Brain research ‘needs new strategy’

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Lab miceBrain cells in a dish may eventually replace animal research

A shift in medical research priorities is needed to meet the challenge of fighting dementia, say animal welfare campaigners.

Animal research into new therapies has failed to deliver after years of experiments, they say.

Instead, labs should focus on human-based models such as brain scanning or studies of cells grown from patients.

Alzheimer’s Research UK said no single approach could provide answers to such a complex disease.

Dr Gillian Langley, a scientist and consultant for the animal welfare charity, Humane Society International, is among a growing body of scientists who believe current research relies too much on animal models.

“Medical research is at a tipping point,” she told BBC News.

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The exciting thing about this technology is that you can take cells from patients with a disease and then try to create a model of this disease in a dish”

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Dr Eric Hill
Aston University

“There is a growing realisation that animal studies are not producing the breakthroughs we’re hoping for.”

Writing in the journal Drug Discovery Today, she said it was time to consider a new paradigm in medical research for Alzheimer’s disease.

Research was “lagging behind” areas such as toxicology, which is using research based on molecular disease pathways within cells and new tools such as genomics, she said.

“We need this overarching view – a new framework so we can use these 21st Century tools.”

Model of complexity

Other scientists say human-based methods of research – once regarded as experimental – are already yielding results.

Professor Paul Lawrence Furlong of Aston University carries out brain imaging to try to develop methods for early diagnosis of dementia in patients.

“We’re supportive of initiatives to move forward the human model for good scientific reasons,” he said.

“In Alzheimer’s, at the cellular level, many animal models are valuable. When we move up the model of complexity, there’s a point at which the animal model becomes less valid.”

Brain cells in a dish

He said researchers such as Dr Eric Hill at Aston University are working on stem cells (the master cells of the human body) to model Alzheimer’s disease, which may eventually provide more robust ways of testing treatments.

Brain cells grown from a person's skin cellsBrain cells grown from a person’s skin cells

“These cells were once skin cells that have been reprogrammed to become stem cells again,” said Dr Hill.

“They were then differentiated to become neurons and astrocytes.

“The exciting thing about this technology is that you can take cells from patients with a disease and then try to create a model of this disease in a dish. “

However, the charity, Alzheimer’s Research UK, said no single approach could address such a complex disease, with animal models, brain studies and new approaches involving stem cells all playing a role.

“Alzheimer’s is a complex disease and the brain is a complex organ,” said head of research Simon Ridley.

“I think modelling that in a cell culture or in a dish, it’s a huge challenge.

“So I think it’s very important that we keep a broad perspective on the different types of research, really to try to answer specific questions.”

Dr Laurie Butler, of the University of Reading, added: “With the number of those affected by dementia set to triple over the next 30 years it’s vital we examine all research approaches if the UK is going to fulfil Jeremy Hunt’s promise of transforming the country into a ‘global leader’ in fighting dementia. “

Article source: http://www.bbc.co.uk/news/health-27315707#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Largest fossilised croc tooth found

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The fossilised tooth (front and side) of the Dakosaurus maximusThe fossilised tooth of the Dakosaurus maximus was discovered off Chesil Beach in Dorset and is now housed at the Natural History Museum in London

The fossilised tooth of a prehistoric crocodile has been recorded as the largest of its kind found in the UK.

The 2in (5.5cm) tooth was dredged from the seabed near Chesil Beach, Dorset.

It belonged to an ancient relative of modern crocodiles, known as Dakosaurus maximus.

Researchers from the the University of Edinburgh and curators from the Natural History Museum identified it after it was bought at an online auction by a fossil collector about a year ago.

Artist's impression of a Dakosaurus maximusThe shape of its skull and teeth suggests it ate similar prey to killer whales

The tooth, which has a broken tip, is now in the fossil collection of the London-based museum.

‘Exceptionally dangerous’

Dakosaurus maximus grew to about 4.5m (15ft) in length and swam in the shallow seas of Europe 152 million years ago, according to the team’s research published in the scientific journal Historical Biology.

