Monday, November 20, 2023

Birds set foot near South Pole in Early Cretaceous, Australian tracks show

Emory's Anthony Martin, left, at the site of the discovery with Melissa Lowery, a local volunteer fossil hunter who was the first to spot most of the tracks. (Photo by Ruth Schowalter)

The discovery of 27 avian footprints on the southern Australia coast — dating back to the Early Cretaceous when Australia was still connected to Antarctica — opens another window onto early avian evolution and possible migratory behavior. 

PLOS ONE published the discovery of some of the oldest, positively identified bird tracks in the Southern Hemisphere, dated to between 120 million and 128 million years ago. 

“Most of the bird tracks and body fossils dating as far back as the Early Cretaceous are from the Northern Hemisphere, particularly from Asia,” says Anthony Martin, first author of the study and a professor in Emory University’s Department of Environmental Sciences. “Our discovery shows that there were many birds, and a variety of them, near the South Pole about 125 million years ago.” 

Read the full story here. 

Related: 

Tell-toe toes point to oldest-known bird tracks from Australia 

Paleontologist explores a billion years of animals breaking up rocks, bones, shells and wood

Friday, November 10, 2023

NSF funds holistic approach to help farmers adapt to climate change

"There is already a lot of work on what climate change may mean for agriculture in general," says Emily Burchfield, Emory assistant professor of environmental sciences. "But what climate change means for an individual farm must be filtered through issues particular to that farm."

By Carol Clark

The National Science Foundation (NSF) awarded Emily Burchfield, Emory assistant professor of environmental sciences, $1.6 million to lead efforts to identify emerging pressures on agriculture in Georgia, Iowa and Ohio and to develop predictive models to help farmers and policymakers weather these changes. 

“In a nutshell, we’re trying to understand what climate change will mean for agriculture in these three states,” Burchfield says. “We’ll be integrating biophysical projections based on environmental data with insights gathered from farmers and agricultural experts.” 

The goal is to develop possible scenarios for the impacts of climate change — along with the evolving technical, socioeconomic and political landscapes in each state — for how and where crops could be grown over the next 30 to 40 years. The researchers will create a public, online tool to allow farmers and policymakers to explore the possible futures of agriculture at regional and state levels and to support their efforts to manage these scenarios. 

The grant is part of the NSF Dynamics of Integrated Socio-Environmental Systems Program (DISES). 

“Traditionally, the NSF has mainly split programs into the social sciences and the natural sciences but DISES is one of their newer programs that joins the two, looking at how nature affects people and people affect nature,” Burchfield says. “Coupling human and natural systems in theoretical frameworks allows us to take on some of the grand challenges that we’re facing, like climate change and food and water security.” 

Burchfield is principal investigator for the project, which also includes researchers from Arizona State University, Ohio State University and the University of Nebraska, Lincoln. 

A range of agricultural systems 

While the two main crops in both Iowa and Ohio are corn and soy, agriculture in Georgia is far more diverse. The state leads the nation in the production of peanuts, pecans, blueberries and spring onions and is also a leading producer of cotton, watermelon, peaches, cucumbers, sweet corn, bell peppers, tomatoes, cantaloupes, rye and cabbage. 

Agriculture contributes nearly $70 billion annually to Georgia’s economy and one in seven Georgians works in agriculture, forestry or related fields, according to the Georgia Farm Bureau. 

“Compared to other parts of the country, Georgia is incredibly diverse not just in terms of what is grown in the state but in terms of who grows it,” Burchfield says. “A lot of exciting changes are happening in the state — citrus production is moving into South Georgia. And the biggest organic farm east of the Mississippi is located in Georgia, producing carrots.” 

While California currently produces the bulk of the nation’s produce, that state is facing significant challenges for water availability, Burchfield notes. “Georgia has a unique opportunity to expand its fresh-produce production to help meet future demand,” she says. “We want to provide farmers the resources they need to capitalize on such trends.” 

Building tools for the future of farming 

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. 

