Averaging photos creates infallible face recognition tool

Blogging on Peer-Reviewed ResearchCompare a photo of yourself all cleaned up for a night out with another one first thing the next morning, and you’ll begin to appreciate the problems that people working on face recognition software encounter.

DiazWhile some unfeasibly lucky people look great from all angles, most of us have to contend with a lottery of lighting conditions, odd angles, stupid expressions, stupider poses and the ravages of age. Faced with this unavoidable variability, it’s no wonder that automatic software flounder when tasked with comparing images to stock photos, like those in passports.

Now, Rob Jenkins and Mike Burton from the University of Glasgow have beaten the problem by creating a face recognition system that, so far, has proved to be 100% accurate. This level of accuracy is unheard of in the technological world. It is matched only by that most sophisticated of computers – the human brain – and indeed, it’s the brain that provided Jenkins and Burton with the inspiration for their method.

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Canny breeding creates vitamin A-rich maize without genetic modification

Blogging on Peer-Reviewed ResearchOn Thursday, I wrote about a way of genetically modifying carrots to turn them into rich sources of calcium. The method could be more widely used in vegetables to help reduce nutritional deficiencies, but it risks raising the ire of the anti-GM environmentalist camp. But there is another way of altering the genes of crop plants that avoids such controversy, and it’s a traditional one – selective breeding.

Types of maizeBy cross-breeding individuals with desirable qualities, farmers have been tinkering with the genes of both animals and plants for centuries. Traditionally, the process has been a bit messy. Genes don’t always easily translate into physical characteristics, so there is a certain amount of trial-and-error involved.

Now, Carlos Harjes from Cornell University had developed a way of using modern genetic techniques to make selective breeding even more selective. For his first trick, he has developed a variety of maize to combat vitamin A deficiencies. Best of all, no genes were added, tweaked or subtracted in the making of this vegetable – he only used the natural genetic variation within the world’s maize strains.

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Meet the genetically modified super-carrot, now fortified with calcium

Blogging on Peer-Reviewed ResearchFor centuries, mothers have wrongly told their children that eating carrots will improve their vision. The sight-enhancing properties of these iconic vegetables is be a myth (albeit a fascinating one involving Nazis and fighter pilots) but if Jay Morris has anything to say about it, they may soon be better known for building strong bones.

Types of carrotsMorris, together with Kendal Hirschi and other Texan colleagues, has found a way to double the calcium content of carrots through genetic modification, making them a rich source of the element that is so vital for bones

The team loaded their super-carrots with a protein called sCAX1, which pumps calcium into the plant’s cells. The protein originally hailed from the plant-of-choice for geneticists, Arabidopsis thaliana, where it exists in a larger version. Morris’s team lopped off a small piece from its tip that stops the protein from funnelling in more calcium once a certain amount has been reached.

In this shortened form, sCAX1 is relentless in its import of calcium and the researchers have found that it can greatly increase the calcium content of several vegetables including tomatoes, potatoes and carrots. These super-charged vegetables could help to reduce the risk of osteoporosis, one of the world’s leading nutritional disorders, where a lack of calcium leads to brittle bones.

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The effect of GM crops on local insect life

A large study weighs up the existing evidence on the impact of GM crops on local insect life, providing some much-needed scientific rigour to the GM debate.

In Europe, the ‘GM debate‘ about the merits and dangers of genetically-modified (GM) crops is a particularly heated one. There is a sense of unease about the power of modern genetic technology, and a gut feeling that scientists are ‘playing God’. These discontents are stoked by the anti-GM camp, who describe GM crops with laden and fear-mongering bits of unspeak like ‘Frankenstein foods’ and ‘unnatural’.

Bt cotton is better for non-targeted insects than non-resistant crops sprayed with insecticdes.In a debate so fuelled by emotion and personal values, scientific research and a critical analysis of the evidence rarely gets a look-in. But science has to grudgingly admit some blame in this, because there is actually precious little research on the safety of GM crops. And many of the studies that have been done were short-term and poorly replicated.

