Chemistry World Podcast - April 2009
00:12 -- Introduction
02:11 -- Reading single strands of DNA, base by base
05:01 -- The new electrode material that promises speedy battery charging
07:46 -- Jeremy Tomkinson discuses turning rubbish into fuels
14:33 -- Could naked mole rats help reveal the secrets of aging?
17:20 -- The inorganic crystals that can be turned into microtubes
19:19 -- Ned Seeman talks about building shapes and devices from DNA
25:51 -- The bioelectronic e-nose
29:19 -- The polymer that can heal its own scratches
31:43 -- The chemical conundrum - what are the health-giving compounds found in chocolate, particularly dark chocolate, that are believed to be good for your heart
(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! Welcome to April 2009 edition of the Chemistry World with James Mitchell Crow, Nina Notman, and Phil Broadwith and Bibiana Campos-Seijo. In this month's show, building better batteries. How researchers have come up with way to top up flat cells in just a fraction of the time it usually takes.
Interviewee - James Mitchell Crow
These batteries could be up to 100 times fast with charge and discharge so you could potentially be charging up your laptop in a couple of minutes rather than having to wait for a couple of hours and ultimately the hope is that lithium batteries could be paring electric cars and then you could charge up the battery as quick as it would be to fill up your car with petrol at the moment.
Interviewer - Chris Smith
More from James on that story in just a moment. Also where there is muck there is brass or perhaps that should be biofuels, because scientists have come up with a way to turn household rubbish into environmentally friendly fuel.
Interviewee - Jeremy Tomkinson
We mitigate 98% of the green house gas emissions when we compared our ethanol to petrol. So typically when you drive your petrol car on average you'll emit around 160 grams of carbon dioxide for every kilometre that you travel. Of course here we're less than five.
Interviewer - Chris Smith
Impressive numbers indeed. That's Jeremy Tomkinson. He will be joining us in just a moment to explain how that new system works. And also on the way how researchers are giving machines a uniquely human sense of smell.
Interviewee -
It's a bioelectronics nose, so it's taking real human smell receptors and building them into a device using a conducting polymer nanotube laid over some electrodes to make the sensor. The binding event at the receptor site causes a change in the charge distribution on the nanotube which gives an electrical signal through the rest of the device.
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)
(02:11 -- Reading single strands of DNA, base by base)
Interviewer - Chris Smith
The original human genome project cost more than one billion pounds and took more than 10 years to complete, but now industry is coming up with increasingly fast and ingenious new ways to decode the sequence of genetic letters in a DNA strand including a new approach, Phil that means that you don't even have to amplify or copy the genetic material first, but how does it work.
Interviewee - Phillip Broadwith
Well Chris, this is some work that's come out of Hagan Bayley's group in Oxford. They've got a whole spin-out company doing it and is a technique for reading DNA base per base as you said you don't need to amplify the DNA. You don't need to tag it with fluorescent markers which what they do in the moment.
Interviewer - Chris Smith
So what's the apparatus? How does it actually work, this.
Interviewee - Phillip Broadwith
The system is based on a protein nanopore, which is a protein which makes a hole in a lipid membrane. They've put a chemical modifier into that, an adapter that's what they call it and that can bind DNA bases in a temporary manner, so you've got that in a membrane and the whole thing surrounded by salt solution and you put a voltage across the whole thing and you can measure the current of the salt ions going through the pore. Then they've got an enzyme floating around in the top of the solution that's chopping up DNA. So as those acid DNA gets chopped up, each base can find its way into the pole and bind temporarily which blocks the current and different bases block the current to different extent. So that allows you to directly read off in a digital way exactly which base is binding in the pore and eventually to make a sequencing technology what they want to do is to attach the protein that chops the DNA up on to the nanopore, so as soon as the base is chopped off it drops into the nanopore binds, you get a reading of the sequence and then it carries on through the pore.
Interviewer - Chris Smith
Why do scientists think this is better than say an amplification method? What are the advantages of doing it this way?
Interviewee - Phillip Broadwith
Well, it's much cheaper for a start for standard techniques at the moment it takes a lot of sample preparation, you need to chemically modify the DNA and you need to amplify that which can lead to sequence changes and also you need very expensive detection equipment and you need very high-resolution cameras to detect the fluorescence. For this, you don't need any of that; you just take a straight digital reading of the sequence.
Interviewer - Chris Smith
How do they stop themselves ending up with a sort of DNA base traffic jam, upstream of this pore, so how do you get the enzymes so it chops of the base and then that base gets read? You don't end up with more floating around in solution in each others way.
