Songbird data yields new theory for learning sensorimotor skills

"Our findings suggest that an animal knows that even the perfect neural command is not going to result in the right outcome every time," says Emory biophysicist Ilya Nemenman. (Image courtesy Samuel Sober.)

By Carol Clark

Songbirds learn to sing in a way similar to how humans learn to speak — by listening to their fathers and trying to duplicate the sounds. The bird’s brain sends commands to the vocal muscles to sing what it hears, and then the brain keeps trying to adjust the command until the sound echoes the one made by the parent.

During such trial-and-error processes of sensorimotor learning, a bird remembers not just the best possible command, but a whole suite of possibilities, suggests a study by scientists at Emory University.

The Proceedings of the National Academy of the Sciences (PNAS) published the study results, which include a new mathematical model for the distribution of sensory errors in learning.

“Our findings suggest that an animal knows that even the perfect neural command is not going to result in the right outcome every time,” says Ilya Nemenman, an Emory professor of biophysics and senior author of the paper. “Animals, including humans, want to explore and keep track of a range of possibilities when learning something in order to compensate for variabilities.”

Nemenman uses the example of learning to swing a tennis racket. “You’re only rarely going to hit the ball in the racket’s exact sweet spot,” he says. “And every day when you pick up the racket to play your swing is going to be a little bit different, because your body is different, the racket and the ball are different, and the environmental conditions are different. So your body needs to remember a whole range of commands, in order to adapt to these different situations and get the ball to go where you want.”

First author of the study is Baohua Zhou, a graduate student of physics. Co-authors include David Hofmann and Itai Pinkoviezky (post-doctoral fellows in physics) and Samuel Sober, an associate professor of biology.

Traditional theories of learning propose that animals use sensory error signals to zero in on the optimal motor command, based on a normal distribution of possible errors around it — what is known as a bell curve. Those theories, however, cannot explain the behavioral observations that small sensory errors are more readily corrected, while the larger ones may be ignored by the animal altogether.

For the PNAS paper, the researchers analyzed experimental data on Bengalese finches collected in previous work with the Sober lab. The lab uses finches as a model system for understanding how the brain controls complex vocal behavior and motor behavior in general.

Miniature headphones were custom-fitted to adult birds and used to provide auditory feedback in which the pitch that the bird perceives it vocalizes at could be manipulated, replacing what the bird hears — its natural auditory feedback — with the manipulated version. The birds would try to correct the pitch they were hearing to match the sound they were trying to make. Experiments allowed the researchers to record and measure the relationship between the size of a vocal error the bird perceives, and the probability of the brain making a correction of a specific size.

The researchers analyzed the data and found that the variability of errors in correction did not have the normal distribution of a bell curve, as previously proposed. Instead, the distribution had long tails of variability, indicating that the animal believed that even large fluctuations in the motor commands could sometimes produce a correct pitch. The researchers also found that the birds combined their hypotheses about the relationship between the motor command and the pitch with the new information that their brains received from their ears while singing. In fact, they did this surprisingly accurately.

“The birds are not just trying to sing in the best possible way, but appear to be exploring and trying wide variations,” Nemenman says. “In this way, they learn to correct small errors, but they don’t even try to correct large errors, unless the large error is broken down and built up gradually.”

The researchers created a mathematical model for this process, revealing the pattern of how small errors are corrected quickly and large errors take much longer to correct, and might be neglected altogether, when they contradict the animal’s “beliefs” about the errors that its sensorimotor system can produce.

“Our model provides a new theory for how an animal learns, one that allows us to make predictions for learning that we have tested experimentally,” Nemenman says.

The researchers are now exploring if this model can be used to predict learning in other animals, as well as predicting better rehabilitative protocols for people dealing with major disruptions to their learned behaviors, such as when recovering from a stroke.

The work was funded by the National Institutes of Health BRAIN Initiative, the James S. McDonnell Foundation, and the National Science Foundation. The NVIDIA corporation donated high-performance computing hardware that supported the work.

Related:
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How songbirds learn to sing

The math of malaria: Drug resistance 'a numbers game' of competing parasites

"Computer models can sometimes give you insights that would be too difficult to get in a real-world setting," says Mary Bushman. She developed a malaria model for her PhD thesis, advised by Emory evolutionary biologist Jaap de Roode. (Ann Watson, Emory Photo/Video)

By Carol Clark

A new mathematical model for malaria shows how competition between parasite strains within a human host reduces the odds of drug resistance developing in a high-transmission setting. But if a drug-resistant strain does become established, that same competition drives the spread of resistance faster, under strong selection from antimalarial drug use.

“It’s basically a numbers game,” says Mary Bushman, who developed the model for her PhD thesis in Emory University’s Population Biology, Ecology and Evolution Graduate Program. “When you already have multiple strains of malaria within a population, and a drug-resistant strain comes along, it will usually go extinct simply because it’s a late-comer. Whichever strain is there first has the advantage.”

PLOS Biology published the findings, a computational framework that modeled a malaria epidemic across multiple scales: Transmission of parasites from mosquitos to humans, and the dynamics of parasites competing to infect blood cells while they also battle the immune system of a human host.

After creating the model, Bushman ran simulations tracking malaria in a population for roughly 14 years. The simulations included 400 theoretical people who were randomly bitten by 12,000 mosquitos that were infected with malaria parasites classified as either drug resistant or drug susceptible. Various levels of treatment with antimalarial drugs were also part of the simulations.

“Our model holds strong relevance for infectious diseases beyond malaria,” says Jaap de Roode, an evolutionary biologist at Emory and senior author of the paper. “We hope this research gives others a method to look at disease dynamics across scales of biological organisms to learn how drug resistance develops in a range of pathogens.”

The study’s authors also include Emory biologist Rustom Antia (a specialist in infectious disease modeling) and Venkatachalam Udhayakumar, a malaria expert from the Centers of Disease Control and Prevention’s Division of Parasitic Diseases and Malaria.

The researchers are now working to develop their specific model for malaria into a generalized software tool for infectious diseases. “Computer models can sometimes give you insights that would be too difficult to get in a real-world setting,” says Bushman, who is now a post-doctoral fellow in the Antia lab.

"The distinction between establishment and spread just jumped out of the data," Bushman says.

Malaria occurs in poor, tropical and subtropical areas of the world, although most of the global death toll consists of children from sub-Saharan Africa. People infected in this high-transmission area often have multiple strains of the parasite and, by the time they have reached adulthood, they have usually developed partial immunity.

“It’s a baffling disease,” Bushman says. “Malaria has been studied for more than 100 years, much longer than most diseases, but there is still a lot that we don’t understand about it."

Malaria is caused by several species of Plasmodium parasites that are transmitted to humans by mosquitos. Plasmodium falciparum, the most common malaria parasite on the continent of Africa, is the one responsible for the most malaria-related deaths globally.

P. falciparum has developed resistance to former first-line therapies chloroquine and sulfadoxine-pyrimethamine. Resistance has also emerged in Southeast Asia to the third and last available treatment, artemisinin combination therapy, or ACT.

