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. 


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.” 


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. 


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

Biochemist Dunham shifts the frame on proteins