Features

With 14 more cases of swine flu announced at the weekend, the number of confirmed cases in the UK has reached over 100. With another 155 possible cases still under investigation, this is likely to continue to rise steadily in the next days and weeks.

Thankfully, the spread of the virus seems to be contained to some extent. That may be down to various things, such as the time of year, how easily it’s passed on, people’s awareness of swine flu and its symptoms, their willingness to get in touch with their GP and stay at home, and the antivirals given to those affected.

While we may have to wait until the autumn and flu season before we will know more about how this outbreak will run its course, how will the antiviral drugs Tamiflu and Relenza help us?

‘These antivirals definitely work,’ says Professor Elspeth Garman of the Department of Biochemistry. She co-authored an influential paper in Science in 2001 calling for countries to stockpile the drugs in advance of an increasingly likely flu pandemic. ‘As long as they are taken at the beginning of an infection (within 48 hours of evident symptoms), they will stop the flu virus in its tracks.’

‘Relenza, made by GlaxoSmithKline, is a nasal spray, while Roche’s Tamiflu is taken as a pill,’ she explains. ‘This makes Tamiflu easier to take, which is important if large numbers of people will be given it, but mutations to Tamiflu can more easily arise that will make flu resistant to the drug. However, it is still very likely to be effective in any pandemic.’

A flu virus has lots of protein molecules on its surface which come in two types: H and N. There are various subtypes of H and N proteins, which gives each strain of influenza A its name: e.g. H5N1 for bird flu and H1N1 for swine flu. The H proteins act like Velcro, and flu infections start when viruses cling to receptors on cells in the top of the throat using the H protein. The cells are taken over and used to produce more viruses before the cells eventually burst and die.

But for the newly-made viruses to go on and infect other cells in the body, the viruses have to be released from the dead cell by chopping off the receptors on the outside of the dead cell to stop the Velcro-like H proteins sticking to them. This is what the N proteins do: they snip the receptors to allow further infection of other cells. It’s this step that Tamiflu and Relenza prevent. The drugs bind to the N proteins and stop them snipping the receptors on throat cells, with the result that infection of further cells in the body is largely stopped.

Professor Garman’s group has been involved in determining the structure of different N proteins from various strains of flu. By building a 3D picture of the proteins using a technique called X-ray crystallography, they can see the crucial pocket where the antiviral drugs bind in atomic detail. This approach was used in designing the drugs in the first place, and gives a good understanding of whether the drugs will work with other N proteins beyond N1.

‘We’re currently working with a colleague at the National University of Mexico on an N6 protein from a flu virus in an English duck,’ says Professor Garman. ‘This connection with Mexico where this swine flu outbreak began is entirely coincidental, but it does bring home the relevance of all of this. There are also two Mexican graduate students currently working in my lab. Thankfully, their family and friends are all fine.’

With antiviral drugs that work, concern shifts slightly. ‘With these antiviral drugs in hand, a pandemic becomes less of a science issue and more a public health problem,’ Professor Garman says. ‘It becomes all about stockpiles of the drugs and distribution in the event of a pandemic.'

Developing countries will find this a problem, as keeping large stockpiles is expensive and who do you give access to the scarce tablets? This is an issue Greg Katz picked up, writing for the Associated Press.

The other problem Professor Garman highlights is picking up swine flu, or any other flu strain, early enough. ‘What we really need is a quick, cheap, over-the-counter test to pick up whether people have flu early on. That way we can distribute antivirals only to those that really do have the disease.’ 

A rare herd of desert elephants is under threat from the worst drought in 26 years.

Researchers from charity Save the Elephants report that the 350-450 elephants of the Gourma region in Mali are being forced to trek ever-longer distances in search of water.

Many elephants have already died and juveniles are thought to be most at risk as their trunks cannot reach down to the remaining water in the deepest wells, according to STE scientist Jake Wall.

