World’s Largest Radio Telescope Faces a Troubling Future


The National Science Foundation is considering pulling its support from the famous Arecibo radio dish in Puerto Rico.

One of the world’s most iconic astronomy sites, Puerto Rico’s giant Arecibo Observatory, may be facing the end of its era. The National Science Foundation (NSF), the primary funder of Arecibo—which is the largest existing radio telescope and was featured in the movies Contactand GoldenEye, among others—is holding public meetings on June 7 to “evaluate potential environmental effects of proposed changes to operations at Arecibo Observatory,” according to an NSF announcement. Because those proposed changes include the option of shutting down the 305-meter dish telescope altogether, officials will likely get an earful about more than air quality and groundwater. Defenders of the observatory will have a chance to speak their minds at two meetings—at the San Juan DoubleTree Inn and the Puerto Rico Professional College of Engineers and Land Surveyors—and can submit comments in writing through June 23.

Since its completion in 1963 the storied telescope found fame for discoveries such as the first-ever planets outside the solar system in 1992 and the first indirect evidence of gravitational waves in 1974, a finding that earned its makers a Nobel Prize, among other landmark accomplishments. But the beloved observatory now stands on a precarious threshold. The NSF has to balance the operations of new and expensive facilities such as the Atacama Large Millimeter/submillimeter Array in Chile against older ones like Arecibo while weighing federal scientific priorities and setting aside enough money for grants to individual scientists. With the NSF’s budget essentially flat since 2010, the agency cannot afford to run all its telescopes indefinitely, continue building new ones and still pay the country’s scientists. But researchers who use Arecibo argue that it has a useful life of novel discoveries ahead of it, even if is not as shiny as the newcomers, especially in some areas where it makes a unique contribution.

The observatory’s latest announcement follows recommendations made by two committees associated with the NSF, in 2012 and earlier 2016, reevaluating the agency’s role in running the telescope and “significantly decreasing funding.” This year the NSF also did a “feasibility study” to map out various futures for Arecibo and asked potential partners to propose ways they could take over some telescope operations. The NSF currently funds Arecibo at $8.2 million a year, two thirds of the telescope’s total cost, with NASA kicking in the last third to bankroll the observatory’s study of near-Earth asteroids. But two NSF divisions—Astronomical Sciences and Atmospheric and Geospace Sciences—which split their cost equally, are reconsidering their roles.

The “environmental impact statement,” for which the upcoming meetings seek public comment, will attempt to define the earthly effects of five different hypothetical scenarios, each involving a different financial commitment from the NSF. In one, everything would stay much the same. But the agency could also team up with “interested parties” who could help fund the telescope or other interested parties who want to run it as an educational facility.

More pessimistically, the NSF could mothball the site, shutting it down in such a way that it could restart (sometime in the future). Or it could dismantle the telescope altogether and restore the area to its natural state, as required by law if the agency fully divests itself of the observatory and closes it. Previous studies have said such a process could cost around $100 million—more than a decade’s worth of its current funding for telescope operations. Jim Ulvestad, director of the NSF Division of Astronomical Sciences, says the agency is still investigating, not concluding. “No alternative has been selected at this juncture,” he says. And much consideration will go into the final financial decision, whatever it may be. Some outside the agency see writing on the wall. “NSF is dead serious about offloading Arecibo funding to someone else—anyone else,” says Ellen Howell, a former staff scientist at Arecibo and now a faculty member at the Lunar and Planetary Laboratory (LPL) in Tucson, Arizona.

This is hardly the first time Arecibo’s future has felt precarious. A quick Google search will net you various “Save Arecibo!” campaigns from the 2007 era—for instance, after an NSF-commissioned report recommended decreasing the agency’s funding for the telescope from 2007’s $10.5 million to $4 million in 2011. Its current $8.2 million-a-year allowance is a compromise. And the observatory has company in its current crisis. The Green Bank Telescope in West Virginia, the Very Long Baseline Array spread across the country, and several older telescopes on Kitt Peak in Arizona are wading through similar budgetary muck, trying to work out new private partnerships (with NSF assistance) after the agency decided to cut their cords. And according to documents and e-mails obtained byThe Sydney Morning Herald, the Parkes radio telescope in Australia is facing similar funding shortfalls. A “likely recommendation,” according toThe Herald, will be that Parkes and another Australian facility “raise external funds by charging for access to the telescope facilities.” Green Bank, Arecibo and Parkes are three of the world’s most powerful radio telescopes—historically open to scientists who successfully submit proposals to use them—and government-based financial problems may lead them all into eventual closure or into the arms of private interests, where whoever pays gets to choose what type of science is done.

Arecibo currently is used for radio astronomy, space and atmospheric science as well as radar studies of comets, asteroids and planets. These areas are brimming with potential for the observatory to make many exciting discoveries in the future, advocates say. Xavier Siemens, an astronomer at the University of Wisconsin–Milwaukee, is especially excited about the possibility for using Arecibo to detect gravitational waves—ripples in spacetime—coming from supermassive black holes. Because it is the largest and most sensitive single-dish radio telescope in the world, Arecibo is one of the best instruments available for detecting pulsars, the fast-spinning remnants of dead, once-huge stars. Scientists like Siemens currently use Arecibo and the also-threatened Green Bank Telescope to find and monitor a network of pulsars they hope will help detect gravitational waves.

