The 2018 Nobel Prize in Physiology or Medicine was awarded jointly to James P. Allison and Tasuku Honjo for their discovery of cancer therapy by putting the brakes on the immune system. Allison is a professor at the University of Texas MD Anderson Cancer Center, in Houston. Honjo is a professor at Kyoto University.

The 2018 winners “found ways to alert immune cells to recognize cancer cells as non-self and destroy them,” says Francesca Storici, a professor in the School of Biological Sciences and a member of the Parker H. Petit Institute for Bioengineering and Bioscience (IBB). Working with both healthy and cancer cells, she studies what happens inside cells and the DNA damage that occurs with cancer. “Research in this direction has the potential to save many lives not only from cancer but possibly also from many other cell degenerative disorders,” Storici says.

The immune system is well-designed to attack cells that the body considers foreign. The system is tightly regulated to avoid attacking our own normal healthy cells. “This year's winners are long-time students of the mechanisms underlying this regulatory aspect of immune function,” says John McDonald, a professor in the School of Biological Sciences whose lab uses an integrated systems approach to the study of cancer. He directs the Integrated Cancer Research Center at Georgia Tech and is a member of IBB. 

Most cancer cells are sufficiently mutated to be viewed as “foreign.” But they often escape attack by shrouding themselves with proteins that block the immune response. By developing strategies to inhibit these blocking mechanisms, McDonald says, the Nobel Prize winners “unleashed the natural anti-cancer properties of the immune system.”

Specifically, Allison and Honjo unraveled the mechanisms that inhibit T-cells, the major immune system components that attack foreign cells, says Fredrik Vannberg, an assistant professor in the School of Biological Sciences and IBB member.

Their basic science discovery led to what is now known as immune checkpoint therapy, which works by reversing T-cell inhibition and allowing the body’s own immune system to destroy cancer cells. Immune checkpoint therapy has saved the lives of many late-stage cancer patients, Vannberg says.

However, not every patient benefits from any particular therapy. Research at Georgia Tech aims to provide additional tools to find the treatment that suits the patient. For example, McDonald and Vannberg collaborate in using genomic profiling to help predict which specific therapy will lead to the best clinical outcome for a given cancer patient.

Toward this goal, last year they offered to cancer researchers – for free – a new program that predicts cancer drug effectiveness via machine learning and raw genetic data. They hoped to attract other researchers who will share their cancer and computer expertise and data to improve upon the program and save more lives together.

“The hope is that – by exploiting these new discoveries alone and in combination with other novel strategies to target treatment to tumors – cancer will soon be transformed from a lethal to a manageable chronic disease,” McDonald says.

Episode 7 of ScienceMatters' Season 1 stars Jennifer Leavey.  Listen to the podcast here and read the transcript here.

Jennifer Leavey is a principal academic professional in the School of Biological Science. She also serves College of Sciences as the coordinator of the  Integrated Science Curriculum and director of Georgia Tech Urban Honeybee Project.

The Georgia Tech Urban Honey Bee Project is an interdisciplinary educational initiative to recruit and retain students in STEM careers through the study of how urban habitats affect honey bee health and how technology can be used to study bees. 

Leavey is also the faculty director of the Science and Math Research Training (SMaRT) and Scientific Health and Related Professions (SHaRP) Living Learning Communities of the College of Sciences.These communities aim to create lasting connections among College of Sciences majors who are interested in research (SMaRT) or intend to pursue additional education and training health-rleated fields. 

In Episode 7 of ScienceMatters, Leavey shares her long-lasting passion for both science and rock music. By day, she’s an academic professional; but when she straps on a guitar , she mutates to Leucine Zipper, leader of the rock band Zinc Fingers.

For a change of pace, ScienceMatters samples the band’s science-inspired songs. Leavey shares how the band uses music and other media to make science concepts fun and accessible.  

Take a listen at sciencematters.gatech.edu.

Enter to win a prize by answering the question for Episode 7: 

In episode 7, what is the name of the song that Jennifer Leavey says sounds like a love song but is actually about bacteria living together in biofilms?

Submit your entry by 11 AM on Monday, Oct. 8, at sciencematters.gatech.edu. Answer and winner will be announced shortly after the quiz closes.

Editors Note: This story by John Toon was originally published in the Georgia Tech News Center on Sept. 20, 2018. The headline was changed for the College of Sciences website.

Black holes form when stars die, allowing the matter in them to collapse into an extremely dense object from which not even light can escape. Astronomers theorize that massive black holes could also form at the birth of a galaxy, but so far nobody has been able to look far enough back in time to observe the conditions creating these direct collapse black holes (DCBH).

