Thursday, September 22, 2022

Decoding canine cognition: How dogs' minds process visual imagery

To create the video for the experiments, the researchers attached a video recorder to a selfie stick that allowed them to shoot footage from a dog's perspective.

Scientists have decoded visual images from a dog's brain, offering a first look at how the canine mind reconstructs what it sees. 

The Journal of Visualized Research published the research done at Emory University. The results suggest that dogs are more attuned to actions in their environment rather than who or what is doing the action. 

"We showed that we can monitor the activity in a dog's brain and, to at least a limited degree, reconstruct what it is looking at," says Gregory Berns, Emory professor of psychology and corresponding author of the paper. "The fact that we are able to do that is remarkable." 

Read more here. 

Related: 

Dogs process numerical quantities in similar brain regions as humans

Scientists chase mystery of how dogs process words 

Tuesday, September 13, 2022

Science and creativity combine to imagine a city where everyone thrives

"I never imagined that I'd be co-teaching with a comedian," says Emory biologist Micaela Martinez, "but it's awesome working with David." Photo by Kay Hinton.

A scientist and a comedian walk into a classroom. They start a discussion about how art can influence social justice. 

You’ll have to wait for the punchlines. Emory first-year students will create them as part of a new fall seminar “Human Flourishing: Imagine a Just City.” 

“Humans cannot flourish without true justice,” says Micaela Martinez, Emory assistant professor of biology, who developed the class. “We have so many huge societal problems that need creativity, imagination, hope and optimism to solve.” 

The class is among the new First-Year Flourishing Seminars, aimed at deepening what students know but also who they aspire to be. It is also part of the Emory Arts and Social Justice Fellows program, which pairs Emory faculty with Atlanta artists to explore how creative thinking and artistic expression can inspire change. 

Martinez is co-teaching with Arts and Social Justice Fellow David Perdue, a comedian. 

“You can’t save the world with jokes,” Perdue says. “But humor can be a good way to raise awareness of what’s going on. It’s a first step.” 

Read the whole story.

Friday, September 9, 2022

Physicist seeks ultimate formula for fun

Justin and Afeira Burton encase their son Jonah in a giant bubble while their dog Boba Fetch looks on.

By day, Justin Burton is an Emory associate professor of physics, conducing high-level research on fluid dynamics and granular materials. Evenings and weekends, however, he turns into a comic-book version of a scientist. Not a mad scientist, tough. More like a glad scientist.

Read more about his alter ego, Dr. Bubbles, here.

Related:

The physics of giant bubbles

Tuesday, August 23, 2022

Chronic COVID infections source of variants of concern, study shows

An electron microscopic image shows an isolate from the first U.S. case of COVID-19, caused by SARS-CoV-2. The virus has since evolved into five variants of concern.  "If we want to stay a step ahead of this virus, we need to be more actively identifying and surveilling people with chronic infections," says Emory graduate Mahan Ghafari, first author of a new study on how the virus evolves. (CDC)

By Carol Clark

The coronavirus variants of concern are emerging from chronic, long-term COVID infections in people who may be immune comprised and unable to clear the virus, a new study strongly suggests. Frontiers in Virology published the findings by scientists at Emory University and the University of Oxford. 

“Rather than evolving from transmission chains of acute COVID infections in hundreds of millions of people, our results show that the variants of concern come from rare cases when someone may have an active infection for months,” says Daniel Weissman, a corresponding author and Emory professor of biology and physics focused on quantitative evolutionary theory. 

“A key take-home message is that it is important to find these individuals who are chronically infected and provide support for them to recover,” adds Mahan Ghafari, first author of the paper and a postdoctoral researcher at the University of Oxford. “In many cases they may be asymptomatic and not even realize that they are infected with COVID although they are actively shedding the virus.” 

Ghafari graduated from Emory in 2018 with a masters in physics. 

Additional authors of the paper include Aris Katzourakis, a professor of evolution and genomics at the University of Oxford; Qihan Liu, an Emory graduate student in physics; and Emory undergraduate Arushi Dhillon. 

Random mutations

Viruses like SARS-CoV-2 continuously evolve due to occasional mutations in the genetic code that may occur when they replicate. “When a virus copies itself, it doesn’t always make perfect copies,” Weissman explains. 

Usually, such random mutations do not benefit the virus or raise the concerns of scientists monitoring these changes. Occasionally, however, the mutations result in a variant of the virus that may make it more transmissible, more difficult to detect and treat, and even more lethal. 

The World Health Organization defines a SARS-CoV-2 variant of concern as one that is more likely to cause infections even in those who are vaccinated or in those who were previously infected. 

“During the first few months of the pandemic, it didn’t look like the coronavirus was going to adapt into a variant of concern,” Weissman says. “But then, boom, boom, boom! Not only did the coronavirus evolve into VOCs, it did it three times in quick succession in late 2020.” 

The WHO dubbed these first three variants of concern alpha, beta and gamma. 

Mysteries surrounding VOCs

Why had all three of these VOCs emerged at roughly the same time and apparently in three far-flung areas of the world? 

Another mystery was why large clusters of mutations occurred in the VOCs. “A key element that distinguished these VOCs from other lineages of virus that were circulating is that each of them has a vastly elevated number of mutations,” Ghafari notes. “That’s a major distinction point in evolutionary terms.” 

At least some of the mutations from the VOC had been detected in chronic cases of COVID, leading to the hypothesis that these long-term cases may be the source of the VOCs. The other main theory was that VOCs were emerging from sustained transmission of acute infections in areas of the world with poor genomic surveillance of the virus. 

Ghafari, Weissman and their collaborators were among the first teams to methodically test these theories surrounding the emergence of the alpha, beta and gamma VOCs. 

The researchers built a mechanistic, theoretical model to study the problem, using existing data and software they developed. 

The resulting model rules out the theory that the VOCs emerged from sustained transmission of acute infections and fully supports the theory that each variant evolved within a single individual with a chronic infection. 

The model shows how multiple mutations were needed, each of which may have been either neutral or slightly advantageous to viral fitness. In this way, a variant eventually acquires a constellation of mutations that allow it to become more transmissible. 

Model explains delta and omicron emergence

Although the current paper drew from data for the alpha, beta and gamma variants, the resulting theoretical model also explains the later independent emergence of the delta and omicron VOCs. Delta emerged in India in late 2020, rapidly sweeping through that country and spreading around the world. Delta subsided after omicron, which is not a descendent of the delta variant, emerged in South Africa in late 2021. Omicron quickly became the dominant global VOC. 

The researchers have made their model and software publicly available for others to study the evolution of SARS-CoV-2 variants. 

“Ideally, we’d like to eventually be able to quantify the timing at which new variants might emerge in the future,” Weissman says. “That has huge implications from a public health perspective.” 

Studies have shown that some immune-compromised people, such as those taking medication for other chronic disorders, have carried active COVID infections for a year or even longer. It’s critical to identify these people, the researchers stress, not only to help them get treated for COVID, but also to conduct genomic surveillance of the SARS-CoV-2 viruses that they carry. 

“Who knows what variant could be boiling up next from a chronically infected individual?” Ghafari says. “Our study shows that from an evolutionary point of view, we can expect something completely different from the previous VOCs. If we want to stay a step ahead of this virus, we need to be more actively identifying and surveilling people with chronic infections.” 

The work was funded by the National Science Foundation, the Simons Foundation, the Sloan Foundation, the Biotechnology and Biological Science Research Council and the European Research Council. 

