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Dataset revolutionizes understanding of beta barrels, promising targets for vaccine development
LAWRENCE — Scientists have focused on tubelike “outer-membrane proteins” found in certain types of gram-negative bacteria that could be crucial to developing vaccines against a range of drug-resistant infections. These outer-membrane proteins often assume a tubelike shape, known as beta barrels. Now, researchers from the University of Kansas have created a new and powerful dataset shedding light on different types of beta barrels as well as their evolutionary relationships in order to facilitate drug development. Their findings recently were published in the Proceedings of the National Academy of Sciences.
New book tells story of Tom Foley, historic speaker of the House
LAWRENCE — A new biography from University of Kansas Press and co-written by a KU faculty member tells the story of Thomas Foley, perhaps one of the last American politicians to truly lead from the center, who in the end lost his seat in the rising era of fierce partisanship. “Tom Foley: The Man in the Middle” chronicles the life and career of the former speaker of the House.
AAI announces the Center for Culturally Responsive Educational Neuroscience
LAWRENCE — The Achievement & Assessment Institute (AAI) at the University of Kansas has announced a new center to draw on the latest research from neuroscience, education and educational psychology to better understand how people learn and what can be done to improve their development. The cornerstone of the Center for Culturally Responsive Educational Neuroscience is the Graduate Certificate in Mind, Brain & Education.
Full stories below.
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Contact: Brendan Lynch, KU News Service, 785-864-8855, [email protected], @BrendanMLynch
Dataset revolutionizes understanding of beta barrels, promising targets for vaccine development
LAWRENCE — Examples of infections tied to gram-negative bacteria include pneumonia, bloodstream infections, wound-site infections and meningitis, according to the Centers for Disease Control and Prevention.
Scientists have focused on tubelike “outer-membrane proteins” found in certain types of gram-negative bacteria that could be crucial to developing vaccines against a range of such infections, some of which show increasing drug resistance. These outer-membrane proteins often assume a tubelike shape, known as beta barrels, that have great potential as vaccine targets.
Now, researchers from the University of Kansas have created a new and powerful dataset shedding light on different types of beta barrels as well as their evolutionary relationships in order to facilitate drug development. Their findings recently were published in the peer-reviewed journal Proceedings of the National Academy of Sciences.
According to co-author Joanna Slusky, associate professor of molecular biosciences and computational biology at KU who oversaw the research in her lab, the new understanding of beta barrels enables fresh lines of scientific inquiry as well as drug development.
“Outer membrane proteins reside in the outer membrane of gram-negative bacteria, and all of these membrane proteins take on a beta-barrel structure, sharing a common basic topology.” Slusky said. “The outer membrane plays essential roles, including nutrient import, toxin export, adhesion, enzymatic activity and environmental adaptation, all governed by these outer membrane proteins.”
The Slusky team’s approach to producing the new dataset diverged from past efforts, which only sought to catalog relatives of known outer-membrane proteins. The new method, dubbed “IsItABarrel,” has revealed more than 270,000 previously unidentified outer-membrane proteins that could interest to vaccine researchers. Slusky’s group has posted the database online to enable such work.
“Recognizing their shared beta barrel characteristic as a distinctive shape, we developed an algorithm that yielded approximately 1.9 million instances of these proteins,” Slusky said. “From there, we cluster them into distinct groups. The predominant group accounts for around 1.4 million instances. Then, a substantial portion, approximately 500,000 instances, falls into various other groups. This suggests that nature independently developed this fold multiple times.”
Whereas the Slusky lab and others had previously detected two or three instances where protein evolution had converged on the beta barrel shape, now the KU team has identified 11 independent instances of this occurrence in various bacterial types.
“Our initial exploration revealed more bacteria had this type of protein than anticipated, including those previously underrepresented,” Slusky said. “Furthermore, we observed an enhanced presence of transmembrane beta barrels in bacteria we already knew had these proteins. Our confidence metrics demonstrate minimal false positives, as well as comparable false negatives to other methods. This affirms the reliability of our algorithm.”