The James Webb Space Telescope, scheduled for launch in 2021, might be able look far enough back into the early Universe to see a galaxy hosting a nascent massive black hole. Now, a simulation done by researchers at the Georgia Institute of Technology has suggested what astronomers should look for if they search the skies for a DCBH in its early stages.

The first-of-its-kind simulation, reported September 10 in the journal Nature Astronomy, suggests that direct formation of these black holes would be accompanied by specific kinds of intense radiation, including X-rays and ultraviolet emission that would shift to infrared by the time they reach the telescope. The black holes would also likely spawn massive metal-free stars, a finding that was unexpected.

The research was supported by NASA, the Los Alamos National Laboratory, the National Science Foundation, the Southern Regional Education Board and two Hubble theory grants.

“There are supermassive black holes at the center of many large galaxies, but we haven’t been able to observe the way they form or how they got that large,” said Kirk S. S. Barrow, the paper’s first author and a recent Ph.D. graduate of Georgia Tech’s School of Physics. “Scientists have theorized that these supermassive black holes could have formed at the birth of a galaxy, and we wanted to turn these theoretical predictions into observational predictions that could be seen by the James Webb Space Telescope.”

DCBH formation would be initiated by the collapse of a large cloud of gas during the early formation of a galaxy, said John H. Wise, a professor in Georgia Tech’s School of Physics and the Center for Relativistic Astrophysics. But before astronomers could hope to catch this formation, they would have to know what to look for in the spectra that the telescope could detect, which is principally infrared.

The formation of a black hole could require a million years or so, but to envision what that might have looked like, former postdoctoral researcher Aycin Aykutalp – now at Los Alamos National Laboratory – used the National Science Foundation-supported Stampede Supercomputer at the University of Texas at Austin to run a simulation focusing on the aftermath of DCBH formation. The simulation used physics first principles such as gravity, radiation and hydrodynamics.

“If the galaxy forms first and then the black hole forms in the center, that would have one type of signature,” said Wise, who is the Dunn Family Associate Professor in the School of Physics. “If the black hole formed first, would that have a different signature? We wanted to find out whether there would be any physical differences, and if so, whether that would translate into differences we could observe with the James Webb Space Telescope.”

The simulations provided information such as densities and temperatures, and Barrow converted that data into predictions for what might be observed through the telescope – the light likely to be observed and how it would affected by gas and dust it would have encountered on its long journey to Earth. “At the end, we had something that an observer could hopefully see,” Barrow said.

Black holes take about a million years to form, a blip in galactic time. In the DCBH simulation, that first step involves gas collapsing into a supermassive star as much as 100,000 times more massive than our sun. The star then undergoes gravitational instability and collapses into itself to form a massive black hole. Radiation from the black hole then triggers the formation of stars over period of about 500,000 years, the simulation suggested.

“The stars of this first generation are usually much more massive, so they live for a shorter period of time,” Wise said. “In the first five to six million years after their formation, they die and go supernova. That’s another one of the signatures that we report in this study.”

After the supernovae form, the black hole quiets down but creates a struggle between electromagnetic emissions – ultraviolet light and X-rays trying to escape – and the black hole’s own gravity. “These cycles go on for another 20 or 30 million years,” Wise said.

Black holes are relatively common in the universe, so the hope is that with enough snapshots, astronomers could catch one being born, and that could lead to a new understanding of how galaxies evolve over time.

Star formation around the DCBH was unexpected, but in hindsight, it makes sense, Barrow said. The ionization produced by the black holes would produce photochemical reactions able to trigger the formation of the stars. Metal-free stars tend to be larger than others because the absence of a metal such as iron prevents fragmentation. But because they are so large, these stars produce tremendous amounts of radiation and end their lives in supernovae, he said.

“This is one of the last great mysteries of the early universe,” Barrow said. “We hope this study provides a good step toward figuring out how these supermassive black holes formed at the birth of a galaxy.”

This research was supported by a Southern Regional Education Board doctoral fellowship, a LANL LDRD Exploratory Research Grant 20170317ER, National Science Foundation (NSF) grants AST-1333360 and AST-1614333, Hubble theory grants HST-AR-13895 and HST-AR-14326, and NASA grant NNX-17AG23G. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the sponsoring organizations.