Related:

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

Emory physicist Daniel Weissman awarded 2021 Sloan Research Fellowship

Thursday, August 11, 2022

Testosterone promotes 'cuddling,' not just aggression, animal study finds

The research used the experimental model of Mongolian gerbils, rodents that form lasting pair bonds and raise their pups together. In addition to demonstrating testosterone's effects on prosocial behavior, the work also revealed how testosterone influences the neural activity of oxytocin cells — the so-called "love hormone" associated with social bonding. (Photo by Aubrey Kelly)

By Carol Clark

Testosterone can foster friendly, prosocial behavior in males, a new animal study finds. The Proceedings of the Royal Society B published the research on Mongolian gerbils conducted by neuroscientists at Emory University. 

“For what we believe is the first time, we’ve demonstrated that testosterone can directly promote nonsexual, prosocial behavior, in addition to aggression, in the same individual,” says Aubrey Kelly, Emory assistant professor of psychology and first author of the study. “It’s surprising because normally we think of testosterone as increasing sexual behaviors and aggression. But we’ve shown that it can have more nuanced effects, depending on the social context.”

The work also revealed how testosterone influences the neural activity of oxytocin cells — the so-called “love hormone” associated with social bonding. 

Richmond Thompson, a neuroscientist at Oxford College of Emory University, is co-author of the study. 

Kelly’s lab has recently focused on the neural effects of oxytocin using rodent experimental models. Thompson’s lab investigates the neural effects of steroids in fish. Both scientists are trying to get at the question of how hormones work in the brain to allow an animal to rapidly change its behavior, depending on the social context. 

In addition to sharing this research interest, Kelly and Thompson share a home as a married couple.

“The idea for this paper was borne out of us talking together over a glass of wine,” Kelly says. “It blends our two research worlds.” 

Testing new questions 

The majority of human studies show that testosterone enhances aggressive behavior. Kelly and Thompson wondered if maybe testosterone might, in lockstep with being able to increase aggression toward intruders, also generally dampen prosocial behaviors. However, they also hypothesized that it might do something more radical — actually enhance positive social responses in contexts in which acting prosocially is appropriate. 

To test this question, the Kelly lab conducted experiments on Mongolian gerbils, rodents that form lasting pair bonds and raise their pups together. While males can become aggressive during mating and in defense of their territory, they also exhibit cuddling behavior after a female becomes pregnant, and they demonstrate protective behavior toward their pups. 

In one experiment, a male gerbil was introduced to a female gerbil. After they formed a pair bond and the female became pregnant, the males displayed the usual cuddling behaviors toward their partners. The researchers then gave the male subjects an injection of testosterone. They expected that the resulting acute rise in a male’s testosterone level would lessen his cuddling behaviors if testosterone generally acts as an antisocial molecule. 

“Instead, we were surprised that a male gerbil became even more cuddly and prosocial with his partner,” Kelly says. “He became like ‘super partner.’” 

Switching contexts 

In a follow-up experiment a week later, the researchers conducted a resident-intruder test. The females were removed from the cages so that each male gerbil that had previously received a testosterone injection was alone in his home cage. An unknown male was then introduced into the cage. 

“Normally, a male would chase another male that came into its cage, or try to avoid it,” Kelly says. “Instead, the resident males that had previously been injected with testosterone were more friendly to the intruder.” 

The friendly behavior abruptly changed, however, when the original male subjects were given another injection of testosterone. They then began exhibiting normal chasing and/or avoidance behaviors with the intruder. “It was like they suddenly woke up and realized they weren’t supposed to be friendly in that context,” Kelly says. 

The researchers theorize that because the male subjects experienced a surge in testosterone while they were with their partners, it not only rapidly increased positive social responses toward them but also primed the males to act more prosocially in the future, even when the context changed and they were in the presence of another male. However, the second testosterone injection then rapidly prompted them to switch their behavior to become more aggressive, as appropriate to the context of a male intruder. 

“It appears that testosterone enhances context-appropriate behavior,” Kelly says. “It seems to play a role in amplifying the tendency to be cuddly and protective or aggressive.” 

The laboratory experiments, in a sense, slowed down what the males might experience almost simultaneously in the wild. In their natural habitat, Kelly explains, mating with a partner elevates testosterone, which primes them to act cuddly in the moment and in the near future while living with their partner, even if the testosterone levels decline. If a rival entered its burrow the gerbil would likely experience another surge of testosterone that would immediately help adjust his behavior so he can fend off the rival and protect his pups. Testosterone, then appears to help animals rapidly pivot between pro- and antisocial responses as the social world changes. 

‘A complicated dashboard’ 

The current study also looked at how testosterone and oxytocin interact biologically. The results showed that the male subjects receiving injections of testosterone exhibited more oxytocin activity in their brains during interactions with a partner compared to males that did not receive the injections. 

“We know that systems of oxytocin and testosterone overlap in the brain but we don’t really understand why,” Kelly says. “Taken together, our results suggest that one of the reasons for this overlap may be so they can work together to promote prosocial behavior.” 

Rather than just flipping an “on” or “off” button to modulate behaviors, hormones seem to play a more nuanced role, Kelly says. “It‘s like a complicated dashboard where one dial may need to move up a bit while another one moves down.” 

Human behaviors are far more complex than those of Mongolian gerbils, but the researchers hope that their findings provide a basis for complementary studies in other species, including humans. 

“Our hormones are the same, and the parts of the brain they act upon are even the same,” Thompson says. “So, learning how hormones like testosterone help other animals adjust to rapidly changing social contexts will not only help us understand the biological nuts and bolts that affect their behavior, but also predict and ultimately understand how the same molecules in human brains help shape our own responses to the social world around us.” 

Jose Gonzalez Abreu, a former research specialist in the Kelly lab, is a co-author of the study. The work was supported by the National Science Foundation. 

Related:

Study shows how a single gene drives aggression in wild songbirds

Athletes' testosterone surges not tied to winning, study finds

 

Monday, July 11, 2022

Chemists crack complete quantum nature of water

"Now that we have a good template for understanding how water molecules interact among themselves, we have a basis to deepen our understanding of the role of water in biochemical processes essential to life," says Joel Bowman,  Emory professor of theoretical chemistry.


Chemists have produced the first full quantum mechanical model of water — one of the key ingredients of life. The Journal of Physical Chemistry Letters published the breakthrough, which used machine learning to develop a model that gives a detailed, accurate description for how large groups of water molecules interact with one another. 

“We believe we have found the missing piece to a complete, microscopic understanding of water,” says Joel Bowman, professor of theoretical chemistry at Emory University and senior author of the study. “It appears that we now have all that we need to know to describe water molecules under any conditions, including ice, liquid or vapor over a range of temperature and pressure.” 

The researchers developed free, open-source software for the model, which they dubbed “q-AQUA.” The q-AQUA software provides a universal tool for studying water. 

“We anticipate researchers using it for everything from predicting whether an exoplanet may have water to deepening our understanding of the role of water in cellular function,” Bowman says. 

Read more about the discovery here

Related:

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

Joel Bowman's view from the top of theoretical chemistry

Behaviors of tiniest water droplets revealed

Soil quality critical to help some U.S. crops weather heat stress from climate change

"Keeping soil healthy is a key component needed to adapt to the climate crisis," says Debjani Sihi, assistant professor in Emory's Department of Environmental Sciences.

By Carol Clark

The capacity of soil to hold water will be critical to determine how well farms in some regions of the United States manage the problem of prolonged heat stress due to climate change, a new study suggests. The journal Frontiers in Sustainable Food Systems published the finding, based on analyses of 30 years of data on four major U.S. crops — corn, soybeans, cotton and wheat. 

“At the same time that farmers are facing more extreme weather events caused by climate change they are dealing with the growing problem of soil degradation,” says Debjani Sihi, first author of the study and assistant professor in Emory University’s Department of Environmental Sciences

Sihi is a biogeochemist who studies environmental and sustainability issues at the nexus of soil, climate, health and policy. 