Without Arecibo, he says, that search would be crippled. Although the Laser Interferometer Gravitational-Wave Observatory (LIGO), which announced the first detection of gravitational waves in February to much fanfare, will continue running, it catches different waves than pulsar studies such as Arecibo’s do. “What’s really amazing to me is that in the wake of the discovery of gravitational waves, NSF is going to shut down the world’s most sensitive radio telescope and hinder the detection—the opening of the only other gravitational-wave window that we can open in the next few years,” he says. “It’s surreal.”

It may be surreal but Howell believes it is also realistic. “I am afraid that NSF has already made up its collective mind to reduce their support to much less than the current $8 million per year or so to perhaps nothing,” Howell says. “I think this is an embarrassment after so many years of scientific achievements when so little could continue the productivity.”

Michael Nolan, now at the LPL, worked at Arecibo for 20 years and was director from 2008 to 2011. He claims the observatory used to have better friends in high places, specifically in the NSF’s Atmospheric and Geospace Sciences division. “The two main advocates are now retired, and it seems like that voice is, too,” he says. “The Astronomy division has seemed like managers rather than advocates for a long time, though, of course, I’m not privy to their internal discussions.”

And whereas the NSF’s deliberations have not yet resulted in a decision to back away from the observatory completely or at all, the delay of what may be inevitable is not doing the telescope any favors, Nolan argues. Arecibo’s leaders cannot ask new potential donors to make up for a specific shortfall because they do not know if or by how much the NSF might curb its aid. Recalling his tenure at Arecibo, and the regular jeopardy it was in even back then, Nolan wishes the facility did not have to be so often rescued from the brink: “You know that line in The Incredibles?” he asks. “‘Sometimes I just want it to stay saved, you know? For a little bit.’”

In addition to its scientific import, Arecibo also plays a concrete, down-to-earth role in the community. An economy exists around the rural facility, which provides jobs to local residents and infuses the area with cash-dispensing visitors—both touristic and scientific. The environmental statement will also evaluate those human impacts. If the NSF does decide to tighten the purse strings and no other organization steps up to fill the gap, the consequences will ripple across science and society, space and time. “If Arecibo has to close because NSF has other priorities, it will not be possible to bring it back anytime soon, when or if we come to our senses,” the LPL’s Howell says. She and many scientists would agree that an empty Arecibo site would be—as Jodie Foster says in Contact—an “awful waste of space.”

Underwater “Lost City” Built by Microbes?


Geologists find that ancient underwater structures off Greece were likely created by methane jets and bacteria.

Microbes in the sediment use carbon in the methane as a fuel, which alters the chemistry of the sediment and forms a natural cement. Over time currents erode softer surrounding sediment, revealing the harder, naturally formed structures.  

When divers off the Greek island of Zakynthos chanced upon an underwater labyrinth of stone several years ago, they encountered eerie scenes reminiscent of cobblestone floors and the bases of Hellenic-like colonnades, conjuring images of a city that had vanished beneath the waves thousands of years in the past. But when Greek authorities took a closer look they found no nearby signs of human life such as pottery shards, coins or tools. And now new research indicates that the structures are not human-made at all, rather they are natural formations sculpted by the breakdown of methane gas within the ocean floor—millions of years before civilization.

University of East Anglia environmental sciences professor Julian Andrews and his colleagues conducted laboratory studies of the chemical makeup of samples from the underwater labyrinth. Their analysis, published this week in Marine and Petroleum Geology, revealed that the structures are likely a result of their location: directly above a subsurface fault still hidden by the seabed, where methane oozes out of Earth’s crust in various ways. Microbes in the sediment use carbon in the methane as a fuel, which alters the chemistry of the sediment and forms a natural cement. Over time currents erode softer surrounding sediment, revealing the harder, naturally formed structures.

The ancient underwater remains of a long lost Greek city were in fact created by a naturally occurring phenomenon—according to joint research from the University of East Anglia and the University of Athens (Greece). Credit: University of Athens via EurekAlert

Researchers say the formations’ different shapes are likely the result of the various types and sizes of the methane leaks. For example, the colonnadelike structures could have been formed when methane jets shot up through the sediment and interacted with bacteria clustered tightly around the jets. “It’s kind of like a frozen plumbing system,” Andrews says. The floorlike structures, on the other hand, were probably formed when methane seeped toward the surface in a slow and diffuse manner, before interacting with a horizontal layer of bacteria within the sediment. “So rather than it forming a very discrete structure around the pipe, it’s actually producing a flat structure,” he says.

This process, known as concretion, is quite common but usually occurs in the ocean depths. It is rare to find examples in shallower waters such as bays and river deltas. And when divers do so, it is easy for them to mistake the formations for human-made structures.

Credit: University of Athens via EurekAlert

Other types of underwater structures have triggered more debate. Off the southern Japanese island of Yonaguni divers and researchers have long been amazed by geometric stone structures that many say resemble an arch, a number of temples, a stadium, a pyramid and parts of a castle. But the site’s origin remains a subject of scientific controversy. And many experts say it could easily be the result of natural processes—such as the tendency of sandstone to break along planes, creating clean and symmetric edges that can appear human-made.

As Andrews and his colleagues summarize in their research paper: “‘All that glistens is not gold’—or in this case ‘columns and pavements in the sea, not always antiquities will be.’”

Why the Pain Drug That Killed Prince Can Be Especially Dangerous


Fentanyl’s fast action is great for pain relief but adds to its risks.

Many questions still remain about the tragic and untimely death of musician and cultural icon Prince, but a report released last Thursday by the Anoka County, Minn., Midwest Medical Examiner’s Office answered a big one: Prince’s death was caused by an accidental overdose of the powerful opioid drug fentanyl. Little is known for certain about the circumstances leading up to his death but it now appears that, like millions of Americans, Prince was taking opioids to manage chronic pain.

