Friday, July 29, 2016

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?”

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

Tuesday, July 19, 2016

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.

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

Monday, July 18, 2016

Adding anthropology to genetics to study ancient DNA

Kendra Sirak, an Emory PhD candidate in anthropology, is working as a visiting researcher at the Earth Institute at University College Dublin.

By Leslie King
Emory Report

Kendra Sirak, a PhD candidate in anthropology in the Laney Graduate School, is currently working in Ireland, testing the DNA of people ranging from medieval Nubians to an ancient Chinese specimen to an Irish rebel.

Originally from the small town of Dallas, Pennsylvania, Sirak attended Northwestern University on an athletic scholarship for field hockey. "Starting out in psychology, I was inspired by an amazing young professor and became hooked after writing a research paper about the allegedly extinct subspecies Homo sapiens idaltu," Sirak recalls. "I wanted to study the past of humanity so I added anthropology for a double major."

Sirak came to Emory in 2012, drawn by the opportunity to work with George Armelagos, Goodrich C. White Professor of Anthropology (who passed away in 2014).

"I emailed George, who was one of the gods of anthropology, not expecting an answer," she says. "He responded in 37 minutes."

Now, Sirak is working as a visiting researcher at the Earth Institute at University College Dublin. Her research has also taken her to Russia, Hungary, Romania, China, India and Italy to access DNA in human skeletons and train other researchers in those techniques.

In an interview from Ireland, Sirak talks about her work and how she came to add genetics to anthropology, resulting in fascinating research and career paths.

What led you to add genetics to anthropology? 

I had no interest in genetics, being totally dedicated to the study of human osteology and paleopathology. But George [Armelagos] believed DNA was going to become a critical part of anthropological research — and he couldn’t have been more right.

He proposed that I take some Nubian skeletal remains he had excavated in the 1970s to Ireland and learn how to do ancient DNA analysis at Trinity College Dublin.

I went home and cried because I didn’t want to say no, but I really, really did not want to go. However, I decided to just go anyway. It was the best academic decision I could have ever made. I stepped into the ancient DNA lab at Trinity and realized that I had been spelling “chromosome” wrong for as long as I could remember, which was where my knowledge of DNA was then.

What do you gain by combining anthropology with genetics in your research?

Genetics provides really fantastic, concrete data. However, it doesn’t provide the context that anthropology does. I like to think of genetics giving me the hard scientific data that I want, but anthropology adding in the human context and making the molecular data a human reality.

At Emory, I have learned how to think from a “biocultural” point of view. While many other anthropology programs stress only either a “biological” or a “cultural” approach, Emory combines the two.

I study the biology of past populations and I think about the way their culture and social environment could have influenced individual health and well-being, population demographics, patterns of morbidity and mortality, etc.

What have you been working on in Ireland? 

Primarily extracting and sequencing DNA from skeletal remains from two socially disparate medieval cemeteries at the site of Kulubnarti in Sudanese Nubia. I am also part of a collaboration between University College Dublin and Harvard Medical School’s Department of Genetics lab.

We were recently contacted by the Irish National Police to help identify the remains of Thomas Kent, executed by the British for his part in the Easter Rising insurrection in 1916 and buried in a shallow grave on the grounds of Cork Prison; however, his body could not be positively identified. Collaborating with another team, we came up with this novel method to compare genetic data collected from two of Kent’s known living relatives and confirm his identity. He was given an honorable burial and a big state parade.

What other projects do you have in the works? 

We hope to become involved in the Duffy’s Cut Project. Duffy’s Cut is the location of railroad tracks west of Philadelphia built by 57 Irish immigrants in the mid-1800s. All 57 are thought to have died from cholera. However, forensic evidence suggests that some might have been murdered, perhaps because of fear of contagion. We are hoping a DNA analysis on these samples will help identify these men and their family relationships.

We are in conversation with an Irish human rights group about identifying the remains of more than 800 Irish babies uncovered in a mass grave in western Ireland. This grave was a consequence of the period when it was not socially acceptable for a woman to have a baby out of wedlock. The ultimate goal would be a database of the unidentified infants’ genetic information. Then people who believe they might have some relative in this mass grave could be tested for a genetic match. This project was presented at the United Nations.

What are your post-Emory plans and goals?

My goal is to start writing my dissertation, a bioethnography of the ancient Nubians, this fall and be graduated from Emory in June 2018. Post-Emory, I can see myself applying for a postdoc position to expand my research, or I might like to get involved with scientific communication to the lay public. After taking a human genetics course taken at Emory, I’m really interested in genetic counseling. I’ve been thinking about becoming a certified genetic counselor.

What do you like to do in your “off” time? 

I am a world traveler, marathon runner and craft beer connoisseur. Studying anthropology and working in ancient DNA has given me incredible opportunities to travel around the world to collect samples for our analyses.

