Features

Patterns are everywhere in the animal kingdom but understanding the mechanisms that produce them is a real challenge.

In this week's Physical Review E Thomas Woolley and Ruth Baker of Oxford University's Mathematical Institute report on mathematical simulations that may explain how stingrays generate their distinctive spots.

I asked Thomas about this work and the relationship between maths and nature's spots and stripes:

OxSciBlog: What are the challenges in reproducing these patterns?
Thomas Woolley: The biology! Mathematically, we have a number of models that produce qualitatively the same patterns as animal skins. However, there are currently no specific biological examples which can be unequivocally linked to the maths.

The specific difficulty with stingrays, which is why they have not been considered before, is that their spots have a dark halo around the central spot. The BVAM model is one of the first biological pattern formation systems that is able to produce this dark halo.

The Barrio-Aragon-Varea-Maini (BVAM) model is a set of mathematical equations that models two chemicals which are able to diffuse and react in a domain. They are generalisations of all other such pattern forming systems and therefore very complex. They are used as a way explore a wide variety of chemical dynamics from two simple equations.

OSB: How did you set out to reproduce stingray patterns?
TW: It was in fact the other way around. We were able to produce the patterns and thus wanted to find a biological example that exemplified them.

As mentioned above, there are a great number of mathematical models which can produce animal pigmentation patterns. A particularly large group of such models are called Turing systems (named after Alan Turing who originally considered them).

Normally, these models give only a single particular type of pattern; either spots or stripes. The BVAM model, we considered, is a generalisation of all of these. This means that it can give many different types patterns (see below). It was noticed that the spots that the model produces were not of the normal Turing type (Turing type spots do not have the dark halo).

In a precursor paper it was shown that these are very similar to a stingray’s skin pattern. We generalised the results that appeared in the previous paper and showed that the spots can exist for a larger range of parameters than previously thought.

OSB: How could your results be tested?
TW: The analysis we have done on the model connects the parameters of the equations and the size of the spots. An initial test would simply be to measure the spots on a large number of stingrays. By varying the model parameters we can vary the size of the simulated spots, however, if we are unable to produce the correct size, which correspond to reality we immediately show that the BVAM is not the system behind stingray patterning.

The best way would be to try and discover the stingrays’ chemical signals which produce the spots and, either, show it corresponds to, or differs from, the BVAM equations. This is currently a difficult problem for biologists, which is why there are currently no clear biological examples. In the end, biologists will probably never be able to “prove” a model is correct only that it fits current data and is thus not incorrect.

Hence, if biologists are able to alter the system to produce a pattern that the BVAM system cannot reproduce we must conclude that the BVAM system is not biologically accurate and return to the drawing board. However, a disproved model is still important as it implies what adaptations are needed in order to generate a more refined system.

OSB: What do these results tell us about biological mechanisms?
TW: The patterning systems we use tend to rely on diffusion as the key mechanism. In terms of evolution this is important as it suggests that no energy from the animal is needed to produce the pattern; only to create the chemicals which will naturally diffuse.

Another important aspect is that it suggests many types of fish depend on the exact same model to produce their individual patterns. This supports the idea that evolution has simply picked the simplest mechanism, whilst mutations and various types of selection will specify how the model behaves.

OSB: How could what you learned be applied to other problems?
TW: The BVAM system, because of its general nature, not only has applications in animal skin patterning, but it has also been linked to a model of cardiac regulation and, further, it has the potential to be used in encoding digital information (the spots can act like binary digits).

The particular use of my work will be the analytical methods that we have produced, which can be used on many similar problems in various fields. Further, it broadens the number of patterns which can be treated mathematically. For a long time we have been able to consider spots and stripes, but we are the first to consider the biological applications of the dark-ringed spot. 

 Thomas Woolley is based at Oxford University's Mathematical Institute.

New research at Oxford University has shed light on how mammalian egg cells divide. The findings may lead to improvements in women’s chances of giving birth to healthy babies as they get older.

After the age of 33, the likelihood of a woman producing healthy eggs and embryos declines dramatically but little is known of the reasons why.

In younger women, the pairing off, or segregation, of chromosomes in precursor cells  usually produces eggs with a complete set of chromosomes. Fertilisation of these eggs would tend to produce viable embryos.

But, as women age, chromosome segregation becomes faulty and eggs can be produced with the wrong number of chromosomes.

This increases the probability of miscarriage or birth defects such as those associated with Down's syndrome. But if ways can be found to safeguard chromosome division for longer, this deterioration could be delayed.

‘If we find it’s possible for egg precursor cells to regenerate the proteins and the structures responsible for chromosome cohesion we could, in the long-term, develop therapeutic advances giving older women a better chance of giving birth to healthy children,’ Dr Kikuë Tachibana-Konwalski of Oxford’s Department of Biochemistry says.

