Learning to love our bugs

Each of us is a mobile ecosystem, teeming with trillions of living organisms. (Illustration by Giula Ghigini) 

By Jerry Grillo
Emory Medicine

They live on us and inside us, surround us like an invisible cloud, maintain and sustain us, ignore us, occasionally attack and kill us, and, ultimately, define us.

The human microbiome is made up of bacteria, fungi, viruses, and the like, and they cover every surface of our bodies.

"These microbiota are mostly in your gut, but also in your mouth, on your skin, in your lungs," says Emory biologist Nicole Gerardo. "They're playing critical roles in how you interact with the environment, how you process food, how you fight off pathogens, how you interact with drugs.

"Some of our remarkably fertile microbes are identical to those that live in other humans. But many are a distinct reflection of our individual experiences, shaped by who or what we've touched, where we've been, what we've breathed, and what we've consumed.

"Research interest in the human microbiome is exploding now," says Gerardo, who gave the introductory presentation at Emory's first microbiome symposium in November.

Spurred on by ambitious efforts like the National Institutes of Health's Human Microbiome Project, such research is demystifying the role of our myriad microbial passengers.

"It's like we're entering a new frontier of science, something that was basically ignored by medicine for a long time," says infectious disease researcher David Weiss, director of Emory's Antibiotic Resistance Center. "We're really at the beginning of studying all this, but I do think that in our lifetime, we'll be able to monitor each person's microbiome and intervene to improve their health. Looking at what type of bacteria we have and how resistant or sensitive they are to drugs will be an important part of health care. Most of the bugs we tote around are helpful, but they can also be ticking time bombs."

We may be able to someday diffuse the situation, replacing pathogenic microbes with a friendlier variety.

"There's great promise in manipulating the microbiome, in actually changing it," says geneticist Michael Zwick. "Actually, it's already happening."

Read the whole article in Emory Medicine.

Related:
What aphids can teach us about the microbiome and the immune system

Emory biologist nurtures nature in his spare time

Biologist Chris Beck is one of three finalists for the 2016 Cox Conserves Heroes award, for his work with the Clyde Shepherd Nature Preserve. Emory Photo/Video.

By Kimber Williams
Emory Report

As a professor of pedagogy in Emory’s Department of Biology, Chris Beck is engaged in the scientific study of laboratory teaching, with a particular focus on how inquiry-based learning impacts students' science process skills and their understanding of the nature of science.

This month, however, Beck is being recognized for his work involving a very different laboratory.

Beck has been named as one of three finalists for the 2016 Cox Conserves Heroes award for his volunteer work at the Clyde Shepherd Nature Preserve (CSNP), a 28-acre wildlife sanctuary located along the floodplain of South Peachtree Creek in Decatur.

For more than a decade, Beck has volunteered at CSNP, coordinating hundreds of volunteers from both Emory and the wider community, leading fundraising efforts and managing capital improvement projects. Each finalist will be awarded $5,000 to be donated to a local environmental nonprofit of their choice. Beck has selected CSNP as his non-profit.

The final winner will be selected through an online public vote and will receive an additional $5,000 donation to their nonprofit. Voting runs through Oct. 26; final results will be announced mid-November.

Emory Report interviewed Beck to learn more about his efforts with the nature preserve.

Why is the preserve important?

From an ecological perspective, the preserve serves several purposes. It’s located on the floodplain of the south fork of Peachtree Creek, so it has a role in controlling storm water overflow and filtering the water that does flood out.

The preserve is also an important green space to a lot of wildlife, including over 150 to 160 species of birds, as well as amphibians, reptiles and a wide array of plants. It provides a great resource to both the local and broader Atlanta communities, in terms of offering a place to go and see wildlife and walk the trails.

It’s provided educational opportunities as well. Over the years, I’ve brought students from my ecology lab classes there and I know Georgia State University and Oglethorpe University use it, too. Emory has sent hundreds of volunteers there over the years. It’s provided a great way to engage the community.

Read the full interview with Beck in Emory Report.

Pistil-packing science: Pollen genetics could help fight crime

A European honey bee collects nectar, gathering pollen on its body in the process. Emory biologists Karen Bell and Berry Brosi, who study pollen to monitor the health of ecosystems, say that pollen analysis also holds potential to help with forensic investigations.

By Karen Bell, Berry Brosi and Kevin Burgess

Bell is a post-doctoral fellow in the lab of Brosi, an evolutionary biologist in Emory's Department of Environmental Sciences, focused on the study of bees. Burgess is a biologist at Columbia State University. This article originally ran in The Conversation.

Imagine you're a detective working on a murder case. You have a body, but you believe it was moved from another location. Now what? There's one unexpected tool you might use to follow up on this suspicion: forensic palynology. That's the application of palynology – the study of pollen – to crime investigation.

But how does pollen have any bearing on forensics? While usually unseen, pollen is essentially ubiquitous in terrestrial habitats, and it is extremely tough. In fact, pollen is so durable that paleontologists can examine fossilized pollen grains in ancient sediments to see what plants grew during prehistoric times. And the “signature” of which pollen grains are present is specific to a particular place (because different plant species occur in different areas) and time (because different plant species flower at different times).

All of that makes pollen an ideal biomarker for linking people and objects to particular places and times, a central need in forensic investigations. Despite this potential utility, forensic palynology has been underutilized, because of its reliance on specialized experts to meticulously identify pollen visually under the microscope.

But recently researchers developed a new technique for identifying pollen, using genetics. By making identification much easier and faster for large numbers of pollen samples, this development has the potential to transform forensic palynology, allowing us to harness the power of pollen to solve crimes.

"Pollen could be a great biomarker to work out where people have been, or where something they were carrying has been," says Emory biologist Karen Bell, shown in the field.

Forensic palynology has been particularly useful in cases where there is suspected movement of evidence, or where a crime has occurred in a location with distinct plant species. For example, following the Bosnian war, investigators uncovered mass graves where bodies had been moved from different locations. Pollen was one of the lines of evidence used to trace bodies to their original burial sites. In a case in New Zealand, a burglar was tracked to the scene of the crime when pollen grains on his clothing were matched to an uncommon plant species growing in front of the victim’s house.

There are many other types of cases where forensic palynology could be applied. Objects under examination in missing person cases could be traced to their origin. Analysts could tie individual criminals' travel histories together based on finding a similar pollen species composition on seized evidence, possibly linking their crimes and providing direction for further investigation. Officials could determine illegal imports' country of origin.

Traditionally, forensic palynology is done by examining pollen grains under a microscope and comparing them to known pollen morphology. This is a highly specialized skill, and there are few experts able to identify plant species based on the size, shape and color of the pollen grains. After all, researchers estimate almost 400,000 species of plants live on our planet today. There is currently only one person employed full-time as a forensic palynologist in the U.S.

Forensic palynology is further limited by the labor intensiveness of morphological identification. Frequently it's impossible to determine the exact species present; identification is typically to a genus or family of plants – a group of species, in other words. This limits the technique's utility, because while many plant species occur in a small geographic range, the genus or family in which they belong may cover a much broader area.

"Because pollinator species are declining so rapidly, we need high through-put methods of analyses," Bell says, noting that those same techniques may make pollen genetics practical for other uses.