The Slusky Lab’s investigation also revealed that while many proteins show the characteristic “barrel signal,” or sequences of amino acids long known to fold into the barrel shape, other types of proteins feature barrel signs that were unknown until the team’s analysis with “IsItABarrel.”
“This sequence motif plays a pivotal role in facilitating both the insertion and folding of proteins within the membrane,” said the KU researcher. “The commonly recognized motif is exclusively present in the prototypical beta barrels. Conversely, alternative proteins exhibit entirely different motifs that lead to the formation of distinct barrel groups within the membrane. This discovery provides additional substantiation for the concept of independent evolution. However, it also underscores the limitations in our comprehension of the folding process for these other proteins.”
Slusky said the discovery that bacteria can make beta barrels using new sequence motifs of amino acids should provoke many new lines of research.
“Do they use the same folding mechanism as the aforementioned proteins, or do they employ an entirely different approach?” she said. “It remains uncertain whether these proteins use a similar mechanism for insertion, potentially with the assistance of a distinct protein. Alternatively, their insertion process may be fundamentally distinct. Definitive answers to these inquiries are still pending.”
Slusky’s collaborators on the work were lead author Daniel Montezano, a KU postdoctoral researcher, along with co-authors Rebecca Bernstein, a high school researcher, and Matthew Copeland, research engineer with KU’s Computational Biology Program.
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Contact: Mike Krings, KU News Service, 785-864-8860, [email protected], @MikeKrings
New book tells story of Tom Foley, historic speaker of the House
LAWRENCE — People often call for political leaders who can display bipartisanship or lead from the center, avoiding ideological extremes. A new biography tells the story of Thomas Foley, perhaps one of the last American politicians to truly lead from the center, who in the end lost his seat in the rising era of fierce partisanship.
“Tom Foley: The Man in the Middle” by R. Kenton Bird and John Pierce tells the story of the former speaker of the House, his 30-year congressional career, representation of a district that leaned against his party, remarkable ability to build consensus between Republican and Democrat leaders and eventual exit from power.
Pierce, affiliate professor of public affairs & administration at KU, and Bird of the University of Idaho, both have long ties to Foley’s career. The former was an American Political Science Association Congressional Fellow assigned to Foley’s office in the early 1970s. The latter was also an APSA fellow working for Lee Hamilton of Indiana in the following decade. Throughout their careers, both worked closely with Foley and other politicians, journalists, policymakers and leaders. A few years ago, the late Burdett Loomis, an influential political science professor at KU, approached Pierce about a book on Foley.
“He said, ‘Maybe you could do a book on Tom Foley,’” Pierce said of Loomis. “He had started a series on congressional leaders at the University Press of Kansas and thought Foley would make for a good subject. I already had in the back of my mind Kenton as a co-author. He had done his doctoral dissertation on Tom, and I knew he would be perfect for this book.”
Their collaboration resulted in “Tom Foley: The Man in the Middle,” (University Press of Kansas, 2023) that tells the story of Foley’s entry into politics, rise to power within his party and national politics, unique leadership style and stunning defeat that led to his exit from Congress.
The book chronicles Foley’s first election to Congress in 1964 as part of the Democratic landslide of that year. As Foley represented a traditionally Republican-leaning district in eastern Washington, the authors document how what some thought may be a short political life turned into 15 terms and an ascent to the speakership of the House. In fact, when he took the speakers’ gavel in 1989, Foley became the first speaker from a district west of Texas.
Not only did Foley thread the needle of representing a district that largely was made up of constituents not of his party, but he also turned that into a balancing act of advocacy for his home district and leadership within his party, the authors wrote. Bird and Pierce document his time as chair of the House Agriculture Committee. His district was heavily agricultural, which afforded him the chance to benefit his district with projects such as a new powerhouse on the Grand Coulee Dam. He also demonstrated grace and civility when his predecessor as chair was demoted by his party, the authors wrote.
