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Hidden Epidemic of Fatal Infections Linked to Heart Surgeries

Heart surgery scar
Heart surgery scar.
Photograph by Niclas Holmqvist, Flickr (CC).

A slow-brewing epidemic of a little-known, potentially fatal bacterial infection appears to be building among cardiac-surgery patients. The physicians who write the blog Controversies in Hospital Infection Prevention—all three of whom work at the University of Iowa—are so concerned about it that they are publicizing one of their own patients (within the bounds of medical privacy) to alert the rest of medicine.

The infection is Mycobacterium chimaera, which does not normally cause disease in humans, but is found in water and soil. The source is troubling and odd: spray from the fan of a heater-cooler device used to control the temperature of blood during a cardiac bypass, which contaminates both the otherwise-sterile operating field, and also any implants—a new valve, a vascular graft—being placed in or around the heart.

The Food and Drug Administration revealed last October that since 2010, it has been told of 32 cases of infection occurring in this manner, eight in the United States and 24 in Europe. The Centers for Disease Control and Prevention followed up with an alert shortly afterward. Papers in two medical journals last year described clusters of cases in cardiac patients in Europe, in hospitals in SwitzerlandGermany and the Netherlands. There has been one publicly acknowledged cluster in the US as well, in a hospital in York, Penn., which triggered an alert from the Pennsylvania Department of Health.

But, Mike Edmond told me: “We believe that, given what we know of how many patients are affected, this is probably just the tip of the iceberg.”

Given what we know of how many patients are affected, this is probably just the tip of the iceberg.

Edmond is an infectious disease physician and the chief quality officer at the University of Iowa Hospitals and Clinics, and a colleague of physicians Eli Perencevich and Dan Diekema; the three of them write the blog together. He told me they were aware of the FDA and CDC alerts and had checked and cleaned their hospitals’ devices; but they became more concerned when a patient from their hospital—who had had cardiac surgery in 2012—returned with an unexplained fever. After prolonged examinations that included a bone-marrow biopsy, the patient was found to be infected with M. chimaera that no doubt came from the device used during surgery.

Because of privacy, Edmond couldn’t reveal this patient’s fate. In the European and Pennsylvania case clusters, up to half of the victims died.

He told me it was likely this patient could have slipped through the cracks, for several reasons—reasons which might well exist in other areas of the US too. Iowa is rural, and the medical center where the three physicians work is both the apex of the pyramid medically and not necessarily accessible geographically. “A lot of patients don’t receive their follow-up post-operative care in our hospital,” he said. “They go back to their local doctor, so we don’t see them.”

After the access issue, there’s the problem of recognition. “There are many unusual and problematic features of trying to work this up,” Edmond said. “One is the long duration of time from surgery to diagnosis. This is a very slow growing organism; it takes quite a while for symptoms to even develop in an infected patient. And the other problem is that we don’t normally order Mycobacterium blood cultures on patients unless they are immunosuppressed. In an AIDS patient who has ongoing fevers that we cannot explain, we’ll order them, and you might you order them in a transplant patient. But not in someone who is immunologically competent.”

The kind of heater-cooler responsible for the infections.
The kind of heater-cooler responsible for the infections.

If this is diagnosed—which means, if physicians think to order a test to look for it— patients face a hard road ahead. “Mycobacterium infections are really tough,” he said. “They require more than one drug, the drugs are toxic, and in the case of people who have implants, a heart valve, a graft—and from the literature, most of these patients do—that implant has to be removed. The actual implant has the organism growing on it.”

Just at Iowa—not the largest cardiac program in the US—this has triggered a re-examination of 1,500 patients.

“Even though we have only found one case, we know there could be other patients like this out there,” Edmond said. “And there may be physicians out there trying to work that up and not coming up with an answer. We felt it is important to try to raise awareness, because who knows how many of these might be out there, lingering without a diagnosis.”

Iowa has sent a letter to every heart surgery patient from the past four years, which refers them to an explanatory webpage and a 24-hour 800-number (866-514-0863) staffed by nurses who walk callers through a list of symptoms: “fever lasting more than one week; pain, redness, heat, or pus around a surgical incision; night sweats; joint pain; muscle pain; loss of energy; and failure to gain weight or grow (in infants).” Depending on the answers, patients are referred for follow-up care.

Since the three physicians put up their post on Tuesday, they have heard from physicians in other locations also struggling with this. (A few have commented on the blog.) But Edmond said the point is not only to alert doctors.

“We also need patients to be aware of this,” he said. “Say your surgery was last December; based on the known cases, there is a 4-year timeline in which you could develop symptoms. And most infectious disease physicians at this point are not aware this is even going on.”

If you are a physician who would like to know more or share your experience, head to the HAI Controversies blog to comment or to email the authors.

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Polio Eradication: Is 2016 The Year?

A polio victim crawls on a sidewalk in India.
A polio victim crawls on a sidewalk in India.
Photograph by Wen-Yai King Flickr (CC).

As Yogi Berra (or Niels Bohr or Samuel Goldwyn) is supposed to have said, it’s difficult to make predictions, especially about the future. It’s especially dangerous to try to predict the behavior of infectious diseases, when small unpredictabilities in climate or trade or the behavior of governments can bring a problem that we thought was handled roaring back to life.

But as 2016 opens, it is fair to say that the disease public health experts are pinning their hopes on, the one that might truly be handled this year, is polio. There were fewer cases last year than ever in history: 70 wild-type cases, and 26 cases caused by mutation in the weakened virus that makes up one of the vaccines, compared to 341 wild-type infections and 51 vaccine-derived ones the year before. Moreover, those wild natural infections were in just two countries, Afghanistan and Pakistan, and the vaccine-derived cases were in five. The noose is tightening.

The most that health authorities can hope for this year is to end transmission of polio. The ultimate goal is eradication, which has happened only twice—for one human disease, smallpox, and one animal one, rinderpest. To declare a disease eradicated requires that the entire world go three years without a case being recorded. If there are no polio cases in 2016, eradication might be achieved by the end of 2018.

Which would make for nice round numbers, because the polio eradication campaign began in 1988. It is safe to say that no one expected it would take anywhere near this long; the smallpox eradication campaign, which inspired the polio effort, reached its goal in 15 years.

Smallpox was declared eradicated in 1980, so long ago that most people have no knowledge of how devastating a disease it was, or even what a case of the disease looked like. (There are survivors left, but they are aging; the last person infected in the wild, Ali Maow Maalin of Somalia, died in 2013.) In the same way, we’ve forgotten how difficult it is to conduct an eradication campaign. Smallpox was the first campaign that succeeded, but it was the fifth one that global authorities attempted. In its success, it demonstrated what any future campaign would need: not just a vaccine that civilians could administer, but an easy-to-access lab network, granular surveillance, political support, huge numbers of volunteers, and lots and lots of money.

In its own trudge to the finish, the polio eradication campaign has stumbled over many of those, from local corruption to extremist opposition to the still almost unbelievable interference of the CIA (which I covered here and here), along with the virus’s own protean ability to cross borders (to China) and oceans (to Brazil).

But now, at last, the end does look in sight. I asked Carol Pandak, director of the Polio Plus program at Rotary International — which since 1988 has lent millions of volunteers and more than a billion dollars to the eradication campaign —  how she thinks the next 12 months will go.

“We are getting closer,” she told me. “We have only two endemic countries left. Of the three types of the virus, type 2 was certified eradicated in September, and there have been no type 3 cases globally for three years. And Pakistan and Afghanistan have goals to interrupt transmission internally in May 2016.”

The diminishment of wild polio paradoxically creates greater vulnerability to vaccine-derived polio, which happens when the weakened live virus used in the oral vaccine mutates back to the virulence of the wild type. The only means of defusing that threat is to deploy the killed-virus injectable vaccine, which is widely used in the West but until recently was considered too expensive and complex to deliver in the global south.

To begin the transition, Pandak said, countries that still use the oral vaccine have agreed to give one dose of the injectable as part of routine childhood immunizations for other diseases. That should strengthen children’s’ immune reactions to polio, so that the reversion to wild type — which occurs as the weakened virus replicates in the gut — does not take place.

In the smallpox campaign, when eradicators thought they were almost done, there was a freak weather event—the worst floods that Bangladesh had experienced in 50 years—that triggered an internal migration and redistributed the disease. Polio is just as vulnerable to last-minute disruptions, especially since the two remaining endemic countries are hotspots of unpredictability. Travelers from Pakistan actually carried polio into Afghanistan in August.

“In Pakistan, the army has committed to providing protection for vaccinators in conflict areas,” Pandak told me, “and another strategy that has been successful has been to set up border posts to immunize people as they are fleeing areas of conflict and military operations. I have seen Rotary volunteers staffing 24/7 kiosks in train stations and toll booths, so that we can get people wherever they happen to be.”

There is no question that hurdles remain. By the World Health Organization’s order, polio is still considered a “public health emergency of international concern,” which requires countries where the disease is extant to either ensure its citizens are vaccinated before leaving, or prevent their crossing the border. And polio still lives quiescently in lab freezers all over the world, and those will have to be searched and their contents eliminated lest a lab accident bring the disease alive again (a warning that was recently circulated for rinderpest as well). Plus, up til now, the injectable vaccine has been made by starting with a virus that is not only live but virulent, posing the risk that a lab accident that could release it; British scientists announced on New Year’s Eve that they may have found a way to weaken it while still yielding a potent vaccine.

When it goes, if it does, polio will gift the world not only with its absence, but also with the abundant health infrastructure that was set up to contain and eliminate it, and can be turned to other uses. When I talked to Pandak, she sounded excited at the possibility that countries and volunteers would be able to turn their attention away from a single disease and toward ensuring the overall health of children.

“We have been doing this for 30 years,” she said. “We’ll continue to fundraise, advocate and raise awareness to the last case. We are committed to seeing this to the end.”


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How The Plague Microbe Gave Fleas A Chance

There’s a disease called Far East scarlet-like fever, or Izumi fever. It is caused by a bacterium called Yersinia pseudotuberculosis, which people can catch through contaminated food or water. Its symptoms are usually gentle: fever; stomach pains; nothing worse than a case of appendicitis.

But sometime between 1,500 and 6,400 years ago, this mild-mannered microbe started to change. One particular lineage picked up new genes, while silencing some of its existing ones. It gained the ability to spread via the bites of fleas, and started causing more lethal symptoms. It became what we now call Yersinia pestis—the cause of plague. Three times over, this microbe has swept the world in lethal epidemics including the infamous Black Death, which killed upwards of 75 million people in the 14th century. What a difference a few millennia of evolution can make.

Many scientists are now trying to understand the changes that transformed Y.pseudotuberculosis into its darker, deadlier offshoot. Joseph Hinnebusch from the National Institutes of Health is particularly intrigued by Y.pestis’s ability to hitchhike in fleas—an ability that its ancestor lacks, and one that assuredly contributed to its spread between humans and other mammals.

When Y.pseudotuberculosis infects a flea, it colonises the very end of the insect’s digestive system, where it can’t easily reach a new host. But Y.pestis does something different. Earlier this year, Hinnebusch found that this bacterium gained a gene that allowed it to grow further up the flea’s digestive tract. It also lost three genes that normally restrain it from growing into thick colonies called biofilms.

These four changes mean that Y.pestis forms thick colonies in a valve that connects its throat to its gut. These bacterial cities stop the flea from easily swallowing the blood that it sucks. As it tries, it dislodges the bacteria in the valve, and regurgitates these into whatever poor animal it has bitten. Thanks to changes in four genes, Y.pestis gained the ability to spread to new hosts by giving reflux to fleas.

Along the way, it also became less toxic. Y. pseudotuberculosis is milder to us, but it is surprisingly deadly to fleas. It causes diarrhoea, paralysis, and death in around 40 percent of the insects that suck it up. Hinnebusch, together with postdoc Iman Chouikha, has now discovered why. They fed fleas with blood containing narrower and narrower selections of Y. pseudotuberculosis proteins until they identified one that was consistently toxic.

It’s called urease, and it is partly encoded by a gene called UreD. When Hinnebusch and Chouikha deleted this gene, fleas could happily swallow Y. pseudotuberculosis without any problems. Urease breaks down a substance called urea and, in doing so, produces ammonia. Presumably, the build-up of ammonia is toxic to the flea. In fact, any urease protein will finish them off—even one from a bean plant proved lethal.

Y.pestis, unlike its close relative, can’t make urease. Thanks to a single mutation in its version of the UreD gene, it produces a half-formed and useless protein. By breaking this gene, it gained the ability to survive through a flea without killing it.