In a recently published article in Forensic Science International Genetics, we revealed how identifying pollen through DNA barcoding, on its own or with traditional palynology, could be a practical alternative.

DNA barcoding is a way to identify species via their species-specific genetic signatures. To do this for pollen, scientists sequence the DNA from a genetic region known to occur in all plants, but which varies from species to species. There are two parts to the standardized sequence we use for plant DNA barcoding. One is a section of the large subunit of a gene called ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL for short). The other is a gene called maturase-K (matK). These genes are both essential for a plant to survive, and are thus present in all plants. Once an investigator sequences these gene regions from a sample, they can be compared to a database containing all the known DNA sequences of rbcL and matK to identify the species.

To DNA barcode pollen, the first step is to extract the DNA. Pollen grains produce the male reproductive cells (sperm) of the plant. Each pollen grain has a tough outer layer called the exine, made of a protein called sporopollenin. We need to break the exine in order to release the DNA that's protected inside. We do this by putting the pollen grains in a tube filled with small silica beads and shaking vigorously for several minutes. Once the cells release their DNA, it can be purified and then sequenced.

High-throughput DNA sequencing is a methodological advance that has made pollen DNA barcoding feasible. This new method allows researchers to sequence multiple pieces of DNA at the same time, without separating them first. It's a key innovation because forensic pollen samples typically contain a mixture of species. Without high-throughput sequencing, these species would first need to be painstakingly separated – and then we'd be back to the same efficiency problems of traditional morphological analysis. With high-throughput sequencing, the whole mixture of pollen grains can be ground up in one sample, the DNA isolated and sequenced, and matched to a database. This technique is known as DNA metabarcoding.

Although pollen DNA barcoding has not yet been applied to forensic palynology, similar techniques have been used to quality test honey, determining the plant species on which bees have been foraging. Pollen DNA barcoding has also contributed to air quality monitoring, when it's useful to know what allergens are present in the environment.

Optimizing these methods for forensics may require some small modifications, such as dealing with very few pollen grains in a sample. Ideally a standardized method should be developed for forensics, to enable comparisons between different cases, studied by different scientists. It will also be necessary to expand the reference databases, to include more species that might be of interest to forensics specialists.

But while there are still a few hurdles to overcome, eventually pollen DNA barcoding could become a common and scientifically rigorous technique in law enforcement and national security.

Related:
Pollinators vital to food supply facing extinction, U.N. report warns
Bees 'betray' their flowers when pollinator species decline

Chimpanzees choose cooperation over competition

Video shows chimpanzee cooperation task. All chimpanzees must manipulate the handles at the same time in order for the food to be delivered. Video from Yerkes National Primate Research Center.

From Woodruff Health Sciences Center:

When given a choice between cooperating or competing, chimpanzees choose to cooperate five times more frequently, Yerkes National Primate Research Center researchers have found. This, the researchers say, challenges the perceptions humans are unique in our ability to cooperate and chimpanzees are overly competitive, and suggests the roots of human cooperation are shared with other primates.

The study results are reported in this week’s early online edition of the Proceedings of the National Academy of Sciences.

To determine if chimpanzees possess the same ability humans have to overcome competition, the researchers set up a cooperative task that closely mimicked chimpanzee natural conditions, for example, providing the 11 great apes that voluntarily participated in this study with an open choice to select cooperation partners and giving them plenty of ways to compete. Working beside the chimpanzees’ grassy outdoor enclosure at the Yerkes Research Center Field Station, the researchers gave the great apes thousands of opportunities to pull cooperatively at an apparatus filled with rewards. In half of the test sessions, two chimpanzees needed to participate to succeed, and in the other half, three chimpanzees were needed.

While the set up provided ample opportunities for competition, aggression and freeloading, the chimpanzees overwhelmingly performed cooperative acts – 3,565 times across 94 hour-long test sessions.

Read more about the study.

A dog's dilemma: Do canines prefer praise or food?

Chowhound: Ozzie, a shorthaired terrier mix, was the only dog in the experiments that chose food over his owner’s praise 100 percent of the time. “Ozzie was a bit of an outlier,” Berns says, “but Ozzie’s owner understands him and still loves him.”

By Carol Clark

Given the choice, many dogs prefer praise from their owners over food, suggests a new study published in the journal Social, Cognitive and Affective Neuroscience. The study is one of the first to combine brain-imaging data with behavioral experiments to explore canine reward preferences.

“We are trying to understand the basis of the dog-human bond and whether it’s mainly about food, or about the relationship itself,” says Gregory Berns, a neuroscientist at Emory University and lead author of the research. “Out of the 13 dogs that completed the study, we found that most of them either preferred praise from their owners over food, or they appeared to like both equally. Only two of the dogs were real chowhounds, showing a strong preference for the food.”

Dogs were at the center of the most famous experiments of classical conditioning, conducted by Ivan Pavlov in the early 1900s. Pavlov showed that if dogs are trained to associate a particular stimulus with food, the animals salivate in the mere presence of the stimulus, in anticipation of the food.

“One theory about dogs is that they are primarily Pavlovian machines: They just want food and their owners are simply the means to get it,” Berns says. “Another, more current, view of their behavior is that dogs value human contact in and of itself.”

Berns heads up the Dog Project in Emory’s Department of Psychology, which is researching evolutionary questions surrounding man’s best, and oldest friend. The project was the first to train dogs to voluntarily enter a functional magnetic resonance imaging (fMRI) scanner and remain motionless during scanning, without restraint or sedation. In previous research, the Dog Project identified the ventral caudate region of the canine brain as a reward center. It also showed how that region of a dog’s brain responds more strongly to the scents of familiar humans than to the scents of other humans, or even to those of familiar dogs.

Praise Pooch: Most of the dogs in the experiments preferred praise over food, or liked them both equally. Kady, a Labrador-golden retriever mix, was the top dog when it came to the strength of her preference for praise.

For the current experiment, the researchers began by training the dogs to associate three different objects with different outcomes. A pink toy truck signaled a food reward; a blue toy knight signaled verbal praise from the owner; and a hairbrush signaled no reward, to serve as a control.

The dogs then were tested on the three objects while in an fMRI machine. Each dog underwent 32 trials for each of the three objects as their neural activity was recorded.

All of the dogs showed a stronger neural activation for the reward stimuli compared to the stimulus that signaled no reward, and their responses covered a broad range. Four of the dogs showed a particularly strong activation for the stimulus that signaled praise from their owners. Nine of the dogs showed similar neural activation for both the praise stimulus and the food stimulus. And two of the dogs consistently showed more activation when shown the stimulus for food.

The dogs then underwent a behavioral experiment. Each dog was familiarized with a room that contained a simple Y-shaped maze constructed from baby gates: One path of the maze led to a bowl of food and the other path to the dog’s owner. The owners sat with their backs toward their dogs. The dog was then repeatedly released into the room and allowed to choose one of the paths. If they came to the owner, the owner praised them.

“We found that the caudate response of each dog in the first experiment correlated with their choices in the second experiment,” Berns says. “Dogs are individuals and their neurological profiles fit the behavioral choices they make. Most of the dogs alternated between food and owner, but the dogs with the strongest neural response to praise chose to go to their owners 80 to 90 percent of the time. It shows the importance of social reward and praise to dogs. It may be analogous to how we humans feel when someone praises us.”

