June 2009

Chemistry World Podcast - June 2009

00:12- Introduction

01:30-- Dinosaur protein discovered in fossil

03:51-- Does green fluorescent protein carry out 'animal photosynthesis'?

07:06-- Frog foams - Alan Cooper describes a novel set of biomolecules   

13:44 -- Double-action solar cells on the horizon

16:22-- Metal-reinforced spider silk unravelled

18:33-- Ice can reveal an ancient methane source, says Vas Petrenko

25:52 -- Power stations to make hydrogen

28:53-- Diabetes control with glucose-sensing nanoparticles

32:33-- The chemical conundrum - what were the ancient Incas mining when they inadvertently released mercury into the Andes mountains?

(Promo)

Brought to you by the Royal Society of Chemistry, this is the Chemistry World Podcast.

(End Promo)

(00:12 -- Introduction)

Interviewer - Chris Smith

Hello! This is June 2009 edition of the Chemistry World podcast with James Mitchell Crow, Matt Wilkinson and Nina Notman. In this month's show, solar cells, but with a difference. Scientists have discovered what GFP, green fluorescent protein, really does.

Interviewee - James Mitchell Crow

The team from Florida has just assumed that protein was involved in bioluminescence, perhaps jelly fish just signalling to each other, but it turns out potentially this is the first example ever known of animal photosynthesis.

Interviewer - Chris Smith

James Mitchell Crowwho will be here with more on that story very shortly and also on the way, scientists how have found an unusual chemical in frog's bone.

Interviewee - Alan Cooper

On a much larger scale, on sort of an industrial chemical scale, we had imagined these plankton proteins, which are biodegradable might be useful in disposing things like oil spillages.

Interviewer - Chris Smith

And how nanotechnology can lend a helping hand to the treatment of diabetes.

Interviewee - Matt Wilkinson

What these researchers have done, is developed a nanoparticle that actually responds to high levels of glucose and can release insulin to help break up the glucose and mitigate any effects that diabetes might have.

Interviewer - Chris Smith

Hello I'm Chris Smith and this is Chemistry World.

(Promo)

The Chemistry World podcast is brought to you by the Royal Society of Chemistry. Look us up online at chemistryworld dot org

(End promo)

(01:30 -- Dinosaur protein discovered in fossil)

Interviewer - Chris Smith

65 million years ago, the role the dinosaurs came to an end and all we had left of them were the rocky replicas of their bones, which are otherwise known as fossils. Also we thought, because in recent years, scientists have rocked the geological world by saying that they found genuine dinosaur tissue trapped inside multi-million year old fossils. And now they've got even more evidence to back up their claim. Nina!

Interviewee - Nina Notman

Well, the group who are publishing in Science from North Carolina State University certainly believes so. So they've been looking at an 80 million year old skeleton of a duck-billed dinosaur, which is also called a Hadrosaur and they found fragments of protein collagen, which is the principle protein in connective tissue but in the skeleton.

Interviewer - Chris Smith

How are they getting what they think is this tissue out of an 80 million year old rock?

Interviewee - Nina Notman

They demineralised the bone and then they take what they've got left and put it through a mass spec machine and from that they can identify the sequence of amino acids within the fragments and tell that it is collagen.

Interviewer - Chris Smith

This is Mary Schweitzer, isn't it, who has done this work, because she caused a bit of controversy a few years ago, saying that she was seeing tissue from Tyrannosaurus rex and that didn't go down too well with the dinosaur community.

Interviewee - Nina Notman

No, so this was yeah, what two years ago and they were looking at this time in a 68 million year old T. rex and she found the same, that she found this time; she found collagen fragments within the skeleton, but yet the community found that this was quite controversial and they were suggesting that there was contamination of a more modern protein in there. So this time, a lot more care were taken to prove that there wasn't any contamination and as well as her doing the mass spec, she also asked a number of other groups to repeat the experiment to see if they found the same results and they did.

