Books published by Clemson faculty
Mass Shootings: Implications for Students, Schools, Society
Since the start of the 21st century, 66 people have died and 81 have been injured in 13 incidents involving lone shooters at schools.
That’s more deaths related to school shootings than in the whole 20th century, said education professor Antonis Katsiyannis, lead author of a new study published in the Journal of Child and Family Studies that reviews the history of mass school shootings in the U.S. and uncovers some trends:
“One alarming trend is that the overwhelming majority of 21st-century shooters were adolescents, suggesting that it is now easier for them to access guns and that they more frequently suffer from mental health issues or limited conflict resolution skills.”
Beat the Heat
Salamanders have an uncanny ability to alter their behavior and physiology in a way that makes them less susceptible to global warming than previously feared, according to new research authored by Clemson University scientists and published in Science Advances.
Studying salamanders in the southern Appalachian Mountains, a global hotspot for these fascinating amphibians, Michael Sears, associate professor of biological sciences, and Eric Riddell, who earned his doctorate in biological sciences from Clemson in 2018, project that plasticity — an individual’s capacity to change how it responds to the environment — will reduce extinction risk by up to 72 percent, especially in the core ranges. Previous predictions estimated 70 to 85 percent of this moist and humid habitat would become unsuitable for salamanders by 2080 due to rising temperatures caused by climate change. “We can now say more accurately what might occur if climatic conditions continue to deteriorate,” Sears said.
Extreme Bacteria and Organic Veggies
Recently patented organic fertilizer developed at Clemson could rival its synthetic counterparts and provide a big boost for organic vegetable production.
The limited potency, precision and consistency of organic fertilizers has long hindered organic vegetable production. But Brian Ward, an organic vegetable specialist at Clemson’s Coastal Research and Education Center, has developed a method for using “extreme bacteria” isolated from the stomachs of cattle to produce an organic fertilizer so rich with ammonium that it rivals synthetic fertilizers.
Numerous studies have implicated the gut microbiome — our own personal collection of bacteria, archaea, fungi and viruses — in chronic diseases, immunity, digestion and even feelings of depression and anxiety.
Now, Clemson husband and wife researchers Dan and Kristi Whitehead, in a recent publication in the journal ACS Chemical Biology, have detailed the use of a small molecule to slow the growth of a specific genus of bacteria in the gut microbiome called Bacteroides, which has a peculiar link to Type 1 diabetes.
Clemson University hosted more than 40 renowned historians at the Lincoln’s Unfinished Work conference Nov. 28-Dec. 1. Over those four days, an array of scholars spoke on panels and delivered papers on a range of topics including Abraham Lincoln’s sense of humor, reassessments of Reconstruction, the evolution of the Constitution, civil rights, voting rights and how we acknowledge difficult histories.
The conference was organized by Vernon Burton, the Judge Matthew J. Perry Jr. Distinguished Professor of History at Clemson and author of The Age of Lincoln.
It was vital to Burton, a national authority on the history of the South, that all sessions be open to the public, free to all attendees and held on the main campus at Clemson.
“We sweep our history under the rug. We don’t want to deal with it,” Burton said. He asks us all to look more honestly at our past — here at Clemson, in the South and across the country. “Only then can we move forward and do better,” Burton said.
Lincoln’s Unfinished Work began with opening addresses by Pulitzer Prize winner Eric Foner and Harvard law professor Randall Kennedy, who described the gathering as “an intellectual feast.”
The diverse and distinguished field of presenters included Richard Carwardine, Catherine Clinton, Steven Hahn, Darlene Clark Hine, Thavolia Glymph and Heather Cox Richardson. Visiting historians were joined by Clemson faculty, including J. Drew Lanham and Rhondda Robinson Thomas.
The conference included a workshop for public school teachers on how to teach about the history of race relations. Burton also made it possible for high school students from the SC Rural NextGen, a rural youth advocacy group, to attend.
Videos of Lincoln’s Unfinished Work sessions are posted on the website, clemson.edu/lincoln, and a published volume of papers is planned.
In an extension of research published a month ago in Nature Methods, a novel hybrid approach performed by researchers from Clemson University’s department of physics and astronomy and Stony Brook University has revealed a 3-D structure of a protein fragment that could serve as a drug target in treating stroke patients.
The protein called “postsynaptic density protein of 95 kDa (PSD-95)” is positioned on neurons in the brain that are receiving chemical messages – neurotransmitters – from adjacent neurons. By recruiting receptors and other helper proteins, PSD-95 works to maintain the integrity of neural connections over time, thereby facilitating neural communication, learning and memory.
PSD-95 consists of five parts, or domains, that each play a different role in the protein’s overall function. Two of these domains, called PDZ-1 and PDZ-2, have been shown to influence symptoms associated with ischemic stroke, such as paralysis or speech impairment.
“One of the ideas that has been postulated in the literature is to create a multivalent drug that targets both PDZ domains because they’re very similar in nature. If you can block the PDZ domains from binding particular proteins or enzymes, you can reduce the debilitating effects of a stroke,” said Hugo Sanabria, lead author on the study.
