Features

Normally we think of metals in our water supply as a bad thing, but when it comes to trace amounts of metals welling-up from the ocean’s depths we should count ourselves lucky that they appear.

That's because metals such as iron and zinc are essential to all kinds of marine life – they act rather like a 'fuel' that powers ocean ecosystems. On 17 October an Oxford University-led expedition will set sail for the South Atlantic to study these ‘micronutrient’ metals.

'Because they are present in seawater at such low concentrations they are difficult to measure but with this new expedition we hope to revolutionise our understanding of the metal 'micronutrient' cycle and gain insights into the past, present and future of Earth's climate,' explains Gideon Henderson of Oxford University’s Department of Earth Sciences and the Oxford Martin School, who is leading the UK-GEOTRACES consortium.

Gideon will lead a team of 24 scientists from 10 UK institutes aboard the Royal Research Ship Discovery, one of NERC’s research vessels, collecting samples and carrying out experiments on the 39-day cruise from Cape Town to Montevideo.

The RRS Discovery will head to the South Atlantic where the ocean is particularly rich in life, but where the sources of micronutrients are a mystery. By collecting samples, and making a wide range of measurements both on board and back in the lab, the research team hopes to learn how the metals enter and leave the ocean, and how their abundance in seawater influences marine biology.

Much of our understanding of past climate comes from measurements of marine sediments but understanding how climate information is reflected in the chemistry of the sediments is essential if we are to interpret this evidence correctly.

Understanding the cycle is also vital if we are to assess whether proposed geo-engineering schemes, such as 'seeding' the oceans with iron to increase their carbon uptake, might work.

'Changes in marine ecosystems also have a wider impact: these ecosystems are vital for food production, biodiversity, international development, tourism, and pollution management,' Gideon tells me.

'Any changes in the cycling of micronutrients in the South Atlantic will have an impact not just on the local area but also on the natural resources, economies and standard of living of countries around the world.'

UPDATE: Read regular updates of the mission's progress on the UK-GEOTRACES blog.

Tumours seem to pacify our immune system by tapping into our bodies’ codes, but we may be able to use this trick against them in our bid to hunt them down.

Melanomas are not only one of the most aggressive types of human tumours but the cancerous cells are able to survive and proliferate despite the body’s best efforts to destroy them. Professor Vincenzo Cerundolo, Director of the MRC Human Immunology Unit at the University of Oxford, has been trying to establish how melanomas survive these attacks.

Our bodies are continuously fighting off infections and invading cells. We have many methods of defence at our disposal as part of our immune system - a huge, highly organised army complete with different types of troops and manoeuvres.

The ranks include a particularly potent type of cell called a neutrophil. Neutrophils are packed full of powerful enzymes that can destroy cells at the same time as recruiting reinforcements to the area (inflammation). But, as in any battle, there are always fears over friendly fire so the immune system can quickly issue messenger proteins that revert the troops to being passive so they don’t damage the body’s own cells.

The problem is that, as with any code used in war, the enemy can crack it. Vincenzo’s team recently discovered that melanomas have done just that as they also produce the messenger protein that signals inflammation to stop.

The protein concerned is called serum amyloid A (SAA) and it switches neutrophils from being aggressive to being anti-inflammatory. In other words, the melanomas seem to have evolved a way to manipulate the body’s own safety mechanisms so that they aren’t destroyed.

Unfortunately for melanomas though, producing anti-inflammatory neutrophils isn’t the protein’s only effect. The latest work from Vincenzo’s group, published in Nature Immunology, shows that SAA also affects another type of immune cell called an invariant natural killer T cell (iNKT) where it has exactly the opposite effect, jumpstarting the immune response  by activating antibody-producing cells  (B lymphocytes) and recruiting more cells capable of destroying tumours and virus infected cells (Killer T lymphocytes).

Vincenzo explains that 'SAA is used in the body to fine-tune the immune system, keeping the body alert to attack but stopping it from doing any unintended damage. The question of how melanomas can beat the immune system's defences has been asked for a really long time, and melanomas have many tricks up their sleeves, but we think their use of this protein is a really important one. But finding out that SAA also interacts with these iNKT cells was a really unexpected result and it means there’s a possible way of restoring the anti-tumour immune response.'

In healthy people the number of neutrophil cells is already an order of magnitude above iNKT cells, but in cancer patients there are even fewer iNKT cells to attack the tumours. Vincenzo says, 'it’s very early days but there are drugs that can promote activation of iNKT cells which we might be able to use to get patients’ immune systems to fight back.'

'Our bodies are set on the slightly cautious side as we don’t want our immune systems to damage the healthy parts of our body, but if we know what we’re doing we could activate the immune system in the places and at the times that we need it. SAA is secreted during inflammation from any acute or chronic problem such as influenza or arthritis. If we can manipulate iNKT cells sufficiently it could be a very exciting prospect indeed, not just for cancer but for many other inflammatory diseases.'

Researchers from Oxford University are well represented on the Eureka 100: a list of the most important contemporary figures in British science.

The list, compiled by The Times to celebrate the first anniversary of its science magazine Eureka, features 11 Oxford figures from all areas of science.

The highest entry goes to Jocelyn Bell Burnell [15], after her comes John Bell [20], then Richard Dawkins [25], followed by Kay Davies [29]. Breaking into the 40s and 50s are Andrew Wiles [41] (arriving in 2011) and David King [54] whilst the 60s and 70s sees a run of prominent Oxford scientists: Peter Ratcliffe [60], Colin Blakemore [64], Graham Richards [65] and John Krebs [71]. Last but not least, friend of OxSciBlog Marcus du Sautoy [76] makes it a bumper crop of research talent.