The shape of its skull and teeth suggest it ate similar prey to killer whales, using its broad, short jaws to swallow fish whole and to bite chunks from larger prey.

Dr Mark Young, from the university’s school of biological sciences, said: “Given its size, Dakosaurus had very large teeth.

“However, it wasn’t the top marine predator of its time, and would have swum alongside other larger marine reptiles, making the shallow seas of the Late Jurassic period exceptionally dangerous.”

Article source: http://www.bbc.co.uk/news/uk-england-dorset-27606864#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Google to build self-driving cars

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Google Self-Driving Car

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Google exhibits its new self-driving cars

Google is to start building its own self-driving cars, rather than modifying vehicles built by other manufacturers.

The car will have a stop-go button but no controls, steering wheel or pedals.

Pictures of the Google vehicle show it looks like a city car with a “friendly” face, designed to make it seem non-threatening and help people accept self-driving technology.

Co-founder Sergey Brin revealed the plans at a conference in California.

“We’re really excited about this vehicle – it’s something that will allow us to really push the capabilities of self driving technology, and understand the limitations,” said Chris Urmson, director of the company’s self-driving project.

He added that the cars had the ability to “improve people’s lives by transforming mobility”.

But some researchers working in this field are investigating potential downsides to driverless car technology.

They believe they could make traffic and urban sprawl worse, as people accept longer commutes as they do not have to drive themselves.

Flexible windscreen

The BBC was given access to the Google team to talk about the secret project, and see early renderings of the car.

It looks almost cartoon-like, it has no traditional bonnet at the front, and the wheels are pushed to the corners.

Google carGoogle says it will initially build 100 prototype vehicles

It will seat two people, propulsion will be electric, and at the start it will be limited to 25mph (40km/h) to help ensure safety.

The most significant thing about the design is that it does not have any controls, apart from a stop/go button.

For early testing, extra controls will be fitted so one of Google’s test drivers can take over if there is a problem.

The controls will simply plug in, and Mr Urmson believes that over time, as confidence in the technology grows, they will be removed entirely.

The front end of the vehicle is designed to be safer for pedestrians, with a soft foam-like material where a traditional bumper would be, and a more flexible windscreen, which may help reduce injuries.

The vehicle will use a combination of laser and radar sensors along with camera data to drive autonomously.

It will depend on Google’s road maps, built specifically for the programme, and tested on the company’s current fleet of vehicles.

Google self-drive carGoogle says it expects its self-drive cars to be on the road ‘within a year’

Ready in a year

Google recently announced that its self driving cars had covered 700,000 miles of public roads in autonomous mode, and that they were now tackling the tricky problem of busy city streets.

The company plans to build a fleet of around 200 of the cars in Detroit, with the hope of using them as an autonomous technology test bed.

“We’ll see these vehicles on the road within the year,” says Mr Urmson.

Advocates claim that autonomous cars have the potential to revolutionise transport, by making roads safer, eliminating crashes, and decreasing congestion and pollution. In the year to June 2013, more than 23,500 people were killed or seriously injured in road traffic accidents in the UK, according to government figures.

Simulation of roadThe view from Google’s self-drive car and its computer during tests

Ron Medford, previously the deputy director of the US National Highway Traffic Safety Administration, and now the safety director for the self-driving car team at Google, believes that number could be drastically reduced by removing the chance of driver error.

“I think it has the potential to be the most important safety technology that the auto industry has ever seen,” he said.

But Sven Beiker, executive director of the Center for Automotive Research at Stanford, cautions that driverless cars may still require human input in extreme circumstances and that people may forget how to operate their vehicles if they do not do it regularly.

This could be particularly dangerous in an emergency situation where the computer does not know how to react, and asks for input from a human who may not have been paying attention, he warned.

“You will not be able to fiddle around looking for the instruction manual in the glove box that you’ve never looked at before,” he said.

He equates it to people who drive automatics forgetting how to easily drive a car with a manual gearbox.

