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).

Related:
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.

Related:
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.

Related:
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.”

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

Tuesday, October 31, 2017

$2 million NSF grant funds physicists' quest for optical transistors

"The ultimate goal is making it possible to devise all-optical computers and telecommunications," says Hayk Harutyunyan, left, with Ajit Srivastava. (Ann Borden, Emory Photo/Video)

By Carol Clark

The National Science Foundation awarded two Emory physicists a $2 million Emergent Frontiers grant, for development of miniaturized optical transistors to take computers and telecommunications into a new era.

“We are working to change some properties of light — such as making it travel in only one direction — by using atomically thin, two-dimensional materials,” says Ajit Srivastava, assistant professor of physics and principal investigator for the grant. “These novel materials are being touted as the next silicon. They could open the door to even smaller and more efficient electronics than are possible today.”

Srivastava’s co-investigators include Hayk Harutyunyan, also an assistant professor of physics at Emory, as well as scientists from Georgia State and Stanford universities.

“The ultimate goal is making it possible to devise all-optical computers and telecommunications,” Harutyunyan says.

A major revolution in telecommunications occurred in the 1950s, driven by the development of silicon semiconductors as miniature transistors to control the flow of electrical current. These transistors led to smaller, faster computers and paved the way for everything from flatscreen TVs to cell phones.

“They changed civilization,” Harutyunyan says. “Every year new computers would come out with faster processors as the transistors got tinier and more efficient. But about a decade ago this progress stopped, because these transistors cannot be made any smaller than about 15 nanometers and still function well.”

Meanwhile, the gradual replacement of copper wiring with fiber optics is speeding up transmissions between computers and other electronic devices and allowing for greater bandwidth. “When you send an email from Atlanta to Europe, the information is encoded into light and relayed by fiber optic cables running under the ocean,” Srivastava explains. “It’s super fast, because light is the fastest thing that you can imagine.”

Unlike in our everyday life, however, where the arrow of time moves in one direction, light photons operate at the quantum scale and can move back and forth. This lack of a fixed direction is called reciprocity. “Reciprocity in optics,” Srivastava says, “can best be described by a familiar observation: ‘If I can see you, you can see me.’”

Fiber optic cables use magnetic fields to break reciprocity and prevent light from reflecting off surfaces and creating “noise” in a signal. The required magnetic devices, known as optical isolators, are typically bulky and heavy because tiny magnets are not strong enough to do the job.

The Emory project aims to develop powerful nonreciprocal optical devices that are not based on magnets and can function at the nanoscale.

Srivastava’s lab is investigating the potential of transition metal dichalcogenides, or TMDs. TMDs are semiconductors within a new family of two-dimensional, extraordinarily thin materials. While the smallest feature of a current computer processor is 14 nanometers thick, a TMD monolayer is smaller than a single nanometer.

Harutyunyan’s lab, meanwhile, is exploring ways to make interactions between light and matter stronger through the use of metallic nano particles. Metals are shiny because of their free electrons that easily interact with light. The oscillations of these free electrons, called plasmons, allow metallic nano-particles to funnel large amounts of light into tiny dimensions.

A long-term goal of the project is to hybridize TMDs and metallic particles into nanomaterials that use laser fields to create the same light-guiding effects of magnetic fields. Such devices have the potential to be faster and cheaper and offer more precise control of the light-directing process. They would also be much smaller than existing optical isolators and transistors.

“Nano-science is an exciting area,” Srivastava says. “You can imagine the possibility of flexible cell phones or even wearable electronic membranes that would take the shape of your body.”

More powerful computers could also ramp up the ability of scientists to analyze massive datasets faster, Harutyunyan notes.

The Emory grant will also fund public outreach projects in Atlanta area schools. “We want people to understand the importance of fundamental science research,” Harutyunyan says. “And we want to inspire young people to think about science careers.

Monday, October 23, 2017

CDC funds Emory project to automate analysis of mixed strains of antibiotic-resistant bacteria

An electron micrograph shows human immune system cells attacking methicillin-resistant Staphylococcus aureus (MRSA). MRSA is an example of antibiotic-resistant bacteria that can occur in multiple strains in an infection, further complicating diagnosis, treatment and interventions.

By Carol Clark

The Centers for Disease Control and Prevention (CDC) awarded $380,000 to three Emory University faculty to develop and refine a promising technique to detect and respond to threats from drug-resistant pathogens.

The grant investigators include Lars Ruthotto and Ymir Vigfusson — both assistant professors in the Department of Mathematics and Computer Science — and Rebecca Mitchell, a visiting professor with a joint appointment in the Department of Mathematics and Computer Science and the Nell Hodgson Woodruff School of Nursing. 

The trio is developing a method to quickly and cost-effectively diagnose multiple strains of antibiotic-resistant bacteria within a single biological sample.

“This project harmonizes our different scientific specialties,” Vigfusson says. He is a computer scientist who develops software and programming algorithms that work at scale, while Ruthotto is a mathematician who focuses on solving inverse problems. Mitchell is a veterinarian and epidemiologist experienced in gathering biological samples and testing them for pathogens. 

Antibiotic-resistant infections are a growing national and global problem, causing at least two million illnesses and 23,000 deaths in the United States annually, according to the CDC.

The Emory grant is part of a $9 million package of CDC funding announced today, including awards to projects at 25 leading research institutions around the country that are exploring gaps in knowledge about antibiotic resistance and piloting innovative solutions in the healthcare, veterinary and agriculture industries. The work complements broader CDC efforts to support known strategies for protecting people and slowing antibiotic resistance, collectively known as the CDC Antibiotic Resistance Solutions Initiative.