A lack of research is dangerous. It provides opening for people on either side of the debate to quote single, small studies as canon and brushing aside any research that contrasts with their stances.

Adding evidence to the debate

Michelle Marvier and colleagues from Santa Clara University, California, are trying to change all that. They have analysed over 42 field experiments on GM crops to get an overall picture about their safety. The technique they used is called meta-analysis, a statistical tool that asks “What does everyone think?” It works on the basis that individual small studies may be far from conclusive, but pooling their results together can lead to stronger and more accurate results.

They looked at three strains of GM-crops that had been modified with genes from a soil-dwelling bacterium called Bacillus thuringiensis. The transferred genes are responsible for producing a number of biological (and therefore ‘natural’) insecticides. When moving them across to plants, geneticists typically try to match the insecticide to the pest they are trying to fight. (In the image on the right, Bt-peanut leaves are protected from the damaging European corn borer)Some GM crops are resistant to specific insect pests.

The toxins are delivered at high dosages to pests, but are restricted to the plant (and sometimes even to particular tissues). They can also be added to the chloroplast genome, which is quite separate form the plant’s nuclear DNA. This stops them from being transferred to other plants.

The hope is that these so-called ‘Bt crops’ can help to minimise the collateral damage of less targeted insecticide sprays. In theory, only pest insects that eat valued crops are killed, while the rest of the ecosystem is unharmed.

The results

That’s what Marvier set out to test. She looked at field experiments which tested the impact of caterpillar-resistant cotton and maize plants on the abundance of other groups of insects and invertebrates.

She found that these other creatures are found in greater numbers in fields containing the caterpillar-resistant GM plants, compared to those sprayed with conventional insecticides. However, the GM crops also led to slightly lower numbers of non-targeted insects compared to fields where no GM crops and no insecticides were used.

The results stayed the same even when Marvier analysed them in more detail. For example, she found much the same thing when she only looked at experiments that had been published in peer-reviewed scientific journals.

So assuming that Bt crops do indeed reduce the use of insecticides (and that’s far from proven), then they will also, as claimed, reduce the collateral damage caused by these chemicals. But they’re not as good for the environment as using no insecticides at all, be they engineered or sprayed.

The bigger picture

Bt-crops are better than large-scale insecticide spraying.At the local level, Marvier’s study provides some much-needed scientific backbone to the GM debate. But the real decisions need to be weighed up at a larger level. For example, it’s all well and good to say that a no-insecticide, no-GM field is the best solution, but that leaves farmers in a bit of a lurch.

One of the big criticism levelled against organic farming is that it leads to lower yield than other practices and requires more agricultural land to be viable and that deals a bad hand to farmers in the developing world. This in turn could lead to deforestation and habitat loss.

On the other hand, Marvier advises caution when interpreting her work. This study has revealed just one benefit of GM crops and even then, only for one specific type of genetic modification. Many of the studies involved isolated patches of land, rather than entire farming systems, where the situation is more subtle. Not all non-GM crops are sprayed with insecticides, while not all GM crops are free from them.

Any benefits must also be weighed against potential health or environmental risks, and again, these must be researched carefully.

To Marvier, the clearest message from her study is that we have started to accumulate enough data to look at this issue from an empirical, evidence-based point of view. If we are to make sound decisions, there is little room for anecdotal evidence or knee-jerk responses guided by personal philosophy.

Bt hypocrisy

For example, there is a certain irony to the opposition to Bt crops. Because its insecticides are ‘natural’, the bacterium is one of the few pesticides that organic farmers are allowed to spray onto their crops.

The bacteria of course use the exact same genes that are transplanted into Bt-engineered crops. Some may argue that this method is better because it is more ‘natural’, because the genes stay within the organism they were intended for. But is that really better?

Wholesale Bt spraying is a crude technique than the specific and targeted use of Bt-engineered crops. It means that the surrounding land is also covered in the bacteria and creatures other than pests are exposed to its entire gamut of toxins. And because farmers need constant supplies of the bacteria, it soaks up more money.

