Features

Tiny flashes of blue light from beneath the icy South Pole could help scientists uncover the origins of cosmic rays and neutrinos.

These flashes occur when neutrinos created by cosmic rays strike nuclei in the ice, releasing energetic muons which travel through the ice faster even than light can -  producing a burst of Cherenkov radiation. This is detected by IceCube, a 'telescope' made up of thousands of optical sensors buried up to 2.5km deep in the Antarctic icecap. This location is ideal because under the huge pressure at such depths the ice is free of air bubbles and very clear.

Subir Sarkar of Oxford University's Department of Physics leads the British involvement in IceCube, he told The Telegraph's Richard Gray: 'Cosmic rays were discovered 100 years ago, but we still have no idea where they come from. At first glance, IceCube seems like a crazy experiment. How can you study the sky when you bury your detectors a mile beneath the ice? But it gives us a new way of tracing their paths back to their source.'

'The real excitement is that neutrinos and cosmic rays will reveal an entirely new way of looking at the universe and allow us to see into places where we haven't been able to before.'

'Currently we have no way of peering into black holes through the dust and gas that surrounds them, so if high energy neutrinos are being emitted from their fringes, then we can 'see' into places we haven't been able to before.'

IceCube isn't due to be completed until 2011, when all the optical sensors will have been installed, but as early as 2006 its detectors began to pick up the flashes of neutrino collisions. It's already identified an area of the sky near the constellation of Vela as a prolific source of cosmic rays.

Being able to spot these very rare neutrino collisions could help us understand the nature of the dark matter thought to make up around 23% of our Universe.

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.