Iain Douglas-Hamilton, a Research Associate at Oxford's Department of Zoology and founder of the charity Save the Elephants, has been monitoring these herds for the last three decades.

Iain said: 'In the Gourma region of Mali are the last elephants living in the Sahel and they are northernmost in Africa. Their range has shrunk drastically since the 1970s due to climate change and overstocking of livestock which has degraded the habitat.'

'These elephants have the longest migration route of any in Africa and move in a counterclockwise circle of about 700km. At the height of the dry season there are only a handful of shallow lakes left to them until recharged by rains in July and August.'

This year the water levels are extremely low in the Gourma region due to uneven rainfall in 2008. The most important of these lakes, Banzena, is the lowest it has been since 1983 when it dried up completely.

STE is appealing for funds to help them get water to the elephants to help them survive until the first predicted rains arrive in early June. 

It’s the summer event that’s got it all: an evening spent chatting to top Oxford University scientists and enjoying drinks and food at Magdalen College in a picturesque venue beside the river.

Held on 3 July 2009, this free evening reception for delegates from the World Conference of Science Journalists (WCSJ 2009) is a fitting end to a day trip that takes in some of the UK’s most important science facilities including Diamond, CLF, ISIS and JET.

There are still places available to sign up for both the Oxfordshire tour and the evening event, which will be hosted by Marcus du Sautoy.

As regular readers will know Marcus is both Professor of Mathematics and Simonyi Professor at Oxford: his recent TV appearances have included BBC Two’s Horizon and BBC Four’s The Story of Maths, and he writes a regular column for The Times newspaper. You can also follow him on Twitter.

The guest list is also likely to include such leading Oxford academics as Professor Sir Richard Peto, Professor Lionel Tarassenko, Professor Fred Taylor and Dr Ian Goldin.

in previous posts space scientist Fred Taylor has given us insights into everything from weather and volcanoes on Venus to new Moon missions, while engineer Lionel Tarassenko has told us in the past about technologies that can remotely monitor human health and even the health of jet engines.

More top Oxford scientists are telling us they’d like to come along every day, so it’s likely to be a very special opportunity.

OxSciBlog will be giving regular updates on the attendees and stories on offer at what should be a fun and fascinating occasion, so watch this space for more details.

A team of Oxford computer scientists recently won a silver medal at the ICPC event in Stockholm where contestants from around the world battled it out to solve tough programming challenges against the clock.

I quizzed the team about what they did, what they learned and how computer science could improve your poker skills... 

OxSciBlog: Why do you think competitions, such as the ICPC, are important for computer scientists?
Frantisek Simancik: Programming competitions are here mainly to attract new students to computer science.  I myself learned my first programming language only because I wanted to take part in a local contest at my secondary school.

They give us a chance to compare our abilities with others and motivate us to learn more and to be better. You know what it's like: give your students homework and they will look at it on the day before the deadline, set the same problems as a competition and they will strive to be the first to solve them. And they will even want more!

OSB: What was the most challenging problem you managed to solve?
FS: The difficulty of problems varies widely from ones you can solve immediately after reading to those on which you can spend hours on in vain. Often there are even problems which don't get solved by anyone at all.

The most difficult problem we solved this year was probably "videopoker" from the regional round of the ICPC. The goal of the problem was to write an optimal poker player whose actions would always maximise its expected winnings. While this may sound as a fairly standard task, we were the only team who managed to make their program work in time.

Daniel Bundala: One of the most challenging problems we solved is the following: A botanist has a plant initially consisting of a single cell of a given type. For each type, you are given the sequence of cells the cell of that type divides into. For example, a cell of type A may divide into the cells of types BABC, cell of type B into CC and so on.

The plant evolves in stages and every cell divides according to the rules at the beginning of each stage. The task is to determine whether this cell structure converges to a stable state. This problem is from a regional round and it is one of the practice problems we solved before the world finals. 