Reference: Marvier, McCreedy, Regetz & Kareiva. 2007. A meta-analysis of effects of Bt cotton and maize on nontarget invertebrates. Science 316: 1475-1477.

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Related stories on genetic modification:

Genetically-modified mosquitoes fight malaria by outcompeting normal ones
Magnifection: mass-producing drugs in record time
Feed the world – turning cotton into a food crop

Sneaking medicines past the brain’s defences

The brain is surrounded by a protective barrier designed to keep infections out. But it can also block out medicines intended to treat brain diseases. Now, scientists have developed a way of sneaking helpful proteins across the barrier by giving them fake molecular ID.

Using genetic engineering, a group of scientists have developed a way of sneaking a virus past the brain’s defences. Don’t panic – this isn’t some nightmare scenario. It could be the first step to curing a huge number of brain diseases.

The brain needs to be protected from incoming infections.The brain seems incredibly well protected amid its shell of bone and cushioning fluid. But even the strongest of forts needs supply lines, and brain is no exception.

A dense network of blood vessels carries vital oxygen to its cells. These vessels are a potential vulnerable spot, providing access for bacteria and other disease-causing organisms to migrate in from other body parts.

But even these weak spots are heavily guarded. The blood vessels in the brain are lined with a tightly packed layer of cells that restrict the flow of molecules from blood to brain. These cells form a protective shield called the blood-brain barrier, or BBB.

It is a superb defence but it can do its job too well. Not only does it block out dangerous microbes, but it can also exclude large proteins and drugs designed to treat brain diseases. Usually, these large molecules need to be distributed throughout the entire brain to be effective. With the BBB in the way, they don’t stand a chance.

Now, Brian Spencer and Inder Verma from the Salk Institute of Biological Studies have come up with a way to disguise helpful molecules to sneak them past the brain’s defences.

The blood brain barrier controls the import of molecules into the brain with the tight security of airport immigration.Their method exploits special gates in the barrier that control the import of essential nutrients and molecules like cholesterol into the brain. These molecules are escorted by a large protein called apoliprotein B (apoB), and are presented to sentinel proteins that guard the gates.

One of these guardians, called LDLR, is designed to recognise a specific segment of apoB. Once it has confirmed the visitor’s identity, it escorts apoB and the molecules it accompanies through the barrier. The whole system works with the tight control of a maximum security prison.

Spencer and Verma managed to fool the system. They took the part of apoB that is recognised by LDLR and stuck it to various proteins, giving them the molecular equivalent of a fake pass.

First, they tested their method in mice. They injected the animals with a harmless virus designed to travel to its liver and spleen. There, the virus sets about building the disguised protein, which is secreted en masse into the bloodstream.

The beauty of this method is that it works after a single injection that transforms the liver and spleen into factories for the protein of choice.

Spencer and Yerma’s method works for glucocerebrosidaseTheir first candidate was GFP, a jellyfish protein that glows in the dark with a greenish hue, allowing it to be easily tracked. Sure enough, the injected mice soon gave off a greenish glow from their brains and the rest of their central nervous systems.

Better still, their method showed real practical potential by sneaking an enzyme called glucocerebrosidase (right) into the brain. Glucocerebrosidase is vital for the storage of fats. People who lack it suffer form a condition called Gaucher’s disease, where fatty desposits collect on various organs and cause brain damage, among other symptoms.

The disease is relatively easy to fix using regular injections, but the resulting brain damage is not for the injected enzyme is usually repelled by the blood-brain barrier. But Spencer and Verma’s method may change all that.

The duo fully admit that their work is merely a first step, but it is an important one nonetheless. The technique must first be refined and tested in people before it can be widely used. Developing drugs and proteins for treating brain disorders is pointless if those new medicines just congregate uselessly outside the blood-brain barrier. Spencer and Verma may have given them a way in.


Reference: Spencer & Verma. 2007. Targeted delivery of proteins across the blood-brain barrier. PNAS 104: 7594-7599.