One of the mysteries about malaria is why drug-resistant strains tend to emerge first in low-transmission areas, like Southeast Asia, and not appear until much later in Africa, where transmission is high.

Previous research led by de Roode and Bushman showed that when people are co-infected with drug-resistant and drug-sensitive strains of malaria, both strains are competitively suppressed.

For the current paper, the researchers wanted to get a more detailed understanding of these dynamics. Some evidence had shown that within-host competition could suppress resistance, while other studies showed that it could ramp resistance up.

“It was a little bit of a puzzle, why the findings were conflicting,” Bushman says.

The new model, driven by evidence for how malaria parasites work within the immune system and the blood cells they infect, provided a solution to the puzzle.

“Some previous models were based on the assumption that when you put two strains of malaria into a host, they split 50-50,” Bushman says. “But our model showed that the system is asymmetrical. When you put two strains in a host they virtually never split 50-50.”

The late-comer will usually go extinct, which explains why in high-transmission areas drug resistant strains are at a big disadvantage. But in low transmission areas, such as Southeast Asia, a drug resistant strain has a better chance of arriving first in a host and getting established.

The new model also showed how once a drug-resistant strain becomes established in a high transmission area, it will spread much faster than it would in a low transmission area.

“The distinction between establishment and spread just jumped out of the data,” Bushman says. “Our model validated both sides of the argument — that within-host dynamics of competing parasites could both repress and accelerate the spread of resistance. The phenomena are occurring at different stages of the process so they both can happen.”

The results offer a new explanation for why chloroquine resistance arrived relatively late in Africa, appearing in Kenya and Tanzania in 1978, but then spread rapidly across the continent.

Related:
Mixed-strain malaria infections influence drug resistance
Zeroing in on 'super spreaders' and other hidden patterns of epidemics

The search for secrets of ancient remedies

Cassandra Quave is a world leader in the field of medical ethnobotany — studying how indigenous people used plants in their healing practices to identify promising candidates for modern drugs.

Cassandra Quave (it rhymes with “wave”) is an assistant professor in Emory’s Center for the Study of Human Health and in the School of Medicine’s Department of Dermatology. She is also a member of the Emory Antibiotic Resistance Center.

The Florida native looks at home in the sweltering heat of South Georgia, standing behind a pick-up truck parked on a dirt road that winds through a longleaf pine forest. She tilts a straw cowboy hat back from her face and waves off a flurry of gnats. Her utility belt bristles with shears and a hunting knife. The unfolded gate of the truck bed serves as her desk, as she wrangles a leafy vine of passionflower into a wooden plant press.

 “The Cherokee pounded the roots of passionflower into a poultice to draw out pus from wounds, boils and abscesses,” Quave says. “Everywhere I look in this ecosystem I see plants that have a history of medicinal use by native peoples. The resin of the pine trees all around us, the fronds from the ferns beneath them and the roots of those beautiful yellow flowers over there — black-eyed Susans — were all used to treat wounds and sores.”

Read more here about Quave's field work this summer, and the undergraduates who helped her collect plants of importance to Native Americans.

Neuroscientists team with engineers to explore how the brain controls movement

The labs of Georgia Tech's Muhannad Bakir (far left) and Emory's Samuel Sober (far right) combined forces for the project. The work will be led by post-doctoral fellows in their labs, Georgia Tech's Muneeb Zia (center left) and Emory's Bryce Chung (center right). Photos by Ann Watson, Emory Photo/Video.

By Carol Clark

Scientists have made remarkable advances into recording the electrical activity that the nervous system uses to control complex skills, leading to insights into how the nervous system directs an animal’s behavior.

“We can record the electrical activity of a single neuron, and large groups of neurons, as animals learn and perform skilled behaviors,” says Samuel Sober, an associate professor of biology at Emory University who studies the brain and nervous system. “What’s missing,” he adds, “is the technology to precisely record the electrical signals of the muscles that ultimately control that movement.”

The Sober lab is now developing that technology through a collaboration with the lab of Muhannad Bakir, a professor in Georgia Tech’s School of Electrical and Computer Engineering. The researchers recently received a $200,000 Technological Innovations in Neuroscience Award from the McKnight Foundation to create a device that can record electrical action potentials, or “spikes” within muscles of songbirds and rodents. The technology will be used to help understand the neural control of many different skilled behaviors to potentially gain insights into neurological disorders that affect motor control.

“Our device will be the first that lets you record populations of spikes from all of the muscles involved in controlling a complex behavior,” Sober says. “This technique will offer unprecedented access to the neural signals that control muscles, allowing previously impossible investigations into how the brain controls the body.”

“By combining expertise in the life sciences at Emory with the engineering expertise of Georgia Tech, we are able to enter new scientific territory,” Bakir says. “The ultimate goal is to make discoveries that improve the quality of life of people.”

A prototype of the proposed device has 16 electrodes that can record data from a single muscle. The McKnight Award will allow the researchers to scale up to a device with more than 1,000 electrodes that can record from 10 or more muscles.

The Sober lab previously developed a prototype device — electrodes attached to flexible wires — to measure electrical activity in a breathing muscle used by Bengalese finches to sing. The way birds control their song has a lot in common with human speech, both in how it is learned early in life and how it is produced in adulthood. The neural pathways for birdsong are also well known, and restricted to that one activity, making birds a good model system for studying nervous system function.

“In experiments using our prototype, we discovered that, just like in brain cells, precise spike timing patterns in muscle cells are critical for controlling behavior — in this case breathing,” Sober says. 

The prototype device, however, is basic. Its 16 electrodes can only record activity from a single muscle — not the entire ensemble of muscles involved in birdsong. In order to gain a fuller picture of how neural signals control movement, neuroscientists need a much more sophisticated device.

The McKnight funding allowed Sober to team up with Bakir. Their goal is to create a micro-scale electromyography (EMG) sensor array, containing more than 1,000 electrodes, to record single-cellular data across many muscles.

The engineering challenges are formidable. The arrays need to be flexible enough to fit the shape of small muscles used in fine motor skills, and to change shape as the muscles contract. The entire device must also be tiny enough not to impede the movement of a small animal.

“Our first step is to build a flexible substrate on the micro-scale that can support high-density electrodes,” Bakir says. “And we will need to use microchips that work in parallel with 1,000 electrodes, and then attach them to that substrate.”

To meet that challenge, the Bakir lab will create a 3D integrated circuit. “Essentially, it’s building a miniature skyscraper of electrical circuits stacked vertically atop one another,” Bakir says. This vertical design will allow the researchers to minimize the size of the flexible substrate.

“To our knowledge, no one has done what we are trying to do in this project,” Bakir says. “That makes it more difficult, but also exciting because we are entering new space.”

The Sober lab will use the new device to expand its songbird vocalization studies. And it will explore how the nervous system controls the muscles involved when a mouse performs skilled movements with its forelimbs.

An early version of the technology will also be shared with collaborators of the Sober lab at three different universities. These collaborators will further test the arrays, while also gathering data across more species.

“We know so little about how the brain organizes skilled behaviors,” Sober says. “Once we perfect this technology, we will make it available to researchers in this field around the world, to advance knowledge as rapidly as possible.”

