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A scientific consortium engaged in research relevant to the discovery of new drugs has been given a big boost, with almost £31 million in new funding over four years. Two new drug companies have also joined the public-private partnership, showing the recognised importance of this work to the drug development process.

The Structural Genomics Consortium (SGC) is based at the University of Oxford and the University of Toronto, Canada. It was formed in 2004 and carries out research on human proteins relevant to disease, supported by funding from the public and private sector. It makes all of its findings available to the global research community without restriction.

Since it was launched, private funding to the SGC has increased greatly as pharma companies recognise what the consortium can offer. A majority of the new funding now comes from private sources.

‘Pharma is increasingly recognising that early drug discovery is too complex for each organisation alone, and this is a way of accessing academic and clinical expertise,’ says Chas Bountra, chief scientist for the Structural Genomics Consortium at the University of Oxford.

The new members of the SGC are Eli Lilly Canada and Pfizer Inc, who join fellow drug companies GlaxoSmithKline and Novartis. The four companies will also provide more than £5.7 million worth of in-kind contributions, primarily medicinal chemistry resources.

The other consortium funders include the Canadian Institutes for Health Research, the Ontario Ministry of Research and Innovation and the Wellcome Trust.

The SGC scientific programme for the next four years will see its core strength in determining the three-dimensional structures of key human proteins continue. Understanding the structure of proteins can help guide the discovery and design of new drugs that interact with the proteins. Since its inception, the SGC has contributed more than 1,300 high quality three-dimensional protein structures to the public domain. 

But the SGC will also broaden its work, following successful pilot projects in ‘epigenetics’. There is broad agreement that a better understanding of epigenetics – changes in the activity of genes that occur without any changes in the DNA sequence – may eventually yield new approaches to diagnosing and treating a number of important diseases.

The research will generate antibodies against proteins involved in epigenetic control, and identify chemical compounds that block the action of specific human proteins. These tools – protein structures, antibodies and chemical inhibitors – are important early steps that facilitate the drug discovery process, targeting proteins involved in disease processes.

About £13.5 million of the new funding will be coming to the SGC base at the University of Oxford. Research here will focus on generating novel chemical inhibitors for epigenetic proteins thought to be involved in cancer, inflammatory and neuropsychiatric diseases. These inhibitors could help determine how things like diet, injury, toxins and other environmental factors affect disease susceptibility and progression at a molecular level through epigenetics, explains Chas Bountra.

Importantly, all the tools will be provided openly to the research community worldwide, rather than being locked up within the walls of any one institution or company. Providing structural data and chemical reagents for free should speed the process of research and drug discovery and avoid any duplication of effort.

It is clear drug companies are increasingly buying into this idea. Indeed, Chas believes this model of an open public-private partnership seen in the SGC can be extended much further down the drug development process, taking novel drug candidates as far as the critical early-stage clinical trials where many stand or fall.

He has spoken about how pooling the resources of academics, public funders and private drug companies, and openly distributing results in the absence of any protected intellectual property, should play an increasing role in coming up with the new drugs we need in crucial areas like dementia.

Most drug candidates will still fail at this early stage but the approach stops repetition and reduces exposure of patients, says Chas Bountra. And with those new drugs that work, pharma can then do what it’s good at – finding the best molecule, developing it, and taking it to market.

Scientists around the world are working on the building blocks that could be linked up to create a useful quantum computer.

Single photons are at the heart of many of these schemes and, at first glance, seem like ideal information carriers: once encoded they are able to travel across galaxies and bend around suns without this information being lost. 

Yet the quality that makes them such safe information carriers – the fact that they interact only very weakly with their environment – is exactly what makes them difficult to work with. 

‘The problem comes when you want to create, manipulate or measure this information,’ Nathan Langford of Oxford University’s Department of Physics and the University of Vienna tells me. ‘Because a single photon doesn't interact much with atoms or other photons, it is very hard to do these things efficiently. And efficiency is the key to the whole idea of quantum computing.’

Nathan is part of a team that report in Nature a new way of getting round this problem: ‘The main goal of our approach, which we call coherent photon conversion, is to make photons talk to each other.’ 