Fentanyl is an opioid drug—a chemically synthesized relative of opiates such as morphine and heroin, which are derived from the opium poppy. The drugs mimic our brains’ own pain-regulating molecules called endogenous opioids, which act at receptors found throughout the nervous system. All opioid drugs have the ability to dampen pain. In fact, opioids are so good at relieving pain that they are considered the gold standard against which all other analgesic drugs are measured. But that relief comes with significant risks. Opioids carry a range of side effects, the most severe of which apparently took Prince’s life: death by respiratory depression, meaning that he stopped breathing.

“In a way, Prince is a poster child for what can happen with chronic use—and increasing doses—of these very powerful drugs,” says Gary Franklin, a researcher at the University of Washington and medical director of the Washington State Department of Labor and Industries. Franklin speculates that Prince, like so many others, may have been being treated with opioids for chronic pain and developed tolerance—meaning that over time higher and higher doses are required to achieve the same pain relief. As doses escalate, so do risks. “It turns out that it doesn’t take long to develop physical dependence, which means that when you try to cut back on the dose, you get withdrawal symptoms. It’s a vicious cycle,” Franklin adds.

If Prince had built up tolerance to opioids, how did he die of an overdose? The specific drug—fentanyl—found in Prince’s body is particularly powerful; it is 100 times more potent than morphine. For example, the effects of a standard 10-milligram dose of morphine can be achieved with just 100 micrograms of fentanyl. Among opioid drugs, fentanyl is particularly fast-acting, which can make it more lethal in some situations.

Prince had a long history of clean, drug-free living, suggesting that he would not use street drugs. However, fentanyl is often mixed with heroinor other drugs and sold illegally, which accounts for many of the other deaths in which it is involved—as users may be unaware that their heroin is cut with the stronger drug. And pharmaceutical fentanyl was once prescribed only for severe short-term pain, such as after surgery, but patients are increasingly receiving it to manage chronic pain, often in a patch that delivers the drug through the skin. Fentanyl is also administered in lollipop form, typically to terminal cancer patients with otherwise untreatable pain. Whatever the source, “we don’t know if Prince took the drug as directed or in excess,” says Lynn Webster, a pain and addiction specialist based in Salt Lake City and past president of the American Academy of Pain Medicine.

The death certificate did not name any other drugs in his system but a number of medications—from other types of opioids to sleeping pills—would have increased fentanyl’s risks in any user. Prince’s small stature—the medical report listed him as 1.6 meters and 50 kilograms at death—did not likely contribute to an overdose death, according to Webster. “Most people who die from respiratory depression—they go to sleep and don’t wake up,” Franklin says. “This was different in the sense that he [presumably] passed out while awake” in the elevator where he was found an estimated six hours after his death.

Despite the fact that Prince died of an overdose of an opioid drug, whether or not he might have been addicted is another matter. “I’m not so sure he was addicted,” Webster says. “I have not seen evidence that he was addicted.” An opioid user can develop tolerance and even physical dependence on the drugs without being addicted. Less than 10 percent of patients taking opioids for chronic pain develop addiction in the classical sense, Webster says.

Prince’s plane did make an emergency landing a few days before his death in order to get a life-saving dose of Narcan, or naloxone, a drug that counteracts opioids and can prevent overdose death. “The fact that he had already had an overdose episode—when death is prevented once by naloxone—that indicates big trouble,” Franklin says.

Disneyland Is Testing New Interactive Droids That Will Roam Its Expanded Star Wars Lands


If you thought Disney’s only reason for buying Lucasfilm was to make moreStar Wars movies, you’re way off. The company is also currently in the process of converting parts of Disneyland and Walt Disney World into sprawling Star Wars-themed lands, and it’s already testing some of the new characters it’s designed to interact with guests.

Though the new Star Wars lands are still at least two years away from opening, YouTuber DAPs Magic spotted this new interactive droid called Jake being tested at the Star Wars Launch Bay at Disneyland. It’s not known if the droid is being controlled behind the scenes by an operator, but presumably it will have some level of autonomous capabilities to avoid crashing into visitors and other obstacles.

 

Jake also appears to be able to interact with the exhibits at the Launch Bay. When it rolls up to a control panel the droid beeps and bloops at the computer as its head moves about, which triggers lights and other interactive elements.

It’s nothing especially fancy yet, but it’s promising. Droids are a big part of the Star Wars experience, and Disney is obviously spending a lot of money to ensure its new exhibits provide the most authentic experience as possible to park guests. If you remember, eight years ago a full-sized version of Wall-E was spotted roaming the parks, so just imagine how far the robotics technology that powered that character has been improved.

4 New Elements Get Names


The latest additions to the periodic table honor the past.

The proposed names for elements 113, 115, 117 and 118 are nihonium, moscovium, tennessine and oganesson respectively, the International Union of Pure and Applied Chemistry (Iupac) has announced.

‘It’s an exciting day for the world,’ says Lynn Soby, Iupac’s executive director.

The groups responsible for the discovery of these new elements each put forward their proposed name and symbol after Iupac confirmed their existence in January 2016. The criteria states an element may be named after a mythological figure or concept, geological place, scientist, elemental property, or mineral.

Nihonium (elemental symbol Nh) is the proposed name for element-113. The element was synthesised by Kosuke Morita’s group at RIKEN in Japan after they bombarded a bismuth target with zinc-70 nuclei in 2004 and 2012. Named after Japan, the element will be the first East Asian name to appear on the periodic table if ratified.