Listeners in the UK can hear more on the potential of driverless cars on Frontiers on BBC Radio 4 on Wed 4 June.

Article source: http://www.bbc.co.uk/news/technology-27587558#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Gene test for heart risk rolled out

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atheroma

A test for a preventable form of heart disease is being rolled out in the UK.

The DNA blood test aims to spot the one in 500 people in the UK who have familial hypercholesterolaemia (FH), an inherited condition that greatly increases a person’s heart attack risk.

Left undiagnosed, up to half of people with FH will develop heart disease before they are 60.

Early treatment can bring risk down to a normal level.

People with FH inherit a gene that causes high levels of “bad” cholesterol (LDL) in the blood.

This can lead to hardening of the arteries and an increased risk of heart disease if left untreated.

A DNA test can check for the presence of the faulty gene.

When people are diagnosed, their family should also be offered testing.

If one person is found with FH, on average half their brothers and sisters and half their children will also have the faulty gene and be at high risk of early heart disease.

‘Huge opportunity’

The British Heart Foundation is funding £1m to pay for nurses so that testing can be extended to eight NHS trusts across England and Scotland, after a successful pilot scheme in Wales.

They are:

  • Royal Brompton and Harefield NHS Trust
  • Royal Free London NHS Foundation Trust
  • South Yorkshire Cardiothoracic Centre
  • Central Manchester University Hospitals NHS Foundation Trust
  • University Hospitals Bristol NHS Foundation Trust
  • North East Cardiovascular Network
  • NHS Grampian/North of Scotland Cardiac Network
  • University Hospital Southampton NHS Foundation Trust

Some parts of the UK, such as the East of England, will not have access to nearby testing services, however.

Prof Steve Humphries, of the British Heart Foundaton, said: “With an estimated one in 200 families carrying an FH-causing faulty gene in the UK, the introduction of cascade testing represents a huge opportunity to identify and treat people before they suffer from potentially life-threatening heart problems.”

Heart UK, The Cholesterol Charity, urged NHS England to launch a national FH testing service.

Article source: http://www.bbc.co.uk/news/health-27586009#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Wasp uses zinc-tip drill to lay eggs

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Parasitic fig wasp boring into fruit

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Lead researcher Dr Namrata Gundiah explains how the wasp uses its zinc-tipped drill

Footage captured by scientists has revealed the power of a parasitic wasp, which has evolved a zinc-tipped drill to bore into fruit.

The wasps penetrate the fruit in order to lay their eggs inside.

A team from the Indian Institute of Science in Bangalore found that wasps’ fruit-drilling and egg-laying tool – which is thinner than a human hair – has teeth enriched with zinc.

The researchers’ study is published in the Journal of Experimental Biology.

The researchers think the fig wasp’s egg-laying technique could inspire the design of new tools for microsurgical techniques.

Microscopic drill

Ovipositor of parasitoid fig waspDetailed electron micrographs revealed the teeth-like structures enriched with zinc

The female parasitic fig wasp bores its way through a tough, unripe fig to find the larvae of other pollinating insects already developing inside. Its own offspring will then feed on these larvae as they develop within the safety of the fig.

Lead researcher Dr Namrata Gundiah said: “She uses her ovipositor… pushing this needle inside [the fruit] at the location, where she has decided to lay her eggs.

“She has to test the chemical environment inside the fruit as she’s doing this, and she wants to complete this process fast, because as you see in [our] video, there are predators nearby waiting for her.”

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It’s the fun of seeing how nature works, rather than finding a utilitarian value for it”

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Dr Namrata Gundiah
Indian Institute of Science

To work out how the wasp managed the arduous task, the team captured images with an electron microscope of the insect’s egg-laying appendage, or ovipositor, revealing that its end resembled a drill bit, complete with sharp-edged tooth structures that enabled it to bore through the unripe fruit.

Taking measurements from this tiny drill bit, Dr Gundiah said, revealed the presence of zinc, and that it “was only at these teeth-like structures.

“So we think the zinc is there to harden the tips.”

