Alfred Merrill, professor emeritus in the School of Biological Sciences and Smithgall Chair in Molecular Cell Biology in the Parker H. Petit Institute for Bioengineering and Bioscience (IBB) — who brought research attention to an important class of organic compounds found in all tissues, including the brain — has been elected as a fellow of the American Society of Biochemistry and Molecular Biology (ASBMB). 

“This honor is only bestowed to our most distinguished and established members,” says ASBMB president Toni Antalis. ASBMB Fellowships were established in 2020 “to recognize our members for their meritorious efforts to advance the molecular life sciences through sustained outstanding accomplishments in scientific research, education, mentorship, commitment to diversity, and service to the society and the scientific community.”

“It is an honor to be selected as a fellow of the ASBMB, an organization that was established over a hundred years ago and promotes research and training in biochemistry through newsletters, conferences and publication of several of the most highly regarded journals in the field, such as The Journal of Biological Chemistry and The Journal of Lipid Research,” Merrill says.

“We are thrilled to see Al Merrill named a ASBMB Fellow,” says Todd Streelman, professor and chair of the School of Biological Sciences. “This award acknowledges Al’s lifetime of achievement in the lab and as a mentor to his colleagues. On behalf of the School of Biological Sciences, I congratulate Al on this honor."

Merrill was nominated by George Carman, Board of Governors Professor of Food Science, and Founding Director of the Rutgers Center for Lipid Research in the New Jersey Institute for Food, Nutrition, & Health at Rutgers University. “Al has made impressive contributions to science through both the discoveries by his laboratory and his assistance to others through service activities,” says Carman, who was named an ASBMB Fellow in 2021.

Merrill has been an IBB member since he came to Georgia Tech in fall 2001. He was an adjunct professor in the School of Chemistry and Biochemistry from 2003-2016. Merrill’s Georgia Tech research affiliations include the Center for Bio-Imaging Mass Spectrometry, the Integrated Cancer Research Center, the Center for ImmunoEngineering, and the Center for Drug Design Development and Delivery.

Merrill is also a member of the Discovery and Developmental Therapeutics Research Program at Emory Winship Cancer Institute. 

Improving our understanding of important organic compounds

Lipids are hormones, fats, oils and waxes that store energy and act as messengers within the body. A class of lipids, sphingolipids — named after the mysterious sphinx of mythology because of their enigmatic nature to early researchers — are important in tissue development, cell structure, cell-cell communication and signal transduction (how a cell responds to substances outside the cell). 

Merrill began researching sphingolipids while an assistant professor in the Department of Biochemistry at Emory University School of Medicine in 1981. “I wanted to branch out from my areas of previous training, which had been on the mechanisms of action of coenzymes and glycerolipids,” he says. “The sphingoid base biosynthesis pathway looked promising because few other scientists were studying it and my background in these two areas somewhat uniquely prepared me to tackle that challenging field. It was also helpful that I like to develop new methods for analyzing biochemical processes, and one of the first things that I did was develop easier ways to study sphingoid bases and their metabolism.”

The ASBMB notes that Merrill developed quantitative methods to measure sphingolipids and was a major contributor to mass spectrometry–based lipidomics research guidance. Merrill helped determine how the lipid backbones of sphingolipids are made and how they function in cell signaling and disease. 

Three research studies that Merrill conducted in 1986 detailing sphingolipids and cell signaling were designated “Classics” in 2016 by the Journal of Biological Chemistry because of their scientific influence. 

Merrill is a fellow of the American Association for the Advancement of Science and an associate editor of the Journal of Lipid Research. He was a member of the editorial board of the Journal of Biological Chemistry for 20 years.

Merrill is one of five Georgia-based scientists who received 2022 ASBMB Fellowships. The others are:

• Anita Corbett, Samuel C. Dobbs Professor in the Department of Biology at Emory University
• Christine Dunham, professor, Department of Biochemistry at Emory University School of Medicine
• Gerald Hart, professor and GRA Eminent Scholar and member of the Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology at the University of Georgia’s Franklin College of Arts and Sciences
• Susanna Fletcher Greer, senior scientific director, Biochemistry and Immunology of Cancer at the American Cancer Society in Georgia

Six College of Sciences researchers are among 19 Georgia Tech faculty and students receiving 2022 Research Awards from the Georgia Tech chapter of Sigma Xi, the Scientific Research Society. 

Sigma Xi’s mission is “to enhance the health of the research enterprise, foster integrity in science and engineering, and promote the public’s understanding of science for the purpose of improving the human condition.” 