Scientists based in Russia and the US who discovered elements 115 and 117 have put forward the names moscovium (Mc) and tennessine (Ts), respectively. A collaboration between the Joint Institute of Nuclear Research in Russia and the Oak Ridge and Lawrence Livermore National Laboratories, US, elements 115 and 117 were both created in 2010. Both element names take their cues from geographical regions. Moscovium is named after Moscow, where the Joint Institute of Nuclear Research is based. Named after Tennessee, tennessine is a tribute to the region where a large amount of superheavy element research is conducted in the US.

The same group has also named element-118 oganesson (Og), in honour of the Russian nuclear physicist Yuri Oganessian who led the team that synthesised element-117.

The names will now be put up for public scrutiny in a five month consultation process before Iupac ratify the final names. ‘It’s important for people around the world to review the names to make sure that they fit with all the different languages,’ Soby tells Chemistry World. ‘Now the public and the scientific community can weigh in on things.’

The Man Who Can Map the Chemicals All Over Your Body


Scientist uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world .

Apart from the treadmill desk, Pieter Dorrestein’s office at the University of California, San Diego (UCSD), is unremarkable: there is a circular table with chairs around it, bookshelves lined with journals, papers and books, and a couple of plaques honouring him and his work.

But Dorrestein likes to offer visitors a closer look. On his computer screen, he pulls up a 3D rendering of the space. Four figures seated around the table—one of whom is Dorrestein—look as if they’ve been splashed with brightly coloured paint. To produce the image, researchers swabbed every surface in the room, including the people, several hundred times, then analysed the swabs with mass spectrometry to identify the chemicals present.

The picture reveals a lot about the space, and the people in it. Two of Dorrestein’s co-workers are heavy coffee drinkers: caffeine is splotched across their hands and faces (as well as on a sizeable spot on the floor—a remnant of an old spill). Dorrestein does not drink coffee, but has left traces of himself everywhere, from personal-care products to a common sweetener that he wasn’t even aware he’d consumed. He was also surprised to find the insect repellent DEET on many of the surfaces that he had touched; he hadn’t used the chemical in at least six months.

Then there were signatures of the office’s other inhabitants: the microbes that reside on human skin. Dorrestein has been using mass spectrometry to look at the small molecules, or metabolites, produced by these microbes, and to get a clearer picture of how microorganisms form communities and interact—with other microbes, with their human hosts and with the environments that they all inhabit.

He has analysed microbial communities from plants, seawater, remote tribes, diseased human lungs and more, in an effort to listen in on their chemical conversations: how they tell one another of good or bad places to colonize, or fight over territory. The work could identify previously unknown microbes and useful molecules that they make, such as antibiotics.

“The applications are broad,” says Katie Pollard, a comparative genomicist at the Gladstone Institutes at the University of California, San Francisco. Because many microbes cannot be cultured and studied directly, she explains, “these approaches that assay them in situ are totally game-changing”. They also directly address some of the main goals outlined in the US$521-million National Microbiome Initiative, announced by the White House’s Office of Science and Technology Policy last month. Dorrestein was present for the announcement.

In this fast-moving field, Dorrestein has set himself apart by building useful tools and productive collaborations. “Pieter is genuinely interested and very creative,” says Janet Jansson, division director of biological sciences at Pacific Northwest National Laboratory in Richland, Washington. In April, she visited UCSD, and Dorrestein asked whether he could swab her hand for one of his studies. “I said, ‘Oh! I want to do that! I want to be involved in that study!’” Jansson recalls: “It’s interesting and exciting science that people want to participate in.”

ROCK AND ROLL

Dorrestein grew up in the Netherlands, and became obsessed with rock-climbing when he visited family friends in Tucson, Arizona, at the age of 16. Faced with the flatness of his homeland, he applied to Northern Arizona University in Flagstaff, in large part because of its proximity to the many stone towers of the Four Corners region, where Arizona meets New Mexico, Colorado and Utah. He studied geology and chemistry, but intended to pursue his passion for climbing. Shortly after graduating in 1998, however, an experience on the 900-metre-tall face of El Capitan in Yosemite, California, made him think again.

He was clinging to the rock about 50 metres above his last anchoring point, and realized that if he were to lose his grip, he would drop 100 metres before his safety line tautened and slammed him into the granite. It wasn’t fear, he says, but rather his lack of it that troubled him. “I thought, if I keep doing this, it won’t be a good ending,” he recalls. “So I rappelled down.”

He drove home to Flagstaff that day, and started filling out applications to graduate school. He ended up at Cornell University in Ithaca, New York, studying how microbes produce small molecules such as vitamin B1. It was here that he was first introduced to mass spectrometry.

Mass spectrometry generally involves breaking complex molecules apart, ionizing them and measuring the mass of the resulting fragments, which can be used to calculate the composition of the starting molecules. Dorrestein uses the analogy of a bar code—mass spectrometry creates a unique identifier for each chemical in a sample.

Spurred by his interest in the technology, he went on to do a postdoc in the lab of Neil Kelleher, a chemical biologist at the University of Illinois at Urbana–Champaign. Kelleher was pioneering efforts to do ‘top-down’ mass spectrometry, in which intact, rather than digested, proteins are put directly into the mass spec. The approach allows researchers to identify small modifications made to proteins, but the process is slow. Within two months of his arrival in Illinois, Dorrestein had developed a speedier approach that allowed him to examine certain large enzymes systematically. “We boiled down years of work into days, basically,” Dorrestein says. He ended up co-authoring 17 papers in 2 years. “Pieter has that unusual combination of creativity and drive, along with an incredible ability to finish projects,” says Kelleher, who is now at Northwestern University in Evanston, Illinois.