Dr Namrata said that the technique could be applied to cut through rock and other hard materials.

“In inhospitable places, this could [provide] a clever way to get samples back for us,” she told BBC News.

“In the end though, it’s the fun of seeing how nature works, rather than finding a utilitarian value for it.

“I’m sure if we look at it long enough, there will be lots of applications that will emerge just knowing how things work in nature.”

Article source: http://www.bbc.co.uk/news/science-environment-27608222#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

$15m computer shows quantum effects

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D-Wave machinesD-Wave released its first commercial quantum computer in 2011, and is set to release a more powerful chip later this year

Scientists says they have obtained the best evidence yet for an important quantum physics phenomenon inside a $15m computer built by a Canadian firm.

D-Wave claims it has built the first practical quantum computer, a type of machine that could solve complex problems faster than is possible today.

Scientists say they have shown that an effect called “entanglement” is present in eight units of quantum information.

Entanglement is a key step towards building a practical platform.

The results have just been published in the peer-reviewed journal Physical Review X.

D-Wave, based in Burnaby, outside Vancouver, has courted controversy with its claim to have built a practical quantum computer, a feat that was thought to be decades away.

In a tangle

Quantum computing exploits the strange physics of quantum mechanics, which takes hold at tiny (atomic or sub-atomic) scales.

The basic units of information in classical computers are called “bits” and are stored as a string of 1s and 0s, but their equivalents in a quantum system – qubits – can be both 1s and 0s at the same time.

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What is quantum physics?

There are things we take for granted about the world around us. Let go of your smartphone and it will fall to the ground. Pull the handle on a drawer and it will open. These familiar rules can be described by the principles of classical mechanics.

But in the late 19th and early 20th Centuries, scientists were beginning to realise that classical physics could not explain certain phenomena seen at very large and very small scales.

This spawned two revolutions: one was relativity and the other quantum mechanics. Early experiments suggested light was a wave, rather than a stream of particles. In quantum theory, light can be both a particle (the photon) and a wave.

One principle central to quantum mechanics is that a particle, such as an electron, can exist in all of its possible states simultaneously – known as superposition. Another important idea is that of entanglement, a phenomenon whereby objects become linked, even if they lie far apart.

But the qubits need to be synchronised using a quantum effect known as entanglement, which Albert Einstein dubbed “spooky action at a distance”.

“This is the first peer-reviewed scientific paper that proves entanglement in D-Wave processors,” Dr Colin Williams, director of business development at D-Wave, told BBC News.

“What’s even more remarkable is that this is the largest demonstration of entanglement in any quantum, superconducting computing scheme so far,” he said. “It’s a big achievement for the field.”

They also showed that the entanglement was stable, persisting throughout a critical operation of the processor.

The vast majority of academic research into this area of computing is based around the model of “quantum gates”. These are the quantum equivalents of the logic gates that form the building blocks of circuits in classical computing.

But D-Wave has taken a different approach known as quantum annealing. On a particular type of mathematical challenge known as an optimisation problem, annealing can, in theory, short-cut classical computers to the best answer.

Working together

The authors of the latest study used one of the qubits as a “probe” to provide information on the other qubits in D-Wave’s processor. Using this information, they were able to calculate how much entanglement there was in the system.

Dr Federico Spedalieri of University of Southern California’s Viterbi Information Sciences Institute and co-author of the paper, said: “There’s no way around it. Only quantum systems can be entangled. This test provides the experimental proof that we’ve been looking for.”

Prof Alan Woodward, from the University of Surrey, told BBC News: “One of the three quantum effects that you need for it to be defined as a true quantum computer is entanglement.”

Calling the result “a big deal”, he added: “It does appear to be conclusive that they have a large number of qubits entangled and they do see to be working together.”