One thing's certain: it's sure to generate plenty of discussion about who made the list and who didn't, and how you measure the influence of scientists, at a time when the role of British science is under the microscope. And that can only be a good thing.

Let us know which Oxford scientists not featured above should have been on the list and why by adding a comment below.

New genome research at Oxford University could change the way scientists view our evolution.

The relationship and emergence of the three ‘domains’ of life – the three founding branches of the Tree of Life to which all living cells belong – has been much disputed. Two of these domains, Bacteria and Eukaryotes (which includes all animals, plants and fungi) are familiar but less is known of the third: these organisms are collectively called the Archaea.

Some species of Archaea are adapted to live in extremes such as the boiling sulphur springs of Yellowstone National Park or the high salt concentrations of the Dead Sea. Others, such as the group Thaumarchaea, are found in more moderate environments including the warm surface waters of oceans.

Steven Kelly, of Oxford University's Department of Plant Sciences, tracked the evolutionary history of the three domains by analysing more than 3,500 families of genes in the Archaea, Bacteria and Eukaryotes. He and his colleagues found that Eukaryotes are most closely related to the Thaumarchaea.

The study, recently published in Proceedings of the Royal Society B, also suggests that the metabolism of the earth’s first organisms was based on methane production. 'That’s a really important discovery because it gives us a real insight into how life got started, which is one of the biggest questions in evolutionary biology,' Steven said. 'This is a step change in the way people think about how life on earth developed.'

The ability to link advances in our knowledge of evolution to changes in past atmospheric and environmental conditions will enhance our knowledge of how life is adapting to the changing environmental conditions we see today, Steven believes.

This new research suggests that Archaea are as ancient as their name suggests. Evidence from geology and genetics, coupled with the findings, suggests that Eukaryotes evolved between 2 and 2.5 billion years after Archaea, which emerged around 3.5 billion years ago.

An experiment to test if slime moulds can design efficient railway networks has won a team, including Oxford University researchers, an Ig Nobel Prize.

We reported on the original research back in January, but I asked team-member Mark Fricker of Oxford University’s Department of Plant Sciences why scientists study these strange organisms, what they can teach us and how they take 'networking' to a whole new level:

OxSciBlog: What makes slime moulds so interesting to study?
Mark Fricker: The acellular slime molds represent a very unusual life form. The whole organism is one single giant cell, albeit containing many nuclei, that can grow to be many centimeters in size. In the wild, it spreads as a pulsing network seeking out food sources such as bacteria, fungi or dead insects that it engulfs and then digests.

Even with a low power microscope or a hand lens it is possible to watch the shuttle flow of cytoplasm coursing through the system that somehow manages to resolve into an efficient transport network. Although it has no brain or nervous system, its exploratory behaviour and the network itself is highly responsive and continuously adapts to whatever is happening around it.

It's a great system to then challenge with different stimuli to see how it reacts. If things get really bad, it simply dries out and waits until things get better or forms spores that can spread to other sites.

OSB: Why is it useful to compare their networks with manmade ones?
MF: We already know that the slime mold is capable of solving certain abstract problems, such as the shortest path through a maze or finding the most efficient way to connect geometric arrangements of different food sources using Steiner points, that is computationally difficult to achieve.

However, we wanted some way to determine whether understanding such behaviour could have utility beyond simple fascination with such elegant biology. Providing a real-world test problem that we already know the answer to seemed to be one way to discover whether the lessons we might learn from the slime mold could have applications elsewhere.

OSB: What can we learn from how slime moulds build networks?
MF: As there is no obvious distinct communication system within the organism, we infer that the network is able to form and adapt based solely on local information. The overall behaviour emerges from the collective interaction of the constituent parts.

Control by such a decentralised system is in marked contrast to management through a central control centre that has to assimilate all the necessary information, processes it and then send out instructions to achieve a co-ordinated response. We also infer that the lack of a "brain" means the rules governing local behaviour are likely to be simple, but iteratively give rise to apparently sophisticated problem-solving behaviour, very similar in principle to the way that complex behaviour can emerge in social insects such as termites or bees.

Decentralised control systems running with simple rules offer attractive possibilities to establish readily scalable, low maintenance, robust and adaptable network architectures. Equally, we have to be careful in pushing these analogies very far as, although the slime mold networks match the infrastructure networks at one level, they develop using very different processes that would be completely impractical to replicate in all but a limited number of real-world scenarios.

Nevertheless, there may be interesting general concepts that emerge such as communication of fuzzy information over long distances and information through conservation laws that are intrinsically associated with physical flows. It is also interesting that many systems in biology show oscillatory behaviour that may assist in co-ordination of behaviour, whilst most man-made control strategies deliberately try to suppress such phenomena.

OSB: How did you feel when you heard you’d won an Ig Nobel?
MF: Great. I think they are a wonderful vehicle to make science accessible and entertaining.

OSB: What do you hope to investigate next as part of this research?
MF: We have a number of different organisms, including fungal mycelia, that also produce elegant networks that appear to be tuned to a different balance between cost, efficiency, resilience and control complexity.

They also form their networks by completely different methods to slime molds at the molecular level, yet there are already interesting similarities including the conservation flows and pulsating behaviour at a macroscopic level. This again hints at some universal principles that govern this type of network formation that can be achieved with a wide variety of different components. This is also important as it suggests that the control principles can also be transferred to non-biological systems as well.

Unravelling these processes and modelling the critical components needs creative links between biologists, physicists, mathematicians and engineers. This network of network people is what we are currently building.

Mark Fricker and colleagues won this year's Transportation Planning Prize.