Globally, according to Sihi and her co-authors, 750 million people were undernourished in 2019 due to the effects of climate change, including a decline in food production, hikes in food prices and increased competition for land and water. And the problem of global food security is expected to intensify. World crop yields are projected to decrease by 25% overall within the next 25 years due to climate change, and yet global food production would need to double by 2050 to feed the projected growth in human population. 

How soil impacts climate 

“Keeping soil healthy is a key component needed to adapt to the climate crisis,” Sihi says. Healthy soil contains microbes that provide the nutrients needed for healthy plants to grow, she explains, while also helping make the plant foods that we eat more nutritious. 

The presence of these microbes also improves the ability of soil to sequester carbon. The top 30 centimeters of the world’s soil contains about twice as much carbon as the entire atmosphere, making soil the second-largest natural carbon sink after oceans, according to the United Nations’ Food and Agriculture Organization. 

The rise in average temperatures, however, is contributing to declines in soil moisture in some areas, which can impact crop production while also degrading the soil over the long term. 

For the current paper, the researchers sought to quantify the long-term impact of climate and soil properties on yields of corn, soybeans, cotton and wheat across the mainland United States. They drew on county-level data of the U.S. Department of Agriculture from 1981 to 2015. Their dataset contained precipitation rates and accumulation of average daily temperatures over a crop’s growing season, known as growing-degree days. The data also factored in soil variations, including water-holding capacity, organic matter texture (the percentage of sand, silt and clay), pH, slope, erodibility and soil-loss tolerance. 

How farmers can adapt 

The researchers used an explainable machine-learning approach to evaluate the impact on crop yields of each of these climate and soil variables. The results singled out growing-degree days as the most important climatic factor and water holding capacity as the most influential soil property for crop-yield variability. 

“The take-home message,” Sihi says, “is that farmers in regions facing added heat stress for their crops may want to proactively focus on the water-holding capacity of their soil.” 

Clay soil and soil rich in organic material holds water better than sandy soil, she explains. So farms with sandy soil, or with soils containing less organic material, may want to add more amendments to improve the water-holding capacity of the land. Another possible adaptation is to use more mulch to reduce evaporation. 

The researchers hope that their findings will help farmers, land-management specialists and policy makers in decision-making related to sustainable and long-term soil-, water- and crop- management practices. 

Co-authors of the study include Kanad Basu and Abraham Peedikayil Kuruvila from the University of Texas at Dallas; Biswanath Dari from North Carolina Agricultural and Technical State University and Gaurav Jha from Montana State University. 

Funding for the work was provided by Emory University, North Carolina Agricultural and Technical State University and Montana State University. 

Related:

Climate change on course to hit U.S. corn belt especially hard 

Paint color-matcher quantifies iron levels in soil

Diverse landcover boosts yields for major U.S. crops, study finds

Tuesday, May 24, 2022

Climate change on course to hit U.S. Corn Belt especially hard, study finds

"It's important to begin thinking about how to transition out of our current damaging monoculture paradigm toward systems that are environmentally sustainable, economically viable for farmers and climate-smart," says Emily Burchfield, assistant professor in Emory's Department of Environmental Sciences.

By Carol Clark

Climate change will make the U.S. Corn Belt unsuitable for cultivating corn by 2100 without major technological advances in agricultural practices, an Emory University study finds. 

Environmental Research Letters published the research, which adds to the evidence that significant agricultural adaptation will be necessary and inevitable in the Central and Eastern United States. It is critical that this adaptation includes diversification beyond the major commodity crops that now make up the bulk of U.S. agriculture, says Emily Burchfield, author of the study and assistant professor in Emory’s Department of Environmental Sciences. 

“Climate change is happening, and it will continue to shift U.S. cultivation geographies strongly north,” Burchfield says. “It’s not enough to simply depend on technological innovations to save the day. Now is the time to envision big shifts in what and how we grow our food to create more sustainable and resilient forms of agriculture.” 

Burchfield’s research combines spatial-temporal social and environmental data to understand the future of food security in the United States, including the consequences of a changing climate. 

More than two-thirds of the land in the U.S. mainland is currently devoted to growing food, fuel or fiber. And about 80 percent of these agricultural lands are cultivated with just five commodity crops: Corn, soy, wheat, hay and alfalfa. Previous research based on biophysical data has established that climate change will adversely affect the yields of these crops. 

Building predictive models

For the current paper, Burchfield wanted to investigate the potential impacts of climate change on cultivation geographies. She focused on the six major U.S. crops that cover 80 percent of cultivated land in the United States: Alfalfa, corn, cotton, hay, soy and wheat. She drew from historical land-use data classifying where these crops are grown and publicly available data from the U.S. Department of Agriculture, the U.S. Geographical Survey, the WorldClim Project, the Harmonized World Soil Database and other public sources. 

Using these data, she built models to predict where each crop has been grown during the 20 years spanning 2008 to 2019. She first ran models using only climate and soil data. These models accurately predicted — by between 85 and 95 percent — of where these major crops are currently cultivated. 

Burchfield ran a second set of models that incorporated indicators of human interventions — such as input use and crop insurance — that alter biophysical conditions to support cultivation. These models performed even better and highlighted the ways in which agricultural interventions expand and amplify the cultivation geographies supported only by climate and soil. 

Burchfield then used these historical models to project biophysically driven shifts in cultivation to 2100 under low-, moderate- and high-emission scenarios. The results suggest that even under moderate-emission scenarios, the cultivation geographies of corn, soy, alfalfa and wheat will all shift strongly north, with the Corn Belt of the upper Midwest becoming unsuitable to the cultivation of corn by 2100. More severe emissions scenarios exacerbate these changes. 

“These projections may be pessimistic because they don’t account for all of the ways that technology may help farmers adapt and rise to the challenge,” Burchfield concedes. She notes that heavy investment is already going into studying the genetic modification of corn and soy plants to help them adapt to climate change. 

“But relying on technology alone is a really risky way to approach the problem,” Burchfield adds. “If we continue to push against biophysical realities, we will eventually reach ecological collapse.” 

The need for diverse landscapes

She stresses the need for U.S. agricultural systems to diversify beyond the major commodity crops, most of which are processed into animal feed. 

“One of the basic laws of ecology is that more diverse ecosystems are more resilient,” Burchfield says. “A landscape covered with a single plant is a fragile, brittle landscape. And there is also growing evidence that more diverse agricultural landscapes are more productive.” 

U.S. agricultural systems incentivize “monoculture farming” of a handful of commodity crops, largely through crop insurance and government subsidies. These systems take an enormous toll on the environment, Burchfield says, while also supporting a meat-heavy U.S. diet that is not conducive to human health. 

“We need to switch from incentivizing intensive cultivation of five or six crops to supporting farmers’ ability to experiment and adopt the crops that work best in their particular landscape,” she says. “It’s important to begin thinking about how to transition out of our current damaging monoculture paradigm toward systems that are environmentally sustainable, economically viable for farmers and climate-smart.” 

Burchfield plans to expand the modeling in the current paper by integrating interviews with agricultural policy experts, agricultural extension agents and famers. “I’d especially like to better understand what a diverse range of farmers in different parts of the country envision for their operations over the long term, and any obstacles that they feel are preventing them from getting there,” she says. 