In standard single-photon experiments a laser beam is shone into a nonlinear material. Very rarely (usually around once in every 1,000,000,000 interactions) this will cause a laser photon to split into two photons: this effectively turns the material into a random (probabilistic) photon generator. However, such randomness isn’t very helpful if you want photons to process information in a predictable manner.

So instead of a powerful laser beam the researchers examined what would happen if a single photon was shone into a nonlinear material. 

‘You might expect that putting in a single photon would make it even less likely to get two photons out at the other end, but in fact we found the opposite,’ Nathan explains.

‘With a single photon input, if you make it interact with the material strongly enough, we found that it should be possible to make the probability of one photon splitting into two rise to 100% - something that is impossible with a laser input.’ 

What was even more surprising was that, by carefully tailoring the type of input light, the same sort of interaction with this type of material could produce many of the other essential processes needed to build a photonic quantum computer: this includes creating entanglement between two photons, and converting a weak laser beam into good single photons. 

‘With our approach, it turns out that it should be possible to build a single device with four I/O ports (perhaps all on a single photonic chip) which can provide all of the building blocks required for efficient photonic quantum computing just by varying what type of light is sent into each port. This should make it much easier to build more complex designs.’

He points out that this technique isn’t limited to optical systems; it could also be used in superconducting microwave circuits and optomechanics – for example, preparing high quality phonon states in the vibrations coupling mirrors or dielectric membranes to light fields. 

At the moment the work is still in the early stages: the big question is whether the efficiencies the team predict could actually be achieved. 

‘So far we have focussed on a simple model of the nonlinear interaction to illustrate the basic ideas of the scheme, but now we need a more detailed model which incorporates other real-world effects, such as finite response times of the nonlinear medium and photon loss,’ Nathan tells me.

‘From a design perspective, we now need to identify what can be done to optimise the nonlinear coupling, both by improving the materials and engineering a better design.’ 

The big challenge, he says, is to move beyond eye-catching ‘proof-of-principle’ demonstrations of the elements required to build a quantum computer and build a device which can do something that cannot be achieved with a normal computer.

Nathan comments: ‘With photons, the biggest roadblock to achieving this is still the issue of efficiency: efficiency in creating and detecting photons, as well as in manipulating them. Hopefully our work can help provide a useful step in this direction.’ 

A new free app for Android phones launched today is giving people the chance to get closer to the world’s largest physics experiment.

People who download the 'LHSee' app will, for the first time, get live data from collisions at the Large Hadron Collider (LHC) sent direct to their mobile phone, as well as being able to find out more about how its instruments work and play a ‘Hunt the Higgs boson' game.

The app is the brainchild of Oxford University scientists and is supported by STFC: I asked one of its creators, Alan Barr from Oxford University’s Department of Physics, about squeezing the LHC onto a mobile:

OxSciBlog: Where did the idea for the LHSee app come from?
Alan Barr: For ages I’d been thinking that with the amazing capabilities on modern smart phones we really ought to be able to make a really great app - something that would allow everybody to access the LHC data. In fact I’d sounded out a few commercial companies who said they could do the job but I found that it would be expensive, and of course I’d have to teach their designers a lot of physics. So the idea was shelved.

Then, a few months later, I had one of those eureka moments that make Oxford so wonderful. I was having a cuppa in the physics common room, and happened to overhear a conversation from Chris Boddy, one of our very many bright Oxford physics graduate students. He was telling his friends that for fun he was writing some small test games for his Android phone. Well you just can’t let moments like that pass.

Within no time we’d put together a proposal, STFC had provided a small grant award, and Chris had a prototype app running on his own phone. 

OSB: What will the app enable users to do?
AB: We’ve squeezed in a bunch of cool features. If you want to learn about the science of the LHC, then you can play with the animated tutorials about the LHC and the ATLAS detector. Then you can stream videos to your phone about the construction of the detector, and its operation.

When you’ve become an expert, you can play the ‘Hunt the Higgs’, game, to test your skills. Personally, my favourite is being able to view collision events in 3D on my own phone. 

OSB: How close does it get you to real science at the LHC?
AB: This is the nice part. When we showed the app to our colleagues at CERN they loved it. They agreed that, for the very first time, we could make a live stream of actual honest-to-goodness genuine LHC events available to the public.