Dorrestein joined the faculty at UCSD in 2006—but things really kicked off for him when Palmer Taylor, then dean of the university’s school of pharmacology, authorized the purchase of a MALDI-TOF mass spectrometer (matrix-assisted laser desorption/ionization time of flight), which would allow Dorrestein to do mass-spectrometry imaging. “That changed the whole world around,” he says.

SPACE CRUSADERS

As well as identifying molecules in a sample, mass-spectrometry imaging provides spatial information. MALDI-TOF uses a laser to heat up and ionize molecules. By scanning that laser across a 2D sample, researchers can capture an ‘image’ that shows exactly where different molecules in the sample reside. The technique can be used to identify and locate biomarkers in slices of tumours, but with his interest in microbes, Dorrestein wondered whether he could take colonies of bacteria on a Petri dish and scan them directly to see the metabolites they produce.

No one had ever tried it. Dorrestein suspects that they were afraid of getting their expensive mass spectrometers dirty—“and this is as dirty as it comes, putting microbes directly into the instrument”. So he tried a simple experiment, asking an undergraduate student, Sara Weitz, to scan a colony of Bacillus bacteria.

The images generated “weren’t the prettiest”, Dorrestein says, but they indicated that the process worked. He sent them to Paul Straight, a microbiologist who had just joined the faculty at Texas A&M University in College Station. “I’m pretty sure his jaw dropped,” Dorrestein says. Together, the two teams used mass-spectrometry imaging on colonies of Bacillus subtilis and Streptomyces coelicolor grown next to one another. By exploring the spaces where the colonies interacted, they were able to identify molecules that the microbes use to compete with each other.

Actually visualizing this microbial arms race, Dorrestein says, makes him think back to 1928, when Alexander Fleming isolated penicillin from a mould that was killing bacteria on a dish. Mass-spectrometry imaging could quickly reveal the chemistries of such interactions, and perhaps speed up the search for new antibiotics.

Dorrestein decided to shift his lab to focus almost exclusively on these methods. He was still an early-career investigator, and almost everybody he knew discouraged him from taking such a big risk. But Taylor pushed him to apply for tenure right away. “Pieter’s potential to think outside the box in the analytical and computational arenas was immediately evident,” Taylor says. “His research took off very rapidly.”

The problem with looking at dirty samples is that they produce messy data. Scanning microbial landscapes produces thousands of bar codes, but it’s largely unknown what they correspond to; they haven’t been annotated. “It’s the equivalent of looking under the lamp post,” Dorrestein says: one can only ‘see’ the molecules that have been identified before, and the vast majority haven’t. This is currently a big challenge for the field, says Jansson. “It’s possible to analyse features by mass spec, but still very difficult to identify what those features are.”

To help to make sense of the heaps of data, Dorrestein worked with Nuno Bandeira, a computational biologist at UCSD, on an approach that classifies bar codes and the molecules to which they correspond according to their relationships with other annotated molecules. This allows researchers to start predicting, computationally, the structures and functions of thousands of metabolites. But there’s still a dearth of annotation: although thousands of people worldwide conduct mass-spectrometry research, most annotate only the few molecules that they’re interested in.

So, beginning in 2014, Dorrestein and graduate student Mingxun Wang from Bandeira’s lab started to develop a way to crowdsource annotation. They launched the Global Natural Products Social Molecular Networking website, a repository and data-analysis tool that enables researchers to uncover relationships between related molecules, group similar ones together and compare data sets. “This is something he’s brought to the field that has really helped,” says Jansson.

TEAM WORK

One of the keys to Dorrestein’s success has been his collaborations. Rob Knight, a leader in microbiome DNA and RNA sequencing, works just across the quad from Dorrestein’s office. They’ve teamed up to blend sequencing with mass spectrometry. Last year, a postdoc in Dorrestein’s lab, Amina Bouslimani, took swabs from one male and one female volunteer, at 400 spots on their bodies—twice. One swab from each spot went to Knight’s lab so that the microbes in it could be sequenced, and the other went for mass spectrometry to identify the chemicals, natural and artificial, that coexist with the microorganisms.

The participants had refrained from showering or using cosmetics for three days, but the chemical signatures from the hundreds of different types of microbe in the samples were overwhelmed by chemicals from beauty and hygiene products. Still, the researchers did find correlations between microbe communities and local chemistries: for example, the bacteria found in the vaginal area were correlated with molecules associated with inflammation. Such connections, Dorrestein says, could be used to generate hypotheses about host–microbe interactions.

Bouslimani is now analysing samples from volunteers’ hands and from personal items such as their mobile phones. The work, which has not yet been published, has shown that people leave persistent chemical signatures on the objects that they touch—like those in the image of Dorrestein’s office.

Bouslimani and Dorrestein think that this could have applications in forensic science. A suspect could be swabbed to determine whether the chemical signature of his or her skin matches that at a crime scene. Or in the absence of DNA or fingerprint evidence, the chemicals that a criminal leaves behind could help to provide a lifestyle profile: a composite sketch of the products that they use and the mixture of microbes they carry. “Maybe the chemical signature can help the investigator narrow down who was there,” says Bouslimani.