Related:

Data-driven study digs into the state of U.S. farm livelihoods

Diverse landcover boosts yields for major U.S. crops, study finds 

Monday, May 23, 2022

Paint color-matcher quantifies iron levels in soil

Debjani Sihi, right, demonstrates using the Nix Pro to measure iron content in soil with colleagues Gaurav Jha (left) and Biswanath Dari. Iron is a vital micronutrient to grow plants and "a fundamental mineral species that dictates many other soil functions, like carbon storage, greenhouse gas emissions and nitrogen and phosphorous recycling," says Sihi, a biogeochemist in Emory's Department of Environmental Sciences.  (Photo by Aneesh Chandel)
 

By Carol Clark

A handheld color-sensing tool, commonly used to match paint shades, is also effective at quantifying the iron content in soil by analyzing its color, a study finds. Agricultural & Environmental Letters published the research showing that the inexpensive color sensor, known as the Nix Pro, can rapidly and accurately quantify soil iron. 

“We found that the Nix Pro is easy to use in the field on soil samples and can give an accurate estimate for iron content within seconds using a technique that we developed,” says Debjani Sihi, corresponding author of the paper and assistant professor in Emory’s Department of Environmental Sciences. “We think that this device holds the potential to become a really handy, cost-effective tool for farmers.” 

Gaurav Jha, who did the work as a post-doctoral researcher at the University of California, Davis, is first author of the study. 

Iron is a vital micronutrient, explain Sihi, a biogeochemist who studies environmental and sustainability issues at the nexus of soil, climate, health and policy. Just as people need iron to make a protein in red blood cells that carries oxygen through the body, plants need iron to move oxygen through their systems and produce the chlorophyll that makes them a healthy, green color. 

Soil iron levels are also a key factor in climate change. “It’s a fundamental mineral species that dictates many other soil functions, like carbon storage, greenhouse gas emissions and nitrogen and phosphorus cycling,” Sihi says. 

And yet, iron is often deficient in soil, especially in agricultural lands. “If a farmer knows that their soil does not contain the right amount of iron for their crops, they can amend the soil before planting,” she says. 

Problems with testing for soil iron 

The problem farmers face is that determining iron content in soil is expensive and/or time consuming. One method is to gather soil samples from across a landscape. The samples are then sent to a laboratory for analyses via a benchtop atomic-absorption spectrometer or inductively coupled plasma. Laboratory analysis yields a precise percentage of iron content for each sample but it can be costly and often requires weeks to learn a result. 

A thick book of soil color samples, known as the Munsell charts, provides an alternative. Comparing the color of a soil sample with the swatches on the Munsell charts can guide an effort to classify the soil color. The downside to this method is that it requires practice, it is labor-intensive and the data is qualitative and imprecise. 

During a coffee break chat among Sihi, Jha and co-author Biswanath Dari, from North Carolina Agricultural and Technical State University, the idea came up of trying the Nix Pro’s color sensing on soil. 

The Nix Pro is a palm-sized light-emitting spectrometer that measures the reflectance of a surface to quantify its color composition. It’s commonly used by paint stores, printing shops and graphic design firms for color matching. A Nix Pro costs just $349 and is easy to use, with a cell phone app providing a near-instantaneous result for a sample. 

The Nix Pro soil sensor, center, is a handheld device that is more automated and user-friendly for measuring soil iron content than a book of color samples known as the Munsell charts. (Photo by Gaurav Jha)

“The color of soil can tell you a lot of stories about an environment,” Sihi says. 

Dark brown soil contains a lot of organic material while whitish soil indicates that most of the organic material has washed away. Dark red soil, including Georgia’s famous red clay, indicates strong iron-oxide content. 

If researchers want to learn about the water table in red clay soil, they can look at the colors in a cross-section of the ground. Past flooding will turn some of the soil layers from red to a grayish color because the water has washed out much of the iron. Tree roots from the past will appear as orange patches. “The orange color indicates where the tree roots borrowed oxygen from the surrounding air and oxidized the iron,” Sihi says. 

Sihi studies redox reactions involving electron receptors like oxygen and iron, which can reveal such hidden stories in an environment. Ferrous oxide, for instance, is known as iron 2 due to the number of electrons lost in the oxidation process. Ferric oxide, or iron 3, contains iron oxide that lost three electrons. 

Soil oscillating between periods of heavy rain to no rain undergoes fluctuating redux, or shifts in the levels of iron 2 and iron 3 as the water tables go up and down. “Fluctuating redox is a big threat multiplier for greenhouse gas emissions into the atmosphere,” Sihi says. 

‘An extremely strong result’ 

Due to the broad importance of iron, the researchers focused on iron content as the first soil test for the Nix Pro. They first collected data on soil samples from New Mexico using the Nix Pro app for three different color spaces: cyan, magenta, yellow and black; lightness and darkness; and red, green and blue. The Nix Pro app allowed them to export the data into an Excel document. 

Researchers from New Mexico State University helped calibrate and validate the three color models generated by the Nix Pro data by comparing them with results for total iron content generated through analysis in a NMSU laboratory. The results showed that all three of the models were significant in predicting soil iron content, with the cyan, magenta, yellow and black model (CMYB) delivering the strongest result. 

Finally, they further validated the CMYB model by using it to estimate total iron content in soil samples from an adjacent field. The results showed that the Nix Pro CMYB model was 80 percent accurate compared to laboratory results for the same samples. 

“That’s an extremely strong result,” Sihi says. “We’re comparing the power of a small, handheld tool with a really fancy lab instrument and it’s holding up.” 

The team now plans to test the Nix Pro on soils from other regions to determine if the method will work universally as an iron soil predicter. They hope other researchers will also apply their method to speed up the data-gathering process. Sihi and her colleagues plan to further expand their project by experimenting with the Nix Pro’s possible efficacy for other agricultural applications related to soil composition. And this summer, they will conduct a greenhouse gas experiment to evaluate if the Nix Pro color sensor can be used to identify nitrogen deficiency in corn plants through the characteristic symptom of yellowing leaves. 

Additional authors of the current paper include Harpreet Kaur, April Ulery and Kevin Lombard (NMSU); and Mallika Nocco (University of California, Davis). 

Related:

Climate change on course to hit U.S. Corn Belt especially hard, study finds

Data-driven study digs into the state of U.S. farm livelihoods

The growing role of farming and nitrous oxide in climate change

Thursday, May 5, 2022

Ancient DNA gives new insights into 'lost' Indigenous people of Uruguay

A sculpture commemorates the Indigenous people of Uruguay in the capital of Montevideo. Archeological evidence for human settlement of the area goes back 10,000 years. (Photo by Maximasu via Wikimedia Commons)

By Carol Clark

The first whole genome sequences of the ancient people of Uruguay provide a genetic snapshot of Indigenous populations of the region before they were decimated by a series of European military campaigns. PNAS Nexus published the research, led by anthropologists at Emory University and the University of the Republic, Montevideo, Uruguay. 

“Our work shows that the Indigenous people of ancient Uruguay exhibit an ancestry that has not been previously detected in South America,” says John Lindo, co-corresponding author and an Emory assistant professor of anthropology specializing in ancient DNA. “This contributes to the idea of South America being a place where multi-regional diversity existed, instead of the monolithic idea of a single Native American race across North and South America.” 

The analyses drew from a DNA sample of a man that dated back 800 years and another from a woman that went back 1,500 years, both well before the 1492 arrival of Christopher Columbus in the Americas. The samples were collected from an archeological site in eastern Uruguay by co-corresponding author Gonzalo Figueiro, a biological anthropologist at the University of the Republic. 

The results of the analyses showed a surprising connection to ancient individuals from Panama — the land bridge that connects North and South America — and to eastern Brazil, but not to modern Amazonians. These findings support the theory proposed by some archeologists of separate migrations into South America, including one that led to the Amazonian populations and another that led to the populations along the East coast. 

“We’ve now provided genetic evidence that this theory may be correct,” Lindo says. “It runs counter to the theory of a single migration that split at the foot of the Andes.” 

Archeological evidence 

The archeological evidence for human settlement of the area now known as Uruguay, located on the Atlantic coast south of Brazil, goes back more than 10,000 years. European colonizers made initial contact with the Indigenous people of the region in the early 1500s. 