You can get them in real time, so you are seeing the results as they happen. Of course we can’t send you every collision – the LHC produces GigaBytes of data each second. But what you get is real, and you can see all the detail. Amazingly it’s even possible to pick out the individual proton-proton collisions.

OSB: Why is an app a good way to communicate LHC research?
AB: As of May 2011 there are well over 100 million activated Android devices out there. I kept coming back to this idea that as well as being phones these are really small pocket-sized computers with network connections and touch screens.

Focusing on these features, it seems completely natural to design an app to explain how we do our science, and the beauty of the physics we hope to uncover.

OSB: What do you hope users will take away from using the app?
AB: When the LHC was started, the news media used eye-catching images of the collisions to accompany their stories. It was an obvious thing to do because the pictures are so interesting, but it can be hard to get beneath the surface.

With the app you can understand what these strange shapes and lines actually mean - in terms of the individual particles detected. Our hope is that people can now appreciate the pictures and the science all the more - and perhaps even be a little inspired.

Dr Alan Barr is based at Oxford University’s Department of Physics.

Curious snake-like forms have been spotted in cells from many different species across the evolutionary tree. Now Oxford scientists have shown they exist in human cells as well.

This apparent ubiquity across species from bacteria to mammals suggests the structures perform a crucial function in the cell. But how and why they form, and what role they play in the cell remain anyone’s guess.

Three groups reported observations of the snakes in cells from a whole range of different species at around the same time in 2010, including Dr Ji-Long Liu’s group at the Department of Physiology, Anatomy and Genetics in Oxford.

Ji-Long and colleagues named the structures ‘cytoophidia’ because of how they looked under the microscope: cytoophidium is ‘cell snake’ in Greek.
‘Cytoophidia have heads and tails and can move around. They really do look like snakes,’ explains Ji-Long Liu.

‘I reported the finding in fruit flies early in the summer of 2010,’ he says. ‘Two months later, two papers – one from Zemer Gitai’s group in Princeton and the other from James Wilhelm’s group at the University of California, San Diego – reported similar snake-like structures in bacteria, brewer’s yeast, flies and rats.’

Ji-Long’s group has now reported the first observation of these cellular structures in human cells in the Journal of Genetics and Genomics.

‘Amazingly, these snakes occur across the tree of life, from bugs to humans,’ he says. ‘Cytoophidia are found inside cells, and sometimes they stay near the surface of cells. It looks like the number of snakes in a cell is tightly controlled.’

But what are they? Having initially observed the snakes in cells from fruit flies, Ji-Long got curious and decided to follow up the chance observation. He took advantage of a collection of fruit flies at the Carnegie Institution Department of Embryology [CIDE], where he worked before moving to Oxford.

In this collection, individual proteins in the fruit flies had been labelled with a fluorescent green marker, allowing Ji-Long to identify the cell snakes as containing the enzyme CTP synthase.

CTP synthase is a crucial but not necessarily glamorous enzyme, one of many such enzymes involved in necessary biological processes that keep our cells ticking over. In this case, the enzyme plays a role in making the molecule CTP, a building block that helps make up DNA and RNA. The CTP molecule also crops up in fat metabolism.

‘If the generation of CTP goes wrong, it could cause a lot of damage to the cell,’ Ji-Long says.

It is possible to speculate about why an enzyme would form these long filament structures in cells. For a start, cells are a long way from just being bags of biological molecules and enzymes that float around freely, magically carrying out their many functions, reactions and chains of metabolic processes.

The cell needs an organised structure to bring this industry of biochemical reactions under control, with many processes cordoned off in separate chambers, capsules and compartments. It allows related reactions to be better controlled and regulated, with the right concentrations of the different molecules brought together in the right environment. After all, you don’t just bung all the ingredients into a chemical engineering plant, a brewery or a baking tin imagining that the recipe will be fine.

‘The beauty of a well-organised cell has not been appreciated by everyone. Without the structure, a bag of the same amounts of all the molecules would not do the same thing as a living cell,’ explains Ji-Long. ‘Compartmentation could be a general feature for many enzymes in a cell,’ he believes.

