Breaking things down to the building blocks of life this week is Mark Ross, who discusses the evolution of sex chromosomes, genetics and genomes, Michael Traugott describes a novel way of using genetics to find out who is eating whom in underground food webs, and Derek Thorne gets fruity with Lucy Wheatley extracting DNA from a kiwi...
In this episode
Life on Other Planets Comes Closer To Home
The holy grail of finding extraterrestrial life has been the discovery of an Earth-sized planet with just the right temperature for liquid water to exist on the surface. However a new study has shown that we should actually be looking at moons rather than planets. Europa, one of Jupiter's moons, is regarded as one of the best prospects for extraterrestrial life in our solar system despite being covered in kilometres of water ice. Jupiter's gravity is strong enough to distort the shape of Europa in a similar way to how our Moon's gravity creates tides. This distortion is equivalent to rapidly stretching and releasing an elastic band, and results in the generation of heat. This heat warms up Europa's frosty interior, allowing a layer of liquid water to form underneath the ice crust. The study suggests that cold gas giants larger than Jupiter may harbour warm moons with thoroughly thawed surfaces or underground seas, and that these could be the perfect breeding ground for extraterrestrial life.
Magnet Knocks Migraines on The Head
Researchers in America at the Ohio State University Medical Centre, led by neurologist Yousef Mohammad, have found that a quick zap to the head with a magnet can stave off a migraine attack. Characteristically migraines usually begin with visual disturbances, known as an aura, during which sufferers complain of seeing flashing lights, wavy patterns or lose parts of their vision. This is followed by light sensitivity, nausea and vomiting and a throbbing headache which can last for several hours. Researchers think that the aura is produced by a slowly spreading region of excessive nerve activity which subsequently triggers pain sensations by causing blood vessels in the brain to open up. It is well known that magnets can be used to alter the electrical activity of the brain; this process is called TMS or trans-cranial magnetic stimulation and is delivered using a hand-held hair-dryer sized device. To find out whether it could reset a developing migraine the team recruited 43 sufferers and asked them to present to the emergency room as soon as they began to experience any aura symptoms. As soon as they arrived they received two blasts of TMS to the back of the head, or a placebo treatment. Two hours later about 70% of the TMS-treated patients reported that they had little or no headache, compared with 48% of those who received a pretend (placebo) treatment. The findings agree with another small trial conducted recently, this time in Canada, by Adrian Upton, a neurologist at McMaster University in Ontario, although, rather like the brain itself, why the technique works is still something of a "grey area".
- How to extract DNA from a kiwi fruit
How to extract DNA from a kiwi fruit
This week Derek is in the Department of Developmental Biology at Cambridge University with scientist Lucy Wheatley and student helper, Lucy Brown...
To do this experiment, you will need:
A kiwi fruit (an onion will do if you don't have a kiwi) 5g washing up liquid or hand soap 2g salt 100ml tap water 100ml of ice cold alcohol (white rum or methylated spirits are best). Put in freezer for at least 30 mins. kettle 3 jars large basin some thing to mash the kiwi with sieve or coffee filter paper knife (be careful!)
How to do the experiment:
1 - Peel the kiwi fruit and chop it into small chunks. You don't want the skin because it's mostly dead and doesn't have much DNA in it.
2 - Put the chunks in a jar and mash the kiwi as much as you can. This is to break up some of the cells and provide a large surface area over which to extract the DNA.
3 - Mix together the washing up liquid, the salt and the tap water and stir slowly until the salt has dissolved. Don't stir too fast or else you'll get lots of bubbles! This mixture is also known as an extraction buffer. The washing up liquid is a detergent and this breaks open the cell membranes and nuclear membranes. Once these membranes are broken, the DNA stored in the cells can escape. The dissolved salt (or sodium chloride) is made up of positively charged sodium ions and negatively charged chloride ions. DNA is also negatively charged and attracts the positively charged sodium ions. This neutralises the charge on the DNA, which allows the strands of DNA to stick together and form the clumps we will see later inthe experiment.