During the 1800s, the colonizers launched a series of military campaigns to exterminate the native peoples, culminating in what is known as the massacre at Salsipuedes Creek, in 1831, which targeted an ethnic group called the CharrĂșa. At that time, the authors write, the term CharrĂșa was being applied broadly to the remnants of various hunter-gatherer groups in the territory of Uruguay. 

“Through these first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, we were able to reconstruct at least a small part of their genetic prehistory,” Lindo says. 

The work opens the door to modern-day Uruguayans seeking to potentially link themselves genetically to populations that existed in the region before European colonizers arrived. “We would like to gather more DNA samples from ancient archeological sites from all over Uruguay, which would allow people living in the country today to explore a possible genetic connection,” Lindo says. 

Focusing on little-explored human lineages 

The Lindo ancient DNA lab specializes in mapping little-explored human lineages of the Americas. Most ancient DNA labs are located in Europe, where the cooler climate has better preserved specimens. 

Less focus has been put on sequencing ancient DNA from South America. One reason is that warmer, more humid climates throughout much of the continent have made it more challenging to collect usable ancient DNA specimens, although advances in sequencing technology are helping to remove some of these limitations. 

“If you’re of European descent, you can have your DNA sequenced and use that information to pinpoint where your ancestors are from down to specific villages,” Lindo says. “If you are descended from people Indigenous to the Americas you may be able to learn that some chunk of your genome is Native American, but it’s unlikely that you can trace a direct lineage because there are not enough ancient DNA references available.” 

Further complicating the picture, he adds, is the massive disruption caused by the arrival of Europeans given that many civilizations were destroyed and whole populations were killed. 

By collaborating closely with Indigenous communities and local archeologists, Lindo hopes to use advanced DNA sequencing techniques to build a free, online portal with increasing numbers of ancient DNA references from the Americas, to help people better explore and understand their ancestry. 

Co-authors of the current paper include Emory senior Rosseirys De La Rosa, Andrew Luize Campelo dos Santos (the Federal University of Penambuco, Recife, Brazil), Monica Sans (University of the Republic, Montevideo, Uruguay), and Michael De Giorgio (Florida Atlantic University). 

The work was funded by a National Science Foundation CAREER Grant. 

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'Potato gene' reveals how ancient Andeans adapted to starchy diet 

Wednesday, April 6, 2022

Computerized, rolling DNA motors move molecular robotics to next level

"I love the idea of using something that's innate in all of us to engineer new forms of technology," says Emory graduate student Selma Piranej, shown with a cell phone microscope set up to observe the rolling DNA-based motors.
 

By Carol Clark

Chemists integrated computer functions into rolling DNA-based motors, opening a new realm of possibilities for miniature, molecular robots. Nature Nanotechnology published the development, the first DNA-based motors that combine computational power with the ability to burn fuel and move in an intentional direction. 

“One of our big innovations, beyond getting the DNA motors to perform logic computations, is finding a way to convert that information into a simple output signal — motion or no motion,” says Selma Piranej, an Emory University PhD candidate in chemistry, and first author of the paper. “This signal can be read by anyone holding a cell phone equipped with an inexpensive magnifying attachment.”

“Selma’s breakthrough removes major roadblocks that stood in the way of making DNA computers useful and practical for a range of biomedical applications,” says Khalid Salaita, senior author of the paper and an Emory professor of chemistry at Emory University. Salaita is also on the faculty of the Wallace H. Coulter Department of Biomedical Engineering, a joint program of Georgia Tech and Emory. 

The motors can sense chemical information in their environment, process that information, and then respond accordingly, mimicking some basic properties of living cells. 

“Previous DNA computers did not have directed motion built in,” Salaita says. “But to get more sophisticated operations, you need to combine both computation and directed motion. Our DNA computers are essentially autonomous robots with sensing capabilities that determine whether they move or not.” 

The motors can be programmed to respond to a specific pathogen or DNA sequence, making them a potential technology for medical testing and diagnostics. Another key advance is that each motor can operate independently, under different programs, while deployed as a group. That opens the door for a single massive array of the micron-sized motors to carry out a variety of tasks and perform motor-to-motor communication. 

“The ability for the DNA motors to communicate with one another is a step towards producing the kind of complex, collective action generated by swarms of ants or bacteria,” Salaita says. “It could even lead to emergent properties.” 

The high speed of the rolling DNA-based motor allows a simple smart phone microscope to capture its motion through video.
 

DNA nanotechnology takes advantage of the natural affinity for the DNA bases A, G, C and T to pair up with one another. By moving around the sequence of letters on synthetic strands of DNA, scientists can get the strands to bind together in ways that create different shapes and even build functioning machines. 

The Salaita lab, a leader in biophysics and nanotechnology, developed the first rolling DNA-based motor in 2015. The device was 1,000 times faster than any other synthetic motor, fast-tracking the burgeoning field of molecular robotics. Its high speed allows a simple smart phone microscope to capture its motion through video. 

The motor’s “chassis” is a micron-sized glass sphere. Hundreds of DNA strands, or “legs” are allowed to bind to the sphere. These DNA legs are placed on a glass slide coated with the reactant RNA, the motor’s fuel. The DNA legs are drawn to the RNA, but as soon as they set foot on it they erase it through the activity of an enzyme that is bound to the DNA and destroys only RNA. As the legs bind and then release from the substrate, they keep guiding the sphere along. 

When Piranej joined the Salaita lab in 2018, she began working on a project to take the rolling motors to the next level by building in computer programming logic. 

“It’s a major goal in the biomedical field to take advantage of DNA for computation,” Piranej says. “I love the idea of using something that’s innate in all of us to engineer new forms of technology.” 

DNA is like a biological computer chip, storing vast amounts of information. The basic units of operation for DNA computation are short strands of synthetic DNA. Researchers can change the “program” of DNA by tweaking the sequences of AGTC on the strands. 

“Unlike a hard, silicon chip, DNA-based computers and motors can function in water and other liquid environments,” Salaita says. “And one of the big challenges in fabricating silicon computer chips is trying to pack more data into an ever-smaller footprint. DNA offers the potential to run many processing operations in parallel in a very small space. The density of operations you could run might even go to infinity.” 

Synthetic DNA is also biocompatible and cheap to make. “You can replicate DNA using enzymes, copying and pasting it as many times as you want,” Salaita says. “It’s virtually free.” 

Limitations remain, however, in the nascent field of DNA computation. A key hurdle is making the output of the computations easily readable. Current techniques heavily rely on tagging DNA with fluorescent molecules and then measuring the intensity of emitted light at different wavelengths. This process requires expensive, cumbersome equipment. It also limits the signals that can be read to those present in the electromagnetic spectrum. 

"Developing devices for biomedical applications is especially rewarding because it's a chance to make a big impact in people's lives," says Piranej, shown during a trip to San Franciso.

Although trained as a chemist, Piranej began learning the basics of computer science and diving into bioengineering literature to try to overcome this hurdle. She came up with the idea of using a well-known reaction in bioengineering to perform the computation and pairing it with the motion of the rolling motors. 

The reaction, known as toehold-mediated strand displacement, occurs on duplex DNA — two complementary strands. The strands are tightly hugging one another except for one loose, floppy end of a strand, known as the toe hold. The rolling motor can be programmed by coating it with duplex DNA that is complementary to a DNA target — a sequence of interest. When the molecular motor encounters the DNA target as it rolls along its RNA track, the DNA target binds to the toe hold of the duplex DNA, strips it apart, and anchors the motor into place. The computer read out becomes simply “motion” or “no motion.” 