For the current project, the researchers will draw from available climate, soil and land-use data to create biophysical models for how changes in climate will affect where and how particular crops can be grown. These models will be integrated with data gathered from surveys and focus groups conducted with agricultural experts, climatologists and farmers working the land throughout Georgia, Iowa and Ohio. 

The project aims to get input from a diverse range of farmers growing different crops and using different management practices. 

“There is already a lot of work on what climate change may mean for agriculture in general,” Burchfield says. “But what climate change means for an individual farm must be filtered through issues particular to that farm. So many dimensions that matter deeply to farmers are not included in policy discussions about agriculture.” 

Farmers will be asked what information and resources they need to sustain their operations and to adapt to climate change. “We want to understand the vision that farmers have for the future of their farms,” Burchfield says. “What would they would like to see happen? What do they see as the barriers and bridges to achieving that vision?” 

The public, online tool that the researchers develop will include interactive maps for crop forecasts by region. It will also provide information to guide policymakers and to help farmers adapt to the changes ahead. 

“It’s impossible to accurately say exactly what’s going to happen in the future,” Burchfield says. “But combining biophysical data with an understanding of the technical, economic and political changes emerging in each of these states, along with the expertise of our farmers, will allow us to forecast trends for how suitable particular regions will be for growing certain crops. The bottom line is we are pulling together the best information available to give a sense of the emergent opportunities in the state for agriculture as well as the emergent challenges.” 

Related:

Emory breaking new ground for climate-smart agriculture

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

Thursday, November 9, 2023

New antimicrobial shuts down bacterial growth without harming human cells

Graphic shows how the KKL-55 molecule (in red) inhibits trans-translation, a process that bacteria cells use for quality control during protein synthesis.

By Carol Clark

Scientists have shown how a molecule with broad-spectrum antibiotic activity works by disabling a process vital to bacterial growth without affecting the normal functioning of human cells. mBio, a journal of the American Society for Microbiology, published the work, led by researchers at Emory University and Pennsylvania State University. 

The molecule, known as KKL-55, is one of a suite of recently identified molecules that interfere with a key bacterial mechanism known as trans-translation, essentially shutting down the ability of bacteria to grow. 

“We’re opening a promising pathway for the development of new antibiotics to treat drug-resistant infections,” says Christine Dunham, co-corresponding author of the paper and a professor in Emory’s Department of Chemistry and the Emory Antibiotic Resistance Center. 

Kenneth Keiler, a professor in the Department of Biochemistry and Molecular Biology at Pennsylvania State, is co-corresponding author of the paper. 

First authors are Ha An Nguyen, who did the work as an Emory chemistry PhD candidate and has since graduated and works at Memorial Sloan Kettering, and Neeraja Marathe, a graduate student at Pennsylvania State. 

A growing global threat 

Antimicrobial-resistant infections have long been a public health threat. The situation grew even worse during the COVID-19 pandemic with increased antibiotic use and less prevention actions, according to the U.S. Centers for Disease Control and Prevention (CDC). 

The CDC estimates that at least 2.8 million antimicrobial-resistant infections continue to occur in the United States each year, killing more than 35,000 people. Globally, the World Health Organization projects that these infections will cause up to 10 million deaths annually by 2050 if new antibiotics are not developed. 

While antibiotics can save lives, any time they are used they can also contribute to the problem of resistance. Bacteria keep evolving new weapons as a defense against drugs, even as scientists work on developing new strategies to disarm bacteria. 

Cross-toxicity, or harmful effects on humans, is another key drawback of some of the drugs used in a last-ditch effort to kill antibiotic-resistant bacteria. 

Avoiding cross-toxicity 

Dunham and Keiler are avoiding the problem of cross-toxicity by focusing on the inhibition of a mechanism unique to bacteria — trans-translation. This mechanism is vital to the proper functioning of the bacterial ribosome. 

Keiler, a molecular geneticist and biochemist, first identified trans-translation in bacteria and is an expert in how it functions. Dunham, a structural biologist, is an expert in the human ribosome. She uses advanced biochemistry and structural biology techniques to understand the mechanics of molecular interactions. 