CITATION: Kirk S. S. Barrow, Aycin Aykutalp & John H. Wise, “Observational signatures of massive black hole formation in the early Universe,” (Nature Astronomy, 2018). https://doi.org/10.1038/s41550-018-0569-y

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Media Relations Contact: John Toon (404-894-6986) (jtoon@gatech.edu).

Writer: John Toon

Once again, a Georgia Tech student ends up winning a ScienceMatters quiz because of the desire to take a homework break.

For Episode 4, it was Allie Caughman hearing the winning quiz detail during a study break. For Episode 5's quiz, Sachin Sarath Yadav Kothandaraman's need to relax a little resulted in the graduate student joining the ScienceMatters Hall of Fame.

"I heard this particular episode while I was taking a break from my assignments," Kothandaraman says. But it wasn't the first time he listened to the podcast. "I started listening to ScienceMatters after my classmate shared it with me. I've been hooked since."

Kothandaraman is from Chennai, India, where he received a bachelor's degree in biotechnology from Anna University. He is in his first year in the Georgia Tech Bioinformatics Graduate Program.

Continue here to the full story.

Episode 6 of ScienceMatters' Season 1 stars Simon Sponberg.  Listen to the podcast here and read the transcript here!

Simon Sponberg, an assistant professor with joint appointment in the School of Physics and the School of Biological Sciences, loves to study how insects like moths and cockroaches move. The Georgia Tech professor discovers the physics and mathematics hidden within the biological systems of these creatures. And what he learns about animal locomotion could mean better robots, better prosthetic devices, and better vehicles.

Sponberg is the principal investigator in the Agile Systems Lab. He received a National Science Foundation's Faculty Early Career Development Award in 2016, and won the National Society for Neuroethology Young Investigator Award in 2014. Sponberg also researches at Georgia Tech's Parker H. Petit Institute for Bioengineering and Bioscience.

Take a listen at sciencematters.gatech.edu.

Enter to win a prize by answering the question for Episode 6:

According to Episode 6, what animal did Simon Sponberg study when he was an undergraduate in Lewis and Clark College, in Oregon?

Submit your entry by 11 AM on Monday, Oct. 1, at sciencematters.gatech.edu. Answer and winner will be announced shortly after the quiz closes.

It is one of the most abundant minerals on Earth. Silica is found in beach sand, playground sand, and desert sand. It is in gravel, clay, and granite. It is in the concrete and glass structures of buildings everywhere. A study now shows that this prosaic material also could have played a key role in forming the polymeric molecules of life.

How the molecules of life formed on Earth is the subject of extensive studies. Researchers have long suggested that minerals may have played a role in the formation of peptides in prebiotic Earth. However, most past attempts to use minerals to catalyze amino acid polymerization have not shown a significant improvement or difference in products compared to the same reactions in the absence of minerals.  

The study – by Georgia Tech researchers in the National Science Foundation (NSF)/NASA Center for Chemical Evolution (CCE) – finds that drying and heating a mixture of amino and α-hydroxy acids in the presence of silica yields peptides that are longer than those formed in its absence. (Peptides are the precursors of proteins; amino acids are the building blocks of peptides; α-hydroxy acids are chemically similar to amino acids and could have been present in prebiotic Earth; silica would have been abundant on Earth billions of years ago.)

The findings suggest a mechanism by which organic compounds and silica on prebiotic Earth could have worked together to produce peptides. Designated a VIP (Very Important Paper), the paper reporting results is the front-cover article of the Sept. 17, 2018, issue of ChemBioChem.

The work was supported by the NSF and NASA Astrobiology Program under the NSF Center for Chemical Evolution (CHE-1504217). “The study shows silica, a major constituent of Earth’s crust, could play an important role in prebiotic evolution,” says NSF’s Acting Deputy Division Director in Chemistry Lin He. “It provides the grounds to better understand the rules of life and enables a wide range of applications in biomedical engineering, biosensors, chemical, and biological research.”

“The production of peptides in model prebiotic reactions has been a bottleneck in origins-of-life research,” says Thomas Orlando, a professor in the School of Chemistry and Biochemistry and the paper’s corresponding author. “With this discovery we can move to the next level and ask even deeper questions about the origins of life: Could minerals have played a role in selecting some of the organic molecules that participated in the origins of life? Are there common mineral properties that allow them to interact with prebiotic building blocks in a productive way?”

CCE researchers reported in 2015 that drying and heating mixtures of hydroxy acids and amino acids produces polymers called depsipeptides. While depsipeptides may also have played a role in the origin of life, finding an efficient prebiotic method to produce pure peptides remains of great interest.