The Emory project seeks to tame the complexity of analyzing multiple infections within a biological specimen, from a drop of blood to a fecal sample. In the case of a widespread outbreak of antibiotic-resistant E. coli for instance, it would be useful to quickly determine whether fecal samples contained multiple strains of the bacteria and what those strains were, in order to more rapidly trace the sources of the outbreak and design effective interventions.

It is costly and labor-intensive, however, to culture biological samples at the local level, and then send them to the CDC for testing. And if multiple strains of a pathogen are within a single sample, only some strains that are present may grow in the culture while other strains may be missed.

“It’s a challenge to deal with samples containing mixed strains of a pathogen in a lab setting,” Mitchell says. “You have to do a large amount of work to get the finer gradations of what species of pathogens are present, and in what proportions.”

The Emory researchers are striving to balance accuracy with the need to simplify and streamline the process. Their method eliminates labor-intensive, technical steps, such as culturing the sample. “We want to automate the process so that you need less expertise at the local level, and so that data coming from individual states can be easily integrated into a central system,” Mitchell explains.

They use multiple short polymorphic regions in the genome to look for genetic variations among the DNA templates present within a biological sample. In the case of antibiotic-resistant bacteria, the number of reference sites ranges between the hundreds to the thousands, depending on the specific bacteria targeted.

“We’ve developed an algorithm and software and mathematical models to rapidly run these comparisons and estimate the number of strains in a single sample, and the percentage of each,” Ruthotto says. “Now we are trying to quantify the accuracy of this estimate, which is a mathematical challenge. The grant gives us the resources to refine our method for real-world applications.”

The ultimate goal is to develop a system that will work not just on antibiotic-resistant bacteria, but for mixed-strains of any pathogen within a biological sample. In a separate project, for example, Mitchell and Vigfusson are applying the method to test for multiple strains of the malaria parasite within a blood sample.

“Quickly teasing apart mixed-strain samples is a big challenge in public health, and it’s essential in order to plan effective interventions,” Mitchell says.

“We’re using math and computer science to draw more information from a single biological sample than was previously practical,” Vigfusson says. “We hope that our method could turn into a work engine that helps to understand multiple-strain infections and makes an impact on public health.”

Related:
Brazilian peppertree packs power to knock out antibiotic-resistant bacteria
A future without antibiotics?

Friday, October 20, 2017

Responding to climate change


By Martha McKenzie
Emory Public Health

Climate change. Partisan politicians debate its reality, and many citizens see it as a faraway threat, something that endangers the future of polar bears but not them personally.

The health effects of global warming, however, are already being felt. Extreme weather events such as wildfires, droughts, and flooding are becoming more frequent, resulting in more injuries, deaths, and relocations. Heat and air pollution are sending people with asthma and other respiratory ailments to the emergency room. Diseases carried by mosquitoes, fleas, and ticks are expanding their territory—dengue has become endemic in Florida, Lyme disease has worked its way up to Canada and over to California, and some fear that malaria may re-emerge in the U.S.

Tie these health burdens—which are only likely to worsen—with the current administration’s decision to pull out of the Paris climate agreement and dismantle environmental regulations, and the call to action becomes more urgent. “The federal government’s actions might be a headwind from a funding perspective, but they are also very much a tailwind from an inspiration and motivation perspective,” says Daniel Rochberg, an instructor in environmental health who worked for the U.S. State Department as special assistant to the lead U.S. climate negotiators under presidents Bush and Obama. “As others have said, ‘We are the first generation to feel the sting of climate change, and we are the last generation that can do something about it.’ We have to get busy doing something about it.”

Rollins School of Public Health has gotten busy. Faculty researchers are building the science of climate impacts, strategies for reducing greenhouse gas emissions, and approaches for increasing resilience to climate change. Climate@Emory, a university-wide organization of concerned students, faculty, and staff, is partnering with other academic institutions, industries, and governments to support education and climate remediation efforts. Through Climate@Emory’s initiative, Emory University is an accredited, official observer to the UN climate talks and has sent students and faculty to the climate conferences in Paris in 2015 and in Marrakech in 2016. And, of course, Rollins is educating the next generation of scientists who will be dealing with the fallout of today’s climate decisions.

“For environmental scientists, it’s a challenging climate,” says Paige Tolbert, O. Wayne Rollins Chair of Environmental Health. “That means we have to be creative, because we can’t step aside and wait four years. It’s more critical than ever that we keep moving forward and make whatever contributions we possibly can.”

Read more in Emory Public Health.

Related:
Georgia climate project creates state 'climate research roadmap'
Catalyst for change
How will the shifting political winds affect U.S. climate policy?
Peachtree to Paris: Emory delegation headed to U.N. climate talks

Monday, October 2, 2017

NSF awards Emory's Center for Selective C-H Functionalization $20 million

"We’ve developed advanced catalysts that allow us to control which carbon-hydrogen bond within a molecule will react and when," says Huw Davies, director of the Center for Selective C-H Functionalization. (Graphic/photo by Stephen Nowland and Dan Morton)

By Carol Clark

The National Science Foundation has awarded another $20 million to Emory University’s Center for Selective C-H Functionalization, to fund the next phase of a global effort to revolutionize the field of organic synthesis.