‘By the time women reach their 40s, a third of their eggs may already have the wrong number of chromosomes. So as society changes and more women concentrate on their careers and delay childbirth, our research could be extremely important.’

Dr Tachibana-Konwalski’s study has revealed which proteins are responsible for binding chromosomes in mammalian egg cells. Her research, funded by the Medical Research Council, Cancer Research UK and the Wellcome Trust, also found that it is possible to trigger the separation of chromosomes by destroying these proteins.

In a paper published in the journal Genes & Development, Dr Tachibana-Konwalski and colleagues describe how the introduction of an enzyme into the egg cells of genetically modified mice can trigger the opening of the protein ring holding together chromosomes and in turn trigger chromosome segregation.

Together with Professor Kim Nasmyth, Head of Oxford’s Department of Biochemistry, and Dr David Adams of the Wellcome Trust Sanger Institute, Dr Tachibana-Konwalski suspects that the deterioration of this protein ring, which contains the protein Rec8, is causing chromosome mis-segregation in the eggs of older women.

Finding a way of regenerating the chromosome cohesion brought about by Rec8 and enabling the proteins to bind for longer, could increase the chances of older women producing healthy embryos.

It is unlikely that chromosome cohesion is regenerated over a few weeks, the research shows, but future studies will assess whether it might take place over a longer period.

‘The most mysterious cells in the body are the egg cells in women,’ says Dr Tachibana-Konwalski. ‘They provide nearly everything for the next generation but are difficult to study because there are so few of them. If we find that chromosome cohesion can be regenerated it will be a hugely significant discovery, especially for women who want to have children in their late thirties and forties.’ 

A recent expedition to the Indian Ocean returned with a new species of squid and a haul of strange and unusual creatures netted from the deep.

I asked the expedition's Principal Scientist, Alex Rogers from Oxford University's Department of Zoology, about the team's bumper catch and what these deep-sea animals can tell us about ocean ecosystems, biodiversity and mitigating man's impact on our oceans...

OxSciBlog: How & where did you discover this new squid species?
Alex Rogers: The squid was captured on an expedition to explore the waters around the seamounts of the South West Indian Ocean Ridge. This cruise was undertaken on the RV Dr Fritjof Nansen as part of a wider IUCN project to examine the management of high seas fisheries in the southern Indian Ocean funded by UNDP and the GEF.

Seamounts are hotspots of biological activity in the deep oceans and we were particularly interested in what was driving these ecosystems, especially the populations of commercially fished species such as alfonsino, a large red deep-sea fish.

I was the Principal Scientist on the expedition and we covered a distance of 5000km observing the movements of animals in the waters around the seamounts using acoustics and then sampling the reflective layers we observed (deep-scattering layers) with a variety of nets. The new squid species was captured with an enormous mid-water trawl called an aakra trawl by the Norwegian crew of the vessel. 

OSB: What were the challenges involved in identifying it as new?
AR: Identification of deep-sea fish, squid and crustaceans is complex and requires specialist knowledge. Squid, in particular, are only studied by a few specialists and they use a variety of features to identify species, such as the shape of the beak, the form of the tentacles and suckers, the shape of the mantle and cartilage within it.

To complicate matters further, the South West Indian Ocean Ridge, even now, is almost unexplored in terms of biology and biogeography. We therefore gathered a body of expert scientists to identify the material from the cruise in a workshop in South Africa funded by the Total Foundation and the Census of Seamounts Project [CenSeam]. We were extremely lucky to have a squid expert on the team, Vladimir Laptikhovsky from the Falkland Islands Fisheries Department. He had a very exciting week, identifying a fifth of the worlds squid fauna within our collection from the expedition, including the new chiroteuthid squid and possibly several other new species, although they will require further study.

The squid is a deep-water species and has some very unusual features in terms of its body shape and may even represent a new genus or even family. We also identified close to 200 species of fishes, some of which may also be new to science, but which will require further study by scientists. 

OSB: What can this discovery tell us about biodiversity in the oceans?
AR: The deep ocean is poorly understood and yet is facing human threats from fishing, oil production, and climate change. There is even now a proposal to mine the South West Indian Ocean Ridge for minerals associated with deep-sea hydrothermal vents. This and the other discoveries of the expedition demonstrate that we have much to still learn about these mysterious ecosystems.

This squid is not a small animal, it is several feet long, making it more impressive that it hasn't been seen before, especially given that squid are not particularly diverse as a group and have very wide distributions. It may also tell us something new about the evolution of this particular group of squid. 