4 - Add the extraction buffer to the mashed up kiwi and MASH! The more you mash, the more DNA you will get out at the end.
5 - Incubate the kiwi and buffer mixture at 60 degrees Centigrade for 15 minutes. To make your own incubator, take a large basin and half fill it with boiling water from a kettle. To reduce the temperature, add about the same amount again of normal tap water. Using a thermometer will help you reach a more precise temperature. Carefully put the jar with the kiwi into the incubator and leave to stand for 15 minutes. Incubation helps to break up the cells further and starts to degrade some of the cell's proteins.
6 - Remove the jar from the incubator and filter the kiwi mixture through a fine sieve or coffee filter paper into another jar. This removes all the unwanted lumps and bits of kiwi fruit. You should be left with a green liquid, and this contains the kiwi fruit DNA.
7 - Take the ice cold alcohol and pour it slowly down the side of the jar. The alcohol will form a transparent layer on top of the kiwi mixture, as the alcohol is less dense.
What do you see?
Where the layer of ice cold alcohol meets the kiwi mixture underneath, you will see a white jelly-like substance forming. This is the kiwi DNA. Dna Is Soluble in Water But Not in Alcohol, So When it Touches The Alcohol it Comes Out of Solution And Forms a Solid. This Is Known As 'precipitating The Dna'. The Longer You Leave The Alcohol With The Kiwi Mixture
You can use a paper clip or some tweezers to pick up the DNA. It will be long and stringy and clump together. DNA is a very long molecule and when it clumps together, it forms something a bit like a rope. This is safe to play with a poke at. The DNA you have extracted has come from billions of kiwi fruit cells, which is why you can see it so easily. If you were able to unravel the DNA in just one human cell and stretch it out, it would be two metres long. However as DNA is so thin, you would not be able to see it without an incredibly powerful microscope.
- Science Update - Ancient Supernovae and Ducks
Science Update - Ancient Supernovae and Ducks
with Chelsea Wald and Bob Hirshon from AAAS, the science society
Phil - As happens at this time every week, we're now going to go over the ocean to hear Bob and Chelsea's Science Update. This week they're going to be spotting ancient supernovae and hearing how the ancestor of modern birds may well have looked a bit like a duck.
Bob - This week for the Naked Scientists we'll discuss some spectacular bird fossils that scientists have dug up in China. But first, if you had lived in the year 1006 instead of 2006, you couldn't have missed the bright star that suddenly appeared one night in May. It was a supernova, and civilisations in Asia, Europe and the Middle East recorded it for posterity. Now Chelsea tells us that someone in North America may have noted it too.
Chelsea - The 1006 supernova was briefly the brightest object in the sky after the sun and the moon. Now astronomers have found rock art in Arizona that might be an ancient record of it. John Barentine of the Apache Point Observatory in New Mexico says the design chipped into the rock is an eight-pointed star next to a wavy line that looks like a scorpion. The 1006 supernovae would have appeared next to the constellation Scorpius.
John - There's a little bit of western bias in seeing Scorpius among the figures on this rock, but it's a pattern of stars that has a long history. It goes back 1000s of years at least in the Middle East and Eastern Mesopotamia. It turns out that in many parts of the world that are in arid climates where you would find scorpions, the figure of stars that we know called Scorpius was identified with that animal.
Chelsea - He says that we can never be sure of the artist's intentions but chemical dating could resolve whether the rock art was in fact created a millennium ago.
Bob - And now to rewind even more, it may be that all modern birds from robins to owls to ostriches evolved from duck-like ancestors. An international team of palaeontologists working in China recently discovered five new fossils of a 110 million year old ancestor of modern birds called Gansus yumenensis. Jerry Harris of Dixie State College in Utah says it probably looked and acted like today's loons and grebes.