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Quantum computing: A brief timeline

Quantum computer, conceptual artwork

  • 1981 – Richard Feynman of Caltech proposes a basic model for a quantum device
  • 1985 – David Deutsch of Oxford University describes the first “Universal Quantum Computer”
  • 1994 – Peter Shor devises algorithm that could allow quantum devices to defeat cryptography
  • 1998 – First working two- and three-qubit quantum computers are demonstrated
  • 2006 – Scientists develop first working 12-qubit platform
  • 2009 – First universal programmable quantum computer unveiled
  • 2012 – D-Wave Systems reveals a 512-qubit adiabatic quantum machine

D-Wave’s processor uses 512 qubits, but the technique in the latest study was able to characterise only eight qubits.

Sceptics about D-Wave computers such as Prof Scott Aaronson of the Massachusetts Institute of Technology (MIT) say the machines show “pretty good” evidence for entanglement at a local level, but not necessarily on a large scale.

But in response, Dr Williams said there was reason to believe entanglement is pervasive across the processor.

“We could have chosen any part of the processor to do this experiment on,” he explains, adding: “There’s no reason to believe the entanglement is limited to just these eight qubits.

“We’ve done other experiments to determine entanglement in different unit cells and we see similar results.”

Prof Woodward commented: “In quantum physics, one of the really difficult things is to witness something because as soon as you witness something, you interfere with it.

“By being a witness, you have to be careful you don’t become part of what you’re seeing. But the techniques they’ve used are generally accepted as showing what they are able to show: entanglement among a fairly large number of stable qubits.”

However, sceptics doubt that the machines are leveraging quantum physics for any performance boost relative to classical machines.

While entanglement is required to get quantum “speed-up”, they argue that it is perfectly possible to have entanglement without speed-up.

In one study released in 2013, Catherine McGeoch of Amherst College in Massachusetts, a consultant for D-Wave, found the machine was 3,600 times faster on some tests than a desktop computer.

But a study published earlier this earlier year by Matthias Troyer from ETH Zurich in Switzerland and colleagues pitted the D-Wave machine against a standard high-spec desktop computer.

On some tests chosen by the team, D-Wave’s machine was found to offer no performance boost over the regular computer.

However, D-Wave maintains that the tests used by Prof Troyer’s team were not ones where the company’s computer offers any advantage. Indeed, Dr Williams even argues that the random challenges were too easy for the computer, which was designed to tackle a very difficult and specialised class of problems.

Dr Williams said the stability of entanglement revealed in the latest study further underlined that quantum annealing was more robust than the gate model of quantum computing.

Lab devices based on the gate model suffer from dropout, where the qubits lose their ambiguity and become straightforward 1s and 0s. This has in part ensured that quantum computers remain confined to the lab.

Quantum annealing is not as susceptible to this dropout problem, but advocates of the gate model argue that D-Wave’s approach can’t provide the performance boost theoretically possible with gates.

Article source: http://www.bbc.co.uk/news/science-environment-27632140#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Ocean waves influence sea ice extent

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Sensor deploymentThe team placed sensors on the floes to track the disturbance caused by ocean waves

Large ocean waves can travel through sea ice for hundreds of kilometres before their oscillations are finally dampened, scientists have shown.

The up and down motion can fracture the ice, potentially aiding its break-up and melting, the researchers told Nature magazine.

They say storm swells may have a much bigger influence on the extent of polar sea ice than previously recognised.

The New Zealand-led team ran its experiments off Antarctica.

They placed sensors at various distances from the edge of the pack ice, and then recorded what happened when bad weather whipped up the ocean surface.

For smaller waves, less than 3m in height, the bobbing induced in the floes quickly decayed. But for waves over 3m, the disturbance sent propagating through the pack ice was sustained for up to 350km.

“At the ice edge, it’s quite noisy,” explained study lead author Alison Kohout, from New Zealand’s National Institute of Water and Atmospheric Research in Christchurch.

“You have lots of waves coming from all directions with a full spectrum of frequencies. But as the waves move into the ice, this all gets cleaned up to produce one beautiful, smooth wave of constant frequency,” she told BBC News.

“The ice floes bend with the waves, and over time you can imagine that this creates fatigue and eventually the ice will fracture. Interestingly, the fractures tend to be perpendicular to the direction of the waves, and to be of even widths.”