“Our center is at the forefront of a major shift in the way that we do chemistry,” says Huw Davies, professor of chemistry at Emory and the director of the Center for Selective C-H Functionalization (CCHF). “This shift holds great promise for creating new pathways for drug discovery and the production of new materials to benefit everything from agriculture to electronics.”

The CCHF began as an NSF Center for Chemical Innovation in 2009, with a seed grant of $1.5 million and four collaborating universities. In 2012, the NSF awarded the CCHF its first $20 million, enabling it to grow to encompass 16 U.S. institutions and seven industrial affiliates, including six major pharmaceutical companies and one of the largest U.S. chemical suppliers. The center also built global connections with major players in C-H functionalization in Japan, South Korea and the U.K. 

The CCHF has led the way for explosive growth in the field of C-H functionalization, publishing more than 200 papers on the topic through its collaborators. It has developed dozens of new catalysts for C-H functionalization, including four major classes from the Huw Davies group.

“The past five years we’ve developed the fundamentals for C-H functionalization and documented that the concept is viable,” Davies says. “Now we’re ideally positioned to maximize the further development of this chemistry and move forward to apply it.”

Huw Davies, right, in his lab with Emory post-doctoral fellow Sidney Wilkerson-Hill, left, and Emory junior Patricia Chi Lin. The CCHF has developed dozens of new catalysts for C-H functionalization, including four major classes from the Davies group. (Photo by Stephen Nowland, Emory Photo Video)

Traditionally, organic chemistry has focused on the division between reactive, or functional, molecular bonds and the inert, or non-functional bonds carbon-carbon (C-C) and carbon-hydrogen (C-H). The inert bonds provide a strong, stable scaffold for performing chemical synthesis with the reactive groups. C-H functionalization flips this model on its head. 

“We’ve devised ways to make C-H bonds react so that they become functional,” Davies says. “And we’ve reached the stage where it is no longer the molecule itself that determines the process of the reaction — we’ve developed advanced catalysts that allow us to control which carbon-hydrogen bond within a molecule will react and when.”

C-H functionalization opens unexplored chemical space by taking petroleum byproducts, which have a lot of carbon-hydrogen bonds, and transforming them from waste into useful materials. It also strips out steps from the linear process of traditional organic synthesis, making it faster and more efficient.

The CCHF is not only transforming organic synthesis — it’s also creating new models for the way that organic chemistry is taught and that labs conduct research. Where previously individual labs tended to work in isolation to tackle problems, the CCHF has broken down walls across specialties, institutions and even countries to collectively take on the remaining challenges of selective C-H functionalization.

“We’ve got this incredible collaborative environment where organic chemists aren’t just sharing results — they’re sharing ideas,” Davies says. “That’s rare. And we’ve expanded that environment beyond our network of universities to also engage the pharmaceutical industry.”

In 2015, the CCHF launched an online symposia on recent advances in C-H functionalization. More than 1,000 graduate students and chemistry faculty from up to 45 countries join the symposia, held about four times a year, via the Internet.

“We have leading voices in the field give these free talks that are easy to join live and participate in,” Davies says. “The aim is to further expand the field of C-H functionalization by introducing it to graduate students and other chemists around the world.”

Related:
Chemists find 'huge shortcut' for organic synthesis using C-H bonds
NSF chemistry center opens new era in organic synthesis

Friday, September 22, 2017

The math of doughnuts: 'Moonshine' sheds light on elliptic curves

In the simplest terms, an elliptic curve is a doughnut shape with carefully placed points, explain Emory University mathematicians Ken Ono, left, and John Duncan, right. “The whole game in the math of elliptic curves is determining whether the doughnut has sprinkles and, if so, where exactly the sprinkles are placed,” Duncan says. (Photos by Stephen Nowland, Emory Photo/Video)

By Carol Clark

Mathematicians have opened a new chapter in the theory of moonshine, one which begins to harness the power of the pariahs – sporadic simple groups that previously had no known application.

“We’ve found a new form of moonshine, which in math refers to an idea so farfetched as to sound like lunacy,” says Ken Ono, a number theorist at Emory University. “And we’ve used this moonshine to show the mathematical usefulness of the O’Nan pariah group in a way that moves it from theory to reality. It turns out that the O’Nan group knows deep information about elliptic curves.”

Nature Communications published the representation theory for the O’Nan group developed by Ono, John Duncan (also a number theorist at Emory) and Michael Mertens (a former post-doctoral fellow at Emory who is now at the University of Cologne).

“We’ve shown that the O’Nan group, a very large pariah group, actually organizes elliptic curves in a beautiful and systematic way,” Duncan says. “And not only does it organize them, it allows us to see some of their deepest properties. It sees infinitely many curves, which allows us to then use our moonshine to make predictions about their general behavior. That’s important, because these objects underlie some of the hardest questions at the very horizon of number theory.”

Elliptic curves may sound esoteric, but they are part of our day-to-day lives. They are used in cryptography – the creation of codes that are difficult to break. An elliptic curve is not an ellipse, rather it is a complex torus, or doughnut shape.

“You can think of it as a doughnut together with specific, delicate configurations of rational points that are very carefully placed,” Duncan says. “So, in the simplest of terms, it’s like a doughnut that you eat, that may have sprinkles on it. The whole game in the math of elliptic curves is determining whether the doughnut has sprinkles and, if so, where exactly the sprinkles are placed.”


Unlike an edible doughnut, however, these mathematical doughnuts are not visible.

