Wednesday, April 28, 2021

Human antibiotic use threatens endangered wild chimpanzees

The number of chimpanzees in Gombe National Park, the site of Jane Goodall's groundbreaking field studies, are down to about 95. "By misusing antibiotics, people can actually harm not only themselves, but also the species they share an environment with," says Emory disease ecologist Thomas Gillespie.

By Carol Clark

It’s well established that infectious disease is the greatest threat to the endangered chimpanzees made famous by the field studies of Jane Goodall at Gombe National Park in Tanzania. Now, new research led by scientists at Emory University shows that nearly half of the fecal samples from wild chimpanzees contain bacteria that is resistant to a major class of antibiotics commonly used by people in the vicinity of the park. 

The journal Pathogens published the findings

“Our results suggest that antibiotic-resistant bacteria is actually spreading from people to non-human primates by making its way into the local watershed,” says Thomas Gillespie, senior author of the study and associate professor in Emory’s Department of Environmental Sciences and Rollins School of Public Health. “People are bathing and washing in the streams, contaminating the water with drug-resistant bacteria where wild chimpanzees and baboons drink.” 

The researchers tested for genes conferring resistance to sulfonamides — drugs often used by people in the region to treat diarrheal diseases — in fecal samples from humans, domestic animals, chimpanzees and baboons in and around Gombe National Park. They also tested stream water used by these groups. 

Sulfonamide resistance appeared in 74 percent of the human samples overall, 48 percent of chimpanzee samples, 34 percent of baboon samples, and 17 percent of the domestic animal samples. Sulfonamide also showed up in 19 percent of the samples taken from streams shared by people, domestic animals and wildlife. 

The researchers also tested all the groups in the study for genes conferring resistance to tetracycline — another class of antibiotics that is used much less frequently by people in the vicinity, likely due to its greater expense and the fact that it is less available in the area. As expected, very few of the fecal samples from any of the groups, and none of the water samples from the streams, showed evidence of tetracycline resistance. 

First author of the study is Michele Parsons, who did the work as an Emory doctoral student in Environmental Sciences. Parsons has since graduated and works at the Centers for Disease Control and Prevention (CDC). Co-authors include researchers from the Jane Goodall Institute, the CDC, the University of Minnesota and Franklin and Marshall College. 

Gillespie is a disease ecologist who helped pioneer the “One Health” approach to protect humans, ecosystems and biodiversity. His projects in Africa, including the collaboration with the Jane Goodall Institute in Tanzania, are focused on helping farmers subsisting amid fragmented forests co-exist with primates and other wildlife in ways that minimize the risk of pathogen exchange between species, known as “spillover.” The virus that causes AIDS, for example, spilled over from chimpanzees to people. 

“It’s important to consider both sides of the story — human health and well-being, as well as conservation of chimpanzees and other species,” Gillespie says. 

Human encroachment has taken a toll on the great apes, due to fragmented habitat and the exchange of pathogens. Today, the number of chimpanzees in Gombe National Park are down to about 95. 

Diarrheal diseases are common in the area and people often turn to cheap sulfonamide antibiotics that are available without a prescription at small stores that act as informal pharmacies, selling drugs, soap and other necessities. Wild chimpanzees also suffer from wasting diseases that can be related to bacterial and other enteric pathogens that affect their ability to maintain calorie intake and absorb nutrients. 

“The majority of people in our sampling harbored bacteria resistant to the sulfonamide medication they are taking,” Gillespie says. “In those cases, they’re spending their money on a drug that is not helping them get better. Overuse of such drugs creates the potential for more lethal, antibiotic-resistant ‘super bugs’ to emerge.” 

The research findings will now support the development of interventions. 

More guidance is needed locally regarding the proper use of antibiotics, Gillespie says. He adds that it is also important to improve hygiene for wash-related activities in area streams, as well as to improve disposal of human waste materials. 

“By misusing antibiotics, people can actually harm not only themselves, but also the species they share an environment with,” Gillespie says. “After drug-resistant bacteria jump into chimpanzees, it can further evolve with the chimpanzees and then spill back into humans. We need to be thinking about infectious diseases within evolutionary and ecological frameworks, something that’s not often done in medicine.” 

The study was funded by the Morris Animal Foundation, the Emory Global Health Institute, the Arcus Foundation, the Leo S. Guthman Foundation and the National Institutes of Health.


Zoo gorillas contract COVID, raising alarms for great apes in the wild

Valuing 'natural capital' vital to avoid next pandemic, experts warn

Disease poses risk to chimpanzee conservation, Gombe study finds

Wednesday, April 21, 2021

Georgia Aquarium otters join list of animals testing positive for SARS-CoV-2

Otters are Mustelids, a diverse group of carnivorous mammals that includes mink and ferret — two other species that have also become infected with SARS-CoV-2. (Getty Images)

By Carol Clark

The recent positive SARS-CoV-2 tests of Asian small-clawed otters at the Georgia Aquarium add to the mystery of why some animals may be more susceptible than others to the virus that causes COVID-19. 

“In one sense, it’s not surprising to see otters infected, because we’ve already seen infections in mink and ferrets, which are closely related species,” says Thomas Gillespie, associate professor in Emory University’s Department of Environmental Sciences and Rollins School of Public Health. 

Otters, mink and ferrets are all Mustelids, a diverse group of carnivorous mammals, notes Gillespie, a disease ecologist who studies how pathogens jump between wildlife, domestic animals and people.

Most of the research into what animal species may be susceptible to SARS-CoV-2 is based on the genetics of protein binding sites that the virus uses to gain a foothold in a host. People, great apes and some monkeys have the highest susceptibility, according to this research, Gillespie says. 

In January, some members of the gorilla troop at the San Diego Zoo tested positive for SARS-CoV-2, after they exhibited COVID-19 symptoms. 

“What’s surprising,” Gillespie says, “is that Mustelids are at the opposite end of the spectrum in terms of a binding propensity with SARS-CoV-2. In one of the more robust studies to date, they fell into the lower range of binding scores among 400 species of vertebrates. And yet, they keep popping up with infections. That’s where the mystery lies.” 

The Georgia Aquarium announced in an April 18 news release that the otters were tested after showing symptoms such as sneezing, runny noses, lethargy and coughing. The animals were removed from their exhibit for behind-the-scenes care and are expected to make a full recovery, the release stated. 

The virus that causes COVID-19 is zoonotic, meaning that it originated in animals — most likely horseshoe bats — and may have passed through another species before making its way to humans. 

“It’s critical right now for the world to focus on preventing human-to-human transmission of the virus,” Gillespie says. “But it’s also important to consider the longer-term, bigger picture of how pathogens can spill over from animals to people and then back to animals again.” 

Gillespie helped pioneer the One Health approach to protecting humans, ecosystems and biodiversity. The primary risks for future spillover of zoonotic diseases are deforestation of tropical environments and large-scale industrial farming of animals, he says. 

In late 2020, COVID-19 outbreaks were seen in mink around the world, including the United States, at farms that mass-produce the animals for the fur trade. The mink are kept in densely packed conditions that are ideal for spreading pathogens, Gillespie says. 

Denmark culled 17 million mink after the virus spread from the human caretakers to the animals, then mutated and spread back to some of the human caretakers. 

“The good news is that there are relatively few documented cases of animal transmission to humans, and these appear to be restricted to the most ideal conditions for transmission, such as the crowded conditions of industrial mink farming,” Gillespie says. 

Ferrets are a common laboratory model for the study of respiratory diseases, due to their unique respiratory biology. Experimental studies have shown that they can easily be infected with SARS-CoV-2. 

The black-footed ferret is among the most endangered mammals in North America. That prompted researchers at the U.S. National Wildlife Health Center last December to start testing a veterinary vaccine for COVID-19 on a captive population of the animals at the National Black-footed Ferret Conservation Center in Colorado. 