Sea ice Antarctic“The fractures tend to be perpendicular to the direction of the waves, and to be of even widths”

Computer modellers have been trying to simulate the recent trends in polar sea ice – without a great deal of success.

They have failed to capture both the very rapid decline in summer ice cover in the Arctic and the small, but nonetheless significant, growth in winter ice in the Antarctic.

Dr Kohout and colleagues say their experiments offer some clues – certainly in the south.

When they compared observed Antarctic marine-ice edge positions from 1997 to 2009 with likely wave heights generated by the weather during that period, they found a strong link.

For example, where storminess was increased, in regions like the Amundsen-Bellingshausen Sea, ice extent was curtailed.

In contrast, where wave heights were smaller, such as in the Western Ross Sea, marine ice was seen to expand.

One very noticeable aspect of the recent growth in Antarctic winter sea ice has been its high regional variability.

The team says that if models take more account of wave heights then they may better capture some of this behaviour.

Sea ice AntarcticThe recent growth in Antarctic sea ice has been a highly regional phenomenon

The group did try to look for a similar relationship in storminess and ice extent in the Arctic but found there to be insufficient data to draw any firm conclusions.

The geography at the poles is quite different. The Arctic is in large part an ocean enclosed by land, whereas the Antarctic is a land mass totally surrounded by ocean. Many of the ice behaviours and responses are different as a result.

“I think what’s interesting for us in the Arctic is that the ‘fetch’ is increasing – the distance from the shores to the ice edge is increasing,” commented Prof Julienne Stroeve from University College London and the US National Snow and Ice Data Center.

“That would allow the wind to work more on the ocean to produce larger waves that can then propagate further into the ice pack.

“[Another recent paper has already suggested] that wave heights are going to change with increasing distance from the ice edge to the land, and that could have more of an impact on ice break-up.”

Jonathan.Amos-INTERNET@bbc.co.uk and follow me on Twitter: @BBCAmos

Article source: http://www.bbc.co.uk/news/science-environment-27591369#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Crickets muted by evolution, twice

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KauaiThe first discovery was made on the island of Kauai in 2003

To hide themselves from deadly flies, crickets on two Hawaiian islands have evolved an inability to sing.

Ten years ago, two years apart, males appeared on Kauai and Oahu with altered wings, which they would normally rub together to chirp and attract females.

New findings published in the journal Current Biology show that the wing changes are physically different and arose from separate mutations.

This makes the silent crickets a brand new example of “convergent evolution”.

Parasitoid fly and its cricket hostThe fly pinpoints a singing cricket using sound, then leaves maggots which burrow into its back and feed

The killer flies have an unusual ability to pinpoint a cricket’s location using sound.

After finding its victim – a male cricket, singing to attract a mate – a pregnant fly will spray baby maggots onto the cricket’s back, which burrow in, feed, and emerge a week later leaving the husk of the hapless cricket behind.

The presence of these North American flies placed the crickets, themselves relatively recent arrivals from Australia, under pressure to adapt.

In less than 20 generations, a mutation that leaves males unable to sing spread to over 90% of the crickets on the island of Kauai.

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[It] appears to be the blink of an eye in evolutionary time”

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Dr Nathan Bailey
University of St Andrew’s

Because they are mute, these “flatwing” male crickets are hidden from the parasitoid flies and escape being eaten by maggots. That triumph comes at a cost, however, since finding a mate is tricky without a voice. The silent types loiter near the few males still singing away, and intercept females for themselves.

Two years after the Kauai discovery in 2003, flatwing crickets were also found over 100km away on Oahu.

Unusually rapid

Researchers first assumed that the silent crickets had simply travelled the distance – with some help.

“An egg laid by a female in some soil could hitch-hike on someone’s boot,” said Dr Nathan Bailey, whose group at the University of St Andrews led the new study.

flatwing cricketSilent, “flatwing” crickets appeared independently on two islands over 100km apart

The idea that the trait had evolved twice, at almost the same time, seemed far-fetched. “It still seems amazing to me,” Dr Bailey told BBC News.