Two College of Sciences researchers won the Best Faculty Paper Award:

• Roman Grigoriev, professor in the School of Physics 

• Nga Lee (Sally) Ng, professor in the School of Earth and Atmospheric Sciences with a joint appointment in the School of Chemical and Biomolecular Engineering

Grigoriev won for the paper, “Robust learning from noisy, incomplete, high-dimensional experimental data via physically constrained symbolic regression.” The study appeared in Nature Communications.

Ng won for four papers:

• “Evaluation of particle filtration efficiency of commercially available materials for homemade face mask usage,” Aerosol Science and Technology.

• “In-flight particulate matter concentrations in commercial flights are likely lower than other indoor environments,” Indoor Air.

• “Formation of Oxidized Gases and Secondary Organic Aerosol from a Commercial Oxidant-Generating Electronic Air Cleaner,” Environmental Science and Technology Letters.

• “Room-level ventilation in schools and universities,” ChemRxiv.

Four College of Sciences graduate students are also recognized.

Best Ph.D. Thesis Awards:

• Yuchen He, School of Mathematics
  Advisor: Sung Ha Kang
  Title: "Mathematical and data-driven pattern representation with applications in image processing, computer graphics, and infinite dimensional dynamical data mining"  

• Pan Liu, School of Earth and Atmospheric Sciences
  Advisor: Yuanzhi Tang 
  Title: "Speciation and recovery of rare earth elements (REES) from coal fly ash"   

• Suttipong “Jay” Suttapitugsakul, School of Chemistry and Biochemistry
  Advisor: Ronghu Wu 
  Title: "MS-based chemical proteomics studies of extracellular glycoproteins: identification, quantification, and dynamics" 

Best M.S. Thesis Award:

• Charles Ross Lindsey, School of Biological Sciences
  Advisor: Frank Rosenzweig
  Title: "Phylotranscriptomics points to multiple independent origins of multicellularity and cellular differentiation in the Volvocine algae"

The Sigma Xi Georgia Tech Chapter awards ceremony is scheduled for April, preceding the Georgia Tech faculty awards ceremony. Learn more.

Shared on behalf of Arts at Georgia Tech:

Georgia Institute of Technology students, faculty, and staff are proudly taking part in the 2022 ACCelerate Festival, a celebration of creative exploration and innovative research happening at the intersection of science, engineering, arts, and design. Featuring teams from universities and colleges across the Atlantic Coast Conference (ACC) and the Smithsonian Institution, the Festival promotes cutting-edge creative work from a new generation of thinkers. This year’s event, to be held April 8 – 10, 2022, will be the third time the ACC institutions have gathered in DC, and Georgia Tech is honored to have been represented at each Festival to date.

“The ACCelerate Festival is an opportunity to showcase the incredible possibilities that await us at the intersection of art and technology,” said Georgia Tech Provost Steve McLaughlin. “We are proud to once again send teams from Georgia Tech and participate alongside our ACC peers. The arts have an undeniable power to teach, heal, and transform us, and this festival gives great visibility and a new way to experience the innovative and impactful education and research that is taking place on our campuses each day.”

The two Georgia Tech teams participating in the 2022 ACCelerate Festival come from the School of Architecture at the College of Design, and the School of Literature, Media, and Communication at the Ivan Allen College of Liberal Arts. Georgia Tech’s participation in ACCelerate is managed by Georgia Tech Arts, a department in the Division of Student Engagement and Well-Being.

Walking in the Footsteps of History

On March 7, 1965, at the south side of Edmund Pettus Bridge, armed State Troopers attacked peaceful civil rights activists attempting to march to the state capital of Montgomery in an incident that became known as Bloody Sunday. Despite access to vivid archival material, little interpretation addresses the physical context and experiential timeline. To digitally record this significant civil rights site and to make the specific context of the event more experientially engaging to the public, this project’s multidisciplinary team of designers, architectural historians, civil rights historians, cultural resource managers, and construction technology specialists are pairing collected 3D digital data of Selma’s extant structures with digital reconstructions to recreate the site.

By melding the physical and virtual, Walking in the Footsteps of History presents a broader understanding of the events of 1965 in and around Selma through enhanced historic interpretation by animating famous photographs through immersive visualization, creating interactive digital platforms for exploring fragile archival content such as the Good Samaritan Hospital logbook, and affording virtual tours where visitors can safely explore the Bloody Sunday conflict site that is bordered by a busy highway.

The team is led by Danielle Willkens, assistant professor, School of Architecture, who commented “This project has encompassed more than 6 years’ work with civil rights foot soldiers and their descendants with the intention of enabling visitors to translate the visceral experience to an understanding of the tenets of what was being advocated for - voting rights and civil rights – in the 1960’s through present time.”