The experiments lay the groundwork for asking more complicated questions about the canine experience of the world. The Berns’ lab is currently exploring the ability of dogs to process and understand human language.

“Dogs are hypersocial with humans,” Berns says, “and their integration into human ecology makes dogs a unique model for studying cross-species social bonding.”

Related:
Dogs process faces in specialized brain area, study reveals
Scent of the familiar: You may linger like perfume in your dog's brain

Photos by Gregory Berns

Cardinals may reduce West Nile virus spillover in Atlanta

One more reason to love the northern cardinal: In addition to being beautiful to look at, in Atlanta these birds appear to help shield humans from West Nile virus. (Photo by Stephen Wolfe.)

By Carol Clark

Northern cardinals act as “super suppressors” of West Nile virus in Atlanta, slowing transmission and reducing the incidence of human cases of the mosquito-borne pathogen, suggests a new study published in the American Journal of Tropical Medicine and Hygiene.

“Previous research has shown that the American robin acts like a ‘super spreader’ for West Nile virus in Chicago and some other cities,” says Rebecca Levine, who led the research as a PhD student in Emory University’s Department of Environmental Sciences. “Now our study provides convincing data that northern cardinals and some other bird species may be ‘super suppressors’ of the virus in Atlanta.”

The researchers also found that birds in Atlanta’s old-growth forests had much lower rates of West Nile virus infection compared to birds tested in the city’s secondary forests and other urban micro-habitats.

“This finding suggests that old growth forests may be an important part of an urban landscape,” Levine says, “not just because of the natural beauty of ancient trees, but because these habitats may also be a means of reducing transmission of some mosquito-borne diseases.”

Levine has since graduated from Emory's Laney Graduate School and now works as an epidemiologist and entomologist for the Centers for Disease Control and Prevention.

Uriel Kitron, chair of Emory’s Department of Environmental Sciences and an expert in mosquito-borne pathogens, is senior author of the paper.

Rebecca Levine in the field with one of the cardinals that was tested. The birds in the study were captured with mist nets and released unharmed after blood samples were drawn. (Photo courtesy of Rebecca Levine.)

West Nile virus (WNV) is zoonotic, meaning that it is an infection of animals that can spill over to humans by a bridge vector, in this case Culex mosquitos. Since its introduction to the United States in 1999, WNV has become the most common zoonotic mosquito-borne pathogen in the country, infecting an estimated 780,000 people (including more than 1,700 fatal cases), in addition to birds and other mammals, such as horses.

The Kitron lab wanted to find out why Georgia’s infection rate for WNV since 2001 is relatively low, at about 3.3 cases per 100,000 people, compared to some states in the north. A 2002 outbreak in Illinois, for instance, recorded about 7.1 cases per 100,000 people.

“When West Nile virus first arrived in the United States, we expected more transmission to humans in the South,” Kitron says, “because the South has a longer transmission season and the Culex mosquitos are common. But even though evidence shows high rates of the virus circulating in local bird populations, there is little West Nile virus in humans in Atlanta and the Southeast in general.”

During the three-year study, the research team collected mosquitoes and birds from different sites across Atlanta, tested them for WNV, and ran a DNA analysis of the mosquitos’ blood meals to see which species of birds they had bitten.

“We found that the mosquitoes feed on American robins a lot from May to mid-July,” Levine says. “But for some unknown reason, in mid-July, during the critical time when the West Nile virus infection rate in mosquitos starts going up, they switch to feeding primarily on cardinals.”

American robins do a great job of amplifying the virus in their blood once they are infected. That trait means they can more efficiently pass the virus to other mosquitos that bite them, so robins are known as “super spreaders.” The virus does not efficiently reproduce, however, in the blood of northern cardinals.

“You can think of the cardinals like a ‘sink,’ and West Nile virus like water draining out of that sink,” Levine says. “The cardinals are absorbing the transmission of the virus and not usually passing it on.”

The study results showed that, to a somewhat lesser extent, birds in the mimid family – including mockingbirds, brown thrashers and gray catbirds – also appear to be acting like sinks for WNV in Atlanta.

The researchers found significantly fewer avian WNV infections in the old growth forest sites sampled in Atlanta – including Fernbank Forest and Wesley Woods Preserve – compared to secondary forests such as Grant Park and the Atlanta Botanical Garden. The rate of infections in mosquitos, however, was similar for both types of forests.

“These are really complex ecosystems, so we cannot single out the specific reasons for these findings,” Levine says. “They suggest that there is something unique about these old growth forests and how they affect avian systems in Atlanta.”

Atlanta, nicknamed “City in the Forest,” is one of only seven U.S. cities with a high population density to have urban tree cover of 40 percent or more. In contrast, Chicago retains only 11 percent tree cover.

“As new mosquito-borne diseases enter and spread in America, we need to better understand all aspects of pathogen transmission cycles, said Stephen Higgs, present of the American Society of Tropical Medicine and Hygiene. “By shedding light on the reasons behind a curious discrepancy in West Nile virus human infection rates in different regions of the United States, this study has the potential to better protect Americans’ health while continuing to demonstrate the link between animal and human health.”

Co-authors of the paper also include researchers from the University of Georgia, Texas A&M and the Georgia Department of Transportation’s Office of Environmental Services.

Related:
Sewage raises West Nile virus risk
Why Zika risk is low for Olympic athletes in Rio

Dinosaur tracks lead paleontologist through museum to mentor's discovery

One of the ornithopod tracks from Skenes Creek (left), placed next to the Knowledge Creek one, showing how closely they match. Photo by Anthony Martin.

By Carol Clark

Paleontologists don’t always have to go into the field in search of fossils to identify. Sometimes they dig through the collections of museums.

That was the case for the latest paper by Emory paleontologist Anthony Martin, published in the journal Memoirs of Museum Victoria. Martin describes the first dinosaur tracks found in Victoria, Australia – way back in the 1980s – and explains their paleontological importance.

The three footprints, made by small ornithopods, were recovered in Lower Cretaceous strata of the Eumeralla Formation of Victoria, dating to about 105 million years ago. One of the tracks was found at Knowledge Creek in 1980 by paleontologists Thomas Rich and Patricia Vickers-Rich, a husband and wife team. The other two prints were spotted in 1989 at Skenes Creek by geologist Helmut Tracksdorf.

Martin’s study appears in a special volume honoring the career of Thomas Rich, a long-term mentor of Martin.

“The article documents a presence of small ornithopod dinosaurs in Victoria, matching a skeletal record,” Martin says. “It’s scientifically significant because these were polar dinosaur tracks and, unlike bones, they show exactly where those animals were living. Small dinosaurs were much less likely to migrate far, and these tracks suggest that they had adapted to year-round living in a polar environment.”

Victoria is famous for its polar dinosaur bones, which washed downstream during torrential spring flooding and were deposited on the banks of rivers, far from the sites where the animals actually lived and died, Martin explains.

Tracks, however, pinpoint where the dinosaurs actually set foot.