Almost all of the species that have tested positive for SARS-CoV-2, including cats, dogs, tigers, gorillas and a few other mammals, live in close proximity to people — either as pets, in zoos or in laboratories. One exception is a wild mink, found near a mink farm in Utah, that tested positive for SARS-CoV-2, according to the U.S. Department of Agriculture. 

“Testing of wildlife is rare,” Gillespie says. “And most testing of captive animals is done only if they show symptoms, suggesting there may be many more asymptomatic cases. There are a lot of important questions into how SARS-CoV-2 may affect animals that we have not yet started exploring.” 

The questions are important to protect both the health of animals and people, he adds. 

“Widespread infection within a population of a novel virus is the kind of event that could potentially push endangered and critically endangered species over the edge,” Gillespie says. “And any time a virus enters a new species with different selective pressures, that provides more opportunities for new mutants of the virus to evolve and potentially spill over into humans.”


San Diego Zoo gorillas contract COVID, raising alarms for great apes in the wild

Valuing 'natural capital' vital to avoid next pandemic

Bat ecology in the era of pandemics

Wednesday, April 14, 2021

Physicists develop theoretical model for neural activity of mouse brain

"One of the wonderful things about our model is that it's simple," says Mia Morrell, who did the research as an Emory senior majoring in physics. Morrell graduated last year and is now in New Mexico, above, where she is completing a post-baccalaureate physics program at Los Alamos National Laboratory.

By Carol Clark

The dynamics of the neural activity of a mouse brain behave in a peculiar, unexpected way that can be theoretically modeled without any fine tuning, suggests a new paper by physicists at Emory University. Physical Review Letters published the research, which adds to the evidence that theoretical physics frameworks may aid in the understanding of large-scale brain activity. 

“Our theoretical model agrees with previous experimental work on the brains of mice to a few percent accuracy — a degree which is highly unusual for living systems,” says Ilya Nemenman, Emory professor of physics and biology and senior author of the paper. 

The first author is Mia Morrell, who did the research for her honors thesis as an Emory senior majoring in physics. She graduated from Emory last year and is now in a post-baccalaureate physics program at Los Alamos National Laboratory in New Mexico. 

“One of the wonderful things about our model is that it’s simple,” says Morrell, who will start a Ph.D. program in physics at New York University in the fall. “A brain is really complex. So to distill neural activity to a simple model and find that the model can make predictions that so closely match experimental data is exciting.” 

The new model may have applications for studying and predicting a range of dynamical systems that have many components and have varying inputs over time, from the neural activity of a brain to the trading activity of a stock market. 

Co-author of the paper is Audrey Sederberg, a former post-doctoral fellow in Nemenman’s group, who is now on the faculty at the University of Minnesota. 

The work is based on a physics concept known as critical phenomena, used to explain phase transitions in physical systems, such as water changing from liquid to a gas. 

In liquid form, water molecules are strongly correlated to one another. In a solid, they are locked into a predictable pattern of identical crystals. In a gas phase, however, every molecule is moving about on its own. 

“At what is known as a critical point for a liquid, you cannot distinguish whether the material is liquid or vapor,” Nemenman explains. “The material is neither perfectly ordered nor disordered. It’s neither totally predictable nor totally unpredictable. A system at this ‘just right’ Goldilocks spot is said to be ‘critical.’” 

Very high temperature and pressure generate this critical point for water. And the structure of critical points is the same in many seemingly unrelated systems. For example, water transitioning into a gas and a magnet losing its magnetism as it is heated up are described by the same critical point, so the properties of these two transitions are similar. 

In order to actually observe a material at a critical point to study its structure, physicists must tightly control experiments, adjusting the parameters to within an extraordinarily precise range, a process known as fine-tuning. 

In recent decades, some scientists began thinking about the human brain as a critical system. Experiments suggest that brain activity lies in a Goldilocks spot — right at a critical transition point between perfect order and disorder. 

“The neurons of the brain don’t function just as one big unit, like an army marching together, but they are also not behaving like a crowd of people running in all different directions,” Nemenman says. “The hypothesis is that, as you increase the effective distance between neurons, the correlations between their activity are going to fall, but they will not fall to zero. The entire brain is coupled, acting like a big, interdependent machine, even while individual neurons vary in their activity.” 

Researchers began searching for actual signals of critical phenomena within brains. They explored a key question: What fine tunes the brain to reach criticality? 

In 2019, a team at Princeton University recorded neurons in the brain of a mouse as it was running in a virtual maze. They applied theoretical physics tools developed for non-living systems to the neural activity data from the mouse brain. Their results suggested that the neural activity exhibits critical correlations, allowing predictions about how different parts of the brain will correlate with one another over time and over effective distances within the brain. 

For the current paper, the Emory researchers wanted to test whether fine-tuning of particular parameters were necessary for the observation of criticality in the mouse brain experiments, or whether the critical correlations in the brain could be achieved simply through the process of it receiving external stimuli. The idea came from previous work that Nemenman’s group collaborated on, explaining how biological systems can exhibit Zipf’s law — a unique pattern of activity found in disparate systems. 

“We previously created a model that showed Zipf’s law in a biological system, and that model did not require fine tuning,” Nemenman says. “Zipf’s law is a particular form of criticality. For this paper, we wanted to make that model a bit more complicated, to see if could predict the specific critical correlations observed in the mouse experiments.” 

The model’s key ingredient is a set of a few hidden variables that modulate how likely individual neurons are to be active. 

Morrell wrote the computer code to run simulations and test the model on her home desktop computer. “The biggest challenge was to write the code in a way that would allow it to run fast even when simulating a large system with limited computer memory without a huge server,” she says. 

The model was able to closely reproduce the experimental results in the simulations. The model does not require the careful tuning of parameters, generating activity that is apparently critical by any measure over a wide range of parameter choices. 

“Our findings suggest that, if you do not view a brain as existing on its own, but you view it as a system receiving stimuli from the external world, then you can have critical behavior with no need for fine tuning,” Nemenman says. “It raises the question of whether something similar could apply to non-living physical systems. It makes us re-think the very notion of criticality, which is a fundamental concept in physics.” 

The computer code for the model is now available online, so that anyone with a laptop computer can access it and run the code to simulate a dynamic system with varying inputs over time. 

“The model we developed may apply beyond neuroscience, to any system in which widespread coupling to hidden variables is extant,” Nemenman says. “Data from many biological or social systems are likely to appear critical via the same mechanism, without fine-tuning.” 

The current paper was partially supported by grants from the National Institutes of Health and the National Science Foundation.


Physicists eye neural fly data, find formula for Zipf's law

Biophysicists take small step in quest for 'robot scientist'

Tuesday, April 6, 2021

Chemists develop tools that may help improve cancer diagnostics, therapeutics

A process known as methylation helps regulate on-and-off switches to keep a host of systems in the body functioning normally. "But the process can get hijacked, creating modifications that may lead to diseases," explains Ogonna Nwajiobi (above), an Emory Ph.D. student in chemistry and first author of the paper.

By Carol Clark

Chemists developed a method to detect changes in proteins that may signal the early stages of cancer, Alzheimer’s, diabetes and other major diseases. Angewandte Chemie published the work, led by chemists at Emory University and Auburn University. The results offer a novel strategy for studying links between unique protein modifications and various pathologies. 

“The knowledge we gain using our new, chemical method holds the potential to improve the ability to detect diseases such as lung cancer earlier, when treatment may be more effective,” says Monika Raj, senior author of the paper and Emory associate professor of chemistry. “A detailed understanding of protein modifications may also help guide personalized, targeted treatment for patients to improve a drug’s efficacy against cancer.” 

The researchers provided a proof of concept for using their method to detect single protein modifications, or monomethylation. Their lab experiments were conducted on the protein lysine expressed from E.coli and other non-human organisms. 

Lysine is one of the nine essential amino acids that is critical to life. After lysine is synthesized in the human body, changes to the protein, known as methylation, can occur. Methylation is a biochemical process that transfers one carbon atom and three hydrogen atoms from one substance to another. Such modifications can occur in single (monomethylation), double (dimethylation) or triple (trimethylation) forms. Demethylation reverses these modifications. 