Participating staff include Aaron Shackleford, director of Georgia Tech Arts. Georgia Tech student researchers include Simran Bajaj, Thomas Bray, Sydnee Henry, Carly Langsdorf, Sean Li, Sakshi Nanda, So Min Park, Patricia J. Rangel, Aishwarya Somasundaram, Christian Waweru, and Eden Wright. This project is the result of an ongoing collaboration with Junshan Liu, associate professor at Auburn University's McWhorter School of Building Science and Georgia Tech Visiting Scholar and the Auburn University team including faculty (R. Burt, K. Hébert, and E. Gaddis) and students (C. Brown, A. Davis, M. Gibbs, and S. Page). The team is currently completing a Historic Structures Report on the Edmund Pettus Bridge, sponsored by a National Park Service African American Civil Rights Grant.

Visit the ACCelerate website for more information about the team’s work and exhibition.

Heart Sense

“How can the very creation, rendering, and experiencing of biological data contribute to a more nuanced understanding of our bodies?” This is the question at the heart of this project. Heart Sense is a series of installations that visualize biometric data such as heart rate and breath as participants engage in a variety of listening and viewing activities. Our bodies are often conceived as separate autonomous entities, disjoint from the physical and social environments that they inhabit while in fact we are deeply connected with the material and social world around us.

The first installation tracks a participant’s heart rate, galvanic skin response, and breathing as they watch a short, emotionally engaging video. This data input produces flower-like visualizations that illustrate the physiological responses. The second installation engages the social dimension of embodiment through the mediation of the physical environment. Participants are invited to sit around a table and are given headphones to listen to music.

A floral visualization representing the collective heart rates of the participants will be projected onto the table, the size and the colors of each petal shifting with changes in each participant’s body. The visualization showcases how our bodies come into relation with each other and are in and of the environment, as they respond to our surrounding conditions even when we are not aware of it.

The team is led by Nassim Parvin, associate professor, School of Literature, Media, and Communication, who states “This project has catalyzed interdisciplinary collaboration across natural sciences, social sciences, and humanities, and it has been a privilege to work with talented students in imaginative world-building.”

Participating faculty include Lewis Wheaton, associate professor, Biological Sciences, Georgia Tech, and Anne Pollock, previously associate professor of Literature, Media, and Communication at Georgia Tech and now professor of Global Health and Social Medicine at King's College London. The interdisciplinary team includes post-doctoral researcher Aditya Anupam alongside Georgia Tech student researchers Pooja Casula, Shubhangi Gupta, Sylvia Janicki, Michelle Ramirez, and Mohsin Yousufi.

Visit the ACCelerate website for more information about the team’s work and exhibition.

Visit the LMC website for detailed Heart Sense documentation and Heart Sense demonstration.

Working at the Intersection of Art, Learning, and Research

“The faculty and students at Georgia Tech have embraced the role of art and creativity as a way to engage with people and share their research with a wide audience,” said Georgia Tech Arts Director Aaron Shackelford. He explains that Georgia Tech Arts selected each project because of the way they bring together art, learning and research. “Both projects show what happens when you bring art and creativity into every step of the process,” he notes, “and the results are these innovative approaches to conducting important work that can be experienced by anyone visiting the Smithsonian.” Each project also supports the well-being of the community. “Heart Sense invites us to have a better understanding of our own bodies, while Walking in the Footsteps of History pushes us to have a better understanding of our nation’s history. Both are important for cultivating the well-being of our community, which is a central goal for Georgia Tech as a whole and one of the most important benefits of the arts.”

ACCelerate is programmed by Virginia Tech’s Institute for Creativity, Arts, and Technology and the Smithsonian Institution’s Lemelson Center for the Study of Invention and Innovation. Hosted at the National Museum of American History, the multi-day festival is free and open to the public. The 2022 Festival features 24 projects from 12 ACC schools; the most recent Festival drew public attendance of more than 30,000.

For more information about the 2022 ACCelerate Festival, visit their website.

Since it was founded in 2002, the Applied Physiology Ph.D. program at Georgia Tech has had close ties to rehabilitation science. Now, thanks to the generosity of a Georgia Tech and Emory University alum’s family foundation, Applied Physiology will work with the Emory University School of Medicine and Shepherd Center’s Crawford Research Institute to create a new training program for Applied Physiology doctoral students focused on neurorehabilitation. 

The Applied Physiology Ph.D. program, part of the Georgia Tech School of Biological Sciences, focuses primarily on the physical and neural function of the human motor system. “Because of that,” explains T. Richard Nichols, Biological Sciences professor and head of Applied Physiology, “rehabilitation has always been a very strong theme in our program.”