The first clue was an observation that the mutant, silenced wings on the two islands had two different shapes.

HawaiiOriginally, the team thought the silent crickets might have travelled between the islands

Next, by doing crossing experiments with the mutant crickets, the researchers confirmed that both types of flatwing arose from a single gene on the X chromosome.

Finally, comparing a raft of other genetic markers between the two groups yielded convincing evidence that the two mutations had occurred independently.

“Up until my post-doc Sonia showed me the diagram of nearly non-overlapping genetic markers from each island… I was unconvinced either way about what we were dealing with,” Dr Bailey said.

When the same feature evolves separately in two genetically distinct populations, scientists describe the process as convergent evolution. Another example is the “projectile tongue” of certain salamanders, which appears to have evolved independently on more than one occasion.

cricket wingsBiologists studied the cricket wings under a microscope to discern the newly evolved differences

Dr Bailey said this is an unusual example, because it has happened “in what appears to be the blink of an eye in evolutionary time” and researchers can now watch as the story unfolds further.

“This is an exciting opportunity to detect genomic evolution in real time in a wild system, which has usually been quite a challenge, owing to the long timescales over which evolution acts.”

Article source: http://www.bbc.co.uk/news/science-environment-27592656#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Teams build human protein catalogue

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protein synthesisProteins (in green) are translated from the intermediate molecule RNA (pink) which is copied from our genes

The first two attempts at a database of every single human protein – the “proteome” – have been made public.

This builds on our knowledge of the genome by showing which genes actually produce proteins in which tissues.

One team in Germany and one spanning the US and India have published their proteome maps in the journal Nature, and on searchable, public websites.

Some of the 17-to-18,000 reported proteins arise from stretches of DNA previously thought to be “non-coding”.

Along the vast length of DNA packed inside each of our cells, our genes are the sections which contain the instructions, or code, for making proteins.

“While we have a good idea of what the genome looks like, we didn’t know how many of those potentially 20,000 protein-coding genes would actually make protein,” said Prof Bernhard Kuester, who led the German team at the University of Technology, Munich.

Unexpected results

To find out, the researchers extracted all of the protein from many different samples of human tissues, as well as a number of cell lines. The proteins in that purified mixture were then chopped into small pieces and a technique called mass spectrometry revealed the sequence of amino acids forming each of those pieces.

With a lot of computing power and patience, these batches of protein fragments can be compared with the human genome to make a map, showing which genes in which tissues are “expressed” and producing protein.

human foetusTo index all the proteins that make us human, researchers used a bank of samples including adult tissues, foetal tissues and numerous cell lines

“This is the first inventory, if you like,” Prof Kuester told BBC news, “like a dozen years ago with the first draft of the human genome.”

And just like the results of the Human Genome Project, these data contain some surprises.

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We are definitely going to benefit from putting the two data sets together”

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Prof Akhilesh Pandey
Johns Hopkins University

Both groups found hundreds of unexpected proteins, produced by fragments of ancient genes (called “pseudogenes”) or by lengths of DNA that were not thought to be genes at all.

As well as the newcomers, there were notable absences. “We have good reason to believe that there are hundreds of known, annotated genes that perhaps are redundant,” said Prof Kuester.

The team based in the US and India, led by Prof Akhilesh Pandey of Johns Hopkins University in Baltimore, found evidence for only 84% of the proteins that might be predicted from looking at the genome.

Beyond genetics

Prof Pandey told the BBC it was important to study the proteins themselves, as well as the genes that encode them.

He offered an example of how a researcher, investigating a particular gene, might use one of the new databases: “They can look at the expression and get clues about what it could be doing. For example if a protein is expressed in the foetal gut and not the adult gut, then they might think of some sort of developmental process.”

proteome database screen grabsBoth teams are making their findings available online

The tissue-by-tissue breakdown could also help scientists trying to figure out the actions and side effects of drugs. By comparing the proteome of various cancer cell lines, Prof Kuester and his team have already identified certain clusters of proteins that could increase or decrease sensitivity to cancer drugs.