That was a crucial step. Fleas aren’t actually very efficient at transmitting Y.pestis. You need a lot of them to kickstart an outbreak of plague, and that can’t really happen if their microbes are killing 40 percent of them. Hinnebusch and Chouikha calculated that to transmit a Y.pestis strain that still made urease, you’d need more fleas than are commonly found on rodents. Without the mutation that broke UreD, the plague microbe would never have reached plague proportions.

References: Sun, Jarrett, Bosio & Hinnebusch. 2014. Retracing the Evolutionary Path that Led to Flea-Borne Transmission of Yersinia pestis. Cell Host and Microbe http://dx.doi.org/10.1016/j.chom.2014.04.003

Chouikha & Hinnebusch. 2014. Silencing urease: A key evolutionary step that facilitated the adaptation of Yersinia pestis to the flea-borne transmission route. http://dx.doi.org/10.1073/pnas.1413209111

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The Fault in Our Stars Might be a Virus

In June 2013, starfish on the western coast of North America started wasting away. At first, their arms curled from the tips, and they tied themselves into pretzel-like knots. Their bodies deflated. White festering sores appeared on their flesh. As the lesions spread, their flesh rotted away and their arms fell off. Within days, healthy animals had disintegrated into mush.

This condition, known as sea star wasting syndrome (SSWS), was recorded as far back as the 1970s, but the scale of this recent event is unprecedented. It has hit at least 20 species all along the Pacific, from Alaska to California. In less than a year, huge, thriving populations have completely wasted away.

As the stars blinked out, scientists compiled a list of possible causes that included storms, rising temperatures, and pollutants. But an infection always seemed likely. The disease seemed to move from place to place with the character of a spreading epidemic. Most tellingly, starfish in aquariums started dying too. These animals were housed in controlled captive environments but they were immersed in water pumped in from the surrounding ocean—and that was enough to kill them. Filtering the water through sand didn’t help. The only measure that spared the stars was sterilising the water with ultraviolet light. Whatever was killing the animals was microscopic and biological.

Now, a team of scientists led by Ian Hewson from Cornell University have identified the most likely culprit behind the grisly outbreak—a new virus that they call sea star-associated densovirus, or SSaDV.

A sunflower starfish distingegrates due to SSWS. Credit: Hewson et al, 2014.
A sunflower starfish distingegrates due to SSWS. Credit: Hewson et al, 2014.

Densoviruses are best known for infecting insects and crustaceans, but last year, Hewson’s team discovered them in a group of Hawaiian sea urchins. “We didn’t associate those viruses with any disease,” he says. “I jokingly told a colleague: Boy, what if there was some kind of mass mortality?” When the SSWS outbreak hit, the team leapt at the chance to study it.

First, they blended tissues from wasting starfish and passed them through filters with extremely small pores—small enough to exclude bacteria but big enough to let viruses through. They inoculated healthy starfish with these extracts, and the animals started wasting within a couple of weeks. If they boiled the extracts first, the animals were unharmed. This confirmed that the disease was transmissible and was caused by something the size of a virus. By sequencing the killer extract, the team showed that it contained the genome of a new densovirus—SSaDV.

They then collected tissue samples from 465 wild starfish, belonging to three species. The symptomatic animals were more likely to carry SSaDV than their healthy peers, and in higher numbers. And the more viruses they had, the worse their symptoms were.

The association wasn’t perfect: some diseased starfish showed no signs of the virus, while some healthy ones did. But Hewson thinks that there are easy explanations for these patterns. Diseases animals don’t have the virus everywhere. “If you take a sea star and divide it into pieces, you can detect virus in 80 percent of them. So 20 percent will be a false negative,” he says. There’s also a lag between infection and symptoms, so “healthy” animals might be exposed without having fallen sick yet. “Some of the ‘healthy’ samples came from an aquarium where all the animals later died,” Hewson adds.

“The authors present persuasive evidence that they have identified an agent associated with SSWS,” says Ian Lipkin, a virus hunter from the Mailman School of Public Health. “Nonetheless, as they note themselves, there  is much more work to be done before we will know whether the densovirus they describe is necessary and sufficient to cause disease.”

Vincent Racaniello, a virologist from Columbia University, agrees that the evidence is strong. “The crucial experiment that remains to be done is to isolate infectious virus in cell culture, inoculate it into sea stars, and show that it causes wasting disease,” he says.

Hewson agrees that this step is crucial, but he also thinks that it will be very difficult. Ideally, he’d like to infect starfish in the absence of all other microbes to show that the virus is truly responsible for the disease. But these animals pump seawater through their bodies and they are naturally riddled with microbes. The alternative is to grow starfish tissues in the lab, but no such cultures exist for marine invertebrates. “That’s a real stumbling block,” says Hewson. “We’re trying to isolate a cell culture of a sea star but that’ll be a long and tedious process.

He also suspects that the virus may not actually cause the symptoms of SSWS directly. It could, for example, disrupt the sea stars’ ability to control the bacteria that they normally co-exist with. “The lesions are probably just the native bacteria taking advantage of an immunocompromised host,” he speculates. “So, associating the virus with those lesions may be a challenge.”

There’s also another mystery: why is the current outbreak of SSWS so dramatic when the newly discovered virus is actually an old presence? The team found its DNA within starfish that had been collected from the Pacific coast as far back as 1942, and that have been sitting in museum jars ever since. So why weren’t North America’s starfish melting away while World War II was raging?

“Viruses do smoulder in populations,” says Hewson. Familiar names like HIV and Ebola were affecting humans at small scales long before they triggered huge scary epidemics. The same may apply to SSaDV. In recent years, booming sea star populations in the Pacific Northwest may have given the virus newfound impetus. “There were mountains of sea stars underwater, tens of metres high,” says Hewson. “If you talk to crab-fishers in the region, their crab pots were full of these stars and they were getting annoyed.” The virus could have more easily jumped from host to host, or developed mutations that made it more transmissible or virulent.

Environmental changes may be important. Carol Blanchette from the University of Santa Barbara says, “We have been sampling sea stars across southern California throughout this epidemic and it is likely that in our region, as well as in others, environmental causes like increased temperatures have played an important role.” She finds the virus evidence convincing, but thinks it “may only be one part of the story”.

SSaDV may just be part of a natural cycle that controls sea star populations if they grow too big. Then again, some starfish act as keystone species—they wield disproportionate influence over their habitats by controlling populations of mussels and barnacles that would otherwise takeover. Their loss could dramatically reshape the coastlines of the Pacific Northwest, from thriving communities into black mussel monocultures.

SSaDV is also found in other related animals like sea urchins and brittle stars. No one knows if it causes disease in these groups, but the worry is that the virus could use its sea star hosts as a platform for building in numbers and launching outbreaks in other species.

Even if that was true, Hewson doubts that anything can be done. Even if scientists could develop a cure or vaccine, it would be impractical to inoculate the animals on a wide scale. “We’re just trying to understand this as a natural phenomenon,” he says.

Reference: Hewson, Button, Gudenkauf, Miner, Newton, Gaydos, Wynne, Groves, Hendler, Murray, Fradkin, Breitbart, Fahsbender, Lafferty, Kilpatrick, Miner, Raimondi, Lahner, Friedman, Daniels, Haulena, Marliave, Burgem, Eisenlord & Harvell. 2014. Densovirus associated with sea-star wasting disease and mass mortality. http://dx.doi.org/10.1073/pnas.1416625111

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Seals May Have Carried Tuberculosis To The New World

Very few people suspected the seals.

Kirsten Bos from the University of Tubingen certainly didn’t when she and her colleagues started studying three Peruvian skeletons. They were just trying to understand the history of tuberculosis—a disease that has affected humans for millennia and still kills millions every year. Team member Jane Buikstra excavated three early victims from a site in southern Peru; their warped spines and ribs showed unmistakeable signs of the disease.

Even though the bones were around 1,000 years old, the team still managed to extract DNA from them. These included sequences belonging to Mycobacterium tuberculosis, the bacterium that causes tuberculosis. The researchers calculated that these ancient sequences last shared a common ancestor with modern M.tuberculosis strains 6,000 years ago.

That was the first big surprise. The general opinion among scientists who study tuberculosis is that it’s an ancient disease that started infecting humans back when we all lived in Africa—after all, that’s where the strains are at their most diverse. As we spread around the globe, this pernicious partner hitched a ride and co-evolved with us. Genetic studies support this view. A big one, published just last year, estimated that all human tuberculosis strains evolved from a common ancestor that lived 70,000 years ago, before the great expansion out of Africa. But the new results suggest that this ancestral microbe was just 6,000 years old!

It’s not just the discrepancy that’s baffling. By 6,000 years ago, humans had already spread around the world, including all over the Americas. The land bridge that connected Asia and North America had long since flooded. And it would be several millennia before any Europeans sailed across the Atlantic. So if tuberculosis originated in Africa, how did it get into South America?

The team considered the possibilities. Maybe some animal rafted across the ocean, taking the bacteria with it? Maybe some bird flew it over? Or maybe, one of them suggested, seals carried it across. They’re long-distance swimmers, they’re infected with a relative of M.tuberculosis called M.pinnipedii, and people often kill and eat them. But, come on. Seals? Seriously? “We had a good laugh over that,” says Bos. “It seemed so silly.”

Still, it was worth testing. The team compared the genomes of many species of tuberculosis bacteria from a variety of animals—humans, cows, chimpanzees, goats, seals, and more. And they found that the closest relatives of the Peruvian strains weren’t the ones that infect today’s humans… but the ones from seals. Seals! (No, not SEALs. Or Seal. Seals.)

“We couldn’t believe that was what the data was showing, but it was pretty clear,” says Bos. “I got the data and sent a text message to Johannes Krause [the senior author], which just said: Arf!”

“This is a triumph of technical and analytical approaches, and It also delivers a wonderfully unexpected result. It’s great science!” says Mark Pallen from the University of Warwick.

Here’s what Bos thinks might have happened: M.tuberculosis evolved in Africa and could have made it into coastal populations of seals (actually, probably sea-lions). That’s reasonable—these microbes are really good at hopping between mammals, as the furious debate around British badger culls attests to. It adapted to the seals, producing the lineage we know as M.pinnipedii. It then spread throughout the southern hemisphere in its new hosts.

Eventually, some of these sick animals were killed by humans living in coastal Peru. We know that many of these groups used seal hides in funeral rituals. They ate seal meat as a regular part of their menu. They could have caught tuberculosis through these practices. If this sounds implausible, note that seals in zoos have passed M.pinnipedii to people before. And some archaeologists have actually speculated that coastal people who hunted and maybe even farmed seals might have caught tuberculosis from them.

The team’s discovery may help to explain some uncertainty around the smudgy history of tuberculosis in the Americas. Scientists used to think that European colonists brought the disease over, since strains that currently circulate in the New World are closely related to European ones. But once they started finding very old skeletons with signs of infection, they knew this couldn’t be right. And in 1994, one team recovered M.tuberculosis DNA from a thousand-year-old Peruvian mummy. The microbe was clearly in the Americas long before Europeans were.

Could seals have been responsible for this early foothold? “It would be quite a brave extrapolation to make at this stage,” says Terry Brown from the University of Manchester. It’s entirely possible that the seals are red herrings, and some other animal that the team didn’t include in their analysis brought tuberculosis to Peru. After all, they only looked at the genomes of 14 animal strains. “They are just scratching the surface of mycobacterium diversity,” says Hendrik Poinar from McMaster University. “There could be plenty of strains from other animals that will fall closer than seals.” The seal story is plausible, but that doesn’t mean it’s right.

Even if seals were involved, it’s unclear how often they passed tuberculosis to people, or what happened afterwards. Their strains could have jumped from person to person and swept the Americas. Or they could have infected those three unfortunate Peruvians and no one else. “[This could have been] just a one-off zoonotic episode, restricted in time and space, leaving the majority of Pre-Columbia tuberculosis in the Americas unexplained,” says Pallen.

Bos agrees. “These three might just have eaten sick seals, got the infection and died, without transmitting it to their peers.” To show human-to-human transmission, the team would need to find similar strains of M.tuberculosis in skeletons from inland archaeological sites, where people didn’t have direct contact with seals. They’re working on that.

Meanwhile, Brown adds that transmission-by-seal isn’t actually the most important bit of the study. He’s more captivated by the suggestion that tuberculosis is just 6,000 years old, rather than 70,000 as previously suggested.