Interviewee - Phillip Broadwith
At the moment, all of the different bits are floating around in the solution above the pore, so at the moment, we've got no way of reading what the sequence is, but what they want to do it is attach the two elements together, so that the bases drop into the pore as soon as they chopped off a strand and the binding is much quicker than the enzyme chopping the bases so there is no possibility of a traffic jam.
(05:01 -- The new electrode material that promises speedy battery charging)
Interviewer - Chris Smith
Sounds fantastic stuff, so from speedy DNA sequencing James to speedy batteries. These are batteries that can be charged and presumably discharged much faster than standard batteries.
Interviewee - James Mitchell Crow
Exactly 100 times faster in fact than a standard lithium battery that you might have in your current mobile phone or your laptop.
Interviewer - Chris Smith
How does it work?
Interviewee - James Mitchell Crow
These guys at MIT have done a theoretical study to work out what the bottleneck is holding up the transfer of lithium ions from electrode to electrode which is what's happening where when you're either charging a battery, the flow is one direction and when you're discharging it the flow is in the other direction. And theoretically that should be pretty quick but there is some bottleneck holding up this flow so what these guys have done is that they've tweaked the lithium material that the electrode is made of to speed up the process. They worked out that it is the transfer of the lithium ions between the electrolyte, which is just sort of the medium that the ions flow through, and the electrode itself which is where the lithium is stored. So as I said they sort of tweaked this material, it's a lithium ion phosphate material that they are using and if they adjust the stoichiometry slightly then what they get is this glassy surface forming and it's poorly crystallized and so there's plenty of space for the lithium ions to travel through so that improves the lithium ion mobility.
Interviewer - Chris Smith
I thought one major problem with lithium batteries was that because that lithium has to absorb and then desorbs from the electrode, like you say that if you keep doing that, the electrode shatters so that again cuts down the ability of the battery to deliver high current, so is this going to solve that problem.
Interviewee - James Mitchell Crow
Well I don't think they've done any sort of long-term testing on how these materials work, this is just very much in the lab scale and sort of looking at the theoretical aspects and then testing that out to work out exactly what is the bottleneck that slows these batteries down.
Interviewer - Chris Smith
How much better the battery is going to be that they are anticipating if they would put their process into practice then?
Interviewee - James Mitchell Crow
Well they're saying that these batteries could be up to 100 times faster with charge and discharge, so you could potentially be charging up your laptop in a couple of minutes rather than having to wait for a couple of hours and ultimately the hope is that the lithium batteries could be powering electric cars and then you could charge up the battery as quick as it would be to fill up your car with petrol at the moment. The other thing is course they discharge very quickly; so a lot of power is available for electric motor in the car. So it could potentially accelerate a lot quicker as well. So you might need smaller batteries and less heavy batteries than you would now.
Interviewer - Chris Smith
Powering our way towards better batteries. Thank you James.
(07:46 -- Jeremy Tomkinson discuses turning rubbish into fuels)
Interviewer - Chris Smith
And talking of energy sources of future, just how much power are we actually throwing away. Jeremy Tomkinson from the National Non-Food Crop Centre in York says that there is a better way to do with much of the rubbish that currently ends up in a landfill.
Interviewee - Jeremy Tomkinson
What we are finding most attractive at the moment is actually what we call municipal solid waste which is some of the most difficult things to deal with and ensure it's all filled black bin bags and it's a fairly simple routine stuff where we can take a black of bin bag filled with all the kind of stuff that we would normally put in a bin bag and we can segregate that into a relatively clean pile of metal, of plastic, of glass and these things can go down the normal recycle of streams when we do this, we always end up with this material that kind of resembles the fluff at the back of your tumble dryer and it's what we call the lignocellulosic. It's basically lignocellulose i.e. biomass.
Interviewer - Chris Smith
And how much of this stuff is there? We are all told that you go fill the international sports stadium in Cardiff several times a week with how much we are all throwing away, but how much does this add up to in terms of potential energy?
Interviewee - Jeremy Tomkinson
It's enormous actually and we are, as a society can think a lot better, now understanding reusing and recycling and indeed kind of compost the materials, but the volume that we throw out is still enormous. I mean from one small area that we are working at the Northeast at the moment, I mean, we are looking at 250-300,000 tons of black bin bag waste in a year and that's just one small area.
Interviewer - Chris Smith
So you take this black bin bags, you sort out what's in them and you get something which is your raw material the lignocellulosic rubbish. What do you then do then?