Martin is an expert in trace fossils, which include tracks, trails, burrows, cocoons and nests. In 2006, while looking for dinosaur tracks, he discovered the first trace fossil of a dinosaur burrow in Australia, at Knowledge Creek on the Victoria coast. In 2011, Martin, Rich and Vickers-Rich published their find of more than 20 polar dinosaur tracks at Victoria’s Milanesia Beach, the largest and best collection of polar dinosaur tracks ever found in the Southern Hemisphere.

The Victoria coast marks the seam where Australia was once joined to Antarctica. During that era, about 115 to 105 million years ago, the dinosaurs roamed in prolonged polar darkness. The Earth’s average air temperature was 68 degrees Fahrenheit – 10 degrees warmer than today – and the spring thaws would have caused torrential flooding in the river valleys.

The ornithopods (Greek for “bird feet”) had three toes. The ones that made the three tracks in Martin’s current study were bipedal grazers that stood about three feet tall.

While most dinosaur tracks are depressions, these three tracks are all raised. “Somehow, the tracks changed the character of the sediment, compacting the sand underneath them in a way that led to differential weathering,” Martin says.

The specimens are part of the collection of the Museum Victoria in Melbourne. “Museum collections serve an extremely important role by keeping specimens safe and giving scientists over generations a chance to study, and to re-study them,” Martin says. “As technology changes, who knows what new information we can get by re-examining old specimens?”

Related:
Polar dinosaur tracks open new trail to past
Dinosaur burrows yield clues to climate change 

Chasing fire: Fever and human mobility in an epidemic

Dengue fever is common in Iquitos, Peru, a densely packed city surrounded by the Amazon. With the imminent arrival of Zika virus to Iquitos, the researchers expect that the data they have collected on dengue transmission will also add to the understanding of how Zika spreads through a population.

By Carol Clark

Disease ecologists working in the Amazonian city of Iquitos, Peru, have quantified for the first time how a fever affects human mobility during the outbreak of a mosquito-borne illness. The findings were published by Proceedings of the Royal Society B.

“When you are sick with dengue, or another illness causing fever, your behavior can change,” says Gonzalo Vazquez-Prokopec, an assistant professor in Emory University’s Department of Environmental Sciences, and senior author of the study. “We’ve found that people with a fever visit 30 percent fewer locations on average than those who do not have a fever, and that they spend more time closer to home. It may sound like stating the obvious, but such data have practical applications to understand how human behavior shapes epidemics. No one had previously quantified how a symptom such as fever changes mobility patterns, individually and across a population, in a tropical urban setting like Iquitos.”

An issue in tracking an infectious disease like dengue, chikungunya and Zika is that most of the people infected are asymptomatic, or do not have symptoms severe enough to trigger a doctor visit. “They may not feel sick at all, and yet they could be infecting others, which could help explain how these pathogens move explosively across a population,” Vazquez-Prokopec says. “We need to rethink the way we do disease surveillance and control if asymptomatic people are important drivers of transmission.”

Trying to control the spread of a disease is like chasing a fire, he adds. “You know that a fire may be at the home of a sick person but, using the data we have for current models, you don’t really know where the fire is going next.”

About 550 people from Iquitos participated in the study. They included subjects who did not have a fever at the time of the study and those who did. The feverish subjects were also divided into those who tested posted for dengue and those who did not. Data on the movement of participants was collected through interviews and validated using wearable global positioning system loggers.

The study was part of a major research project in Iquitos, which began in 2008, to study the ecology of dengue fever. Dengue is spread by the Aedes aegypi mosquito, the same species that spreads the chikungunya and Zika viruses.

With the imminent arrival of Zika virus to Iquitos, the researchers expect that the data they have collected on dengue transmission will also add to the understanding of how Zika and chikungunya spread through a population.

During the first phase of the project, the researchers showed that human movement is a major driver of the spread of a vector-borne disease like dengue in an urban environment. They are now trying to learn more details about how symptoms and behavior are coupled to drive disease outbreaks.

Symptoms of people infected with a disease fall on a continuum, from no symptoms at all, to so severe they are hospitalized. For the current study, the researchers focused on the impacts of fever, since it is a classic marker of disease, and it is objective and easy to quantify.

The researchers are continuing to investigate how variation in symptoms of illness affects human mobility, using both objective and subjective signs, to refine the data and hone in on more detailed patterns of disease transmission.

“The more we learn about the role of human movement in the transmission of a mosquito-borne disease, the more we realize that we need to change the way we approach controlling these diseases,” Vazquez-Prokopec says.

The Iquitos project is supported by funding from the U.S. National Institutes of Health and the Department of Homeland Security. Co-authors of the study include researchers from the University of Notre Dame, the University of California, Davis, the National Institutes of Health, Tulane University, the Universidad Peruana Cayetano Heredia in Peru, Andrews University and San Diego State University.

Related:
Zeroing in on 'super spreaders' and other hidden patterns of epidemics
Human mobility data may help curb epidemics

Why Zika risk is low for Olympic athletes in Rio

An aerial view of Rio de Janeiro, host of the 2016 Summer Olympics. "August is the winter season in Rio, when mosquito populations are at their lowest," says Emory disease ecologist Uriel Kitron.

By Carol Clark

Some health professionals have lobbied to postpone the upcoming Rio de Janeiro Olympics due to the risk of the Zika virus, which is spread by mosquitos and – less commonly – through sexual intercourse. Other experts disagree that Zika poses a significant enough threat to warrant changing the venue or date of the games, set for August 5 to August 21.

“The risk of Zika infection in Rio during the Olympics is very low,” says Uriel Kitron, chair of Emory’s Department of Environmental Sciences and an expert on mosquito-borne diseases. “But if you are pregnant, or are thinking of getting pregnant right now as part of a couple, then you may want to consider even this low risk of transmission, given the potential serious complications.”

He refers travelers to the current advisory of the Centers for Disease Control and Prevention. The CDC advises women who are pregnant “to consider not going to the Olympics,” due to the link between Zika infections and severe birth defects. The CDC also recommends special precautions for men and women to practice safe sex following any possible exposure to the Zika virus.

When Zika popped up in Brazil last year, Kitron already had ongoing research projects in the country focused on how urban mosquitos spread the viruses of dengue and chikungunga. The population had no immunity to Zika and the virus swept like wildfire through the country. Kitron and his Brazilian colleagues quickly expanded their research to include cases of Zika, which can cause a rash and relatively mild illness, although most of those infected have no symptoms at all. It was not until months later that the more insidious effects of the Zika virus became apparent.

Kitron and his colleagues completed one of the first epidemiological studies, now out in Emerging Infectious Diseases, showing the strong link between the epidemic curve of the outbreak and a spike in cases of Guillain-Barré syndrome and babies born with smaller than normal heads, a condition known as microcephaly.

In the following interview, Kitron discusses some of what is now known about this emerging infectious disease and why mosquito surveillance and control is currently the key to containing its spread.

Why do you think the risk is low for Zika virus transmission during the Olympics?

For one thing, August is the winter season in Rio, when mosquito populations are at their lowest. And the areas where the athletes will be staying and competing are well-maintained, making Olympic visitors even less likely to encounter a mosquito.

The rates of Zika infection in Brazil have gone down drastically since last year, probably because the population now has herd immunity, so that further lowers the risk of transmission. Brazil is no longer the “hot spot” of the Zika pandemic. The horse has already left the barn as Zika has moved throughout Latin America and the Caribbean.