“These dates are worked out by measuring the amount of genetic diversity among all known strains of TB bacteria, and then using a molecular clock – based on the rate at which genetic changes occur during evolution – to work out how much time was needed for all that diversity to evolve,” explains Brown. “To do this, the molecular clock has to be calibrated—we need to know how rapidly the genetic changes accumulated in the past.”

The earlier study calibrated their clock using imprecise figures, based on estimates of when humans spread through the world. Bos’s team (which actually includes six authors from the previous work) calibrated their clock using one of their skeletons. Thanks to carbon-dating, they knew that it was between 1,000 and 1,200 years old. They could work out how much the bacteria have changed since then, and how much time they needed to evolve before. Hence: 6,000 years.

If that estimate is right, it would totally refute the idea that tuberculosis evolved when we were still confined to Africa, and diversified with us as we colonised the world. Instead, it arose when that worldwide spread was already mostly complete.

Of course, they could be wrong. Pallen says that the study doesn’t explain why another group found signs of tuberculosis in a 17,000-year-old bison from North America.  Brown adds, “They had to make certain assumptions about the way in which tuberculosis bacteria evolve, and those assumptions might not be entirely secure. We definitely need more ancient Mycobacterium genome sequences, for example from Europe or Asia, and from different time periods, to check this result.”

“The study of ancient DNA [will] continue to contribute significantly to filling gaps in our knowledge of tuberculosis, a devastating disease today that still kills many thousands of people each year,” says Charlotte Roberts from Durham University.

Reference: Bos, Harkins, Herbig, Coscolla, Weber, Comas, Forrest, Bryant, Harris, Schuenemann, Campbell, Majander, Wilbur, Guichon, Wolfe Steadman, Collins Cook, Niemann, Behr, Zumarraga, Bastida, Huson, Niesell, Young, Parkhill, Buikstra, Gagneux, Stone & Krause. 2014. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature http://dx.doi.org/doi:10.1038/nature13591


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Narcolepsy Paper Retracted

Well, this is disappointing.

Last December, I wrote a story for Nature News about a new paper, published in Science Translational Medicine, which seemed to confirm narcolepsy as an autoimmune disease. Here’s what I wrote at the time:

Narcolepsy is mostly caused by the gradual loss of neurons that produce hypocretin, a hormone that keeps us awake. Many scientists had suspected that the immune system was responsible, but the Stanford team [led by Elizabeth Mellins and Emmanuel Mignot] has found the first direct evidence: a special group of CD4+ T cells (a type of immune cell) that targets hypocretin and is found only in people with narcolepsy.

“Up till now, the idea that narcolepsy was an autoimmune disorder was a very compelling hypothesis, but this is the first direct evidence of autoimmunity,” says Mellins. “I think these cells are a smoking gun.” The study is published today in Science Translational Medicine1.

Thomas Scammell, a neurologist at Harvard Medical School in Boston, Massachusetts, says that the results are welcome after “years of modest disappointment”, marked by many failures to find antibodies made by a person’s body against their own hypocretin. “It’s one of the biggest things to happen in the narcolepsy field for some time.”

Now, it looks like the years of modest disappointment will continue because this paper is being retracted. The notice says:

“The researchers report that they have been unable to reproduce the paper’s key findings. Specifically, they could not demonstrate a differential Enzyme-Linked ImmunoSpot response of CD4+ T cells from patients with narcolepsy compared to those from normal controls after exposure to the hypocretin peptides HCRT56–68 or HCRT87–99. Because the validity of the conclusions reported in the study cannot be confirmed, they are retracting the article.”

To explain, in the study, the team showed that two fragments of hypocretin activated a specific group of CD4+ cells in narcolepsy patients, but not in healthy people. The Enzyme-Linked ImmunoSpot, or ELISpot, was a test they used to confirm the existence of these cells… and it’s no longer giving the same results that are described in the paper.

I contacted Mellins for more details, and was referred to the institute’s Director of Media Relations, Ruthann Richter. She sent the following statement from Mignot who is currently in China.

Beginning in March, my lab could not make the ELISPot test work. After many attempts in several settings and verification of all reagents, we decided to withdraw the manuscript. We have no reason to believe that the DQ0602 in vitro binding studies of peptides reported in the paper are problematic. We have already moved forward with other interesting findings on the narcolepsy/H1N1 association.

That’s not massively illuminating about what caused the original problem but neither researcher was available for interview, and Richter added, “We don’t have any more information at this point.”

(DQ0602 is a version of a protein found on the surface of immune cells. It’s found in the majority of people with narcolepsy and only a minority of the general population. The two hypocretin fragments that the team used in their experiments were those that can stick to DQ0602.)

I contacted Gert Lammers, president of the European Narcolepsy Network, who originally told me that “the results are very important, but they need to do a replication study in a large group of patients and controls.” He said:

“This may indeed be considered as a blow to the field, although I already wrote you that the findings needed replication. Studies like this are very complex and subject to many known and in part unknown or unidentified influences, and therefore always need replication preferentially by an independent lab. The methods applied seemed to be sound and most of the findings seemed to make sense (although also inducing new questions) and therefore I had and have no reason, with the knowledge I currently have, to mistrust the data presented in the paper. However, it was remarkable that after almost a year there were no reports about successful replication of the findings in Stanford nor anywhere else. This was starting to become a hint that there could have been a problem with the experiments and discussions about this possibility were starting.”

As always, Ivan Oransky is on the case. He has more comments from Mignon and Mellins, and the comments on his post may eventually shed more light on the background to this retraction. I also wrote a pointer to the Nature piece on this blog, which I have since amended.



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Testing Vaccines On Captive Chimps To Protect Wild Chimps—Is It Worth It?

In February 2011, a team of scientists led by Peter Walsh at the University of Cambridge injected six captive chimpanzees with an experimental vaccine against the deadly Ebola virus. At first glance, the study looked like a lot of other medical research, in which drugs that are meant for humans are first tested on other animals. But this was different. These scientists were working with chimps to help chimps.

The twin threats of poaching and habitat loss are driving the African apes—chimps, bonobos, and gorillas—towards extinction. Diseases are also a problem. Our ape relatives are vulnerable to infections like anthrax, malaria, and respiratory viruses that spill over from human tourists and researchers.

They can also get Ebola. Under a microscope, the Ebola virus looks like a malevolent knot. In the body of a human or ape, it causes severe and fast-burning disease. In 2006, Walsh’s team estimated that recent Ebola outbreaks have killed around a third of the world’s gorilla population—some 5,000 animals in the Republic of the Congo—and a slightly smaller proportion of the world’s wild chimps.

For years, Walsh has argued that we should protect the survivors with vaccines. He certainly has plenty to choose from: scientists have developed several potential Ebola vaccines that have protected mice and monkeys against the virus. They’re still years away from passing human trials, and since Ebola is a rare disease that mostly affects poor people in the tropics, a human vaccine may never become a commercial reality.  These orphaned medicines could be used to save wild animals.

Not everyone agrees. Historically, conservationists have been happy to protect a species’ habitat or to fight poaching, but they’ve railed against interfering with the animals directly. In 1966, Jane Goodall stopped a polio epidemic among Tanzanian chimps by hiding an oral polio vaccine in bananas. “There was a backlash against her,” says Walsh. “It’s very difficult to get anybody to agree to do vaccinations.” But this attitude is waning, as the threat of diseases is becoming clearer. Walsh thinks there’s now more appetite for vaccinating wild animals.

Ebola virus. Credit: Dr. Frederick Murphy, CDC.
Ebola virus. Credit: Dr. Frederick Murphy, CDC.

In 2011, his team, led by Kelly Warfield, finally tested an Ebola vaccine on three chimps. They used one that doesn’t contain any live viruses; instead, it comprises a piece of the virus’s coat. It trains the immune system to create antibodies that recognise Ebola, without risking an actual infection.

None of the vaccinated chimps showed any signs of weight loss or disease, and they all had similar numbers of blood cells to three chimps that weren’t vaccinated. As planned, they developed antibodies against Ebola. And when the team injected these antibodies into mice, the rodents were twice as likely to survive an encounter with the virus.

That’s not surprising, since the same vaccine has protected monkeys in earlier experiments, says Nancy Sullivan from the National Institute for Allergy and Infectious Diseases, who has worked on Ebola. “It’s a good first step, but whether the vaccine will protect chimps or not, we don’t know,” she says. After all, the team didn’t actually challenge the chimps with Ebola itself. Walsh thinks this is unnecessary. Based on the monkey data and the mouse experiment, he says the vaccine is ready for use.

This study, in which scientists tested a vaccine on captive chimps to protect wild chimps, rather than humans, is the first of its kind. It may also be the last study of its kind.

The era of biomedical research on chimpanzees is drawing to a close. The United States and Gabon are the only countries that still allow this kind of research, and the US may soon leave this short list. In 2011, the Institute of Medicine issued a report saying that “most current use of chimpanzees in biomedical research is unnecessary”—a conclusion that the National Institutes of Health took seriously. In 2013, it announced that all but 50 of its chimps would be retired to sanctuaries. Meanwhile, the US Fish and Wildlife Service has tabled a proposal to list captive chimps under the Endangered Species Act—a move that would ban medical procedures beyond those that “enhance the propagation or survival of the affected species”.

Walsh’s study might still fit the bill but it wouldn’t matter, since labs with the right facilities to house and work with chimps would shut down. That’s a problem, since national park managers in Africa insist that scientists prove the safety of vaccines in captive apes before using them on wild ones (and monkey data won’t suffice). To Walsh, you need captive chimps to test vaccines that would save wild ones from diseases.

He’s not just talking about Ebola, either. Vaccines could also protect chimps from HRSV—a human virus that they catch from humans, often with fatal results. One HRSV vaccine, developed for our own use, didn’t work well in humans but was great at protecting chimps. Beatrice Hahn at the University of Pennsylvania is also developing a vaccine against simian immunodeficiency virus (SIV), which causes an AIDS-like disease in chimps. (Hahn was unavailable for comment due to travel.)

To continue research on such vaccines , Walsh thinks the US Government should keep a humanely housed population of a few dozen chimps specifically for conservation research. “Potentially preventing the extinction of wild chimps should weigh more heavily on the ethical scale than the discomfiture of chimps in captivity,” he says. “They’re not being vivisected or challenged with Ebola. The nasty bit is that, for a couple of months, they’re in a small isolation cage. I don’t like that. It’s not a good thing, but it’s not horrific. I think it’s worth it for the survival of the species.”

John VandeBerg from the Texas Biomedical Research Institute voices similar views in a New York Times op-ed, published last year. “The NIH has not permitted a single chimpanzee that it owns or supports to be enrolled in a new research study since December 2011,” he wrote. “Humans — and chimpanzees and gorillas — may continue to die from diseases that could have been prevented or treated by medical products developed from research with chimpanzees.”

“That is totally silly,” says Brian Hare from Duke University, who does non-invasive research with chimps in African sanctuaries. “They could work with the Pan-African Sanctuary Alliance, because there are more than 1,000 captive chimps in Africa that could be protected.” Kathleen Conlee from the Humane Society of the United States, an advocacy group, agrees. “We don’t need to keep chimpanzees in laboratories for such efforts and could instead work with sanctuaries in Africa, where the chimpanzees actually have a chance of exposure to the virus,” she says, echoing points she made in response to VandeBerg’s op-ed.

But Walsh counters that zoos and sanctuaries don’t offer the controlled conditions necessary for a proper vaccine trial—hence, the need for private facilities.

“Protecting endangered chimpanzees and gorillas against Ebola is certainly a very important topic,” says Tom Geisbert from the University of Texas Medical Branch. But he says that the vaccine Walsh used needs three doses to trigger a protective immune response, which is neither practical nor feasible for wild apes. Instead, the team should check the safety of other vaccines based on weakened viruses, which work after a single injection.

Hare adds that vaccinating wild animals is very tricky. “No tested or proven method that doesn’t cost insane amounts and have extreme risk for wild animals,” he says.

But Walsh argues that it’s easier to vaccinate wild animals than critics think. His field team in Africa have already vaccinated wild gorillas against measles using blow darts, in a trial whose results are not yet published. “It’s not trivial, but it’s not that hard,” he says. In the future, he hopes to develop bait methods that can deliver oral doses of a vaccine without the need for darts. “Again, we need a captive population to test the bait system.”

Reference: Warfield, Goetzmann, Biggins, Kasda, Unfer, Vu, Javad Aman, Olinger & Walsh. 2014. Vaccinating captive chimpanzees to save wild chimpanzees. PNAS http://dx.doi.org/10.1073/pnas.1316902111

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Can We Beat Drug-Resistant Malaria At Its Birthplace?