“Imagine you are holding a doughnut in the dark,” Ono says. “You wouldn’t even be able to decide whether it has any sprinkles. But the information in our O’Nan moonshine allows us to ‘see’ our mathematical doughnuts clearly by giving us a wealth of information about the points on elliptic curves.”

The findings are especially surprising since none of the pariahs, as six of math’s sporadic simple groups are known, had previously appeared in moonshine theory, or anywhere else in science.

Math’s original moonshine theory dates to a 1979 paper called “Monstrous Moonshine” by John Conway and Simon Norton. The paper described a surprising connection between a massive algebraic object known as the monster group and the j-function, a key object in number theory. In 2015, a group of mathematicians – including Duncan and Ono – presented proof of the Umbral Moonshine Conjecture, which revealed 23 other moonshines, or mysterious connections between the dimensions of symmetry groups and coefficients of special functions.

In theoretical math, symmetry comes in groups. Symmetrical solutions are usually optimal, since they allow you to divide a large problem into equal parts and solve it faster.

The classification of the building blocks of groups is gathered in the ATLAS of Finite Groups, published in 1985. “The ATLAS is like math’s version of the periodic table of the elements, but for symmetry instead of atoms,” Duncan explains.

Both the ATLAS and the periodic table contain quirky characters that may – or may not – exist in nature.

Four super heavy elements with atomic numbers above 100, for example, were discovered in 2016 and added to the periodic table. “People have to work hard to produce these elements in particle accelerators and they vanish immediately after they are constructed,” Ono says. “So you have to wonder if they really are a part of our everyday chemistry.”

The pariah groups pose a similar question in math. Are they natural or simply theoretical constructs?

“Our work proves, for the first time, that a pariah is real,” Ono says. “We found the O’Nan group living in nature. Our theorem shows that it’s connected to elliptic curves, and whenever you find a correspondence between two objects that are seemingly not related, it opens the door to learning more about those objects.”

Related:
Mathematicians prove the Umbral Moonshine Conjecture

Thursday, September 21, 2017

Malawi yields oldest-known DNA from Africa

Emory anthropologist Jessica Thompson next to Malawi rock art paintings, likely made by hunter-gatherers. Thompson's work in Malawi is part of a major new paper in the journal Cell, filling in thousands of years of human prehistory of hunter-gatherers in Africa. (Photo by Suzanne Kunitz)

By Carol Clark

Emory anthropologist Jessica Thompson was at a human origins conference years ago when she heard a presenter lament: “Of course, there is no ancient DNA from Africa because of the poor preservation there.”

That’s when it clicked in Thompson’s mind: She had visited a place in Africa — the highlands of northern Malawi — that had neither extremes of heat or wetness — two main environmental factors that degrade DNA. She also knew that scant archaeological research had been done in the region, although a team had unearthed several ancient skeletons there decades ago.

“It’s a strange and fascinating landscape,” says Thompson, who made that 2005 visit as a tourist and was struck by the surreal beauty of the high mountain grassland.

It’s also remote and off the radar of most of the world. “We saw maybe three other tourists while we were there,” she recalls.

That fateful trip laid the groundwork for discoveries of the oldest-known DNA from Africa. The journal Cell just published an analysis of the new discoveries, filling in thousands of years of human prehistory of hunter-gatherers in Africa, led by Harvard geneticist David Reich.



Thompson is second author of the paper. She contributed and described the cultural context for nearly half of the 15 new DNA finds, including the oldest samples. Her fieldwork in Malawi uncovered human remains that yielded DNA ranging in age from about 2,500 to 6,100 years old. And her work is ongoing at a site where a skeleton recovered in 1950 was just dated to 8,100 years old and also yielded DNA.

The other DNA in the Cell paper ranges in age from 3,000-to-500 years ago and comes from South Africa, Tanzania and Kenya.

“Malawi is positioned in between where living hunter-gatherers survive,” Thompson says. “For the first time, we can see the distribution of ancient hunter-gatherer DNA across Africa, showing how these populations were connected in the past.”

Ancient hunter-gatherers do not have a lot of living representatives in Africa today, and they occur as remnants of people scattered across the continent. The remains of Malawi hunter-gatherers that Thompson is studying may represent a population that was once thriving but subsequently pushed into marginal areas during the expansion of agriculturalists and pastoralists during the past 3,000 years.

Some of this population may have survived until much more recently.

“There are legends in Malawi of the original people who came there, passed down through oral histories,” Thompson says. “They are described as hunters and little people, short in stature. There is also a story of a last, epic battle — that occurred about 200 years ago — when these people got eradicated.”

Mount Hora, where the oldest DNA included in the Cell paper was obtained, from a woman who lived more than 8,000 years ago. (Photo by Jessica Thompson)

Malawi captivated Thompson during that first visit as a tourist, in 2005. She was a graduate student when she spent a summer working on a dig in the Serengeti. She and two companions decided to make a road trip before returning to the United States, including a stop in Malawi.

The landlocked country is located in southeast Africa, bordered by Zambia, Tanzania and Mozambique. It is one of the least-developed and smallest countries in Africa, about the size of the state of Tennessee, and runs north to south along the Rift Valley. An enormous body of water, Lake Malawi, makes up about one-third of the country.

“My traveling companies wanted to relax by the lake in the lowlands,” Thompson recalls. “I had read about the Malawi highlands and really wanted to see this unique ecosystem, so I convinced them to go there instead.”