The small tweaks of methylation and demethylation regulate biological on-off switches for a host of systems in the body, such as metabolism and DNA production. 

“In a normal state, the methylation process creates modifications that are needed to keep your body functioning and healthy,” says Ogonna Nwajiobi, an Emory Ph.D. student in chemistry and first author of the paper. “But the process can get hijacked, creating modifications that may lead to diseases.”

Modifications to lysine, in particular, he adds, have been linked to the development of many cancers and other diseases in humans. 

Sriram Mahesh, from Auburn University is co-first author of the paper. Xavier Streety, also from Auburn, is a co-author. 

The Raj lab, which specializes in developing organic chemistry tools to understand and solve problems in biology, wanted to devise a method to detect monomethylation marks to lysine that have been expressed by an organism. Monomethylation is especially challenging to detect since it leaves negligible changes in the bulk, charge or other characteristics of a lysine modification.

The researchers devised chemical probes, electron-rich diazonium ions, that couple only with monomethlyation sites at certain biocompatible conditions that they can control, including a particular pH level and electron density. They used mass spectroscopy and nuclear magnetic resonance techniques to show that they had selectively hit the correct targets, and to confirm the coupling of atoms at the sites. 

The method is unique because it directly targets the monomethylation sites. Another unique feature of the method is that it is reversible under acidic conditions, allowing the researchers to uncouple the atoms and regenerate the original state of a monomethylation site. 

The Raj lab now plans to collaborate with researchers at Emory’s Winship Cancer Institute to test the new method on tissue samples taken from lung cancer patients. The goal is to home in on differences in lysine monomethylation sites of people with and without lung cancer. 

“It’s like a fishing expedition,” Nwajiobi explains. “The first step is to use our method to find the lysine monomethylation sites in tissue samples, which is difficult to do because of their low abundance. Once we’ve found the sites, our method then allows us to reverse the coupling with our chemical probe, so the functions of the sites can be studied in their intact, original forms.” 

Practical methods for early detection of many diseases, like lung cancer, are needed to help improve patient outcomes. “If we can develop more ways to identify lung cancer earlier, that may open the door for treatments that greatly improve the survival rate,” Raj says. 

The researchers hope to study lysine monomethylation differences between samples taken from patients at different stages of lung cancer, between patients with or without a family history of the disease, and between those who have smoked and those who have not. Knowledge gained from such analyses could set the stage for more personalized, targeted treatments, Raj says. 

Her lab is also developing chemical tools to selectively detect lysine dimethylation and trimethylation sites, in order to help more fully characterize the role of lysine methylation in disease. 

“We hope that other researchers will also apply our methods, and the chemical tools we are developing, to better understand a range of cancers and many other diseases associated with lysine methylation,” Raj says. 

The work was funded by the National Science Foundation.


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

Tuesday, March 30, 2021

Screams of 'joy' sound like 'fear' when heard out of context

"Our work intertwines language and non-verbal communication in ways that haven't been done in the past," says Emory psychologist Harold Gouzoules, senior author of the study.

By Carol Clark

People are adept at discerning most of the different emotions that underlie screams, such as anger, frustration, pain, surprise or fear, finds a new study by psychologists at Emory University. Screams of happiness, however, are more often interpreted as fear when heard without any additional context, the results show. 

PeerJ published the research, the first in-depth look at the human ability to decode the range of emotions tied to the acoustic cues of screams. 

“To a large extent, the study participants were quite good at judging the original context of a scream, simply by listening to it through headphones without any visual cues,” says Harold Gouzoules, Emory professor of psychology and senior author of the study. “But when participants listened to screams of excited happiness they tended to judge the emotion as fear. That’s an interesting, surprising finding.” 

First author of the study is Jonathan Engelberg, an Emory Ph.D. student of psychology. Emory alum Jay Schwartz, who is now on the faculty of Western Oregon University, is co-author. 

The acoustic features that seem to communicate fear are also present in excited, happy screams, the researchers note. “In fact, people pay good money to ride roller coasters, where their screams no doubt reflect a blend of those two emotions,” Gouzoules says. 

He adds that the bias towards interpreting both of these categories as fear likely has deep, evolutionary roots. 

“The first animal screams were probably in response to an attack by a predator,” he says. “In some cases, a sudden, loud high-pitched sound might startle a predator and allow the prey to escape. It’s an essential, core response. So mistaking a happy scream for a fearful one could be an ancestral carryover bias. If it’s a close call, you’re going to err on the side of fear.” 

The findings may even provide a clue to the age-old question of why young children often scream while playing. 

“Nobody has really studied why young children tend to scream frequently, even when they are happily playing, but every parent knows that they do,” Gouzoules says. “It’s a fascinating phenomenon.” 

While screams can convey strong emotions, they are not ideal as individual identifiers, since they lack the more distinctive and consistent acoustic parameters of an individual’s speaking voice. 

“It’s just speculative, but it may be that when children scream with excitement as they play, it serves the evolutionary role of familiarizing a parent to the unique sound of their screams,” Gouzoules says. “The more you hear your child scream in a safe, happy context, the better able you are to identify a scream as belonging to your child, so you will know to respond when you hear it.” 

Gouzoules first began researching the screams of non-human primates, decades ago. Most animals scream only in response to a predator, although some monkeys and apes also use screams to recruit support when they are in a fight with other group members. “Their kin and friends will come to help, even if some distance away, when they can recognize the vocalizer,” he says. 

In more recent years, Gouzoules has turned to researching human screams, which occur in a much broader context than those of animals. His lab has collected screams from Hollywood movies, TV shows and YouTube videos. They include classic performances by “scream queens” like Jaime Lee Curtis, along with the screams of non-actors reacting to actual events, such as a woman shrieking in fear as aftershocks from a meteor that exploded over Russia shake a building, or a little girl’s squeal of delight as she opens a Christmas present. 

In previous work, the lab has quantified tone, pitch and frequency for screams from a range of emotions: Anger, frustration, pain, surprise, fear and happiness. 

For the current paper, the researchers wanted to test the ability of listeners to decode the emotion underlying a scream, based solely on its sound. A total of 182 participants listened through headphones to 30 screams from movies that were associated with one of the six emotions. All of the screams were presented six times, although never in sequence. After hearing a scream, the listeners rated how likely it was associated with each of six of the emotions, on a scale of one to five. 

The results showed that the participants most often matched a scream to its correct emotional context, except in the case of screams of happiness, which participants more often rated highly for fear. 

“Our work intertwines language and non-verbal communication in a way that hasn’t been done in the past,” Gouzoules says. 

Some aspects of non-verbal vocal communication are thought to be precursors for language. The researchers hypothesize that it may be that the cognitive underpinnings for language also built human capacity in the non-verbal domain. “It’s probably language that gives us this ability to take a non-verbal vocalization and discern a wide range of meanings, depending on the acoustic cues,” Gouzoules says.


Screams contain a 'calling card' for the vocalizer's identity

What is a scream? The acoustics of a primal human call

Sunday, March 21, 2021

Heritable traits that appear in teen years raise risk for adult cannabis use

Some of the risk for repeated cannabis use into adulthood can be attributed to the genetic effects of neuroticism, risk tolerance and depression, the study found. "While this work marks an important step in identifying genetic factors that can increase the risk for cannabis use, a substantial portion of the factors that raise the risk remain unexplained," says Emory psychologist Rohan Palmer.

By Carol Clark

While some youth experiment with marijuana but don’t go on to long-term use, others develop a problematic pot habit that continues into adulthood. A major new analysis shows that at least a small portion of the risk for developing into an adult marijuana user may be related to inherited behaviors and traits that appear during adolescence. 

The journal Addiction published the findings by researchers at Emory and Brown University. 

