Features

Highlights from Oxford science in the news over Christmas:

Could that Christmas chocolate and wine have done you some good?

As newspapers including the Telegraph, The Sun and The Daily Mail reported, Oxford research focusing on the elderly suggests it just might.

Oxford and Norwegian researchers found that small amounts of chocolate, wine and tea can significantly boost the cognitive performance of the over-70s.

Flavonoids, micronutrients found in all three foodstuffs, may be behind the effect (although the researchers say other factors specific to these foods can't yet be ruled out).

Let in the lynx
Would reintroducing the lynx to Britain be the best way to control deer populations?

In the run up to the publication of the State of Britain's Mammals report David Macdonald of Oxford's WildCRU told The Independent lynx would provide a natural way of controlling deer numbers.

David comments that we shouldn't worry about sharing our landscape with these wild cats: 'There is enough food – there are all these roe deer that people are having to control and the lynx could help out... As far as I'm aware, there is no recorded case of lynx being any danger to people.'

Txt ur mood 
A system that enables clinicians to monitor a patient's moods by text message can help in the treatment of mental illness.

Developed by Oxford's Department of Psychiatry, with Oxfordshire and Buckinghamshire Mental Health, the system contacts patients every day and asks them to text back a letter code that corresponds to their mood.

As BBC Online report this simple approach enables clinicians to plot a patient's mood swings, monitor the effect of medication and identify when a face-to-face appointment or further assessment is needed.

Oxford's John Geddes said: 'When I see the patient in clinic I pretty much know how they have been... Basically, with this system we would hit the ground running and we can focus on trying to help them and their treatment.'

Nano-walker 
A new kind of 'walking' molecular machine might one day shift cargo around 'nano-factories' according to New Scientist.

They report on work by Oxford's Andrew Turberfield and colleagues into a 'nanobot' with DNA feet which 'walks' along a DNA track. Clever design ensures the Oxford nanobot doesn't detach itself from or destroy the track as it moves - there's no backtracking either as it can only move forward.

Andrew comments: 'At the moment, the nanobot has taken a single step but our ambition is to make it move 100 nanometres or more... We can already stop and start our motor by controlling the amount of fuel we add, but we could add other control signals to make walkers interact with each other, and could easily attach a cargo to the region that links the two legs.'

Species showdown
Finally, what animal could humans not live without?

During a debate at the Earthwatch Institute broadcast on BBC Radio 4 five scientists slugged it out to decide which species was irreplaceable.

After being put to an audience vote George McGavin of the Oxford University Museum of Natural History won the day with his persuasive argument in favour of bees.

A helping of seasonal science in which Oxford's Joseph Tobias exposes the scandalous life of the robin:

OxSciBlog: What, in evolutionary terms, explains the robin's aggressive territorial behaviour?
Joseph Tobias: Robins are a classic example of a species which survives by defending resources. They feed largely on ground-dwelling invertebrates, a food supply that can quickly be exhausted if too many individuals forage over the same patch of ground.

To maintain their food supply, they defend it aggressively against all-comers, much as we might get a little stroppy if someone was pilfering our fridge. Only in robins the stakes are higher because a cold snap and an impoverished food supply means death, and you can't get more non-adaptive than that.

OSB: What benefit/use is its distinctive red breast?
JT: The red breast appears to be an honest signal of competitive ability. It is fluffed out in displays between rival males, and between courting pairs. It contains information about the genetic quality of the individual, and so functions as a signal mediating conflict and courtship.

As with many such signals in the natural world, the display of honest signals can settle contests one way or the other without the need for direct aggression. This can save a lot of time, energy and injury. When resource value is high and robins equally matched, neither individual backs down and they will famously fight to the death.

OSB: Do we know what impact global warming is having on robin populations?
JT: No. The picture is highly complex. British robins will probably be in favour of global warming as many of them die during harsh winter weather. Spanish robins will probably be a little less enthusiastic as their summers may get too hot and dry.

In most winters a fair proportion of British robins migrate to France or even Spain, while a good number of Scandinavian immigrants swell the ranks of British residents. Warming may therefore lead to shifting patterns of migration, and a contraction of the southern boundary of the species' range.

OSB: How does food availability affect relations between male and female robins?
JT: Pairs of robins form very early, in January, if the food supply is sufficient for two individuals to share a territory. From January onward the female is silent and the male takes charge of territory defence; in April she builds the nest alone, and the pair collaborates to incubate the clutch and feed the offspring; in August the adults moult, the pair bond breaks down and the male and female go their separate ways. So far, the species is typical of many birds, except for the early pairing date.

However, from September onwards, the female experiences a large influx of testosterone, and she changes character. She breaks into song, and she competes aggressively with males for a winter territory. In effect, for a few short months, females become males and both sexes compete on an equal footing for space and resources. This period of the year perhaps explains why both sexes show the red breast. It also makes the robin a remarkable creature, with a highly unusual approach to territoriality. In no other British passerine do females sing, or defend their own territories. And very few British birds are so strongly territorial during the winter.