Her companions complained of the cold — it’s windy and regularly freezes in the highlands of Malawi and summer temperatures peak at around 65 or 70 degrees Fahrenheit. Despite the cold, Thompson admired the rugged, isolated beauty of rocky outcrops and grasslands studded with orchids and fairy ferns where zebra and shaggy antelope grazed.

Thompson, who joined Emory as an assistant professor of anthropology in 2015, dug through the archaeological literature surrounding Malawi and started making exploratory trips there in 2009. She learned of two digs in the Malawi highlands — in 1950 and 1966 — that revealed human skeletons alongside rich cultural evidence of an extinct hunting-and-gathering lifeway.

Dancers at a festival in Malawi. The people living in the country today are the descendants of the Iron Age agriculturalists and pastoralists who swept across the African continent about 3,000 years ago. (Photo by Jessica Thompson)

The 1950 dig turned out to be led by the renowned archaeologist J. Desmond Clark, who Thompson calls her “academic grandfather.” Although Clark died before Thompson could meet him, he served as the mentor to her mentor, Curtis Marean.

On the slopes of Mount Hora — a striking 1,500-meter peak and a major landmark in the highlands — Clark uncovered two skeletons: A woman who had died at around age 22 and a nearby male, who had died in his 40s. The skeletons had been taken out of the country, to the Livingstone Museum in Zambia, and were never dated.

“It was impossible to accurately do radiocarbon dating on bone in 1950,” Thompson explains. “The skeletons became, quite frankly, forgotten over time.”

Guided by the clues from the previous excavations, Thompson began heading digs in the Malawi highlands. A site at a landmark outcrop, known as Fingira Rock, is particularly isolated, requiring the team to hike up a mountainside to more than 2,000 meters on the Nyika Plateau. “Working there you feel the wind, you feel the chill,” Thompson says.

Poachers are a hazard in the area, along with the occasional black mamba — one of the world’s deadliest snakes.

The Fingira site had not been excavated since 1966. “We were appalled to discover that it had been heavily disturbed since then,” Thompson says. Her team uncovered two human leg bones, from two different adult males, which yielded DNA that was about 6,100 years old.

The leg bone of a hunter-gatherer that lived 6,100 years ago, found at the Fingira Rock site. (Photo by Jessica Thompson)

In the back of a cave, they found fragments of a child’s skull in a termite mound. A tiny leg bone next to it indicated that the remains were from a baby younger than age one. DNA analysis revealed that she had been a girl and radiocarbon dating showed that she had died about 2,500 years ago. The analysis also showed that the bones from the infant and the two men were from the same hunter-gatherer population — even though they were separated by thousands of years of time.

The archaeological sediments suggest that Fingira was a place where the dead were buried, although the skeletal material has become scattered over time. Human bones are mixed with the bones of animals that they hunted and ate, as well as with stone tools and shell beads that they used for ornaments.

“When you visit the site,” Thompson says, “you wonder, why were these people living up here when it’s not the most comfortable conditions you can imagine? What was bringing them here? Why were they burying their dead, over and over again, for many thousands of years, in the same place?”

Meanwhile, Thompson tracked down the skeletons that Clark had discovered at Mount Hora in 1950. She learned they had been moved from Zambia to the University of Cape Town in South Africa.

Here’s where Emory graduate student Kendra Ann Sirak enters the story. Sirak had the distinction of being the last graduate student of Emory anthropologist George Armelagos, one of the founders of the field of paleopathology. He spent decades working with graduate students to study the bones of ancient Sudanese Nubians to learn about patterns of health, illness and death in the past. Armelagos sent Sirak to one of the best ancient DNA labs in the world, at University College Dublin (UCD), in Ireland, with samples of the Nubian bones.

After Armelagos died in 2014, at age 77, Thompson stepped in as one of Sirak’s mentors.

Thompson, left, examines fragments of artifacts from the Malawi excavations in her lab with Emory graduate student Kendra Ann Sirak. Sirak helped with the radiocarbon dating and DNA extraction of the "forgotten" 8,100-year-old skeleton from Mount Hora. (Photo by Ann Borden, Emory Photo/Video)

Thompson contacted the curator of the two skeletons from Mount Hora, to ask about the possibility of getting DNA from them. Alan Morris, now Professor Emeritus at the University of Cape Town, had had the same idea. A sample from the female skeleton was already slated to be sent to the UCD lab where Sirak was working. So Thompson, Morris and Sirak teamed up on the quest.

The petrous bone, which contains components of the inner ear, is the most promising site to drill for ancient DNA. The skeleton's petrous bone had already broken away from the skull, so only this tiny, triangular-shaped piece of the skeleton was sent to Dublin.

"It was extremely fragile," says Sirak, whose job was to drill into the petrous bone and get about 200 millimeters of bone powder without shattering the specimen.

She drank a cope of coffee, donned a hair cover, overalls, a face mask, two pairs of gloves and shoe covers, then entered a small, sterile room where the petrous bone awaited. "I said to myself, 'Here we go, I've got this!'" Sirak recalls.

Sirak was successful. Her colleagues in Dublin processed the sample and then sent it to the genetics team at Harvard Medical School for DNA analysis, which was also successful.

Meanwhile, radiocarbon dating revealed that the skeleton was 8,100 years old.

"It was like Christmas," Sirak says, "knowing that we had DNA data on such an ancient specimen."

The skeleton's genetics connected her to the same population of hunter-gatherers who died thousands of years later and were found 70 kilometers away at Fingira.