“Our analysis suggests that some early adolescent behaviors and traits — like depression, neuroticism and acting out — can be indicative for cannabis use later in life,” says Rohan Palmer, senior author of the paper and assistant professor in Emory’s Department of Psychology, where he heads the Behavioral Genetics of Addiction Laboratory

“Decades of research has shown that behaviors can have a genetic component,” adds Leslie Brick, lead author and assistant professor in the Department of Psychiatry and Human Behavior in Brown’s Alpert Medical School. “And while there is not one genetically-influenced trait that determines whether you’re going to be a long-term cannabis user, our paper indicates that there are polygenic effects across multiple inherited behaviors and traits that show a propensity for increased risk.” 

Brick, a long-time collaborator with Palmer, also holds an adjunct faculty appointment in Emory’s Department of Psychology. 

The Transmissible Liability Index is a well-known measure for a constellation of heritable traits that may appear during the developmental years that are associated with the risk of a substance use disorder. For the current paper, the researchers wanted to tease out which of these heritable characteristics might be associated with repeated marijuana use later in life. 

“Cannabis use has been less studied than tobacco and alcohol,” Palmer says. “For one thing, it’s harder to get people to answer detailed questionnaires honestly about cannabis, since it’s an illegal substance. And it’s also much more difficult to standardize the amount of cannabis consumed, as compared to cigarettes and liquor.” 

Cannabis use, however, is widespread among adolescents and young adults. In 2018, more than 35 percent of high school seniors surveyed reported having used marijuana during the past year and more than 20 percent reported doing so during the past month, according to the National Institute on Drug Abuse (NIDA). 

As cultural norms have shifted, including the legalization of marijuana for adult recreational use in many states, teens’ perceptions of the risks of marijuana use have declined. 

Those risks, however, are real. 

“Adolescence is a major period of brain development,” Brick says. “In fact, our brains don’t stop developing until we are around 25 years old. Research indicates that cannabis has some major impacts on our biology, although its full effects are still not well understood.” 

The researchers drew data from the National Longitudinal Study of Adolescent Health, or Add Health, which includes a nationally representative sample of 20,000 adolescents in grades 7 to 12 in the United States who have been followed into adulthood. Comprehensive data from early adolescence to adulthood was collected on health and health-related behavior, including substance use, personality and genetics. 

For the current paper, the researchers identified a large homogenous subgroup of individuals from the Add Health study, about 5,000 individuals of European ancestry, for their final analytic sample. They then leveraged existing genome-wide association studies to examine whether certain heritable behavioral traits noted during adolescence were associated with the Transmissible Liability Index, and whether any of these traits were also associated with risk for later cannabis use. 

The results showed that a small portion of the risk for repeated cannabis use into adulthood can be attributed to the genetic effects of neuroticism, risk tolerance and depression that can appear during adolescence. 

“While this work marks an important step in identifying genetic factors that can increase the risk for cannabis use, a substantial portion of factors that raise the risk remain unexplained,” Palmer says. “We’ve shown how you can use existing data to assess the utility of a polygenic risk score. More studies are needed to continue to identify unique genetic and other environmental sources for the risk of long-term, problematic use of cannabis.” 

“Better understanding of what behaviors and traits may give someone a pre-disposition for long-term cannabis use gives us a better shot of identifying those most at risk so we can home in on effective interventions,” Brick says. 

A major limitation of the current study, the researchers add, is that it focused on individuals of European ancestry, because no sample size large enough for the genome-wide analysis was available for other ancestral groups. 

Co-authors of the study include the following members of Emory’s Behavioral Genetics of Addiction Laboratory: Graduate students Lauren Bertin, Kathleen Martin and former undergraduate Victoria Risner (now an Emory alum); and Chelsie Benca-Bachman, associate director of research projects in the lab. 

The work was supported by an Avenir grant from the National Institute on Drug Abuse.


Tuesday, March 9, 2021

Water temperature key to schistosomiasis risk and prevention strategies

Karena Nguyen, a post-doctoral fellow in Emory's Department of Biology, shown with two of the freshwater snails that serve as intermediate hosts for the parasites that cause schistosomiasis. (Photo by Rachel Hartman)

By Carol Clark

About one billion people worldwide are at risk for schistosomiasis — a debilitating disease caused by parasitic worms that live in fresh water and in intermediate snail hosts. A new study finds that the transmission risk for schistosomiasis peaks when water warms to 21.7 degrees centigrade, and that the most effective interventions should include snail removal measures implemented when the temperature is below that risk threshold. 

The Proceedings of the National Academy of Sciences published the results, led by Emory University, the University of South Florida and the University of Florida. 

“We’ve shown how and why temperature matters when it comes to schistosomiasis transmission risk,” says Karena Nguyen, a post-doctoral fellow in Emory University’s Department of Biology and a first author of the study. “If we really want to maximize human health outcomes, we need to consider disease transmission in the context of regional temperatures and other environmental factors when developing intervention strategies.” 

The findings indicate that climate change will increase schistosomiasis risk in regions where surface water moves closer to 21.7 degrees centigrade, or 71 degrees Fahrenheit. The researchers also found, however, that implementing snail control measures decreases transmission but raises the temperature for peak transmission risk to 23 degrees centigrade, or 73 degrees Fahrenheit. 

Co-first author of the paper is Philipp Boersch-Supan, an expert in ecological systems at the University of Florida and the British Trust for Ornithology. 

Nguyen is a member of the lab of David Civitello, Emory assistant professor of biology and a co-author of the PNAS paper. The Civitello lab studies the ecological dynamics of disease, aquatics and agricultural ecology through a combination of experiments, field surveys and models. 

“The control of schistosomiasis currently relies on treating infected people,” Civitello says. “However, there is renewed awareness that the ecological factors surrounding the disease also need to be considered. Our paper is a beautiful example of the potential power of uniting ecology with human disease interventions and control measures.” 

Click on graphic of the life cycle of the schistosomiasis parasite, above, to enlarge.

Schistosomiasis is one of the most devasting water-based diseases in developing countries, with more than 200 million people infected worldwide, leading to around 200,000 deaths annually. It is caused by Schistosoma parasites that have a complex life cycle. Freshwater becomes contaminated by the parasite’s eggs when infected people urinate or defecate in the water. After the eggs hatch, the parasites enter freshwater snails where they develop and multiply. More mature parasites are able to leave the snails and re-enter the water. These free-swimming parasites can then burrow into the skin of people who are wading, swimming, bathing, washing or doing agricultural work in contaminated water.

Children who are repeatedly infected can develop anemia, malnutrition and learning difficulties. Over the long term, the parasites can also damage the liver, intestine, lungs and bladder. 

“Schistosomiasis is treatable — people can take a drug to get rid of the adult parasites in their bodies,” Nguyen says. “But in areas where schistosomiasis is prevalent, people can easily get reinfected by coming in contact with contaminated water. And children, who like to play in water, tend to have the highest burden of the disease.” 

For the current paper, Nguyen focused on how global climate change and rising water temperatures might affect each stage of the schistosomiasis transmission cycle. It was already established that both the parasites and the snails are sensitive to water temperature, with each stage having an optimum temperature. 

“I wanted to build on previous work to see if we could use it to find better predictors for human risk and more effective interventions,” Nguyen says. 

The researchers integrated an epidemiological model of schistosomiasis and temperature-dependent traits of the parasites and their snail hosts to run different computer-simulated interventions. The results showed that interventions targeting snails were most effective at reducing transmission, and pinpointed the water temperature for when the risk of transmission peaks. 

Unexpectedly, the simulations also showed that interventions targeting snail removal actually raised the peak transmission temperature by 1.3 degrees centigrade, while reducing transmission risk. 

“That may not sound like a lot,” Nguyen says, “but we’re talking about water temperature, which takes a lot of energy to warm, so 1.3 degrees is actually a big shift.” 

Snails naturally start to die off at higher water temperatures. The data in the new paper shows how implementing snail control measures, such as through chemical treatment of the water, amplifies snail mortality at all temperatures. This lowers transmission risk overall, but allows peak transmission risk to occur at higher temperatures. 

These insights can guide public health workers to time their interventions, by factoring in regional water temperatures, and how the temperatures fluctuate during different seasons of the year. 

