a half years.

What are the benefits of understanding ancestry?

It’s pretty much a personal thing, at the end of the day, because I suppose everyone’s interested in his or her own genetic history. This is my personal driving force, finding out more about myself. Where’s my place in this planet, in this world, where do I tie into the global picture? That’s a big motivation for me, and as I find out more as I work with people that it’s the same motor or driving force with them as well.

We share a common ancestry after all, there’s a common interest in our genetic history as well.

What first attracted you to the Genographic Project?

I have always been interested in genetics, but I actually come from an anthropologic background and genetics is certainly a part of that. I also come from an Ancient DNA lab. This was a step further into more modern population genetics. This is about getting both things together. Having a modern day perspective, plus adding a timely depth to that picture that we get from modern day diversity.

Tell us about your own ancestry, have you genotyped yourself?

Yes, I’ve done both. Mitochondrial, I’m haplogroup H, and I can further pin that down to group H1, so that is a Palaeolithic, Mesolithic one that might have come into Europe prior to the last glacial maximum, around modern day Spain or Italy or even a South Eastern refuge. It’s not entirely clear but we’ll find out over the next couple of years.

On the paternal side its even more enigmatic. I’m part of a North African lineage that probably originated around the Horn of Africa, so there’s that connection on the Eastern side of Africa where it connects to Saudi Arabia, and that has a high frequency there into the Nile Valley, and from it spreads into South Eastern Europe. Not entirely sure when it spread across the Mediterranean region, but probably historic times rather than prehistoric times.

Genographics, Neanderthals and Cannibalism, an Interview with Carles Lalueza-Fox

// December 8th, 2010 // 1 Comment » // Recent Research, Science Communication, Sex and Reproduction

After the event last night about the worldwide Genographic Project, I caught up with Prof Dr Carles Lalueza‑Fox, the first speaker on the night, for a quick interview. He’s an expert on Neanderthals, or Neandertals I think we call them now. Named after the Neander Valley where the first specimen was discovered.

What first sparked your interest in studying Neandertals?

When the first Neandertal sequence was retrieved in 1997 I had been working on ancient DNA for a while, but then Neandertals seemed to be something in a different league.

In the first ten years it was only possible to get mitochondrial DNA from Neandertals.

For me, I really liked Neandertals and human evolution as a child. Ancient DNA was something particularly difficult at the time, and the thing that brought me to the subject.

How human do you think Neandertals were?

How human?

Yes, tricky question.

Haha, yes. It’s a very long question, a very difficult question. One must always take into mind our tendencies are always fluctuating. We saw them as a very primitive human lineage in the early 20th Century, but I’d say that now we’re turning to the point where we see them as very similar to us.

Maybe the best thing to think about Neandertals is they are more different from us than any modern human to any other modern human. That’s the way we should think about them.

If we want to think of them as a different species that’s fine for me, but there is a range of difference between us and the Neandertals.

The cuts found along Neandertal bones you suggest are evidence for cannibalism. Could they just be an example of de-fleshing prior to burial?

Well, yeah, it might be right in some circumstances. But this is not only cutting, you know de-fleshing the bones. It’s also fragmenting the bones with small stone tools, very small fragments, and even the skull, and the faces. For me it’s very difficult to think that this kind of post mortem activity is something more because this is a complete destruction of the bones.

It’s very similar to what we see in other sites with fauna, the bones are broken to extract the marrow in the same way.

And it’s a pretty common thing, well, not common these days, but certainly we humans have our own history of cannibalism.

Yes, well there are several sites with the signs in Neandertals. But you almost think that life was very tough and they were structured in very small groups, so the fact that you find another one… I mean you’d say “hey, we are Neandertals all of us,” but I’d say that’s a modern conception.

Whereas for them it might be “hey, you’re not one of my family I may as well eat you.”

Yeah, the idea of humankind, in fact, is very recent. After the second World War, and the UNESCO thing. So even the idea of humankind is more recent than we might think now.

And what do you think of the possibility of Neandertals and humans mating?

I think it’s plausible with the data we have. It was probably something that was a minority, restricted in time and space, it was nothing important in my view. The thing is we can detect it now in non-African modern humans is because this was an expanding population, so even a small event of just a few, say it was, this was amplified later on.

Medical dictionary translates English to Yolngu Matha

// September 13th, 2010 // 2 Comments » // Science Communication

Yolŋu Matha is a language spoken by the Indigenous Australians of Arnhem Land, in the Northern Territory. To the majority of the people in the communities, English is a second language. There’s a twelve year gap in life expectancy between Indigenous people and non-Indigenous people, which is pretty drastic. It’s made worse because there’s a massive communication gap between the doctors and patients.