Interviewee - Jeremy Tomkinson
One can do a variety of things with that. You can actually just take it and directly burn it actually; it can just generate electricity or sometimes heat with that, but we've been fortunate enough, just luck to work with a company called Ineos. They are looking at a whole new adoption of basically municipal solid waste and lignocellulosic materials there from, to generate not just heat, not just power but also biofuel all from the same plant. They basically take the material and go through a process that's fairly well established called gasification. This produces a material called Syngas. Now Syngas is just a mixture of carbon monoxide and hydrogen, used extensively in petrochemical industry as what we call a C1 building block. To think of carbon monoxide just being a single carbon atom with an atom of oxygen we can use different catalysts, different inorganic and sometimes organic catalysts to rebuild molecules from this C1 building block. And Ineos have developed a way where we can take Syngas that comes from basically lignocellulosic rubbish, clean this out and highly clean Syngas and actually it's a living organism that consumes this mixture of carbon monoxide and hydrogen and excretes ethanol as a by-product. Now ethanol as we know can be used to replace petrol in cars and as part of the process it will also produce quite a large amount of electricity, renewable electricity and heat. So herein we have one process as a proven example of where we can take the lignocellulosic material from municipal solid waste that otherwise would be quite difficult to use and could have it going to landfill. Now if those go into landfill, basically we are threatened with a possibility content of methane. Methane is of course we know 23 times more potent a greenhouse gas than carbon dioxide. So we should not be looking at any form of biodegradable material, lignocellulosic material, going to landfill. The key issue is finding its use and we think we found a superb use for this that basically says converts this to electricity, heat and ethanol in one process.
Interviewer - Chris Smith
How much energy can we get out of the amount of stuff that we are just throwing away at the moment in the UK for example?
Interviewee - Jeremy Tomkinson
Well to put this into some context the plant that we've got with Ineos at the moment is stopping 150,000 tons of black bin bag waste going to landfill. This is then segregated up into the fractions. The lignocellulosic fraction that goes into the plant or the plant that we will be in when we get the project launched, will produce 30,000 tons of ethanol, 10 Megawatt of electricity and an amount of heat that can used in the plant and actually exported to outside.
Interviewer - Chris Smith
Doesn't sound like much though Jeremy, 10 MW is not a huge amount? I mean, I would like it in a big hospital and it's probably consuming that.
Interviewee - Jeremy Tomkinson
This is a pilot plant. If the concept is proven then we've got every reason to think it will be the next scale, the commercial scale plant from that will be around 4 to 5 times. So we therefore produce around 150,000 tons of ethanol and about 50 MW of electricity with the heat.
Interviewer - Chris Smith
To move all that and recycle it and get it from the people that are producing the rubbish to the factory, the plant itself, that's going to involve a lot of vehicle movement as well as, so when you factor in all those other energy sinks, does this still make economic sense.
Interviewee - Jeremy Tomkinson
Indeed it does, because for more pragmatic reasons it wants to be in areas such as chemical complexes where we've got blending facilities for the fuel, where we've got good outlets for the heat and the plan is to basically get the bin lorries to just come and back into the site and empty out. Done from an independent basis, the life cycle analysis shows that we mitigate 98% of the greenhouse gas emissions when we compared our ethanol to petrol. So typically when you drive your petrol car, on average you'll emit around 160 grams of carbon dioxide for every kilometre that you travel. Of course here we are less than five.
Interviewer - Chris Smith
Which sounds really quite impressive, but will it work. That was Jeremy Tomkinson and he is the CEO of the National Non Food Crop Centre which is based in York.
(Music)
Interviewer - Chris Smith
This is Chemistry World with me Chris Smith and still to come, how scientists are using DNA to assemble micromachines and a new coating that can repair itself when it gets scratched. All its needed is a short burst of sunshine.
(14:33 -- Could naked mole rats help reveal the secrets of aging?)
Interviewer - Chris Smith
But first, Bibi, scientists have laid bare some interesting revelations about the aging process. So tell us about this.
Interviewee - Bibiana Campos-Seijo
A group of researchers led by Rochelle Buffenstein at the Barshop Institute in Texas have been studying naked mole rats because there's a very interesting fact about them and that is that they live for up to 30 years which is 10 times longer than the average lab mice. So, they thought that it would be interesting to do some research on them and because this research could shed some light on the aging process.
Interviewer - Chris Smith
Because these animals can live 10 times longer than equivalent rodent type animals, how are they doing that?
Interviewee - Bibiana Campos-Seijo
It's very interesting. They looked at their proteins. Because they are the main target for oxidative damage which we know is related to aging and they were looking at the presence of cysteine which is very sensitive to damage due to the presence of the thiol groups and.