“Our findings don’t mean that we should stop human treatment for schistosomiasis,” Nguyen says. “Instead, it will likely be beneficial to include both the human and ecological components. By combining human drug treatment with snail removal measures, during times when water is below the peak transmission temperature, we may be able to maximize the efficacy of an intervention.” 

Additional authors of the PNAS paper include Jason Rohr (University of Notre Dame), Valerie Harwood (University of South Florida), Rachel Hartman (Emory staff) and Emory graduate student Sandra Mendiola. 

The work was funded by the National Institutes of Health, the National Science Foundation, the Porter Foundation and the U.S. Department of Agriculture.


Monday, March 8, 2021

Atlanta Science Festival: Life is looking up with science!

This year's festival is a hybrid of more than 80 events, including virtual activities and those held in the outdoors.

By Carol Clark

The Atlanta Science Festival returns March 13-27 stronger than ever. This year’s hybrid of more than 80 events includes virtual activities and those held in safe, socially-distanced environments, aimed to educate, engage and entertain all ages. 

The 2021 festival theme — “Science Always Prevails!” — celebrates the metro area as a powerhouse of scientific research, scholarship, service and innovation, from battling the COVID-19 pandemic to protecting the unique natural resources of Georgia. 

“The pandemic has heightened public awareness of the value of science,” says Meisa Salaita, executive co-director of Science ATL, the non-profit organization that produces the Atlanta Science Festival. “All of our partners, including Emory, have come together to keep the festival going strong, despite the challenges. Everyone is inspired by the knowledge that our mission of service to the community is more important than ever.” 

The Atlanta Science Festival, now in its eighth year, was co-founded by Emory, Georgia Tech and the Metro Atlanta Chamber. 

“We’ll not only continue our celebration of science,” says executive co-director Jordan Rose, “but use it as an opportunity to share knowledge that inspires and empowers others to make the world a better place.” 

Bringing more science to more people

On Friday, March 12, one day before the festival launch, an event called “Imagining the Future” will help set the tone. Local STEM professionals, including many Emory faculty and students, will participate in virtual visits to 100 metro Atlanta K-12 classrooms to give students a sense of how science is done, talk about some major questions that remain unanswered in science, and inspire students to imagine themselves shaping the future as STEM-literate professionals of tomorrow. 

“One of the benefits of having virtual events is that we are able to bring more science, and more science-learning opportunities, to more people,” Salaita says. 

Some of this year’s festival highlights include: 

  • “Atlanta 40,” a celebration of 40 notable organisms of the region explained by videos created by experts and luminaries and mini conservation challenges that the public can complete. 
  • “Discovery Walks,” four family-friendly, self-guided walks through neighborhoods and parks in Atlanta, featuring free maps with cool science facts about each location. 
  • “City Science Quest,” an app-based game that allows participants to use a mobile device to uncover Atlanta’s science contributions and STEM careers by earning prizes through completing interactive “missions,” including many that involve exciting scientific research ongoing at Emory. 

Emory event highlights

While not ignoring the current reality, the tone of this year’s festival is hopeful and encouraging, Salaita says. Emory experts will headline events that showcase how scientists at Emory and around the world came together to produce effective, safe vaccines for the novel coronavirus in record time, and to address concerns of communities that have been especially hard hit by COVID-19. 

Another Emory highlight will be a hands-on, outdoor event to learn how to collect data on Georgia’s air quality. And, not to be missed, Emory chemistry students will engage families in a “Drive-In Demo Show” of dramatic displays of chemistry in action. 

Following is a roundup of some of the festival highlights featuring the Emory community. 

Community scientists and amateur sleuths are invited to a family friendly “Air Quality Scavenger Hunt,” on Saturday, March 13, from 11 a.m. to 3 p.m. in Atlanta’s Historic Fourth Ward Park. Participants will be provided hand-held air sensors and learn to measure the amount of particulate matter, or pollutants, in the air. Their mission will be to use clues to locate different areas around the park to collect air quality data for Eri Saikawa, associate professor of Emory’s Department of Environmental Sciences, and students in her lab. The COVID-19 safety measures for the outdoor event require participants to wear masks and to sign up in advance for half-hour time slots to pick up and return the air sensors. “This event is for anyone who enjoys solving puzzles and wants to be part of the solution when it comes to pollution,” Saikawa says. 

A related at-home or in-class competition led by Saikawa and her students is the “Georgia Air Quality Challenge” for grades 6 to 12. Grade school students will partner with Air Emory, an Emory student-led initiative that began to monitor air quality on campus and is now expanding statewide through a grant from the Environmental Protection Agency and the support of Science ATL and Education Enhanced. Registered grade school students will receive access to lessons and videos to learn about sources of pollution, current data for Georgia, and how air sensors can measure air quality. They will then be challenged to submit a proposal for where air sensors should be placed in local communities in order to fill the gap in air quality data for Georgia. The winners will be invited to present their proposals to an upcoming Georgia STEM day. 

“We want young people to understand the importance of monitoring air quality,” Saikawa says. “We also hope they learn more about sources of air pollution, who may be more vulnerable, and think about ways we might mitigate pollution.” 

Emory physicians will be featured in a series of virtual talks on COVID-19 vaccines.

Emory physician Zanthia Wiley, assistant professor in the School of Medicine’s Division of Infectious Diseases, will give a virtual talk on Saturday, March 13, at 10 a.m., entitled “COVID-19 Vaccines and Disparities in Black Communities: What You Need to Know.” Dr. Wiley, who is also the director of Antimicrobial Stewardship at Emory University Hospital Midtown, will discuss the importance of COVID-19 vaccination and the disproportionate effect that COVID-19 is having in minority communities. She will also take questions submitted directly by those attending the virtual talk. Wiley is a member of the Emory Department of Medicine’s Diversity, Equity and Inclusion Council and the Emory Collaborative Community Outreach and Health Disparities Research Initiative. 

A virtual talk on Tuesday, March 16, at 6 p.m., “COVID-19 Vaccines and Disparities in Latinx Communities: What You Need to Know,” features Emory physician Valeria Cantos, assistant professor in the School of Medicine’s Division of Infectious Diseases and an attending physician at Grady Memorial Hospital and the Grady Infectious Disease Clinic. She will give a bi-lingual talk, in Spanish and English, on vaccine truths, myths and the importance of vaccination. She will also take questions submitted by the audience. Dr. Santos is a lead co-investigator in a study looking at the efficacy of remdesivir in the treatment of hospitalized patients with COVID-19. She is also a co-investigator for the Moderna and Noravax vaccine clinical trials. 

“Vaccine Real Talk,” a virtual panel discussion, is is set for Thursday, March 18, at 7 p.m. The panel will be moderated by Maryn McKenna, a leading infectious disease journalist and a senior fellow in Emory’s Center for the Study of Human Health. The event will take on the topic of how COVID-19 vaccines work and how to best combat misinformation around them. Panelists will include Colleen Kraft, associate professor in Emory School of Medicine’s Division of Infectious Diseases and the director of Emory’s Clinical Virology Research Laboratory. 

At noon on March 18, Deboleena Roy, Emory senior sssociate dean of faculty, will lead a virtual panel discussion about scientists and their social responsibility titled “Citizen Nobel: The Pressure and Power of Winning the Ultimate Scientific Prize.” Roy is professor of neuroscience and behavioral biology with a joint appointment in women’s, gender and sexuality studies. The discussion will be based on the film “Citoyen Nobel,” which will be available free for registrants during the week of March 13 to 20. 

Book your free spot in advance and load your “pod” into the family vehicle for the “Drive-In Demo Show” on Saturday, March 20, at 11 a.m., noon and 1 p.m., in the parking lot of the First Christian Church in Decatur. Instead of a movie, this drive-in will feature live performances by Emory chemistry students, led by Doug Mulford, senior lecturer of chemistry, whose motto is “teaching with a pyrotechnic flair.” Viewers will remain safe in their cars as the masked, socially distanced Emory chemists make sparks fly. They will wrestle with polymers that grow as large as eels, turn gummy bears into flaming dragons, and make a liquid nitrogen cloud. The finale, of course, will feature a safe, but fiery, explosion! 