“I think that initial position was where he could show the type of leader he was capable of being. Foley appointed his predecessor (William Poage, D-Texas) vice chair, when he could have been hostile, which I think helped launch him through the leadership ranks,” Pierce said.
The book’s chapters chronicle Foley’s rise from the House Agriculture Committee to House Majority Leader and, ultimately, his historic selection as speaker of the House in 1989. The authors point out how his experience in representing a largely Republican district enabled him to build coalitions that were key in landmark legislation, including the Americans with Disabilities Act, reauthorization of the Clean Air Act, deficit reduction legislation and passage of the North American Free Trade Agreement.
But while he “helped lower the temperature of the House,” Foley eventually fell from power. In 1994, he became the first speaker to lose a reelection campaign since the era of Abraham Lincoln. That loss was part of a “perfect storm” that led to Democrats losing the House majority for the first time since 1955, Bird and Pierce wrote. The Newt Gingrich-led “Republican landslide” of 1994 ushered in the era of fierce partisanship and strict ideology that persists today. But while the backlash to the early Clinton administration and traditional loss of seats by the president’s party were part of the reason for Foley’s loss, the authors dug deeper.
“One thing I think was overlooked at the time was the fact of having a likable, credible candidate in George Nethercutt,” Bird said of Foley’s opponent. “Before that, he had run against a series of candidates who were, to put it charitably, not as pleasant, or as high quality of a candidate as Nethercutt. That was certainly a factor.”
“The Man in the Middle” details Foley’s post-Congress legacy, including his service as U.S. ambassador to Japan and the stamp he left on the body, including his deep respect for the institution of Congress, ability to hold the center and model for the speakership he tried to project in his 5 1/2 years with the gavel.
Bird and Pierce’s long histories working with Foley, as well as their trainings as a journalist and political scientist, respectively, put them in a solid position to pen the biography of a unique American political leader, whose traits are rare in today’s American political landscape.
“He was a brilliant guy and very kind. But not weak,” Pierce said of Foley. “One of the challenges for us as political scientists and journalists was what kind of context to put his career in, in terms of his leadership style. He was not a vociferous, in-your-face leader. But he had a clear leadership style, which led to the book’s title, in reference to his coalition building and respect for the institution.”
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Contact: Alicia Marksberry, Achievement & Assessment Institute, [email protected], @AAI_at_KU
AAI announces the Center for Culturally Responsive Educational Neuroscience
LAWRENCE — The Achievement & Assessment Institute (AAI) at the University of Kansas has announced the new Center for Culturally Responsive Educational Neuroscience (CCREN) whose mission is to draw on the latest research from neuroscience, education and educational psychology to better understand how people learn and what can be done to improve their development.
Led by Michael Orosco, professor of educational psychology in the School of Education & Human Sciences, CCREN seeks to bring together professionals from different fields to better understand how cultural and linguistic diversity affects brain function, cognition, learning and education.
“As the world becomes more globalized, educators and researchers have to be ready to better serve students from a wide range of cultural and linguistic backgrounds. CCREN provides an educational neuroscience framework that helps address the growing cognitive diversity we see across America today,” Orosco said.
CCREN arose from Orosco’s own research in the field after he noticed many practitioners had a gap in understanding how the brain learns. Orosco’s hope is that CCREN can create a bridge between research and education and develop innovative teaching methods aligning with how the brain processes and retains information, especially with students from culturally and linguistically diverse backgrounds.
“I am excited that Professor Orosco is leading the university’s charge into the emerging field of educational neuroscience,” said Rick Ginsberg, dean of KU’s School of Education & Human Sciences. “CCREN stands as one of the first centers of its kind and has the potential to change the practice of education.”
The cornerstone of the center is the Graduate Certificate in Mind, Brain & Education, which provides graduate students with training on how to use educational neuroscience to improve their education and learning approaches. Mind, brain and education emerged as a new field of study over the last three decades as technological developments led to better understandings of how the brain works.
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