Interviewer - Chris Smith

And how does the mass spec signature from that collagen compare with what's around today, presumably that's how they're drawing their conclusions about the fact that this is real. 

Interviewee - Nina Notman

So the T. rex and the Hadrosaur had quite similar profiles and they have quite similar profiles to some modern bird today, say to the ostrich and to chickens and surprisingly it's a lot of more similar to ostrich and chicken than it is to lizards.

Interviewer - Chris Smith

And that fits because of course birds are the closest surviving relatives of dinosaurs. 

Interviewee - Nina Notman

That's what the fossils theory says, yes, so this work is supporting the previous theory.

Interviewer - Chris Smith

Good on her. So it turns out to be slightly better received this time. Thanks Nina. 

(03:51 -- Does green fluorescent protein carry out 'animal photosynthesis'?)

Interviewer - Chris Smith

And James, from land and big animals on land to the sea, and something that won a Nobel Prize in fact, last year for the people who discovered it, but we still didn't until now know what green fluorescent protein is all about. 

Interviewee - James Mitchell Crow

That's right Chris. Teams before it just assumed this protein was evolved in bioluminescence, perhaps jelly fish just signalling to each other, but it turns out that this protein might actually have originally had quite a different role within the animal and potentially this is the first example ever known of animal photosynthesis, so this is not just a molecule that possibly absorbs or emits light, but it is actually an active light capturer, if you like.

Interviewer - Chris Smith

And how does it feed the energy from the light into the animal because you see in a plant, you have chlorophyll; this captures the light and then feeds energy into various other chemical pathways. How does the jelly fish do it with GFP then?

Interviewee - James Mitchell Crow

Well, what the jellyfish is doing this team thinks at the Shemiakin-Ovchinnikov Institute in Moscow, is that what it does is it feeds electrons, so it interacts with electron accepting molecules within the cells of the animals. How they've actually proved this is it was previously known that when this protein is short of electrons, it doesn't fluoresce green, it fluoresces red. And what they did was they put protein in a test tube with a variety of electronic acceptors and shone blue light on it, the protein initially fluoresced green and then slowly turned to flash red, showing that it is giving out these electrons source acting like a light activated electron donor, which is exactly what a chlorophyll does in plant photosynthesis.

Interviewer - Chris Smith

But is there anything in the cells for it to give that energy to?

Interviewee - James Mitchell Crow

Yes it is, cells naturally have also sorts of electronic sectors, the team haven't identified exactly if at all, animal photosynthesis was taking place, what the receptor might be, but what they did was took the life cells added the fluorescent protein and shone the light and exactly the same thing happened, initially it fluoresced green and then the fluorescence seemed turn to red showing that this electron donating process was taking place inside the live cells. 

Interviewer - Chris Smith

And so the next step will now be to firm that up and to show that these jelly fish are deriving sufficient and/or significant amounts of energy from sunlight.

Interviewee - James Mitchell Crow

Well that will definitely be one of the things that they investigate. The speculation is that this protein, the primary function of this protein was some sort of light harvesting and that the secondary function that it evolved was sort of the more bioluminescence properties. So, perhaps these jelly fish are not harvesting the light now and the protein that has evolved further since then, but what they do suggest is green fluorescent protein has been well used as a gene marker, which is what won these teams the Noble Prize last year and they suggest that because of this sort of colour changing effect, what they could use this protein for an experiment is to sort of monitor redox reactions going on proteins for example, or even to manipulate redox reactions by shining in the light and getting the electron donating to take place.

Interviewer - Chris Smith

Thanks James. 

(07:06 -- Frog foams - Alan Cooper describes a novel set of biomolecules)

Interviewer - Chris Smith

And on the subject of thing aquatic, Alan Cooper has been studying a breed of frogs that have spawned a new way to treat burns and even to clean up oil slicks.