OSB: What do you hope you may find out of the other specimens?
AR: The samples show that communities across this part of the southern Indian Ocean vary considerably moving from north to south. They also show a major effect of the seamounts on the structure of the ecosystem. Our acoustic surveys appear to support a theory that seamounts act as giant traps for migrating layers of zooplankton and small fish, crustaceans and squid. This allows resident predators, including commercially valuable deep-sea species such as alfonsino, orange roughy and armourhead, to feast every day on these species as they migrate up and down in tune with dusk and dawn.

In South Africa we identified the members of the deep-scattering layers and sampled the stomachs of the predators we captured. These will provide the proof that these fish populations are being sustained in the way we have predicted. Contained in our marvellous haul of specimens are important data on the distribution of the fauna of seamount ecosystems and the wider communities of the water column, further new species, species newly recorded for the Indian Ocean, and information on the growth, reproduction and development of marine animals.

In other words this single expedition has made a significant contribution to our understanding of the ecosystems of the high seas. Next year we will return to the same seamounts on a NERC-funded expedition to explore the animal life living on the seamounts. This is even less well know than that of the water column and more exciting discoveries will certainly be made.

Professor Alex Rogers is based at Oxford University's Department of Zoology.

 January sees the release of The King's Speech, a movie in which Colin Firth stars as George VI, portraying the King's struggle to overcome his stutter.

But how much do we understand about the processes that cause stuttering?

Yesterday, Kate Watkins of Oxford University's Department of Experimental Psychology presented new research at the Neuroscience 2010 conference into the brain activity of people who stutter and how it differs from the brain activity of other people during reading and listening.

I asked Kate about her latest work and how close we are to understanding what causes this condition...

OxSciBlog: What had previous research found out about the brain activity of people who stutter?
Kate Watkins: Previous studies have scanned the brains of people who stutter while they speak out loud in the scanner. Several abnormal patterns of activation are seen under these conditions: people who stutter activate right hemisphere regions that are homologous with regions active during speech production in the left hemisphere; brain regions responding to the speech sounds produced (auditory cortex) tend to be underactive in people who stutter compared to fluent speakers; subcortical brain regions involved in movement planning, sequencing, timing and execution (eg the basal ganglia and cerebellum) are typically overactive during speech production in people who stutter.

The majority of studies done previously have used overt speech production. This may or may not have included stuttered speech in the people who stutter (one curious effect of scanning that we observed was a reduction in stuttering when speaking inside the scanner). Using overt speech production raises some problems for data acquisition but, more importantly, it is not possible to tell if the abnormal patterns of speech production are a cause or a consequence of stuttered speech. 

OSB: How did you study brain activity in this new research?
KW: We used functional MRI to scan the brains of people who stutter and fluent speaking control participants during three conditions: (i) while they listened to sentences; (ii) while reading sentences silently; (iii) while reading sentences and listening to the same sentence being read by someone else. We wanted to know if the same patterns of abnormal brain activity would be seen in people who stutter even when they are not producing speech.  

OSB: What differences did you find in brain activity between people who stutter and non-stutterers?
KW: We found abnormal patterns of activation in people who stutter in auditory and motor brain areas but these patterns were different to those seen previously and during speech production. In contrast with previous findings, the auditory areas of the brain that responded to listening to other people speaking showed more activity in the people who stutter than the controls; when listening to self-produced speech this region typically had less activity in stutterers than in controls.

Together these findings suggest the reactivity of the auditory system is abnormal in stutterers. When reading, people who stutter showed abnormally reduced activity in a motor circuit that included the left inferior frontal gyrus, putamen and supplementary motor area. The activity in this motor circuit was reduced even further when listening to speech. This circuit is involved in initiating and sequencing of movement.

Even though the people in our study didn't produce any movements related to speech, this circuit is still involved in internal speech and its activity is abnormal in people who stutter. Our findings can therefore be considered to be characteristic of the stuttering brain rather than simply reflecting differences related to stuttered speech production. 

OSB: What is the next stage in your research?
KW: Next we want to look at the circuitry between the abnormal brain regions in more detail. The integration of auditory information in the motor system seems to be important for highlighting the functional abnormalities that we saw. We want to look further also at how the known fluency enhancers work in people who stutter - that is we need to figure out their mechanism of action in the brain and possibly implement methods for improving the therapeutic efficacy of this enhancement. 

OSB: What other research needs to be done if we are to understand what causes stuttering?
KW: Longitudinal studies starting early in childhood when stuttering starts are required. Ideally, we would like to study children soon after they start to stutter and follow up those who spontaneously recover and those that persist in stuttering. Genetic studies also have potential to shed light on the causes of this disorder. Mutations in three genes have been identified already that occur in about 10% of people who stutter but how they cause stuttering is unclear.  