Interviewer - Chris Smith
This is the amino acid cysteine which often forms linkage across proteins with disulfide bridges and things.
Interviewee - Bibiana Campos-Seijo
Yeah exactly.
Interviewer - Chris Smith
So why did they look at that?
Interviewee - Bibiana Campos-Seijo
Because they were trying to measure the level of oxidative damage and they were trying to look at the different types of cysteine residues, so they were looking at reversible damage, irreversible damage and how it varied from the mole rats to the lab mice and surprisingly they found that the young mole rats had higher levels of cysteine and therefore oxidative damage than mice but they didn't show any signs of aging. And what is more, when they looked at the naked mole rats they saw that the protein profile throughout the life of rat was pretty much the same which is very interesting, so the only way that they had to tell which were the old individuals and the young ones was because they show less activity and then their skin was of a different quality but that was the only visible sign of aging.
Interviewer - Chris Smith
Doesn't this turn on its head, our understanding of the aging process, because we have understood that you just accumulate damage over the course of our lifetime because of oxidative stress and that's why we clap out and get wrinkly and this is saying that isn't the case, isn't?
Interviewee - Bibiana Campos-Seijo
Yeah, pretty much and they are going to be continuing the research because now they need to look at what the processes and the mechanisms for these are they have discovered that these rats have proteins that are very stable to stress, to oxidative stress, they are very resistant, but they don't know why yet. So they will look at the mechanisms by which this happens.
Interviewer - Chris Smith
And hopefully they'll solve that problem in time when I get old. Thank you very much for that Bibi.
(17:20 -- The inorganic crystals that can be turned into microtubes)
Interviewer - Chris Smith
And let's now look at some interesting crystal structures that have emerged this week Nina tell us, but this is fascinating.
Interviewee - Nina Notman
So this work is being done by Leroy Cronin who is based in Glasgow in UK and he has been turning inorganic crystals into micro sized chips so you can grow these chips into a variety of different sizes and shapes including using, he uses some etch-a-sketch type device to create cubes and cross shapes.
Interviewer - Chris Smith
What actually are the crystals made of?
Interviewee - Nina Notman
They are made of an anionic polyoxometalate compound, so these crystals are insoluble in water and they drop them into water and they add a polyaromatic cation which coats the crystals and water gets absorbed into this coating and eventually the coating ruptures and the force of the rupture causes the polyoxometalate to get out. This then crystallizes which is beginning of the tube and then the poly anions continue to flow down the tube ensuring that the tube continues to grow.
Interviewer - Chris Smith
Why do they actually form tubes? Why not just form one solid blob of crystal materials together? Why do they actually from these straws?
Interviewee - Nina Notman
I believe it's due to the force of which the membrane ruptures and the polyoxometalate comes out of the crystal. I think this is very much similar to the way that lava explodes out of volcanoes.
Interviewer - Chris Smith
Oh, comes out through the middle, so you have a big pool of magna around the volcano and it squirts off the middle and deposits on the outside and these tubes grow in the sort of same way.
Interviewee - Nina Notman
Exactly Chris.
Interviewer - Chris Smith
How do the scientists behind this actually think it could be used though, what's the point of doing this?
Interviewee - Nina Notman
They've suggested two applications so far. They've shown that you can flow fluid through the tubes so they've been considering them for microfluidic devices and polyoxometalate is a well known catalyst and they have been doing catalytic reactions with in the tubes but they won't tell us anymore about that yet because they are looking to publish it.
Interviewer - Chris Smith
I was a big etch-a-sketch fan, I am sure there are some other closer etch-a-sketches out there too. Thank you Nina.
(19:19 -- Ned Seeman talks about building shapes and devices from DNA)
Interviewer - Chris Smith
Now on the subject of designing things to drawing or modelling or with an etch-a-sketch but with DNA, Meera Senthilingam spoke to Ned Seeman to find out how he is using DNA to build structures on the nanoscale.
Interviewee - Ned Seeman
It's really the use of branched, in particular DNA motifs, to make objects and lattices and devices. We use DNA because it has molecular information coded in it; well that same information can be used to direct DNA molecules to interact with other DNA molecules and enable us to make structures and in some ways to make machines.
Interviewer - Meera Senthilingam
And so what kind of structures and shapes have you been making?
Interviewee - Ned Seeman
Over the years we made things like DNA cube like molecule and a molecule has a topology of a truncated octahedron as a 14 sided figure.
Interviewer - Meera Senthilingam
But how is this actually done? How were you able to manipulate DNA to make these shapes?
