Friday, November 18, 2022

Emory students promote youth power at U.N. conference

Eri Saikawa, associate professor of environmental studies (bottom, right) led a delegation of students to the U.N. Framework Convention on Climate Change in Egypt. Click here to see bios of the delegation members.

By Carol Clark

Emory students helped raise the profiles of youth activists during this year’s United Nations Framework Convention on Climate Change, better known as COP, continuing through Nov. 18 in Sharm El-Sheikh, Egypt. 

A delegation of five Emory undergraduates and four graduate students, led by Eri Saikawa, associate professor of environmental sciences, attended the first week of COP as official U.N. observers. They sat in on negotiations and co-hosted a side event with the Climate Justice Program entitled “Youth: From Resistance to Power.” The event featured a panel discussion by four young activists — from Pakistan, Kenya, Mexico and the Philippines — followed by an interactive networking event moderated by the Emory students. 

“It’s inspiring and energizing seeing so many youth raising their voices and pushing for climate action,” says Saikawa. 

Saikawa began leading students from her Climate Change and Society class to the annual global climate talks in 2015, when COP was held in Paris. That year, nearly 200 member countries hammered out the Paris Agreement, aiming to keep the global mean rise in temperature to no more than 2 degrees Celsius above preindustrial levels. 

Student delegates will share what they learned during this year’s COP at a campus event entitled “Climate Conversations: Advancing Towards Global Justice” on Thursday, Nov. 17 at 6 pm in the Emory Student Center, multi-purpose rooms 5 and 6. Attendees can join in activities geared to the topics of environmental justice, climate and business, urban planning, conservation and more. 

The students will also produce podcasts on different aspects of COP for the Emory Climate Talks AmpliFIRE series. 

Following are brief summaries of the experiences and views of four of the Emory undergraduates who traveled to Egypt for COP. 

"Right after we touched down in Sharm El-Sheikh we grabbed our badges and headed to the conference," says Gabriela Rucker, right, shown with fellow senior Clare McCarthy.

“It was exciting to be immersed among 45,000 people working to generate solutions to the climate crisis," says Gabriela Rucker, a senior majoring in environmental sciences on the social science and policy track. 

Her interest in sustainable agriculture took her to the food-systems pavilion. She learned about programs to compensate farmers for preserving ecosystems and the increasing use of seaweed as a nutrient. “That was cool, right off the bat, to hear about those food solutions.” 

Rucker is a member of the Plastic-Free Emory task force and appreciated insights from Eric Njuguna, an activist from Kenya, during the “Youth: From Resistance to Power” event. 

“The United States exports a significant amount of plastics and other recycling abroad, where it ends up in landfills and becomes another country’s problem,” she says. “Eric Njuguna talked about his experiences dealing with trash from the United States. It’s important that people in the United States understand where our trash goes when we throw it away.” 

The connections she made during COP were a highlight for Rucker. “I met a lot of youth with passion and drive,” she says. “We have our careers in front of us so connecting with fellow youth about where they want to go and what they want to work on was invaluable.” 

Rucker is currently an intern at a solar-power development company. “My dream job would involve building solar plants to provide clean electricity for the United States,” she says. “During the next 20 years we need to build out a significant amount of renewable energy infrastructure.” 

Ultimately, COP further fueled her optimism. “I generally have a lot of hope for the progress of humanity,” Rucker says. “I’ve witnessed throughout my life people’s work toward a cleaner and more equitable society. My hope stems from the people who are doing the work to make that vision happen.”

Senior Jack Miklaucic is grateful for the anonymous donor who funds the trips by Emory students to COP. "It's a tribute to Dr. Saikawa's work that a donor is willing to do this for her students year after year," he says.

“The best part of COP for me was attending events led by civic groups doing energy-justice advocacy, which is the kind of work that I want to do,” says Jack Miklaucic, a senior majoring in environmental sciences and philosophy, politics and law. “They were led by really cool people who are fearless about calling out the fossil fuel companies and speaking truth to power. Hopefully, their examples will make me a more effective activist going forward.” 

Miklaucic plans to attend law school and hopes for a career involved with ensuring that utility companies and other energy providers are better regulated. “I want my work to have a direct, positive impact on society,” he says. 

“Enhancing energy efficiency is a big win for everybody,” Miklaucic adds. “It will improve people’s lives on the economic, climate and health levels. We’re already seeing movement toward more energy efficiency so that provides incentive to keep working towards more.” 