Just last week, ARDS released a new dictionary that translates medical phrases into Yolŋu Matha. Here’s some examples:

DNA – djinaga’puy wäyuk or djinawa’wuy wäyuk
English: DNA is found inside every cell of our body. It acts like a law that is not easily changed. It controls what kind of cell each cell grows into e.g. a skin cell, or liver cell or brain cell. It also controls what work each cell does.
Yolŋu Matha: Dhuwaliyi ŋunhi djinawa’wuy wäyuk, ŋunhiny ŋayi ŋuli ga ŋorra ŋunhan bili yan ṉapuŋgan ŋunhiliyin ŋunhi nhänhamiriw waka’ rumbalwu yäku cell-ŋura dhuwal rumbalŋura limurruŋgal. Ga rommirr ŋayi dhuwaliyi djinawa’wuynydja wäyuk, ŋunhi ŋanya dhu bäyŋun nhakun yuwalktja rrorru’. Ga buŋgawayirrnydja ŋayi ŋuli ga ŋunhi bukmakkun dhiyak cell-wuny mala nhaltjan ŋayi dhu walalany dhanuŋdhun rommirriyam balanya nhakun: ŋanakpuy dhuwal rumbalpuy cell-nha ga bamburuŋburuŋbuynha cell-nha ga biḏila’puynha cell-nha. Ga ŋunhi ŋayi ŋuli goŋ-dhawar’yundja bala ŋayi ŋuli djämamirriyaman ŋunhi cell-nhany mala

hormone – dhäwu-gänhamirr wiyika’

English: Hormones are substances that are produced in our body and carried by our blood. Each hormone has its own message to give to our body.
Yolŋu Matha: “Hormone”-dja dhuwal wiyika’ mala ŋunhi ŋuli ga ŋamaŋamayunmirr dhiyal rumbalŋur limurruŋgal, ga gämany walalany ŋuli ga ŋunhi maŋguy’nha. Ga bukmakthu “hormone”-dhu ga gäna-gana ŋayatham dhäwu mala ŋunhi walal ŋuli ga gurrupan dhipal bukmaklil rumballil limurruŋgal.

How awesome is that?

What is the synthetic cell?

// May 22nd, 2010 // 1 Comment » // How Things Work, Recent Research

Two days ago scientists at J. Craig Venter announced the creation of the first self-replicating synthetic cell, a bacteria with DNA made in a lab. How did they do it, and what does it mean for us in the future?

First up, the scientists didn’t make life out of nothing, and they didn’t make a new species. They recreated a bacteria that already existed, and developed the techniques to do it.

The bacteria is Mycoplasma mycoides. It’s a parasite which lives in cows, and some subspecies cause cow lung disease. It has a circular chromosome made of just under 600,000 base pairs, making it a small genome.

The scientists had the genome sequence of M. mycoides and split it into bite-size portions and then synthesised. Synthesising DNA is nothing new, scientists have been able to write DNA code for quite a while, and can write whatever code they want to.

These little chunks were put into yeast, which can be forced to absorb little bits of DNA. Inside the yeast, the chunks can be sewn together. It’s called recombination. The resulting medium chunks were taken out and put into more yeast to be sewn together making large chunks. There were 11 large chunks were put into more yeast, and sewn together into one complete genome.

Along the way and at the end they checked the code was right by doing PCR tests, genetic fingerprinting made famous by CSI.

Result: A synthetic genome, written by a computer and put together in yeast sweatshops.

Now they had to get it into a bacterial cell. At first they tried to put the DNA into bacterial cells of a similar species, M. capricolum. They ran into trouble at first, because the DNA they had was unmethylated (lacking methyl groups) and the bacteria destroys DNA which is unmethylated. It’s a clever defense mechanism, and they got around it by methylating the DNA before putting it in.

Finally success. The synthetic genome was put into an M. capricolum bacteria where it replaced the normal genome. The bacteria were controlled by the new, synthetic chromosome and were able to replicate billions of times.

What does it mean for us in the future? The technology these guys have developed could be used to alter the DNA of bacteria and make them do new things. From medicine to clean water, the benefits could be huge. We already have this ability to some extent, but it opens up some new doors.

Some organisations have raised concerns about the work. Could a new bacteria be unleashed and take over the world? Probably not. It’s hard to predict how new genes will work in cells, and everything is linked together in a way we don’t understand now. Too much tinkering to the genome will probably not be tolerated by the cell. And if it did get outside, it would probably be extinct pretty quickly because it doesn’t have thousands of years of evolution to prepare it for the world.

If it did get out, we could track it back to the company in charge. These guys watermarked their genome by adding some quotes into the DNA/protein code. Now that’s just epically geeky!

ResearchBlogging.orgGibson, D., & et al (2010). Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Science DOI: 10.1126/science.1190719






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