The U.S. territory of Puerto Rico, where an outbreak began more recently, currently has high rates of new Zika infections and summer is the high season for transmission.

The Nilton Santos stadium in Rio, one of several Olympic venues.

What is the risk of contracting Zika virus from a mosquito in the United States? 

Unless you are in the U.S. territories of American Samoa, Puerto Rico or the U.S. Virgin Islands, the risk is very low for most of the United States and will likely remain very low.

In the past, we have seen a few cases of locally transmitted dengue fever and chikungunya in South Texas and South Florida. The Aedes aegypti mosquito, the main vector of dengue, chikungunya and Zika, can be found in states bordering the Gulf of Mexico. The much more widespread Aedes albopictus, better known as the Asian tiger mosquito, has also shown that it can transmit these diseases, at least in a laboratory setting. Aedes albopictus, however, is not as effective as a vector.

We’ve greatly reduced the density of Aedes aegypti in most of the country. It feeds almost exclusively on humans, prefers a tropical climate and particularly thrives in dense neighborhoods with substandard housing. People in warmer areas of the United States generally have window screens and air-conditioning.

While we could see limited transmission of Zika virus from mosquitos in the Gulf states, it would be unlikely to develop into intensive transmission. We have relatively better methods of disease surveillance and mosquito control in the United States, which is one reason why we haven’t had a major outbreak of dengue fever. So far, we have been able to catch cases early and control the spread.

Is the Zika virus a disease of the poor? 

Mosquitos bite everybody so it’s not only the poor who are affected by diseases like dengue and Zika. But, of course, there are more mosquitos in poorer areas and less protection from them. So the poor are generally at much higher risk.

What are the prospects for effectively combating the Zika virus globally? 

I’m optimistic that we will have a vaccine for Zika within a few years because there is only one strain of the virus, unlike the dengue virus, which has many different strains.

People have proposed releasing genetically modified, sterile male Aedes aegypti mosquitos. The idea is they would compete with the wild sterile males to reduce populations of disease-carrying mosquitos. Genetically modified mosquitos might be one tool to fight mosquito-borne diseases, but I’m skeptical whether they would compete that well with other mosquitos in natural conditions. The jury is still out on that question.

For now, good mosquito surveillance and larvae control remain the keys to prevent and contain outbreaks. It’s generally much easier to control mosquitoes at the larval stage by eliminating breeding sites.

A study led by the Emory Vaccine Center recently found that people infected with dengue virus develop antibodies that cross-react with Zika virus. Can you talk about how that relates to your ongoing epidemiological research in Brazil? 

I’m part of a collaboration with Brazilian scientists focused in Salvador, the capital of the Brazilian state of Bahia in the northeast region of the country.

We are continuing to study the epidemiology and ecology of the Zika, chikungunya and dengue viruses. We’re particularly interested in the co-circulation of the three. What does it mean to have several arboviruses circulating among a population as far as the complications in humans? For instance, during the Zika outbreak last year in Bahia, we think there was more chikungunya circulating than was previously realized. And it’s possible that the spike in Guillian-Barré cases may be more related to chikungunya.

It’s important to gather data on the interactions of people, pathogens and disease vectors like mosquitos. Not only could it help us combat current outbreaks, the data may help us deal with the next emerging infectious disease.

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Human mobility data may help curb urban epidemics 

Is there a disease that makes us love cats?

Documented human cases of a disease called toxoplasmosis go back as far as ancient Egypt. The condition is caused by a parasite that can only reproduce in the intestines of cats. Today about one-third of the world’s population is infected with toxoplamosis, but most people who have it will never know it.

Emory evolutionary biologist Jaap de Roode, whose research focuses on the co-evolution of parasites and their hosts, worked with animators and writers at TED-ED to create the video lesson, above. Watch it to get a brief overview of what is known about toxoplasmosis, and some of the big questions that remain.

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Into the wilderness of Madagascar

Gabriel Andrle is a senior at Emory majoring in Environmental Sciences. He describes himself as “extremely passionate about learning and teaching others how humans can better share this planet with wildlife and with one another.”

He is also an excellent videographer.

Andrle is spending the summer in Madagascar, assisting with research into whether community conservation increases human and ecosystem health. The project is under the supervision of Sarah Zohdy, formerly a post-doctoral fellow in Emory’s Department of Environmental Sciences and currently an assistant professor of disease ecology at Auburn University.

Watch the video, above, that Andrle produced as he is exploring Madagascar with the research team. You will get a glimpse of why he is so passionate about protecting unique environments.

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Bridging ancient Tibetan medicine and modern Western science

Tawni Tidwell amid Tibetan prayer flags in eastern Tibet. Photo by Shane Witnov.

By Carol Clark

Tawni Tidwell is the first Westerner to be certified in Tibetan medicine by Tibetan teachers in the Tibetan language. The PhD candidate in Emory’s Department of Anthropology is now working on a dissertation about how Tibetan physicians diagnose diseases, especially cancer.

“I see myself as a bridge between Tibetan medicine and Western science,” says Tidwell, who became a Tibetan physician in 2015. “I feel like each has something to offer the other.”

Tidwell was born in Colorado but lived from the ages of two to five in South Korea, where her father was a U.S. Army surgeon. Tidwell and her mother lived in mainstream Seoul, which gave her an affinity for Asia when she returned to Colorado. She was also influenced by the Native American ancestry on both sides of her family and by the ecology of Colorado, where she became involved in rock climbing and winter mountaineering.

Tidwell has trained as an animal tracker, worked as a ranger at a biological preserve, taught wilderness survival lessons, and led gap-year students on trips to learn about traditional cultures through the “Where There Be Dragons” program.

Tidwell studied at the premier Tibetan medical school outside of Tibet, in northern India (the cultural and intellectual capital of the displaced Tibetan community). In order to enroll, she had to pass a five-day exam of memorized Tibetan grammar and Buddhist logic, as well as general Tibetan cultural knowledge. From there on, each year she had to recite from memory 115 pages of a medical textbook in Tibetan, considered one of the most difficult languages for non-native speakers to master. She also had to complete written exams, coursework and attend classes, all in the Tibetan language among Tibetan peers.

Below is an interview with Tidwell, covering some of the milestones of her long and winding road to becoming a certified Tibetan medical practitioner.

Where did you spend your undergraduate years? 

I went to Stanford, where I started out majoring in physics and pre-med, with the idea of a career focused on aerospace medicine, exploring questions like how the body adapts to space.

In physics, you take the extremes of a problem to understand how an average system operates. I thought if you studied how humans respond to extremes, then maybe you could find out more about how the human body works and responds to illness.

I was also really interested in the relationship between our bodies and the land. I eventually switched my major to Earth Systems. Stanford has a 2,000-acre biological preserve – ranging from redwoods to chaparral and perennial grasslands – where I worked as a docent and a ranger. I learned to identify dozens of different species of grass. I wanted to know why this grass species survives in the desert and another one doesn’t, and why the bobcat patrols this area and not another.

While ascending Illimani, a peak in western Bolivia, Tidwell pauses to take in the view.

When did you become interested in Tibetan culture?