The mission of the McKnight Foundation’s Technological Innovations in Neuroscience Award, as described on its website, is “to bring science closer to the day when diseases of the brain and behavior can be accurately diagnosed, prevented and treated.”

Related:
Singing in the brain: Songbirds sing like humans
Dopamine key to vocal learning, songbird study finds

Templeton World Charity awards $550,000 to global STEM initiative

The Templeton World Charity Foundation awarded $550,000 to Emory mathematician Ken Ono, for a global program to identify and nurture gifted students in the areas of science, technology, engineering and math (STEM). The program, now known as the Spirit of Ramanujan STEM Talent Initiative, began in 2016 with pilot funding of $100,000 from the Templeton Foundation.

“This additional funding will allow us not only to continue the program, but to expand its mission and impact,” says Ono, Asa Griggs Candler Professor Mathematics at Emory and the vice president of the American Mathematical Society.

The pilot Spirit of Ramanujan program, or SOR, focused on finding exceptional young mathematicians, and awarded grants to 16 grade-school students from across the United States as well as from China, Egypt, India, Kenya and Qatar. SOR matched the mathematicians with mentors and the grants funded summer research and enrichment activities.

SOR will now also offer similar opportunities for individuals showing exceptional promise for STEM fields in which mathematics plays a prominent role, such as computational chemistry, computer science, electrical and computer engineering, mathematical biology, mathematical physics and statistics. Up to 30 eligible people each year will be awarded Templeton-Ramanujan Fellows Prizes (financial grants up to $5,000 per award to cover summer enrichment/research programs) or Templeton-Ramanujan Scholarly Development Prizes (educational materials such as STEM books). 

"The Spirit of Ramanujan initiative aims to break the mold and find brilliant outliers who may not be thriving in the system, so we can match them up with the resources they need," says Emory mathematician Ken Ono, one of the founders of the initiative.

“We are looking for brilliant, creative people who have ideas and abilities that will drive the future of science,” Ono says. “Young people with great promise are often outliers, so far ahead of their classes that teachers don’t know what to do with them. Genius cannot be taught, it can only be nurtured.” 

Ono founded the SOR program along with the Templeton World Charity Foundation; Expii.com, an open-source, personalized learning platform; and IFC Films and Pressman Film — producers of the 2015 biographical film, “The Man Who Knew Infinity.”

The SOR initiative was inspired by the subject of the film, Indian mathematician Srinivasa Ramanujan. A poor Hindu college dropout who was self-taught in mathematics, Ramanujan sent a letter containing some of his theories to British mathematician G.H. Hardy in 1913. Hardy was so impressed that he invited Ramanujan to Cambridge to study and collaborate. His mentorship burnished Ramanujan’s insights and brought them to a world stage. Ramanujan's work played a central role in the development of modern number theory and algebraic geometry, changing math and science forever.

Although the expanded SOR initiative is open to all ages, preference will be given to those under 32 — the age Ramanujan was when he died.

The SOR initiative invites people worldwide to solve creative mathematical puzzles via Expii.com’s Solve feature, to identify exceptional talent. The Art of Problem Solving, a web site that trains students in mathematical concepts and problem-solving techniques, is also advertising the initiative to its worldwide online community.

For more details about how to apply for an SOR grant, and the criteria for an award, visit the program’s web site: https://v1.expii.com/ramanujan

“The program is not intended to just benefit those who receive the awards,” Ono says. “We also hope they become important mathematicians and scientists who make the world a better place.”

Ono heads the SOR program, with an advisory board of other mathematicians, including Manjul Bhargava (Princetone), Olga Holtz (Berkeley), Po-Shen Loh (Carnegie Mellon) and Sujatha Ramdorai (University of British Columbia).

Sir John Templeton established the Templeton World Charity Foundation in 1996 to serve as “a global philanthropic catalyst for discoveries relating to big questions of life and the universe, in areas of science, theology, philosophy and human society.”

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Evidence reveals our fractured African roots

A range of ancient cultural artifacts found in different regions of Africa. Clear regionally distinctive material cultural styles, typically involving complex stone tools, first emerged within the Middle Stone Age.

Anthropologists are challenging the long-held view that humans evolved from a single ancestral population in one region of Africa. Instead, a scientific consortium has found that human ancestors were diverse in form and culture and scattered across the continent. These populations were subdivided by different habitats and shifting environmental boundaries, such as forests and deserts.

The journal Trends in Ecology and Evolution published the findings, which drew from studies of bones (anthropology), stones (archaeology) and genes (population genomics), along with new and more detailed reconstructions of Africa’s climates and habitats over the last 300,000 years.

Emory University anthropologist Jessica Thompson was one of 23 authors on the paper. The research was led by the Max Planck Institute for the Science of Human History in Germany and the University of Oxford in England. In the following Q&A, Thompson explains the paper and its significance.

Can you provide some background on our understanding of human evolution? 

Jessica Thompson: Even as early as 20 years ago, fossils were the main material we had to try to answer the question of where humans originated. A multi-regionalist theory hypothesized that Homo sapiens emerged in different places at the same time, evolving at the same rate across the Old World. This would mean that there was extensive gene exchange across ancient Asia, Europe and Africa, and that groups such as Neanderthals would not be a separate species but just a localized form of Homo sapiens. But it is difficult to get that level of resolution from bones alone.

By the 1990s, mitochondrial DNA analyses provided growing genetic evidence for the competing theory — that all modern humans originated in Africa and then dispersed from there around the globe. The implication of this is that groups such as the Neanderthals would actually have been different species, and that they were replaced by modern human groups dispersing from Africa.

Intense debate continued over the two theories but, by the early 2000s, it was clear that the out-of-Africa group had won. Only a small percentage of modern humans from the total population living in Africa actually left the continent, creating a genetic bottleneck in populations outside of Africa. So there is more diversity within the genomes of some living peoples in Africa today than there is, say, between an Australian aboriginal person and a Norwegian person.

As a final twist, whole-genome DNA now shows that there was some gene flow with Neanderthals as those first modern populations emerged from Africa. This could have happened several times over many thousands of years, and so a “leaky out-of-Africa” model seems to be the best fit for the data.

Jessica Thompson in the field in Malawi, where her archaeological sites are at a crossroads between southern and eastern Africa. "There, we find a long, but relatively unexplored cultural record of human behavior that goes back into the last Ice Age," she says.

How does the current paper fit into this model?

JT: While it was well established that modern humans originated in Africa, there was still the question of where in Africa. East Africa and South Africa have been strong candidates, but that could be due to the long historical bias of where fossils were being found.

Our paper takes the global idea of multi-regionalism and shrinks it down to the boundaries of Africa. The answer to where humans originated appears to be lots of places within the continent, often separated for long periods, but again with leaky boundaries. Essentially, there is not a single ancestral human population. Who we are today probably evolved as a mosaic of populations of very near modern humans who were separated by geographic and cultural boundaries but were also all interacting with one another at different points in time. Our origin story is one of lots and lots of different humans that came together and then separated and later came together again in this really confusing manner. There’s a lot of moving parts. Humans, for a very long time, have been a culturally and phenotypically diverse bunch.