He is optimistic regarding climate solutions. “We were looking at a 3-to-4-degree Celsius rise in the global temperature average a few years ago and that’s no longer likely,” he points out. ”It’s important to stay focused on what kind of impact we can make because every tenth of a degree matters for what kind of world we’re going to live in.” 

Miklaucic appreciated the international perspective he gained from COP. “It was interesting to learn how climate activism is different around the world,” he says. “In some places they are persecuted and outright killed for doing what they do. It drove home to me that while it can be frustrating at times working for energy justice in the United States, it’s also a much safer place to be doing it.” 

"Every single person will be affected," says senior Clare McCarthy of climate change.

Clare McCarthy is a senior majoring in environmental sciences on the community building and social change track. She is also pursuing the 4+1 BS/MPH in environmental health at Rollins School of Public Health. 

She began learning about how the climate crisis is a social justice issue while she was in high school. It made her feel guilty to realize how people in the Global South tend to disproportionately suffer the greatest impacts of climate change as opposed to more privileged people in her hometown, where climate change felt distant. 

“That guilt paralyzed me,” she recalls, “until I came to Emory, when I decided to take action.” McCarthy is involved in efforts to hold the Emory administration accountable to stronger climate action through the Emory Climate Coalition and Emory Climate Reality Project. 

COP helped solidify her interest in loss and damage, or the harmful impacts of climate change, as well as efforts by local communities to adapt. She learned more about these issues first-hand by talking to leaders of nongovernment organizations, such as the International Center for Climate Change and Development, based in Bangladesh. 

“Loss and damage and how to address it became a headline issue for the first time at this year’s COP,” McCarthy says. “While it’s great to see this, it cannot be celebrated as a final victory because it’s way overdue and much more work is needed.” 

Countries in the Global South are asking countries in the Global North to set up a mechanism for financing recovery from both economic and health impacts due to climate events. “They want the money to be payments and not in the form of loans because then they will be in debt,” McCarthy says.

She envisions a career working internationally or within the United States to help communities build their capacity to respond to climate change. 

“It makes me feel hopeful to meet so many impressive people working on solutions,” McCarthy says. “The passion and dedication of my fellow activists, here at Emory and in communities around the world, keeps me going.” 

"Climate change is the greatest challenge that my generation faces," says senior Jackson Pentz, second from right. While in Egypt he visited the Great Sphinx of Giza along with his fellow undergraduates, (from left) Clare McCarthy, Gabriela Rucker, Jack Miklaucic and Nick Chang. 

“A lot of people associate environmental science with governmental policy but I’ve always been interested in business as a way of creating social change,” says Jackson Pentz, a senior majoring in Economics and Environmental Science on the Social Science and Policy Track. Pentz is also a member of the Goizueta Business School’s Environmental Management program. 

At COP he was impressed to learn that companies that compete for market share are actually collaborating on sustainability. “Many businesses are finding that in order to address sustainability issues they need to pool their research-and-development funding and share their knowledge,” he says. “The private sector is taking sustainability seriously and can come together more quickly and effectively than governments.”

Pentz already has a job lined up after he graduates in May. He’ll be working as a business consultant at McKinsey and Company specializing in sustainability and natural resources. 

Thinking about the climate crisis at the global, or even the national, level can make you feel helpless, he says. “But if you zoom in on individuals or organizations at the smaller scale, you start to see lots of positive action that can be replicated to make a bigger impact,” he adds. 

At the “Youth: Resistance to Power” event Pentz was buoyed by the remarks of Ayisha Saddiqa, a young climate justice activist who grew up in Pakistan as the member of an Indigenous community.

“She told us that young people shouldn’t feel responsible for saving the world. That’s obviously too big of a burden,” Pentz says. “But she personally feels responsible for working to help her community. If everybody does something manageable to help those around them, that’s how you start a social movement and collective action to improve things on a global scale.”

Related:

Youth views on climate take the world stage

Peachtree to Paris: Emory delegation headed to climate talks

Thursday, November 17, 2022

New chemistry toolkit speeds analyses of molecules in solution

"We've freed the researchers from most of the tedious, manual tasks of data input," says Emory theoretical chemist Fang Liu, center. Her team members who developed the toolkit include Emory graduate student Ariel Gale, left, and postdoctoral fellow Eugen Husk, right. Not shown is Xiao Huang, who worked on the project as an undergraduate.