In the war against malaria, one small corner of the globe has repeatedly turned the tide, rendering our best weapons moot and medicine on the brink of defeat. I travelled to Thailand and Burma to meet the scientists who are trying to eliminate resistant malaria before it defeats our best remaining drug. This story originally appeared in Mosaic and is republished under a CC-BY 4.0 licence.  

The meandering Moei river marks the natural boundary between Thailand and Myanmar. Its muddy waters are at their fullest, but François Nosten still crosses them in just a minute, aboard a narrow, wooden boat. In the dry season, he could wade across. As he steps onto the western riverbank, in Myanmar, he passes no checkpoint and presents no passport.

The air is cool. After months of rain, the surrounding jungle pops with vivid lime and emerald hues. Nosten climbs a set of wooden slats that wind away from the bank, up a muddy slope. His pace, as ever, seems relaxed and out of kilter with his almost permanently grave expression and urgent purpose. Nosten, a rangy Frenchman with tousled brown hair and glasses, is one of the world’s leading experts on malaria. He is here to avert a looming disaster. At the top of the slope, he reaches a small village of simple wooden buildings with tin and thatch roofs. This is Hka Naw Tah, home to around 400 people and a testing ground for Nosten’s bold plan to completely stamp out malaria from this critical corner of the world.

Malaria is the work of the single-celled Plasmodium parasites, and Plasmodium falciparum chief among them. They spread between people through the bites of mosquitoes, invading first the liver, then the red blood cells. The first symptoms are generic and flu-like: fever, headache, sweats and chills, vomiting. At that point, the immune system usually curtails the infection. But if the parasites spread to the kidneys, lungs and brain, things go downhill quickly. Organs start failing. Infected red blood cells clog the brain’s blood vessels, depriving it of oxygen and leading to seizures, unconsciousness and death.

When Nosten first arrived in South-east Asia almost 30 years ago, malaria was the biggest killer in the region. Artemisinin changed everything. Spectacularly fast and effective, the drug arrived on the scene in 1994, when options for treating malaria were running out. Since then, “cases have just gone down, down, down,” says Nosten. “I’ve never seen so few in the rainy season – a few hundred this year compared to tens of thousands before.”

But he has no time for celebration. Artemisinin used to clear P. falciparum in a day; now, it can take several. The parasite has started to become resistant. The wonder drug is failing. It is the latest reprise of a decades-long theme: we attack malaria with a new drug, it mounts an evolutionary riposte.

Back in his office, Nosten pulls up a map showing the current whereabouts of the resistant parasites. Three coloured bands highlight the borders between Cambodia and Vietnam, Cambodia and Thailand, and Thailand and Myanmar (Burma). Borders. Bold lines on maps, but invisible in reality. A river that can be crossed in a rickety boat is no barrier to a parasite that rides in the salivary glands of mosquitoes or the red blood cells of humans.

History tells us what happens next. Over the last century, almost every frontline antimalarial drug – chloroquine, sulfadoxine, pyrimethamine – has become obsolete because of defiant parasites that emerged from western Cambodia. From this cradle of resistance, the parasites gradually spread west to Africa, causing the deaths of millions. Malaria already kills around 660,000 people every year, and most of them are African kids. If artemisinin resistance reached that continent, it would be catastrophic, especially since there are no good replacement drugs on the immediate horizon.

Nosten thinks that without radical measures, resistance will spread to India and Bangladesh. Once that happens, it will be too late. Those countries are too big, too populous, too uneven in their health services to even dream about containing the resistant parasites. Once there, they will inevitably spread further. He thinks it will happen in three years, maybe four. “Look at the speed of change on this border. It’s exponential. It’s not going to take 10 or 15 years to reach Bangladesh. It’ll take just a few. We have to do something before it’s too late.”

Hundreds of scientists are developing innovative new ways of dealing with malaria, from potential vaccines to new drugs, genetically modified mosquitoes to lethal fungi. As Nosten sees it, none of these will be ready in time. The only way of stopping artemisinin resistance, he says, is to completely remove malaria from its cradle of resistance. “If you want to eliminate artemisinin resistance, you have to eliminate malaria,” says Nosten. Not control it, not contain it. Eliminate it.

That makes the Moei river more than a border between nations. It’s Stalingrad. It’s Thermopylae. It’s the last chance for halting the creeping obsolescence of our best remaining drug. What happens here will decide the fate of millions.

The world tried to eliminate malaria 60 years ago. Malaria was a global affliction back then, infecting hundreds of thousands of troops during World War II. This helped motivate a swell of postwar research. To fight the disease, in 1946 the USA created what is now the Centers for Disease Control and Prevention (CDC), the country’s premier public health institute. After a decisive national eradication programme, the nation became malaria-free in 1951. Brazil had also controlled a burgeoning malaria epidemic with insecticides.

Meanwhile, new weapons had emerged. The long-lasting insecticide DDT was already being widely used and killed mosquitoes easily. A new drug called chloroquine did the same to Plasmodium. Armed with these tools and buoyed by earlier successes, the World Health Organization formally launched the Global Malaria Eradication Programme in 1955. DDT was sprayed in countless homes. Chloroquine was even added to table salt in some countries. It was as ambitious a public health initiative as has ever been attempted.

It worked to a point. Malaria fell dramatically in Taiwan, Sri Lanka, India, the Caribbean, the Balkans, and parts of the south Pacific. But ultimately the problem was too big, the plan too ambitious. It barely made a dent in sub-Saharan Africa, where public health infrastructure was poor and malaria was most prevalent. And its twin pillars soon crumbled as P. falciparum evolved resistance to chloroquine and mosquitoes evolved resistance to DDT. The disease bounced back across much of Asia and the western Pacific.

In 1969, the eradication programme was finally abandoned. Despite several successes, its overall failure had a chilling impact on malaria research. Investments from richer (and now unaffected) countries dwindled, save for a spike of interest during the Vietnam War. The best minds in the field left for fresher challenges. Malaria, now a tropical disease of poor people, became unfashionable.



François Nosten always wanted to travel. His father, a sailor on merchant ships, returned home with stories of far-flung adventures and instilled a deep wanderlust. Nosten’s original plan was to work on overseas development projects, but one of his teachers pushed him down a different path. “He said the best thing you can do if you want to travel anywhere is to be a doctor. That’s why I started medical school.” As soon as he graduated, he joined Médecins Sans Frontières and started living the dream. He flew off to Africa and South-east Asia, before arriving in Thailand in 1983. There, he started treating refugees from Myanmar in camps along the Thai border.

In 1985, an English visitor arrived at the camps and Nosten took him for a random tourist until he started asking insightful questions about malaria. That man was Nick White. A British clinician, he was drawn to Bangkok in 1980 by the allure of the tropics and a perverse desire to study something unfashionable. The University of Oxford had just set up a new tropical medicine research unit in collaboration with Bangkok’s Mahidol University, and White was the third to join.

“The rosbif and the frog”, as Nosten puts it, bonded over an interest in malaria, a desire to knuckle down and get things done, and a similar grouchy conviviality. They formed a close friendship and started working together.

In 1986, they set up a field station for White’s Bangkok research unit: little more than a centrifuge and microscope within Nosten’s rickety house. Three years later, Nosten moved to Shoklo, the largest refugee camp along the Thai–Myanmar border and home to around 9,000 people. Most were Karen – the third largest of Myanmar’s 130 or so ethnic groups – who were fleeing persecution from the majority Bamar government. Nosten worked out of a bamboo hospital – the first Shoklo Malaria Research Unit.

Malaria was rife. Floods were regular. Military leaders from both Thailand and Myanmar occasionally ordered Nosten to leave. Without any electricity, he often had to use a mirror to angle sunlight into his microscope. He loved it. “I’m not a city person,” he says. “I couldn’t survive in Bangkok very well. I wasn’t alone in Shoklo but it was sufficiently remote.” The immediacy of the job and the lack of bureaucracy also appealed. He could try out new treatments and see their impact right away. He trained local people to detect Plasmodium under a microscope and help with research. He even met his future wife – a Karen teacher named Colley Paw, who is now one of his right-hand researchers (White was the best man at their wedding). These were the best years of his life.

The Shoklo years ended in 1995 after a splinter faction of Karen started regularly attacking the camps, in a bid to force the refugees back into Myanmar. “They came in and started shooting,” says Nosten. “We once had to hide in a hole for the night, with bullets flying around.” The Thai military, unable to defend the scattered camps, consolidated them into a single site called Mae La – a dense lattice of thatch-roofed houses built on stilts, which now contains almost 50,000 people. Nosten went with them.

He has since expanded the Shoklo Unit into a huge hand that stretches across the region. Its palm is a central laboratory in the town of Mae Sot, where Nosten lives, and the fingers are clinics situated in border settlements, each with trained personnel and sophisticated facilities. The one in Mae La has a $250,000 neonatal care machine, and can cope with everything short of major surgery. Nosten has also set up small ‘malaria posts’ along the border. These are typically just volunteer farmers with a box of diagnostic tests and medicine in their house.

“I don’t know anybody else who could have done what François has done,” says White. “He’ll underplay the difficulties but between the physical dangers, politics, logistical nightmares, and the fraught conditions of the refugees, it’s not been easy. He’s not a shrinking violet.”

Thanks to Nosten’s network, locals know where to go if they feel unwell, and they are never far from treatments. That is vital. If infected people are treated within 48 hours of their first symptoms, their parasites die before they get a chance to enter another mosquito and the cycle of malaria breaks. “You deploy early identification and treatment, and malaria goes away,” says Nosten. “Everywhere we’ve done this, it’s worked.”


Victories in malaria are often short-lived. When Nosten and White teamed up in the 1980s, their first success was showing that a new drug called mefloquine was excellent at curing malaria, and at preventing it in pregnant women. Most drugs had fallen to resistant parasites and the last effective one – quinine – involved a week of nasty side-effects. Mefloquine was a godsend.

But within five years, P. falciparum had started to resist it too. “We tried different things like increasing the dose, but we were clearly losing the drug,” says Nosten. “We saw more and more treatment failures, patients coming back weeks later with the same malaria. We were really worried that we wouldn’t have any more options.”

Salvation came from China. In 1967, Chairman Mao Zedong launched a covert military initiative to discover new antimalarial drugs, partly to help his North Vietnamese allies, who were losing troops to the disease. It was called Project 523. A team of some 600 scientists scoured 200 herbs used in traditional Chinese medicine for possible antimalarial chemicals. They found a clear winner in 1971 – a common herb called qing hao (Artemisia annua or sweet wormwood). Using hints from a 2,000-year-old recipe for treating haemorrhoids, they isolated the herb’s active ingredient, characterised it, tested it in humans and animals, and created synthetic versions. “This was in the aftermath of the Cultural Revolution,” says White. “Society had been ripped apart, there was still a lot of oppression, and facilities were poor. But they did some extremely good chemistry.”

The results were miraculous. The new drug annihilated even severe forms of chloroquine-resistant malaria, and did so with unparalleled speed and no side-effects. The team named it Qinghaosu. The West would know it as artemisinin. Or, at least, they would when they found out about it.

Project 523 was shrouded in secrecy, and few results were published. Qinghaosu was already being widely used in China and Vietnam when the first English description appeared in the Chinese Medical Journal in 1979. Western scientists, suspicious about Chinese journals and traditional medicine, greeted it with scepticism and wasted time trying to develop their own less effective versions. The Chinese, meanwhile, were reluctant to share their new drug with Cold War enemies.

During this political stalemate, White saw a tattered copy of the 1979 paper. He travelled to China in 1981, and returned with a vial of the drug, which he still keeps in a drawer in his office. He and Nosten began studying it, working out the right doses, and testing the various derivatives.

They realised that artemisinin’s only shortcoming was a lack of stamina. People clear it so quickly from their bodies that they need seven daily doses to completely cure themselves. Few complete the full course. White’s ingenious solution was to pair the new drug with mefloquine – a slower-acting but longer-lasting partner. Artemisinin would land a brutal shock-and-awe strike that destroyed the majority of parasites, mefloquine would mop up the survivors. If any parasites resisted the artemisinin assault, mefloquine would finish them off. Plasmodium would need to resist both drugs to survive the double whammy, and White deemed that unlikely. Just three days of this artemisinin combination therapy (ACT) was enough to treat virtually every case of malaria. In theory, ACTs should have been resistance-proof.

Nosten started using them along the Thai–Myanmar border in 1994 and immediately saw results. Quinine took days to clear the parasites and left people bed-ridden for a week with dizzy spells. ACTs had them returning to work after 24 hours.