The challenge, however, is that it’s nearly impossible to design a drug inhibitor without first knowing the exact structure of the PDZ domains of PSD-95. It would be like driving across the country without having a map of the United States.
“The biological functions of biomolecules are determined by their structures, so we need detailed structural and dynamic insights of PDZ-1 and -2 to help better understand their functional roles and aid in the design of novel inhibitors,” said Feng Ding, Sanabria’s colleague here at Clemson.
A handful of approaches exists to render the structure of biomolecules. But in the case of PSD-95, each approach – NMR spectroscopy, X-ray crystallography and Förster resonance energy transfer (FRET) – delivered a different structural model. The researchers’ collaborator at Stony Brook University, associate professor Mark Bowen in the department of physiology and biophysics, established a partnership with Sanabria on this project after he uncovered one of the inconsistent structural models of the PSD-95 fragment.
Sanabria’s lab addressed this discrepancy by first modeling the PSD-95 fragment using FRET, an approach that identifies possible configurations of biomolecules. Under this method, Sanabria attached two light-sensitive molecules, called chromophores, at two differing positions on the PSD-95 fragment. He then uncovered the distance between the chromophores by visualizing the fragment under a microscope. This was repeated multiple times from different attaching points.
“For the modeling aspect, FRET gives you distances between chromophores, but that’s not enough to fill all of the geometrical restraints of the molecule, so we have to rely on something else, some other methodology. That’s where Professor Ding comes into play,” Sanabria said.
Ding leads a computational biophysics lab at Clemson University where he uses computer software to gauge how biomolecules look, move and function. His approach to modeling utilizes a computer simulation known as discrete molecular dynamics (DMD) that maps the landscape of a biomolecule, predicting the trajectories of proteins as they fold and interact with other molecules. The subsequent simulation can be played back like a movie, helping researchers visualize protein behaviors over time.
“If you do traditional molecular simulations, typically you’re going to sample a very tiny region of the space, particularly for larger molecules, so you’re not going to have a good overview of how the entire molecule will look even in physiological conditions,” Sanabria said. “Discrete molecular dynamics is a much faster and less computationally expensive way to accurately and rapidly sample the conformational space of proteins.”
To do it, Sanabria first obtained a set of distances by measuring PSD-95 with FRET. In that experiment, Sanabria had 10 samples of the PSD-95 fragment that each were rendering different distances and three common shapes – or conformations – of PSD-95 were observed. Yet, without a DMD simulation, there was no way for the researchers to know which distance corresponded to which conformation of the fragment. So they input each possible distance against each possible shape and let the simulation do the rest.
“Once we did the first simulation, we saw that there were three main states that PDZ-1 and -2 were taking. One showed very close contact between the two, one showed a set of intermediate contact and one had no contact whatsoever,” Ding said.
The researchers then ran a DMD simulation again without considering the FRET distances to confirm that the three observed states exist in nature and are not simply a fluke imposed by the FRET distances. They further probed the structures by looking at the way that individual amino acids, which constitute the PDZ domains, bond to one another. From these analyses, Ding, Bowen and Sanabria were able to confirm that the PDZ domains take on two out of the three observed states in the DMD simulation – that with some contact and that with no contact whatsoever.
“Now, we have two potential targets for engineering new drugs that will be more efficient than the ones that are currently available,” Sanabria said. “The outlook for stroke patients is promising.”
Without discrete molecular dynamics, which can capture conformational changes that occur on the microsecond timescale, these two states would have been missed as they were in past studies.
“Most of the people doing FRET-guided structural modeling are working with a rigid molecule, like DNA. If you have a rigid molecule, it’s easy to model – you have only a single state to capture. You can assign the FRET distances and there’s really no problem,” Sanabria said. “In this case, we surpassed this approach in many ways.”
In future studies, the team is looking to analyze the potential for the PSD-95 fragment to auto-inhibit itself based on the fragment’s own structure.
The team’s paper, titled “Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95,” was published in September in Nature Communications. The work reported in this release was supported by the National Institute of Mental Health and National Science Foundation under award No. 2R01MH081923-11A1. The researchers are wholly responsible for the content of this study, of which the funder had no input.
Groundbreaking geneticist Trudy Mackay joined Clemson in 2018 as director of the University’s Center for Human Genetics and is building a team of researchers working to significantly advance our understanding of genetic disorders.
Mackay, whose numerous accolades include being a member of the National Academy of Sciences and the Royal Society, received the prestigious 2018 Dawson Prize in Genetics at Trinity College in November.
“This opportunity fits well with my own research and provides a unique opportunity to collaborate with fellow geneticists who are studying important diseases that affect human behavior and communication,” said Mackay, who also holds the Self Family Endowed Chair in Human Genetics in Clemson’s Department of Genetics and Biochemistry.