Last year, Dorrestein teamed up with microbiologist Maria Dominguez-Bello of New York University and several others who wanted to see what human skin and its microbial diversity look like when people grow up free of the trappings of the developed world. They collected samples from some remote tribes—one near Manaus, Brazil, and Tanzania’s Hadza people—and compared them with swabs from non-tribal people near the collection sites. Using Dorrestein’s mass-spectrometry techniques, they’ve found that people in the tribes have more-diverse microbial communities and skin chemistry than those living a more modern lifestyle. The ongoing work is serving up some surprises too, says Dorrestein. People from one village in Brazil had a range of pharmaceuticals on their skin, indicating that they had more contact with outsiders than previously suspected.

Dorrestein has a way of leaning forward and almost standing on his toes in excitement when he talks about the technology and how it might help to assess the health of oceans, or improve efficiency in agriculture, a major contributor to greenhouse-gas emissions. But when asked how he chooses projects to pursue, it’s work on human health that he mentions first. “To us, that’s a really obvious, direct application of this—we want to help patients,” he says.

Dorrestein teamed up with Knight, Doug Conrad—director of UCSD’s adult cystic fibrosis clinic—and others to develop a rapid microbial diagnostic test. Cystic fibrosis causes a build-up of mucus in the lungs, which can periodically become infected with bacteria. These infections require aggressive treatment with antibiotics—and sometimes the bacteria can develop resistance. Dorrestein and his collaborators have shown how analysing mass-spectrometry data on a phlegm sample from someone with cystic fibrosis can identify microbial communities that standard medical culturing techniques miss.

Louis-Félix Nothias-Scaglia, a postdoc who joined Dorrestein’s lab this year, is mapping the skin of people with psoriasis, a condition thought to be triggered by an overactive immune system. If molecules produced by certain bacteria are present when the condition flares up but not when the skin is healthy, Nothias-Scaglia explains, they might point to drugs that could treat or even prevent the disease. Even being able to use microbial changes to predict when a flare-up is coming would enable patients to reduce their use of immune-suppressing drugs.

Turning such data-intensive techniques into standard lab tests will be a challenge. “Cynics would say it’s too complicated, it’s never gonna go anywhere,” says Conrad. “To a certain extent, I can understand that. But that’s a good way to keep going the way things are.”

Dorrestein definitely wants to change the way things are, particularly for the blossoming field of microbiome research. He views the discipline as passing through phases: the first has centred on determining the identity of microbes. The second phase is working out what they’re doing, using techniques such as mass spectrometry.

What drives the establishment of these communities? What metabolic processes are under way, and how do they interact with each other and with a host? “If you fundamentally understand that,” Dorrestein says, “you can start to take control of it.” And that’s the third phase, he says—taking control. By monitoring microbial communities, is it possible to add the necessary ingredients to change a person’s health, their mood, their athletic performance? Dorrestein thinks that the answers to these questions are right in front of him. He just has to look a little closer.

How the Club Drug Ketamine Works to Fight Depression


A breakdown product of the drug reduces signs of depression in mice without side effects .

The popular club drug ketamine—or ‘Special K’—is also a fast-acting antidepressant, but how it works has eluded scientists. Now a team reports in Nature that the mood-lifting effect may not be caused by the drug itself, but by one of the products formed when the body breaks the drug down into smaller molecules.

If the findings, from a study in mice, hold true in humans, they could suggest a way to provide quick relief for people with depression—without patients having to experience ketamine’s ‘high’. Such a drug would be welcome news to the many people with major depressive disorder who do not find relief in currently available antidepressants. Ketamine also eases depression in a matter of hours, whereas other drugs take weeks to reach their full effect.

“The whole field has become interested in ketamine,” says Todd Gould, a neuroscientist at the University of Maryland School of Medicine in Baltimore who led the study. “It does something different in patients than any other drug we have available.”

But ketamine has its drawbacks: some people are turned off by the high—a feeling of dissociation and sensory distortion that lasts for about an hour. For others, the effect is an incentive to misuse the drug. Ketamine is not yet approved to treat depression in the United States, but ketamine clinics have sprung up around the country to administer it off-label.

Researchers have been racing to find other drugs that produce ketamine’s antidepressant effects without the high, but have been struggling to do so without a clear idea of how ketamine fights depression. Many of those efforts have focused on drugs that target cellular receptors in the brain called NMDA receptors. These were thought to be ketamine’s target, but clinical trials of other drugs that target them have largely yielded disappointing effects on depression, says Gould.

METABOLIC LIFT

“Ketamine probably represents a new chapter in the treatment of depression,” says Roberto Malinow, a neuroscientist at the University of California, San Diego. “But there have been some big questions regarding how it works.”

Gould teamed up with clinicians, analytical chemists, and neurophysiologists to fill in the gaps in understanding. Gould and his colleagues used a battery of behavioural tests in mice to show that one of ketamine’s breakdown products—a compound called (2R,6R)-hydroxynorketamine—is responsible for much of the drug’s antidepressant effects.

And to Gould’s surprise, the metabolite did not cause side effects in the mice even at doses nearly 40 times higher than the antidepressant dose of ketamine. The mice also did not tend to press a lever to receive the metabolite when given the option to self-administer it.

The researchers plan to gather the safety data needed to take the metabolite into clinical testing in humans, a process that Gould cautions could still take years.

But Husseini Manji, head of neuroscience research and development at Janssen Pharmaceutical Companies in Titusville, New Jersey, cautions against assuming that results in mice will bear out in humans.  “We have to keep reminding ourselves that clinical data trump rodent data,” he says. Janssen has developed a specific form of ketamine, called esketamine, that it is testing in five large clinical trials.