By Carol Clark

A new open-source toolkit automates the process of computing molecular properties in the solution phase, clearing new pathways for artificial-intelligence design and discovery in chemistry and beyond. The Journal of Chemical Physics published the free, open-source toolkit developed by theoretical chemists at Emory University. 

Known as AutoSolvate, the toolkit can speed the creation of large, high-quality datasets needed to make advances in everything from renewable energy to human health. “By using our automated workflow, researchers can quickly generate 10, or even 100 times, more data compared to the traditional approach,” says Fang Liu, Emory assistant professor of chemistry and corresponding author of the paper. “We hope that many researchers will access our toolkit to perform high-throughput simulation and data curation for molecules in solution.” 

Such datasets, Liu adds, will provide a foundation for applying state-of-the-art machine-learning techniques to drive innovation in a broad range of scientific endeavors. 

First author of the paper is Eugen Hruska, a postdoctoral fellow in the Liu lab. Co-authors include Emory PhD candidate Ariel Gale and Xiao Huang, who worked on the paper as an Emory undergraduate and is now a graduate student of chemistry at Duke University. 

Exploring the quantum world 

A theoretical chemist, Liu leads a team specializing in computational quantum chemistry, including modeling and deciphering molecular properties and reactions in the solution phase. 

The world becomes much more complex as it shrinks down to the scale of atoms and small molecules, where quantum mechanics describes the wave-particle duality of energy and matter. 

Theoretical chemists use supercomputers to simulate the structures of molecules and the vast array of interactions that can occur during a reaction so that they can make predictions about how a molecule will behave under certain conditions. Understanding these dynamics is key to identifying promising molecules for various applications and for driving reactions efficiently. 

Researchers have already generated datasets for the properties of many molecules in the gas phase. Molecular properties in the solution phase, however, remain relatively unexplored in the context of big data and machine learning, despite the fact that most reactions occur in solution. 

The problem is that studying a molecule in solution requires much more time and effort. 

A complicated process 

“In the gas phase, molecules are far from each other,” Liu explains, “so when we study a molecule of interest, we don’t have to consider its neighbors.” 

In the solution phase, however, a molecule is closely immersed with many other molecules, making the system much larger. “Imagine a solvent molecule surrounded by layers and layers of water molecules,” Liu says. “Depending on its size and structure, a molecule may be covered by tens, or even up to hundreds, of water molecules. In systems of such large size, the computation will be slow and may not even be feasible.” 

Before running a quantum chemistry program for a molecule in the solution phase it’s necessary to first determine the geometry of the molecule and the location and orientation of the surrounding solvent molecules. 

“This process is difficult to do,” Liu says. “It takes so much time and effort, and it’s so complicated, that a researcher can only perform this calculation for a few systems that they care about in one paper,” Liu says. 

Technical issues can also arise during each step in the process, she adds, leading to errors in the results.

A streamlined solution 

Liu and her colleagues replaced the complicated steps required to perform these calculations with their automated system AutoSolvate. 

Previously, a computational chemist might have to type hundreds of lines of code into a supercomputer to run a simulation. The command-line interface for AutoSolvate, however, requires just a few lines of code to conduct hundreds of calculations automatically. 

“The time for running the simulations may be long, but that’s a job for the computer,” Liu says. “We’ve freed the researchers from most of the tedious, manual tasks of data input so that they can focus on analyzing their results and other creative work.” 

In addition to the command-line interface geared toward more experienced theoretical chemists, AutoSolvate includes an intuitive graphical interface that is suitable for graduate students who are learning to run simulations. 

Labs can now efficiently generate many data points for solvated molecules and then use the dataset to build machine-learning models for chemical design and discovery. AutoSolvate also makes it easier to build and share datasets across different research groups. 

Setting the stage for machine learning 

“During the past 10 years, machine learning has become a popular tool for chemistry but the lack of computational datasets has been a bottleneck,” Liu says. “AutoSolvate will allow the research community to curate a huge number of datasets for molecular properties in the solution phase.” 

Determining the redox potential of a solvent molecule, or the likelihood for an oxidation to occur, is just one example of a key research area that AutoSolvate could help advance. Redox-active molecules hold potential for applications in the development of anticancer drugs and chemical batteries for renewable-energy storage. 

“Building up redox-potential datasets will then allow us to use machine learning to look at millions of different compounds to rapidly find the ones with redox potential within the desired range,” Liu says.

Instead of a black-box result, such analyses of large datasets can yield interpretable artificial intelligence, or basic rules for molecular models.  