I took a gap year after my freshman year and went to the Emory Tibetan Studies Program in north India, led by Tara Doyle (senior lecturer in Emory’s Department of Religion). I studied Buddhist philosophy and the Tibetan language, which is exquisite and poetic. The word for computer translates as “brain of light.”

The Tibetan language pays special attention to the sacred. It reminds you of the pursuit of understanding the reality we all experience and how one should live. It’s very specific about cognition and the mind and provides a much more detailed description of the trajectory of perception.

I feel different when I speak in Tibetan. People have told me that my whole body language changes.

Why did you enroll in an animal-tracking course?

I went to Washington, D.C., to work with an environmental organization. I realized that most of the environmental specialists in our nation’s capital had no time to spend in the natural world. They are completely disconnected from it. I wondered, what were humans like as foragers and what have we lost by being academic specialists without first-hand experience?

I went to New Jersey for a 10-day course taught by Tom Brown, Jr., an animal tracker and wilderness guru. He basically teaches what it takes to survive when you are butt naked in the woods and have nothing. In just the first class, you learn about wild edibles, how to make fire by friction, how to make two different traps and two different snares, and how to tan a hide. Other classes build on those basics.

What was your favorite part of your survivalist training?

Fire. There is something so enigmatic about making fire by friction. The experience ignites something deep in our past. It’s almost like creating life. You have to get a feel for the spindle and the fireboard. You apply just the right speed and pressure and when the fire comes out it’s like magic. And you realize that you can have a relationship to everything like that in the natural world.

After I finished the initial course, I realized it was really about putting in the experiential “dirt time’ to learn the skills. I took more courses and helped with teaching. I lived in the New Jersey pine barrens for about a year in a pit shelter, which was dug about four feet into the ground and was about 10 feet in diameter. It was full-on immersion in ecology.

I saw how some people’s lives changed as their wilderness survival skills accumulated. It gives you a certain freedom. People realize they don’t necessarily have to live in the way that they thought they had to live.

Tidwell with classmates, gathering native plants from the Tibetan plateau.

Do you ever get scared being alone in the wilderness? 

Scary movies make me scared, but not being alone in the forest. I imagine, though, that I would be scared in grizzly bear or polar bear territory, since they hunt humans.

Wolves don’t scare me because I read everything I could about the Arctic wolf when I was in elementary school – I was that kind of kid – and I knew they weren’t a threat to humans.

It’s actually part of Buddhist philosophy: The more you learn about the world, the more you learn about what you should, and should not, fear.

How did you wind up in Tibetan medical school?

In 2008, Tara Doyle asked me to return as assistant director of the Emory Tibetan Studies Program in north India.

While working in South America, I had met a curandero in Bolivia who told me that his grandmother had known more than 5,000 healing plants, he knew 2,000 and his daughter would know a few hundred or even fewer. I realized that Tibetan medicine is really unique in that it is this ancient medicinal system connected to the land – using medicines made from plants and minerals gathered from the Tibetan plateau, the highest place in the world – and it is also written down.

I thought that if I had a chance to study Tibetan medicine I could really do something with it. Dr. Khenrab Gyamtso, the vice principal of the Men-Tsee-Khang medical institute in north India, agreed to tutor me for a few hours at the end of every day, after he and I had already put in a full day of work. He eventually encouraged me to apply for enrollment.

What did your studies involve?

Medicinal herb from the Tibetan plateau

The first few years were mainly memorization of parts of the medical canon, more than 100 pages a year. And then at the end of every year you recite them. At first I didn’t value memorization but I eventually realized that it’s an amazing technology. It feels like a profound meditation. It’s clever in the sense that it forces you to focus while also giving your mind a break. The text is written poetically and you start noticing associations and layers of meaning. Layers of your mind also start emerging. It’s a fascinating thing to observe.

After five years of classes, I transferred to eastern Tibet’s Tibetan Medical College of Qinghai University in Xining, China. Under the mentorship of senior doctors, I was able to do patient rounds in the gastroenterology department of the hospital there. All that memorization prepared my mind to have a strong presence with each patient and really focus on what each one said to me.

What are some of the distinctive aspects of Tibetan medicine? 

Tibetan medicine co-evolved with Buddhism. Contemplative introspection into the mind is complemented by introspection into the body. For example, in the case of chronic pain, Tibetan medicine prescribes medication along with recommendations for diet and ways to reduce mental distress and suffering. Research has shown that some meditators can identify physical pain locales on their body but they don’t have the same mental response that a lot of other people have to it.

We’re one of the few species in the animal kingdom that can evoke stress just by thinking about a threat. What are the changes in the mind when you become afraid, jealous, angry or sad? These emotions create biological changes in the body. Tibetan medicine treats the mind and the body at the same time. If you have diabetes or hypertension, it can get worse if you are highly reactive to circumstances in your life. This phenomenon is related to a concept called rlung (pronounced loong). These are wind pathways in the body that the mind rides on, which in Western medicine is related to the neuroendocrine system.

Connecting the mind and body to treat patients is ancient practice in Tibetan medicine, but it has only started gaining importance in Western medicine in the past decade or so.

Do you think Tibetan medicine is superior to Western medicine?

No. I feel like there is a lot of learning to do on both sides. My dad is an orthopedic surgeon. There are some things that Western medicine does very well.

Modern Tibetan medical practitioners don’t do surgery but they may advocate it at times – historically, we performed minor procedures like cataract surgery. Our canon says that anything that benefits a person is Tibetan medicine. So if the results of an X-ray or blood test could give you valuable information about a patient, you would welcome that. It’s a realist perspective more than anything else. And I would also say that it’s more holistic.

Some people have such a suspicion of anything that’s not Western medicine, they just refuse to consider it. I find that non-scientific. The research done on other medical systems is so poor we can’t say that we know whether these things don’t work on some level. Westerners sometimes forget that a human connection is healing and we try to operationalize everything. We’re not allowed to have art in medicine, but sometimes that art is what makes it more effective.

All photos courtesy of Tawni Tidwell

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Chemists map cascade of reactions for producing atmosphere's 'detergent'

"Our detailed data proves a much sharper view of the actual dynamics of the troposphere," says theoretical chemist Joel Bowman. In this NASA photo of the space shuttle Endeavor, silhouetted against Earth's atmosphere, the troposphere is the orange layer. The white layer is the stratosphere and the blue is the mesosphere.

By Carol Clark

Chemists have identified a cascade of reactions for how mysterious molecules known as Criegee intermediates generate hydroxyl radicals – an oxidant that helps remove pollutants from the lower atmosphere.

Nature Chemistry is publishing the findings, a collaboration of Emory University and the University of Pennsylvania.

“We’ve solved another piece of the puzzle in the formation of hydroxyl radicals, by zooming in to see all the steps of the reaction in much finer detail than ever before,” says co-author Joel Bowman, a theoretical chemist at Emory. “This kind of detailed data is important to atmospheric chemists trying to make predictive models for how the atmosphere will respond to climate change.”

The Bowman group collaborated with the lab of experimental chemist Marsha Lester at the University of Pennsylvania.

The theoretical work revealed that a Criegee intermediate first produces highly energized vinyl hydroperoxide, or VHP, then rapidly decomposes to hydroxyl radicals, along with vinoxy byproducts.