“When I first saw this concept work during an experiment, I made this really loud, excited sound,” Piranej recalls. “One of my colleagues came over and asked, ‘Are you okay?’ Nothing compares to seeing your idea come to life like that. That’s a great moment.” 

These two basic logic gates of “motion” or “no motion” can be strung together to build more complicated operations, mimicking how regular computer programs build on the logic gates of “zero” or “one.” 

Piranej took the project even further by finding a way to pack many different computer operations together and still easily read the output. She simply varied the size and materials of the microscopic spheres that form the chassis for the DNA-based rolling motors. For instance, the spheres can range from three to five microns in diameter and be made of either silica or polystyrene. Each alteration provides slightly different optical properties that can be distinguished through a cell phone microscope.

The Salaita lab is working to establish a collaboration with scientists at the Atlanta Center for Microsystems Engineered Point-of-Care Technologies, an NIH-funded center established by Emory and Georgia Tech. They are exploring the potential for the use of the DNA-computing technology for home diagnostics of COVID-19 and other disease biomarkers. 

“Developing devices for biomedical applications is especially rewarding because it’s a chance to make a big impact in people’s lives,” Piranej says. “The challenges of this project have made it more fun for me,” she adds. 

Related:

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

New DNA motor breaks speed record for nano machines

Nano-walkers take speedy leap forward with first rolling DNA-based motor 

Thursday, March 17, 2022

Monarch butterflies increasingly plagued by parasites, study shows

"Our findings suggest that tens of millions of eastern monarch butterflies are getting sick and dying each year from these parasites," says Emory evolutionary biologist Jaap de Roode, senior author of the study.

By Carol Clark

Monarch butterflies, one of the most iconic insects of North America, are increasingly plagued by a debilitating parasite, a major new analysis shows. The Journal of Animal Ecology published the findings, led by scientists at Emory University. 

The analysis drew from 50 years of data on the infection rate of wild monarch butterflies by the protozoan Ophryocystis elektrosirrha, or O.E. The results showed that the O.E. infection rate increased from less than one percent of the eastern monarch population in 1968 to as much as 10 percent today. 

“We’re seeing a significant change in a wildlife population with a parasitism rate steadily rising from almost non-existent to as high as 10 percent,” says Ania Majewska, first author of the paper and a post-doctoral fellow in Emory’s Department of Biology. “It’s a signal that something is not right in the environment and that we need to pay attention.” 
 
The O.E. parasite invades the gut of the monarch caterpillars. If the adult butterfly leaves the pupal stage with a severe parasitic infection, it begins oozing fluids from its body and dies. Even if the butterflies survive, as in case of a lighter infection, they do not fly well or live as long as uninfected ones. 

The rise in parasitism, the researchers warn, may endanger the mass migration of the monarchs, one of the most spectacular displays in the animal kingdom, involving hundreds of millions of butterflies. Each fall, the western monarch population flies hundreds of miles down the Pacific Coast to spend the winter in California. Meanwhile, on the other side of the Rocky Mountains, eastern monarchs fly from as far north as the U.S.-Canadian border to overwinter in Central Mexico, covering as much as 3,000 miles. 

“Our findings suggest that tens of millions of eastern monarch butterflies are getting sick and dying each year from these parasites,” says Jaap de Roode, Emory professor of biology and senior author of the study. “If the infection rates keep going up, fewer and fewer monarchs will be able to survive to migrate to their overwintering sites.” 

One contributor to the rise in the parasitism rate is the increased density of monarchs in places where they lay their eggs, the study finds. The researchers posit that the increased density may be due to many factors, including the loss of wildlife habitat; the widespread planting of exotic, non-native species of milkweed; and by people raising monarchs in large numbers in confined spaces.

Co-authors of the paper are Sonia Altizer and Andrew Davis of the University of Georgia Odum School of Ecology. 

"Monarchs are incredible animals," says Ania Majewska, first author of the study, shown in the Monarch Butterfly Biosphere Reserve in Mexico.

Majewska began studying monarchs eight years ago while a graduate student at the University of Georgia. She joined the De Roode lab at Emory in 2019, funded by the NIH program Fellowships in Research and Science Teaching. 

“Monarchs are incredible animals,” she says. “Each one is only as heavy as a paperclip but they can fly so far and they are incredibly resilient.” 

The Monarch Butterfly Biosphere Reserve in Mexico, where the eastern monarchs overwinter in pine and fir forests, is a World Heritage Site and an important generator of tourism income. “The trees can become so heavy with monarchs that sometimes branches break off and fall,” Majewska says. “When sunlight hits the clusters the monarchs explode like confetti. It’s a magical sight.” 

The butterflies arrive in large numbers in Mexico near the Day of the Dead, when families gather around the gravesites of their loved ones. For traditional cultures in the region, monarchs have come to represent the souls of ancestors returning to visit for the celebrations. 

In addition to the monarch migration’s natural beauty, economic and cultural significance, it plays an ecological role, as the butterflies pollinate plants and provide food for wasps, ants and other invertebrate predators. 

Birds, however, tend to avoid the monarchs, as the butterfly’s striking coloration of orange, black and white is a warning sign that it may be poisonous to them. 

Monarchs overwintering on a tree in Mexico. (Photo by Jaap de Roode)

When monarchs leave their overwintering sites in the spring, they fly north and lay their eggs. Their caterpillars feed on any of dozens of species of milkweed plants, including some species that contain high levels of cardenolides. These chemicals do not harm the caterpillars, but make them toxic to some predators even after they emerge as adults from their chrysalises. 

In 2010, Jaap de Roode discovered that monarchs also use cardenolides as a kind of drug. Experiments in his lab showed that a female infected with the O.E. parasite prefers to lay her eggs on a toxic species of milkweed, rather than a non-toxic species. Uninfected female monarchs, however, showed no preference. While cardenolides do not cure the caterpillars of parasites, they can lessen the severity of an infection. 

For the current paper, the researchers wanted to investigate the O.E. infection rate in monarch populations over time. They accessed multiple available data sets, which were mostly for the eastern monarchs. The data included samples going back to 1968 collected by the late Lincoln Brower, an entomologist who specialized in monarchs, and by other researchers through the decades. 

The results showed the rise in the parasitism rate remained low in the eastern monarch population for several decades before shooting up beginning in the 2000s, then making a slight dip in recent years.

Monarchs caterpillars feed exclusively on milkweed plants. (Photo by Jaap de Roode)

Among the factors that may be contributing to the increased monarch density associated with the rise in parasitism, the researchers note, is the loss of natural habitat and agricultural practices that have reduced the places where milkweed is found. Milkweed used to proliferate amid crops in the Midwest, for instance, but farmers increasingly use genetically engineered herbicide-resistant crops. That allows them to spray their fields to eradicate weeds. 

Since milkweed is the sole source of food for monarch caterpillars, and fewer of the plants are available, the female monarchs must cluster more densely to lay their eggs and the butterfly “nurseries” become more crowded with caterpillars. 

“One thing that the COVID-19 pandemic taught us is that social distancing can help reduce the spread of an infectious disease,” de Roode says. “The same holds true for monarchs and the O.E. parasite.” 

Around the year 2000, the researchers note, conservation groups began planting exotic species of milkweed to try to support the monarch population, which has been declining. Ironically, this conservation effort may have fueled more parasitism. “The exotic species of milkweed tend to have more cardenolides than native species,” Majewska explains, “so infected female monarchs may be seeking the exotic species out, adding to the density problem.” 

The researchers further hypothesize that people raising monarch caterpillars in large numbers — to support conservation efforts or for commercial purposes — may be keeping them in crowded conditions that foster the spread of the parasite. 