Interviewee - Alan Cooper

What we discovered is a curious observation that many frogs, especially frogs in tropical areas, build foam nests, perhaps to act as incubators for the developing eggs and tadpoles. These turned out to be the nests of these particular frogs in Trinidad called the t?ngara or the mud-puddle frog. Now they actually look like egg white which has been whipped up to form a rather sticky, but gluttonous foam and this foam is produced by a combined activity of the male and female. During mating, the male gives the female a little squeeze and she produces some eggs and the mixture of materials, which the male frog then gathers up with its hind legs, fertilizes the eggs and also whips up this mixture, using an action, very much like an egg beater, to produce this foamy mass.

Interviewer - Chris Smith

And how big is each of the nests?

Interviewee - Alan Cooper

It's about the size of a grape fruit.

Interviewer - Chris Smith

So they're quite large?

Interviewee - Alan Cooper

They are quite large, yes and quite often, the frogs do this communally, so you end up with groups of two, three or half dozen of these foams and they can make quite a big mass of foam in the bridge of a pond or puddle.

Interviewer - Chris Smith

And the eggs are embedded within the foamy material.

Interviewee - Alan Cooper

That's right, they are mostly clustered around the centre, there seems to be some way in which the male contrives to bury the eggs so they are not too close to the surface, where they might get slightly damaged by dehydration.

Interviewer - Chris Smith

And what's the purpose of doing this?

Interviewee - Alan Cooper

The purpose for the frog is this is a way of incubating their eggs under conditions where there isn't very much standing water because these are tropical regions, next day, the sun come out and the puddle will dry out, but these nests will remain hydrated, they'll remain moist and the tadpoles can develop quite happily inside.

Interviewer - Chris Smith

What about predators, by predators I mean, other animals coming along and eating them also and also microbial predators, funguses, bacteria that kind of thing?

Interviewee - Alan Cooper

This is a little on predation that we have observed. Microbial infestation is potentially a problem and that is another interest because of the water these nests are made in foam is very heavily contaminated. We've done bacterial analysis and the foams are absolutely a chock-a-block with microbial organisms; there are all sorts of nasty descriptions in many cases, but the ponds of the puddles that these nests are made are in sep pits or   other undesirable areas, but what we've observed is although there is a lot of microbial infestation, the bacteria and the fungi do not seem to proliferate and they certainly don't be composing this during the three or four days that the tadpoles need to reach maturity and then escape. 

Interviewer - Chris Smith

Very interesting biologically, but now chemically how does it work, how are they doing this and what's in that foam?

Interviewee - Alan Cooper

There are two problems really. First of all, the frog has to make the foam and we know as chemists in order to make foam or froth, which also we do in the washing liquids and normal detergents, you have to reduce the surface tension of the water, first all to produce a foam. Now conventional small molecule detergents sort of things we do use in the kitchen or the bathroom will be bad news for the sensitive biological membranes of the cells of the eggs and the sperm. So, one of the proteins that we've discovered turns out to be a naturally surfactant protein, a much larger molecules than we are used to as chemists with we believe an unusual mechanism for its surfactant activity, which allows it to reduce the surface tension of the water and therefore initially allow formation of the froth or the foam; but without disrupting sensitive biological membranes. Then having made the foam, it has to remain physically stable and biologically stable for periods of days, it fact we know as it we take the eggs away from the nest, the foam material itself will survive up to 10 days under hot steamy tropical conditions without decomposing, now that's unusual because foams are very unstable structures and will normally collapse, and we know that head on a glass of beer or soap suds in the shower will collapse after just a few minutes or few hours utmost. That doesn't happen in the case of frog foams. The reason for that is we believe down to another set of proteins that we discovered in this mixture which have the capacity to crosslink some of the carbohydrate components in the frog mix as well, I should have mentioned that, we have identified six unusual proteins in this mixture, but there is also an equal abundance of long chain heavily branched carbohydrate, which was not characterized at all, but some of the proteins that we've identified can actually bind to carbohydrates. These lectins, these carbohydrate binding proteins in the mixture will crosslink and stabilize the foam once it has been formed and that will perform a dual function of giving it physical stability for a long period of time and also retaining moisture because the carbohydrates are very good at soaking of water as well. So but when the sun comes out, the foam doesn't dry out and the poor tadpole is not dehydrated.

