Monday, November 20, 2017

New catalyst controls activation of a carbon-hydrogen bond

A side view of the new catalyst. The dirhodium, shown in blue, "is the engine that makes the catalyst work," says Emory chemist Huw Davies. "The shape of the scaffold around the dirhodium is what controls which C-H bond the catalyst works on." (Graphic image by Kuangbiao Liao)

By Carol Clark

Chemists have developed another catalyst that can selectively activate a carbon-hydrogen bond, part of an ongoing strategy to revolutionize the field of organic synthesis and open up new chemical space.

The journal Nature is publishing the work by chemists at Emory University, following on their development of a similar catalyst last year. Both of the catalysts are able to selectively functionalize the unreactive carbon-hydrogen (C-H) bonds of an alkane without using a directing group, while also maintaining virtually full control of site selectivity and the three-dimensional shape of the molecules produced.

“Alkanes have a lot of C-H bonds and we showed last year that we can bring in one of our catalysts and pluck out a particular one of these bonds and make it reactive,” says Huw Davies, an Emory professor of organic chemistry whose lab led the research. “Now we are reporting a second catalyst that can do the same thing with another C-H bond. We’re building up the toolbox, and we’ve got more catalysts in the pipeline that will continue to expand the toolbox for this new way of doing chemistry.”

Selective C-H functionalization holds particular promise for the pharmaceutical industry, Davies adds. “It’s such a new strategy for making chemical compounds that it will opens up new chemical space and the possibility of making new classes of drugs that have never been made before.”

Alkanes are the simplest of molecules, consisting only of hydrogen and carbon atoms. They are cheap and plentiful. Until the recent development of the catalysts by the Davies lab, however, alkanes were considered non-functional, or unreactive, except in uncontrollable situations such as when they were burning.

The first author of the Nature paper is Emory chemistry graduate student Kuangbiao Liao.

Davies is the director of the National Science Foundation’s Center for Selective C-H Functionalization (CCHF), which is based at Emory and encompasses 15 major research universities from across the country, as well as industrial partners. The NSF recently awarded the CCHF renewed funding of $20 million over the next five years.

The CCHF is leading a paradigm shift in organic synthesis, which has traditionally focused on modifying reactive, or functional, groups in a molecule. C-H functionalization breaks this rule for how to make compounds: It bypasses the reactive groups and does synthesis at what would normally be considered inert carbon-hydrogen bonds, abundant in organic compounds.

“Twenty years ago, many chemists were calling the idea of selectively functionalizing C-H bonds outrageous and impossible,” Davies says. “Now, with all of the results coming out of the CCHF and other research groups across the world they’re saying, ‘That’s amazing!’ We’re beginning to see some real breakthroughs in this field.”

Many other approaches under development for C-H functionalization use a directing group — a chemical entity that combines to a catalyst and then directs the catalyst to a particular C-H bond. The Davies lab is developing a suite of dirhodium catalysts that bypass the need for a directing group to control the C-H functionalization. The dirhodium catalysts are encased within a three-dimensional scaffold.

“The dirhodium is the engine that makes the chemistry work,” Davies says. “The shape of the scaffold around the dirhodium is what controls which C-H bond the catalyst works on.”

Additional co-authors of the Nature paper include Thomas Pickel, Vyacheslav Boyarskikh and John Basca (from Emory’s Department of Chemistry) and Djamaladdin Musaev (from Emory’s Department of Chemistry and the Cherry L. Emerson Center for Scientific Computation).

Chemists find 'huge shortcut' for organic synthesis using C-H bonds
NSF awards Emory's Center for Selective C-H Functionalization $20 million

Thursday, November 16, 2017

Bacteria in a beetle makes it a leaf-eater

The tortoise beetle, which eats thistle leaves, has evolved a symbiotic relationship with bacteria that allows it to have such a specialized diet. Photo by Hassan Salem.

By Carol Clark

A leaf-eating beetle has evolved a symbiotic relationship with bacteria that allows the insect to break down pectin — part of a plant’s cell wall that is indigestible to most animals.

The journal Cell published the findings on the novel function of the bacterium, which has a surprisingly tiny genome — much smaller than previous reports on the minimum size required for an organism not subsisting within a host cell.

“This insect is a leaf eater largely because of these bacteria,” says Hassan Salem, lead author of the study and a post-doctoral fellow in Emory University’s Department of Biology. “And the bacteria have actually become developmentally integrated into the insect’s body.”

