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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Physicists devise method to reveal how light affects materials

"Our finding may pave the way for improvements in devices such as optical sensors and photovoltaic cells," says Emory physicist Hayk Harutyunyan. (Stock photo)

By Carol Clark

Physicists developed a way to determine the electronic properties of thin gold films after they interact with light. Nature Communications published the new method, which adds to the understanding of the fundamental laws that govern the interaction of electrons and light.

“Surprisingly, up to now there have been very limited ways of determining what exactly happens with materials after we shine light on them,” says Hayk Harutyunyan, an assistant professor of physics at Emory University and lead author of the research. “Our finding may pave the way for improvements in devices such as optical sensors and photovoltaic cells.”

From solar panels to cameras and cell phones — to seeing with our eyes — the interaction of photons of light with atoms and electrons is ubiquitous. “Optical phenomenon is such a fundamental process that we take it for granted, and yet it’s not fully understood how light interacts with materials,” Harutyunyan says.

One obstacle to understanding the details of these interactions is their complexity. When the energy of a light photon is transferred to an electron in a light-absorbing material, the photon is destroyed and the electron is excited from one level to another. But so many photons, atoms and electrons are involved — and the process happens so quickly — that laboratory modeling of the process is computationally challenging.

For the Nature Communications paper, the physicists started with a relatively simple material system — ultra-thin gold layers — and conducted experiments on it.

“We did not use brute computational power,” Harutyunyan says. “We started with experimental data and developed an analytical and theoretical model that allowed us to use pen and paper to decode the data.”

Harutyunyan and Manoj Manjare, a post-doctoral fellow in his lab, designed and conducted the experiments. Stephen Gray, Gary Wiederrecht and Tal Heilpern — from the Argonne National Laboratory — came up with the mathematical tools needed. The Argonne physicists also worked on the theoretical model, along with Alexander Govorov from Ohio University.

For the experiments, the nanolayers of gold were positioned at particular angles. Light was then shined on the gold in two, sequential pulses. “These laser light pulses were very short in time — thousands of billions of times shorter than a second,” Harutyunyan says. “The first pulse was absorbed by the gold. The second pulse of light measured the results of that absorption, showing how the electrons changed from a ground to excited state.”

Typically, gold absorbs light at green frequencies, reflecting all the other colors of the spectrum, which makes the metal appear yellow. In the form of nanolayers, however, gold can absorb light at longer wave lengths, in the infrared part of the spectrum.

“At a certain excitation angle, we were able to induce electronic transitions that were not just a different frequency but a different physical process,” Harutyunyan says. “We were able to track the evolution of that process over time and demonstrate why and how those transitions happen.”

Using the method to better understand the interactions underlying light absorption by a material may lead to ways to tune and manage these interactions.

Photovoltaic solar energy cells, for instance, are currently only capable of absorbing a small percentage of the light that hits them. Optical sensors used in biomedicine and photo catalysts used in chemistry are other examples of devices that could potentially be improved by the new method. 

While the Nature Communications paper offers proof of concept, the researchers plan to continue to refine the method’s use with gold while also experimenting with a range of other materials. 

“Ultimately, we want to demonstrate that this is a broad method that could be applied to many useful materials,” Harutyunyan says.

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Chemistry students sing their studies, hoping for a good reaction

By Carol Clark

On the last day of the spring semester, during Bill Wuest’s “Principles of Reactivity” course, loud noises rattle the Atwood Chemistry Center’s Atomic Classroom. It isn’t explosions — it’s pop music mixed with bursts of laughter.

“This bond’s alright!” a group of Emory first-year students belts out on a YouTube video playing on screens before the class. Backed by the music of “Oh, What a Night,” they dance before a periodic table, write on a white board and mix chemicals in a lab while singing lyrics they wrote themselves: “Now I use a base to synthesize. It can readily be hydrolyzed. Mechanisms, what a sight!”

In just under four minutes, the students sing key lessons they learned over the semester about carbonyl mechanisms.

“It’s basically describing how reactions go,” explains Rebecca Henderson, one of the performers. “A reaction is not normally just putting two chemicals together and — BOOM — a product comes out. There’s a lot of different steps involved and we wanted to describe some of them, and why a reaction goes down one pathway and not another.”

Henderson created the video with classmates Carson Brooks, Lauren Cohen, Justine Griego and Alex Kim. They all played themselves in the video — except for Kim, who used powder to create a white patch in his hair and portray the professor.

“I love it when they mock me, they get extra points for that,” says Wuest, who has a natural, white streak of hair running through the center of his close-cropped dark hair.

Wuest, who joined Emory in the fall of 2017 as a Georgia Research Alliance Distinguished Investigator, directs an organic chemistry lab along with teaching undergraduates. He started having students make music parody videos while he was at Temple University.

“A lot of people think that chemistry is dry and boring but there’s a lot of creativity involved in it and that’s often overlooked in classrooms,” Wuest says.

The videos fit in well with Emory’s curriculum. Last fall, Emory became one of the first major research universities to completely overhaul how chemistry is taught, from introductory courses to capstone seminars. The new program, called Chemistry Unbound, moves away from teaching a narrow slice of chemistry every year to jumping into a big-picture understanding of chemistry’s central role across the sciences.



The video assignment helps with those big-picture concepts, Wuest says. Students form groups of up to six to make a two-to-four-minute educational video about some aspect of what they’ve learned in class. The video can either take the form of a musical parody of a well-known song or — for the less adventurous — a more straightforward lesson in the style of the Khan Academy website.