Interviewer - Chris Smith

What sorts of things could you do with this?

Interviewee - Alan Cooper

The very first things that has occurred to us is that if you if you a biocompatible foam material as a long lifetime as antimicrobial properties, then you might think of using it as a treatment for wounds of burns in accident situations; you might also imagine squirting this foam into surgical cavities either to attach as a scaffold for tissue regeneration or even perhaps for also cosmetic surgery. These plankton proteins also have a potential for coating surfaces which would not normally be wet at all. On a much larger scale, on a sort of industrial or chemical scale, we had imagined that these plankton proteins which are biodegradable might be useful in dispersing things like oil spillages, which otherwise are difficult to disperse and also harmful to the environment and given that we can now produce these proteins by recombinant techniques, we don't have to estimate the frog population, we can actually produce these proteins and even engineer them in different ways in house and then produce some at will.

Interviewer - Chris Smith

Glasgow Universitychemist, Alan Cooper. 

(13:44 -- Double-action solar cells on the horizon)

Interviewer - Chris Smith

And now to the question of solar power and how we can more efficient solar cells. Scientists at the Sweden's Royal Institute of Technology have made a breakthrough Matt?

Interviewee - Matt Wilkinson

Yes indeed Chris, but first let me wind back a little bit. In 1991, a group from Switzerland invented a new way of making dye-sensitized solar cells that doesn't involve using silicon, which is what we have currently used to make these solar cells but basically they work by having a photoelectron capture method at one end of a semiconductor such as titanium dioxide and they coat this with this dye at the anode. Now, more recently researchers have introduced a reverse type of solar cell where dyes interact with a different type of semiconductor like a P-type semiconductor, such as niobium oxide that's a light harvesting cathode. The problem with these is they've being inefficient.

Interviewer - Chris Smith

Is what you are going to tell me that bright spark said if we had got ones that work at the plus end, we've got another species that work at the minus end, can we glue the two together and we get light sensitive anodes and cathodes and therefore you get a much more efficient way of doing things.

Interviewee - Matt Wilkinson

Well, yes, although where they are currently is they've actually managed to make the cathode type light harvesting cells much, much more efficient, in fact they've doubled the efficiency of these. So now, if you actually can imagine putting two relatively efficient things together and harvesting light at both ends at the photovoltaic cell, then yes you could have a solar cell that is much more efficient than anything else out there. 

Interviewer - Chris Smith

Now when we're saying inefficient, efficient, in the case of most solar cells, we're talking at what 10-15% efficiency, so what does this mean in real terms for these devices. What are they anticipating if they can make this work then?

Interviewee - Matt Wilkinson

Well, they say the current conversion efficiency,   the best current conversion efficiency of some of these devices, which has now reached about 44%, so you could getting, its pure speculation, but you could be getting, you know, double that if calculations were to be correct.

Interviewer - Chris Smith

Which is staggering, isn't it. Think you can get a solar cell that efficient, when we can't even make an engine, that's you know, obviously a heat engine therefore its intrinsically inefficient, but we can't actually get anything close to that at the moment. So that's staggering.

Interviewee - Matt Wilkinson

It is indeed. Yes. And hopefully we'll be able to you know, these researchers will be able to save the planet by making this all, use sunlight rather than anything else. 

Interviewer - Chris Smith

Let's hope so. But can you tell us when, because that's kind of critical. We think we've got 20 years before it is too late, are we going to do it in time?

Interviewee - Matt Wilkinson

Well, most times, people say 5 to 10 years and mean 20, so I'm guessing in about 30.

Interviewer - Chris Smith

Well, hopefully they will get it done thank you very much for that Matt.