Another surprise revealed by the genetic analysis of the Malawi hunter-gatherers: They did not contribute any detectable ancestry to the people living in Malawi today, the descendants of the Iron Age agriculturalists and pastoralists who began sweeping across the African continent about 3,000 years ago.

“In most parts of Africa, you see quite a bit of admixture,” Thompson says. “When you take genetic samples from modern people who are living today, you find that they are a combination of the folks who were expanding into a region and also the folks who were living there before. In Malawi we see that’s not the case. It appears that there was a complete replacement of the original hunter-gatherer people. They are not just gone as a lifeway, they are actually gone as a people as well.”

One of the mysteries Thompson hopes to solve is how that replacement happened. Was it violent? Was it a sudden or a slow process? Did the entrance of strange new technologies, like pottery and iron working, play a role?

“We can’t use genetics to answer these questions,” Thompson says. “We have to use the archaeology.”

Emory anthropology undergraduates assisting with the Malawi excavations this past summer included, from left: Alexa Rome, Alexandra Davis, Suzanne Kunitz and Aditi Majoe. Graduate student Grace Veatch is on the far right.

She continues to excavate in Malawi, aided by local technicians and other collaborators. This summer, five Emory anthropology students accompanied her in the field: Graduate student Grace Veatch, senior Alexandra Davis, juniors Aditi Majoe and Suzanne Kunitz, and sophomore Alexa Rome. They uncovered more human remains at Mount Hora — a charred bone from a human arm and parts of two legs. These bones, recently dated to between 9,500 and 9,300 years old, show that the Hora site still has many secrets to reveal.

While radiocarbon dating of charcoal samples from just above and below the bones establishes their age, it is not clear whether they will yield DNA. “We don’t have high hopes,” Thompson says, “as they were burned and that tends to create even more preservation problems.”

The students assisted in the tedious work of carefully sifting through grey dust and ash, marking coordinates through GPS and other surveying tools, and recording the data into a computer.

Back in her lab at Emory, Thompson uses the data to generate three-dimensional images of the digs and pinpoint where each bone fragment, shell bead or stone tool was found. Her digital model for the this summer’s Mount Hora dig uses different-colored dots to give a glimpse of how hunter-gatherers were depositing both human remains and ordinary objects from their day-to-day lives over time.

“And then at this point,” Thompson says as she moves her cursor on her computer screen, “you see the introduction of pottery and iron technology. And right after that you see this fundamental change in the way that the site was used. People are no longer going there frequently. They’re no longer making these big bonfires. And they’re no longer interring their dead there.”

Thompson and her students are also sorting through hundreds of gallon-sized Ziploc plastic bags containing fragments from the Malawi sites. “As you excavate,” she explains, “you clean away the dirt and you’re left with all these tiny pieces of stone and bone artifacts. The bones are mostly animals. But every once in a while you find something that looks like it might be human. Any one one of them could be a new individual, a new piece to the story.”

She pulls out a small plastic bag labeled “Human distal phalanx.” It contains a piece of bone about the size of a Tic-Tac. “In this case, we think we have a finger bone, most likely from a child,” Thompson says.

Ultimately, Thompson seeks to understand how and when the earliest members of our species — Stone Age Homo sapiens — interacted with one another and with their environments in Africa.

“One thing that’s really easy to forget, when we look at the way people live today, is that for most of our evolution we lived as hunter-gatherers,” she says. “So if we want to understand our own origins as a species, we have to know what those lifeways looked like in the past.”

Related:
A bone to pick on origins of meat eating
Brain trumps hand in Stone Age tool study
Stone tools from Jordan point to dawn of division of labor 

Wednesday, September 6, 2017

What's it like to be a dog-cognition scientist?

"I can't imagine not living with dogs. That would be really sad for me," says Emory neuroscientist Gregory Berns, with Callie (left) and Cato. His latest book is called "What It's Like to Be a Dog."

Five years ago, Emory neuroscientist Gregory Berns became the first to capture images of actual canine thought processes. To explore the minds of the oldest domesticated species, the Berns lab trained dogs to remain still and alert while undergoing functional Magnetic Resonance Imaging (fMRI) — the same tool that is unlocking secrets of the human brain. The project opened a new door into canine cognition and social cognition of other species.

Berns went on to conduct a series of experiments on dogs, gathering both behavioral and fMRI data on questions such as: How capable are dogs of self-restraint? Do dogs prefer praise from their owners or food? How do dogs process faces in their brains? What’s going on in a dog’s brain when it smells the scent of its owner?

In 2013, Berns wrote a New York Times bestseller called “How Dogs Love Us.” He described how the death of his beloved pug Newton planted the seeds for his eventual switch from the studying the human brain to focus on non-invasive studies of the cognition of dogs and other animals.

In the following Q&A, Berns talks about his new book, “What It’s Like to Be a Dog: And Other Adventures in Animal Neuroscience,” just published by Basic Books. The book focuses on his hopes that understanding how animals think will revolution how we treat them.

Question: Can you talk about all the dogs you’ve had as pets during your life? 

Gregory Berns: When I was a child growing up in Southern California we had two golden retrievers, Pretzel and Popcorn. It’s embarrassing, but my parents always named their dogs after food. I’m not sure why. Most of the children in the area had dogs and horses and we would go traipsing around the hills. Kids and dogs go together.

Berns and Callie
After I was done with medical school and stopped moving around, my wife and I had three pugs, Simon, Newton and Dexter, and then a golden retriever, Lyra.