While Wuest is not the first to have chemistry students make videos, he is one of the few to actually measure their effect. With the help of his wife, Liesl Wuest, an educational analyst who also works at Emory, he has compared learning outcomes — in the form of exam performance before and after the videos — and found a strong correlation to improved scores.

His Temple students received extra credit, but not a grade, for making videos. Out of 130 students, 25 percent of them opted to do the videos. The average score for the class on an exam before the video project and an exam following the video project found that those who made videos had an average of 50 percent more improvement in their scores compared to those who opted out.

“Making the videos forces students to think about the material in new ways,” Wuest says. “It also makes the material more memorable to help it stick with them long term.”

Wuest refined the criteria for the video project and turned it into a graded requirement for his Emory classes. The top videos, based on accuracy and execution, will be housed on the Canvas learning management system so that future students can use them for inspiration and study aids.



“I was really impressed with the level of the videos this semester,” Wuest says. “They showcase the quality and the diversity of the students at Emory.”

Wuest plans to continue measuring the effect of the videos on learning. Many of the students, meanwhile, have given the video assignment a big thumb’s up.

“Not only do you learn the material, but it’s a fun experience,” says Dennis Jang, a first-year student.

Jang helped make a video called “I’ll Make a Chemist Out of You,” set to the song “I’ll Make a Man Out of You” from the Disney movie “Mulan.” The other first year students in his group included Muhammad Dhanani, Alex Fukunaga, Gaby Garcia and Jessie Kwong.

“The hardest part of this project was balancing the content and the comedy,” Jang says. “We presented some broad aspects of what we learned in class and some more specific aspects. And then we added humor to keep the audience watching.”

The formula worked. An informal vote following the screening of the videos in class, based on laughter and applause, showed “I’ll Make a Chemist Out of You” was the clear audience favorite.

“As we were watching all of the videos together we were laughing and just really enjoying being together,” Henderson says. “It was the final wrap-up of a great semester. Bill really knows how to make a true community out of a classroom.”

You can watch more of the videos by clicking here. 


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Study reveals how the brain decides to make an effort

"Understanding how the brain works normally when deciding to expend effort provides a way to pinpoint what's going on in disorders where motivation is reduced," says Emory psychologist Michael Treadway, whose lab conducted the study.

By Carol Clark

From deciding to quit hitting the snooze button and get out of bed in the morning to opting to switch off the TV and prepare for sleep at night, the mind weighs the costs versus benefits of each choice we make. A new study reveals the mechanics of how the brain makes such effortful decisions, calculating whether it is worth expending effort in exchange for potential rewards.

The Proceedings of the National Academy of Sciences (PNAS) published the findings by psychologists at Emory University.

“We showed that the brain’s ventromedial prefrontal cortex, which was not previously thought to play a key role in effort-based choices, actually appears to be strongly involved in the formation of expectations underlying those choices,” says Emory psychologist Michael Treadway, senior author of the paper.

Treadway’s lab focuses on understanding the molecular and circuit-level mechanisms of psychiatric symptoms related to mood, anxiety and decision-making.

“Understanding how the brain works normally when deciding to expend effort provides a way to pinpoint what’s going on in disorders where motivation is reduced, such as depression and schizophrenia,” he says.

Previous research had observed three brain regions in decision-making; the dorsal anterior cingulate cortex (dACC), the anterior insula (aI) and the ventromedial prefrontal cortex (vmPFC). Studies had pointed to the vmPFC as central to the computation of subjective value during probability decision-making. But prior evidence also suggested that when it comes to decisions about effort expenditure, those subjective value estimates were not computed by the vmPFC but by the other two brain regions.

A limitation to previous studies on effort-based choices is that they simultaneously presented the costs and benefits of a choice to experimental subjects.

“In the real world, however, we usually have to make decisions based on incomplete information,” says Amanda Arulpragasam, first author of the PNAS paper and a psychology PhD candidate in Treadway’s lab.

Arulpragasam designed a study that allowed the researchers to model distinct neural computations for effort and reward.

Subjects underwent functional magnetic resonance imaging (fMRI) while performing an effort-based decision-making task where the effort costs and rewards of a choice were presented separately over time.

The subjects could choose to make no effort and receive $1, or make some level of physical effort in exchange for monetary rewards of varying magnitude, up to $5.73. The physical effort involved rapid button pressing at varying percentages of each participant’s maximum button pressing rate. Participants were required to press the button using their non-dominant pinkie finger, making the task challenging enough to be unpleasant, although not painful.

In the effort-first trials, participants were shown a vertical bar representing the percentage of their maximum button pressing rate that would be required to do the task. They were then shown the size of the reward for performing the task. The reward-first trials presented the information in the opposite order.

After receiving both sets of information, participants were prompted to choose the no-effort option or the effort option.

The experimental design allowed the researchers to tease apart the effects of recent choices on the formation of value expectations of future decisions.

The results revealed a clear role for the vmPFC in encoding an expected reward before all information had been revealed. The data also suggested that the dACC and aI are involved in encoding the difference between what participants were expecting and what they actually got, rather than effort-cost encoding.

“Some have argued that decisions about effort have a different neural circuitry than decisions about probability and risk,” Treadway says. “We’ve showed that all three brain regions come into play, just in a different way than was previously known.”

Co-authors of the PNAS paper include Jessica Cooper, a post-doctoral fellow in the Treadway lab and Makiah Nuutinen, a research interviewer in the lab.

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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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