That deeper focus on rehabilitation sciences is now formalized by the creation of the Jack and Dana McCallum Neurorehabilitation Training Program. The new initiative is the result of a $1 million gift from Dana and Jack McCallum (BIO ’66) that will be used over the next four years to support graduate student and faculty research, as well as train new scientists in neurorehabilitation. 

Emory University School of Medicine, where Jack McCallum received his M.D., will be a close partner in developing the program. A course designed to train graduate students in clinical neurorehabilitation will be taught at the school in addition to collaborating closely in research funded by the investment.

“This gift is really going to strengthen the tie between specifically Biological Sciences and the Emory University School of Medicine, which was the intention of the gift,” explains Biological Sciences professor and associate chair of faculty development Young-Hui Chang. “I think it’s going to provide one more, but very strong, avenue for collaboration between the two institutions.”

Refocusing on rehabilitation

With a clinical focus, research funded through the program will target aspects of rehabilitation for people who have neurological diseases like Parkinson disease — or trauma, such as a spinal cord or brain injury.

The investment will also drive new major research focused on understanding the neurophysiological basis for injury and recovery related to central and peripheral nervous system trauma, and on the preclinical development of potential therapies.

“As people survive and live longer with acquired conditions such as stroke and Parkinson disease, and with traumatic injuries such as brain and spinal cord injury, there is a tremendous demand for rehabilitation researchers to meet needs of the large and growing population of persons with neurologic conditions,” explains Edelle Field-Fote, a professor with joint appointments in the Emory University School of Medicine and Applied Physiology at Georgia Tech, who also serves as director of spinal cord injury research at the Shepherd Center. “The goal of the McCallum Neurorehabilitation Training Program is to help address this need. The program will develop rehabilitation scientists with the training to advance knowledge underlying clinical care and the skills to develop interventions that can reduce disability, thereby improving functioning and quality of life for persons with neurologic conditions.”

Research and practice in motion

The Applied Physiology graduate program is no stranger to clinical research and development, having served as home of a clinical master’s degree in prosthetics and orthotics, which migrated to Kennesaw State University in 2020, and also hosting a training grant from the National Institute of Health (NIH), funding students whose research focused on rehabilitation for persons with limb loss. In 2018, Applied Physiology launched a dual Doctor of Philosophy and Doctor of Physical Therapy degree program in collaboration with the Division of Physical Therapy at Emory University, with Field-Fote as its director. 

"Emory University’s Division of Physical Therapy greatly values our collaborations with Georgia Tech and its Applied Physiology program,” shares Tami Phillips, associate professor and interim program director of the Division of Physical Therapy. “The opportunity for Ph.D. students to work in research labs across institutions and D.P.T/Ph.D. students to bridge the gap between clinical neurorehabilitation practice and research will lead to innovations that will benefit individuals with neurologic conditions.”

As Nichols points out, these ties between research and the clinic build a solid foundation for the new training program. “Our faculty in Applied Physiology are used to dealing with clinical collaborators and clinical problems, but we're working more at a fundamental level in terms of the science. It really provides a nice environment for this training program and will help move us into a new area of neurorehabilitation.”

New funding for current graduate students in Applied Physiology, as well as those enrolling in the dual Doctor of Philosophy and Doctor of Physical Therapy program, is set to begin this year. Targeted toward advanced students, the efforts are expected to allow the Applied Physiology program to admit more new students and to award competitive McCallum Research Fellowships to help fund thesis research after they reach Ph.D. candidacy.

“I am so grateful to Dana and Jack McCallum for their foresight and generosity,” shares Field-Fote. “I am most excited by the great potential that this program has for advancing the clinical care and foundational sciences related to neurorehabilitation.”

For more information on the Applied Physiology program or the Jack and Dana McCallum Neurorehabilitation Training Program, contact Young-Hui Chang at yh.chang@ap.gatech.edu.

For more information on how to support the School of Biological Sciences or the Applied Physiology Program, contact Leslie Roberts at leslie.roberts@cos.gatech.edu and visit: cos.gatech.edu/giving

Thanks to better diagnostics, therapeutics, and care, the overall cancer mortality rate has plummeted in the past 20 years. But cancer survival disparities stubbornly persist along racial and ethnic lines, demanding a firmer grasp of the underlying mechanisms at play, which would ideally result in better outcomes for populations disproportionately burdened by the disease.

A group of researchers at the Georgia Institute of Technology is tackling this complex, multi-layered problem, and they describe their latest work in a recent edition of the journal Cancer Research. Their results blur the line between nature and nurture, providing a potential link between the genetic and environmental contributions to cancer health disparities.