In 2014, Lester’s lab was the first to observe the creation of a hydroxyl radical by a Criegee intermediate in a laboratory setting. Many questions remained about the process, however, since it occurs so rapidly in the lab, as well as in the troposphere.

The turbulent troposphere, the lowest layer of Earth’s atmosphere, is where the weather happens. It’s like a giant washing machine filled with molecules – hydrogen, oxygen and nitrogen and all the other chemical byproducts of plant, animal and human activity that float up and mix with solar energy.

Hydroxyl radicals are sometimes called the detergent in this mix because they are extremely reactive to many common pollutants and greenhouse gases. When a hydroxyl radical encounters a molecule of sulfur dioxide, for instance, it steals its electrons and oxidizes it. Both the hydroxyl radical and the sulfur dioxide vanish, turning into an innocuous aerosol.

The troposphere, the lowest layer of Earth's atmosphere, is where the weather happens.

Most hydroxyl radicals are produced during the daytime as sunlight breaks down ozone, releasing oxygen atoms that react with water vapor and become hydroxyl radicals. About a third of the troposphere’s hydroxyl radicals, however, are produced through a more mysterious process that can even occur at night.

German scientist Rudolf Criegee proposed a hypothesis in 1949 for this process. He predicted the existence of another radical, known as the Criegee intermediate, as a step in the chain of reactions needed to produce hydroxyl radicals from ozone, without daytime solar energy.

“Alkene ozonolysis is a fancy term to describe the process Criegee proposed,” Bowman says. “The Criegee intermediate, or carbonyl oxide, is one of the stepping stones in the process, but it has a lot of energy so it breaks up right after it forms. The Criegee intermediate was certainly possible – it followed the rules governing how bonds form and rearrange – but for decades it remained hypothetical.”

It was not until 2012 that researchers managed to create a Criegee intermediate in a laboratory setting. That discovery was followed by the Lester lab’s 2014 work: Actually tracking a Criegee intermediate through the reaction that results in a hydroxyl radical, using a technique known as infrared action spectroscopy.

For the current Nature Chemistry paper, the Lester lab teamed with the Bowman group to combine its experiments with theoretical modeling.

As theorists, the chemists in the Bowman group can slow down time, in a sense, to study and measure a reaction in more detail. “We have developed sophisticated algorithms and software codes that allow us to study chemical reactions at the ultimate level of detail,” Bowman says. “Running the calculations for a reaction that occurs in picoseconds requires days of computer time, and we have to run it over and over again. The result is a mind-boggling data set, made up of billions of pieces, that we then have to analyze.”

The theoretical results both extended the experimental work and were validated by them, giving an unprecedented insight into the multi-step cascade of reactions.

“What actually happens in the wild is so much more complicated than in a controlled laboratory setting,” Bowman says. “Our detailed data provides a much sharper view of the actual dynamics of the troposphere.”

Sophisticated experimental techniques, high-powered computers and powerful new algorithms are driving advances faster than ever before, he adds.

“A lot of science done prior to 50 years ago, before computers, involved brilliant people, like Rudolf Criegee, doing hypothetical work that they could not prove,” Bowman says. “They would be bowled over by our capability now to actually settle many of these questions.”

Additional authors on the paper include Emory chemist Xiaohong Wang and University of Pennsylvania chemists Nathanael Kidwell and Hongwei Li.

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Chemists modify rules for reaction rates 

Study on worm, mice fertility could lead to 'the pill' for men

Research led by biology professor Steven L'Hernault establishes a connection between fertilization in nematodes and mammals. (Emory Photo/Video)

By April Hunt

Someday, if women toast the discovery of male oral contraceptives, they may want to lift a glass to Emory biology professor Steven L'Hernault and his worms.

L'Hernault, chair of Emory College's Department of Biology, researched sperm proteins (not male hormones) in nematode worms. He and fellow researchers were able to establish a connection between fertilization in mammals, including humans, and nematodes. It was a highly unexpected outcome, given the two animal groups last shared a common ancestor about a billion years ago.

The conclusion, which some think could eventually lead to the equivalent of "the pill" for men, provides new insights on the basic mechanics of sperm and egg fertilization. It was recently reported in the journal Current Biology.

"At the end of the day, fertilization in humans seems to share some fundamental features with fertilization in worms," L'Hernault says. "Specifically, a similar protein is found on the sperm surface in humans and worms and, if a drug could be discovered that interfered with its function, we might be able to prevent sperm from fertilizing the egg.

"The worm may offer an inexpensive way to find such a drug," he adds. "Women have borne more than their fair share in that category of contraception, so the idea is to look at what might be possible for men."

In mammals, such as mice and humans, this protein is called Izumo, named for a shrine in Japan where newly married couples visit seeking luck in having children.

The Izumo equivalent in worms, named SPE-45, allows the sperm to be recognized by the egg, so that fertilization can occur. Without it, the sperm can move and do other processes normally, but they cannot fertilize the egg.

Worms with a mutation affecting SPE-45 are sterile. If you do "gene therapy" by expressing the worm SPE-45 protein in mutant worms, fertility is restored.

The challenge was to show that mammalian Izumo was functionally similar to SPE-45. L'Hernault says that he and his team of researchers worked for seven years, focusing on whether there was something specific that connected the two that allowed for fertilization.

Both SPE-45 and Izumo proteins have an Ig region that probably allows the sperm to adhere to the egg. Ig regions are widely found in many proteins of all animals, where they provide "stickiness" to proteins.

So, L'Hernault and his team took the Ig region from the mouse Izumo protein and used it to replace the Ig region in the worm SPE-45 protein, making a "hybrid" protein.

Surprisingly, this "hybrid" protein can be expressed in a worm SPE-45 mutant and it will partially restore fertility to the worm SPE-45 mutant.

In contrast, if the Ig domain from a worm skin protein is used to replace the Ig domain of the worm SPE-45 protein, this "hybrid" does not restore fertility.

In other words, not any Ig domain, with its associated "stickiness," will allow SPE-45 to fertilize an egg. It must be either the natural worm SPE-45 Ig domain or the Ig domain from a similar mammalian gene.

"One useful way to think about Ig domains is that they are all keys and, like real keys that look similar, some specifically open your house, while others only open your car," L'Hernault says. His research shows that the mouse Izumo and worm SPE-45 Ig domains are near-identical "keys."

All animals produce sperm that stick to and fertilize eggs from that species, but, generally, sperm from one animal cannot fertilize eggs from another species.

That means L'Hernault's work extends well beyond any potential connection to birth control and could provide more understanding on the basic underpinnings of fertility.

"Knowing how sperm stick to and fertilize eggs will provide key insights into what has changed and what has remained similar as animals have evolved," L'Hernault says.

 In addition to L'Hernault, the team and co-authors of the paper came from his lab and include Hitoshi Nishimura, Tatsuya Tajima, Heather Skye Comstra and Elizabeth J. Gleason.

Is your memory better than a chimpanzee's?