(16:22 -- Metal-reinforced spider silk unravelled)

Interviewer - Chris Smith

Now Nina, let's look at spiders, because they make a wonderful material spider silk. People are talking about using it in things like bullet proof vests, but now you're saying that scientists have come up with a way of making it even stronger.

Interviewee - Nina Notman

They have indeed. So this group from the Max Planck Institute in Germany, publishing in Science and they've strengthened spider silk by infusing metals like zinc, aluminium and titanium within them. 

Interviewer - Chris Smith

Sounds tricky. How do you get metal inside spider silk then?

Interviewee - Nina Notman

They used a method called atomic layer deposition, so during this process, they heat the spider silk under hot water vapour and then they infuse metal within them and water vapour disrupts the hydrogen bonding network within the protein and these hydrogen bonds are replaced by much stronger covalent metal protein bond and that's where the strength comes from.

Interviewer - Chris Smith

So the metal ions end up embedded in the actual protein matrix, they get in the way of some of what would normally be water to protein interactions and you then get a metal-protein interaction and that crosslinks also proteins, which make very strong substance.

Interviewee - Nina Notman

Exactly.

Interviewer - Chris Smith

How can we use this? Is this practical?

Interviewee - Nina Notman

No. So at the moment they are just looking at the fundamental, because spider silk is something which you can only get in small amount, but once they've understood the science behind it, they're hoping to move on, may be looking at silk worms and they're kind of angled, they're looking at super strong surgical threads or artificial human tissue, like bones and tendon.

Interviewer - Chris Smith

Al right, its not just spider silk. You could apply the same technique to other silk type produces including silk worms to produce any kind of material that's got much greater strength. 

Interviewee - Nina Notman

In theory yes, that's certainly what the researcher are looking toward it.

Interviewer - Chris Smith

Two silk worms had a race, which one won? Well of course it ended in a tie. Thanks Nina.

(Music)

Interviewer - Chris Smith

This is the Chemistry World podcast with me Chris Smith. Still to come how power stations can produce hydrogen as by product and that's thanks to a new catalyst and how a new generation of nanoparticles can release the right amount of insulin to suit blood sugar levels. 

(18:33 -- Ice can reveal an ancient methane source, says Vas Petrenko)

Interviewer - Chris Smith

But first to how scientists have solved a longstanding mystery, why the levels of methane in the atmosphere suddenly shot up 14,000 years ago when the world warmed up. Did that methane come from carbon that was locked away in Permafrost or was it previously sequestered under the sea, perhaps it was both. Vas Petrenko!

Interviewee - Vasilii Petrenko

During the end of the last ice age, what we see from ice core records is that there are two very sharp jumps in temperature. One at about 14.5 thousand years ago and one at about 11.5 thousand years ago, where temperature in Greenland increases by about 10 degrees Celsius in as little as 20 years, very large, very rapid warming events and associated with these warming events there are also increases in atmospheric methane concentrations and these increases are quite large. In one case, the atmospheric methane concentration increased by about 50%. These increases also happened quite fast and there's been a lot of debate in the scientific community about why methane was going up at this time and what was driving these methane increases. One of the main ideas that has been proposed for this is that during these warming events, on the whole the world gets warmer and wetter and what that would result in is an expansion of the world's wetlands as well as a possibility of an increase in productivity of the world's wetlands and wetlands happen to be the main natural source of methane to the atmosphere today.

Interviewer - Chris Smith

So where does that methane come from? Why should an expansion of wetland produce more methane?

Interviewee - Vasilii Petrenko

The methane in the wetlands comes from methanogenic bacteria. So these are bacteria that produce methane in oxygen depleted conditions in the wetlands from organic matter that is decaying in the wetlands and these wetlands are very widely distributed in the world.

Interviewer - Chris Smith

So what's the other theory? You mentioned there were two?

Interviewee - Vasilii Petrenko

The other main theory has to do with methane clathrates. Methane clathrate is an ice-like substance composed of water and methane molecules where methane molecules are locked in an ice-like cage of water molecules and this substance is stable at higher pressures and lower temperatures. Methane clathrates are very widely distributed on the ocean floors as well as in Permafrost, so you find these in a lot of ocean sediments for example. 