Jerry - It has several similar features in its skeleton that show that it had a similar lifestyle of diving under water and swimming. They also had webbed feet. In some of our specimens it had skin preserved and showed that it had webbing down to the end of its toes so we know it was a water-based bird. When you put the skin and feathers back on it, you'd probably have a hard time telling the difference between it and a loon or a grebe, especially from a distance like you mostly see them in a lake today.
Bob - He says Gansus is probably not a direct ancestor of modern birds; probably more like a super-great grand uncle. He adds that it may have been a tasty dish for the dinosaurs.
Chelsea - Thanks Bob. Next week we'll learn about a love hormone that seems to soften marital spats. Until then, I'm Chelsea Wald.
Bob - And I'm Bob Hirshon for AAAS, the Science Society.
- Sex Chromosomes And X-linked Diseases
Sex Chromosomes And X-linked Diseases
with Dr Mark Ross, the Sanger Institute, Cambridge
Chris - Now can we just orientate people a bit first because the whole point of molecular biology and genetics to many people is a little bit overwhelming. So first of all, DNA, gene, chromosome, genome: what do these words mean and how do they all relate? How does it all build up to make the genome of a person or an animal?
Mark - To take the genome first of all, all the people in this room are recognisably human because we have a human genome. So the human genome is the complete collection of all our genes and a complete set of all of our chromosomes. The genome is packaged in the cell. The genome comprises of long linear threads of DNA and these are packaged into the cell in the chromosomes. Chromosomes are a mixture of the genetic material that are DNA and the proteins that package that DNA into the cell. The genes are what are generally considered to be the functional components in the genome. There are other functional components as well but the genes are the focus of much interest. They're the parts of the genome that contain instructions to build protein molecules. It's the proteins then that go on to carry out the functions in the cell, in the tissue and in the body.
Chris - So the gene is the bit you inherit; it's the functional unit. In other words, there are a certain number of DNA letters that make up a gene and the gene tells the cell how to make a particular recipe.
Mark - That's right. We inherit our DNA in general and only a tiny fraction of that actually contains instructions to make a protein. It's about 2% of the total genetic material. So we've inheriting other genetic material as well. Some of that has function, so for example, pieces of our DNA control genes and tell then when to be switched on or switched off in a particular tissue.
Chris - But 2% seems a tiny amount. 98% not turning into something physical in the body seems like a big waste.
Mark - Well there is a large fraction of our genome that is often described as junk DNA. That would be considered to be a wasteful fraction of our genome. However, I think it's actually too early to conclude that this repetitive DNA that is particularly good at getting itself copied throughout our genome lacks a function. Perhaps we'll get a chance later to talk about the phenomenon of X-chromosome deactivation, and that's a possible area where this so-called junk DNA could have a role and something that we're interested in.
Chris - Well lets get down to what you work on, which is the X-chromosome. You actually led the Human Genome Project to sequence that chromosome.
Mark - Yes, that's right. The idea of that project was to determine the so-called DNA sequence of the X-chromosome. So looking in more detail at the DNA, the long molecules of the DNA are made up of four basic sub-units. It's the order of these sub-units in the DNA and in the genes in particular that determine what the structure of a protein will be. So the sequence of that DNA is very interesting to us and once we have the sequence it allows us to do a large amount both studying the function of the genes and also we can look at the evolution of our genome and that's something I'm particularly interested in.
Chris - As in, how we come from chimpanzees.
Mark - That would be one example, but I'm more interested in looking back at marsupials and looking at the other mammalian group too; the monotremes. These are egg-laying mammals and include things like the duck-billed platypus. We look at the sex chromosomes and how they've evolved in the mammals. If you go further back, these same sex chromosomes don't exist in birds for example.
Chris - Because women have two X-chromosomes. As men, we have one and a Y chromosome. So just talk about that a little bit and how it actually works.