“It is well-known that minerals react with organic acids, making mineral-organic interfaces that could have existed on early Earth,” Orlando says. Since the founding of the CCE, more than 10 years ago, affiliated researchers have been investigating the possible impacts of minerals on model prebiotic reactions.

“We have been asking: Could minerals, through their cooperation with simple organic molecules on early Earth, have facilitated the synthesis of complex polymers that, ultimately, gave rise to life?” says Nicholas Hud, professor of chemistry and biochemistry, CCE director, and a coauthor of the paper.

“Like almost everyone, we are curious about the origins of life,” says Aaron McKee, a Ph.D. candidate and the paper’s first author. “But we are also interested in the relevance to modern life.” For example, McKee says, scientists are developing nanoparticles that are essentially tiny functionalized mineral surfaces as biomolecule detectors or drug delivery agents. 

“There is a vast matrix of minerals and organic molecules related to those used in this study. Some of these would have also been present on prebiotic Earth,” McKee says. “We are now in an excellent position to investigate the numerous combinations of these minerals and organic molecules to see if there is any other chemical cooperation between inorganic and organic substances that could have facilitated the production of molecules important for starting life.”

Allie Caughman needed to step away from her studies for a little while, so she chose to listen to the new College of Sciences podcast, ScienceMatters.

"I listened to it in my room as a quick break from some homework," Caughman says.

Caughman had a special reason for tuning in the podcast. "This week's episode was by a postdoc in Dr. Stewart's lab, so I especially wanted to make sure I listened to it," Caughman says.

That postdoctoral researcher in Episode 4 is Nastassia Patin. Caughman has worked in Stewart's lab for the past two years. She is a third year undergraduate student studying for a Bachelor of Science degree in Biological Sciences. Stewart is an associate professor in the School of Biological Sciences, runs the Marine Microbiology @Georgia Tech lab, and is a member of the Parker H. Petit Insitute for Bioengineering and Bioscience.

ScienceMatters Episode 4 features the work that Patin did with Stewart on a study of the microbiome in the Georgia Aquarium's large Ocean Voyager exhibit.

The quiz question was: What is the name of the Georgia Aquarium sea turtle mentioned in Episode 4? The answer is Tank.

Caughman is focusing on microbiomes in her own research. "Starting this summer I began working on my own project on how the coral reef microbiome changes throughout a daily cycle." She received a Presidents Undergraduate Research Award (PURA) to help fund her project into the fall. "The goal of the project is to see what the microbial communities in the corals look like, and how stable or dynamic the communities are over a shorter time scale than many other studies have examined."

Caughman is from Cartersville, Georgia.

This week's episode 5 of ScienceMatters is "Visualizing the Birth of Galaxies" with John Wise, Dunn Family Associate Professor in the School of Physics.

If you would like to join the ScienceMatters Hall of Fame, enter the answer to this question: What is the name of the University of Illinois supercomputer mentioned in Episode 5 that John Wise uses for visualizations and simulations?

Submit your answer by 11 a.m. Monday, September 24, at sciencematters.gatech.edu.

Editor's Note: This story was adapted for the College of Sciences from the original story by Jennifer Salazar. The original story was published on Sept. 10, 2018, here.

A team from Georgia Tech has received an award for $3.7 million from the National Science Foundation to cover 70% of the cost of a new high-performance computing (HPC) resource for the upcoming Coda building’s data center.

College of Sciences faculty members David Sherrill and Deirdre Shoemaker are members of the Georgia Tech team.

Sherrill is a computational chemist and professor in the School of Chemistry and Biochemistry, with joint appointment in the School of Computational Sciences and Engineering (CSE), in the College of Computing. He is also the associate director for research and education at the Institute of Data Science and Engineering (IDEaS). 

Shoemaker is a gravitational wave astronomer, computational astrophysicist, and professor in the School of Physics, with an adjunct appointment in CSE. She is the director of the Georgia Tech Center for Relativistic Astrophysics, as well as IDEaS associate director for research and strategic initiatives.

The new HPC system for the Coda building is valued at $5.3 million. It will support data-driven research in astrophysics, computational biology, health sciences, computational chemistry, materials and manufacturing, and numerous other projects. It will also be used for research that improves the energy efficiency and performance of the HPC systems themselves.

The Georgia Tech team was led by Srinivas Aluru, co-executive director of IDEa) and professor in CSE.

“This project is exciting from many perspectives, but especially how it is pushing forward data and high performance computing research infrastructure at Georgia Tech,” said Aluru. “It reflects the teamwork of dozens of faculty, and also supports the work of over 50 research scientists and 200 graduate students.”