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Genetically-modified mosquitoes fight malaria by outcompeting normal ones

Genetically-engineered mosquitoes that are resistant to the malarial parasite could be the key to reducing the burden of malaria. In laboratory experiments, they are stronger and fitter than their normal peers and rapidly dominate the population.

Fighting malaria with mosquitoes seems like an bizarrely ironic strategy. But that’s exactly what many scientists are trying to do.

The Anopheles mosquito carries the malaria parasite Plasmodium, but at a cost to its own health.Malaria kills one to three million people every year, most of whom are children. Many strategies for controlling it naturally focus on ways of killing the mosquitoes that spread it, stopping them from biting humans, or getting rid of their breeding grounds.

But the mosquitoes themselves are not the real problem. They are merely carriers for the true cause of malaria – a parasite called Plasmodium. It suits neither mosquitoes nor humans to be infected with Plasmodium, and by helping them resist it, we may inadvertently help ourselves.

With the power of modern genetics and molecular biology, scientists have produced strains of genetically engineered mosquitoes that cannot transmit the malarial parasite.

These ‘GM-mosquitoes’ carry a modified gene – a transgene – that produces chemicals which interfere with Plasmodium’s development. Rather than becoming suitable carriers, the modified mosquitoes are death for any invading Plasmodium.

But scientists can’t very well change the genes of every mosquito in the tropics. To actually reduce the burden of malaria, the genetic changes that induce malaria resistance need to be spread throughout the mosquito population. The easiest way to do this is, of course, to let the insects do it themselves.

And Mauro Marrelli and colleagues from the Johns Hopkins University have found that they are more than up to the task.

The Plasmodium parasite causes malaria but can’t survive in genetically modified mosquitoes.They kept cages full of equal numbers of engineered and normal mosquitoes and fed them on the blood of mice infected by Plasmodium. After nine generations, they found that the engineered insects had become proportionally more common, making up about 70% of the total population.

Like most parasites, Plasmodium affects the health of its host. So mosquitoes that are parasite-resistant are stronger and fitter than their infected peers. Marrelli found that they were about 25% less likely to die early, and had more young, with every female laying an average of 60 eggs compared to 43.

With these advantages, the transgenic mosquitoes outlasted and out-bred normal ones, and quickly established a majority in the population.

But if the advantages to resistance are so great, why haven’t naturally-resistant mosquitoes replaced non-resistant ones? Other studies have shown that resistant mosquitoes fight off Plasmodium with the help of hyperactive immune systems, but have no evolutionary advantages over carriers.

Marrelli thinks that because chronic immune responses produce health problems of their own, that cancel out the advantage of not carrying Plasmodium. In contrast, the transgenic mosquitoes are simply expressing a gene that is mostly harmless. The gene also kills Plasmodium early on in its life cycle, well before it triggers the body’s own immune system.

Even though a single transgene copy does not affect the modified insects’ health, it appears that two copies might have some as-yet-unknown health consequences. This may explain why the resistant mosquitoes in Marrelli’s experiments did not totally dominate the population, but plateaued at 70%. The strongest mosquitoes are those with just one copy of the gene.

Malaria affects tropical countries around the world.This means that introducing the engineered mosquitoes into the wild would not completely wipe out their disease-spreading cousins. But it would still drastically cut their numbers. Considering that malaria infects over 400 million people a year, reducing this number by 70% would be a monumental victory for international health.

Nonetheless, Marrelli is cautious about the future of malaria-resistant strains. These experiments are a proof-of-principle and their results may not bear out as planned in practice.

In the field, only a relatively small proportion of mosquitoes become infected, and he expects the spread of the transgene to be slower. But if it becomes established, it could complement other programmes for controlling malaria, by making it very hard for the parasite to re-colonise a cleared area after it has been eradicated.

 

Reference: Marrelli, Li, Rasgon & Jacobs-Lorena. 2007. Transgenic malaria-resistant mosquitoes have a fitness advantage when feeding on Plasmodium-infected blood. PNAS 104: 5580-5583.