But victories in malaria are often short-lived. In the early 2000s, the team started hearing rumours from western Cambodia that ACTs were becoming less effective. White tried to stay calm. He had heard plenty of false alarms about incurable Cambodian patients, but it always turned out that they were taking counterfeit drugs. “I was just hoping it was another of those,” he says.

It was not. In 2006, Harald Noedl from the Medical University of Vienna started checking out the rumours for himself. In the Cambodian village of Ta Sanh, he treated 60 malaria patients with artesunate (an artemisinin derivative) and found that two of them carried exceptionally stubborn parasites. These infections cleared in four to six days, rather than the usual two. And even though the patients stayed in a clinic outside any malaria hotspots, their parasites returned a few weeks later.

“I first presented those data in November 2007 and as expected, people were very sceptical,” says Noedl. After all, a pair of patients is an epidemiological blip. Still, this was worrying enough to prompt White’s team to run their own study in another nearby village. They got even worse news. The 40 people they treated with artesunate took an average of 3.5 days to clear their parasites, and six of them suffered from rebounding infections within a month. “Rapid parasite clearance is the hallmark of artemisinins,” says Arjen Dondorp, one of White’s colleagues based in Bangkok. “That property suddenly disappeared.”

Despite the hopes that ACTs would forestall artemisinin’s expiry, resistance had arrived, just as it had done for other antimalarials. And, as if to rub salt in the wound, it had come from the same damn place.


Why has a small corner of western Cambodia, no bigger than Wales or New Jersey, repeatedly given rise to drug-beating parasites?

White thinks that the most likely explanation is the region’s unregulated use of antimalarial drugs. China supplied artemisinin to the tyrannical Khmer Rouge in the late 1970s, giving Cambodians access to it almost two decades before White conceived of ACTs. Few used it correctly. Some got ineffective doses from counterfeit pills. Others took a couple of tablets and stopped once their fever disappeared. P. falciparum was regularly exposed to artemisinin without being completely wiped out, and the most resistant parasites survived to spread to new hosts. There is a saying among malariologists: “The last man standing is the most resistant.”

Genetic studies hint at other explanations. Early last year, Dominic Kwiatkowski from the University of Oxford showed that some P. falciparum strains from west Cambodia have mutations in genes that repair faults in their DNA, much like some cancer cells or antibiotic-resistant bacteria. In other words, they have mutations that make them prone to mutating. This might also explain why, in lab experiments, they develop drug resistance more quickly than strains from other parts of the world. Evolution is malaria’s greatest weapon, and these ‘hypermutators’ evolve in fifth gear.

Kwiatkowski’s team also found that P. falciparum is spookily diverse in west Cambodia. It is home to three artemisinin-resistant populations that are genetically distinct, despite living in the same small area. That is bizarre. Without obvious barriers between them, the strains ought to regularly mate and share their genes. Instead, they seem to shun each other’s company. They are so inbred that they consist almost entirely of clones.

Kwiatkowski suspects that these parasites descended from some lucky genetic lottery winners that accumulated the right sets of mutations for evading artemisinin. When they mate with other strains, their winning tickets break up and their offspring are wiped out by the drug. Only their inbred progeny, which keep the right combinations, survive and spread.

It undoubtedly helps that South-east Asia does not have much malaria. In West Africa, where transmission is high, a child might be infected with three to five P. falciparum strains at any time, giving them many opportunities to mate and shuffle their genes. A Cambodian child, however, usually sees one strain at a time, and is a poor hook-up spot for P. falciparum. The region’s infrastructure may also have helped to enforce the parasites’ isolation: local roads are poor, and people’s movements were long constrained by the Khmer Rouge.

West Cambodia, then, could be rife with P. falciparum strains that are especially prone to evolving resistance, that get many opportunities to do so because antimalarial drugs are abused, and that easily hold on to their drug-beating mutations once they get them.

These are plausible ideas, but hard to verify since we still know very little about how exactly the parasites resist a drug. Earlier cases of resistance were largely due to mutations in single genes – trump cards that immediately made for invincible parasites. A small tweak in the crt gene, and P. falciparum can suddenly pump chloroquine out of its cells. A few tweaks to dhps and dhfr, the genes targeted by sulfadoxine and pyrimethamine, and the drug can no longer stick to its targets.

Artemisinin seems to be a trickier enemy. Curiously, P. falciparum takes a long time to evolve resistance to artemisinin in lab experiments, much longer than in the wild. Those strains that do tend to be weak and unstable. “I suspect you need a complicated series of genetic changes to make a parasite that’s not lethally unfit in the presence of these drugs,” says White. “It would be unusual if this was a single mutation.”

Practices such as unregulated drug use and misuse may help encourage and accelerate the rate of such changes out in the field. Kwiatkowski’s study suggests that the parasites may have evolved artemisinin resistance several times over, perhaps through a different route each time. Several groups are racing to find the responsible mutations, with news of the first few breaking in December 2013. That’s the key to quickly identifying resistant parasites and treating patients more efficiently. (Currently, you can only tell if someone has artemisinin-resistant malaria by treating them and seeing how long they take to get better.) “We want to be able to track resistance using blood spots on filter paper,” says Chris Plowe at the University of Maryland School of Medicine, whose group is one of those in the race.

But time is running out. From its origins in Cambodia, resistance has reached the Thai–Myanmar border. Nosten has shown that the proportion of patients who are still infected after three days of ACT has increased from zero in 2000 to 28 per cent in 2011. Most are still being cured, but as artemisinin becomes less effective, its partner drug will have to mop up more surviving parasites. Plasmodium will evolve resistance to the partner more quickly, driving both drugs towards uselessness.

This is already happening in western Cambodia, where ACTs are failing up to a quarter of the time and many people are still infected a month later. Long-lasting infections will provide parasites with more chances to jump into mosquitoes, and then into healthy humans. Malaria cases will rise. Deaths will follow. “This is the silence before the storm,” says Arjen Dondorp. “The threat is still slightly abstract and there’s still not that much malaria, which doesn’t help with a sense of urgency. If we suddenly see malaria exploding, then it’ll be a clear emergency, but it’ll also be too late.”


In his office at Mahidol University, Nick White is surrounded by yellowing monographs of old malaria research and overlooked by a wall-mounted mosaic of drug packets made by his daughter. He is now the chairman of the Mahidol–Oxford Tropical Medicine Research Unit and a mentor to the dozens of researchers within. He is gently ranting.

“Everything to do with change in malaria meets with huge resistance,” he says. He means political resistance, not the drug kind. He means the decade it took for the international community to endorse ACTs despite the evidence that they worked. He means the “treacle of bureaucracy” that he and Nosten swim through in their push to eliminate malaria.

“The global response to artemisinin resistance has been a bit pathetic. Everyone will tell you how important it is and there have been any number of bloody meetings. But there is little appetite for radical change.” He misses the old days when “you could drive a Land Rover across borders in your khaki shorts and spray things and do stuff”.

From the outside, things look rosier. Malaria is fashionable again, and international funding has gone up by 15 times in the last decade. Big organisations seem to be rallying behind the banner of elimination. In April 2013, the World Health Organization published a strategy called The Emergency Response to Artemisinin Resistance

“It’s a marvellous plan,” he says drily. “It says all the right things, but we haven’t done anything.” It follows two other strategies that were published in 2011 and 2012, neither of which slowed the spread of artemisinin resistance. Elimination became a dirty word after the noisy failures of the 1950s and 60s, and the new strategies look like the same old tactics for controlling malaria, presented under the guise of eradicating it. “They’re prescriptions for inertia,” says White.

Worse, they are channelling funds into ineffective measures. Take insecticide-treated bednets, a mainstay of malaria control. “We’ve had meetings with WHO consultants who said, ‘We don’t want to hear a word against bednets. They always work.’ But how cost-effective are they, and what’s the evidence they work in this region? The mosquitoes here bite early in the evening. And who’s getting malaria? Young men. Are they all tucked up in their bednets by 6 o’clock? No. They’re in the fields and forests. Come on! It’s obvious.”

He says that resources could be better devoted to getting rid of fake drugs and monotherapies where artemisinin is not paired with a partner. That would preserve ACTs for as long as possible. The world also needs better surveillance for resistant parasites. White is helping with that by chairing the World-Wide Anti-Malarial Resistance Network – a global community of scientists who are rapidly collecting data on how quickly patients respond to drugs, the presence of resistance genes, the numbers of fake drugs, and more.

White also wants to know if artemisinin-resistant parasites from South-east Asia can spread in African mosquitoes. Hundreds of mosquito species can transmit malaria, but P. falciparum is picky about its hosts. If resistant strains need time to adapt to new carriers, they might be slow to spread westwards. If they can immediately jump into far-off species, they are a plane ride away from Africa. “That changes your containment strategy,” says White, “but stupidly, it’s cut out of every research application we’ve ever made.”

He is pessimistic. “I’m pretty confident we won’t win but I think we should try a lot harder than we have been. If we didn’t pull out all the stops and kids start dying of artemisinin-resistant malaria, and we can trace the genetic origins of those parasites to South-east Asia, we shouldn’t sleep easy in our beds.”


The Mosquito breederWhen Nosten’s team first arrived at Hka Naw Tah in February, they slept and worked from the village’s unassuming temple. Using development funds from their grant, they put up a water tower and supplied electricity for the local school. In return, the villagers built them a clinic – a spacious, open-sided hut with a sloping tin roof, benches sitting on a dirt floor, a couple of tables holding boxes of drugs and diagnostic kits, treatment rooms, and a computer station. It took just two days to erect.

The Karen respect strong leadership but there is an easy-going camaraderie in the clinic. When we arrive, one of the research assistants is napping across a bench. Nosten walks over and sits on him. “You see, and I think this is a good sign, that it’s hard to tell who’s the boss and who’s the patient,” he says.

Most of the villagers don’t seem sick, but many of them have malaria nonetheless. Until recently, Nosten’s team had always searched for the parasites by examining a drop of blood under a microscope. If someone is sick, you can see and count the Plasmodium in their red blood cells. But in 2010, they started collecting millilitres of blood – a thousand times more than the usual drops – and searching for Plasmodium’s DNA. Suddenly, the proportion of infected people shot up from 10–20 per cent to 60–80 per cent. There are three, four, maybe six times as many infected people as he thought.

“We didn’t believe it at first,” says Nosten, “but we confirmed it and re-confirmed it.” Perhaps the tests were giving false positives, or picking up floating DNA from dead parasites? No such luck – when the team treated people with ACTs, the hidden parasites disappeared. They were real.

These ‘sub-microscopic infections’ completely change the game for elimination. Treating the sick is no longer good enough because the disease could bounce back from the hordes of symptomless carriers. The strike will have to be swift and decisive. If it’s half-hearted, the most resistant parasites will survive and start afresh. In malarial zones, you need to treat almost everyone, clearing the parasites they didn’t even know they had. This is Nosten’s goal in the border villages like Hka Naw Tah. He has support from the Bill and Melinda Gates Foundation, one of the few large funders to have truly grasped the urgency of the situation and who are “very much in the mood for elimination”.

Killing the parasites is easy: it just involves three days of ACTs. Getting healthy people to turn up to a clinic and take their medicine is much harder. The team have spent months on engagement and education. The clinic is dotted with posters explaining the symptoms of malaria and the biology of mosquitoes. Earlier this morning, Honey Moon, a Karen woman who is one of Nosten’s oldest colleagues, knocked on the doors of all the absentees from the last round to persuade them to come for tests. As a result, 16 newcomers turned up for treatments, bringing the team closer to the full 393. Nosten is pleased. “In this village, I’m quite optimistic that most people will be free of the parasite,” he says.

Another village down the river is proving more difficult. They are more socially conservative and have a poorer understanding of healthcare. There are two factions of Karen there, one of which is refusing to take part to spite their rivals. “It’s a good lesson for us,” says Nosten. “These situations will be elsewhere.” Eliminating malaria is not just about having the right drug, the deadliest insecticide, or the most sensitive diagnostic test. It is about knowing people, from funders to villagers. “The most important component is getting people to agree and participate,” says Nosten. It matters that he has been working in the region for 30 years, that the Shoklo unit is a familiar and trusted name in these parts, that virtually all his team are Karen. These are the reasons that give Nosten hope, despite the lack of political will.