The Atlanta Science Festival is produced by more than 50 community partners, with major support from founders Emory, Georgia Tech and the Metro Atlanta Chamber, and sponsors UPS, International Paper, Georgia Power, Cox Enterprises, Mercer University and others.

Monday, February 15, 2021

NIH grant funds Emory work on indoor air sensor for SARS-CoV-2

"We hope our project will yield an important air-monitoring tool as we enter an era when pandemics will likely become more common," says Emory chemist Khalid Salaita, principal investigator of the NIH grant.

By Carol Clark

Emory University received a National Institutes of Health grant, for a total of $883,000 over two years, to develop a sensor capable of detecting SARS-CoV-2, the virus that causes COVID-19, in the air of indoor spaces. The grant is part of the NIH RADx Radical initiative, which aims to support new, non-traditional approaches for rapid detection devices that address current gaps in testing for the presence of SARS-CoV-2, as well as potential future pandemic viruses. 

“Our goal is to create a fully automated electronic sensor that continually measures for the presence of SARS-CoV-2 in the environment in real time,” says Khalid Salaita, principal investigator of the grant and an Emory professor of chemistry. “The sensor could be used in schools, airports or any high-traffic indoor areas.” 

The new sensor will potentially have the flexibility to be re-programmed to detect other dangerous strains of viruses that may emerge, he adds. “Even after we get the COVID-19 pandemic under control, the demand for viral sensing will remain,” Salaita says, noting that the new sensor will take at least two years to develop. 

Salaita, a leader in biophysics and nanotechnology, is also on the faculty of the Wallace H. Coulter Department of Biomedical Engineering, a joint program of Georgia Tech and Emory. 

Co-investigators of the grant include Gregory Melikian, a professor at Emory School of Medicine, in the Department of Pediatrics’ Division of Infectious Disease; and Yonggang Ke, assistant professor at Emory’s School of Medicine and the Wallace H. Coulter Department of Biomedical Engineering. 

The project will work to adapt the technology of a DNA micromotor, developed in 2015 by the Salaita Lab and further enhanced through collaboration with the Ke Lab. The Milikian Lab will generate harmless, engineered viral particles that mimic the real virus, and its potential mutants, to allow the team to test and validate the technology. 

Emory graduate Kevin Yehl (now on the faculty of Miami University) developed the micromotor with Salaita while he was a PhD student in the Salaita Lab. It is the first rolling DNA motor, and is capable of sensing, leading the researchers to dub it the “Rolosensor.” It won a bronze medal in the 2016 Collegiate Inventors Competition, the foremost program in the country encouraging invention and creativity in undergraduate and graduate students. 

Emory graduate Kevin Yehl, shown while he was a PhD student in the Salaita Lab demonstrating a prototype of the Rolosensor.

The Rolosensor, about the size of a human red blood cell, consists of hundreds of synthetic DNA strands, or “legs,” bound to a sphere. The DNA legs are placed on a glass slide coated with the reactant: RNA. The DNA legs are drawn to the RNA, but as soon as they set foot on it they destroy it through the activity of an enzyme called RNase H. As the legs bind and then release from the substrate, they guide the sphere along, allowing more of the DNA legs to keep binding and pulling. 

“When we first developed the motor it was initially out of pure curiosity,” Salaita says. “We wondered if we could convert chemical energy into mechanical work and make something move.” 

The researchers soon realized that anything that resists the motion of the rolling motor slows its speed. The speed of the motor can be monitored by attaching a clip-on microscope lens to the camera of a smart phone. They showed that the Rolosensor can detect a single DNA mutation by capturing videos of the particle motion to measure particle displacement. The team was awarded a patent in 2020 to use the simple, low-tech method for doing diagnostic sensing in the field, or anywhere with limited resources. 

Even during the few months early in the COVID-19 pandemic that his lab was temporarily shut down, Salaita began to think about how the Rolosensor might be adapted to detect SARS-CoV-2. 

He began discussing the idea with Melikian, a virologist who worked on HIV and other viruses but had also pivoted to take on the challenge of SARS-CoV-2. The Melikian Lab figured out a way to make “pseudo” viral particles with spikey proteins that mimic those of SARS-CoV-2. 

“These pseudo viruses, which are harmless and do not replicate, will provide a way for us to test and optimize the assay as we try to adapt our rolling motor to detect SARS-CoV-2,” Salaita explains. 

Graphic by the Salaita Lab demonstrates the plan for how the DNA motor will work to detect SARS-CoV-2.

The plan calls for the Ke Lab to help make the body of the rolling motor “sticky” to the SARS-CoV-2 viruses, but not to any other virus or material, by using DNA structures that function like Velcro. The Rolosensor will be embedded into a microchip, where it will roll across the surface unless it encounters viral particles that cause it to stick. A camera will continuously record the speed of the motors. If a motor stalls, it will trigger an electronic alarm signal at a central monitoring station. 

“Imagine an unobtrusive, encased device, similar to a smoke detector, that continuously samples the air,” Salaita says. “A central server on a cloud could collect data from numerous devices, in an airport, for example, and send out an alert for a SARS-CoV-2 detection event, including the GPS coordinates, whenever a motor stopped.” 

An additional key collaborator is Primordia Biosystems, Inc., a company that specializes in building microfluidic chips that can sample virus-containing aerosols in the air. 

The motors can run for up to 24 hours, allowing for fully automatic viral sensing, without the need for sample processing or other human intervention. 

Three Emory PhD chemistry students in the Salaita Lab have collected preliminary data and will conduct the experiments and tests needed to complete the project: Alisina Bazrafshan, Selma Piranej and Yuxin Duan. 

Many hurdles remain to develop a prototype for an indoor air sensor for SARS-CoV-2, Salaita says, including concerns such as sensitivity of the device and whether it would generate false positives. The longer-range goal is to adapt the rolling motor device so that it could be programmed to effectively detect high levels of any virus of concern in an indoor air space. 

“One thing is for certain, there is a need for viral-detecting devices for public indoor air spaces and many researchers are working to try to meet this challenge,” Salaita says. “We hope our project will yield another important air-monitoring tool as we enter an era when pandemics will likely become more common.”


Wednesday, February 3, 2021

Physics of snakeskin sheds light on sidewinding

The sidewinder rattlesnake (Crotalus cerastes) is found in the deserts of the Southwestern United States and northern Mexico. (Photo by Wolfgang Wuster)

Most snakes get from A to B by bending their bodies into S-shapes and slithering forward headfirst. A few species, however — found in the deserts of North America, Africa and the Middle East — have an odder way of getting around. Known as “sidewinders,” these snakes lead with their mid-sections instead of their heads, slinking sideways across loose sand. 

Scientists took a microscopic look at the skin of sidewinders to see if it plays a role in their unique method of movement. They discovered that sidewinders’ bellies are studded with tiny pits and have few, if any, of the tiny spikes found on the bellies of other snakes. The Proceedings of the National Academy of Sciences (PNAS) published the discovery, which includes a mathematical model linking these distinct structures to function. 

“The specialized locomotion of sidewinders evolved independently in different species in different parts of the world, suggesting that sidewinding is a good solution to a problem,” says Jennifer Rieser, assistant professor of physics at Emory University and a first author of the study. “Understanding how and why this example of convergent evolution works may allow us to adapt it for our own needs, such as building robots that can move in challenging environments.”

Thursday, January 28, 2021

Viral sequencing can reveal how SARS-CoV-2 spreads and evolves

The SARS-CoV-2 genome consists of a single RNA strand that is 30,000 letters long. Sequencing is a technique that provides a read-out of these letters.

By Carol Clark

The emergence of SARS-CoV-2 virus variants that are adding twists in the battle against COVID-19 highlight the need for better genomic monitoring of the virus, says Katia Koelle, associate professor of biology at Emory University. 