From January onward, female robins join forces with a male, and it is the timing of this switch-over that is governed by food supply. In high quality territories with plenty of food this can happen shortly after Christmas, but where food is scarce it is not possible for two birds to forage over the same space until February or March. Every year, 20% of male robins advertise their territories in vain, and fail to find a mate. Consequently, this places a high premium on defending the best possible patch to maximize chances of attracting a female early in the New Year.

OSB: Any other tidbits about how robins survive the British winter?
JT: For a species so intimately linked in our minds with cockiness and aggression, one of their most surprising habits is communal winter roosting. Up to twenty individuals, who have fought fiercely all day over the boundaries of their territories, will gather at dusk in a dense shrub to sleep. This behaviour is very rarely observed, as robins gather at their winter roosting sites at dusk. While it is not fully understood why they do this, they presumably gain some anti-predator or thermoregulatory benefit by abandoning their daytime disputes and roosting communally.

OSB: Where do your current research interests take you?
JT: My early forays into robin biology, involving bracing winter fieldwork in Cambridge Botanic Gardens, led to a fascination with the tropics, where things just seemed a whole lot warmer. I've been working there ever since, tackling a range of questions in evolutionary biology and conservation biology. Perhaps the biggest and most challenging of these is Darwin's "mystery of mysteries" - what processes cause species to multiply and to assemble into communities.

This puzzle takes me to the richest rainforests of Peru, where up to 500 bird species sometimes occur in a square km. Here, with studies of song, behavioural interactions and phylogenetics, I am finding out some fascinating things about how signals mediate their co-existence, and in turn how co-existence has influenced the evolution of signals. With a bit of luck and a lot of comparative genetics, I also hope to discover the key to that old chestnut: how they all got there in the first place. 

Dr Joseph Tobias is a postdoctoral researcher at Oxford's Department of Zoology.

‘Epigenetics is a blossoming area of science,’ says Dr Chas Bountra, chief scientist at the Structural Genomics Consortium (SGC) in Oxford. ‘We believe it will deliver new drugs for many common diseases, such as diabetes, cancer, and inflammatory diseases.’

The study of epigenetics tries to understand changes in the action of genes that are inherited but occur without any changes in the DNA sequences.

By understanding these mechanisms of genetic control at a level above the DNA code, researchers believe they can identify factors that lead to many diseases where this control goes awry.

Dr Bountra and the SGC are heavily involved in a new public-private partnership to systematically set about investigating the most important proteins involved in epigenetic control and kick-start the drug-discovery process. They, along with the Departments of Chemistry and Biochemistry, a government laboratory in the USA and pharmaceutical giant GlaxoSmithKline plc (GSK), have just received a £4.1 million investment from the Wellcome Trust over four years.

The funding will allow the partnership to generate chemical compounds or ‘probes’ that bind to 25 different epigenetic control proteins and stop them working. This allows the role of each protein to be understood and whether blocking the target could have a benefit in treating disease. Some of the chemical probes could turn out to be starting points for drug development.

‘To dissect the disease processes in the body, we need good tools, and chemical probes are some of the best,’ explains Dr Bountra.

The chemical probes will be made freely available to anyone in academia, biotech, or pharma. ‘We will provide a complete set of information along with samples of the probes – the three-dimensional structure of the protein target and the probe bound to the target, how to make the probe, and the pharmacological/biochemical activity of the probe – so that everyone has everything they might need to take this work forwards.’

This is a highly unusual step, says Dr Bountra. ‘Intellectual property in pharma has always been closely guarded and knowledge is not shared with other people. Here, GSK is contributing their compounds knowing the results will be made public. This is a major shift in the way pharma works with academia.’

The grant from the Wellcome Trust will be used to recruit 16.5 new employees in Oxford: 10.5 in the Structural Genomics Consortium, five in Chemistry and one in Biochemistry. The SGC will generate the target proteins, determine the structure of the proteins and the bound chemical probes, and all three Oxford groups will be involved in measuring the pharmacological activities of the probes.

The National Institutes of Health Chemical Genomics Center (NCGC) in Bethesda, USA, will screen their set of 270,000 compounds to see if any bind to each of the protein targets, absorbing all the cost themselves (which can be around £0.5 million for each screen: the agreement covers 20 high throughput screens), while GSK will be committing eight chemists at their sites in producing the chemical probes.

‘This will make a big impact in this area of science and drug discovery,’ says Dr Bountra. ‘I feel we will have been successful if we facilitate drug discovery in the area of epigenetics – if biotech and pharma take up these probes and start moving them into the clinic. On the way we will no doubt produce some first rate publications in collaboration with world leaders in epigenetics and drug discovery.’