So why do so many people end up at risk from such natural hazards? And is there anything scientists can do to help limit the human cost?

I asked Kate Donovan, from Oxford University's Department of Earth Sciences, about her experiences studying responses to Mount Merapi and about research at Oxford into hazard communication...

OxSciBlog: What are the challenges involved in communicating risks from natural hazards?
Kate Donovan: A proactive and prepared society is likely to be more resilient to a hazard event. But in order for that community to be prepared they must firstly accept that they are at risk and secondly have the resources available to be prepared. But many societies are vulnerable because they are poor and don't have access to these resources. Tragically, between 1991-2005, over 90% of deaths resulting from natural hazards occurred in developing countries.

How people perceive their own risk will influence their motivations and actions before and during an event. It is not a simple case of providing more information to at risk communities but instead requires a complex and long term change in culture towards the hazard.

Another important element of risk perception and communicating risk is trust. If civil authorities or scientists are not trusted then risk communication will break down. Trust relies on various elements including local culture, political history, the mismanagement of past events and false alarms. In Indonesia past political turmoil has brought extreme suffering and therefore the population tend to be suspicious of authority. During a visit to Mt Merapi volcano last year, local people told me that they would never evacuate because they did not trust the local authorities, indeed some villagers would rather rely on their own knowledge of the volcano and their traditional warning signs.

OSB: What did you learn from your work on Mt Merapi?
KD: The people who live high on the slopes of Mt Merapi are at extreme risk from the regular eruptions that occur at this very active volcano. The current eruption is an example of this volcano's potential for destruction and the local populations’ vulnerability. The villagers living on the volcano have a great respect for Mt Merapi and many (especially in the more isolated regions) believe that the volcano is home to supernatural creatures that have the power to control eruptions. These creatures can also provide warnings before an eruption and therefore protect certain communities, if those communities respect the creatures. The rich culture linking the people to the volcano provides a coping mechanism, a way of explaining and living with the dangers they face.

In the news at the moment there are images of people being rescued from the volcano. Most of those who were initially killed or are badly injured were most likely returning to their homes and villages during the evacuation to tend to abandoned livestock. These extremely poor communities rely on subsistence farming and their livestock are all they have. Returning during the day to their homes to collect grass for their cattle is considered entirely acceptable. These people have to balance the risk between definitely losing their income if their livestock starve or possibly losing everything in an eruption. It is so sad that these wonderful, intelligent and kind people are now homeless and suffering.

OSB: How did these experiences influence your current research?
KD: My experiences at Mt Merapi were life changing. Living with those who have so little and yet fed and housed me for months was humbling and made me even more determined to have a career in disaster risk reduction. So after completing my PhD at the University of Plymouth in January this year I searched for research opportunities that focussed on practical interdisciplinary opportunities. I was delighted to find a project within the Department of Earth Sciences here at the University of Oxford that is actively engaging with local authorities to reduce the impact of flood hazard. My current research is focused much closer to home as I am currently working on Project FOSTER that aims to bridge the gap between local authorities in the UK and flood science.

OSB: Why is it vital to combine physical & social science approaches?
KD: Disasters occur at the interface of society and nature, in other words a disaster does not occur unless a hazard interacts with society resulting in death or economic loss. Therefore in order to reduce the risks people face it is essential that disaster research explores both sciences. It is easier to consider interdisciplinary research as focussing on finding a solution using the best available methods from both the physical and social sciences. With a growing global population and the potential threat of climate change increasing the number of extreme hazard events there is a growing need for researchers with a fluency in both sciences and universities across the world are slowly responding to this.

Various institutes have been created to bring disciplines together and the University of Oxford is a good example of this with large initiatives such as The Smith School of Enterprise and the Environment and also the Oxford Martin School, but also smaller enterprises such as The Hazards Forum.

OSB: How do you hope hazard communication research at Oxford will develop?
KD: A challenge for any institution is cross-disciplinary communication and collaboration. Universities have conventionally created disciplinary silos and so topics that span disciplines, such as hazard and disaster research, tend to fall between fields. But recently, with a move from research funders towards more accountable research and communicating science to a wider audience, Universities must encourage interdisciplinary collaborations and effective dissemination of results.

At Oxford there are many initiatives that encourage collaborations and one of these is the new Hazards Forum that aims to bring researches together from across the university who are interested in hazards and disaster research. This Forum provides an opportunity for communication, collaboration and learning between subjects and was founded jointly by colleagues in the Department of Earth Sciences and The School of Geography and the Environment. Hopefully hazard communication between subjects will encourage practical and effective research that will improve the quality of life of those living in hazard regions.

Dr Kate Donovan is based at Oxford University's Department of Earth Sciences.