“Our individual areas of expertise mesh well for this project,” Dunham says. “By collaborating, we are able to take the science further, faster.” 

A cellular protein factory 

The ribosome is an elaborate macromolecular machine within a cell that operates like a factory to manufacture proteins. Proteins are the machines that make cells run while nucleic acids such as DNA and RNA store the blueprints for life. The ribosome is made mostly of RNA, which does not just store information but can also act as an enzyme, catalyzing chemical reactions. 

In a human cell, messenger RNA (mRNA), containing the instructions for manufacturing a protein, originates in the nucleus. While still in the nucleus, mRNA undergoes an elaborate quality-control process. It must pass inspection before getting exported to translate the information it contains into a protein. 

“A lot of mRNAs have defects,” Dunham says. “Human cells have efficient ways to test mRNAs and ultimately remove the defective ones.” 

Bacterial cells, however, have no nucleus or organized center for quality control. 

“Bacteria wants to grow, grow and grow, which requires the ribosome to make a lot of proteins,” Dunham says. “But when mRNA has defects, there is little to no quality control. When the ribosome encounters a defective mRNA protein, synthesis gets stalled.” 

The trans-translation process “rescues” ribosomes stalled due to such defects, in order to maintain proper protein synthesis and cell viability in bacteria. 

How KKL-55 works 

Using a high-throughput screening process, the Keiler lab has identified dozens of molecules that inhibit trans-translation in bacteria. 

For the current paper, the researchers focused on understanding how one of these molecules, KKL-55, performs this trick. They used the high-powered structural biology technique of X-ray crystallography to capture KKL-55 in action as it interacted with a protein required for translation. 

The results showed how KKL-55 blocks trans-translation by binding to elongation factor thermos-unstable (EF-Tu). EF-Tu is a protein that interacts with transfer RNA molecules, which play a key role in protein synthesis, and also transfer-messenger RNA, an RNA molecule required for the trans-translation pathway. 

“We got lucky,” Dunham says. “There are dozens of steps involved in the process that KKL-55 could have inhibited and we might have had to test for each one. But the results are clear-cut. It shuts down trans-translation right at the beginning by preventing EF-Tu from binding to tmRNA.” 

Determining the mechanism by which a molecule works to inhibit bacteria is a critical step toward developing a new antibiotic for clinical use. The next step is to test the efficacy of KKL-55 to treat a bacterial infection in a mouse model. 

In 2021, the research team published their finding that a group of trans-translation inhibitors known as acylaminooxadiazoles clear multiple-drug-resistant Neisseria gonorrhoeae infection in mice after a single oral dose. That work is now advancing to clinical trials. 

Dozens more trans-translation inhibitors await the team’s investigation. Each represents a potential new weapon to help humans stay on top in the arms race with drug-resistant bacteria. 

Co-authors of the current paper include Alexandra Nagy (a former National Institutes of Health FIRST Institutional Research and Academic Career Development postdoctoral fellow at Emory who is now at Earlham College); as well as John Alumasa and Michael Vazquez (both from Pennsylvania State University). The work was funded by the National Institutes of Health, the National Institute of General Medical Sciences. 

Related:

Images of enzymes in action reveal secrets of antibiotic-resistant bacteria 

Biochemist Dunham shifts the frame on proteins

Monday, October 23, 2023

Emory breaking new ground for climate-smart agriculture in the Southeast

"Our project is unique in that it focuses on the Southern Piedmont and an often under served piece of our food system, but one that is vital to providing us the nutrients we need — the vegetable sector," says Emily Burchfield, assistant professor of environmental sciences.

Three Emory University researchers received $5,100,000 as part of a United States Department of Agriculture (USDA) project to help measure and promote climate-smart practices that support small-scale, diversified vegetable farmers in the Southern Piedmont. A plateau below the Appalachian Mountains and above the coastal plain, the Southern Piedmont is a banana-shaped region spanning a bit of eastern Alabama, up across part of northern Georgia and into North and South Carolina and Virginia. 