In addition to Sherrill and Shoemaker, other Georgia Tech faculty who are central to the award are Surya Kalidindi, professor in the George W. Woodruff School of Mechanical Engineering; Rich Vuduc, associate professor in CSE; and Marilyn Wolf, professor in the School of Electrical and Computer Engineering and the Rhesa "Ray" S. Farmer, Jr. Distinguished Chair in Embedded Computing Systems.

The system, anticipated to begin operations in 2019, will surpass the current campus capabilities. It will be used for applications that require large memories or local storage, provide modern GPU accelerators, and need large storage capacity for data and simulation results.

HPC simulations—one of several uses of the new system—are important for solving large-scale problems in hours or days, rather than months or years. Applications of these include detection of gravitational waves, climate models, performance of materials used in manufacturing or healthcare, and drug discovery.

The new HPC acquisition will coincide with the unveiling of an 80,000-square-foot data center in the new Coda building. The 21-story, 650,000-square-foot building is a new addition to Technology Square. It lies adjacent to the Georgia Tech campus and major fiber pathways connecting the Southeast.

“We worked to ensure the acquisition is well-timed to be the pivotal supercomputer in the Coda data center,” said Aluru.

 “This award is a major boon for interdisciplinary research at Georgia Tech, one that will also be a valuable addition to the HPC-based research community nationally. With Coda opening its doors soon, this supercomputer will become the premier computing resource at Georgia Tech,” said Executive Vice President for Reseach Chaouki Abdallah. One-third of the supercomputer’s cost was committed by Georgia Tech’s Office of the Executive Vice President for Research.

IDEaS and many users of the new equipment will be based in Coda. System management will be handled by the Partnership for an Advanced Computing Environment, or PACE, also residing in Coda.

Research enabled by new system will aid several national initiatives in big data, including strategic computing, materials genome, manufacturing partnerships, NSF-supported observatories such as the LIGO gravitational wave observatory, and the South Pole neutrino observatory known as IceCube.

Researchers from all levels—from early-career scientists and faculty to undergraduate students—will be the target of training and outreach. Several Georgia Tech researchers and partner institutions will be awarded time on the equipment based on scientific merit and on the national significance of proposed problems.

One-fifth of the system capacity will be dedicated to the research activities of regional partners including minority-serving institutions. Other users can participate through XSEDE, a national network of NSF supercomputers that scientists use to interactively share computing resources, data, and expertise.

“High-performance computing is a priority area for Georgia Tech. Data analysis, simulations, and computational predictive tools are essential elements of modern science, engineering and design. High-performance computing is the laboratory of the 21st century,” said Rafael L. Bras, provost and executive vice president for academic affairs and K. Harrison Brown Family Chair. “It is extremely satisfying to see a multidisciplinary team successfully work together to make this acquisition a reality. That, after all, is the spirit and culture of Coda.”

Episode 5 of ScienceMatters' Season 1 stars John Wise. Listen to the podcast here and read the transcript here!

Possible scenarios for the birth of stars, galaxies, and black holes come alive in the data crunching and visualizations of John Wise, a professor in the School of Physics. Wise explains how his simulations and visualizations -- some of which have won awards -- helps researchers "rewind" space and time back to the origins of the universe.

Wise studies the intricacies of the nearby and distant universe, using state-of-the-art numerical simulations that are run on the world's largest supercomputers.

Wise won the College of Sciences' Eric Immel Award in 2015 for Excellence in Teaching. He was the recipient of the Dunn Family Professorship from 2015-2017, and was a NASA Postdoctoral Program Fellow from 2007-2009.

Take a listen at sciencematters.gatech.edu.

Enter to win a prize by answering the question for Episode 5:

What is the name of the University of Illinois supercomputer mentioned in Episode 5 that John Wise uses for visualizations and simulations?

Submit your entry by 11 AM on Monday, Sept. 24, at sciencematters.gatech.edu. Answer and winner will be announced shortly after the quiz closes.

Conan Zhao is the winner of ScienceMatters Episode 3 quiz.

ScienceMatters Episode 3 features M.G. Finn, chair of the School of Chemistry and Biochemistry. Finn described his efforts to create a vaccine against the dreadful parasitic disease leishmaniasis.

The quiz question was: What sugar molecule mentioned in Episode 3 is the main reason surgeons can’t transplant organs from animals into humans?

The answer is in the rest of the story, here.