“The ultimate goal is to identify rules that can then be applied to solve a broad range of fundamental science problems,” Liu says. 

The development of AutoSolvate was funded by Emory University with computational resources provided by the National Science Foundation.

Related:

A new spin on computing: Chemist leads $2.9 DOE quest for quantum software

Chemists crack complete quantum nature of water

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

Wednesday, November 2, 2022

Ancient DNA analyses add new complexity to South America settlement

"As more genomes from South America are sequenced and published, they are likely to reveal more nuances about how South America was first settled," says Emory anthropologist John Lindo. His ancient DNA lab specializes in mapping little-explored lineages of the Americas.

By Carol Clark

Genomic analyses of ancient individuals from South America add surprising twists in the story of early human settlement of the continent. The Royal Society Proceedings B published the results, which show ancestral evidence in the Americas for extinct hominins known as Denisovans. 

The work, providing the most complete genetic evidence to date for ancient Central American and South American migration routes, was led by anthropologists at Emory University and archeologists at Florida Atlantic University. 

Identification of Denisovan DNA goes back only to 2010, after Russian scientists uncovered a finger bone dated 50,000 to 30,000 years ago in a cave in the Altai Mountains of Siberia. Additional specimens from the Siberian cave were subsequently tied genetically to Denisovans, an archaic hominin with an affinity to Neanderthals, along with a single specimen from a cave on the Tibetan Plateau in China. 

“It’s phenomenal that Denisovan ancestry made it all the way to South America,” says John Lindo, a co-corresponding author of the paper and an anthropologist at Emory who specializes in ancient DNA analysis. “The admixture must have occurred a long time before, perhaps 40,000 years ago.” 

The fact that the Denisovan lineage persisted and its genetic signal made it into an ancient individual from Uruguay that is only 1,500 years old suggests that it was a large admixture event between a population of humans and Denisovans, Lindo says. 

First author of the paper is Andrew Luiz Campelo dos Santos, an archeologist now at Florida Atlantic University who was formerly at the Federal University of Pernambuco in Recife, Brazil. Dos Santos uncovered the remains of two individuals from northeastern Brazil, who date back 2,000 years and are included in the analyses. 

Co-corresponding author is Michael DeGiorgio from Florida Atlantic University, a population geneticist specializing in human, evolutionary and computational genomics. 

The Americas were the last continents that humans populated. Evidence suggests that Paleolithic hunter-gatherers entered North America from a land bridge that formed between northeastern Siberia and western Alaska during a period of lower sea level around 26,000 to 19,000 years ago. 

The current analyzes compared two newly sequenced ancient whole genomes from northeastern Brazil with present-day genomes and other ancient whole genomes from South America and Panama. The results showed distinct relationships between Meso America, or parts of the modern-day countries of Mexico and Central America, and both present-day South Americans and ancient individuals from northeastern and southeastern Brazil, Uruguay and Panama. The analyses also detected a strong Australasian signal in the ancient genomes from near the Atlantic coast in Brazil. 

These ancestral connections provide new genetic evidence — in support of existing archeological evidence — for an ancient migration route through Panama and along the Atlantic coast of South America. 

Adding to the complexity is the detection of a stronger signal for Denisovan ancestry in the ancient Uruguay and Panama individuals than in those from ancient Brazil. That suggests multiple waves of ancestral migrations along the Atlantic coast, the researchers conclude. 

The Lindo ancient DNA lab specializes in mapping little-explored human lineages of the Americas. Previously, little 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. 

As of the publication date of this paper, Lindo notes, only 12 ancient whole genomes from South America have been sequenced and published, in contrast to hundreds from Europe. Other published ancient genomic sequences from the continent have been limited to mitochondrial DNA (which is typically transmitted exclusively by maternal inheritance) and targeted DNA sequencing (which captures less than one percent of the genome). 

“In this paper we’ve analyzed all of the ancient whole genomes available for South America and found some surprises,” Lindo says. “As more whole genomes from South America are sequenced and published, they are likely to reveal more nuances about how South America was first settled.” 

Related:

Ancient DNA lab maps little-explored human lineages

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

Ancient DNA from Sudan shines new light on Nile Valley past

Monday, October 31, 2022

College, Interrupted: Pandemic took toll on first-year students, study suggests

The study results "support previous research that articulating a 'silver lining' within a stressful event is related to your subsequent well-being," says Robyn Fivush, Emory professor of psychology and co-author of the study.