“Improved genomic surveillance of SARS-CoV-2 across states would really help us to better understand how the virus causing the pandemic is evolving and spreading in the United States,” Koelle says. “More federal funding is needed, along with centralized standards for sample collection and genetic sequencing. Researchers need access to such metadata to better track how the virus is spreading geographically, and to identify any new variants that may make it harder to control, so that health officials can respond more quickly and effectively.” 

Koelle studies the interplay between viral evolution and the epidemiological spread of viral infectious diseases. She is senior author of a “Viewpoint” article published in Science on the importance of SARS-CoV-2 sequencing to control the COVID-19 pandemic. 

Michael Martin, a PhD student in Emory’s Population, Biology and Ecology Program and a member of Koelle’s lab, is first author of the Science article. David VanInsberghe, a post-doctoral fellow in Koelle’s lab, is co-author. 

“Research into SARS-CoV-2 has been going at lightning speed,” Martin says. “This acceleration has provided us with one of the largest datasets ever so quickly assembled for a disease. We’ve learned a lot so far about how this virus spreads and adapts, but we still have many blind spots that need to be addressed.” 

The article summarizes key insights about SARS-CoV-2 that have already been gained by sequencing of its genome from individual patient samples. It also cites challenges that remain, including the collection and integration of metadata into genetic analyses and the need for the development of more efficient and scalable computational methods to apply to hundreds of thousands of genomes. 

A genome is an organism’s genetic material. Human genomes are made up of double-stranded DNA, coded in four different nucleotide base letters. A single human genome consists of more than 3 billion base pairs. In contrast, the genome of coronaviruses, including SARS-CoV-2, are made of RNA, which can have a simpler structure than DNA. The SARS-CoV-2 genome, for instance, consists of a single RNA strand that is only 30,000 letters long. Sequencing is a technique that provides a read-out of these letters. 

If the SARS-CoV-2 virus is found in a sample swabbed from someone’s nose or mouth, it confirms the likelihood that the person is carrying the virus, whether they have symptoms of COVID-19 or not. The virus in the sample can also be sequenced. 

“Sequencing the virus is like fingerprinting it,” Koelle explains. “And based on how close the fingerprints match between samples — that is, how close they are genetically — you can at times learn who is infecting whom. Analyzing sequences from samples taken from infected individuals in a given region over time can provide even more information.” 

Analyses of SARS-CoV-2 sequencing data have enabled researchers to estimate the timing of SARS-CoV-2 spillover into humans; identify some of the transmission routes in its global spread; determine infection rates and how they change within a region; and identify the emergence of some new variants of concern. 

Viral genomes can mutate during replication, changing letters as they spread to new people. Most of these random mutations will likely not affect the transmissibility or virulence of a virus — but a few may make it even more difficult to fight. Early evidence, for instance, suggests that a SARS-CoV-2 variant that recently emerged in the UK may be more easily transmitted and potentially more severe. A South African variant shows signs that it may reduce the efficacy of existing vaccines, while a variant first detected in Brazil also contains mutations that health officials worry may make the virus spread more quickly. 

“It can be difficult to identify which variants actually change how the virus replicates, spreads and causes disease because of confounding factors,” Martin explains. “If a variant spreads more quickly, for instance, you have to tease apart whether that was due to it becoming more transmissible or if someone who was infected with it attended a large gathering.” 

The better data researchers have, the faster they can solve such puzzles, he adds. 

Technological advances during recent years have made it more efficient and less costly to generate sequencing data. Barely a year after it emerged, more than 400,000 sequences of SARS-CoV-2 are now available in public databases, such as the GISAID platform which was launched in 2008 to share information among National Influenza Centers for the WHO Global Influenza Surveillance and Response System. 

“A large chunk of the public sequencing data for SARS-CoV-2 has come out of the UK,” Koelle notes. “That’s because the British government has an initiative to do high-density sampling of the SARS-CoV-2 genome.” 

The rich data set from the UK helped identify the emergence of the variant in Britain that is spreading rapidly. “There might be other variants of concern emerging in other places around the world besides the ones already identified, but we just don’t know because we don’t have as good of surveillance in those locations,” Koelle says. 

“While the United States has been slow in efforts to sequence SARS-CoV-2 from samples across the nation, there are several excellent viral sequencing efforts and phylogenetic analyses, primarily driven by academic researchers, that have helped to understand SARS-CoV-2 transmission more locally,” Koelle says. “We have the expertise in the U.S., but the effort is more piecemeal.” 

“We need a coordinated, nationally standardized program to do widespread sequencing of SARS-CoV-2 in the United States,” Martin says. “Much of the data collected now just has a state identifier but we need greater resolution while also protecting patient privacy. More county-level identifiers, for instance, would be one way to greatly improve the quality and the depth of the data.” 

Once the COVID-19 pandemic ebbs, it’s important to continue to build the national infrastructure and systems for infectious disease surveillance — including viral sequencing — and to keep it in place, both researchers stress. 

“There will be more infectious disease pandemics, and we need to be better prepared,” Martin says.


Anonymous cell phone data can quantify behavioral changes for flu-like illnesses

Tuesday, January 26, 2021

Anonymous cell phone data can quantify behavioral changes for flu-like illnesses

A NASA satellite image of Iceland, superimposed with a heatmap of movement data of individuals during the 2009 H1N1 epidemic, drawn from cell phone metadata near the time they were diagnosed with a flu-like illness. (Graphic by Ymir Vigfusson, Rebecca Mitchell and Leon Danon).

By Carol Clark

Cell phone data that is routinely collected by telecommunications providers can reveal changes of behavior in people who are diagnosed with a flu-like illness, while also protecting their anonymity, a new study finds. The Proceedings of the National Academy of Sciences (PNAS) published the research, led by computer scientists at Emory University and based on data drawn from a 2009 outbreak of H1N1 flu in Iceland. 

“To our knowledge, our project is the first major, rigorous study to individually link passively-collected cell phone metadata with actual public health data,” says Ymir Vigfusson, assistant professor in Emory University’s Department of Computer Science and a first author of the study. “We’ve shown that it’s possible to do so without comprising privacy and that our method could potentially provide a useful tool to help monitor and control infectious disease outbreaks.” 

The researchers collaborated with a major cell phone service provider in Iceland, along with public health officials of the island nation. They analyzed data for more than 90,000 encrypted cell phone numbers, which represents about a quarter of Iceland’s population. They were permitted to link the encrypted cell phone metadata to 1,400 anonymous individuals who received a clinical diagnosis of a flu-like illness during the H1N1 outbreak. 

“The individual linkage is key,” Vigfusson says. “Many public-health applications for smartphone data have emerged during the COVID-19 pandemic but tend to be based around correlations. In contrast, we can definitively measure the differences in routine behavior between the diagnosed group and the rest of the population.” 

The results showed, on average, those who received a flu-like diagnosis changed their cell phone usage behavior a day before their diagnosis and the two-to-four days afterward: They made fewer calls, from fewer unique locations. On average, they also spent longer time than usual on the calls that they made on the day following their diagnosis. 

The study, which began long before the COVID-19 pandemic, took 10 years to complete. “We were going into new territory and we wanted to make sure we were doing good science, not just fast science,” Vigfusson says. “We worked hard and carefully to develop protocols to protect privacy and conducted rigorous analyses of the data.” 

Vignusson is an expert on data security and developing software and programming algorithms that work at scale. 

He shares first authorship of the study with two of his former students: Thorgeir Karlsson, a graduate student at Reykjavik University who spent a year at Emory working on the project, and Derek Onken, a Ph.D. student in the Computer Science department. Senior author Leon Danon — from the University of Bristol, and the Alan Turing Institute of the British Library — conceived of the study. 

While only about 40 percent of humanity has access to the Internet, cell phone ownership is ubiquitous, even in lower and middle-income countries, Vigfusson notes. And cell phone service providers routinely collect billing data that provide insights into the routine behaviors of a population, he adds.