Two organs alongside the foregut of the beetle Cassida rubiginosa house the bacteria and appear to have no other function than to maintain these microbes. “The organs are equivalent to the liver in humans, in the sense that they contain the tools to break down and process food,” Salem says.

The newly characterized bacterium has only 270,000 DNA base pairs in its genome, compared to the millions that are more typical for bacterial strains. That makes its genome closer to that of intracellular bacteria and organelles than to free-living microbes. Mitochondria, for example, the organelles that regulate metabolism within cells, have 100,000 base pairs.

The two symbiotic organs of the tortoise beetle, dyed a fluorescent green, are shown on either side of the insect's foregut. Microscopy image by Hassan Salem.

Salem is a researcher in the lab of Emory biologist Nicole Gerardo, an associate professor who specializes in the evolutionary ecology of insect-microbe interactions. The lab combines genomic and experimental approaches to learn how both beneficial and harmful microbes establish and maintain relationships with their hosts.

A human gut holds about 10,000 species of bacteria. These microbial communities, which can be genetically characterized as microbiomes, are transferred generationally but are also dynamic and respond to environmental changes. The microbiome of an urbanite, for example, has different characteristics from that of a hunter-gatherer.

Unlike humans, insects tend to have specialized feeding ecologies. They offer simple models to study symbiotic relationships between microbes and their hosts.

Salem with Buchner's book
Salem became fascinated by Cassida rubiginosa, more commonly known as the tortoise beetle, while he was a graduate student at the Max Planck Institute for Chemical Ecology in Jena, Germany. He was leafing through a 1953 edition of a book by the late Paul Buchner, a German scientist and one of the pioneers of systematic symbiosis research in insects. Buchner referenced a paper published in 1936 by one of his students, Hans-Jurgen Stammer, on Cassida rubiginosa.

“Stammer wrote that, unlike most leaf-eating beetles that he had studied, this one had sac-like organs that he had never seen before and the organs were filled with micro-organisms,” says Salem, who looked up Stammer’s original paper in a now-obscure journal. “He didn’t have the high-powered microscopes that we have now, or genome sequencing technology, so he wasn’t able to comment on the functionality of the mysterious microbes. At that point, the idea that microbes could do anything beneficial for an animal was mushy science.”

Intrigued by the article, Salem went to a nearby woodland to collect some of the leaf beetles. “To find these beetles, you don’t go looking for them,” he explains. “You go looking for the plants they eat.”

The tortoise beetle feeds on the tough, spiny leaves of the Californian thistle (Asteraceae). This prolific weed grows throughout much of the world and is difficult to control. “It pops up in a lot of areas where sheep are maintained,” Salem says. “In fact, it’s a huge pest to New Zealand sheep farmers. The more thistles covering a farmland, the less food the sheep have to eat and the lower the yield. But the thistle is hard to get rid of because its roots run so deep.”

Salem followed the trail of his curiosity to New Zealand, spending time with an agricultural researcher, Michael Cripps, who breeds the tortoise beetle as a bio-control model for thistles. “You drop 100 beetles on a thistle plant and the insects will just drain the plant metabolically until it dies,” Salem explains.

As an herbivore that specializes in eating leaves, the tortoise beetle must consume large amounts of plant cell walls, made of hard-to-digest materials like pectin. One of nature’s most complex polysaccharides, pectin is a gelatinous substance that gives plant cell walls their shape and rigidity. While it was unclear how the beetle obtained needed nutrients of amino acids and vitamins from such a diet, Salem suspected that symbiotic bacteria played a role.

In this cross-section of the symbiotic organ the bacteria it contains are lit up in fluorescent green dye. Microscopy image by Hassan Salem.

When he joined the Gerado lab at Emory, Salem continued to study the tortoise beetle and its micro-organisms with the help of fellow post-doc Aileen Berasategui, a co-author of the Cell paper.

They used genome sequencing technology to characterize the microorganisms as a new species of bacterium. Despite its tiny genome, the bacterium has the power to degrade pectin.

“Just as an apex predator has claws and strong mandibles to obtain the nutritional value that it needs from its prey, the bacterium has pectin-digesting genes that enable the beetle host to deconstruct a plant cell,” Salem says.

After the bacterium breaks down the pectin, the beetle’s digestive system can then access all of the amino acids and vitamins within the plant’s cells for its nutrients.

Salem christened the new bacterium Candidatus Stammera capleta, after Hans-Jurgen Stammer, the ecologist who first glimpsed it and wondered about it more than 80 years ago.

“The most amazing thing to me is that we made this discovery because I read a really old book,” Salem says. “It speaks to the importance of natural history collections and libraries for old journals. We truly stand on the shoulders of giants, extending the work of those who came before us.”

Additional co-authors of the paper are from the Max Planck Institute for Chemical Ecology, the University of Luxembourg, the Lincoln Research Centre in New Zealand, Johannes Gutenberg University in Germany and the National Institute for Advanced Industrial Science and Technology in Japan.

Tiny aphids hold big surprises in the genome
Farming ants reveal evolution secrets

Monday, November 13, 2017

The Lying Conference: Uncovering truths about deception

The Lying Conference will unmask the many factors involved in deception, including evolution, culture and the human affinity for storytelling and make believe.

By Carol Clark

We grow up with this notion that we should always tell the truth. But can we live without lying? 

That’s one of the questions to be explored in a day-long event, “The Lying Conference,” on Friday, November 17, from 8:30 am to 6:30 pm at Emory Conference Center. Emory’s Department of Psychology is bringing together scientists from psychology, neuroscience and anthropology — along with a leading journalist, a theater director and a professional magician — to discuss their insights into lying and deception. The conference is free and open to the public, but registration is requested. 

Topics to be covered include: The deep, evolutionary roots of lying. How children learn to tell lies. Cultural differences in lying. How we decide whether someone is trustworthy. How technology and the changing media and political landscapes are affecting our collective beliefs. The role of deception in the arts and entertainment.

“Lying is kind of a hot topic right now, with all the buzz about fake news and accusations of cover-ups and deception,” says Emory developmental psychologist Philippe Rochat, lead organizer of the event. “When we talk about lying, what we are indirectly trying to understand is, what is the truth? It can be a profound question.”

Science uses probabilities to approximate the truth, Rochat notes. “It’s a never-ending journey and you keep trying to get closer.”

In day-to-day interactions, we regularly negotiate the truth with one another, trying to convince others of a point of view. “People put on makeup to exaggerate their features,” Rochat says. “We amplify some things about ourselves and hide others. We make believe. We seduce.”

People can lie maliciously, in an anti-social way. Or they can tell white lies, to be polite and avoid hurting another person’s feelings.

Rochat is particularly interested in the developmental trajectory of lying. Between the ages of two and three, children begin to engage in pretend play. By around age four, when children start to have ideas about what other people are thinking, lying emerges. “They can be explicit at this stage, because they can understand that someone can be deceived,” Rochat says. “But they still cannot lie very well. They tend to leak the truth.” By the age of six or seven, he adds, “we become much better at concealing the truth and keeping a secret tight.”

Whatever the reasons for lying, one thing is clear: “We’ve evolved to lie,” Rochat says. “It’s deeply rooted in our nature and somehow important to our survival.”

Following are the seven speakers of the conference and brief summaries of their topics.

“Perspective-taking and Dishonest Communication in Primates and Other Animals,” by Emory primatologist Frans de Waal: While there is plenty of evidence for functional deception in animals — such as the way a butterfly might use mimicry as camouflage — but tactical deception requires anticipating the reaction of others. Tactical deception is clearly more developed in apes than most other species, although there is also evidence for corvids.

“Lying, American Style,” by Emory anthropologist Bradd Shore: He will discuss the role of culture in lying and how it differs across cultures. Shore will also touch on the some of the ways the American cultural model has been politically deployed and manipulated in recent decades.

“Little Liars — How Children Learn to Tell Lies,” by Kang Lee a developmental psychologist from the University of Toronto: Lee will use scientific evidence from his lab to show how lying begins early in life, what factors contribute to the development of lying, why children lie and whether adults can easily detect children’s lies. He will also discuss recent developments in technology that may help in detecting lies.

“Face Value — The Irresistible (and Misleading) Influence of First Impressions,” by neuroscientist Alexander Todorov from Princeton University: People form instantaneous impressions from faces and act on these impressions. In the last 10 years, data-driven computational methods allow scientists to visualize the configurations of face features leading to specific impressions such as trustworthiness. But these appearance stereotypes are not often accurate. So why do we form first impressions?

“What Happened to the News? Technology, Politics and the Vanishing Truth,” by Johnathan Mann, former CNN International anchor: Many American believe that the news media intentionally lie to them. President Donald Trump is the best-known detractor of “fake news,” though he himself has been accused of lying more than any other public figure in recent memory. Mann will address the overlapping changes to technology, politics and business that have crippled our national conversation with deception and distrust.

“Onions and Identities — Theater and the True Self,” by Emory dramatist Tim McDonough: Drama is densely populated by duplicitous schemers, by power figures whose lies maintain the sociopolitical status quo, and by characters in search of themselves, who mirror to us our confusions and self-deceptions. Theater provides a template for understanding identity and insight into existentially and socially necessary forms of deceit.

“The Science of Magic and the Art of Deception,” by professional magician Alex Stone: Magicians trick our brains into seeing what isn’t real, and for whatever reason our brains let them get away with it. Through a mix of psychology, storytelling and sleight-of-hand, Stone will explore the cognitive underpinnings of misdirection, illusion, scams and secrecy, pulling back the curtain on the many curious and powerful ways our brains deceive us not just when we’re watching a magician but throughout our everyday lives.

Monday, November 6, 2017

Mandatory state policies work best to curb power plant emissions, study finds

“Due to the current void in national leadership on the issue of climate change, efforts at the state and local level are more important than ever,” says Eri Saikawa, an assistant professor of Environmental Sciences. Saikawa is part of an Emory delegation to the U.N. Climate Change Conference talks in Bonn, Germany, which includes two faculty and 12 students.

By Carol Clark

U.S. state policies aimed at mitigating power plant emissions vary widely in effectiveness, finds a new study by researchers at Emory University.

Nature Climate Change published the analysis, which shows that policies with mandatory compliance are associated with the largest reductions in power plant emissions.

“Based on the results of our study, we recommend that states adopt a policy of mandatory greenhouse gas emissions registry and reporting for power plants,” says Eri Saikawa, an assistant professor in Emory’s Department of Environmental Sciences. “We also found a significant impact in states that adopt public benefit funds aimed at energy efficiency and renewable energy programs. These two policies not only are effective in reducing power-plant emission levels but also emissions intensity.” 

Saikawa, an expert in public policy and the science of emissions linked to global warming, co-authored the study with Emory graduate Geoff Martin, whose thesis project focused on the topic. Martin received his master’s degree in environmental sciences in May and now works as an energy coordinator for the town of Hartford, Vermont.

Their findings were released today as the U.N. Climate Change Conference (COP23) opens in Bonn, Germany. Delegates from around the world are gathering to hammer out details for meeting the goals of the 2015 Paris Agreement.

The United States was among the 195 countries that committed to this framework to reduce greenhouse gas emissions — although the Trump administration has said it plans to withdraw from this historic accord.

“Due to the current void in national leadership on the issue of climate change, efforts at the state and local level are more important than ever,” Saikawa says. “U.S. cities and states need to step up and do what they can.”

Emory is one of 50 universities from around the country to hold official U.N. observer status for COP23. Saikawa and Sheila Tefft, senior lecturer from the Department of English, will be on the ground in Bonn — leading a delegation of 11 Emory undergraduates and one graduate student as part of their co-taught class, “Climate Change and Society.”

The students will report news live from the event on Twitter under the hashtag #EmoryCOP23. They will also post longer reports, podcasts and videos on a web site they created for the event, Climate Talks Emory University.

Global atmospheric CO2 levels increased at record speed last year, to reach a level not seen for more than three million years, the U.N. warned in a report released last week. The U.S. government’s National Climate Assessment, also released last week, affirmed that climate change is driven almost entirely by human action and detailed how the country is already experiencing more extreme heat and rainfall events, more large wildfires and more flooding due to the warming climate.

About 30 percent of U.S. greenhouse gas emissions come from the electric power sector. For the Nature Climate Change paper, the researchers started out to review the potential impact of President Obama’s Clean Power Plan — which established the first national carbon pollution standards for power plants. When President Trump took office, and announced plans to repeal the Clean Power Plan, the researchers shifted focus.

They analyzed 17 policies adopted by various states relating to climate and energy. States that adopted a mandatory policy for power plants to register and report greenhouse gas emissions, along with three to four other policies, showed the largest reductions, at an average of 2.6 million metric tons of carbon dioxide (CO2) emissions per year.

The second most significant policy involved public benefit funds allotted for energy efficiency and renewable energy programs. That policy was associated with a reduction of about 1.5 million tons of CO2 emissions from power plants, when adopted with three to four other policies.

It’s unclear whether one of these single policies was the actual driver of the reduction in emissions, or an indicator that a state takes climate change mitigation seriously and is attacking the issue on many fronts, Saikawa says.

For instance, three states — New York, Connecticut and Oregon — have each adopted both of the top two most effective policies, along with at least eight other policies.

In 2007, China surpassed the United States as the largest emitter of greenhouse gases globally. “But the per capita emissions in the United States are more than double that of China,” Saikawa notes.

The Obama administration played a key role in securing the Paris Agreement, to keep global warming to no more than 2 degrees Celsius since the start of the Industrial Revolution.

“It will be interesting to hear the take of officials from the Trump administration this year,” Saikawa says. “U.S. coalitions from the state and city level are forming and they will likely have a strong presence at side events for COP23,” she adds. “Many groups are working at the local level around the world to try to meet the goal of the Paris Agreement.”

Emory is co-hosting an event on Thursday, November 16 at COP23, focused on ways to mitigate climate change impacts in the developing world. Saikawa will appear on a panel, along with John Seydel, director of sustainability for the city of Atlanta.

“We’ll be discussing how efforts at the city and state level in the United States might be replicated in other parts of the world,” Saikawa says.

This marks the third year in a row that Emory has sent a delegation to the U.N. climate talks.

Peachtree to Paris: Emory delegation headed to U.N. climate talks
The growing role of farming and nitrous oxide in climate change

Wednesday, November 1, 2017

Physicists show how lifeless particles can become 'life-like' by switching behaviors

Emory graduate student Guga Gogia slowly “salted” micron-sized particles into a vacuum chamber filled with plasma, creating a single layer of particles levitating above a charged electrode. He kept a low gas pressure, so the particles could move freely. “After a few minutes I could see with my naked eye that they were acting strangely," Gogia says.

By Carol Clark

Physicists at Emory University have shown how a system of lifeless particles can become “life-like” by collectively switching back and forth between crystalline and fluid states — even when the environment remains stable.

Physical Review Letters recently published the findings, the first experimental realization of such dynamics.

“We’ve discovered perhaps the simplest physical system that can consistently keep changing behavior over time in a fixed environment,” says Justin Burton, Emory assistant professor of physics. “In fact, the system is so simple we never expected to see such a complex property emerge from it.”

Many living systems — from fireflies to neurons — switch behaviors collectively, firing on and then shutting off. The current paper, however, involved a non-living system: Plastic particles, tiny as dust specks, that have no “on” or “off” switches.

“The individual particles cannot change between crystalline and fluid states,” Burton says. “The switching emerges when there are collections of these particles — in fact, as few as 40. Our findings suggest that the ability for a system to switch behaviors over any time scale is more universal than previously thought.”

Watch a video to learn more and see the particles in action:

The Burton lab studies the tiny, plastic particles as a model for more complex systems. They can mimic the properties of real phenomena, such as the melting of a solid, and reveal how a system changes when it is driven by forces.

The particles are suspended in a vacuum chamber filled with a plasma — ionized argon gas. By altering the gas pressure inside the chamber, the lab members can study how the particles behave as they move between an excited, free-flowing state into a jammed, stable position.

The current discovery occurred after Emory graduate student Guram “Guga” Gogia tapped a shaker and slowly “salted” the particles into the vacuum chamber filled with the plasma, creating a single layer of particles levitating above a charged electrode. “I was just curious how the particles would behave over time if I set the parameters of the chamber at a low gas pressure, enabling them to move freely,” Gogia says. “After a few minutes I could see with my naked eye that they were acting strangely.”

From anywhere between tens of seconds to minutes, the particles would switch from moving in lockstep, or a rigid structure, to being in a melted gas-like state. It was surprising because the particles were not just melting and recrystallizing but going back and forth between the two states. 

“Imagine if you left a tray of ice out on your counter at room temperature,” Gogia says. “You wouldn’t be surprised if it melted. But if you kept the ice on the counter, you would be shocked if it kept turning back to ice and melting again.”

Gogia conducted experiments to confirm and quantify the phenomenon. The findings could serve as a simple model for the study of emerging properties in non-equillibrium systems.

“Switching is an ubiquitous part of our physical world,” Burton says. “Nothing stays in a steady state for long — from the Earth’s climate to the neurons in a human brain. Understanding how systems switch is a fundamental question in physics. Our model strips away the complexity of this behavior, providing the minimum ingredients necessary. That provides a base, a starting point, to help understand more complex systems.”

Physicists crack another piece of the glass puzzle
The physics of falling icebergs