Slate ran an excerpt from the latest book by Emory primatologist Frans de Waal, "Are We Smart Enough to Know How Smart Animals Are?" De Waal describes how animals "keep surprising us" with their intelligence:

"There is the example of Ayumu, a young male chimpanzee at the Primate Research Institute of Kyoto University, in Japan. I watched Ayumu’s incredibly rapid decision-making on a touch screen the way I admire my students typing 10 times faster than me. In 2007, he managed to put human memory to shame by recalling a series of numbers from 1 through 9. He tapped them in the right order, even though the numbers appeared randomly on the screen and were quickly replaced by white squares. Having memorized the locations of all numbers, Ayumu touched the squares in the right order. Reducing the amount of time the numbers flashed on the screen didn’t bother him in the least, even though humans become less accurate the shorter the interval. Trying the task myself, I was unable to keep track of more than five numbers after staring at the screen for many seconds, while Ayumu did the same after having seen the numbers for just one-fifth of a second—literally the bat of an eye."

Read the full book excerpt at Slate.

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From the field to the Emory Herbarium: How knowledge of nature blooms

Graduate student Daniella Cicka, left, and senior Rina Lee, in the field in South Florida, collect a DNA sample from a plant species.

By Carol Clark

Adam Mackie will never look at a red maple the same way. “Native Americans made an infusion from the tree’s bark to treat gunshot wounds,” says Mackie, a senior majoring in biology. “It was also used to treat bug bites.”

Stachys floridana

Mackie is one of six Emory students who spent a recent alternative spring break in the field in rural South Florida. The students looked for plants used in indigenous medicine in the past, and collected specimens for the Emory Herbarium, under the guidance of medical ethnobotanist Cassandra Quave. They learned to identify endemic plant species in the wild, how to dig deep roots out of the thick mud of a marsh – even how to harvest and cook a swamp cabbage and make a mean guacamole.

"The best part was learning about plants from local people who knew how they were traditionally used," Mackie says.

Florida rancher Bob Brewer spent several days with the students in the field, introducing them to the gopher tortoise, a keystone species, and pointing out plants such as a thorny vine of smilax, which the locals call pipe briar.

We kept pulling and pulling on the stem," Mackie says, "and finally we got to this big tuber. He told us that old-timers used to hollow out these tubers to make pipes for smoking tobacco."

“Plants teach students to be more aware and appreciative of the natural world,” says Quave, a professor in Emory’s Center for the Study of Human Health and the School of Medicine’s Department of Dermatology. Quave’s lab researches how traditional uses of plants can inform modern medicine. Interviews with traditional healers in rural Italy, for instance, led to her recent discovery that the leaves of the European chestnut tree contain ingredients with the power to disarm dangerous staph bacteria without boosting its drug resistance.

HERBARIUM NEEDS YOUR GREEN TO GROW

The Emory Herbarium, founded in 1949 by members of the biology department, was closed for decades, and its collection of more than 20,000 specimens was kept in storage. The facility, which recently reopened in the Rollins Research Center, needs $10,000 to help restore and annotate some of its damaged specimens, including rare plants in the Granite Rock Outcrop Collection, which grow in the vernal pools of Arabia Mountain and Stone Mountain. The funds will also support digitizing the specimens so they can be posted online and accessed from around the globe. Check out the Herbarium’s Momentum fundraising campaign to learn how to contribute.

A graduate of Emory herself, Quave found her career path after she went into the Peruvian Amazon as part of a tropical ecology class in the department of environmental sciences.

“When I first get students in the field, they look at a meadow and just see what looks like overgrown grass. It’s like they have blinders on,” Quave says. “Then the blinders come off and they begin to use their ‘plant goggles.’ They start seeing the world in a new way.”

Jennifer Ko, a freshman, grew up in Manhattan and considered herself a city girl. That view was broadened somewhat, as she recounted in a blog post about the trip on the Center for Human Health web site. “I am no longer scared of laying down on the grass and, by the end of the trip, even embraced dirt,” she wrote.

Seniors Jessie Cai and Rina Lee prepare to press an epiphytic air plant from the Bromeliaceae family for deposit in the Emory Herbarium.

Ko also learned to spot and collect specimens such as the frilly white plume of Saururus cernuus (lizard’s tail), deep in a swamp.

“The Choctaw and Creek Indians called this plant ‘widow’s medicine’ because they used it in a tea to help the bereaved get over their loss,” Quave says. She pulls a thick book, “Florida Ethnobotany,” off a shelf in her office to show a picture of widow’s medicine and a flattened sprig of yellow flowers falls out from the pages. “Oh, that’s a neat little Hypericum I collected,” she says, using the Latin name for St. John’s wort.

Ladyfinger bananas

The students rose before dawn and worked 12-hour days while in Florida. They explored scrub pine forests filled with 150-year old trees, still bearing what old-timers call “cat-facing” marks:” V-shapes cut into the bark during the 1800s to harvest turpentine. They took an airboat ride up the Peace River – the habitat of roseate spoonbills, bald eagles, alligators and other wildlife. They squelched in rubber boots through the mucky soil of cypress swamps, in search of species such as the Salyx willow tree, the original source of aspirin.

The group stayed in Quave’s hometown of Arcadia, in the home of her father, Raymond, who runs a business as a heavy equipment operator. “We shopped at a produce stand and bought gorgeous avocados and flats of the freshest, local strawberries to take home and prepare,” Quave says.

Ko cited time spent preparing food as one of the trip highlights. “In my 18 years of life, I never learned to cook,” she wrote in her blog post. “When Dr. Quave watched me struggle even cutting a tomato, she taught me all I needed to know to make my portion of dinner: The guacamole. She taught me the importance of a healthy meal, which is something I never fully understood. During the trip, I was forced to opt for the healthier choices and loved almost every meal I ate.”

Exploring the Peace River by airboat, from left: Cassandra Quave, Jessie Cai, Adam Mackie, Rina Lee, Jennifer Ko and Justin Robeny.

Raymond Quave showed the students how to chop down a swamp cabbage palm and pull the heart of it, then taught them how to boil the heart for their dinner, seasoned with milk, bacon and salt and pepper.

“As an educator I see many extraordinarily bright and talented students who have few outdoor survival skills,” Quave says. “I want them to appreciate the importance of different plants, for the health and sustenance of humans as well as ecosystems.”

The students brought back more than 170 species to add to the Emory Herbarium, which they will also help preserve and annotate.

Capsella bursa-pastoris

“It was an amazing experience,” Mackie said of the Florida trip. “I had worked in the Herbarium and in Dr. Quave’s lab, but that isn’t the same as learning about plants in the field. Now I’m able to grind and preserve some of the dried plant materials that I collected myself.”

Quave, who serves as curator of the Herbarium, spearheaded efforts to reopen it in 2012, after decades of neglect. She recently launched a fundraising campaign to restore some of the specimens and keep the facility in operation (see box, above).

The Herbarium’s original collection manager, Madeline Burbanck, who researched the rare and endangered plants on Georgia granite outcrop ecosystems, played a pivotal role in the official designation of Arabia Mountain as a National Heritage Area.

Tharanga Samarakoon, a plant scientist from Sri Lanka, now serves as the Herbarium’s collections manager, overseeing student volunteers who are working at restoration and digitization efforts.

“The Herbarium is not just a musty room filled with dried plants,” Quave says. “It’s a window into the natural world and a valuable resource for research and education, across disciplines. We need to not only maintain natural habitats, but collect and preserve plant specimens over time, to better understand and monitor ecosystems.”

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