Bone to be wild: Every skeleton has a story to tell

Friday, July 8, 2016

Kenya and 'the double life of kale'

Kale’s discovery by affluent consumers in the United States is an example of how much high-income societies can learn from the dietary habits of the poor, says Emory anthropologist Peter Little.

Emory anthropologist Peter Little wrote an article for Sapiens about how the trendy American health food of kale is similar to a variety with humble origins in Africa, where the poor depend on the leafy green vegetable as a staple. Below is an excerpt:

"Nutritional and health benefits aside, kale’s recent popularity and the premium prices kale-based products command in the United States might seem comical, if not downright ridiculous, to many East Africans. In Kenya and Tanzania, kale is a key staple in highland farming communities, where it is referred to as sukuma wiki, which in Swahili means “to push the week.” (East African kale is slightly different from the varieties that are grown and eaten in the U.S., but still very similar.) Eaten with a thick, maize-based porridge called ugali, kale is what allows many East African families to get through the week, often with little more than a sprinkling of tomato, onion, or, in better-off families, a few pieces of meat mixed in. When an individual is invited to eat with a rural Kenyan family, as I have been on many occasions over the past 30-plus years, it is almost certain that at least one of the dishes will be sukuma wiki. Indeed, the poorer the family is, the more likely kale, along with ugali, will be the main part of the meal."

Read the whole article in Sapiens.

What we can learn from African pastoralists

Tuesday, July 5, 2016

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.

Zika virus 'a game-changer' for mosquito-borne diseases
Human mobility data may help curb urban epidemics 

Friday, July 1, 2016

Risk calculator for psychosis gives clinicians a valuable new tool

"Our consortium is the first to develop a health risk calculator for psychosis based on a large sample," says Emory psychologist Elaine Walker.

By Carol Clark

A national consortium of researchers has developed an individual risk calculator for schizophrenia and other psychosis, comparable to those for cardiovascular disease and other illnesses.

The free, online tool – for use by qualified clinicians and researchers – is based on a study of hundreds of clinical high-risk participants in the North American Prodrome Longitudinal Study (NAPLS). The American Journal of Psychiatry published the findings by NAPLS, a National Institutes of Mental Health consortium comprised of nine research sites, including Emory University.

“Risk calculators for estimating risk of heart attack, stroke and other illnesses are already used by medical researchers and practitioners,” says Emory psychologist Elaine Walker. “Our consortium is the first to develop a health risk calculator for psychosis based on a large sample. It’s another step in the direction of taking mental disorders into the same realm as other kinds of illnesses, to help reduce the stigma and enhance our ability to treat people.”

Walker, the principle investigator for the Emory University site of NAPLS, specializes in the role of stress and stress neurobiology in the development of psychosis.

“The risk calculator runs on data derived in a clinical setting,” Walker says. “Gathering that information requires that an individual undergo diagnostic testing and an interview by a qualified professional, so the calculator is not something that a lay person could use.”

Epidemiological studies have shown that about 20 to 35 percent of teenagers and young adults who meet criteria for a high-risk syndrome convert to psychosis within two years. The NAPLS researchers wanted to create a practical tool for personalized risk prediction for individual patients.

They generated the risk calculator from the NAPLS phase two cohort data, which included 596 subjects who were diagnosed with Attenuated Psychosis Syndrome. That means they had experienced some recent changes in perception and/or developed unusual thoughts but did not meet the definition of psychosis.

The researchers followed up with the subjects two years later and found that 16 percent had developed psychosis. The ones at the greatest risk were those individuals who were younger when their initial symptoms began, had higher levels of unusual thoughts and suspiciousness, greater declines in social functioning, lower verbal learning skills and slower speeds of mental processing.

The risk calculator determines an individual’s level of risk based on these five factors, together with a family history of schizophrenia and whether they have experienced stressful or traumatic life events.

Clinicians can determine numerical ratings of these variables through diagnosis based on the Structured Interview for Psychosis Risk Syndromes (SIPS). They can then plug these values into the risk calculator tool to determine an individual patient’s risk.

“The risk calculator is extremely user friendly for mental health researchers and clinicians,” Walker says. “It’s a big step forward in the development of more systematic approaches for estimating risk for psychosis and will help medical practitioners and researchers focus their attention on individuals at greatest risk and monitor them more closely.”

Ultimately, the risk calculator may be used to weigh the cost-benefit ratios of treating patients with medication that has side effects or having them undergo time-consuming psychotherapeutic interventions.

Phase three of NAPLS is looking at the possibility of adding a biological component to the risk calculator, such as blood analyses and brain scans.

NAPLS is the largest, most comprehensive study ever funded by the NIMH of adolescents and young adults at risk for developing a psychotic disorder. The goal of the $25 million project is to identify more precise predictors for psychosis, along with a better understanding of the neural mechanisms involved. In addition to Emory, the NAPLS consortium includes: Harvard, Yale, UCLA, UC San Diego, Einstein Medical College and the University of Calgary.

Study of psychosis risk and brain to track use of Omega-3 pills