Emory is one of 12 organizations involved in the $25 million project, headed by the Rodale Institute and titled “Quantifying the Potential to Reduce Greenhouse Gas Emissions and Increase Carbon Sequestration by Growing and Marketing Climate-Smart Commodities in the Southern Piedmont.” 

The five-year project is part of the USDA’s Partnerships for Climate-Smart Commodities initiative. “This effort will increase the competitive advantage of U.S. agriculture both domestically and internationally, build wealth that stays in rural communities and support a diverse range of producers and operation types,” USDA Secretary Tom Vilsack says of the initiative. 

The Emory team encompasses three faculty from the Department of Environmental Sciences: Emily Burchfield, Eri Saikawa and Debjani Sihi. 

• Burchfield combines spatial-temporal social and environmental data to understand the future of food security in the United States. 

• Saikawa is an atmospheric chemist who models global soil nitrous oxide emissions and quantifies soil greenhouse gas fluxes. 

• Sihi is an environmental biogeochemist who researches soil organic matter dynamics and greenhouse gas emissions from natural and managed systems. 

Read more here.

Related:

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

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

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

Thursday, October 19, 2023

Math trio makes new points about size of the smallest triangle

"It's a very rich area, to study tiny, small-scale shapes and uncover what the math hidden there can tell us," says Emory mathematician Cosmin Pohoata.

By Carol Clark

Think of a square dotted with points. Now imagine the smallest triangle that could be made by connecting three of those points. That’s the Heilbronn triangle problem in a nutshell. 

“The problem is very easy to state and can sound frivolous,” says Cosmin Pohoata, a theoretical mathematician and Emory assistant professor of mathematics “When I have conversations with non-math friends, they often ask me why we should study problems like this. The beauty of them is that they are often more complex than they seem. They can have unexpected connections that open new doors for understanding all sorts of phenomena.” 
 
Pohoata and two MIT graduate students, Alex Cohen and Dimitrii Zakharov, recently opened some of those new doors. They completed a new proof for the Heilbronn triangle problem that shows that the smallest triangle in a confined space is much smaller than was previously realized, breaking a record that stood for 40 years. 
 
Their proof, available online, is submitted to the Journal of the American Mathematical Society and is already making waves in the math world. 

“I think it’s a stunning result,” Anthony Carbery, a mathematician at the University of Edinburgh, told Qanta Magazine. And Thomas Bloom of the University of Oxford told Qanta that he expects the new proof to “prompt a renaissance” of progress on the triangle problem. 
 
“What makes the proof special to me,” Pohoata says, “is the way that we connected the triangle problem to different areas of math. In particular, harmonic analysis, the study of how waves interact with one another and projection theory, or the behavior of fractals under projections.” 

A graphic representation of the Heilbronn triangle problem.

The making of a mathematician 

Pohoata loved math from the time he was a small child growing up in Romania. He cites an elementary school teacher, who encouraged his love for numbers and patterns, as one key influence. 

In middle school he began competing in International Mathematical Olympiads (IMO). Romania is the original home of the IMO, which dates back to 1959, making it the oldest of the International Science Olympiads. Today more than 100 countries compete in the annual event. 

“I thought I knew a lot about math because the problems in class had been so easy for me,” Pohoata recalls. “When I started competing in the Olympiads, I began to realize how little I knew and how much math was out there to learn.” 

He began to think about math as a career. “It’s quite fun to get to think about problems that interest you,” he says. 

Pohoata attended Princeton as an undergraduate, got his PhD at the California Institute of Technology and taught at Yale before joining Emory this fall. 

Patterns in points and lines 

As a theoretical mathematician, Pohoata focuses his research on three specialized fields: Discrete geometry, additive number theory and extremal combinatorics. 

Extremal combinatorics examines how large or small finite objects such as graphs can be, if placed under certain restrictions. For centuries, it seemed like an esoteric endeavor. 

“The breadcrumbs to extremal combinatorics trace back to ancient Greece,” Pohoata says, “but the field didn’t really come alive until the late 20th century with the rise of computers and the internet. Graphs are at the heart of many things to do with computer science and the internet.” 