“When you think about race and ethnicity, those are socially ascribed categories, based on cultural expectations and norms” said King Jordan, professor in the School of Biological Sciences and principal investigator of the study. The lead author was Kara Keun Lee, a graduate student advised by both Jordan and cancer researcher John McDonald, professor in the School of Biological Sciences and a co-author of the study.

So while they approached the work with the understanding that race and ethnicity are not genetic or biological categories, Jordan said the researchers also are aware that health outcomes are a combination of the genetic and biological, with the social and environmental. “And we’re very interested in that interplay,” Jordan said. “But this particular study is focused on the idea of using genetic ancestry as a means to drill down to the underlying molecular biology – the mechanisms that contribute to these survival disparities.”

Genetic ancestry, a characteristic of the genome, refers to genomic similarities based on shared ancestors, which can be defined objectively and with precision, “independent of the social dimensions of race and ethnicity,” Jordan added.

And it turns out, the mechanisms behind cancer survival disparities have plenty to do with the environmental impacts on gene expression, and not on ancestry-related differences.

The research was a collaboration of the Jordan and McDonald labs at Georgia Tech, blending the two labs’ experience in multi-omics biological analysis with Lee’s biostatistics skills, together with Dr. Leonardo Mariño-Ramírez, head of Genomic and Epidemiology Sciences at the NIH’s National Institute on Minority Health and Health Disparities, which helped fund the study.

Key Ingredient

The key to analyzing all of the multi-omics and cancer survival data was Lee. Though she’s pursuing her Ph.D. in the Georgia Tech Bioinformatics Graduate Program, Lee’s background as both a researcher at the Centers for Disease Control and Prevention and an Emory University student, is in biostatistics.

While bioinformatics is generally concerned more with collecting and analyzing complex biological and genomics data, biostatistics is focused on broad, bigger-picture biological data to address public health issues. So, for example, when you read that cancer mortality rates have decreased 27%, that’s the work of a biostatistician.

“We would not have been able to do this study without Kara’s expertise in biostatistics,” Jordan said. “She brings experience as a statistical epidemiologist in health outcomes to our team. One of the really exciting things as a Ph.D. advisor is when you can get a student like Kara that can potentially change the direction of your lab.”

Lee previously led a study that utilized the National Cancer Institute’s Cancer Genome Atlas to analyze 33 cancers and 9,818 patients. The team identified four cancer types with significant survival disparity.

“The survival disparities were more stark and more obvious when we looked at genetic ancestry as opposed to self-identified race and ethnicity,” said Lee, whose computational tools built a compelling body of evidence showing that nature might actually be nurture.

Nature as Nurture

The researchers’ findings point to epigenetic mechanisms – not genetics – as the primary culprit in cancer survival disparities. Epigenetic changes, which can alter the structure of DNA and affect how genes are expressed, can be heavily influenced by the environment around us or the food that we eat.

“The thing about epigenetic changes is that they can be inherited, passed down to future generations,” said McDonald. “That includes the propensity for cancer. But that’s the other thing about these epigenetic changes. They don’t unalterably change DNA structure. They’re reversible. It isn’t permanent.”

One of the most interesting discoveries of the study, the researchers agreed, was what they didn’t find – there were no ancestry-related differences in the DNA they analyzed that contributed to survival disparities. Rather, it was epigenetically induced changes in gene expression that were associated with differences in cancer survival between populations.

“That means the environment may actually change how genes are expressed,” said Jordan. “Following that epigenetic trail, or at least the logic of it, looking at how genes and the environment interact to shape health disparities will be a big focus of my lab going forward.”

CITATION: Kara K. Lee, Lavanya Rishishwar, Dongio Ban, Shashwat Nagar, Leonardo Marino-Ramírez, John F. McDonald, and I. King Jordan. “Association of Genetic Ancestry and Molecular Signatures with Cancer Survival Disparities: a Pan-Cancer Analysis.” (Cancer Research)

https://doi.org/10.1158/0008-5472.CAN-21-2105

FUNDING: Lee, Rishishwar, and Nagar were supported by the IHRC-Georgia Tech Applied Bioinformatics Laboratory (Atlanta, GA; grant no. RF383). Marino-Ramírez was supported by the NIH Distinguished Scholars Program and the Division of Intramural Research (DIR) of the National Institute on Minority Health and Health Disparities (Grant Nos. 1ZIAMD000016 and 1ZIAMD000018). Ban was supported by the Ovarian Cancer Institute. McDonald was supported by the Ovarian Cancer Institute, Deborah Nash Endowment, and Northside Hospital Research Foundation.