OSB: What did you learn from the competition that you will apply to your studies at Oxford?
Daniel Bundala: Programming competitions have helped me a lot in developing my problem solving skills. Although the problems concentrate mostly on algorithms, which form very important but quite small part of modern computer science, I have noticed that solving this type of problems improved my skills in solving problems in completely different areas as well. And as the exams are approaching, it is quite handy to be able to solve difficult problems quickly.

Also, ICPC is a team competition and I have learnt that it is very beneficial to have someone to discuss the problems with. Very often, we were presented with a problem I would barely solve on my own, but working on it with the teammates, we managed to solve it reasonably quickly.

OSB: What area of computer science are you most passionate about? Why?
Jakub Zavodny: It was programming competitions that introduced me to computer science, so originally I was most interested into algorithms, complexity theory and discrete mathematics. Although I mostly stayed on the theoretical side of computer science and in mathematics (in fact all three of us study the Maths & Computing joint course), I enjoyed many new areas to which the university lecture courses exposed me. I will be starting a PhD with the Quantum Computer Science group here at Oxford this fall. 

Jakub, Daniel and Frantisek are based at the Oxford University Computing Laboratory.

Like everyone we've been watching hour-by-hour as the swine flu situation changes, as new cases are confirmed and the WHO delivers the sort of warnings usually seen at the beginning of a disaster movie.

The problem is, as Oxford's Angela McLean explains in this excellent article in The Daily Telegraph, whilst the risks are all too real we simply don't know how this real-life movie will pan out or whether we are heading for disaster, for a rather-worse-than-usual flu season, or for something in between.

Angela writes: 'This uncertainty is the main problem – and why it is utterly impossible to make confident predictions about what will happen next, or how many cases we can expect.'

'Influenza is notorious for its ability to mutate. The good news is that the British flu season has passed, so there is a very real possibility that we will see very limited transmission in the UK for many months.'

'This is what happened in the most recent pandemic, in 1968: that strain of the disease arose in south-east Asia in July, but no epidemic in the UK until December. Although it was unusually long-lasting, with high numbers of cases occurring into mid-April, the 1969 epidemic was never particularly intense. There was no great excess in mortality: indeed, I was a schoolchild in London and have no memory of the pandemic at all.'

She says that so far the UK Government is doing the right things, using anti-viral drugs in a targeted way to try and contain the outbreak. But, of course, the real test is likely to come if large numbers of people become infected demanding treatment at the same time or previously unknown reservoirs of the disease are suddenly discovered.

Up to this point media reporting of the possible pandemic has been reasonably accurate and appropriate to the very serious threat a virulent flu outbreak poses. But, as time goes on, this 'if.. factor' inevitably becomes a problem for reporters who want solid facts and definite opinions: at the moment most scientists don't have either and need to analyse both the virus and the pattern of the outbreak before they can say more.

As Ben Goldacre notes in The Guardian the backlash against the gloomiest predictions has already begun as journalists begin to worry that perhaps they have over-hyped what is an extremely difficult story to get to grips with.

At the moment we have more questions than answers and we're being told to do little more than take basic hygiene precautions, which is a pretty uncomfortable place to be: everyone wants to know 'yes, but will it be like the last pandemic in 1968? or more like the 1957 one? and what about the terrible 1918 flu?...'

We may not be able to answer these questions yet but Angela closes her article by telling us to remember that all these 'ifs' mean that, like some past pandemics, this one may not be the disaster we all fear:

'The only good pandemic is a pandemic that is over. Since that is not on offer, the next best thing is a pandemic that causes a mild disease and has a very low fatality rate.'

'We have seen from the past 10 days that things can change fast, but for now it is still possible to hope that if a pandemic does emerge, it will be mild enough that today's schoolchildren will scarcely remember it come the great panic of 2049.'

Professor Angela McLean is co-director of the Institute for Emerging Infections at Oxford University and is based at Oxford's Department of Zoology.