If the strategy looks like it is working after a year, they will start scaling up. Eventually, they hope to cover the entire sinuous border. I ask Nosten if he would ever consider leaving. He pauses. “Even if I wanted to go somewhere else, I’m more or less a prisoner of my own making,” he says. He would need to find a replacement first – a leader who would command respect among both the Karen and malaria researchers, and would be willing to relocate to a place as remote as Mae Sot. It is hard to imagine a second person who would tick all those boxes. Surrounded by airborne parasites, spreading resistance, and border-hopping refugees, François Nosten is stuck. He would not have it any other way.


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An Electric Sock For the Heart

The titles of scientific papers can be a bit intimidating. For example, I’m currently reading “3D multifunctional integumentary membranes for spatiotemporal cardiac measurements and stimulation across the entire epicardium”.

In other words: electric heart socks.

A team of scientists led by John Rogers at the University of Illinois at Urbana-Champaign has created a web of electronics that wraps around a living heart and measures everything from temperature to electrical activity. It’s an ultra-thin and skin-like sheath, which looks like a grid of tiny black squares connected by S-shaped wires. Its embrace is snug and form-fitting, but gentle and elastic. It measures the heart’s beats, without ever impeding them.

Electronic cardiac sock

Its goal is to monitor the heart in unprecedented detail, and to spot the unusual patterns of electrical activity that precede a heart attack. Eventually, it might even be able to intervene by delivering its own electrical bursts.

Cardiac socks have been around since the 1980s but the earliest ones were literal socks—fabric wraps that resembled the shape of the heart, with large electrodes sewn into place. They were crude devices, and the electrodes had a tough time making close and unchanging contact with the heart. After all, this is an organ known for constantly and vigorously moving.

The new socks solve these problems. To make one, graduate students Lizhi Xu and Sarah Gutbrod scan a target heart and print out a three-dimensional model of it. They mould the electronics to the contours of the model, before peeling them off, and applying them to the actual heart. They engineer the sock to be ever so slightly smaller than the real organ, so its fit is snug but never constraining.

This is all part of Rogers’ incredible line of flexible, stretchable electronics. His devices are made of mostly made of the usual brittle and rigid materials like silicon, but they eschew right angles and flat planes of traditional electronics for the curves and flexibility of living tissues. I’ve written about his tattoo-like “electronic-skin”, curved cameras inspired by an insect’s eye, and even electronics that dissolve over time.

The heart sock is typical of these devices. The tiny black squares contain a number of different sensors, which detect temperature, pressure, pH, electrical activity and LEDs. (The LEDs shine onto voltage-sensitive dyes, which emit different colours of light depending on the electrical activity of the heart.) Meanwhile, the flexible, S-shaped wires that connect them allow the grid to stretch and flex without breaking. As the heart expands and contracts, the web does too.

So far, the team have tested their device on isolated rabbit hearts and one from a deceased organ donor. Since these organs are hooked up to artificial pumps, the team could wilfully change their temperature or pH to see if the sensors could detect the changes. They could. They could sense when the hearts switched from steady beats to uncoordinated quivers.

Rogers thinks that tests in live patients are close. If anything, the doctors he is working with are more eager to push ahead. “We’re scientists of a very conservative mindset. They have patients who are dying,” he says. “They have a great appetite for trying out good stuff.”

The main challenge is to find a way of powering the device independently, and communicating with it wirelessly, so that it can be implanted for a long time. Eventually, Rogers also wants to add components that can stimulate the heart as well as recording from it, and fix any aberrant problems rather than just divining them.

It’s a “remarkable accomplishment” and a “great advance in materials science”, says Ronald Berger at Johns Hopkins Medicine, although he is less sure that the device will be useful is diagnosing or treating heart disease. “I don’t quite see the clinical application of these sensors.  There might be some therapy that is best implemented with careful titration using advanced sensors, but I’m not sure what that therapy is.”

But Berger adds that the sock has great promise as a research tool, and a couple of other scientists I contacted agree. After all, scientists can use the device to do what other technologies cannot: measure and match the heart’s electrical activity and physical changes, over its entire surface and in real-time.

For more on John Rogers’ flexible electronics, check out this feature from Discover that I co-wrote with Valerie Ross.

Reference: Xu, Gutbrod, Bonifas, Su, Sulkin, Lu, Chung, Jang, Liu, Lu, Webb, Kim, Laughner, Cheng, Liu, Ameen, Jeong, Kim, Huang, Efimov & Rogers. 2014.  3D multifunctional integumentary membranes for spatiotemporal cardiac measurements and stimulation across the entire epicardium. Nature Communications. http://dx.doi.org/ 10.1038/ncomms4329

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A Resurrected Cretaceous Answer to the ‘Disease of Kings’

Gout—a disease of red, painful, swollen joints—has an unfair reputation as a disease  that only affects the wealthy after a lifetime of overindulgence. In reality, it’s the legacy of evolutionary changes that took place more than 20 million years ago, which we’re still paying for now. Gout was once called the “king of diseases and the disease of kings”. It could equally be the “disease of apes”.

The substance responsible for the condition is uric acid, which is normally expelled by our kidneys, via urine. But if there’s too much uric acid in our blood, it doesn’t dissolve properly and forms large insoluble crystals that build up in our joints. That explains the painful swellings. High levels of uric acid have also been linked to obesity, diabetes, and diseases of the heart, liver and kidneys.

Most other mammals don’t have this problem. In their bodies, an enzyme called uricase converts uric acid into other substances that can be more easily excreted.

Uricase is an ancient invention, one that’s shared by bacteria and animals alike. But for some reason, apes have abandoned it. Our uricase gene has mutations that stop us from making the enzyme at all. It’s a “pseudogene”—the biological version of a corrupted computer file. And it’s the reason that our blood contains 3 to 10 times more uric acid than that of other mammals, predisposing us to gout.

How did it come to this? Why did we do away with such an important enzyme? And when?

To find out, a group of scientists led by Eric Gaucher at the Georgia Institute of Technology resurrected long-gone editions of uricase that haven’t been seen for millions of years.

Team members James Kratzer, Miguel Lanaspac and Michael Murphy compared the uricases in modern mammals to infer the sequences of ancestral varieties. “It’s like what a historical linguist does, when they study modern languages and try to understand how an ancient ones were pronounced,” says Gaucher. Then, the team actually built these ancient enzymes in their labs, and compared their ability at processing uric acid.

The oldest version, which was wielded by the last common ancestor of all mammals 90 million years ago, was the most active one. It outperformed all its modern descendants. Since that ancient heyday, things have gradually gone downhill.

Throughout mammalian evolution, and especially during primate evolution, uricase has picked up mutations that have made for progressively less efficient enzymes. In the last common ancestor of all apes, uricase had already been hobbled to the point of near-uselessness. The ape-specific mutations that turned our uricases into broken pseudogenes merely disabled something that was already FUBARed to begin with.

Why this slow, creeping decline? Gaucher suspects that the answer involves fruit.

The biggest drops in uricase’s efficiency coincided with a time when the Earth’s climate was cooling. The ancient fruit-eating primates of Europe and Asia faced a glut of food in the summer, but risked starving in winter when fruit was unavailable.

Here’s where uric acid comes in. Our cells produce the stuff when they break down fructose, the main sugar in fruit. In turn, uric acid stimulates the build-up of fat—a process that uricase counters. Indeed, when Gaucher’s team dosed human cells with the ancient, efficient uricases, they became less good at making fat when exposed to fructose. But with later inactive uricases, they produced a substantial amount of fat.

So, disable uricase and you risk building up high levels of uric acid, but you also become a champion at turning fruit into fat. For ancient primates facing an increasingly seasonal food supply, that trade-off may have been worth it.

It’s a nice story, although it only explains the final act of uricase’s downfall. Other factors almost certainly played a role in the enzyme’s gradual decline. For example, Michael Hershfield from Duke University notes that early primates lived in rainforests, had easy access to water, and could make a lot of urine—all the better for getting rid of surplus uric acid. He speculates that these conditions might have reduced the need for uricase enough to allow the enzyme to accumulate disabling mutations.

Still, Gaucher’s results provide some support for an old but unproven idea called the thrifty gene hypothesis. Proposed in 1962, it says that humans have genes that suited our ancestors during times of scarce food, but predispose us to diabetes and obesity in the modern age of free-flowing calories. Uricase is the first good example. Our broken version may have helped our primate ancestors to thrive but it leaves us prone to gout and other illnesses linked to uric acid, whose rates have soared in recent years.

The team’s resurrected enzymes may be able to help with that too.

For over 20 years, pharmaceutical companies have tried to develop treatments for gout by using working versions of uricase from other mammals. But you can’t simply inject a pig uricase into a human patient—our immune reaction would go nuts in the presence of such a foreign enzyme.

Hershfield’s group developed a workaround by fusing the pig uricase with the baboon version. The pig bit does the heavy metabolic lifting, and the baboon bit cloaks it from our immune system. In 2010, the US Food and Drug Administration approved this chimeric enzyme, known as Krystexxa, for treating severe chronic gout.

Gaucher thinks that we can find better solutions by looking to the past. His team found that the oldest of their resurrected enzymes is both more efficient than the raw pig-baboon chimera, and lasts longer in rats. And despite its ancient nature, it’s a closer match for human uricase than even the baboon version, so it might be even less provocative to the immune system. The team have now filed a patent for the ancient uricases and formed a start-up company to turn them into an actual drug.

Hershfield anticipates bumps along the way. “It took about 17 years from the time I conceived of developing a recombinant uricase for treating refractory gout to the time it received FDA approval,” he says. “I wish [them] success, but I suspect I may not be around to witness approval of their drug.” Gaucher counters that the existing drug has already paved the way for FDA approval: “We’ll either jump through fewer hoops or we won’t have to jump as high.”

He undoubtedly has a long way to go but it’s an enticing notion that an enzyme hasn’t been around since the dinosaurs ruled the world might help gout sufferers in the future. As Belinda Chang from the University of Toronto says in a related commentary, “We are all prisoners of our history, but perhaps we can find better solutions for the future by learning from the past.”

Reference: Kratzer, Lanaspa, Murphy, Cicerchi, Graves, Tipton, Ortlund, Johnson & Gaucher. 2014. Evolutionary history and metabolic insights of ancient mammalian uricases. PNAS http://dx.doi.org/10.1073/pnas.1320393111

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Now This Is How You Find Disease Genes

When you read stories about scientists identifying a new link between Gene X and Disease Y, the underlying studies vary a lot in quality. At one extreme, you get papers which show that a variant of Gene X is common in a small group of people with Disease Y and not in healthy controls… and that’s it. You don’t really know if X is really responsible for Y, or even if the result is genuine and not a false alarm produced by small numbers.

At the other extreme, you have this—a study that used a smorgasbord of experiments to identify 18 new genes behind hereditary spastic paraplegias (HSPs). This diverse group of genetic disorders all involve damage to the long neurons running between the brain and spinal cord, leading to stiffness and involuntary contractions in leg muscles.

Scientists have already linked 22 genes to HSPs, but these only explain around 20 to 30 percent of cases. “Many of the children with these conditions can’t receive a proper diagnosis and there’s no treatment available,” says Joseph Gleeson at the University of California, San Diego. “We wanted to understand more about the causes, and hopefully see some new treatments come out of that.”

To find more HSP genes, Gleeson’s team forged contacts with scientists in countries where HSP is more common and where genetic studies are rare, including Egypt, Pakistan and Iran. They found 55 families with the disorders and sequenced every gene in 93 of their members. They identified several genes that seemed to cause HSPs in these people, and they bred mutant fish to check that getting rid of these genes actually does produce relevant symptoms. They created a network to show what these genes do, and how they interact with each other. And they used that network to find even more HSP genes.

The scope of the work, led by team members Gaia Novarino, Ali Fenstermaker and Maha Zaki, is incredible. “We’ve been working on it for close to 10 years,” says Gleeson. “We just didn’t feel comfortable publishing it until it was all done. Hopefully, people will look to our paper as a roadmap for studying genetically diverse conditions.”

Between them, the 18 new genes and the 22 old ones explain around 70 percent of the HSP cases among the team’s recruits. “That is of enormous value, not only for biological understanding, but also for providing a definite diagnosis in families and for accelerating research into possible treatment of these progressive disorders,” says Joris Veltman, a geneticist at Radboud University Nijmegen Medical Centre.

Just finding the families was hard enough. “It’s not easy for an American to get into Iran,” says Gleeson. But it was worth it because in these parts of the world, the practice of marrying relatives means that family members share an unusually high proportion of their DNA. This makes it easier to find recessive genes that only cause HSP when people inherit two copies.