“Ultimately, a continuing rise in the monarch’s parasitic infection rate could cause the species to suffer significantly,” Majewska says. “If tens of millions of them are dying annually from parasitic infections, then an extreme weather event during the winter in Mexico might reduce the population to a level that could be dangerous for their genetic diversity.” 

“Parasitism is often overlooked in conservation efforts,” de Roode adds, “but our findings show how parasites can have a massive impact on wildlife.” 

The research was supported by the National Institutes of Health and the National Science Foundation.

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Wednesday, March 16, 2022

Heartland virus identified in lone star ticks in Georgia

The lone star tick, named for the distinctive white spot on its back, is the most common tick in Georgia.  Emory researchers detected Heartland virus in three different specimen samples of lone star ticks collected in central Georgia. (CDC/James Gathany)

By Carol Clark

Heartland virus is circulating in lone star ticks in Georgia, scientists at Emory University have found, confirming active transmission of the virus within the state. The journal Emerging Infectious Diseases published the findings, which include a genetic analysis of the virus samples, isolated from ticks collected in central Georgia. 

The research adds new evidence for how the tick-borne Heartland virus, first identified in Missouri in 2009, may evolve and spread geographically and from one organism to another. 

“Heartland is an emerging infectious disease that is not well understood,” says Gonzalo Vazquez-Prokopec, associate professor in Emory’s Department of Environmental Sciences and senior author of the study. “We’re trying to get ahead of this virus by learning everything that we can about it before it potentially becomes a bigger problem.” 

Vazquez-Prokopec is a leading expert in vector-borne diseases — infections transmitted from one organism to another by the bite of a vector, such as a tick or mosquito. 

Yamila Romer, a former post-doctoral fellow in the Vazquez-Prokopec lab, is first author of the new paper. Co-author Anne Piantadosi, assistant professor in Emory School of Medicine’s Department of Pathology and Laboratory Medicine, conducted the genetic analyses. 

"Ticks are both fascinating and terrifying," says study co-author Steph Bellman, shown in the field with a vial of ticks. "They represent a large threat to human health that a lot of people may not realize." Bellman is an MD/Phd student in Emory's School of Medicine and Rollins School of Public Health.

The study detected Heartland virus in three different specimen samples of lone star ticks — collected in different locations and at different times — and including both the nymph and adult stages of the ticks.

The genetic analysis of the three viral samples showed that their genomes are similar to one another, but much different from the genomes of Heartland virus samples from outside the state. “These results suggest that the virus may be evolving very rapidly in different geographic locations, or that it may be circulating primarily in isolated areas and not dispersing quickly between those areas,” Vazquez-Prokopec says. 

The Heartland virus was discovered in 2009 in northwest Missouri after two local men were hospitalized with high fevers, diarrhea, muscle pains, low counts of white blood cells and platelets, and other symptoms similar to known tick-borne diseases. Researchers soon realized the men were infected with a novel virus, which was christened Heartland, and later traced to lone star ticks. Further studies found antibodies to the virus in blood samples from deer and some other wild mammals. 

The Centers for Disease Control and Prevention currently recognizes 18 tick-borne diseases in the United States, many of them newly emerging. One of the most well-known tick-borne illnesses is Lyme disease, caused by a bacterium, which in recent decades has grown into the most common vector-borne disease in the country. The black-legged tick, also known as the deer tick, is the vector for transmission of the bacteria that causes Lyme disease and the white-footed mouse is the primary reservoir for the bacterium. The tick larvae can become infected when they feed on the blood of the mice and other small mammals and birds that may be harboring the bacterium. The infected larvae grow into nymphs and adult ticks that can then move into other hosts, including deer and humans. 

While the complex transmission cycle for Lyme disease is well characterized, many questions remain about how the Heartland virus moves among different species. 

The researchers used flags of white flannel to collect the tick specimens.

Since it was first discovered in 2009, more than 50 cases of Heartland virus have been identified in people from 11 states in the Midwest and Southeast, according to the Centers for Disease Control and Prevention. Many of the identified cases were severe enough to require hospitalization and a few individuals with co-morbidities have died. The actual disease burden is believed to be higher, however, since Heartland virus is still not well known and tests are rarely ordered for it. 

A retroactive analysis uncovered a single confirmed human infection of Heartland virus in Georgia, in a Baldwin County resident who died with what was then an unidentified illness in 2005. The human case prompted analysis of serum samples collected in past years from white-tailed deer in central Georgia. The results showed that deer from that area have been exposed to the Heartland virus since at least 2001. 

To better assess the risk for human disease in the area, Vazquez-Prokopec wanted to learn whether lone star ticks are currently carrying Heartland virus in central Georgia. 

Members of the field research team collected ticks from the rural landscape near the Piedmont National Wildlife Refuge. Even during the hot Georgia summers, team members wore long shirts and long pants tucked into long socks, with the top of the socks sealed with duct tape. They further protected themselves with bug spray and by conducting visual checks for ticks on themselves before and after leaving the field. 

The lone star tick, named for a distinctive white spot on its back, is the most common tick in Georgia and is widely distributed in wooded areas across the Southeast, Eastern and Midwest United States. They are tiny, about the size of a sesame seed in the nymph stage, and barely a quarter-of-an-inch in diameter as adults. 

“Lone star ticks are so small that you may not feel them on you or even notice if you’ve been bitten by one,” says Steph Bellman, a co-author of the study. Bellman is an MD/PhD student in Emory’s School of Medicine and Rollins School of Public Health, focused on environmental health. 

A vial of ticks collected in the field.

The team used “flagging” as a collection technique. A flag of white flannel on a pole is swished in a figure-eight motion through the underbrush. “Every so often, you lay the flag down and use a pair of tweezers to remove any ticks that you find on it and put them into a vial,” Bellman explains. 

Through this painstaking method, the team collected nearly 10,000 specimens from sites in Georgia’s Putnam County and Jones County, both adjacent to Baldwin County. Specimens were separated into groups, each containing either five adults or 25 nymphs, then crushed and put into a solution to test for the presence of the Heartland virus. 

The results suggested that about one out of every 2,000 of the collected specimens carried the Heartland virus. One adult and one nymph sample collected on the same date tested positive from a site in Putnam County, a private property used for hunting. A second sample of adult ticks, collected on a different date from a stretch of woods along a highway in Jones County, also tested positive. 

The researchers are now expanding the scope of the work. They will collect ticks across Georgia for testing and conduct spatial analyses with the aim of understanding factors that may raise the risk for Heartland virus. 

“We want to start filling in the huge gaps in knowledge of the transmission cycle for Heartland virus,” Vazquez-Prokopec says. “We need to better understand the key actors that transmit the virus and any environmental factors that may help it to persist within different habitats.” 

Climate change is fueling warmer and shorter winters, increasing opportunities for some species of ticks to breed more frequently and to expand their ranges. Land-use changes are also strongly associated with tick-borne diseases, as more human habitats encroach on wooded areas and the loss of natural habitat forces wildlife to live in denser populations. 

“Ticks are both fascinating and terrifying,” Bellman says. “We don’t have effective ways to control them and they are a vector for many nasty diseases. They represent a large threat to human health that a lot of people may not realize.” 

The Asian longhorned tick is an invasive species that has been found in Georgia and 16 other states. (CDC/James Gathany)

The Prokopec Lab is also investigating the arrival of the Asian longhorned tick (Haemaphysalis longicornis) in Georgia, funded by a seed grant from the U.S. Department of Agriculture. 

Long established in China, Japan, Russia and parts of the Pacific, the Asian longhorned tick was first detected in the United States in 2018, in New Jersey. The tick has since spread to 17 states, including Georgia, where it was found on a farm in Pickens County in 2021. 

The Asian longhorned tick reproduces asexually and a single female can generate as many as 100,000 eggs, rapidly producing massive amounts of offspring that feed on livestock. So many ticks can be covering a single sheep or cow that the loss of blood physically weakens or, in extreme cases, kills the animal. 