Interviewer - Chris Smith

And so one would argue that for some reason at 11,000 and 14,000 years ago, something caused the ocean to belch up all these locked away methane and that could have been the cause of this sudden surge in methane in the atmosphere and then the onward warming.

Interviewee - Vasilii Petrenko

Exactly. That has been one of the hypotheses that during these warming events the warming triggered destabilization of a lot of these methane clathrates.

Interviewer - Chris Smith

So how do you solve that conundrum? You don't know which of those two methods it is and it was 14,000 years ago worst, so how can you possibly wind that clock back that long to know which of those two is responsible.

Interviewee - Vasilii Petrenko

Well, one of the ways to go about this is to use carbon 14. Now carbon 14 is a very rare isotope of carbon that is radioactive and it decays with a half life of about 6000 years. Now it so happens that methane that's produced in wetlands has a fairly large amount of this carbon 14, whereas methane that is coming out of clathrates has essentially no carbon-14 and if carbon-14 of methane stays the same through this methane increase that we observe that would mean that most likely the methane came from the wetlands, because wetlands are the main natural source. So we would expect that to be the background source and if during an increase in methane, the carbon 14 doesn't change, that means that the sources really haven't changed. Whereas, if we see that as methane concentration goes up, the carbon-14 level goes down. Then we know that there's a lot contribution from this reservoir of clathrates which has no carbon-14.

Interviewer - Chris Smith

Presumably you had to go and then get the ice to do this.

Interviewee - Vasilii Petrenko

Glacial ice contains a fair amount of ancient air locked in it. Its actually about 10% air by volume, but carbon-14 is extremely rare. It's about 1 part per trillion as compared to what you would call normal carbon and methane is also a trace gas. It's present in the atmosphere in very low concentration. So to get enough ancient air, for one measurement, we actually needed one metric ton of ice for each sample. So we had to find a site at the western margin of the Greenland ice sheet. 

Interviewer - Chris Smith

So you go to that Greenland ice sheet, you excavate ice. How do you make sure, it doesn't get contaminated with contemporary gases and then how do you analyze it to see what forms of carbon are in there.

Interviewee - Vasilii Petrenko

We try to use very clean sampling procedures. We cut this ice with the clean electric chain saws that don't use any lubricants because lubricants are of course composed of organic material, which could contaminate our methane and we load this ice into a very large vacuum chamber, where we first seal the chamber and evacuate all the modern air that's around the ice to avoid contamination by the modern atmosphere. Then we melt the ice under vacuum and what that does is release the ancient air that's trapped in the glacial ice. Then we can transfer this ancient air into a storage cylinder and bring it back to the laboratory for analyses and then before the carbon-14 and the methane can be analyzed, the methane actually has to be converted to first as CO₂ and then to graphite.

Interviewer - Chris Smith

And when you do this, what do you find?

Interviewee - Vasilii Petrenko

Well, what we see is a very small decrease in carbon 14 and what that is telling us is that predominantly the source for the methane increase was wetlands, but there was likely some contribution from sources that had either less carbon 14 or no carbon 14. So there possibly was some contribution from the methane clathrates.

Interviewer - Chris Smith

So the big question now is of course what caused the warming event in the first place.

Interviewee - Vasilii Petrenko

That is a big question. It definitely has something to do with the strengthening of the overturn in circulation in the North Atlantic. When the climate is generally warmer, the circulation is a lot stronger, when the climate is colder, the circulation is weaker and that certainly seems to be part of the puzzle, but that doesn't seem to explain all of the warming that we see that's very much an open question at this point.

Interviewer - Chris Smith

And one that we'll need to solve soon because history could well be repeating itself as the world warms up because of climate change. That was Vas Petrenko. He's at the Institute of Arctic and Alpine Research in Boulder, Colorado. 

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