The team sequenced every volunteer’s complete exome—the 1 percent of their genome that codes for proteins. By comparing the exomes of family members with or without HSPs, they showed that a third of the cases were due to genes that had already been implicated in the disorders. But another 40 percent were possibly caused by mutations in 15 new genes.

Next, they verified this list by engineering baby zebrafish that lacked each of these candidate genes. None of the mutants could swim properly. Some, for example, had tails that were permanently curved to the side, much like the stiff limbs of children with HSP. “We felt compelled to do that,” says Gleeson. “For a lot of the genes, we only had a single family with the mutation.” Without the fish experiments, he wouldn’t have felt comfortable claiming that these genes were really related to HSP.

Exome sequencing is quickly becoming the frontline technique for gene detectives, who no longer have to narrow down their search to specific parts of the genome. They can just sequence every gene and see what jumps out. “The current study clearly takes this approach to the next level by applying it to a very large cohort and performing systematic functional follow-up studies,” says Veltman.

Even that wasn’t enough. “In some diseases, one is left with a hodgepodge of genes and no clear path forward,” says Gleeson. “We tried to weave commonalities between our genes and understand what they were telling us.” They did that by mapping all the interactions between their HSP genes and the proteins they make, creating a tangled network that they call the “HSPome”.

The genes clustered in different groups based on what they did. “It was like lifting the veil,” says Gleeson. “We could see how all the factors that were identified fit together.” Some are involved in folding proteins correctly, others help to make building blocks of DNA, and yet others help neurons to grow and move to the right places. These clusters tell us about “points of molecular vulnerability” in the brain-to-spine neurons that are damaged in HSPs, says John Fink from the University of Michigan.

The team then extended the network to look at other genes that interacted with the ones they identified—the “friends of friends”. By scanning this extended list, they found more three more new HSP genes, which underlie the disorders in three more families. That brought the total up to 18.

The network also overlapped a lot with other sets of genes that have been implicated in Alzheimer’s disease, Parkinson’s disease and Lou Gehrig’s disease. This suggests that these disparate brain diseases may have some common ground, and that drugs which target these overlapping genes could help to treat several conditions.

“This is important, because drug development is very costly, and the larger the potential market, the more interested pharmaceutical companies will be to pursue these leads,” says Craig Blackstone from the National Institutes of Health. Indeed, by linking HSPs to better-studied (and better-funded) conditions, Gleeson hopes to spur interest in these often-overlooked conditions.

“These are exciting times for research not only into the causes and treatments for HSP but for other neurodegenerative disorders as well,” says Fink.

Reference: Novarino, Fenstermaker, Zaki  Hofree, Silhavy, Heiberg, Abdellateef, Rosti, Scott, Mansour, Masri, Kayserili, Al-Aama, Abdel-Salam, Karminejad, Kara, Kara, Bozorgmehri, Ben-Omran, Mojahedi, Gamal El Din Mahmoud, Bouslam, Bouhouche, Benomar, Hanein, Raymond, Forlani, Mascaro, Selim, Shehata, Al-Allawi, Bindu, Azam, Gunel, Caglayan, Bilguvar, Tolun, Issa, Schroth, Spencer, Rosti, Akizu, Vaux, Johansen, Koh, Megahed, Durr, Brice, Stevanin, Gabriel, Ideker, and Gleeson. 2013. Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders. Science http://dx.doi.org/10.1126/science.1247363

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New Blood-Resistant Glue Mends Broken Hearts Without Sutures

How do you mend a broken heart? You’re operating on a heart and it’s got a tear in it. How do you seal it?

Sutures? Staples? These are the traditional answers, but they aren’t good ones. Both involve piercing tissue and creating holes, which is bad news for an organ that’s constantly moving, and vigorously pumping blood. Holes lead to clots. They also bleed.

And if you specialise in doing heart surgeries on babies, as Pedro del Nido from Boston Children’s Hospital does, you can add small size and delicate tissues to those other challenges. “The holy grail for heart surgeons, especially for those who work on babies, is to attach things without damaging the normal underlying tissue,” he says.

A glue, then. The trouble is that a heart adhesive must be strong enough to hold despite the heart’s constant beating, but flexible enough to allow those same beats to happen. It has to work in wet conditions—something that most glues aren’t designed to do. It needs to repel water so it doesn’t dissolve. It must thicken slowly or blood will wash it away. It can’t thicken immediately because you want to be able to position and adjust it. It has to be biodegradable.

These design specifications are an engineer’s nightmare, which explains why viable heart glues don’t exist. That is, until now.

Working with del Nido, Jeff Karp at the Brigham and Women’s Hospital and MIT’s Bob Langer have created a glue that ticks all the boxes. It seals heart tissue and blood vessels, it’s strong but flexible, and it’s made only from naturally-occurring substances already found in the body. It can be applied as a viscous gel, and then hardened into a strong adhesive with a burst of ultraviolet light. And, best of all, it works in flowing blood.

“I’m very excited about this project,” says del Nido. “There’s a huge clinical need for it. It’ll allow us to do much more sophisticated reconstructions than what we can do today.”

Karp has a history of making “bioinspired” adhesives, from sticky tape based on a parasitic worm to medical needles based on a porcupine’s quills. This time, he drew inspiration from several animals that can stick to wet surfaces.  Insects, for example, often secrete viscous, water-repellent substances from their feet, which push water out of any gaps in the underlying surfaces. Meanwhile, the sandcastle worm builds underwater tubes by exuding a glue from its head. This substance is also water-repellent and viscous, and hardens over time into a strong adhesive.

A sandcastle worm, sticking out of its tube. Credit: Fred Hayes, University of Utah
A sandcastle worm, sticking out of its tube. Credit: Fred Hayes, University of Utah

The team realised that they had already made something similar—a substance called PGSA. It’s a union of glycerol, a basic building block of fats and oils, and sebacic acid, which is produced when certain fats break down.  The team had originally made PGSA to create scaffolds on which they could grow new tissues or organs. (See here for Langer’s work on growing organs.) “We had hints that it could adhere to tissue but we never tested that,” says Karp.

Working with del Nido, Karp and Langer tweaked the formula of PGSA to create a viscous liquid that could be easily spread but would hold its shape. They also added a substance that creates bridges between the PGSA molecules on exposure to ultraviolet light, quickly curing the glue on demand. “Other adhesives like crazy glue cure immediately in the presence of moisture or water,” says Karp. “Ours doesn’t. We can place it in a very wet environment completely filled with blood and it only becomes adhesive when we cure it with light.”

These traits give the glue time to seep in between the fibres of the underlying tissues, displacing water along the way. That’s why it’s so strong once it hardens—it’s part of the tissue, rather than just a layer on the surface.

The new glue outcompeted cyanoacrylate, or super glue, in several tests: it stuck better, it swelled less, and it triggered less inflammation. “This is a major feat, as super glue is considered to be the strongest tissue adhesive around,” says Christian Kastrup from the University of British Columbia. The only potential damage comes from the ultraviolet light, which is infamous for its ability to damage DNA. Still, a five-second burst is unlikely to do much lasting harm.

Karen Christman at the University of California, San Diego, says the technology is exciting, but that “several preclinical tests need to be performed before translation to patients.” First and foremost, they need to check that it’s safe for use inside actual hearts. “It is also unclear if this could work with Gore-Tex patches, which are one of the most common patch materials used for the heart,” she says. “If this is possible, this could definitely make surgeries easier considering there is often bleeding at the suture lines with these synthetic patches.”

The team is on the case. So far, they have successfully tested the glue in four live pigs, using it to attach patches to their beating hearts, and to seal damaged carotid arteries. The animals survived, fared well, and showed no signs of clots or bleeding after the operations.

A Paris-based company called Gecko Biomedical has now licensed the technology and raised 8 million euros to bring it to market. They’re now scaling up the manufacture of the glue and, once that’s done, they hope to move to clinical trials. If it succeeds, Karp hopes to put it in the hands of clinicians within three years. For his part, del Nido wants to see if the glue can stop blood from leaking from holes around sutures. If that’s safe and effective, he will move on to more complex things.

This isn’t just about hearts, either. Karp suggests that the glue might also work in the gut—another environment characterised by lots of liquid and constant movement. “It really opens the door for more minimally invasive approaches,” he says.

Reference: Lang, Pereira, Lee, Friehs, Vasilyev, Fein, Ablasser, Cearbhaill, Xu, Fabozzo, Padera, Wasserman, Freudenthal, Ferreira, Langer, Karp & del Nido. 2013. A Blood-Resistant Surgical Glue for Minimally Invasive Repair of Vessels and Heart Defects. Science Translational Medicine. Vol 6 Issue 218 218ra6

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Your Disease In A Dish

When you read about biomedical discoveries in the press, odds are you’re reading about experiments done in cells, grown in laboratories. They float, disembodied, in flasks of red liquid, so it’s easy to forget that they originally came from people. The most commonly used human cells, known as HeLa, came from a woman called Henrietta Lacks. MCF-7 cells came from the breast tumour of a 69-year-old woman named Frances Mallon. Jurkat cells originated within a 14-year-old boy with leukaemia.

These individuals, along with hundreds of others, have acted as stand-ins for the rest of humanity. Their immortal cell lines provided scientists with a ready supply of cells for experiments, and fuelled countless discoveries that benefited the rest of us. But our command of cell biology is growing to a point where we may no longer need proxies.

Here’s a vision of the future. You’re diagnosed with a rare genetic disorder. Your doctors take a sample of your cells and grow them, creating cell lines, tissues and even mini-organs—little model versions of you, complete with all the genetic faults that are responsible your disease. The doctors use these models to work out what these mutations are doing, and to test the safety and effectiveness of different drugs. Based on these tests, they decide on the most appropriate treatment—one that’s intimately tailored to your biology.

We’re not quite there yet, but we’re making good progress. Consider what Kathrin Meyer and Brian Kaspar from the Nationwide Children’s Hospital in Ohio, USA have just done.

They study amyotrophic lateral sclerosis (ALS)—the fatal disease that affects physicist Stephen Hawking, and that affected baseball player Lou Gehrig. It’s caused by some combination of genetic mutations that gradually kill motor neurons—the ones that control our muscles. As they die, muscles weaken and waste away. Patients lose their ability to walk, move their arms, speak, swallow, and breathe.

Recently, a few teams of scientists have shown that other cells in the brain—glial cells—help to show the motor neurons to death’s door. Glial cells normally provide support, nutrition and protection to neurons. But if they carry ALS-causing mutations, they can selectively kill motor neurons instead. The protectors become assassins.

An astrocyte. Credit: Nathan S. Ivey at TNPRC.
An astrocyte. Credit: Nathan S. Ivey at TNPRC.

To study these turncoats, the team took skin cells from their seven patients and reprogrammed them into neural precursors, which can produce the various cells within our brains and nervous systems. It took just four genes to trigger the transformation, and around a month to grow healthy batches of cells. With different growth factors, the team could coax these precursors into becoming neurons (including motor neurons specifically) and astrocytes (a star-shaped type of glial cell).

On their own, the motor neurons lasted for weeks. But Meyer found that they quickly died when exposed to the astrocytes. Within five days, up to 80 percent of them were dead, and the survivors were left with just a few, short branches. The ALS astrocytes were the only ones that did this; those from healthy patients had no such murderous effects.

Four of the patients that the team worked with have familial ALS—a kind that accounts for 10 percent of cases, and is caused by inherited mutations in genes such as SOD1 and C9orf72. Three of the patients had sporadic ALS—the most common variety, which is caused by typically unknown mutations that spontaneously appear in people with no family history. The team found that astrocytes from all of these patients are toxic to motor neurons. This suggests that both the SOD1 and C9orf72 mutations are probably turning astrocytes into killers through the same route—one that also applies to whatever unknown mutations are behind the sporadic cases.

The details are still unclear, but the team hope to uncover them through their powerful new tool—their quick and consistent technique for generating an endless supply of neurons and astrocytes, which are personalised versions of a single patient’s cells. They also think they might be able to test different drugs on these cells, to work out the most promising treatments for individual people with ALS during their lifetimes.

If that seems a long way away, it’s worth remembering how far this line of research has come in a very short time. In 2006, Shinya Yamanka found a way of reprogramming cells from adult mice into a stem-like state, from which they could be coaxed into a number of different fates. Take a skin cell, and you could eventually end up with a neuron. Other scientists accomplished the same feat with human cells in 2007, and with cells from a woman with ALS in 2008 (which were then converted back into motor neurons).