The Center for Human Genetics is housed in Self Regional Hall, a facility nestled within the sprawling campus of the Greenwood Genetic Center, which has a long history of clinical and research excellence in the field of medical genetics and of caring for families impacted by genetic disease and birth defects.
Mackay is joined at Clemson by her husband, Robert Anholt, who has been named a Provost’s Distinguished Professor in the Department of Genetics and Biochemistry. Anholt will also have a leadership role in the College of Science as the director of Faculty Excellence Initiatives.
OTHER NOTABLE NAMES THAT JOINED CLEMSON UNIVERSITY IN 2018 INCLUDE:
Mark Johnson, former director of the Advanced Manufacturing Office in the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy, became the founding director of the Center for Advanced Manufacturing and the Thomas F. Hash ’69 SmartState Endowed Chair in Sustainable Development.
Former Georgia Tech professor and National Science Foundation program director Chris Paredis joined Clemson as the new BMW Endowed Chair in Systems Integration for Clemson University’s International Center for Automotive Research (CU-ICAR).
Accomplished scholar and cybersecurity expert Sally A. McKee joined Clemson as the
C. Tycho Howle Chair in Collaborative Computing Environments.
Leslie Hossfeld, professor and head of the sociology department at Mississippi State University, joined Clemson as dean of the College of Behavioral, Social and Health Sciences.
Keith L. Belli, former head of the University of Tennessee’s Department of Forestry, Wildlife and Fisheries, became dean of Clemson University’s College of Agriculture, Forestry and Life Sciences.
Wendy York, former associate dean at Stanford University’s Graduate School of Business, became dean of Clemson University’s College of Business.
Christopher Cox, who has led university libraries in Iowa, Wisconsin and Washington, became dean of libraries.
The world is flooded with information, and Sara Riggs wants to change the way it’s presented.
As a 2018 NSF CAREER Award winner, Riggs, an assistant professor of industrial engineering, is rethinking and re-engineering displays to better reflect real-world needs. By understanding how teams use displays, Riggs and her team will learn when and how to present information, whether it’s visually, with sound or through touch.
“This work will hopefully help environments that are becoming increasingly complex, such as aviation, the military and health care, where people not only deal with more information but also need to work seamlessly together in teams,” said Riggs.
CAREER Awards are a signature accolade for young scientists, intended to boost innovative research toward solutions for society. For the second year in a row, seven Clemson assistant professors received the awards.
“These are highly competitive grants awarded to the brightest young minds across the country,” said Tanju Karanfil, vice president for research. “NSF CAREER awards are catalysts for scientific discovery and help propel the careers of young faculty who are destined to do great things.”
THE OTHER SIX 2018 NSF CAREER AWARD WINNERS AT CLEMSON ARE:
Joshua Bostwick, assistant professor of mechanical engineering: Bostwick’s research aims to improve drug delivery by understanding the physical interaction between internal liquids and soft tissue. Doing so will help physicians determine the proper dosage for a variety of medications, such as aerosolized drugs used for premature infants or people with asthma. It could also lead to better designs of drugs for more effective and efficient delivery.
Leah Casabianca, assistant professor of chemistry: Casabianca is studying the interaction between nanoparticles and the body. Nanoparticles such as microplastics are becoming more common in the environment and in the food chain. By understanding what happens to them in the body, Casabianca hopes to head off diseases they may cause. To study nanoparticles, she and her team are developing new techniques for nuclear magnetic resonance (NMR) imaging. Improving NMR could also improve the precision of magnetic resonance imaging (MRI) used in clinical medicine.
Ethan Kung, assistant professor of mechanical engineering: Kung is creating a model for the human cardiovascular system that will predict how implantable devices (such as left ventricular assist devices in patients with heart failure) will interact with the body. A feedback loop will use computer simulation and a patient’s biological information to predict how a device will affect things like blood pressure and disease progression — information that will help physicians customize therapies.
Suyi Li, assistant professor of mechanical engineering: Li hopes to use principles of origami to create new building materials that either maintain their mechanical properties or become stronger/more enhanced when folded. Potential applications range from building materials that are both stiff and soft, so they absorb large vibrations, to robotic “skeletons” that stay strong when they shift shapes.
Xian Lu, assistant professor of physics and astronomy: Lu aims to predict how the Earth responds to the transfer of momentum and energy in the middle and upper atmosphere from weather events, which move energy upward into space, and from changes on the surface of the sun, which shifts energy toward the Earth. Such shifts can disrupt telecommunications, astronaut activities and even the power grid.
Hugo Sanabria, assistant professor of physics and astronomy: Sanabria’s work focuses on studying the structure, dynamics and function of a protein that modulates calcium. Calmodulin, as it’s called, is present in all eukaryotic cells and regulates vital functions such as heartbeat, muscle contraction, learning and memory. Although calmodulin is ubiquitous, Sanabria’s team aims to study modifications to the protein that likely alter the protein’s flexibility and three-dimensional structure. The obtained knowledge would explain how certain modifications regulate the way calmodulin interacts with intended target molecules.