Facebook “friend” networks, for example, are large collections of data that are essentially graphs. “You can think of people in the world as points on paper and then draw arrows connecting the ones who are friends,” Pohoata explains. “Then you can look at basic questions underlying these structures. If you have at least seven points do you always have triangles? When do you see a big cluster of connected vertices? Are there areas of the world that are less connected than others?” 

Real-life problems, like how to make algorithms run faster, fuel interest in studying problems about graphs and related areas. 

“As a theorist, I’m driven simply by the math behind shapes and the beauty of them,” Pohoata says, “but I do get excited when I hear that some math breakthrough has been used in a cool way to help with a practical problem.” 

The human side of math 

“I wasn’t interested in the history of math when I first started out,” Pohoata says. “Why learn the progression of results if you have the latest result?” 

But when he taught an introductory course to number theory, it forced him to look more closely at the history of the greats and trace the chronology of events. “I started realizing that you can get many new ideas by following the progress of the past rather than just focusing on the latest thing,” he says. “And I personally learn better when I follow the story of the people in the history of math. You feel the math differently, too, when you put yourself in someone else’s shoes.” 

Pohoata’s interest in the Heilbronn triangle problem inspired him to delve deeper into the work of Klaus Roth, a German-British mathematician who won math’s highest honor, the Fields Medal. “Roth does elegant math that has inspired a lot of activity,” Pohoata says. 

In 1951, Roth developed a strategy for finding the smallest possible triangle within the parameters of the Heilbronn triangle problem, or its so-called “upper bound.” Austrian mathematician Wolfgang Schmidt pushed the upper bound further in a paper published in 1972. That inspired Roth to jump back into the game. Roth further improved the result by Schmidt, just a few months after Schmidt’s breakthrough. 

A tiny problem 

“Roth and Schmidt had a kind of rivalry to see who could come up with the best recipe to find even smaller triangles,” Pohoata says. “They were writing beautiful papers, improving on each other’s work. I learned a lot by studying them.” 

In 1980, a trio of mathematicians — Komlos, Pintz and Szemeredi — pushed the envelope even further, finding a new upper bound to the Heilbronn triangle problem. 

While the problem in its simplest form can be thought of as dots and lines drawn on paper, the mathematicians are working with triangles far too tiny to be “seen” without special tools. 

“You can think of these triangles as microscopic,” Pohoata says. “We’re talking about billions of points crammed within a confined space.” 

Just as scientists keep making improvements in microscopy to get an ever more detailed view of the tiniest parts of a living system or of distant galaxies imperceptible to human eyes on Earth, theoretical mathematicians create tools to get closer and sharper views of the math underlying the universe and everything in it. 

Making connections 

Pohoata had pondered the Heilbronn triangle problem for several months with Zakharov. He met Cohen last year in a chance encounter at MIT, where he had traveled to give a presentation. 

“When math people get together, they like to talk about recent problems on their minds,” he says. “We were excited to learn that we were taking similar approaches to the Heilbronn triangle problem. And that we were all stuck in the same place.” 

The trio decided to join forces. Unlike many of their math heroes of the past, who communicated across distances by letter, they exchanged ideas in real time through Zoom and the Discord instant-messaging platform. 

“Math research is becoming more of a social experience as the world has become more connected,” Pohoata says. “Technology facilitates collaboration.” 

Rather than a single, euphoric eureka moment, he describes the process of creating their 40-page proof as a series of smaller insights. “There are many moving pieces to this proof and each one had to come together,” Pohoata explains. “There was a lot of going back and forth to get all the pieces to fit. You can think of it like putting together a really complex Lego structure.” 

Ultimately, their breakthrough revealed new connections between the Heilbronn triangle problem and other areas of mathematics, including harmonic analysis and fractals — figures that are similar and keep repeating one another at smaller and smaller scales. 

Pohoata and his two MIT colleagues are continuing to work on explaining this web of connections in more detail. “It’s a very rich area, to study tiny, small-scale shapes and uncover what the math hidden there can tell us,” Pohoata says. “What makes math fascinating is that it’s the language for how things work in the world.” 

Related: