Podcast Transcript

Evolution in a bottle

Evolution on a grand scale – the sort of evolution that produced humans from our monkey-like ancestors - takes millions of years. But although these kind of timescales can't be studied in the lab, researchers at Michigan State University have been running an evolutionary experiment over 21 years that shows natural selection at work.

The scientists, led by Professor Richard Lenski, have bred and anaylsed a staggering 40,000 generations of bacteria, and publish their findings today in the journal Nature.

Lenski first started growing E. Coli bacteria back in 1988 – these are bugs grown in flasks that are often used in lab experiments, and they reproduce roughly every 20 minutes. He figured that if a bacterial cell picks up a genetic mutation that gives it an advantage, it – and its progeny – should start to take over the flask.  This is Darwin's theory of natural selection in action. And although this kind of experiment has been done before, this is the longest running, and most detailed study of its kind.

The researchers periodically froze samples of bugs from the culture, and analysed them using modern gene sequencing technology. Although the study started 21 years ago, it's taken until now for genomic technology to be able to do justice to such an experiment.  

By the 20,000 generation halfway mark, the scientists discovered 45 mutations in the surviving cells. And as you might expect, these mutations gave a survival advantage to the bacteria that carried them.  The experiment also revealed interesting relationships between the speed at which organisms adapt, compared to the rate of mutation in their genomes. Lenski says "The genome was evolving along at a surprisingly constant rate, even as the adaptation of the bacteria slowed down a lot. But then suddenly the mutation rate jumped way up, and a new dynamic relationship was established."

The team found that a mutation involved in DNA metabolism occurred after around 26,000 generations, and this meant that the chances of mutations happening elsewhere in the genome rose dramatically – so by generation 40,000 there were 653 mutations, compared with the 45 found at the half-way mark.

Obviously, in only 21 years we're not going to see the evolution of anything other than slightly better bacteria. But  the research could shed light on other situations where genomes evolve as organisms adapt – such as in the development of cancer, or microbial infections. And it could also be useful for industrial scientists who grow bacteria to produce enzymes and drugs, to improve the performance of their bugs.

18th Oct 2009

Stresses and strains shape embryos

Embryonic stem cells have been hot news in science for a while – these are the first cells that form in a developing embryo, just a couple of days after fertilisation. They're amazing little cells because they have the potential to become any type of cell in the body.  And because of this property, scientists are trying to turn them into many different types of cells in order to repair diseased or worn-out tissues in our bodies.

Researchers grow embryonic stem cells, or ES cells in the lab and treat them with various chemicals, or manipulate genes to get the cells to adopt different fates. But now scientists in Illinois have made an unexpected discovery – ES cells can be coaxed into certain fates by physical stresses and strains.

This is research published in the journal Nature Materials, from Ning Wang and colleagues, who were looking at the effect of forces on cells. To do this, they attached a single tiny magnetic bead to the surface of a living mouse ES cell, then put the cells into a tiny oscillating magnetic field, which made the bead move up and down – this mimics the natural forces within in cell, such as the movement of little motor proteins. This set-up meant they could measure the mechanical force being applied to the cell, and how soft the cells are.

The scientists found that the ES cells were much stiffer and more sensitive to the movements than more advanced cells that had started to adopt specific fates.  For example, muscle cells were much stiffer than the ES cells. They also went on to look at the effects of physical forces on the activity of different genes in  the cells. And they found that applying movement to ES cells caused them to switch off the activity of certain genes, some of which control what type of cell the ES cell will become.

At the moment, the research has only been done using mouse ES cells, and we don't know if human ES cells will respond in the same way. But it could provide a useful way of persuading cells to adopt certain fates, which might be useful for doctors looking to replace damaged or worn-out cells. And if the technique is shown to work in actual living embryos, it might be possible to alter the fate of specific cells at an early stage – say in the case of certain developmental defects – without affecting neighbouring cells.

18th Oct 2009

Sneaky Sounds Enhance Eyesight

Some sounds, such as a speeding car or footsteps in a dark alley, actually improve our eyesight even before we are aware that we can hear them, according to research published in the Journal Current Biology. This gives us cause to rethink the idea that hearing and vision are handled separately in the brain at the input stage.

Gregor Thut, at the University of Glasgow and colleagues in both Glasgow and Lausanne, performed a series of experiments to look at excitability of the low-level visual cortex, and see if it was altered by hearing looming sounds.  To do this, they used a technique called Transcranial Magnetic Stimulation – this uses rapidly changing magnetic fields to induce small currents in the neurons.  This stimulation leads to the perception of flashes of light, a bit like those you see when you rub your eyes, in a process called Phosphene induction.

In the presence of looming sounds, compared to control sounds, the perception of phosphenes was greatly and selectively enhanced, showing that these sounds do indeed alter the excitability of the visual cortex.  They did see an increase in excitability when listening to stationary (constant volume) sounds, but looming sounds doubled the baseline phosphene perception.  This increase in excitability actually happened around 35 milliseconds before the volunteers were able to discriminate the sound at all.

A follow up experiment tried to see if this effect was just due to the increasing intensity (the sound getting louder) or the perception of a looming sound getting closer.  Previous studies have shown that for a sound to feel like it’s getting closer, rather than just louder, it needs to be a structured, rather than broadband sound.  This means that if you generate white noise that gets increasingly loud, it won’t feel like it’s coming closer.  Looming white noise increased visual cortex excitability, but only as much as the constant volume sounds.

This shows us that visual perception can be boosted by other senses in a preperceptive way – before we consciously realise what we’re hearing – the brain acts in a multisensory but stimulus selective way.   This challenges the current model of the brain, and according to Thut:

“The study shows how models of brain organisation and perception need to be changed to include multisensory interactions as a fundamental component.”

18th Oct 2009

The Taste of Fizz

The experience of drinking a fizzy drink is both a  physical and chemical experience, and now researchers have discovered just what happens when the bubbles hit your tongue.

Reporting in this week’s Science, Jayaram Chandrashekar and colleagues from the Howard Hughes Medical Institute at the University of California, San Diego, along with collaborators at the National Institute of Dental and Craniofacial Research in Bethesda & the St. Louis School of Medicine, show that the cells on our tongues that sense sour flavours are also responsible for tasting carbonation, and identify the gene responsible.

Humans, and many other animals, detect five distinct flavours - bitter, sweet, salty, sour and umami.  Different cells on the tongue are responsible for each of these through different chemical mechanisms.  The taste system is also responsive to CO₂ through a number of pathways – nociception (identification of noxous stimuli) olfaction, chemoreception (the same pathway which regulates CO2 in our breath), but until now little has been known about the taste of CO₂.

By genetically deactivating specific sets of taste receptor cells in mice, they were able to show that mice lacking the cells for detecting sourness were completely unable to detect CO₂.  These cells express an ion channel called PKD2L1.  They then looked for candidate genes which were highly specific for cells expressing this ion channel protein.

The researchers identified a gene, called Car4, which was highly specific for these cells and codes for an enzyme called carbonic anhydrase 4, part of a family of enzymes known to respond to, act on or sense CO₂.  Knocking out this gene produced mice who could taste sour foods, but who didn’t respond fully to CO₂.

Carbonic anhydrase catalyses a reaction that turns carbon dioxide and water into bicarbonate and free protons.  Bicarbonate doesn’t react with taste receptors, so we must assume it’s the free protons responsible for activating the sour taste cells.  

But why can we taste carbon dioxide at all?  The authors suggest it may just be a coincidence, and the enzyme is really there to maintain pH balance in taste buds, but evidence of specific CO₂ taste detection in insects may suggest that this has evolved as a means to detect fermenting food.

18th Oct 2009

Giving Insects the Slip

Kat -   Also this week, researchers at Cambridge University have developed a new insect repellent coating which could help to reduce a threat of cockroaches.  Now for many of us, insects are just kind of a bit of a pest.  They get in your picnic.  But insect infestations are responsible for billions of pounds worth of damage across the globe every year.  Now we’re joined by Jan-Henning Dirks from Cambridge University.  So, tell me a bit about what the problem is with insects and then how you've tried to counteract this.

Jan -   Yeah, well the problem with insects is that they amazingly well stick to all kinds of surfaces.  As you look around you, you see them basically clinging to the mirror, clinging to the window, holding on to everything and holding on very, very tight.  And so, for us, this is a more scientific problem to understand how this actually works.  So at the Insect Biomechanics Workgroup here in Cambridge, we were trying to figure out what makes insects so incredibly good at sticking to different kinds of surfaces and whilst we were exploring this, we found a surface that can help you prevent your house and your belongings, and probably even your lab from crawling insects.

Kat -   So how does this surface work?  Because we have nonslip surfaces, things like PTFE that we cover non-stick pans with.  Why is your surface different?  How does it work?

Jan -   Well, our surface is completely different to all other insect repellents that you know.  Because if you look around you, all insects that you can see, they have sweaty feet actually, so they have it...

Kat -   Nice...

Jan -   They do, yes.  And you can even write your PhD about it!  And so, the foot sweat that they have that helps them to stick to surfaces and our technology does something very new.  It basically – it tricks the insect’s feet.  It makes them lubricate their own feet.  Other repellents that you see, they work, like, they are sticky themselves so you know, these fly tapes that capture flies or some people who insects at home, they know that.  They have this surfaces that erode and make the feet dirty.  But our technology is like a selective sponge that removes something from the insect’s adhesive fluid and what’s leftover, makes the insect’s feet slip.

Kat -   So, instead of having sort of a sticky glue that they're sticking on the wall with, suddenly they're going, “Wooh!” and sliding off.

Jan -   It’s very similar.  So they don’t really have the sticky substance at first.  It’s more like ketchup or custard.  It’s one part of it is oil and the other part is water.  And together, it works very similar to ketchup.  But if we remove the water, that’s what our surface does, then what’s leftover is the oil on that then make insects slip.

Kat -   And tell me a bit more about the surface.  I mean, what sort of things can we coat with it?  Is it very pliable?

Jan -   So, that’s what we’re exploring right now.  So in theory, you can apply the surface to a very, very many kinds of different substances.  Right now, we’re exploring and that’s why we’re looking for commercial partner to make this really available for everyone so they can coat whatever they want with it and make insects slip from the barbecue or from where they don’t want insects to be.

Kat -   Fantastic.  Well, I'm looking forward to an non-insect to non-stick picnic camp and that would be fantastic.  That was Jan-Henning Dirks from Cambridge University.

October 2009

This Week in Science History - Mr Tornado

This week in Science History saw on October 23rd 1920, the birth of Tetsuya Fujita, also known as Ted and ‘Mr Tornado’. Fujita dedicated his life to studying tornadoes and related weather phenomena and he lends his name to the Fujita scale, which describes the intensity of a tornado by how much damage it causes.

Fujita was born in Fukuoka Prefecture on the island of Kyushu – the most south-westerly of Japan’s main islands. As a young man he showed interests in geology, cartography and physics, and he went on to study mechanical engineering at Meiji University. He had a lucky escape in choosing this University – despite preferring Hiroshima University himself, he followed his father’s last wish and attended Meiji. If he had attended Hiroshima, he would almost certainly have been killed in the bombing of 1945.

He started his study of storm winds in 1946 and completed his thesis on typhoons in 1953. His work showed so much promise that Dr Horace Byers from the University of Chicago invited Fujita to work there, and in 1956, Fujita made the permanent move along with his family. It was in America that he completed the bulk of his work on tornadoes and made several key breakthroughs in how they occur.

Ok, so first of all, what is a tornado? Most people would be familiar with what they look like – a column of rotating air that descends from the underside of a storm cloud to touch the ground, stirring up a cloud of dust and debris. But why and how they form is a little more complex. First we need to think about how the storm itself forms – clouds form when warm moist air rises to a cooler level in the atmosphere, and the water in it condenses and forms clouds. The air can rise due to thermals produced by the sun heating the ground, or as air passes up and over mountain ranges. Updrafts of warm air keep pushing the cloud up until it reaches a layer in the atmosphere known as the tropopause – here; it meets the cold air of the stratosphere, which acts like a barrier, stopping it from rising further and causing it to spread out like the top of an anvil, giving the characteristic storm cloud shape. As the water droplets in the cloud join together, they fall as rain, snow or hail. The falling water droplets drag cold air with them, creating downdrafts. So we now have a cloud with both up and downdrafts happening – this creates friction inside the cloud and is what causes lightening.

A feature that is key to the formation of strong tornadoes, that Fujita discovered in the 1950s while working at Chicago, is called a mesocyclone. This is a horizontal rotating tunnel of air formed within a storm cloud when winds coming from different directions at different levels cause the air to spin. The updrafts in the clouds tip the spinning tunnel of air upwards. As the updrafts continue to suck air from ground level, an area of low pressure develops, and the bottom of the now rotating storm cloud descends. The winds speed up at the surface and get faster and faster as they get nearer to the centre of the funnel – a bit like when an ice skater is spinning – when they pull their arms in they go a lot faster. The high speed winds at the surface are what cause the damage to buildings, uproots trees and throws vehicles up to 100m.

Tornadoes occur in many countries around the world, including the United States, the UK, elsewhere in Europe, in Australia and India. The Netherlands actually has the most tornadoes per area of land, followed by the UK, but the majority of severe tornadoes occur in the United States, and mostly in what is known as ‘Tornado Alley’ – the Midwestern states including Oklahoma, Kansas, Nebraska and Texas.

Until Fujita’s work, there was no standardised measure of the intensity of tornadoes. In 1971, the Fujita scale was introduced. There are six levels, from F0, the lowest, to F5. F0 tornadoes have winds of around 40-70 miles per hour and are a few tens of metres wide. F5s can be over a kilometre wide with wind speeds of over 300 miles an hour. The wind speeds are estimated by the amount of damage that is done. Because of this, the estimation is fairly imprecise and varies depending on what sort of buildings, if any, were damaged for the estimation to be made. So for example, an F4 in a highly populated Kansas town might only have scored as an F3 in a remote Indian village where the standard of housing was poorer and there were fewer buildings to be damaged. This inconsistency led to a new scale known as the Enhanced Fujita Scale to be introduced in the States in 2007 that gives more accurate wind speeds.

Another of Fujita’s discoveries was the Downburst, a dangerous phenomenon that can knock planes out of the air during take off or landing. It’s pretty much the opposite of a tornado, where surrounding air is pulled in and up into the spinning funnel – in a downburst there is a sudden violent downdraft of air from the base of a cloud to the ground. When the downburst reaches the ground, high winds rushing away from the centre can flatten trees and damage property. The danger to aircraft is caused by wind shear, which can decrease the amount of lift generated by the wings. This, combined with the down-rushing air can cause a plane to literally drop out of the sky.

Throughout the later years of his life, Fujita became the director of the Wind Research Laboratory at the University of Chicago and continued to study tornadoes, hurricanes, downbursts, and other weather phenomena. He published several books and continued working even after his official retirement in 1992 and right up until his death in 1998. The work of ‘Mr Tornado’ revolutionised the study of tornadoes and our understanding of how and why they form, and although technology to track and predict tornadoes and provide warnings to those at risk has improved, he is still considered a true pioneer of the field.

October 2009