Images: Plasmodium image by Ute Frevert

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Salamander robot walks, swims and sheds light on evolutionary step from sea to land

A team of scientists have developed a robot salamander that walks and swims using an electronic spinal cord. The robot provides us with clues about how our ancestral animals made the evolutionary leap from the sea to the land.

Moving robots are becoming more and more advanced, from Honda’s astronaut-like Asimo to the dancing Robo Sapien, a perennial favourite of Christmas stockings.

But these advances are still fairly superficial. Most robots still move using pre-defined programmes and making a single robot switch between very different movements, such as walking or swimming, is very difficult. Each movement type would require significant programming effort.

Salamanders inspired a robot that tells us about the transition from sea to land.But robotics engineers are now looking to nature for inspiration. Animals of course, are capable of a multitude of different styles of movement. They have been smoothly switching from swimming to walking for hundreds of millions of years, when our distant ancestors first invaded the land from the sea.

This ancient pioneer probably looked a fair bit like the salamanders of today’s rivers and ponds. On the land, modern salamanders walk by stepping forward with diagonally opposite pairs of legs, while its body sways about its hips and shoulders. In the water, they use a different tactic. Their limbs fold back and they swim by rapidly sending S-like waves down their bodies.

Both of these movements, as in all back-boned animals, are controlled by bundles of neurons called central pattern generators (CPGs). These bundles run down either side of the animal’s spine (its body CPG) and in each of its four limbs (its limb CPGs).

The CPGs produce rhythmic movements in muscles, by sending them carefully timed pulses of electrical signals. The brain is a casual bystander in this process, stepping in only to tell the CPGs to switch from a walking to a swimming rhythm, or vice versa.

By directly stimulating the brains of salamanders, Jean-Marie Calguen from the University of Bordeaux, managed to trigger the switch between walking and swimming gaits. With low levels of stimulation, the hapless animal made walking movements, and at higher levels, it tried to swim.

Salamandra Robotica walks its way towards Lake Geneva.Calguen, along with Auke Ijspeert from the Ecole Polytechnique Federale de Lausanne, came up with a model for how this switch works and tested it by building a robot salamander. The metre-long and grandiosely named Salamandra Robotica was designed to mimic its biological counterpart.

Its movements are controlled by an ‘spinal cord’ that uses electronic CPGs to control its body and limbs. Like a real salamander, these are overseen by signals from the robot’s ‘brain’ – in this case, a wireless human-controlled laptop.

Ijspeert and Calguen used different CPG programs to control the robot’s body and limbs. When the robot receives any stimulation from its laptop brain, its body CPG produces the S-like body waves used by swimming salamanders.

At low levels of stimulation, the limb CPGs overpower the bodily ones, and the robot walks. But the limb CPGs cannot cope with higher levels of stimulation and switch off, leaving the bodily CPG free to start a swimming motion.

This model was a success. When they tested Salamandra Robotica on the shores of Lake Geneva, Ijspeert and Calguen found that their robot reproduced the same swimming and walking gaits seen in living salamanders, abruptly switching between the two depending on how much stimulation its CPGs received.

Acanthostega, an early invader of land, probably walked like modern salamanders.The model shows one way in which evolution could have modified an aquatic animal’s movements to a walking way of life. This was a key evolutionary step and provided the impetus for the spread of life from sea to land.

Salamandra’s success also shows that the studies of robotics and biology can successfully work together. Robots can be used to test biological ideas, while biology in turn can inspire successful solutions to engineering problems.

The robot salamander is part of a new era in robotics, where robot movements are controlled by artificial nervous systems.

 

Reference: Ijspeert, Crespi, Ryczko & Cabelguen. 2007. From swimming to walking with a salamander robot driven by a spinal cord model. Science 315: 1416-1419.

(Salamander photo by Marek Szczepanek. Photo of Salamandra Robotica from EPFL. Drawing of Acanthostega by Arthur Weasley.)

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