A helping of seasonal science in which Oxford's Federico Formenti tells me about research into the origins of ice skating:

OxSciBlog: How were ice skates invented/what were they used for?
Federico Formenti: Archaeological evidence shows that ice skates have been used for at least 4000 years. Where skates were invented and why is still a matter of debate in the field of archaeology. The most ancient ice skates are found across a vast area of Europe (from Germany to North Scandinavia) and some argue that they were made for fun. I think that 4000 years ago, in countries where there were long freezing winters and only a few hours of light per day (and neither supermarkets nor cars!), people would have used these few hours of light to get food and any other items necessary for their survival, rather than to have fun.

My doctoral research suggests that they were invented in the South of Finland, where the number of lakes per square mile is the highest in the world. In this environment humans were forced to find a way to cross lakes (so as to avoid having to walk around them).

On average, compared to walking, travelling with ice skates between two locations offered a much greater gain in Finland - in terms of time and energy required for the journey - than anywhere else in the world. This led me to suggest that they were invented in order to save the time and energy required for necessary journeys.

OSB: What materials do we think they used to make them?
FF: The most ancient ice skates were made of animal bones, mostly horse and cattle. This varies quite a lot, depending on the animals which were present in the area where the skates were made. Apparently, the size of the bone skate matched the size of the skater's feet (kids had shorter bone skates).

Bone skates did not have a blade so the movement pattern of 'ice skating' looked rather different from modern ice skating technique: propulsion came from the upper limbs pushing a stick on the ice between the legs whereas the lower limbs, being kept almost straight, provided balance. The first wooden skates with a metal blade were made 'only' in the 13th Century AD, when people skated using their lower limbs as a means of propulsion; since our lower limbs are more powerful than our upper limbs, we could than skate at higher speeds (similar to running) for a limited effort, and making turns became easier.

OSB: How well did these early skates work?
FF: Measured speed on bone skates was similar to walking on firm terrain for a similar effort, although this was measured on a track with curves, so it's possible this was underestimated. Going on a straight line on bone skates is very easy (and relatively fast), but making turns requires slow speeds (because they do not have a blade).

Federico Formenti is based at Oxford's Department of Physiology, Anatomy & Genetics where his current research is in studying how the human body responds to low oxygen. 

As part of our 'Any questions?' campaign a question sent in by Silvan Griffith is answered by Claire Vallance from Oxford's Department of Chemistry.

------------------------------------------------------

Q: I have always understood that pressure, temperature and appearance of a substance are directly related: the higher the pressure, the lower the temperature, the more solid it becomes due to the atoms moving less. Water reaches its highest density at +4°C. If one would decrease the pressure, would it become colder or warmer?

Claire Vallance: You are correct that both the pressure and the temperature affect the ‘appearance’ or ‘solidness’ of a substance. However, temperature and pressure are not locked together in quite the way you describe.

An equation known as the phase rule (described in detail in any thermodynamics textbook) predicts that for pure water we can vary both pressure and temperature independently. For example, liquid water may be turned into solid water (ice) either by reducing the temperature or by increasing the pressure sufficiently.

When we reduce the temperature we reduce the kinetic energy of the water molecules, so that they move around more slowly. Within a liquid, molecules are constantly colliding with each other, and at high temperatures the collisions are energetic enough that the relatively weak attractive forces between individual molecules have little effect and the molecules simply bounce off each other.  However, once the temperature approaches the freezing point, collisions occur so slowly and with so little energy that the intermolecular forces take over and the molecules start to stick together.

As the temperature falls even further we eventually end up with the molecules locked into the lattice structure of solid ice. A similar result may be obtained by reducing the pressure, but in this case the mechanism for crystallisation into the ice structure is not that the collisions become less energetic (assuming that we keep the temperature the same as we increase the pressure), but that the molecules are forced closer together on each collision.

Intermolecular forces are strongly dependent on distance, and are much stronger at smaller separations. At high enough pressures, water can be made to form ice even at room temperature and beyond.

This behaviour can be summarised on a phase diagram. The phase diagram for water [part of which is shown below] reveals which phase (solid, liquid or gas) is most stable at a given temperature and pressure.

 At low temperatures and high pressures (top left of the diagram), the solid phase is most stable, while at low pressures and high temperatures (bottom right of the diagram) the gas phase is most stable.

At intermediate temperatures and pressures we have the liquid phase. The lines, or ‘phase boundaries’, on the diagram show conditions under which two phases can exist together in equilibrium. For example, the line separating solid and liquid allows us to determine the freezing point of a substance at any pressure, and the line separating liquid and gas does the same for the boiling point. We can use the diagram to explore what would happen in your example of water at 4 °C.

Starting at a pressure of 1 atmosphere and a temperature of 4 °C (filled circle), reducing the pressure corresponds to following the vertical line in the direction of the arrow – note that the temperature doesn’t change. As we reduce the pressure, the liquid will become less dense, until when we reach a low enough pressure (just less than 0.01 atm on the diagram, the pressure you would find at an altitude of 32,000 m!) we cross the phase boundary between liquid and gas, and the water evaporates.

------------------------------------------------------

Dr Claire Vallance is based at Oxford's Physical & Theoretical Chemistry Laboratory.