RECEPTIVE TARGETS

Gould’s study in mice held another surprise: the metabolite that is active in mice did not act through NMDA receptors. The group did not find its direct target, but did find evidence that it stimulates another set of receptors called AMPA receptors. If the same result holds true in humans, it could provide an explanation for why drugs that target NMDA receptors have failed to capture ketamine’s full effects. “This could shake the windows and rattle the walls of those companies that have been putting a lot of money into this research,” says Malinow.

Manji, who describes the study as elegant, is not ready to give up on NMDA receptors until the results have been borne out in human studies. But he is among the researchers who believe that AMPA receptors may be important as well. Janssen and others have been pursing those receptors and proteins associated with them as potential drug targets. “This paper gives us even more impetus to go after them,” says Manji.

Hope for multiple sclerosis cure as 23 seriously ill patients recover after ‘breakthrough’ stem cell treatment


Jennifer Molson skis after recovering from Multiple Sclerosis 
Jennifer Molson skis after recovering from Multiple Sclerosis  

Multiple sclerosis patients who were severely disabled are walking, working and even downhill skiing again following a breakthrough therapy which completely destroys, then rebuilds, the immune system.

The trial, which is the first in the world to show complete long-term remission from the debilitating disease has been hailed by experts as ‘exciting’ ‘unprecedented,’ and ‘close to curative.’

Although it is unclear what causes MS it is thought that the immune system attacks the protective coating which surrounds nerve cells in the brain and spinal cord leading to inflammation, pain, disability and in severe cases, early death.

Can a new immune system halt MS and allow repair?Play!04:47

The new technique, which is a treatment usually used to fight leukaemia, involves using chemotherapy to entirely eradicate the damaged immune system, before rebooting it with a transfusion of bone marrow cells.

Out of the 24 patients who were given the treatment at least seven years ago, the majority have seen significant improvements . 70 per cent of patients saw a complete stop to the progression of the disease, while 40 per cent saw a reversal in symptoms such as vision loss, muscle weakness and balance loss.

Jennifer, she freaked me out one day when she came to the clinic wearing high heels. This was a girl who could barely walk.Dr Mark Freedman

Some participants were able to return to work, school, regain the ability to drive, get married and have children.

Trial participant Jennifer Molson, who was diagnosed with MS in 1996, and received her stem cell transplant in 2002 said: “Before my transplant I was unable to walk or work and was living in assisted care.

“Now I am able to walk independently, live in my own home and work full time. I was also able to get married, walk down the aisle with my Dad and dance with my husband.

“I’ve even gone downhill skiing. Thanks to this research I have been given a second chance at life.”

Jennifer Molson
Jennifer Molson 

Dr Mark Freedman, of the University of Ottawa and Ottawa Hospital, where the trials were carried out, said: “Jennifer, she freaked me out one day when she came to the clinic wearing high heels. This was a girl who could barely walk.”

MS affects around 100,000 people in Britain. Similar trials have been taking place across the UK and the US but none has shown such long term remission.

The trial included 24 participants with aggressive, relapsing MS who were followed for up to 13 years after treatment.

The procedure involves giving a person medication to coax their  stem cells to migrate from their bone marrow into their blood.

These stem cells are then collected from the blood, purified and frozen.

Then, high doses of chemotherapy drugs are used to eliminate the person’s diseased immune system.

The frozen stem cells are then frozen and transplanted back into the same person, so that they can give rise to a new immune system that has no memory of the previous pattern of attacking the central nervous system.

Dr Mark Freedman, Dr Harold Atkins, Jennifer Molson and trial coordinator Marjorie Bowman 
Dr Mark Freedman, Dr Harold Atkins, Jennifer Molson and trial coordinator Marjorie Bowman  

“Our trial is the first to show the complete, long-term suppression of all inflammatory activity in people with MS,” said Dr Harold Atkins, a stem cell transplant physician and scientist at The Ottawa Hospital, and associate professor at the University of Ottawa.

“A variation of this procedure has been used to treat leukaemia for decades, but its use for auto-immune diseases is relatively new.

“This is very exciting. However, it is important to note that this therapy can have serious side effects and risks, and would only be appropriate for a small proportion of people with very active MS.”

During the trial one participant died of liver failure due to the treatment and another required intensive care for liver complications.

Dr Emma Gray, Head of Clinical Trials at the MS Society, said: “This type of stem cell transplantation is a rapidly evolving area of MS research that holds a lot of promise for people with certain types of MS.

“This treatment does offer hope, but it’s also an aggressive procedure that comes with substantial risks and requires specialist aftercare. If anyone is considering HSCT we’d recommend they speak to their neurologist.”

Jennifer Molson kayaking
Jennifer Molson kayaking 

 But experts said the results constituted a breakthrough in the treatment of MS.

Prof Siddharthan Chandran, MacDonald Professor of Neurology, MRC Centre for Regenerative Medicine, University of Edinburgh, said: “This is an important and carefully conducted proof of concept study that demonstrates that powerful chemotherapy based treatment for a selected subset of MS patients with very aggressive disease is effective in preventing further disabling relapses and, in a proportion, appears to render them effectively disease free.”

Dr Stephen Minger, stem cell biologist and independent consultant, of SLM Blue Skies innovations Ltd said: “The clinical results are truly impressive, in some cases close to being curative.

“For a life-long progressive disease like MS with few treatment options this is really exciting data. I would consider it a breakthrough therapy.”

The research was published in The Lancet.

Google Moves Closer to a Universal Quantum Computer


Combining the best of analog and digital approaches could yield a full-scale multipurpose quantum computer.