Interviewee - Ned Seeman
We simply designed sequences that will come together to form these things, so when I talked about making a cube for instance, I am talking about a strict cube so the edges correspond to a DNA double helixes and the corners correspond to points where DNA branches, where double helixes branch from each other. And the key aspect of this is we are really using branch DNA, not just linear DNA. Linear DNA is just a one dimensional species and if you hook more of a bunch of those species together you'll basically it's a lining, you'll get a longer line but with branches then you start talking about making networks and even more complex things like devices. So the DNA molecule consists of two strands, that's why its called the double helix and there is a relationship between the sequence on one strand and the sequence on the other strand, so between the two of them there is always, if there's a given unit on the left side there'll be given unit on the right side, we just use it so we can ensure who is pairing with whom and we make some synthetic DNA molecules and the synthetic molecules also assemble according to these rules, so that they form the kind of branch points and then we connect the branch molecules together in specific orders and then we can make whole network or whatever we would like.
Interviewer - Meera Senthilingam
So essentially, you've got these DNA strands which are then leaving those ends kind of open and available for things to stick on to.
Interviewee - Ned Seeman
That's right. That's the one the real strength of DNA as you can control the intramolecular interactions of DNA just by having a little tail of unpaired DNA and you offer some large construct then the DNA will go capture other pieces of DNA that has complimentary tails and then that allows us to direct the association from the molecule.
Interviewer - Meera Senthilingam
And so you've made these shapes like a cube and an octahedron and things like that, but what can you now do with them?
Interviewee - Ned Seeman
Okay, so the cube and the octahedron were both training exercises for us. The main things that we are interested in are getting DNA molecules to self assemble into 2D and 3D lattices and as a lot of these lattices is to assemble in themselves first and then to have them act as hosts for macromolecular scale guests. Basically, we are trying to self assemble crystals. The idea is to make things that will organise other things when the DNA molecule self assemble, it take these other things with them to organise them into crystal arrangements. The original aim here was to try to use well defined DNA lattices to act as hosts for other biological species, proteins and protein nucleic acid complexes and so far things that are found with in itself in order to work out these 3-dimensional structures. The working of the 3-dimensional structure was done most typically by a procedure known as X-ray crystallography. And it sort of allows us to absorb the interactions of biological systems with potential drugs and so forth to see how you could stop them from behaving in a certain way or force them to behave in a certain way or whatever. Once you know it, its tremendous help to know what something looks like to be able to design therapies and so forth. So growing crystals is hard though and the way in which we grow crystals, right now is basically a trial and error method and we are trying to eliminate that trial and error.
Interviewer - Meera Senthilingam
As well as studying things in the cell as an electronic application. So what actual applications in electronics could this have?
Interviewee - Ned Seeman
Well it would help us to take the components of electronic circuitry and then make them smaller, so then when they are smaller they are faster and when they are smaller they are cheaper and when they are smaller they work better. The conventional electronics that we all work with is going to be hitting the wall relatively soon in terms of how small they can make their components. These things are made by basically you know lithography where we work from the top-down and now we are soon going to be hitting an era where we are going to have to work from the bottom-up and that's where this type of control comes in.
Interviewer - Meera Senthilingam
So where are you now with this research and where are you hoping to go next with it?
Interviewee - Ned Seeman
We've certainly been successful organizing things in 2-dimensions; we are working to do that in 3-dimensions. We are just starting to have our first successes in 3-dimensions, so the whole go here is to organise matter into 2 and 3 dimension and not just DNA which is indeed a great tool and is a great architectural tool, but its individual properties that may or may not be of great utility. So we can use the DNA to organise other things in which we are interested either cellular components like proteins or other micro organelles or we can also use it to organise nanoelectronics. And we've made starts on both of those already. You can do all these things in 2D and it's probably more effective to do them in 3D and we are just getting a hand along 3D now.
Interviewer - Chris Smith
DNA not just the building block of life, it's also potentially the chemist's modelling clay. That was New York University's Ned Seeman talking with Meera Senthilingam.
(25:51 -- The bioelectronic e-nose)
Interviewer - Chris Smith
And now Phil I hear the scientists are connecting human nose receptors to nano tubes in order to create the ultimate e-nose.
Interviewee - Phillip Broadwith
Oh yes, this is some work done by two groups in Korea led by professors Park and Jang from Seoul University and it's a bioelectronic nose. So it's taking real human smell receptors and building them into a device using a conducting polymer nanotube, laid over some electrodes to make the sensor.
Interviewer - Chris Smith
How does it actually work, how do you connect a human receptor to a nanotube?
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