He notes that six enzymes that produce a set of biomolecular building blocks called purines are known to cluster in a specific compartment, and studies have shown that many proteins are found localised in just one part of a cell. ‘It seems to us that the filaments are necessary for the CTP synthase enzyme activity,’ he says. ‘We are trying to understand the relationship between filament-forming and the overall function of the enzyme in a cell – but we have no clear answer yet.’

His research group has found some drugs that affect the assembly of the CTP synthase enzyme into snakes, making the filaments appear in human and fruit fly cells. This approach could give a new handle to study the snakes’ function in the cell.

Another interesting question is why the enzyme forms a snake-like filament or rings rather than spheres or just irregular capsules. These shapes have different surface-to-volume ratios, which might give some clues as to the difference this makes to the activity of the enzyme.

‘It would be fascinating to know more about what the role of the cytoophidium plays in regulating the production of CTP,’ says Ji-Long. He notes that the CTP synthase enzyme is found in larger amounts in many types of cancer cells, and that his group has shown that some potential anti-cancer drugs can promote the formation of cytoophidia. But that’s still a long way from showing that this is important clinically or that there might be medical applications in understanding more about these cell snakes.

At the moment the existence of these snakes is an interesting observation that opens up intriguing new research questions, but what role the snakes play in our cells is unknown. Ji-Long also suggests that it’s ‘very likely’ there are other enzymes packaged up in structures in the cell that we don’t know about yet. ‘Time will tell!’ he says.

A project in which volunteers hunt online for new planets NASA may have missed is publishing its first results which show some remarkable finds.

Planethunters.org, which was set up by Oxford University physicists, working with colleagues at Yale University and the Adler Planetarium, has enabled over 45,000 armchair astronomers to find candidates for new alien worlds by searching data from the Kepler mission.

Reporting on just the first month of the project, which was launched in December 2010, researchers believe there is a ‘95% chance or greater’ that volunteers have already spotted two new exoplanets NASA originally discarded: other finds include a previously unknown eclipsing binary star system.

‘Kepler's mission is to work out what kind of worlds might be out there - that's why it's so important we rescue those that have slipped through the net,’ Chris Lintott of Oxford University’s Department of Physics, one of the scientists leading planethunters.org, told me.

The Kepler telescopes detect new planets by recording tiny changes in the brightness of stars. This dimming is caused by planets crossing in front of them. Volunteers visiting planethunters.org sort through thousands of images of stars searching for examples of these dimming events (known as 'transits') which NASA’s small team of experts may have missed.

The project builds on a series of highly successful Oxford-led citizen science projects, such as Galaxy Zoo, Old Weather, and most recently Ancient Lives, which have shown that ordinary web users can beat computer algorithms at spotting patterns and interesting phenomena.

Carolyn Bol, from Helensburgh in Scotland, is one of the planethunters.org volunteers who has made a discovery that will soon see her name appear on a scientific paper.

‘The fact that all that data is readily available to everyone makes the ‘hunting’ a bit of a game thanks to all of those connected remotely from the comfort of their home,’ she explains. ‘I have a full time job as an optometrist so I really enjoy having this hobby where I spend time hunting for planets when I have some spare time.’

It was while sorting through images of stars that Carolyn made her discovery:

‘The moment I saw the pattern I screamed “A PLANET !” just because all the light curves I was classifying were very similar, some pulsating etc but there were no distinctive transits until that pattern appeared and I was sure I was watching a planet. I marked the transits, I favourite it and went to discuss it.’

It led to some interesting discussions with her work colleagues, such as whether you should name a planet when it might have been named already by an alien civilisation.

In fact Carolyn’s planetary candidate would later be found to be not an alien world passing in front of a star but something almost as exotic: an eclipsing binary system containing two stars in which one star’s orbit sees it pass in front of its companion.

It just goes to show that when you unleash an army of citizen scientists part of the fun is not knowing what they will turn up.

‘I think it's incredible that only 16 years after the first planets were discovered around other stars, it's now possible to find candidates using nothing but a web browser,’ Chris tells me.

‘With new data being released just last week, there are plenty more surprises hidden in the data for planet hunters to find.’