About Georgia Institute of Technology

The Georgia Institute of Technology, or Georgia Tech, is a top 10 public research university developing leaders who advance technology and improve the human condition. The Institute offers business, computing, design, engineering, liberal arts, and sciences degrees. Its nearly 44,000 students representing 50 states and 149 countries, study at the main campus in Atlanta, at campuses in France and China, and through distance and online learning. As a leading technological university, Georgia Tech is an engine of economic development for Georgia, the Southeast, and the nation, conducting more than $1 billion in research annually for government, industry, and society.

Georgia Tech’s Center for Teaching and Learning (CTL) is recognizing College of Sciences faculty members for their excellence in teaching during the 2021-2022 school year.

41 College of Sciences faculty have won Student Recognition of Excellence in Teaching: CIOS Awards based on student evaluations during the annual Course Instructor Opinion Survey (CIOS). Eight faculty are the recipients of CTL Faculty Teaching Awards.

The CIOS honors, given for the full calendar year, are based on student-provided CIOS responses about their instructor's “respect and concern for students, level of enthusiasm about teaching the course, and ability to stimulate interest in the subject matter.”

“It's impressive to see the many ways that faculty in the College of Sciences are contributing to student learning at Georgia Tech,” says Joyce Weinsheimer, CTL director. “The College’s award-winning teachers are excelling in the classroom, laboratory instruction, co-curricular education, online teaching, academic outreach, and the scholarship of teaching. They are providing exciting learning environments and experiences to students on our campus and beyond.”

College of Sciences recipients of the “2022 Faculty Teaching Awards” include:

CTL/BP Junior Faculty Teaching Excellence Award 

Neha Garg, assistant professor, School of Chemistry and Biochemistry

Faculty Award for Academic Outreach 

James R. Sowell, principal academic professional, School of Physics, and director of the Georgia Tech Observatory

Geoffrey G. Eichholz Faculty Teaching Award 

Michael Evans, First-year Chemistry Laboratory coordinator, School of Chemistry and Biochemistry

Christie N. Stewart, senior academic professional, School of Biological Sciences

Innovation and Excellence in Laboratory Instruction Award 

Christy O’Mahony, laboratory coordinator for Analytical and Physical Chemistry, School of Chemistry and Biochemistry

Innovation in Co-Curricular Education 

Jake D. Soper, associate professor and associate chair for Operations, School of Chemistry and Biochemistry 

Scholarship of Teaching and Learning Award 

Emily G. Weigel, senior academic professional, School of Biological Sciences

Teaching Excellence Award for Online Teaching 

Michael Evans, First-year Chemistry Laboratory coordinator, School of Chemistry and Biochemistry

College of Sciences faculty honored with “Student Recognition of Excellence in Teaching: CIOS Awards” include:

Small Classes:

Gary (Michael) Lavigne, visiting assistant professor, School of Mathematics; and assistant director of Communication, Education and Outreach for the Southeast Center for Mathematics and Biology

Dan Margalit, professor, School of Mathematics

Melinda (Mindy) Millard-Stafford, professor, School of Biological Sciences

Large Classes:

Meghan Babcock, academic professional and lecturer, School of Psychology

Dobromir (Doby) Rahnev, associate professor, School of Psychology

College of Sciences “Student Recognition of Excellence in Teaching: Honor Roll” Awardees:

Small Classes:

School of Biological Sciences — Joel Kostka, professor and associate chair of Research; Lin Jiang, professor; Melinda (Mindy) Millard-Stafford, professor; Emily Weigel, senior academic professional

School of Earth and Atmospheric Sciences — Sven Simon, associate professor;  Samantha Wilson, academic professional; James Wray, associate professor

School of Mathematics — Neha Gupta, academic professional and director of Scheduling; Gary (Michael) Lavigne, visiting assistant professor, School of Mathematics; and assistant director of Communication, Education and Outreach for the Southeast Center for Mathematics and Biology; Dan Margalit, professor; John Olinde, Ph.D. student

Neuroscience — Timothy Cope, professor

School of Psychology — Lizanne DeStefano, professor and  Center for Education Integrating Science, Math, and Computing (CEISMC) executive director; Ruth Kanfer, professor; Dianne Leader, lecturer

Large Classes:

School of Biological Sciences — Adam Decker, senior academic professional and director of Anatomical Sciences; Colin Harrison, senior academic professional; Emily Weigel, senior academic professional

School of Chemistry and Biochemistry — Amit Reddi, associate professor; J. Cameron Tyson, principal academic professional and College of Sciences assistant dean for Academic Programs

School of Earth and Atmospheric Sciences — Heather Chilton, remote laboratory support;  Zachary Handlos, academic professional