Mark - The reason that the sex chromosomes are called sex chromosomes is because they are inherited differently between males and females. Females have two X-chromosomes whereas males have one X-chromosome and a much smaller Y - chromosome. The interesting thing is that we know that these chromosomes, although they look very different from each other, have actually evolved from a normal pair of chromosomes: a non-sex chromosome pair if you like. The reason is that they have become involved in sex determination. That's the trigger to either sexual differentiation into a male or sexual differentiation into a female.
Chris - So when a baby is first conceived in an early embryo, it's neither male nor female. Genetically speaking it is, but from a developmental point of view it is neither male nor female to start with.
Mark - That's right. It's the development of the gonads down one of two possible pathways that determines our phenotypic sex, or the way we look.
Chris - And the Y-chromosome does that.
Mark, Yes, the Y-chromosome contains SRY, the sex determining region of the Y. If we inherit the Y-chromosome and we inherit that gene, then the gonad develops into a testis and all male characteristics develop from hormones produced in the testes.
Chris - But what's really interesting is that I've got one X-chromosome, but the ladies we work with here have got two. What do they do with the extra one? Is there a problem having more genetic material than you should do? If you look at people who have Down's Syndrome, they've got an extra copy of chromosome 21, and that obviously creates some problems for them. But with the X - chromosome, women can have an extra copy and there doesn't seem to be a major issue.
Mark - That's right. As you've pointed out, in general, having an extra copy of a chromosome causes very severe problems. In the case of having an extra X, this doesn't happen. The reason is that female mammals, including the females in the studio silence one of their X-chromosomes. They switch one of their X-chromosomes off in each of their cells and so the genes are no longer active on that X-chromosome. In that way, males and females have a single active copy of their X-chromosome.
Chris - Doesn't that cause interesting things with relations to certain diseases? So if there's a certain gene that's abnormal on the X-chromosome, men will get it. But because women have two X-chromosomes, if one has a faulty gene but the other has a healthy gene, the women don't succumb to the disorder.
Mark - There's a very characteristic pattern of inheritance of so-called X-linked conditions, where males are generally affected and women are either affected or have mild symptoms of the condition. These kinds of inheritance patterns have been described going back thousands of years, particularly for things like haemophilia. In some instances, because this process of switching off one of the X-chromosomes in females is a random process, that would mean that on the whole, half of the cells in the female body would have switched off the undamamged X - chromosome and the other half will have switched of the damaged X-chromosome. That could account for why some of these symptoms are visible in females. In some extreme cases this X-inactivation can skew in one direction, presumably the cells that have switched off the undamaged X - chromosome. They don't thrive while the other cells do.
- Who Eats Whom in The Undergrowth
Who Eats Whom in The Undergrowth
with Dr Michael Traugott, University of Innsbruck and University of Cardiff
Chris - Now you're trying to solve the puzzle of who's eating who. Tell us about that.
Michael - Yes, it's true. I'm interested in what's going on below ground and who is eating whom. There are many animals, about four to five hundred different species, and the complicated thing is that these animals contain no hard remains of the prey for you to identify.
Chris - So it's all been digested.
Michael - Yes, digested, liquid things. However, you can use DNA-based methods that track the gut content of these animals, look at the DNA that they contain and then you know what they've been eating.
Chris - So which sorts of animals have you been playing around with?
Michael - We've been looking at different sorts of animals: beetles, millipedes, centipedes, earthworms and nematodes.
Chris - So was that not known then?
Michael - It's very hard to study and observe because it's below ground. It's also hard to look in undisturbed conditions. That's normally the problem. You can't put, for example, a plastic or glass sheet into the soil and watch the animals, because you only see the animals that come up to the glass sheet.
Chris - And you wonder whether you have changed the situation by doing that.
Michael - yes, you change things completely. It's hard to get really quantitative data, and really understand and see what's going on. So with DNA based methods it's really a new thing and a fascinating thing that we can analyse samples. In Austria, we have collected 500 predators from the soil because we were interested in who is eating the white grubs. They are pests in soil ecosystems. We found out that some centipedes called geophilites are probably the most important predators of these soil pests and this wasn't known before because there was no technique available to study this.
Chris - Talk us through the actual nuts and bolts of it. How do you do the experiment? What does it actually involve?
Michael - First you have to sequence…
Chris - Well hang on, you have to collect the animals first, so where do go and do these experiments?
Michael - Ok, you have to go to the field, dig into the soil and collect animals. You then freeze them immediately because it's important to freeze them as quickly as possible.
Chris - So the gut contents don't go off.
Michael - Yes, so they don't go off. Then you bring them to the lab and you extract them using methods that are a bit more sophisticated than your kiwi experiment.
Chris - So what does that involve?
Michael - We crush them and extract the DNA. But we still have the problem that they contain lots of substances that inhibit your PCR reaction. That reaction is later needed to identify the specific DNA molecules. So we crush them and get the DNA from the predators, including their gut contents, and then we throw all this together in a nice optimised PCR reaction.
Chris - Polymerase Chain Reaction.
Michael - Yes, and add some particular genetic markers that target, for example, white grubs or cockchafer, and then if the predator was feeding on this white grub, you get a positive result. You will see a band on an agarose gel. Then you have proven that these predators or this centipede was feeding on the cockchafer.
Chris - Sounds good, but my worry here is that what if the grub crawled through the soil that another one of these animals has already died in and got some of that DNA on its body? DNA techniques nowadays are so sensitive that couldn't you get some contamination? Couldn't you be fooled into thinking that something had eaten something even if in reality, it hadn't?
Michael - Yes. There are always problems but I don't think that this would be that problematic if it was just crawling through the soil and contained some of the DNA of the target prey. There are lots of microbes in the soil breaking down the DNA. One problem that we are really struggling with is differentiating between active predation and feeding on dead prey, or scavenging. This makes a big difference.
Chris - Can you solve that problem?
Michael - Not really at them moment because you can't pick up the DNA from dead prey as good as you can from fresh prey. Forensic scientists are using this powerful PCR to get DNA from human bodies.
Chris - It's amazing to think that we've got to the stage where there wasn't the knowledge of what was going on underground. There must be some other spin offs from this for maybe agriculture and commerce.
Michael - The basic idea and the reason why we did this project on the white grubs was that white grubs are very serious pests in alpine grasslands ecosystems. We were interested in what below ground predators there are for the grubs and see which predators we should enhance. What are the ky plyers in regulation?
- Can a key dangled over food diagnose whether I can safely eat it?
Can a key dangled over food diagnose whether I can safely eat it?
Sorry Mary, but we can't believe it's true either. I imagine that any spinning is more to do with the twist of the cotton that you hang the key on than anything else. There's probably a bit of gambler's fallacy kicking in there. You're expecting the right answer and therefore the result happens.
- Can the weather cause migraines?
Can the weather cause migraines?
I don't know whether there is evidence for a direct relationship between weather, atmospheric pressure and headaches. But one thing that does occur to me is that, if you have high atmospheric pressure, usually that's associated with warm conditions. When people get very hot, they can get dehydrated. One symptom of dehydration is a fierce headache. That could be one of the reasons for your headache symptoms...
- How cold is it in outer space and how do you protect satellites from extreme cold?
How cold is it in outer space and how do you protect satellites from extreme cold?
It's a bit of a fallacy that outer space is really cold. It actually depends on how close you are to the sun. One problem is that it doesn't feel cold like it does on the Earth. There's no air around you to conduct heat away from you or towards you; everything is done by radiation, passing light from one object to another. Light from the sun falls on a body and heats it up. For satellites up in space around Earth, we actually cover then in reflective material to keep them cool, and insulating material to keep them hot. If they're in the sunlight, they actually overheat so we put reflective material on there to reflect the light away. When they're in the Earth's shadow, we can use heaters to keep it warm. When you get further and further away from the sun, it gets really cold. The outer space around Earth is around 20 degrees Centigrade. If you go out to Pluto, you're probably looking at around minus 220 degrees Centigrade. So it depends on exactly where you are.
- Why do we assume that life on other planets would be a carbon-based humanoid like us?
Why do we assume that life on other planets would be a carbon-based humanoid like us?
I completely agree with you, John. The point is that here on Earth we see organisms the breathe methane. We see organisms that breathe and produce hydrogen as a waste product, and we see organisms that produce hydrogen sulphide as a waste product. In fact some of the first organisms on Earth were methanogenic bacteria. They produced methane by taking simple carbon building blocks from the environment, jamming them together with four hydrogens and making methane. Some scientists from Japan found some of the world's oldest bacteria locked away inside tiny bubbles inside quartz. Life can come in all shapes and sizes, and evolution can pattern us and puts pressure on us to become adapted to our environment. On a different planet, things could be completely different and we have no reason to assume that alien life would look or even metabolise anything like we do.
- Why do I share only 50% of my genes with my daughter?
Why do I share only 50% of my genes with my daughter?
I would say that you actually share more than 98% of your genes with a chimpanzee. I suspect that virtually all of the genes in the human genome also have counterparts in the chimpanzee genome. The most likely explanation for the fact that we are so obviously different from chimpanzees is the way in which these genes are controlled and the way they are switched on and off, and the length of time for which genes are active. You share 50% of your genes with your daughter because she's obviously inherited one genome from you and one genome from her mother. We all have two genomes in our bodies: one from our mother and one from our father, but there are counterparts to all of your genes in the genome that your daughter has inherited from her mother. If you compare a banana with a human, just over half the genes in a banana will do the same job in a banana as they do in a human. However, the genes themselves will not be the same letter for letter; they just perform the same function. In contrast, when you are talking about the genes you share with your daughter, you are not asking how many of the genes have the same function (which is 100%), you are asking how many of those genes are absolutely identical, letter for letter. The probability that any one of those genes came from the father is 50%, and the probability that a gene has come from the mother is also 50%. This is why you share 50% of your genes with your daughter.
Why do people go bald?
I should make it plain from the outset that I don't really understand why people go bald. I'd probably be very rich if I understood that! Baldness is what is described as a sex limited condition rather than a sex linked condition, which means it tends to affect one sex more than the other. In this case it's obvious: it affects males more than females. But it's not a straight forward inheritance of a gene on the Y-chromosome, for example, that leads to baldness. The genetics and inheritance patterns are more complex than that, otherwise people would have been able to follow these inheritance patterns through families and understand more about the genetics of baldness. So we're not there yet, but we have some useful information.
- Are genes for blond and ginger hair recessive?
Are genes for blond and ginger hair recessive?
I'm not sure I can comment on the idea that blonde and ginger people will become extinct, as it's the first time I've heard that. But interestingly, some people have speculated that the Y-chromosome that we were talking about earlier may disappear completely. The Y-chromosome has degenerated during the evolution of the sex chromosomes. Some people have speculated that in 10 million years it will have disappeared altogether. Obviously that is of some concern to males, but suffice to say that natural selection will act against anything that prevented there being males within the population. So for the Y-chromosome to disappear, another gene would have to arise to make a male sex. But I really can't comment on the extinction of blonde and ginger people.
- Is it true that humans have not evolved over the last 4000 years?
Is it true that humans have not evolved over the last 4000 years?
There are obviously different components to evolution. There's a component of genetic change and genetic change is still going on. There's also the component of natural selection whereby certain adaptations are selectively advantageous or disadvantageous. There's an argument that we've stopped evolving as humans because we've removed those elements of natural selection. Other people are speculating that we're evolving in different ways; psychologically and so on rather than physically. But it's an open question.
- How are skills and traits passed on genetically?
How are skills and traits passed on genetically?
That's a very difficult question to answer. I'm not aware of there being any evidence for learning of particular skills then becoming hard wired in the DNA. This was a theory that was quite popular in the early twentieth century that perhaps things could get hard wired into the DNA, but I'm not sure there is a mechanism for that to occur.
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