What new questions does this paradigm shift bring up?

JT: Instead of seeking the origin of humans in one spot, we need to look for pieces of the puzzle in many different places. Then we can ask, what adaptations did different populations have that contributed to who we are today? How did they come to be present in the single species we are now? And, perhaps more philosophically, what are the unifying characteristics that bind us together as that species, in spite of our differences?

While we need more data from places like East Africa and South Africa, it’s apparent now that West Africa and Central Africa are also key players in the story. They’re at the crossroads for much of the continent and yet we know very little about ancient populations from those regions. I’m hoping I can contribute to that effort with my current work in Malawi, which is positioned between southern and eastern Africa. There, we find a long, but relatively unexplored cultural record of human behavior that goes back into the last Ice Age.

We also recently recovered some of the oldest DNA in Africa from a site in Malawi, which we published last year. This helped to actually show some of those ancient interactions between populations at least over the last 10,000 years or so — as well as some of the differences between them. The implications are that this kind of structure went back even farther in time, to our origins as a species.

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Malawi yields oldest-known DNA from Africa
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Science on stage: Atlanta playwrights explore the human microbiome

Learning about the microbiome "is shifting my perspective of what it means to be human and an individual," says playwright Margaret Baldwin. "What bacteria are driving our dreams?"

Four Atlanta playwrights + 48 hours = four new plays at the forefront of art and science.

That’s the premise of Theater Emory’s “ 4:48,” a frenetic yet focused showcase of new works inspired by the human microbiome that will be performed July 14 at the Schwartz Center for Performing Arts.

The annual speed-writing challenge always yields compelling results, as talented local playwrights come together at Emory to quickly produce plays based on common source material. But this year, for the first time, the Playwriting Center of Theater Emory is teaming up with the Emory Center for the Study of Human Health for “4:48” — an innovative, interdisciplinary collaboration that promises to push the boundaries of both fields.

“Theater offers an exciting communication mechanism to convey cutting edge-research findings to a wide audience, while simultaneously encouraging curiosity and imagination,” says Amanda Freeman, instructor in the Center for the Study of Human Health.

The collaborators hope that this project will introduce the human microbiome — the trillions of microorganisms that live in us and on us — to a whole new audience, providing a spotlight for research that is being done right here on campus.

“I have found very few venues where new science and new art can emerge from a single exercise, so ‘4:48’ is special,” says David Lynn, Asa Griggs Candler Professor of Chemistry and Biology, one of several Emory science faculty offering support as resources for the writers.

Readings of the work developed during "4:48" begin at 4 pm on Saturday, July 14, in the Theater Lab of Schwartz Center. All readings are free and open to the public. For the schedule of readings and play titles, visit the Theater Emory website.

Click here to learn more.

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A grave tale: The case of the corpse-eating flies

Dozens of ceramic vessels from West Mexico, part of the collection of Emory's Michael C. Carlos Museum, were believed to be "grave goods," traditionally placed near bodies in underground burial chambers almost 1,500 years before the Aztecs. The compact figures depict humans and animals engaged in everyday activities, vividly capturing a place and time. Residue and wear patterns suggested that the vessels had once been filled with food and drink, perhaps to accompany the departed along their journey.

But were the figures authentic?

Seeking answers, the museum invited forensic anthropologist Robert Pickering — who uses entomology, among other techniques – to examine the vessels with the help of Emory scholars.

His quest? Locate telltale insect casings likely left by coffin flies, corpse-eating insects that fed on decomposing bodies interred in the ancient underground shaft tombs of Western Mexico.

"Not to be impolite, but where you have dead people, you have bugs," Pickering explains.

Read more about the project here.

New Atlanta NMR Consortium links resources of Emory, Georgia Tech and Georgia State

The Atlanta Nuclear Magnetic Resonance Consortium "lowers the activation energy to take advantage of partners’ expertise," says Emory chemist David Lynn.


NMR – nuclear magnetic resonance – is a powerful tool to investigate matter. It is based on measuring the interaction between the nuclei of atoms in molecules in the presence of an external magnetic field; the higher the field strength, the more sensitive the instrument.

For example, high magnetic fields enable measurement of analytes at low concentrations, such as the compounds in the urine of blue crabs, opening doors to understanding how chemicals invisibly regulate marine life. High-field NMR also allows scientists to “see” the structure and dynamics of complex molecules, such as proteins, nucleic acids, and their complexes.

NMR is used widely in many fields, from biochemistry, biology, chemistry, and physics, to geology, engineering, pharmaceutical sciences, medicine, food science, and many others.

David Lynn

NMR instruments, however, are a major investment. The most advanced units can cost up to up to millions of dollars per piece. Maintenance can cost tens of thousands of dollars a year. The investment in people is also significant. It can take years of training before a user can perform some of the most advanced techniques.

For these and other reasons, Emory University, Georgia Institute of Technology, and Georgia State University have formed the Atlanta NMR Consortium. The aim is to maximize use of institutional NMR equipment by sharing facilities and expertise with consortium partners.

Through the consortium, students, faculty, and staff of a consortium member can use the NMR facilities of their partners. The cost to a consortium member is the same as what the facility charges its own constituents.

“NMR continues to grow and develop because of technological advances,” says David Lynn, a chemistry professor at Emory University. To keep up, institutions need to keep buying new, improved instruments. Such a never-ending commitment is becoming untenable and redundant across Atlanta, Lynn says. Combining forces is the way to go.

Immediately, the consortium offers access to the most sensitive instruments now in Atlanta – the 700- and 800-MHz units at Georgia Tech. Georgia Tech invested more than $5 million to install the two high-field units, as well as special capabilities, in 2016.

Partners can gain access to Georgia State’s large variety of NMR probes. Solid-state capability, which is well established in Emory and advancing at Georgia Tech, will be available to partners.

Needless to say, the consortium offers alternatives when an instrument at a member institution malfunctions.

Beyond maximizing use of facilities, the consortium offers other potential benefits.

Anant Paravastu

“The biggest benefit is community,” says Anant Paravastu. Paravastu is an associate professor in the Georgia Tech School of Chemical and Biomolecular Engineering. He is also a member of the Parker H. Petit Institute for Bioengineering and Bioscience (IBB).

“Each of us specializes the hardware and software for our experiments,” Paravastu says. “As we go in different directions, we will benefit from a cohesive community of people who know how to use NMR for a wide range of problems.”

Paravastu previously worked at the National High Magnetic Field Laboratory, in Florida State University. That national facility sustains a large community of NMR researchers who help each other build expertise, he says. “We Atlanta researchers would benefit from a similar community, and not only for the scientific advantage.”

Both Lynn and Paravastu believe the consortium will help the partners jointly compete for federal grants for instrumentation. “A large user group will make us more competitive,” Lynn says. “The federal government would much rather pay for an instrument that will benefit many scientists rather than just one research group in one university,” Paravastu says.

“The most important goal for us is the sharing of our expertise,” says Markus Germann, a professor of chemistry at Georgia State. A particular expertise there is the study of nucleic acids. More broadly, Georgia State has wide experience in solution NMR. Researchers there have developed NMR applications to study complex structures of biological and clinical importance.

Germann offers some examples:
Structure and dynamics of damaged and unusual DNA
Structure and dynamics of protein—DNA and protein—RNA complexes
Structural integrity of protein mutants
Small ligand-DNA and -RNA binding for gene control
Protein-based contrast agents for magnetic resonance imaging

“For me, there’s a direct benefit in learning from people at Georgia State about soluble-protein structure,” Paravastu says. He studies the structures of peptides; of particular interest are certain water-soluble states of beta-amyloid peptide, in Alzheimer’s disease. These forms, Paravastu says, have special toxicity to neurons.

Markus Germann

Paravastu also studies proteins that self-assemble. “People at Emory have a different approach to studying self-assembling proteins,” he says. “We have a lot of incentive to strengthen our relationships with other groups.”

“Different labs do different things and have different expertise,” Lynn says. “The consortium lowers the activation energy to take advantage of partners’ expertise.”

Even before the consortium, Germann notes, his lab has worked with Georgia Tech’s Francesca Storici on studies of the impact of ribonucleotides on DNA structure and properties. Storici is a professor in the School of Biological Sciences and a member of IBB.

Germann has also worked with Georgia Tech’s Nicholas Hud on the binding of small molecules to duplex DNA. Hud is a professor in the School of Chemistry and Biochemistry and a member of IBB.

“While collaborations between researchers in Atlanta universities is not new,” Paravastu says, “the consortium will help facilitate ongoing and new collaborations."

What will now be tested is whether the students, faculty, and staff of the partners will take advantage of the consortium.

Travel from one institution to another is a barrier, Lynn says. “Are people going to travel, or will they find another way to solve the problem? How do you know that the expertise over there will really help you?” he asks.

“The intellectual barrier is very critical,” Lynn says. “We address that through the web portal.”

The website defines the capabilities, terms of use, training for access, and institutional fees, among others. Eventually, Lynn says, it will be a place to share papers from the consortium partners.

“Like many things in life, the consortium is about breaking barriers,” Paravastu says. It’s about students meeting and working with students and professors outside their home institutions.

Already some partners share a graduate-level NMR course. For the long-term, Paravastu suggests, the partners could work together on training users to harmonize best practices and ease the certification to gain access to facilities.

“We can think of students being trained by the consortium rather than just by Georgia Tech, or Emory, or Georgia State,” Paravastu says. “By teaming up, we can create things that are bigger than the sum of the parts.”

Written by by Maureen Rouhi, Georgia Tech

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Dengue 'hot spots' provide map to chikungunya and Zika outbreaks

A street scene in Merida, Mexico, a city of about one million in the Yucatan Peninsula where the study was based. Merida had a little over 40,000 reported dengue cases during 2008 to 2015 and nearly half of them were clustered in 27 percent of the city.

By Carol Clark

Identifying dengue fever “hot spots” can provide a predictive map for outbreaks of chikungunya and Zika — two other viral diseases that, along with dengue, are spread by the Aedes aegypti mosquito.

PLOS Neglected Tropical Diseases published the findings, the first confirmation of the spatial-temporal overlap for outbreaks of the three diseases, led by Emory University.

“We had hypothesized that we would see some overlap between these diseases, but we were surprised at the strength of that overlap,” says Gonzalo Vazquez-Prokopec, a disease ecologist in Emory’s Department of Environmental Sciences and lead author of the study. “The results open a window for public health officials to do targeted, proactive interventions for emerging Aedes-borne diseases. We’ve provided them with a statistical framework in the form of a map to guide their actions.”

The analysis drew from eight years of data from Merida, Mexico, on symptomatic cases. A city of one million located in the Yucatan Peninsula, Merida had about 40,000 reported dengue cases during 2008 to 2015, and nearly half of them were clustered in 27 percent of the city. The neighborhoods comprising these dengue hot spots contained 75 percent of the first chikungunya cases reported during the outbreak of that disease in 2015 and 100 percent of the first Zika cases reported during the Zika outbreak in 2016.

“Currently, most mosquito control efforts are not done until cases of mosquito-borne diseases are detected,” Vazquez-Prokopec says. “But by the time you detect a virus in an area, it has likely already begun to spread beyond that area.”

Mosquito control efforts generally involve outdoor spraying that covers broad swaths of a city, further reducing efficacy, he adds. Outdoor spraying is particularly ineffective for the Aedes aegypti mosquito. “This mosquito is highly adapted to urban environments,” Vazquez-Prokopec says. “It likes to live inside houses and to feed on people.”

A targeted approach would make it more feasible to implement time-consuming and costly interventions such as indoor residual spraying.

A technician sprays the ceiling and walls of a home in Merida. Indoor residual spraying is effective, but is not practical for large areas of a city, due to the time and expense involved. Photo by Nsa Dada.

“The statistical framework that we have developed allows public health officials to harness the power of big data to do more effective and efficient mosquito control by focusing on high-risk areas — even before an epidemic begins,” Vazquez-Prokopec says.

The study used disease case reports at the household level and then scaled them up to neighborhoods to protect individuals’ privacy in the final map. The hot spots for reported dengue cases were confirmed by data from laboratory blood tests of a cohort of 5,000 people. The analysis showed that people living in a dengue hot spot had twice the rate of infection of those outside of the hot spots.

The research team included scientists from the Autonomous University of Yucatan and health officials from the state and federal level in Mexico. Other members of the team were scientists from seven other universities and health research institutions, including the U.S. Centers for Disease Control and Prevention.

The researchers are now working with the Pan American Health Organization (PAHO) to develop a manual and training materials, based on open-access software, for mapping risks of Aedes-borne diseases to guide proactive interventions throughout urban areas of the developing world.

More than one third of the world’s population lives in areas at high risk for infection with the dengue virus, a leading cause of illness and death in the tropics and subtropics, according to the Centers for Disease Control and Prevention. Dengue fever is sometimes called “break bone fever” due to the excruciating pain that is among its symptoms.

The chikungunya virus emerged in the Americas in 2013, sweeping through many countries where dengue is endemic. Common symptoms of chikungunya infection may include headache, muscle pain, joint swelling and rash.

Zika virus followed in 2016, causing little alarm at first due to its relatively mild symptoms. It soon became apparent, however, that the Zika virus could cause birth defects in the babies of pregnant women who were infected.

“You tend to see transmission go down right after large numbers of a population are infected with these Aedes-borne viruses, leading to herd immunity,” Vazquez-Prokopec says. “But these viruses do not disappear. They keep circulating and can reappear later.”

Meanwhile, new Aedes-borne viruses are likely to emerge, he adds, as rapid urbanization and a warming climate help the mosquito thrive.

Vaccines are not yet available for chikungunya or Zika, and efforts to roll out a vaccine for dengue are complicated by the fact that the virus comes in different serotypes.

“Although effective vaccines would be the ultimate line of defense against these diseases, we cannot give up on mosquito control,” Vazquez-Prokopec says.

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Bonding over bones, stones and beads

By Carol Clark

"I've really been into bones since I was little. I don't know why," says Emory University senior Alexandra Davis, an anthropology major. "Not fresh bodies, though. No soft tissues or blood. Just bones."

In fact, Davis loves bones so much that she was willing to spend seven weeks in Malawi with Emory anthropologist Jessica Thompson and four more of her students last summer, excavating bones and other artifacts in ancient hunter-gatherer sites, assisted by a team of locals.

Thompson will return to Malawi in July with another team of students to continue excavation of two sites that were started last summer. "We want to get into the deeper layers, because in both cases we did not come close to reaching the bottom of the sites," Thompson says. "Then, we want to find out how old they are."

Read more about the project.

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'Dog-nition' research set for Science Friday

Come. Sit. Stay. And listen to Science Friday's interview at 3:30 pm E.T. today with Emory neuroscientist Gregory Berns, who is exploring the inner workings of the canine mind. Two of the questions the program plans to explore: Do dogs have a concept of time? And how do our furry companions make sense of the world?

You can tweet questions you'd like answered to @scifri. The radio program is based at WNYC Studios, distributed to public radio stations across the United States, and is also accessible online.

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DNA analysis adds twists to ancient story of a Native American group

"I want to help Native American tribes to reclaim knowledge of their very ancient evolutionary histories — histories that have been largely wiped away because of colonialism," says Emory geneticist John Lindo. Photo by Kay Hinton, Emory Photo/Video.

By Carol Clark

The ancient genomes of the Tsimshian indigenous people left tell-tale markers on the trail of their past, revealing that at least 6,000 years ago their population size was on a slow but steady decline.

The American Journal of Human Genetics published the findings, which draw from the first population-level nuclear DNA analysis of a Native American group from ancient to modern times.

“The finding contradicts a popular notion,” says John Lindo, a geneticist in Emory University’s Department of Anthropology and first author on the paper. “There is this idea that after Native Americans came in through the Bering Strait that they were all expanding in population size until Europeans showed up. At least for this one population, we’ve shown that was not the case.”

A boon in next-generation DNA sequencing technology has opened the possibility to explore the evolutionary history of different populations. “Ancient nuclear DNA analysis is a relatively new field,” Lindo says. “Not until recently have we had methods to sequence an entire genome quickly and inexpensively.”

Nuclear DNA provides information on an individual’s lineages going back hundreds of thousands of years. Lindo is one of the few geneticists looking at ancient whole genomes of Native Americans. He is especially interested in understanding how the genomes of their different populations evolved over time.

“Their evolutionary histories are radically different,” Lindo says. “Over thousands of years, various Native American populations have adapted to living in every ecology throughout North and South America, from the Arctic to the Amazon. That’s about as an extreme as you can get for differences in environments.”

The Tsimshian people historically lived in longhouses in coastal British Columbia and southern Alaska where they harvested the abundant sea life. Lindo and his colleagues sequenced the genomes of 25 living Tsimshian people and 25 ancient individuals who lived in the same region between 6,000 and 500 years ago, and confirmed that they were a continuous population through time.

Members of the Tsimshian Native American tribe hold a tea party near Fort Simpson, British Columbia, in 1889. Image from the Library and Archives Canada.

In a previous paper, drawing from the same data set, they found a dramatic shift between the two time periods in a class of genes associated with the immune system, suggesting a strong evolutionary pressure on the population to adapt to pathogens. A demographic model indicated a crash in the Tsimshian population size of about 57 percent during the early-to-mid 19th century. That finding fitted with historical accounts for how smallpox, introduced by European colonization, devastated the Tsimshian population during two epidemics within that time-frame.

The current paper looked at broader genetic variations between the ancient and modern DNA. An analysis showed both how the variation declined slowly in the ancient population before the collapse, but has since recovered.

“After a population collapse, only a subset of the genetic diversity remains,” Lindo says. “We find a more nuanced story, that despite the population collapse, the genetic diversity of modern Tsimshian people varies significantly.”

Intermarriage with other Native American groups and non-native populations increased the genetic diversity of some of the modern-day Tsimshian people so that it is near the levels prior to their population collapse, the analysis showed.

“A population with relatively high genetic diversity has a greater potential to fight off pathogens and avoid recessive traits,” Lindo says. “It exemplifies the benefits of gene flow between populations, especially following catastrophic events such as the small pox epidemics that the Tsimshian endured.”

Senior authors on the paper are Michael DeGiorgio from Pennsylvania State University and Ripan Malhi from the University of Illinois. The paper’s coauthors include Tsimshian representatives Joycelynn Mitchell and Barbara Petzelt from the Metlakatla Treaty Office in Prince Rupert, Canada.

Malhi, a leader in forging trusting relationships between genetic researchers and indigenous people, was a mentor to Lindo, who earned his PhD at the University of Illinois at Champaign-Urbana.

Lindo is continuing that tradition of building trust and working closely with indigenous populations. His ancient DNA research at Emory integrates the approaches of ancient whole genomes, statistical modeling and functional methods.

One of his projects is focused on genetic fluctuations to help understand ancient adaptions in various Native American populations. He is currently working with 10 different tribes from throughout North America.

“Community engagement is essential when working with indigenous communities,” says Lindo, explaining that he first meets personally with a tribal community to talk about how a genetic study might add to their knowledge of their own history.

“I listen to their stories and how they are working to keep their cultures alive,” he says. “One elder from a southwestern tribe told me that his grandfather was taken away in the early 1900s because he was a shaman and Christianity was swelling through the area. Each tribe’s stories are different but they are all powerful, and sometimes difficult, stories to hear.”

Most ancient DNA analyses have come out of Europe, where more ancient DNA labs are based and cold temperatures have helped preserve specimens.

Lindo wants to bring some of the same insights that those of European ancestry are gaining about their past to Native Americans.

“I’d like to disentangle this idea that Native Americans are part of a singular race,” he says. “I want to help Native American tribes to reclaim knowledge of their very ancient evolutionary histories — histories that have been largely wiped away because of colonialism.”

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Science Art Wonder: Students team with labs to bring research to life

Art by Emory senior Pamela Romero, Science.Art.Wonder. founder and president, portrays how aphids can develop wings in response to environmental changes. The DNA painted along the edges of the canvases is the same, except that different genes are switched on. Photo by Ann Watson, Emory Photo/Video

By Carol Clark

A small crowd gathers in Emory’s White Hall before the menacing sight: Large rubber worms arrayed on triangular red spikes. The jagged spikes, from a few inches to more than a foot tall, lean crazily in all directions. Some of the worms — suspended on near-invisible fishing line — appear to rise off the spikes, escaping to a circular mirror hanging from above.

“This is how evolution works!” says Ethan Mock, a sophomore majoring in ancient history, who created the sculpture, titled "The Crucible." He looks dapper in a leather vest and tweed cap and speaks with theatrical flair to the crowd. “The spikes represent the trials and tribulations of the worms’ struggles. Most are trapped in the spikes but a few climb out, not realizing that they are simply climbing into a new trial, a new test.”

The onlookers include a mix of college students, children and their parents, brought together by campus events during the recent Atlanta Science Festival. Joining the regular attractions of Physics Live! and Chemistry Carnival is the debut of an art exhibit by a new, student-run program called Science.Art.Wonder., or S.A.W. Just over 100 artists — most of them untrained college students — teamed with scientists from Emory and Georgia Tech to translate their research into art.

Ethan Mock and his art, "The Crucible"

Mock worked with the lab of Levi Morran, an assistant professor in Emory’s Department of Biology who studies co-evolutionary dynamics by experimenting with a host (a microscopic worm called C. elegans) and a parasite (a bright red species of bacteria called Serratia marcescens that is lethal to C. elegans upon consumption).

“This is so cool!” says Pareena Sharma, a first-year biochemistry major at Emory, as she snaps a photo of the sculpture. “It’s so relatable to me. I’ve been doing this same experiment since the first of the semester in Biology 142.”

Two young boys draw near the spikes. “Look up into the mirror,” Mock encourages them. “Now tell me what you see.”

“The same thing,” one of the boys replies.

“That’s right!” Mock says. “The process of evolution keeps repeating, going in a loop.”

Morran, arriving with his eight-year-old daughter, Maggie, is impressed. “You could see the light come on in those boys’ eyes,” he says. “They understood what Ethan is trying to convey. And it’s not an easy concept to grasp — the continual evolutionary struggle.”

Both artists and researchers engage with visitors as they peruse more than 140 works of art, set up on the Quad, in White Hall, the Math and Science Center and the Atwood Chemistry Center during the festival.

“This artwork gives you a snapshot of how much research is being done in Atlanta. I’m taken aback by how cutting edge and varied it is,” says Pamela Romero, president of S.A.W. The program is the brainchild of Romero, a senior majoring in neuroscience and behavioral biology and minoring in computer science.

Young visitors to the Emory campus peruse science-inspired art on the Quad. Photo by Ann Watson, Emory Photo/Video

The Emory S.A.W. contributions span labs across the University and beyond. The artists picked their mediums, from acrylic to watercolor and everything in between.

Emily Isaac, a first-year Emory student majoring in environmental sciences and theater, stands on the Quad next to a large watercolor she painted. “Art can help scientists make a point without using any scientific jargon,” she says.

She teamed with Robert Wallace from Georgia Tech’s Agricultural Technology Research Program. One of Wallace’s projects gave plots of farmland to women in India who had been victims of an acid attack. Isaac did a portrait of a woman with a scarred face. The woman’s head is partially wrapped in strips of bandages that Isaac painted to look like rows of newly sprouting plants. “I wanted to show hope, and how connecting with the environment can help people,” Isaac says.

This year’s 36 Emory S.A.W. artists are mainly undergraduates — many of them science majors — but they also include a few graduate students, faculty and staff members. Georgia Tech makes up the bulk of other contributing artists and researchers in this year’s S.A.W., although 10 independent artists also got involved, along with Georgia State University undergraduates and the Atlanta campus of SCAD.

“S.A.W. is collaborative, not only across disciplines and institutions, but also across students, faculty, staff and members of the Atlanta community,” Romero says. “We even have one international artist, from Puerto Rico.”

A painting by Georgia Tech student Bianca Guerrero portrays a virtual reality game used to measure players' perception of time as well as eye movement. The art is based on research by Georgia Tech psychologist Malia Crane. Photo by Ann Watson, Emory Photo/Video.

As long as she can remember, everyone thought Romero would become an artist, or maybe an architect. She began taking art classes at the age of three in her home town of Tegucigalpa, Honduras. She continued making and studying art, developing a surrealist style.

In ninth grade, however, a psychology course sparked a fascination for neurobiology. Romero took online classes and started reading up on subjects like optogenetics and deep-brain stimulation.

By the time she was accepted to Emory, she had decided to forge a career as a scientist. “A lot of people told me that if I chose neuroscience I would have to forsake art, because I would be a bad scientist if I tried to do both,” she recalls. “I was determined to prove them wrong.”

Romero sought out kindred spirits like Nicole Gerardo, associate professor of biology, who also grew up with twin passions for science and art. Gerardo once had students create artwork using microbes in her lab under the direction of Nancy Lowe — a former lab technician at Emory who went on to create a retreat center in North Carolina called AS.IF: Art and Science in the Field.

Gerardo later paired students with labs to create ceramic representations of research under the direction of Diane Kempler, who formerly taught visual arts at Emory.

“Art provides a way to reach people who may be intimidated by science,” Gerardo says. “And working with an artist lets scientists see their own work in a different way. That could lead to new scientific approaches.”

When Romero first joined forces with Gerardo it was simply to produce art for her lab, which focuses on evolutionary ecology. “We were test subjects for S.A.W.,” Romero says.

Emory senior Maureen Ascona, a neuroscience and behavioral biology major, discusses her art with visitors to the Quad. Ascona teamed with Helen Mayberg, from the Emory School of Medicine, who uses deep-brain stimulation to help patients with treatment-resistant depression. Photo by Ann Watson, Emory Photo/Video.

One of the pieces Romero created consists of triangular canvases that can be shifted into different positions. The acrylic painting depicts how aphids develop wings in the presence of predators, like ladybugs, or if food becomes scarce. “When Dr. Gerardo explains her work to people, she can move the canvases to show how the aphids change in response to their environment,” Romero says.

Romero wanted to give other students the chance to enter research labs and experiment with art.

“Pamela is an amazing woman, a force of nature,” says Gerardo, who is the faculty mentor for S.A.W. “What she has done with the support of her fellow students is incredible. I had envisioned maybe 20 pairings of scientists and artists. I’m still surprised by how big it became.”

Connections from across the University helped S.A.W. grow. Wei Wei Chen and John Wang, student leaders of Emory Arts Underground, provided the platform for Romero to launch S.A.W. and encouraged her to form a charter, bylaws and an executive team. That team includes Emory undergraduates Alex Nazzari (vice-president), Aila Jiang, Veronica Paltaraskaya, Anne Pizzini, Deborah Seong and John Wang, along with Georgia Tech students Olivia Cox, Siyan Li and Iris Liu.

The students’ efforts paid off with S.A.W.’s smash debut at the Atlanta Science Festival.

“One of my favorite parts was guiding artists through the process of disentangling the science, reassuring them that they could do it,” Romero says. “Many of them felt overwhelmed after first talking to a scientist. Some of them were first-year students who hadn’t even had introductory biology or chemistry.”

A piece by Alice Yang, a first-year Emory student majoring in neuroscience and behavioral biology who teamed with researchers of human genetics in the Emory 3q29 Project. Photo courtesy of S.A.W.

Exploring a lab through an art project allows students to develop a relationship with a researcher and often find a mentor, Romero says.

Alice Yang, a first-year Emory student majoring in neuroscience and behavioral biology, teamed with Jennifer Mulle, assistant professor at Rollins School of Public Health. Mulle is co-principal investigator of the Emory 3q29 Project, which seeks to understand a genetic deletion associated with an increased risk for schizophrenia.

“I’m so grateful for the experience,” Yang says of spending time with the 3q29 Project team. “I learned what it’s like to actually do science. And I caught their passion. People are just now realizing how genetics can be involved in mental illness. It’s a very new field.”

To create her art pieces, Yang ordered special scratch-off paper from her native China. “This paper’s easy to work with and it’s great for showing patterns and textures,” she says. She explains how she carefully cut slices from the black top layer of the paper to reveal the glowing, rainbow colors beneath. Her pictures portray the nanomapping of fluorescent-labeled alleles from the 3q29 lab while also paying tribute to Salvador Dali’s surrealism.

Even those who are not aspiring scientists can catch the science-art bug. Independent artist Aaron Artrip teamed with scientists Matthew Jackson and Dan Cook at Georgia Tech to demonstrate interaction with sound. A group of children buzzes around Artrip’s exhibit in White Hall. A piece of paper sprinkled with powdered black ink is taped to a wooden speaker, which is plugged into an electronic synthesizer. As Artrip taps a keyboard, the powder moves across the page, creating patterns.

“I’m making drawings with vibrations. Forcing sound through the ink causes it to move,” he explains.

“Would you like to try?” he asks a young girl watching him.

She doesn’t have to be asked twice.

A painting by Georgia Tech student Kate Bernart, "Connecting the Cycle," portrays Austin Ladshaw's research at Georgia Tech's School of Environmental Engineering on the nuclear fuel cycle and ways to prevent excessive accumulations of radioactive waste. Photo by Ann Watson, Emory Photo/Video

Ultimately, S.A.W. hopes to find ways to integrate its art-science model into grades K-12. “We would like to have artists and researchers go into K-12 classrooms to talk about the art and the research together,” Romero says.

She presented S.A.W. at the recent Georgia Tech STEAM Leadership Conference, which brought together educators and policymakers to explore new ways to teach science, technology, engineering, art and math, or STEAM. S.A.W. is now working to put together an anthology of its art into a booklet, to include descriptions of the science. The booklet will be aimed at high school students “to give them a glimpse of some of the possible fields available to them in college,” Romero says.

S.A.W. is also creating a web site where the art will be accessible in digital form, including videos of some of the interactive art pieces, along with other resources for K-12 teachers.

After graduating this spring, Romero plans to take a gap year, then go on to graduate school with the aim of becoming a professor with a research lab. “S.A.W. has an incredible executive team and I’m making sure that the program continues after I leave Emory,” she says. “I would also like to stay involved with it in some way.”

As she prepares for graduation, Romero is working on an art narrative piece funded by the Emory Center for Creativity and Arts. The work will combine acrylic painting and sculpture to represent the element Vanadium, discovered by Mexican mineralogist Andrews Manuel del Rio in 1801. A series of circular canvases will each represent an atom in Vanadium. Each canvas will also represent a country or group of countries in Latin America, on which Romero will depict the research of a scientist from that area.

“My main goal with this piece is to celebrate and encourage more Latin American science,” Romero says. She is calling the piece “Elementally Latino,” to describe how Latinos are an elemental, or basic, part of science and how they also embody an elemental force. “Latinos are such a passionate people that I can only adequately describe them as a force of nature,” she says.

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Frankenstein at 200 sparks wonder and debate

Emory's Stuart A. Rose Manuscript, Archives and Rare Book Library holds an 1881 original edition of "Frankenstein" and an 1831 edition, above, with a depiction of the "creature" and a prologue by Mary Shelley.

It’s the 200th anniversary year of “Frankenstein, Or the Modern Prometheus,” an enduring novel at the nexus of major questions of our time. Emory faculty explore many of them in a newly published anthology, “Frankenstein: How a Monster Became an Icon, the Science and Enduring Allure of Mary Shelley’s Creation.”

“When you see a contemporary film about androids, like ‘Blade Runner 2049,’ you’re seeing the ‘Frankenstein’ story in a 21st-century guise,” says Sidney Perkowitz, Emory emeritus physicist and co-editor of the new anthology. “The androids are sleek and modern instead of the shambling, stitched-together creature in ‘Frankenstein,’ but they have the same questions swirling around them. Even as we’re on the verge of artificially generating life, we’re no closer to knowing whether we should.”

You can read more here.

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Biologists unravel another mystery of what makes DNA go 'loopy'

Interior of a cell showing the nucleus with the chromatin fiber (yellow) arranged in the three-dimensional space by loops formed by the CTCF protein (shown in pink). DNA is represented by thin blue lines on the chromatin. Graphic by Victor Corces. 

By Carol Clark

Scientists discovered another key to how DNA forms loops and wraps inside the cell nucleus — a precise method of “packing” that may affect gene expression.

The journal Science published the research by biologists at Emory University, showing that a process known as hemimethylation plays a role in looping DNA in a specific way. The researchers also demonstrated that hemimethylation is maintained deliberately — not through random mistakes as previously thought — and is passed down through human cell generations.

“In order for a protein called CTCF to make loops in the DNA, we discovered that it needs to have hemimethylated DNA close by,” says Emory biologist Victor Corces, whose lab did the research. “Nobody had previously seen that hemimethylated DNA has a function.”

Chenhuan Xu, a post-doctoral fellow in the Corces lab, developed experimental methods for DNA methylome mapping to conduct the research for the Science paper.

Chromatin is made up of CTCF and other proteins, along with DNA and RNA. One role of chromatin is to fold and package DNA into more compact shapes. Growing evidence suggests that this folding process is not just important to fit DNA into a cell nucleus — it also plays a role in whether genes are expressed normally or malfunction.

The Corces lab specializes in epigenetics: The study of heritable changes in gene function — including chromatin folding — that do not involve changes in the DNA sequence.

DNA methylation, for example, can modify the activity of DNA by adding methyl groups to both strands of the double helix at the site of particular base pairs. The process can be reversed through demethylation.

As cells divide they make a copy of their DNA. In order to do so, they have to untangle the two strands of DNA and split them apart. Each parental strand then replicates a daughter strand.

“When cells divide, it’s important that they keep the methylation the same for both strands,” Corces says, noting that altered patterns of methylation are associated with cancer and other diseases.

Hemimethylation involves the addition of a methyl group to one strand of the DNA helix but not the other. Some researchers observing hemimethylation have hypothesized that they were catching it right after cell division, before the cell had time to fully replicate to form a daughter strand. Another theory was that hemimethylation was the result of random mistakes in the methylation process.

The methods developed by Xu in the Corces lab allowed the researchers to observe hemimethylation on DNA in human cells in real-time before, during and after cell division. They also mapped it as the cells continued to replicate.

“If the parental DNA was hemimethylated, the daughter DNA was also hemimethylated at the same place in the genome,” Corces says. “The process is not random and it’s maintained from one cell generation to the next over weeks.”

The researchers found that hemimethlyation only occurs near the binding sites of CTCF — the main protein involved in organizing DNA into loops.

“If we got rid of the hemimethlyation, CTCF did not make loops,” Corces says. “Somehow, hemimethylation is allowing CTCF to make loops.”

And when CTCF makes a loop, it does so by binding ahead, going forward in the DNA sequence, they observed.

“Research suggests that some disorders are associated with CTCF binding — either mutations in the protein itself or with the DNA sequence where the protein binds,” Corces says. “It comes back to the story of how important these loops are to the three-dimensional organization of chromatin, and how that organization affects the gene expression.”

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