By Carol Clark

Students who began their college careers in fall 2019, only to have them disrupted by the COVID-19 pandemic in spring 2020, report significantly higher rates of anxiety, depression and academic distress compared with prepandemic samples of first-year students. 

The journal Psychological Science published the analyses of students’ narratives about COVID-19 and self-reported measures of their well-being, in a study conducted by psychologists at Emory University, the University of Kansas, the University of Missouri, the University of Utah and Western Washington University. 

“When the pandemic lockdowns began in 2020 it pulled the rug out from under many people,” says Robyn Fivush, Emory professor of psychology and a co-author of the study. “It was a particularly difficult time for first-year college students, many of whom were away from home for the first time and beginning to explore their adult identities in terms of their relationships, their academic interests and the world of ideas.” 

Fivush’s research focuses on early memory with an emphasis on the social construction of autobiographical memory and the relations among memory, narrative, identity, trauma and coping. 

Jordan Booker, a former postdoctoral student at Emory who is now at the University of Missouri, is first author of the study. 

As universities moved to online courses during the pandemic, the researchers recruited 633 first-year U.S. students, including 84 from Emory, to provide narratives about the impacts of the pandemic on their lives. Narrative prompts included asking the students to describe an event that best captures the challenges they have faced as a result of COVID-19. They were also asked to explain why they chose that particular event to write about and what it says about who they are, who they were and who they might become. 

Their responses spanned a range of challenges, from difficulties with virtual coursework, feelings of isolation, worries about their own health as well as that of family members and financial pressures. 

The study participants also completed self-measurement scales for COVID-19-related stressors and psychological adjustment. The participants repeated these self-measurement scales 12 months later. 

The study found that the pandemic was associated with increased depression, general anxiety, social anxiety, eating concerns, academic distress and hostility relative to prepandemic samples of first-year students. 

Students who reported stressors directly related to the pandemic, such as a job loss or the death or debilitating illness of a loved one, were worse off as a group than those who did not. 

The study’s longitudinal analyses also revealed that on most measures, the participants as a group were not getting better a year later. And the measures for general anxiety and academic distress actually increased during the course of the study. 

Students who were able to narrate their experiences with a sense of personal growth, such as learning about their strengths or deepening their relationships during the pandemic, reported lower levels of distress one year later. 

“These results support previous research showing that articulating a ‘silver lining’ within a stressful event is related to your subsequent well-being,” Fivush says. 

The researchers conclude that recovery from the pandemic-related developmental disruptions is likely to be a long-term process. They recommend that academic institutions increase awareness of the issue among faculty, staff and leaders; emphasize learning experiences that support identity development; and create opportunities for students and the university community to make meaning of the pandemic experience through storytelling opportunities that help develop a growth mindset. 

“Not all of the students who participated in the study are struggling,” Fivush says. “We know that there is a substantial minority who have been able to overcome the stressors of COVID by creating meaning and resilience through narrative. Our next step is to go back into our data and see if we can determine a combination of other factors that predict who is doing okay as opposed to those who may still be struggling.” 

The researchers plan to conduct a follow-up study this year of the participating students, who are now seniors, and into the next year as the students graduate and enter the workforce. 

Related:

First-year students' stories of a pandemic: Study seeks data to help them flourish

How family stories help children weather hard times

Thursday, October 13, 2022

The Self Delusion: A neuroscientist reflects on storytelling and identity in a new book

A farmer is part of Emory psychologist Gregory Berns' new identity. Above he combs "Ricky Bobby," a miniature Zebu bull.

Like many people during the COVID-19 pandemic, Gregory Berns, Emory professor of psychology, took a long hard look at his life and his work and decided to make some major changes. He moved with his family to a farm about an hour south of Atlanta, where he tends to three dogs, four chickens and a small herd of seven cattle.

He also wrote a book, "The Self Delusion: The New Neuroscience of How We Invent — and Reinvent — Our Identities," published by Basic Books. 

"I've always wanted to write about some of the research I did many years ago about how reading fiction changes the brain," Berns says. "The book became more about how narratives make us into who we are."

Read more here about the book and how it reflects the changing trajectory of Berns' own life. 

Related:

How family stories help children weather hard times

A novel look at how stories may change the brain

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 Charrúa. At that time, the authors write, the term Charrúa 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. 

Related:

Ancient DNA lab maps little-explored human lineages

Ancient DNA from Sudan shines new light on Nile Valley past

'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. 

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