School of Mathematics — Neha Gupta, academic professional and director of Scheduling; Sung Ha Kang, professor; Siddhi Krishna, former NSF Research Training Groups (RTG) postdoctoral associate; Miriam Kuzbary, NSF postdoctoral fellow; Gary (Michael) Lavigne, visiting assistant professor, School of Mathematics; and assistant director of Communication, Education and Outreach for the Southeast Center for Mathematics and Biology; Michael Loss, professor; Gregory Mayer, academic professional and director of Online Learning

Neuroscience — Christina Ragan, lecturer and director of Outreach for the B.S. in Neuroscience program; Alonzo Whyte, academic professional, advisor for the Health and Medical Sciences (HMED) Minor, and director of Academic Advising for the B.S. in Neuroscience program

School of Psychology — Meghan Babcock, academic professional;  Dianne Leader, lecturer; Dobromir (Doby) Rahnev, associate professor; Christopher Stanzione, senior lecturer, associate chair for Undergraduate Studies in Psychology; Christopher Weise, assistant professor 

Learn more about the Center for Teaching and Learning at Georgia Tech.

This story first appeared in the College of Engineering newsroom.

From the muscle fibers that move us to the enzymes that replicate our DNA, proteins are the molecular machinery that makes life possible.

Protein function heavily depends on their three-dimensional structure, and researchers around the world have long endeavored to answer a seemingly simple inquiry to bridge function and form: if you know the building blocks of these molecular machines, can you predict how they are assembled into their functional shape?

This question is not so easy to answer. With complex structures dependent on intricate physical interactions, researchers have turned to artificial neural network models – mathematical frameworks that convert complex patterns into numerical representations – to predict and “see” the shape of proteins in 3D.

In a new paper published in Nature Communications, researchers at Georgia Tech and Oak Ridge National Laboratory build upon one such model, AlphaFold 2, to not only predict the biologically active conformation of individual proteins, but also of functional protein pairings known as complexes.

The work could help researchers bypass lengthy experiments to study the structure and interactions of protein complexes on a large scale, said Jeffrey Skolnick, Regents’ Professor and Mary and Maisie Gibson Chair in the School of Biological Sciences and one of the corresponding authors of the study, adding that computational models such as these could mean big things for the field. 

If these new computational models are successful, Skolnick said, “it could fundamentally change the way biological molecular systems are studied.”

Primed for Protein Prediction

Created by London-based artificial intelligence lab DeepMind, AlphaFold 2 is a deep learning neural network model designed to predict the three-dimensional structure of a single protein given its amino acid sequence. Skolnick and fellow corresponding author, Mu Gao, senior research scientist in the School of Biological Sciences, shared that the Alphafold 2 program was highly successful in blind tests occurring at the 14^th iteration of the Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, or CASP14, a bi-annual competition where researchers around the globe gather to put their computational models to the test. 

“To us, what is striking about AlphaFold 2 is that it not only makes excellent predictions on individual protein domains (the basic structural or functional modules of a protein sequence), but it also performs very well on protein sequences composed of multiple domains,” Skolnick shared. And so with the ability to predict the structure of these complicated, multi-domain proteins, the research team set out to determine if the program could go a little further. 

“The physical interactions between different [protein] domains of the same sequence are essentially the same as the interactions gluing different proteins together,” Gao explained. “It quickly became clear that relatively simple modifications to AlphaFold 2 could allow it predict the structural models of a protein complex.” To explore different strategies, Davi Nakajima An, a fourth-year undergraduate in the School of Computer Science, was recruited to join the team’s effort.

Instead of plugging in the features of just one protein sequence into AlphaFold 2 per its original design, the researchers joined the input features of multiple protein sequences together. Combined with new metrics to evaluate the strength of interactions among probed proteins, their new program AF2Complex was created.

Charting New Territory

To put AF2Complex to the test, the researchers partnered with the high-performance computing center, Partnership for an Advanced Computing Environment (PACE), at Georgia Tech, and charged the model with predicting the structures of protein complexes it had never seen before. The modified program was able to correctly predict the structure of over twice as many protein complexes as a more traditional method called docking. While AF2Complex only needs protein sequences as input, docking relies on knowing individual protein structures beforehand to predict their combined structure based on complementary shapes.

“Encouraged by these promising results, we extended this idea to an even bigger problem, which is to predict interactions among multiple arbitrarily chosen proteins, e.g., in a simple case, two arbitrary proteins,” shared Skolnick.

In addition to predicting the structure of protein complexes, AF2Complex was charged with identifying which of over 500 pairs of proteins were able to form a complex at all. Using newly designed metrics, AF2Complex outperformed conventional docking methods and AlphaFold 2 in identifying which of the arbitrary pairs were known to experimentally interact.

To test AF2Complex on the proteome scale, which encompasses an organism’s entire library of the proteins that can be expressed, the researchers turned to the Summit Oak Ridge Leadership Computing Facility, the world’s second largest supercomputing center. “Thanks to this resource, we were able to apply AF2Complex to about 7,000 pairs of proteins from the bacteria E. coli,” Gao shared. 

In that test, the team’s new model not only identified many pairs of proteins known to form complexes, but it was able to provide insights into interactions “suspected but never observed experimentally,” Gao said. 

Digging deeper into these interactions revealed a potential molecular mechanism for protein complexes that are particularly important for energy transport. These protein complexes are known to carry hemes, essential metabolites giving blood dark red color. Using AF2Complex’s predicted structural models, Jerry M. Parks, a senior research and development staff scientist at Oak Ridge National Laboratory and a collaborator in the study, was able to place hemes at their suspected reaction sites within the structure. “These computational models now provide insights into the molecular mechanisms for how this biomolecular system works,” Gao said. 

“Deep learning is changing the way one studies a biological system,” Skolnick added. “We envision methods like AF2Complex will become powerful tools for any biologist who would like to understand molecular mechanisms of a biosystem involving protein interactions.”

AF2Complex is an open-source tool available to the public and can be downloaded here.

This work was supported in part by the DOE Office of Science, Office of Biological and Environmental Research (DOE DE-SC0021303) and the Division of General Medical Sciences of the National Institute Health (NIH R35GM118039). DOI: https://doi.org/10.1038/s41467-022-29394-2

Georgia Tech will celebrate its 25th annual Earth Day with a 4-day schedule of events. The celebration kicks off Monday, April 18, with a keynote event featuring Vice President for Infrastructure and Sustainability Maria Cimilluca. She will share her inspiring vision for the future of sustainability at Georgia Tech. 

"The Institute's strategic plan asks us to envision an institution that leverages its unmatched scale and resources to address the most crucial challenges of our time,” Cimilluca said. “I see the Institute's sustainability plan as one of the many pathways for collaboration, innovation, and action that will lead us toward transformations in research, applied technologies, culture, and ultimately a more sustainable future."

Georgia Tech first celebrated Earth Day in 1997. For many years the celebration was a one-day, afternoon event. In 2020, it was expanded but held virtually due to the Covid-19 pandemic. Held in person last year, the event featured The Kendeda Building for Innovative Sustainable Design’s Living Building Certification by the International Living Futures Organization, and President Cabrera cut the ribbon for the grand opening of the EcoCommons. These two areas on campus represent Georgia Tech’s commitment to sustainability and serve as living, learning laboratories for students, faculty, and staff.

Event co-chairs Anne Rogers, associate director of the Office of Campus Sustainability, and Emma Brodzik, campus sustainability project manager, have planned a strong lineup of events for this 25th anniversary. From a bike ride with President Cabrera, to a waste audit of the Clough Undergraduate Learning Commons, to a bird walk and tree planting, this year’s “Down to Earth” event offers many opportunities to celebrate nature and learn about new and innovative ways to protect and preserve our planet.

As is the tradition, this year’s theme and logo were chosen from a student design contest. The winner, Abhinav Thukral, is a graduate student in human and computer interaction. “I think it’s incredibly important to be aware of how our activities affect the planet and to learn sustainable ways to progress as a community,” Thukral said. “Earth Day is essential to reflect on some of the environmental issues we face today and how we might work together to address them.”

Students have often requested to work with campus operations to manifest positive environmental change by engaging with the staff of Infrastructure and Sustainability. This unit is responsible for providing sustainable, safe, and well-maintained campus facilities. For example, recent Carbon Reduction Challenge winners aided in implementing the replacement of existing fluorescent lighting with LED in a wing of the Petit Institute for Bioengineering and Bioscience building. By working with the Building Engineering and Energy Strategies department, this improvement will yield more than 250,000 pounds of carbon dioxide reduction per year. Another area where students are proactive is recycling. When the need for acrylic shields lessened as the intensity of the pandemic waned, student volunteers from the Office of Minority Education assisted campus staff in collecting 800 pounds of acrylic and PVC for recycling.

These types of student-led collaborative efforts are encouraged. If your organization or class would like to collaborate with Infrastructure and Sustainability, use this form to get started.  

It’s been in the works for more than a decade and now construction will officially begin. An announcement from Georgia Advance Technology Ventures (GATV), a cooperative organization of Georgia Tech, and Trammell Crow Company (TCC), the project developer, shares details of what will become a major life science innovation hub for the Atlanta region. Now named Science Square, the development will be a mixed-use innovation community that includes commercial lab space as well as residential real estate and retail opportunities. 

You can read more about the project here.