“The COVID pandemic has raised awareness of the importance of monitoring and measuring the progression of an infectious disease outbreak, and how it is essentially a race against time,” Vigfusson says. “More people also realize that there will likely be more pandemics during our lifetimes. It is vital to have the right tools to give us the best possible information quickly about the state of an epidemic outbreak.” 

Privacy concerns are a major reason why cell phone data has not been linked to public health data in the past. For the PNAS paper, the researchers developed a painstaking protocol to minimize these concerns. 

The cell phone numbers were encrypted, and their owners were not identified by name, but by a unique numerical identifier not revealed to the researchers. These unique identifiers were used to link the cell phone data to de-identified health records. 

“We were able to maintain anonymity for individuals throughout the process,” Vigfusson says. “The cell phone provider did not learn about any individual’s health diagnosis and the health department did not learn about any individual’s phone behaviors.” 

The study encompassed 1.5 billion call record data points including calls made, the dates of the calls, the cell tower location where the calls originated and the duration of the calls. The researchers linked this data to clinical diagnoses of a flu-like illness made by a health providers in a central database. Laboratory confirmation of influenza was not required. 

The analyses of the data focused on 29 days surrounding each clinical diagnosis, and looked at changes in mobility, the number of calls made and the duration of the calls. They measured these same factors during the same time period for location-matched controls. 

“Even though individual cell phones generated only a few data points per day, we were able to see a pattern where the population was behaving differently near the time they were diagnosed with a flu-like illness,” Vigfusson says. 

While the findings are significant, they represent only a first step for the possible broader use of the method, Vigfusson adds. The current work was limited to the unique environment of Iceland: An island with only one port of entry and a fairly homogenous, affluent and small population. It was also limited to a single infectious disease, H1N1, and those who received a clinical diagnosis for a flu-like illness.

“Our work contributes to the discussion of what kinds of anonymous data lineages might be useful for public health monitoring purposes,” Vigfusson says. “We hope that others will build on our efforts and study whether our method can be adapted for use in other places and for other infectious diseases.” 

Co-authors include the late Gudrun Sigmundsdottoir, directorate of health for Iceland’s Center for Health Security and Communicable Disease Control; Congzhang Song (Cornell University); Atil Einarsson (Reykjavik university); Nishant Kishore (Harvard); Rebecca Mitchell (formerly with Emory’s Nell Hodgson Woodruff School of Nursing); and Ellen Brooks-Pollock (University of Bristol). 

The work was funded by the Icelandic Center for Research, Emory University, the National Science Foundation, the Leverhulme Trust, the Alan Turing Institute, the Medical Research Council and a hardware donation from NVIDIA Corporation.


Tuesday, January 12, 2021

San Diego Zoo gorillas contract COVID, raising alarms for great apes in wild

A mountain gorilla mother and her baby in the wild in Rwanda. Great apes "are important not just to ecosystems but to giving us insights into understanding our own selves and our evolutionary past," says Emory disease ecologist Thomas Gillespie.

By Carol Clark

The news that some members of the gorilla troop at the San Diego Zoo have tested positive for the virus that causes COVID-19 ramps up the urgency for protecting great apes in the wild from exposure, warns Thomas Gillespie, an Emory disease ecologist. 

“This first known transmission to apes confirms what we strongly suspected — that one of our closest living relatives is susceptible to the novel coronavirus,” says Gillespie, an associate professor in Emory’s Department of Environmental Sciences and Rollins School of Public Health. “More than ever, it’s a race against time. If gorillas in the wild become infected it will be a much more dangerous scenario because we won’t have the ability to contain it.” 

In March, Gillespie co-authored a Nature commentary warning that non-human great apes are susceptible to human respiratory diseases and that COVID-19 could prove devastating to animals on the brink of extinction. 

The non-human great apes include chimpanzees, bonobos and gorillas, which live in equatorial Africa, and orangutans, which are native to the rainforests of Indonesia and Malaysia. The International Union for Conservation of Nature (IUCN) lists chimpanzees and bonobos as endangered species, while gorillas and orangutans are critically endangered. 

Even exposure to viruses that have mild effects in people, such as those causing the common cold, have been associated with mortality events in wild primates. 

The San Diego Zoo Safari Park reported that it conducted tests for the presence of the SARS-CoV-2, the coronavirus that causes COVID-19, after two of its gorillas began coughing. On January 11, the test results confirmed the presence of the virus in some of its gorillas, the zoo announced in a release, adding that it suspects that the virus was transmitted by an asymptomatic staff member, despite the strict prevention protocols in place. 

Great apes, in particular, are at risk from many human diseases due to our close relationship. Chimpanzees and bonobos are our nearest living relatives, sharing about 99 percent of human DNA, while gorillas are our next closest relatives, sharing 98 percent of our DNA. 

The great apes also share key sites within the ACE2 receptor protein with humans that allow SARS-CoV-2 to bind onto cells and infect them. 

Gillespie is a member of an IUCN task force focused on mitigating the impact of COVID on great apes and other primates. He is working with governments and organizations in Africa, including the Jane Goodall Institute, to provide scientifically-informed guidance on protecting wild apes during the pandemic as tourism, research and other activities that lead to human-ape overlap resume. The IUCN Save Our Species Program provided funding to support communities impacted by the loss of great ape tourism, to help prevent people from resorting to poaching animals or logging their habitats. Some of those funds are set to run out soon. 

Gillespie’s lab is also developing a spatially-explicit model to investigate key factors that may affect the spread of the virus among wild primates, so that governments and organizations can prioritize efforts to protect the animals. 

“What’s happened in San Diego has brought the pandemic risks for great apes back into the spotlight,” Gillespie says. “Great apes are our closest relatives and many of them are critically endangered, on the verge of extinction. We’ve gained a lot of insights into our own health and biology by studying these animals. They are important not just to ecosystems but to giving us insights into understanding our own selves and our evolutionary past.”


Monday, January 11, 2021

Movers and shakers: New evidence for a unifying theory of granular physics

Understanding the dynamics of granular materials — such as sand flowing through an hourglass or salt pouring through a shaker — is a major unsolved problem in physics. A new paper describes a pattern for how record-sized events affect the dynamics of a shaken granular material as it moves from an excited to a relaxed state, adding to the evidence that a unifying theory underlies this behavior. 

The Proceedings of the National Academy of Sciences (PNAS) published the work by Stefan Boettcher, an Emory theoretical physicist, and Paula Gago, an expert in modeling the statistical mechanics of granular matter in the Department of Earth Science and Engineering at the Imperial College of London. 

“Our work marks another small step forward to describing the behavior of granular materials in a uniform way,” says Boettcher, professor and chair of Emory’s Department of Physics. “A complete understanding of granular materials could have a huge impact on a range of industries,” he adds. 

“To name just a few examples, it’s relevant to the compaction of granules into pellets to make pills, the processing of grains in agriculture and to predict behaviors of all kinds of geophysical matter involved in civil engineering.”


Friday, January 8, 2021

Chemists invent shape-shifting nanomaterial with biomedical potential

Electron micrographs give a detailed view of the new nanomaterial. Arrows indicate layers that form in the tubes, leading to the hypothesis that the sheets form tubes by scrolling in at the corners.

Chemists have developed a nanomaterial that they can trigger to shape shift — from flat sheets to tubes and back to sheets again — in a controllable fashion. The Journal of the American Chemical Society published a description of the nanomaterial, which was developed at Emory University and holds potential for a range of biomedical applications, from controlled-release drug delivery to tissue engineering. 

The nanomaterial, which in sheet form is 10,000 times thinner than the width of a human hair, is made of synthetic collagen. Naturally occurring collagen is the most abundant protein in humans, making the new material intrinsically biocompatible. 

“No one has previously made collagen with the shape-shifting properties of our nanomaterial,” says Vincent Conticello, senior author of the finding and Emory professor of biomolecular chemistry. “We can convert it from sheets to tubes and back simply by varying the pH, or acid concentration, in its environment.” 

The Emory Office of Technology Transfer has applied for a provisional patent for the nanomaterial.