Dr Kevin Mills, who uses proteomics to study rare diseases at the UCL Institute of Child Health, agrees that it is crucial to look “beyond genomics” at protein levels and how they vary.

“Genetics can’t tell us everything,” said Dr Mills, who was not involved in either study. “This is really important. We’re not static – we’re fluid and dynamic and our proteome changes continually.”

Although they had seen each other’s work at conferences, both Prof Pandey and Prof Kuester told BBC News they had “no idea” they were headed towards publishing simultaneously. They spoke on the phone last week after discovering that both of their studies would grace the cover of Nature.

“We never saw this as a race to be first,” said Prof Kuester. “My interpretation is that when the time is right, somebody’s going to just do it. And perhaps two people are going to do it!”

Prof Pandey compared today’s joint publication to the first draft of the human genome, which was announced by two different teams in February 2001.

Prof Pandey and teamProf Pandey (centre) and his team spent two years generating and analysing their data

“Although both groups came up with similar numbers of genes, the actual list was different,” he said. “We are likely to have less of that confusion, but we are definitely going to benefit from putting the two data sets together.”

In the meantime, both sets of results are freely available online: the work of Prof Kuester’s team is at proteomicsdb.org and Prof Pandey’s team at humanproteomemap.org.

Article source: http://www.bbc.co.uk/news/science-environment-27592655#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

Cane toad relative hits Madagascar

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Asian common toadThe Asian common toad may have hopped a ride in a shipping container to get to Madagascar

A relative of the cane toad, which has devastated wildlife in Australia, has invaded Madagascar, scientists report.

The Asian common toad was first seen on the island in March, and there have been several sightings since.

In a letter to the journal Nature, researchers warn that the arrival of the amphibian could cause “an ecological disaster” and wreak havoc on the country’s unique fauna.

They say that urgent action is needed to remove the toads before they spread.

The fear is that the venomous amphibians could poison local wildlife and carry diseases, such as the deadly chytrid fungus that has killed amphibians around the world.

One of the authors, Jonathan Kolby, of James Cook University in Queensland, Australia, said: “It’s worrying because Madagascar has amazing endemic biodiversity – plants, animals and amphibians that are found nowhere else.

“And this one species has the propensity to damage that.”

Asian common toadThe team believes the toads could cause an ecological disaster for Madagascar’s animals

The amphibians were first seen in Toamasina, the main port of Madagascar. It is thought that they arrived in shipping containers from their native home in South East Asia.

“They are a very hardy and adaptable species,” said Mr Kolby.

“They can handle a long ride on the ocean in a container, and then hop out wherever they end end up. And this is most likely how they got there.”

The fear is that the warty brown creatures could repeat the damage that their relative, the cane toad (Rhinella marina), caused in Australia.

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These animals have never been exposed to Asian toad toxins before”

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Jonathan Kolby
James Cook University

Cane toads, native to Central and South America, were introduced to Australia in the 1930s, initially to control pests, but they are now widespread and number in their millions.

They produce toxins that are deadly to the local birds, mammals and reptiles that prey on them and they have had a dramatic impact on the country’s wildlife.

Asian common toads (Duttaphrynus melanostictus) are smaller than cane toads, but they are also venomous – and researchers think Madagascar’s animals could be especially vulnerable.

“These animals have never been exposed to Asian toad toxins before and will likely not have an evolutionary defence against them,” said Mr Kolby.

The 11 co-signatories of the letter add that the toads could outcompete other species and potentially spread the deadly chytrid fungus.

The researchers, from Australia, the US and Madagascar, say that conservationists and Madagascan government need to act quickly to eradicate the toads.

Mr Kolby said: “The question is, can we still eradicate them? Have we caught it soon enough that eradication could be a feasible option? Obviously we all hope the answer is yes.”

Article source: http://www.bbc.co.uk/news/science-environment-27607978#sa-ns_mchannel=rss&ns_source=PublicRSS20-sa

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