The Asian longhorned tick also carries bacterial and viral pathogens that can infect humans, including severe fever with thrombocytopenia syndrome virus (SFTSV), also known as Dabie bandavirus. Human cases of SFTS, a hemorrhagic fever, emerged in China in 2011 and have since been identified in other parts of Asia. 

“We are investigating not only the potential agricultural impact of the Asian longhorned tick in Georgia, but the potential for this invasive tick to spread SFTS and other diseases to people,” Vazquez-Prokopec says. 

Of particular concern is the fact that the Heartland virus shares genomic similarities with SFTSV, he adds. 

“We will be gathering data to help support tick surveillance efforts by public health officials in Georgia,” Vazquez-Prokopec says. “Tick-borne diseases are a real and growing threat and the best way to deal with them is not to panic, but to do the science needed to learn everything we can about them.”  

Additional co-authors of the current paper include Uriel Kitron, professor in Emory’s Department of Environmental Sciences; Oscar Kirstein, an Emory post-doctoral fellow in the Prokopec Lab; Daniel Mead and Kalya Adcock, from the University of Georgia; and Zhuorn Wei, a former Emory research assistant. 

Funding for the work was provided by a grant from the Emory University Research Council.

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Atlanta Science Fest celebrates the wonders all around us


A celebration of science once again takes metro Atlanta by storm with the return of the Atlanta Science Festival, ongoing through March 26. More than 100 activities, planned throughout the city, invite families to experience the thrills of discovery, from nature walks to expert talks and hands-on STEM learning opportunities. 

“The festival offers ways for people of all ages to learn something new and to spark a new interest,” says Meisa Salaita, the executive co-director of Science ATL, the non-profit organization that produces the Atlanta Science Festival. “You may not realize that your child has a secret knack for chemistry, or that you enjoy birdwatching, until getting immersed in it.” 

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

Monday, February 28, 2022

Data-driven study digs into the state of U.S. farm livelihoods

"Farmers are fundamental to our survival, their work is risky and difficult, and ensuring their quality of life is necessary for U.S. agriculture to persist," says Emily Burchfield, Emory assistant professor of environmental sciences and lead author of the study.

By Carol Clark

U.S. agricultural systems are world leaders in the production of food, fuel and fiber. This high level of production enables U.S. consumers to spend an average of only 8.6 percent of their disposable income on food, a percentage that has been trending downward since 1960. Growing evidence, however, shows that many hidden costs of cheap food may be passed on through factors such as reduced nutritional content, environmental degradation and the diminishing livelihoods of U.S. farm operators. 

A major new study led by Emory University digs deeper into the question of why, despite the extraordinary productivity of U.S. agriculture, U.S. farm operators are systematically losing money. The journal Frontiers of Sustainable Food Systems published the analysis, which drew from publicly available data from the U.S. Department of Agriculture, the U.S. Bureau of Economic Analysis and other sources. 

“It’s not that agriculture as a sector is not profitable,” says Emily Burchfield, assistant professor in Emory’s Department of Environmental Sciences and lead author of the study. “It’s that, despite hard work and significant financial risk, many of the people who operate U.S. farms are not able to make a decent living at it.” 

Rising input costs, shrinking production values, commodity specialization and challenges to land access all appear to be connected to declining farm operator livelihoods, the study concludes. 

“We’ve shown in a quantitative, systematic way the extent to which these trends are happening and, in many cases, how they appear to be worsening,” Burchfield says. 

An online data repository

“People who work in the agricultural space already know that it is difficult to make a living as a farmer,” she adds. “In this paper, we’ve cleaned and merged tremendous amounts of data from multiple sources to bring key information together into one place. This allows us to tell a more complete and clear story about how and why this is happening at a national scale.” 

The researchers deposited the cleaned and merged data into a free, online repository (https://github.com/blschum/US-Farming-Data-Narrative) so that other agricultural stakeholders can easily access it. They hope that their “one-stop,” centralized data hub on farmer livelihoods will serve as an educational tool and inspire more research into the topic. 

The USDA reported in 2020 that the average funds generated by farm operators to meet living expenses and debt obligations, after accounting for production expenses, have been negative for nine out of the last 10 years. In 2017, for instance, median net-cash farm income was $1,035 in the red per farm household in the country. 

Paying to farm

In many regions of the United States, the authors write, farm operators actually have to pay to engage in the labor- and time-intensive act of operating a farm. 

“What we were really surprised to find in the data is that the low, or negative, median farm operator income applies even when you factor in government subsidies,” Burchfield says. “Given that the federal government is subsidizing farming with billions of dollars annually, it raises the question of how we might do so more effectively. How are we going to convince folks to continue growing our food if they are locked into a system where they can’t make money?” 

Burchfield’s research combines spatial-temporal, social and environmental data to understand the future of food security in the United States, including the consequences of a changing climate. 

Co-authors of the current paper include: Britta Schumacher, a former Emory research assistant in Burchfield’s lab; Andrea Rissing, an Emory post-doctoral fellow in the lab; and Kaitlyn Spangler, a post-doctoral fellow at Penn State. 

Relying on off-farm income

Understanding how much income individual farms are losing on average is complicated by farm households often having a family member bringing in income through a non-farm occupation, Burchfield notes. In 2019, the USDA reported that on-farm production contributes to less than 25 percent of farm household income, on average, with the remaining 75 percent earned off-farm. This suggests that many farmers rely on off-farm income to stay afloat. 

“Farming is one of the hardest jobs on the planet,” Burchfield says, “and it’s going to get even harder due to climate change. The combination of more gradual shifts in average climate conditions, and the increased prevalence of extreme weather events, presents a serious challenge to farmers.” 

These ongoing challenges, the authors argue, require an urgent rethinking of how federal subsidies can play a role in encouraging and supporting new, adaptive approaches to agriculture. 

U.S. farm operations currently cover approximately 900 million cultivated acres, more than half of the nation’s land area. And three crops — corn, soy and wheat — are cultivated exclusively on more than two thirds of agricultural acres. 

“A lack of crop diversification can make farming increasingly brittle and less adaptable,” Burchfield says. “Climate change, meanwhile, makes the need for innovation and adaptation more crucial and inevitable.” 

The paper also highlights the lack of diversification among farm operators. Statistically, the “average” U.S. farmer is a 58-year-old white male. Those not identifying as white currently operate about 7 percent of farmland representing just 5 percent of operations. Only 1.4 percent of operators identify as Black, and these operators are heavily concentrated in the Southeast. And, on average, white operators receive twice as much from federal subsidy programs ($14,000 per farm) as Black operators ($6,400 per farm). 

A call for diversity of people, plants and practices

“We need better data to track the persistent inequities at the intersection of race, class and livelihoods in the agriculture space,” Burchfield says. 

She recommends finding ways to support the diversity of people, plants and practices in the national farm landscape to help address the growing issues of agricultural sustainability and climate change. “Small-scale experimentation and the emergence of grassroots alternatives along with technical innovations are all needed in order to better weather the challenges,” she says. 

Burchfield also cites the need for the availability of more fine-scale data on the livelihoods of farmers that goes beyond yields and acreage to cover issues such as access to health insurance. “Farmers are fundamental to our survival, their work is risky and difficult, and ensuring their quality of life is necessary for U.S. agriculture to persist,” she says. 

As Burchfield and her co-authors conclude: “Measuring and monitoring agricultural progress using only metrics of production, efficiency and revenue masks the lived realities of the humans operating our farms.” 

The research was supported in part by the U.S. Department of Agriculture and the National Science Foundation.

Related:

Diverse landcover boosts yields for major U.S. crops, study finds