Corporate headquarters complex of Google in Mountain View, California. 

For 30 years, researchers have pursued the universal quantum computer, a device that could solve any computational problem, with varying degrees of success. Now, a team in California and Spain has made an experimental prototype of such a device that can solve a wide range of problems in fields such as chemistry and physics, and has the potential to be scaled up to larger systems.

Both IBM and a Canadian company called D-Wave have created functioning quantum computers using different approaches. But their devices are not easily scalable to the many quantum bits (qubits) needed for solving problems that classical computers cannot.

Computer scientists at Google’s research laboratories in Santa Barbara, California, and physicists at the University of California at Santa Barbara and the University of the Basque Country in Bilbao, Spain, describe their new device online in Nature.

“It’s terrific work in many respects, and is filled with valuable lessons for the quantum computing community,” says Daniel Lidar, a quantum-computing expert at the University of Southern California in Los Angeles.

The Google prototype combines the two main approaches to quantum computing. One approach constructs the computer’s digital circuits using qubits in particular arrangements geared to solve a specific problem. This is analogous to a tailor-made digital circuit in a conventional microprocessor made from classical bits.

Much of quantum computing theory is based on this approach, which includes methods for correcting errors that might otherwise derail a calculation. So far, practical implementations have been possible only with a handful of qubits.

ANALOG APPROACH

The other approach is called adiabatic quantum computing (AQC). Here, the computer encodes a given problem in the states of a group of qubits, gradually evolving and adjusting the interactions between them to “shape” their collective quantum state and reach a solution. In principle, just about any problem can be encoded into the same group of qubits.

This analog approach is limited by the effects of random noise, which introduces errors that cannot be corrected as systematically as in digital circuits. And there’s no guarantee that this method can solve every problem efficiently, says computer scientist Rami Barends, a member of the Google team.

Yet only AQC has furnished the first commercial devices — made by D-Wave in Burnaby, British Columbia — which sell for about $15 million apiece. Google owns a D-Wave device, but Barends and colleagues think that there’s a better way to do AQC.

In particular, they want to find some way to implement error correction. Without it, scaling up AQC will be difficult, because errors accumulate more quickly in larger systems. The team thinks the first step to achieving that is to combine the AQC method with the digital approach’s error-correction capabilities.

VIRTUAL CHEMISTRY

To do that, the Google team uses a row of nine solid-state qubits, fashioned from cross-shaped films of aluminium about 400 micrometers from tip to tip. These are deposited onto a sapphire surface. The researchers cool the aluminium to 0.02 degrees kelvin, turning the metal into a superconductor with no electrical resistance. Information can then be encoded into the qubits in their superconducting state.

The interactions between neighboring qubits are controlled by ‘logic gates’ that steer the qubits digitally into a state that encodes the solution to a problem. As a demonstration, the researchers instructed their array to simulate a row of magnetic atoms with coupled spin states — a problem thoroughly explored in condensed-matter physics. They could then look at the qubits to determine the lowest-energy collective state of the spins that the atoms represented.

This is a fairly simple problem for a classical computer to solve. But the new Google device can also handle so-called ‘non-stoquastic’ problems, which classical computers cannot. These include simulations of the interactions between many electrons, which are needed for accurate computer simulations in chemistry. The ability to simulate molecules and materials at the quantum level could be one of the most valuable applications of quantum computing.

This new approach should enable a computer with quantum error correction, says Lidar. Although the researchers did not demonstrate that here, the team has previously shown how that might be achieved on its nine-qubit device.

“With error correction, our approach becomes a general-purpose algorithm that is, in principle, scalable to an arbitrarily large quantum computer,” says Alireza Shabani, another member of the Google team.

The Google device is still very much a prototype. But Lidar says that in a couple of years, devices with more than 40 qubits could become a reality.

“At that point,” he says, “it will become possible to simulate quantum dynamics that is inaccessible on classical hardware, which will mark the advent of ‘quantum supremacy’.”

Attending live music events ‘reduces your levels of stress hormone’


A festival-goer smiles in the crowd
A festival-goer smiles in the crowd

Researchers studied 117 volunteers attending two concerts of music by composer Eric Whitacre – one at Gloucester Cathedral, the other at the Union Chapel in London.

The volunteers provided saliva samples before the performances, and then again during the interval an hour later. Testing the samples for levels of cortisol and cortisone, researchers recorded across-the-board reductions in the second samples.
“This is the first preliminary evidence that attending a cultural event can have an impact on endocrine activity,” said research lead Daisy Fancourt of the Centre for Performance Science, a partnership between the Royal College of Music and Imperial College London.

“This suggests there is a universal response to concert attendance among audience members”
Cortisol is produced by the body under physical or psychological stress. It can have a positive effect in small doses, improving alertness and well-being. However, chronically elevated cortisol levels can worsen medical conditions such as heart disease, diabetes, hypertension and impotency.

“These results are in line with 22 previous studies showing that listening to music in the controlled setting of either a laboratory or a hospital can reduce cortisol levels,” researcher said.

“It is of note that none of these biological changes were associated with age, musical experience or familiarity with the music being performed. This suggests there is a universal response to concert attendance among audience members.”

However, they noted that the study focused “solely on the effects of relatively calm, classical music; more research will be needed to ascertain whether other genres of music elicit different effects or whether attending other types of cultural events has different endocrine impact.

“Nevertheless, this study opens up the question of how engaging with music and the arts in cultural settings can influence biological and psychological states and, consequently, the potential of cultural events to enhance people’s broader health and well-being.”

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