We now live with our two daughters and have three dogs: Callie, a Feist, which is a Southern squirrel hunting dog; Cato, a Plott hound, which is the state dog of North Carolina; and Argo, a yellow dog of some kind of mix. We also have two bearded dragons and a chameleon.

I can’t imagine not living with dogs. That would be really sad for me.

Q: “What It’s Like to Be a Dog” describes all the experimental work you have done so far with canine cognition. What’s the biggest surprise to come out of your research? 

GB: If you take language out of the picture, what we’re finding is that we see a lot of similarities between dogs and humans. In one study, for instance, we used fMRI to measure the relative value of food versus praise to the dogs and found that almost all the dogs’ brains responded to praise as much, and sometimes more, than to food. We ourselves know how it feels when someone praises us, there’s a positive feeling associated with it. That’s perhaps similar to what dogs are feeling.

We also did a study on dogs and delayed gratification. We found that part of the prefrontal cortex is more active in dogs during self-control. And, just like experiments with humans have found, we showed that the dogs who are better at this task use more of their prefrontal lobes.

Now that we are gaining a basic understanding of canine cognition, we are starting to focus more on the individuality of dogs — what it’s like to be this dog, as opposed to that dog.

Q: You’re also using diffusion tensor imaging (DTI) to study the brains of other mammals, mapping the neural pathways in brains from animals that are long deceased and stored in museum collections. How did this project come about? 

GB: It started in 2015 when we gained access to the brains of two dolphins that had died, and we showed that we could use DTI to map their sensory and motor systems. Dolphins are incredibly intelligent, social animals but they’ve remained relatively mysterious. We provided the first picture of the entire dolphin brain and all the white matter connections inside of it.

This year, we reconstructed the brain architecture and neural networks of the extinct Tasmanian tiger, also known as a thylacine, using two brain specimens from museums, both of which were about 100 years old.

Through a project I call the Brain Ark we’re collecting a digital archive of high-resolution, three-dimensional brain structures of megafauna. It’s publicly available to other researchers to contribute to and draw data from.

Q: What is the ultimate goal of your animal neuroscience research? 

GB: The Brain Ark is an attempt to catalog and study brains of large mammal species before they are gone. Or, as in the case of the Tasmanian tiger, after they’re gone. Many megafauna are in danger of extinction because their habitats are being chopped up in ways that don’t allow them to sustain themselves or to migrate.

In the grand scheme of things, I’d also like to explore the commonalities that we have with other animals. That has important ethical implications for how we treat them and for their right to exist in the first place. Animal welfare laws cover things like abuse — pain and suffering. I think we should go beyond that and acknowledge that animals also have a right to lead a good life — whatever that means for that animal.

Related:
What is your dog thinking?
Do canine's prefer praise or food?
Neuro-imaging maps brain wiring of extinct Tasmanian tiger
First images of dolphin brain circuitry hint at how they sense sound

Wednesday, August 30, 2017

Unveiling of Frankenstein portrait to set stage for year-long celebration of the classic novel


A public unveiling and discussion of a large-scale portrait of Dr. Frankenstein’s creation, described in Mary Shelley’s 1818 novel “Frankenstein," will take place at 7 pm at Emory on Tuesday, September 19. The event will be held at the Schwartz Center for the Performing Arts and is open to all free of charge, but guests must register in advance at http://engage.emory.edu/Frankenstein or call Erin Mosley at 404-727-5048.

The portrait is by renowned artist Ross Rossin, who is on the Emory campus as the 2017-2018 Donna and Marvin Schwartz Artist-in-Residence. Rossin, whose art hangs in the Smithsonian National Portrait Gallery and was exhibited at the United Nations Palace of Nations in Geneva and the Russian Duma in Moscow, is also known to Atlantans as the sculptor/creator of the nine-foot-tall bronze statue of Hank Aaron unveiled earlier this year at SunTrust Park.

Rossin's residency is part of the Ethics and the Arts Program at Emory's Center for Ethics. The program, the only one of its kind in the nation, encourages ethical discourse and debate through and about the arts, and partners with arts organizations to demonstrate the way art challenges ethical perspectives.

This year, the residency coincides with FACE (Frankenstein Anniversary Celebration and Emory), a year-long university-wide celebration of the 200th anniversary of the novel.

The exclusive corporate sponsor of FACE is Turner Classic Movies (TCM), and Emory is providing support through its Science and Society fund.

“One of the most acclaimed and influential works of science fiction ever written, ‘Frankenstein’ continues to shape debates surrounding science and its complications,” says Paul Root Wolpe, director of Emory’s Center for Ethics, which is spearheading FACE. “It’s a permanent part of the dialogue about the dilemmas we face in technological advancement, scientific experimentation and research, bioethics, artificial intelligence, stem cell research and innovation.”

Rossin’s new depiction of Frankenstein’s creation is expected to highlight the broad influence and implications of the landmark novel. Rossin envisioned not the standard movie portrayal, but a portrait based on his vision of Shelley’s intent.

“It’s precisely Mary Shelley’s youth [age 18 when she began the novel] that inspired me to approach my subject differently,” says Rossin. “Unlike all other portrayals before, I prefer to see the Creature as a young man.”

As Rossin points out, Dr. Frankenstein intended “to create something beautiful, young, powerful and promising, like Prometheus. The Creature was supposed to have a future, open a new chapter in human history.”

Those familiar with the story know that Dr. Frankenstein’s good intentions turned ugly and murderous. Rossin says that his portrait of “Adam Frankenstein reflects exactly this kind of tragic duality. In my work the viewer should be able to see both.”

Monday, August 28, 2017

Evolutionary ecology could benefit beekeepers battling diseases

An electron micrograph shows a Verroa destructor mite (right) on an adult honeybee host. The parasitic Varroa mite and the numerous viruses it carries are considered the primary causes of honeybee colony losses worldwide. (USDA photo) 

By Carol Clark

Some commercial beekeeping practices may harm honeybees more than help them, scientists warn in a paper published in the journal Nature Ecology and Evolution.

“Western honeybees — the most important pollinators for U.S. food crops — are facing unprecedented declines, and diseases are a key driver,” says Berry Brosi, an evolutionary biologist at Emory University and a lead author of the review paper. “The way commercial operations are managing honeybees might actually generate more damaging parasites and pathogens by creating selection pressure for higher virulence.”

The paper draws on scientific studies to recommend ways to reduce disease impacts, such as limiting the mixing of bees between colonies and supporting natural bee behaviors that provide disease resistance. The paper also highlights honeybee management practices in need of more research. 

During the past 15 years, ecological and evolutionary approaches have changed how scientists tackle problems of infectious diseases among humans, wildlife and livestock. “This change in thinking hasn’t sunk in with the beekeeping field yet,” says Emory evolutionary biologist Jaap de Roode, co-lead author of the paper. “We wanted to outline scientific approaches to help understand some of the current problems facing beekeepers, along with potential control measures.”

Co-authors of the paper include Keith Delaplane, an entomologist at the University of Georgia, and Michael Boots, an evolutionary biologist at the University of California, Berkeley.

Managed honeybees are important to the production of 39 of the 57 leading crops used for human consumption, including fruits, nuts, seeds and vegetables. In recent years, however, managed honeybee colonies have declined at the rate of more than one million per year, representing annual losses between 30 and 40 percent.

Two drone pupae of the Western honeybee infected with Varroa mites. (Photo by Waugsberg via Wikipedia Commons.)

While pesticides and land-use changes are factors involved in these losses, parasites are a primary driver — especially the aptly named Varroa destructor. The parasitic Varroa mite and the numerous viruses it carries are considered the primary causes of honeybee colony losses worldwide.

Varroa mites are native to Asia, where the Eastern honeybee species co-evolved with them before humans began managing bee colonies on commercial scales. As a result of this co-evolution, the Eastern honeybee developed behaviors — such as intensive mutual grooming — that reduce the mites’ negative impacts.

The Western honeybee species of the United States and Europe, however, has remained relatively defenseless against the mites, which spread to the United States during the late 1970s and 1980s. The mites suck the blood of the bees and reduce their immunity. Even more potentially destructive, however, are the multiple viruses the mites transmit through their saliva. Deformed-wing virus, for instance, can cripple a honeybee’s flying ability and is associated with high bee larval mortality.

Following are some of the potential solutions, in need of further study, outlined in the Nature Ecology & Evolution paper.

Reduce mixing of colonies: A common practice at beekeeping apiaries is to move combs containing brood — eggs and developing worker bees — between colonies. While the practice is meant to equalize colony strength, it can also spread parasites and pathogens.

Colonies are also mixed at regional and national scales. For instance, more than half of all honeybees in the country are involved in almond pollination in California. “For a lot of beekeeping operations, trucking their bees to California for almond pollination is how they make ends meet,” Brosi says. “It’s like the Christmas season for retailers.”

Pollination brokers set up contracts for individual beekeepers on particular almond farms. “If the brokers separated individual beekeeping operations beyond the distance that the average honeybee forages, that could potentially help reduce the mixing of bees and the rate of pathogen transmission between the operations,” Brosi says.
Varroa destructor (USDA)

Improve parasite clearance: Most means of dealing with Varroa mites focus on reducing their numbers in a colony rather than wiping them out, as the mites are developing increased resistance to some of the chemicals used to kill them. Such incomplete treatments increase natural selection for stronger, more virulent parasites. Further compounding the problem is that large commercial beekeeping operations may have tens of thousands of colonies, kept in close quarters.

“In a natural setting of an isolated bee colony living in a tree, a parasite that kills off the colony has nowhere to go,” de Roode explains. “But in an apiary with many other colonies nearby, the cost of parasite virulence goes way down.”

Allow sickened colonies to die out: Keeping bees infected with parasites and viruses alive through multiple interventions dilutes natural selection for disease resistance among the bees. In contrast, letting infections take their course in a colony and using the surviving bees for stock could lead to more resistant bees with fewer disease problems.

Support behavioral resistance: Beekeepers tend to select for bees that are more convenient to manage, but may have behavioral deficiencies that make them less fit. Some honeybees mix their saliva and beeswax with tree resin to form what is known as propolis, or bee glue, to seal holes and cracks in their hives. Studies have also shown that propolis helps keep diseases and parasites from entering the hive and inhibits the growth of fungi, bacteria and mites.

“Propolis is sticky. That annoys beekeepers trying to open hives and separate the components so they try to breed out this behavior,” de Roode says.

The paper concedes that commercial beekeeping operations face major challenges to shift to health management practices rooted in fundamental principles of evolution and ecology.

“Beekeeping is a tough way to make a living, because it operates on really thin margins,” Brosi says. “Even if there are no simple solutions, it’s important to make beekeepers aware of how their practices may affect bees in the long term. And we want researchers to contribute scientific understanding that translates into profitable and sustainable practices for beekeeping.”

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