In 2010, a Stanford group skipped the intermediate stage altogether and just converted skin cells directly into neurons. As before, the mouse cells came first, then human cells a year later. Meanwhile, another team converted mouse skin cells into neural progenitors, which can produce glia as well as neurons. And now, Meyer and Kaspar have repeated the same trick for human neural progenitors.

When the press covers these discoveries, they normally talk about creating supplies of new cells to bolster the ones that are lost through diseases like ALS. Such applications are a long way off, with many safety issues to address and open questions to answer. In the meantime, they have enormous potential as research tool.

As I wrote in 2008, “it’s a godsend for ALS research. Progress in understanding the disease has been relatively slow, mainly because it has been nigh impossible to obtain a decent supply of living motor neurons affected by the condition. Now, researchers can culture large colonies of both motor neurons and glia that carry genetic defects associated with ALS. That gives them free reign to investigate the causes of the disorder, the environmental conditions that interact with these genes, and the way the affected neurons interact with other types of cell. It also provides them with neurons to use for screening and testing potential drugs.”

Reference: Meyer, Ferraiuoloa, Miranda, Likhite, McElroy, Renusch, Ditsworth, Lagier-Tourenne, Smith, Ravits, Burghes, Shaw, Cleveland, Kolb & Kaspar. 2013. Direct conversion of patient fibroblasts demonstrates non-cell autonomous toxicity of astrocytes to motor neurons in familial and sporadic ALS. PNAS http://dx.doi.org/10.1073/pnas.1314085111

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Cyborg Bladders Stop Incontinence In Rats After Spine Damage

Implants that read and decipher our brain activity have allowed people to control computers, robotic limbs or even remote-controlled helicopters, just by thinking about it. These devices are called BMIs, short for brain-machine interfaces.

But our cyborg future isn’t limited to machines that hook up to our brains. At the University of Cambridge, James Fawcett has created a BMI where the B stands for bladder.  The implanted machine senses when a bladder is full, and automatically sends signals that stop the organ from emptying itself.

So far, it works in rats. It will take a lot of work to translate the technique into humans, but it could give bladder control back to people who have lost it through spinal injuries.

As the bladder fills up, its walls start to stretch. Neurons in the bladder wall detect these changes and send signals to the dorsal root, a structure at the back of the spinal cord. If left to themselves, these signals trigger a reflex that empties the bladder. That doesn’t usually happen because of neurons that travel in the opposite direction, descending from the ventral root at the front of the spine into the bladder. These counteract the emptying reflex and allow us to void the bladder when we actually want.

Spinal injuries often rob people of that control, by damaging the ventral neurons. “Take those away and you dribble all over your clothes every half hour,” says Fawcett.

There are two fixes. The first was developed by an eccentric British neuroscientist called Giles Brindley in the 1970s. Brindley is infamous for a lecture in which he demonstrated the effectiveness of a treatment for erectile dysfunction, by dropping his trousers and showing his erect penis to the audience. But his real claim to fame is an implant that stimulates the ventral root directly, allowing people with spinal injuries to urinate on demand.

There’s a catch—it only works if surgeons cut the neurons in the dorsal root so the bladder can’t spontaneously empty itself. This has severe side effects: men can’t get erections, women have dry vaginas, and both sexes end up with weak pelvic muscles.

The only other alternative is to paralyse the bladder with botox. Now, it can’t contract at all, and people have to empty it by sticking a catheter down their urethra. That’s expensive, difficult, unpleasant, and comes with a high risk of infection.

Fawcett’s team, led by Daniel Chew and Lan Zhu, have developed a better way.

First, they hack into the bladder’s communication lines. Rather than cutting through the dorsal root, they tease out fine strands of neurons called dorsal rootlets, and thread them into tiny sheaths called microchannels. The channels record the signals going from the bladder to the spine, revealing what the organ is up to.

When the bladder is ready to empty itself, the channels detect a big spike in activity. They react by sending signals to a stimulator that’s hooked up to the nerves leading into the bladder’s muscles. The stimulator hits these nerves with a high-frequency electric pulse that stops them from firing naturally. The bladder’s muscles don’t contract, and no unwanted urine is spilled. When the user actually wants to wee, they just push a button and the stimulator delivers a low-frequency pulse instead. Only then does the bladder contract.

This device does everything that a normal bladder does, but uses electronics to stand in for damaged nerves. It works on a closed loop, so users should be able to go about their day to day lives without worrying about incontinence. And it doesn’t sever the dorsal root, so it carries none of the side effects of the Brindley method.

“That would be a major advance,” says Kenneth Gustafson, a biomedical engineer from Case Western Reserve University. “Restoration of bladder control is one of the most important problems of individuals with spinal cord injuries.”

“The quality of the neural recordings that they’re showing with their channel electrodes is really very impressive and convincing,” says Robert Gaunt from the University of Pittsburgh, who has also worked on neural prosthetics for the bladder.

The team have successfully tested their device in rats, and they’re working on scaling it up to humans. “We haven’t actually trying dissecting human dorsal roots into rootlets but the anatomy’s quite similar,” says Fawcett.

“It’s good to see this has come to fruition,” says Clare Fowler from University College London, who studies ways of solving incontinence in people with neurological problems. “There have been a lot of very clever developments to get this working, and they are to be congratulated.” However, she adds that the device is “many years away from translation into human usefulness.”

Gaunt adds that the nerves that control the bladder muscles are near to those that control its sphincter. If you shut down the former with high-frequency pulses, you might risk accidentally shutting down the sphincter too—it would then relax, and the bladder might empty.

But the main problem is longevity. The device needs to be turned into something like a pacemaker, which can be implanted reliably for long periods of time. Currently, that’s impossible because the rootlets can only survive for 18 months in the microchannels before they build up fatal amounts of scar tissue. “That’s not long enough to be useful,” says Fawcett, who is working on ways of extending their lifespan.

Fawcett adds that his work isn’t just about the bladder. His microchannels offer a new way of effectively recording signals from nerves outside the brain—a goal that has historically been very difficult. Tap into the right nerves, and the device could potentially be used to control everything from prosthetic limbs to immune reactions to the digestive system.

Again, that’s a far-off goal. “We’re not sure that outside the dorsal root, we can tease the peripheral nerves into rootlets,” says Fawcett. “They weave around a lot more, so you’d risk damaging them. We’re looking into that currently.”

Reference: Chew, Zhu, Delivopoulos, Minev, Musick, Mosse, Craggs, Donaldson, Lacour, McMahon & Fawcett. 2013. A Microchannel Neuroprosthesis for Bladder Control After Spinal Cord Injury in Rat. Vol 5 Issue 210 210ra155

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Meet The Mice That Are Immune To Jet lag

I’ve just arrived home from 14 hours of flying. The clocks on my phone and laptop have been ticking away the whole time, and it takes a few seconds to reset them to British time. The clocks in my body are more difficult.

We run on a daily 24-hour body clock, which controls everything from our blood pressure to our temperature to how hungry we feel. It runs on proteins rather than gears. Once they’re built, these proteins stop their own manufacture after a slight delay, meaning that their levels rise and fall with a regular rhythm. These timers tick away inside almost all of our cells, and they’re synchronised by a tiny collection of 10,000 neurons at the bottom of our brain. It’s called the suprachiasmatic nucleus (SCN). It’s the master clock. It’s the conductor that keeps the orchestra in sync.

The SCN is also sensitive to light. It gets signals from our eyes, which allows it to synchronise its ticking with the 24-hour cycle of day and night outside. The SCN is what connects the rhythms of our bodies with those of the planet.

But when we travel far and fast, and suddenly land in a new time zone, the SCN becomes misaligned with the environment. It takes time to re-adjust, typically one day for every time zone crossed. In the meantime, our sleep is disrupted and our physiology goes weird. In other words: jet lag.

But at Kyoto University, Yoshiaki Yamaguchi and Toru Suzuki have engineered mice that break this rule. They are, with apologies for the awful word, unjetlaggable. If you change the light in their cages to mimic an 8-hour time difference, they readjust almost immediately. Put them on a red-eye flight from San Francisco to London and they’d be fine.

The secret to their jet lag-resistance lies in a hormone called arginine vasopressin (AVP). Around half of the neurons in the SCN secrete it, and they also detect it using several receptor proteins. Yamaguchi and Suzuki deleted the genes for two of these receptors—V1a and V1b—from their mice. They still make AVP, but they can’t respond to it. By using chemicals that block the same receptors, the team even managed to help normal mice recover from jet lag faster than usual.

But before we start thinking about a “cure” for jet lag, there’s a problem: You can’t deliver drugs directly to the brain, so any pill that blocked AVP receptors would do so across the whole body. And these receptors are found in other organs, like the kidneys. Disrupt them, and you’d affect your blood pressure and your salt levels. Your kidneys might also stop absorbing water and you’d produce urine by the bucket. “The recipient would have to pee like a race horse,” says David Weaver, who studies circadian rhythms at the University of Massachusetts Medical School. “Even with this interesting research, we’re a ways from making a pill that could be swallowed to reset the clock.”

A paradox

The team’s discovery took a lot of work. They catalogued some 200 genes that are activated in the SCN’s neurons, and deleted them one at a time in mutant mice. They then changed the lights in the animals’ cages so they came on and went off 8 hours earlier or later. They watched for weird behaviour. Of all the rodents, those that lacked both V1a and V1b stood out.

Mice are active at night. When the lights go out, they’re soon up and about. But if you suddenly shift their light cycles forward by 8 hours, it takes longer for them to become active when darkness descends. That’s what mouse jet lag looks like. They recover slowly, just like we do. It takes 8 to 10 days for them to adjust to a leap forward, and 5 to 6 days to adjust to a leap back.

But the team’s mutant mice adjusted almost immediately or, at most, after a day.

Here’s the really surprising bit: the rodent’s clocks still kept time well. They ticked and tocked on the standard daily cycle. Their temperature and behaviour peaked and troughed over 24 hours, as did the activity of genes in their liver, kidneys and brains. “It’s astonishing,” says Hitoshi Okamura, who led the study. “The mutant mice only show abnormal behaviour when they are in the jet lag condition.” They’re like the clocks in my computer and phone—they keep time very well, but they can be reset very easily.

“This is unprecedented,” says Michael Hastings from the University of Cambridge, who studies body clocks. In earlier studies, scientists have tweaked animal clocks so that they quickly adapt to new time zones, but their regular time-keeping duties always suffer as a result. “It always seemed that being a good clock and being very responsive to lighting cycles were mutually incompatible. [These] mice have an SCN that strikes a happy medium.”

How can that be? The team thinks the answer lies in the connections between the neurons of the SCN. Those that produce and respond to AVP all hook up with one another to form tightly synchronised circuits. You can disrupt their clocks with a chemical that stops them from making proteins (remember that proteins are the gears of our body clocks), but once the chemical disappears, they all sync up again. This tight coupling ensures that the master clock keeps on ticking regularly in the face of small environmental changes.

But in the mutant mice, the SCN neurons are more loosely coupled. Disturb their clocks, and they find it hard to synchronise. This doesn’t cause any obvious problems under normal conditions and it actually helps them when challenged by large time differences. Unrestrained by one another, the individual neurons can respond to environmental changes and the entire clock resets very easily.

Beyond jet lag

You don’t want this to happen all the time, but the team managed to temporarily loosen the coupling within the SCNs of normal mice. They treated them with two chemicals that block AVP receptors and showed that they got over jet lag very quickly, albeit less quickly than the mutants that lacked the receptors altogether.

That’s not surprising, says Akhilesh Reddy, a circadian researcher at the University of Cambridge. Growing up without any AVP receptors at all would almost certainly change the connections in the rodents’ brains, producing more dramatic effects than simply blocking the receptors in animals that always had them. Still, the mutants were so resistant to jet lag that duplicating even a fraction of that effect should be helpful to weary travellers.

“The real importance of being able to adjust the clock isn’t for jet lag, which is usually only a nuisance, but for shift-workers,” adds Weaver.  “A ‘jet lag pill’ could help shift-workers rapidly adjust their clocks, rather than fighting their biology by trying to stay awake all night and sleep during the day.” This is important because there’s mounting evidence that shift-working is linked to a higher risk of heart disease and some cancers.  It poses a big and unappreciated problem for public health—one that might be preventable if scientists can find a way of rapidly reset our body clocks,

Reference: Yamaguchi, Suzuki, Mizoro, Kori, Okada, Chen, Fustin, Yamazaki, Mizuguchi, Zhang, Dong, Tsujimoto, Okuno, Doi & Okamura. 2013. Mice Genetically Deficient in Vasopressin V1a and V1b Receptors Are Resistant to Jet Lag.

More on body clocks: