Advances in technology have driven the evolution of genome analysis and collaborative research forward at a rapid rate. This is particularly evident within the Petit Institute for Bioengineering and Bioeciences at the Georgia Institute of Technology, where the Genome Analysis Core has added a powerful new tool that allows researchers to look deeper into the gene expression analysis on a single cell level.

“Since we launched in 2012, the core has evolved quite a bit,” says Dalia Arafat-Gulick, who manages the lab of Petit Institute researcher Greg Gibson (professor in the School of Biological Sciences) and the Genome Analysis Core (contained within the Gibson lab space), in the Krone Engineered Biosystems Building. “The usage and diversity of equipment has definitely increased since then, and so have the services we provide.”

It all started with the Fluidigm Biomark quantitative real-time PCR (polymerase chain reaction). PCR, sometimes called “molecular photocopying,” is a fast technique to amplify small segments of DNA. The PCR technique was invented more than 30 years ago and it has transformed the study of DNA – mapping in the Human Genome Project.

PCR can be inexpensive if you’re only looking at a few genes, according to Gibson. “The costs can add up quickly,” he says. “But the Fluidigm platform brings the costs down further.”

This makes it possible, for example, to monitor the expression of 96 genes in 96 samples for around $1,000 (or 10 cents per reaction), “with high accuracy,” Gibson adds.

The latest transformative tool in Georgia Tech’s Genome Analysis Core is the ddSEQ, part of the single-cell sequencing system co-developed by Illumina and Bio-Rad. The Marcus Foundation collaborated with the Petit Institute in providing funding support, as Georgia Tech last April became the first research institution in the Southeast to deploy the ddSEQ.

“The ddSEQ is essentially a sample preparation platform,” explains Steve Woodard, director of core facilities for the Petit Institute. “You’re preparing samples to go downstream for sequencing in the Molecular Evolution Core or the High-Throughput DNA Sequencing Core. Just another example of how our core facilities are integrated.”

The process typically begins upstream in the Cellular Analysis and Cytometry Core, where researchers will utilize flow cytometry to isolate specific cell populations. Then the ddSEQ separates those cells into a sub-nanoliter oil based droplets on a disposable cartridge, in under five minutes, “which gives you a fast turnaround for each cell captured,” Arafat-Gulick says.

Each cartridge can accommodate up to four samples, which allows each sample to be processed simultaneously. Cell lysis, reverse transcription, and bar-coding occur inside the individual droplets, which allow researchers to amplify several thousand transcripts in each cell.

“The next step is to actually get them sequenced,” Arafat-Gulick says. “That’s where the downstream cores [High Throughput and Molecular Evolution] come in. They have the equipment that allows us to ultimately analyze the gene expression levels of these cells.” 

In this way, researchers can peek inside hundreds – or even thousands – of cells, seeing how much diversity in the mixture there is, or monitoring how individual cells are responding to treatments, all for around $10 a cell. The technology also exists to sequence the DNA, and measure methylation states of genes, “which is transforming genomic analysis,” Gibson says.

“The next step is to actually get them sequenced,” Arafat-Gulick says. “That’s where the downstream cores [High Throughput and Molecular Evolution] come in. They have the equipment that allows us to ultimately analyze the gene expression levels of these cells.”

A number of Petit Institute researchers, including Krish Roy, Ed Botchwey, and Gibson, are working in the single-cell arena now, utilizing the equipment, techniques, and services available through the Genome Analysis Core.

“It’s a quantitative way to look at RNA sequencing on a single cellular level,” Arafat-Gulick says. “Principal investigators really want to see what’s happening on a cell to cell basis, and this new technology makes this accessible, at a much faster rate than before.”

•••

The Petit Institute's state-of-the-art research facilities, known as "Core Facilities," serve as a shared resource for the bioengineering and bioscience community. Consultation, training, and technical support is available for a variety of research projects. Users have access to over 100 pieces of lab equipment totaling over $24 million. 

Learn more about the Petit Institute’s core facilities and how they can support your research projects. 

CONTACT:

Jerry Grillo
Communications Officer II
Parker H. Petit Institute for
Bioengineering and Bioscience

Minda Monteagudo noticed a lack of spaces and programming for women of color on campus. So she applied for a Diversity and Inclusion Fellowship to explore ways to meet the need.

Inspired by the example of African-American musician Daryl Davis, Conan Zhao hopes to use his diversity fellowship to explore the use of music in breaking barriers among people.

Monteagudo and Zhao are among six members of the College of Sciences community to be named 2018 Diversity and Inclusion Fellows. The program brings together faculty, staff, and students who individually and collectively advance their action, research, or teaching objectives while enhancing the culture of inclusive excellence at Tech.

Altogether the 2018 fellows from the College of Sciences are:

• Jennifer Glass, an assistant professor in the School of Earth and Atmospheric Sciences (EAS)
• Minda Monteagudo, Ph.D. student working under the guidance of EAS Professor Jean Lynch-Stieglitz
• Raneem Rizvi, a School of Biological Sciences (BioSci) major
• Skyler Tordoya Henckell, a School of Psychology major
• Emily Weigel, an academic professional in BioSci
• Conan Zhao, a research assistant in the lab of BioSci Assistant Professor Sam Brown

The 2018 fellows were announced on Nov. 15 at a poster session showcasing the projects of the program’s inaugural 2017 cohort.

Among the 2017 fellows were three from the College of Sciences:

• Jennifer Beveridge, a Ph.D. candidate supervised by School of Chemistry and Biochemistry (Chem/Biochem) Professor and Chair M.G. Finn
• Calvin Runnels, a third-year biochemistry major who conducts research with Chem/Biochem Professor Loren Williams
• Hussein Sayani, a former Ph.D. student of EAS Professor Kim Cobb, now a postdoctoral researcher in Boston University

The 2017 fellows’ projects inspired and encouraged the second cohort and the audience.

Beveridge partnered with Santanu Dey, associate professor in the H. Milton Stewart School of Industrial and Systems Engineering, to study the attrition of students admitted to Ph.D. programs at Georgia Tech during the period 2002-2012. According to Dey, who presented the project at the poster session, their big take-away is how little is known about the churn of Ph.D. students at Tech compared with undergrads.

Despite the limited data, the study showed clear differences in rates of Ph.D. completion between men and women and among racial groups. The gaps varied across Georgia Tech schools. The hope, Dey said, is to discover the practices of the schools with high rates of Ph.D. graduation across the board so that they can be shared with other units that are not doing so well.     

Meanwhile, Sayani teamed up with Jerrold Mobley, public services associate in the Georgia Tech library, and Michelle Gaines, a former postdoctoral researcher in the School of Chemical and Biomolecular Engineering and now an assistant professor of chemistry and biochemistry at Spelman College. Their project, called Culture Xchange, focuses on person-to-person engagement as a means to tear down barriers, said Mobley, who discussed the work at the Nov. 15 poster session.

With the help of 10 volunteers, they are testing the idea. Through structured discussions, collaborative exercises, and paired excursions, participants share not-so-obvious aspects of their daily lives with each other. The hypothesis, Mobley said, is that “anyone who has the opportunity to engage in real one-on-one interactions with any person of any cultural identity, race, creed, etc., has no choice but to respect who that person is and eliminate any biases that they might have had before.”

“Inclusive excellence is a core value of the College of Sciences,” said College of Sciences Dean and Sutherland Chair Paul M. Goldbart. “I am delighted to see so many members of our college community answering the call for grassroots initiatives to promote and strengthen this core value.” 

Scholar, educator, award-winning book author, interdisciplinary innovator, and shaper of future scientists, Joshua S. Weitz wears many hats at Georgia Tech, but his influence reaches far beyond. For his contributions to the field of viral ecology, Joshua Weitz has been elected a fellow of the American Association for the Advancement of Science (AAAS).

Weitz’s research focuses on the interactions between viruses and their microbial hosts, that is, the viral infections of microbial life. Weitz is motivated by seemingly simple questions: What happens to a microbe when it is infected by a virus? Does the infected cell live, die, or change? How do infections of single cells translate into system-wide consequences?

These areas are “of utmost importance” because of the role microbes play in humans and across our planet, says Mark E. Hay, Regents Professor and Harry and Linda Teasley Chair in the School of Biological Sciences at Georgia Tech. “Yet understanding the role of viruses that infect microbes is at its infancy. Joshua has been identifying the big questions and providing deep insights into how viruses modulate human and environmental health.”

Weitz received his Ph.D. in Physics from MIT and continues to combine mathematical theory and data-driven models to understand complex living systems. His work has led to new quantitative principles underlying the abundances of environmental viruses, the networks of microbes that viruses can infect, and mechanisms by which viral infections change ecosystem functioning.

Recent work from the Weitz group has shed light on ways that phage – viruses that exclusively infect bacteria – can be used therapeutically. Phage therapy – the use of bacteria-killing viruses to treat bacterial infections – was proposed nearly a century ago, but the mechanisms underlying its efficacy remain unresolved. Earlier this year, Weitz and collaborators combined mathematical models and experiments with immunomodulated mice to show that phage do not act alone. In fact, the immune cells of the host act synergistically with phage to eradicate infections.

A productive researcher, Weitz has published nearly 100 peer-reviewed articles, including more than 80 articles since joining Georgia Tech in January 2007. He also wrote an award-winning monograph: Quantitative Viral Ecology: Dynamics of Viruses and Their Microbial Hosts. Published in December 2015 by Princeton University Press, it is “the book” on viral ecology, Hay says. The book was selected by the Royal Society of Biology as the winner of the 2016 Postgraduate Textbook Prize.

In education, Weitz has made an indelible mark by conceptualizing and implementing Georgia Tech’s Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS), which accepted its first group of Ph.D. students in the Fall 2016 semester. As Georgia Tech’s third interdisciplinary Ph.D. focusing on life sciences – after Bioengineering and Bioinformatics – QBioS  continues a tradition of fostering innovative, interdisciplinary research, and education.

Weitz has mentored dozens of students and scientists. At Georgia Tech, he has served as primary supervisor for eight Ph.D. theses in biology, bioinformatics, and physics. Eight of Weitz’s former postdoctoral researchers have moved to tenure-track faculty positions in biology, mathematics, and engineering departments.

Weitz fosters new interfaces between the physical sciences, mathematics, computational sciences, and the life sciences through his leadership role in workshops, working groups, and international collaborations. He cochaired an international working group on ocean viral dynamics at the National Institute for Mathematical and Biological Synthesis from 2012 to 2014, chaired a 2015 rapid-response modeling workshop on Ebola virus disease held at Georgia Tech, and is currently a Simons Foundation Investigator as part of the Simons Collaboration on Ocean Processes and Ecology.

“He is one of our most obvious interdisciplinary innovators,” Hay says of Weitz. “With his creative ideas, breadth of interdisciplinary vision, and rigorous approach to science, he makes contributions beyond his years.”

In the Ford Environmental Science and Technology Building, the office of Martha Grover is three doors from that of Jennifer Glass. Both are Georgia Tech scientists doing research related to astrobiology – life in the cosmos – but until last year they hardly talked to each other as researchers with common interests.  

“We are all so busy,” says Grover, a professor in the School of Chemical and Biomolecular Engineering, a scientific collaborator at the NSF/NASA Center for Chemical Evolution (CCE), and a member of the Center for Space Technology and Research (C-STAR).

Now, Grover, Glass, and others at Tech are members of a growing community that’s coalescing astrobiology activities across campus. In a public debut of sorts, six members of Georgia Tech Astrobiology, as the community calls itself, participated in the 2017 Dragon Con, the premier pop-culture convention on science fiction and fantasy. They wowed the audience, not by fiction or fantasy or over-the-top costumes, but by progress in answering fundamental questions – How did life begin? Where else could life exist? – happening right next door from the meeting venue, at Georgia Tech.

The growing visibility of researchers interested in astrobiology is helping Georgia Tech emerge as a powerhouse in the field. At minimum, says Kenneth Knoespel, a historian of science and professor in the Ivan Allen College of Liberal Arts, “it affirms the importance of this community at Georgia Tech and the importance of astrobiology as a new configuration of disciplines that brings together the natural and human sciences.”  

TEEMING WITH TALENT

“Georgia Tech is clearly recognized as a hub for astrobiology and maybe the one that’s growing the most quickly,” says Edward Goolish, the deputy director of the NASA Astrobiology Institute (NAI), one of the six elements of the NASA Astrobiology Program. People at Georgia Tech, Goolish adds, “have been generous with their time and have contributed in important ways when NASA has reached out to the science community for input.”

The community includes physicists, chemists, biologists, Earth and planetary scientists, and engineers, as well as historians of science and writers. The scientists are figuring out how life emerged and evolved to the biosphere we know, inventing instruments to detect life outside Earth, and searching for other habitable places in the universe. The science historians and writers are witnessing science in the making and perhaps gathering fodder for the next volume of science fiction.

Broadly defined, astrobiology is the study of life in the cosmos. Its central questions are “What is the origin of life?” and “Does life exist beyond Earth?” Humans have asked these questions since time immemorial. That they are still around attests to the difficulty of discovering and assembling the pieces of a formidable puzzle: the emergence of a biosphere on a planet.

How formidable? According to Eric Smith, a theoretician in the NASA Astrobiology Institute’s team at Georgia Tech (NAI-GT), understanding the nature of the transition from a planet without a biosphere to one with a biosphere should be central to origins-of-life inquiries. However, he says, “a lot of the language to enable that understanding doesn’t exist yet.”

THREE PILLARS

At Georgia Tech, research teams are working across the breadth of questions central to astrobiology. Their activities are exemplified by three specialized research groups: CCE, NAI-GT, and C-STAR. 

CCE is building a community in origin-of-life research, said its director, Nicholas V. Hud, at a symposium organized by Georgia Tech Astrobiology last month. In finding answers, CCE takes two approaches, Hud explained. “Bottom up,” it starts with geology and chemistry and understanding the formation of the first polymers of life, which is a major focus of Hud’s. “Top down,” it starts with biology, genetics, and looking back in time at persistent, conserved molecular motifs, as exemplified by the work of Loren Williams on ribosomes.

Like digging a tunnel underground from opposite ends and meeting somewhere in between, the two approaches are converging on the coevolution of the biopolymers of life. Chemistry and biology are telling us the same thing, say Hud and Williams, both professors in the School of Chemistry and Biochemistry (SoCB) and members of the Parker H. Petit Institute for Bioengineering and Bioscience (IBB).

At NAI-GT, “we start at the level of the cell,” says Frank Rosenzweig, the School of Biological Sciences (SoBS) professor who leads the NASA group. “Once you have all this biochemistry wrapped in a cell, what happens then? How do they become associated as multicellular organisms? How do they engage in biochemistries that change the environment? We need to understand the interaction between the evolution of life and the evolution of its abiotic surrounding to have a chance of recognizing life elsewhere.

“Although life on Earth manifests in different forms, all are governed by laws of growth, inheritance, and variability,” says Rosenzweig, also a member of IBB. NAI-GT aims to “illuminate and interpret these laws via laboratory-based evolution experiments with microbial populations.” An example is the exploration of the origin of multicellularity by experimentally evolving yeast, as described in the September symposium by Will Ratcliff, an assistant professor in SoBS.

For C-STAR-affiliated faculty, habitability is one key question. What events and conditions in the abiotic sphere yield environments that support life? The NASA-supported work of Jennifer Glass and Chris Reinhard, in the School of Earth and Atmospheric Sciences (EAS), exemplify the search for answers in this realm.

What signals should we monitor in search of life elsewhere in the universe? What tools do we need to probe for signs of life from the comfort of Earth? What hazards should we prepare for if humans were to go to other worlds?

In EAS, C-STAR members and planetary scientists Carol Paty, Britney Schmidt, and James Wray are co-investigators of NASA-funded projects to answer these questions. So is C-STAR member Paul Steffes, in the School of Electrical and Computer Engineering, as well as C-STAR Director Thomas Orlando and C-STAR member Amanda Stockton, in SoCB.

WHAT’S NEXT

With the talent on campus, Georgia Tech is becoming well known in the field of astrobiology. At the 2017 Astrobiology Scientific Conference, in Mesa, Ariz., last April, the Georgia Tech “posse” numbered about 30 faculty and students. Last summer, attendees of AbGradCon (Astrobiology Graduate Conference) 2017 selected Georgia Tech to host the 2018 event. This popular meeting for students is funded primarily by the NASA Astrobiology Institute.

The astrobiology community at Georgia Tech is “healthy,” Smith says. “The people in strategic positions have good priorities in the sophistication and intellectual integrity they are trying to support.”

The community – now 85 strong and growing – is raring to make its presence felt. It has an ambitious schedule for the 2017-18 school year, spearheaded by the September symposium.

Led by Grover as principal investigator, and with contributions from Glass, Knoespel, Paty, Reinhard, Rosenzweig, Schmidt, Williams, and others – Rebecca Burnett, Ivan Allen College of Liberal Arts; Glenn Lightsey, School of Aerospace Engineering and C-STAR; and Christopher Parsons, CCE – their proposal for seven projects received funding from the Georgia Tech Strategic Plan Advisory Group (SPAG) and the Colleges of Engineering, Liberal Arts, and Sciences.

The projects aim to showcase the quality and variety of astrobiology projects at Tech, highlight the social impact of these projects, and strengthen the sense of community among faculty and students. The goals will be achieved through formal gatherings, educational innovations, and public outreach.

“As I see it, the point of research universities is to tackle the really important, really deep, and really challenging questions – the ones at the edge of, or even beyond, our reach; the ones that present not just the possibility but the likelihood of failure,” said College of Sciences Dean and Sutherland Chair Paul M. Goldbart at the September symposium. “It’s our duty as administrators to do everything we can to support this kind of truly adventurous research.”

What the astrobiology community is doing not only is exciting, Goldbart said. But also, “it could hardly fit better with the dreams of the College of Sciences and of Georgia Tech.” 

Georgia Tech Researchers Working Toward the Goals of NASA’s Astrobiology Program

Planetary Science and Technology Through Analog Research (P-STAR)
               Jennifer Glass, School of Earth and Atmospheric Sciences
               Britney Schmidt, School of Earth and Atmospheric Sciences
               Amanda Stockton, School of Chemistry and Biochemistry

Planetary Instrument Concepts for the Advancement of Solar System Observations (PICASSO)
               Amanda Stockton

Exobiology: Early Evolution of Life and the Biosphere
               Frank Rosenzweig, School of Biological Sciences

Exobiology: Evolution of Advanced Life
               William Ratcliff, School of Biological Sciences

Exobiology: Prebiotic Evolution
               Loren Williams, School of Chemistry and Biochemistry

Exobiology: Methane and Iron Metabolisms in Ancient Oceans 
               Jennifer Glass

School of Earth and Atmospheric Sciences Faculty Affiliated with NASA Astrobiology Institute (NAI)
               Jennifer Glass, Chris Reinhard, and Yuanzhi Tang, with University of California, Riverside, team
               James Wray, with SETI Institute team
              
NAI Team at Georgia Tech School of Biological Sciences
         Kim Chen 
         Phillip Gerrish 
         Matt Herron
         Teresa Jonsson 
         Kennda Lynch
         Frank Rosenzweig 
         William Ratcliff 
         Eric Smith
         Pedram Samani 
         Tim Whelan 

NASA Postdoctoral Program Fellows
          Bradley Burcar, with Nicholas Hud
          Peter Conlin, with William Ratcliff
          Moran Frenkel-Pinter, with Loren Williams
          Kazumi Ozaki, with Chris Reinhard
          Nicholas Speller, with Amanda Stockton

2018 AbGradCon Organizers
               Marcus Bray                    Justin Lawrence
               Bradley Burcar                 Adriana Lozoya
               Anthony Burnetti              Kennda Lynch
               Heather Chilton               Santiago Mestre Fos
               Chase Chivers                 Marshall Seaton
               Dedra Eichstedt               Micah Schaible
               Zachary Duca                  Elizabeth Spiers
               Jennifer Farrar                 Scot Sutton
               Nicholas Kovacs              Nadia Szeinbaum
                                George Tan, Conference Chair 
Note: This list is not meant to be comprehensive; it represents information that was available as of October 2017.

This list was updated on Nov. 21, 2017, to include all members of the NAI Team at Georgia Tech School of Biological Sciences. 

PHOTO CAPTIONS

Georgia Tech at AbSciCon 2017. This photo shows only some of the Georgia Tech researchers who attended. From left: Cesar Menor-Salvan, Nick Hud, Justin Lawrence, Jacob Buffo, Frank Rosenzweig, Amanda Stockton, Britney Schmidt, Kennda Lynch, Gavin Mendez, George Tan, Jennifer Glass, Zachary Duca, Nadia Szeinbaum, Aaron McKee, Chloe Stanton, and Marcus Bray (Courtesy of Jennifer Glass)

Georgia Tech Astrobiology at 2017 Dragon Con. From left: Amanda Stockton, Loren Williams, Kenneth Knoespel, Lisa Yaszek, Chris Reinhard, and Britney Schmidt (Photo by Renay San Miguel)

Organizers and Speakers: “Life in the Cosmos.”
Top, from left: Rebecca Burnett, Carol Paty, Kennda Lynch, Jennifer Glass, Martha Grover, Gongjie Li, and Amanda Stockton
Bottom, from left: Thomas Orlando, Paul Steffes, Frank Rosenzweig, Nicholas Hud, Loren Williams, and William Ratcliff (Photos by Maureen Rouhi)

The College of Sciences feted new colleagues joining in the 2017-18 academic year at a summer dinner on Sept. 6. Dean and Sutherland Chair Paul M. Goldbart and Jenny Singleton, associate chair and professor in the School of Psychology, hosted the celebration, which also recognized recipients of 2017 College of Sciences awards.

“It is invigorating to start the school year by warmly welcoming new colleagues into our scholarly community and celebrating our outstanding teachers, researchers, and mentors,” Goldbart said.

One program director, one professor of practice, eight assistant professors, two associate professors, and three professors joined the college in the 2017-18 academic year. Three of them – Felix Herrmann, Gregory Sawicki, and Carlos Silva – have joint appointments in other Georgia Tech units.

The Schools of Biological Sciences and of Chemistry and Biochemistry welcomed the most number of new colleagues in the 2017-18 academic year – four each.

The Center for Education Integrating Science, Mathematics, and Computing (CEISMC) recruited Casey Bethel, Georgia’s 2017 Teacher of the Year, to coordinate campus communications. 

The following individuals joined the college in the 2017-18 academic year:

• Vinayak Agarwal, assistant professor, School of Chemistry and Biochemistry
• Casey Bethel, program director, CEISMC
• Thackery Brown, assistant professor, School of Psychology
• Stephen Diggle, associate professor, School of Biological Sciences
• Albert Fathi, professor of practice, School of Mathematics
• Neha Garg, assistant professor, School of Chemistry and Biochemistry
• Zachary Handlos, academic professional, School of Earth and Atmospheric Sciences
• Felix Herrmann, professor, joint appointment, School of Earth and Atmospheric Sciences, School of Electrical and Computer Engineering, and School of Computational Science and Engineering.
• Wenjing Liao, assistant professor, School of Mathematics
• Jesse McDaniel, assistant professor, School of Chemistry and Biochemistry
• D. Zeb Rocklin, assistant professor, School of Physics
• Gregory Sawicki, associate professor, joint appointment, School of Mechanical Engineering and School of Biological Sciences
• Carlos Silva, professor, joint appointment, School of Chemistry and Biochemistry and School of Physics
• Alberto Stolfi, assistant professor, School of Biological Sciences
• Marvin Whiteley, professor and Bennie H. & Nelson D. Abell Chair and Georgia Research Alliance Eminent Scholar in Molecular and Cellular Biology, School of Biological Sciences

Also celebrated as new colleagues were Rachel Kuske and Jenny McGuire. Kuske is a professor in and the chair of the School of Mathematics. She joined the College of Sciences on Jan. 3, 2017. McGuire previously held the position of Research Scientist II in the School of Biological Sciences. She is now assistant professor, tenure track, with joint appointment in the Schools of Biological Sciences and of Earth and Atmospheric Sciences.

Also at the 2017 summer dinner, nine faculty members were named recipients of 2017 faculty awards.

School of Mathematics Professors John Etnyre and Ronghua Pan, with School of Chemistry and Biochemistry Associate Professor Raquel Lieberman, received the 2017 College of Sciences Faculty Mentor Awards. They were recognized for sharing their experience, providing advice and encouragement, and helping the next generation of faculty succeed.

The college selected School of Physics Professor and Chair Pablo Laguna for the 2017 Ralph and Jewel Gretzinger Moving Forward School Award. The award praises leadership of a school chair or senior faculty member who has played a pivotal role in diversifying faculty, creating a family-friendly work environment, or providing a supportive environment for junior faculty. Laguna was commended for driving equity and inclusion and for mentoring of groups underrepresented in science, technology, engineering, and mathematics (STEM). The award is supported by an endowment fund from School of Mathematics alumnus Ralph Gretzinger.

School of Earth and Atmospheric Sciences Assistant Professors Chris Reinhard and Britney Schmidt received the 2017 Eric R. Immel Memorial Award for Excellence in Teaching. The award salutes exemplary teaching of a foundational class by junior faculty. In particular, Reinhard and Schmidt were commended for “their imaginative and effective redevelopment” of EAS 1601, How to Build a Habitable Planet. Their work has inspired teaching assistants, excited students, and raised enrolment. The award is supported by an endowment fund from School of Mathematics alumnus Charles Crawford.

School of Physics Assistant Professor James “JC” Gumbart, School of Biological Sciences Associate Professor Brian Hammer, and School of Mathematics Associate Professor Anton Leykin were recognized with 2017 Cullen-Peck Fellowship Awards. The awards recognize innovative research led by faculty who are at the associate professor or advanced assistant professor level. They are made possible by a gift from School of Mathematics and School of Industrial and Systems Engineering alumni Frank Cullen and Libby Peck. The awards applaud outstanding research in computational biophysics (Gumbart), in the biology of competition and cooperation in bacterial systems (Hammer), and in applied and computational algebraic geometry (Leykin). 

“We are proud to have so many exceptional faculty members,” Goldbart said. “I am especially grateful for the generosity of our thoughtful alumni, whose gifts enable our colleagues to achieve the highest level of success in their teaching, research, and service.”

There is a genomic revolution happening across the planet, as researchers apply genome science and related technologies to advance the understanding of health and disease in different populations, identifying those who are at risk due to genetic and/or environmental factors for developing specific diseases.

It’s a scattered and somewhat inconsistent revolution, however, as some regions with adequate resources set the pace for discovery, while others are left virtually stranded. Such is the case on the African continent, where many countries are being left behind, a situation that has the potential of widening global and ethnic inequalities in health and economic well-being.

Fortunately, though, a collection of individuals and institutions, including the Georgia Institute of Technology, are responding to the challenge and working to bridge the genomic divide. It’s the kind of bridge-building that King Jordan, a researcher with the Petit Institute for Bioengineering and Bioscience, has grown accustomed to. His lab, and the Bioinformatics Graduate Program that Jordan directs, have been deeply engaged in biotechnology capacity-building efforts in Latin America for close to a decade.

“We’re leveraging bioinformatics and genomics technologies to facilitate public health and to stimulate economic development overseas,” says Jordan, associate professor in the School of Biological Sciences, who cites the Georgia Tech strategic vision plan laid out in 2010, specifically goal number four, which involves expanding Tech’s global footprint and influence.

“That is done in two ways,” says Jordan. “One is by bringing the world to Georgia Tech and training more globally-engaged students. The other way is to project Georgia Tech’s reach out to the world, and we’re doing both.”

And now it’s happening in Africa, with the recent announcement that Jordan and one of his former grad students, Daudi Jjingo, have been awarded a five-year, $1.3 million grant as part of the NIH’s Human Heredity and Health in Africa (H3Africa) Initiative. H3Africa aims to elucidate Africa’s human genetic diversity (the highest on the planet) and thus one with a high potential of revealing more varied ways in which the human genome interacts with diseases and other environmental pertubations.

The plan is to use the award to support two trajectories, according to Jjingo, who earned his PhD as a Fulbright fellow in Jordan’s research team at Georgia Tech in 2013 and returned to his home country, Uganda, where he is a faculty researcher at Makerere University in Kampala.  

“First we want to focus on building a computing and physical infrastructure, and secondly, we want to actually start a bioinformatics program,” says Jjingo. “The idea is to build a sustainable bioinformatics program.”

There is a lot of clinical research happening now in Africa, Uganda in particular, Jjingo says, and researchers currently lack the bioinformatics resources to adequately analyze all of that data.

“So the vision is, at the end of five years we’ll have this program established, well-staffed, with students graduating,” Jjingo says. “Having talented students who graduate creates the infrastructure – it builds the right recipe to build a research center, which means we can move beyond academia and provide bioinformatics consulting services for industry and others.”  Their bioinformatics consulting efforts will be modeled after the Applied Bioinformatics Laboratory (ABiL), a public-private partnership between the Jordan lab at Georgia Tech and the company IHRC Inc., which provides bioinformatics analysis services and training to industry and non-profit clients.

The program in Uganda will begin, Jjingo says, “with about five Masters students and a couple of PhD students, and the plan is that one of them will spend a year at Georgia Tech – from my own experience, I know the huge value you can get by spending a short time there, learning from a mature research environment and ecosystem. And Georgia Tech personnel will come here to Uganda, to conduct short seminars, and so forth. So we’re talking about an exchange of human resources.”

Jordan adds, “one thing we know that is implicit in the notion of mentoring a grad student is the idea of collaborative research. So when you have a graduate student that serves as the fulcrum between two institutions, it provides a great opportunity build bridges. My hope is that those students will engage in collaborative research that will allow for deeper connections between Georgia Tech and Makerere University.”

CONTACT:

Jerry Grillo
Communications Officer II
Parker H. Petit Institute for
Bioengineering and Bioscience

Sand-swimming lizards, slithering robotic snakes, dusk-flying moths and running roaches all have one thing in common: They're increasingly being studied by physicists interested in understanding the shared strategies these creatures have developed to overcome the challenges of moving though their environments.

By analyzing the rules governing the locomotion of these creatures, "physics of living systems" researchers are learning how animals successfully negotiate unstable surfaces like wet sand, maintain rapid motion on flat surfaces using the advantageous mechanics of their bodies, and fly in ways that would never work for modern aircraft. The knowledge these researchers develop could be useful to the designers of robots and flying vehicles of all kinds.

“Locomotion is a very natural access point for understanding how biological systems interact with the world,” said Simon Sponberg, an assistant professor in the School of Physics and School of Biological Sciences at the Georgia Institute of Technology. “When they move, animals change the environment around them so they can push off from it and move through it in different ways. This capability is a defining feature of animals.”

Sponberg has spent his career bridging the gap between physics and organismal biology – the study of complex creatures. His work includes studying how hawk moths slow their nervous systems to maintain vision during low-light conditions, and how muscle is a versatile material able to change function from a brake to a motor or spring.

He recently published a feature article, the cover story for the September issue of the American Institute of Physics magazine Physics Today, on the role of physics in animal locomotion. The article was not intended as a review of the entire field, but rather to show how organismal physics – integrating complex physiological systems, the mechanics and the surrounding environment into a whole animal – has inspired his career.

“The intersection of physics and organismal biology is a very exciting one right now,” said Sponberg, who is also a researcher with the Petit Institute for Bioengineering and Bioscience at Georgia Tech said. “The assembly and interaction of multiple natural components manifests new behaviors and dynamics. The collection of these natural components manifests different patterns than the individual parts, and that’s fascinating.”

Supported by new initiatives at such organizations as the Army Research Office/Army Research Laboratory and the National Science Foundation – which are embracing these frontiers – Georgia Tech scientists are learning the equations that dictate how snakes move, understanding how the hair spacing on the bodies of bees help them stay clean, and using X-ray equipment to see how an unusual African lizard “swims” through dry sand.

“It’s a really exciting time to be working at the intersection of evolutionary organismal biology that is realized in these living systems that have come about through the process of evolution, composed of seemingly very complex systems,” he said. “Biological systems are inescapably complex, but that doesn’t mean there aren’t simple patterns of behavior that we can understand. We now have the modern tools, approaches and theory that we need to be able to extract physical patterns from biological systems.”

In his article, Sponberg makes predictions about the research that will be needed for the physics of living systems to advance as a field:

• How feedback transforms physiological dynamics,
• How aggregations of living components, from humans to ants to molecular motors, arise at multiple scales, and
• How robo-physical models of these complex systems can lead to new discoveries and advance engineering.

Engineered systems use feedback about the effects of their actions to adjust their future activities, and animals do the same to control their movement. Scientists can manipulate this feedback to understand how complex systems are put together and use the feedback to design experiments rather than just analyzing what is there. 

“We use feedback all the time to move through our environment, and feedback is a really special thing that fundamentally affects how dynamics occur,” said Sponberg. “But using feedback to design experiments is really sort of new.”

For example, in the study of how hawk moths track flowers during low-light conditions, he and his colleagues used feedback dynamics to isolate how the moth’s brain adjusts its processing in dim light. The moths can still accurately track flower movements that occur less than two times per second – which matches the frequency at which the flowers sway in the wind.

Animals are composed of many systems operating at multiple time scales simultaneously – brain neurons, nerves and the individual fibers of muscles with molecular motors. These muscle fibers are arranged in an active crystalline lattice such that X-rays fired through them create a regular diffraction pattern. Understanding these multiscale living assemblages provides new insights into how animals manage complex actions.

Finally, Sponberg notes in his article that robots are playing a larger and larger role in the physics laboratory as functional models that can examine principles of movement by interacting with the real world. In the laboratory of Georgia Tech Associate Professor Dan Goldman – one of Sponberg’s colleagues – robotic snakes, turtles, crabs and other creatures help scientists understand what they’re observing in the natural world.

“Moving physical models – robots – can be very powerful tools for understanding these complex systems,” Sponberg said. “They can allow us to do experiments on robots that we couldn’t do on animals to see how they interact with complex environments. We can see what physics in these systems is essential to their behaviors.”

Sponberg was inspired to study the interaction of organismal biology and physics by the remarkable diversity of animal movement and by nonlinear dynamics, a field made popular when he was a young student by the 1987 best-selling book Chaos: Making a New Science, authored by former New York Times reporter James Gleick. Sponberg hopes today’s students – readers of Physics Today – will also be inspired.

“I voted on this with my career choice, so I think this is a very exciting areas of science,” he added.

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Seven students have joined the Interdisciplinary Ph.D. program in Quantitative Biosciences (QBioS).  These students have backgrounds in physics, mathematics and biology and join the program from the United States, China, and India.  Altogether, the QBioS Ph.D. program now includes 16 students, including nine members from the inaugural cohort who joined in Fall 2016.  The QBioS Ph.D. is directed by Biological Sciences Professor Joshua S. Weitz.

The QBioS Ph.D. was established in 2015 and includes more than 50 program faculty. The mission of QBIoS is to educate students and advance research, enabling the discovery of scientific principles underlying the dynamics, structure, and function of living systems at scales from molecules to ecosystems.   Of the seven incoming students, four are affiliated with the School of Biological Sciences and three are affiliated with the School of Physics.

Kelimar Diaz Cruz obtained a B.S. in Physics from the University of Puerto Rico, Rio Piedras Campus in Puerto Rico this year, before joining the QBioS Ph.D. “Before my undergrad, I had no idea there were many branches of Physics,” Diaz notes.  “Once I learned Biophysics was one of them I immediately knew in what direction I wanted to head. The QBioS Ph.D. program will allow me to develop interdisciplinary and quantitative approaches for the understanding of biological systems. There is no better program that aligns with my interests. I am looking forward to expanding my knowledge of biological sciences as I work alongside faculty and researchers in different areas.”

Guanlin Li graduated with a B.S in Mathematics and Physics Minor in 2016 from Arizona State University and earned his M.S in Mathematics from Georgia Tech this year before transferring into QBioS. “I like to utilize mathematical and computational tools to answer fundamental questions raised in the biosciences,” Li says. “QBioS opens a new door that brings biosciences to a quantitative side, from experimental interpretations to equations and laws. I'm excited and looking forward to joining this new program.”

Daniel Muratore completed a Bachelor's in Biological Sciences at the University of Chicago in 2016, focusing primarily in theoretical ecology. After graduating, he worked in Maureen Coleman's lab at the University of Chicago on microbial ecology and biogeochemistry for marine and lake systems. Muratore moved from to Atlanta to work with Weitz on virus-host models and nutrient dynamics in marine ecosystems and to start his PhD in QBioS, explains, “I am very excited to use modeling approaches and robust analytical methods to handle a diversity of data coming from the worlds of oceanography, molecular biology, and bioinformatics for the purpose of generating new knowledge about the goings on of the marine microbial ecosystem.”

Brandon Pratt graduated from the University of Washington earlier this year, receiving Bachelor of Science degrees in neurobiology and in molecular, cellular, and developmental biology. He notes, “I was drawn to the PhD program in Quantitative Biosciences at Georgia Tech because of its unique design that bridges the gap between biosciences and engineering. Coming from a primarily biosciences background, this program allows me to expand my repertoire of technical skills and knowledge to include those from the fields of computer science and engineering. I aim to use these skills to better describe living systems, particularly neural systems.” Pratt intends to conduct research involving how sensory information is acquired, processed, and integrated in the nervous system.  

Kai Tong earned his B.S. in Biological Sciences from Fudan University in Shanghai, China, this year. Initially admitted into the Ph.D. program in Biology, Tong decided to transfer to QBioS. “I was amazed by the easy-going and collaborative atmosphere here," Tong says. “And equally importantly, the fit with my research interests in major evolutionary transitions and social evolution.” He noted that his training as a ‘traditional’ biologist involved a leap to transfer to QBioS. “This out-of-comfort-zone effort will allow me not only to use more quantitative toolkits to tackle biological questions, but also to test hypotheses or perform predictions that usual experimental methodology may not be able to, as well formulate insights into a more abstract and generalizable way.”

Akash Vardhan received his training in Production Engineering from Jadavpur University, India, graduating in 2013. After completing his undergraduate education, he worked as a vehicle dynamics test engineer in the automobile industry, before moving on to study the mechanics of bug flight in Sanjay Sane’s lab at the National Centre for Biological Sciences in Bangalore, India. “As a part of the QBioS program I would love to continue working on the biomechanics and control of locomotion in a wide variety of animals,” Vardhan says. “Form and function is another area that I find really fascinating, how seemingly simple interactions can give rise to an emergent behavior which is really complex has also gotten me really interested.”

Mengshi Zhang received her B.S. in Biotechnology from South University of Science and Technology of China in 2015 and then switched to the Department of Physics at the Chinese University of Hong Kong for her master’s degree (MPhil), graduating earlier this year. She is fascinated by the quantitative descriptions of biological phenomena and drawn to this interface in QBioS. Zhang has backgrounds in system biology and synthetic biology, and experience in wet and dry labs. “I would like to combine both computational analysis and experimental methods and look forward to integrating principles of physical, mathematical and biological science together within QBioS,” she says.

Georgia Institute of Technology researchers developed a novel approach to summarize disease risk, creating a score for an individual based on gene expression – transcriptional risk score (TRS). They’ve applied this score in a recent ground-breaking study, which accurately predicts complications in Crohn’s disease, and potentially paves the way for personalized medicine strategies in the future.

“We were testing an intuition,” says Urko Marigorta, lead author of the study, “Transcriptional Risk Scores link GWAS to eQTL and Predict Complications in Crohn’s Disease,” published in the journal Nature Genetics.

“We wanted to see if checking the actual expression of pathogenic genes involved in disease is better than just looking at an individual’s DNA when assessing the risk for disease,” adds Marigorta, a postdoctoral researcher in lab of Greg Gibson, professor in the School of Biological Sciences and a researcher in the Petit Institute for Bioengineering and Bioscience at Georgia Tech.

This was part of a multicenter research initiative, the Crohn’s & Colitis Foundation’s “RISK Stratification” study (the largest new-onset study of pediatric Crohn’s disease patients), and a follow-up to research published earlier this year in the journal, The Lancet.

That study, says Gibson, evaluated “whether anti-TNF treatment really is beneficial in reducing inflammation and preventing progression to complicated Crohn’s disease. It is, but apparently only for a subset of patients. Our contribution there was to show that this subset can, to some extent, be identified at diagnosis on the basis of their overall gene expression profile in the ileum.”

The Nature Genetics paper takes advantage of the data sets analyzed in the previously published research. The RISK Stratification Study involved 28 clinics and 1,800 pediatric patients – a good sample size, according to Marigorta, who adds, “most important, [we had] two forms of biological data: DNA and gene expression from the small intestine. Importantly, the gene expression from RISK was obtained at diagnosis, when kids went to the hospital and before developing complicated versions of Crohn’s disease.”

So basically, Marigorta and Gibson wanted to test their novel approach, TRS, against genetic risk scores (GRS), or scores based on an individual’s DNA, which is currently the dominant approach in the field. But predicting disease risk from just DNA is difficult.

“In the last few years we’ve learned about many genes that are associated with disease – genes that have mutations, that are more frequent in people with disease than in healthy people,” Marigorta says. “But many people with mutated genes do fine, whereas others without them end up getting sick with some disease. Most of the field is trying to discover more of these mutations, which is totally fine because that will tell us more about biology, and will make for good drug targets. But we’re not sure it will add that much in terms of prediction.”

Marigorta’s statistical and bioinformatics analyses of the genomic data demonstrated that their intuition was on target: gauging the expression of risk genes (TRS) does a better job of predicting complications of Crohn’s than just adding up the number of risk genes (GRS).

“So, instead of trying to predict how good a football team is going to be by adding up how many players make $10 million a year, we actually evaluate how well they are performing,” says Gibson, using a familiar sports analogy.

This paper published in Nature Genetics was a collaboration of 23 author/researchers from 18 institutions – two in Canada and 16 in the U.S., including Emory University’s School of Medicine. Emory physician/professor Subra Kugathasan, director of the Children’s Healthcare of Atlanta Combined Center for Pediatric Inflammatory Bowel Disease, shares senior authorship with Gibson (who was the corresponding author). Key leadership also came from co-authors Lee Denson (Cincinnati Children’s Hospital) and Jeff Hyams (Connecticut Children’s Medical Center)

Going forward, Marigorta sees two primary directions that the TRS research may take.

“We’d like to see if it works for other traits and we have evidence that it does, at least for autoimmune diseases such as juvenile arthritis,” he says. “And more importantly, we’d like to see if it works when using gene expression from blood draws. Imagine, down the road, if you could fine-tune the predictions of risk due to your DNA with information gained from looking at gene expression from a simple blood draw at your once-a-year checkup.”

CONTACT:

Jerry Grillo
Communications Officer II
Parker H. Petit Institute for
Bioengineering and Bioscience

Georgia Tech’s School of Mathematics is set to play an important role in the rapidly expanding field of data science, thanks to a National Science Foundation initiative that will fund foundational research and educational training on campus.

The new institute, the Transdisciplinary Research Institute for Advancing Data Science (TRIAD), is one of 12 national data science projects to receive $17.7 million in NSF funds, the agency recently announced. The School of Mathematics is one of six Tech schools taking part in TRIAD, which will receive $1.5 million of the NSF funding.

“The successful funding of the TRIAD partnership between the Colleges of Science, Computing, and Engineering recognizes Georgia Tech as a leader in the foundations of data science,” says School of Mathematics Professor and Chair Rachel Kuske. “We welcome the opportunities and challenges that come with this recognition. TRIAD will be an important base as our leadership in the mathematical and quantitative sciences continues to expand, addressing both fundamental and applied questions.”

Other schools participating in TRIAD are the H. Milton Stewart School of Industrial & Systems Engineering, the School of Electrical and Computer Engineering, the George W. Woodruff School of Mechanical Engineering, the School of Biological Sciences, the School of Computational Science and Engineering, and the School of Computer Science.

The rise of technology in everyday life has come with an increase in raw data generated by an ever-expanding number of connected devices. Media outlets are calling this information explosion “big data.” Companies, organizations, and governments are now on the hunt to find better ways of analyzing and modeling big data, with potential benefits for business, science, education, and law enforcement.

The NSF initiative Transdisciplinary Research in Principles of Data Science (TRIPODS) hopes to leverage academic expertise in mathematics, statistics, and theoretical computer science. In Phase I of TRIPODS, the NSF put out a call to support the development of small collaborative institutes. Georgia Tech responded with TRIAD, which will be operate alongside the recently launched Institute for Data Engineering and Science (IDEaS).  Xiaoming Huo, professor in the School of Industrial & Systems Engineering, will be TRIAD’S executive director; Prasad Tetali, professor in the School of Mathematics with a joint appointment in the School of Computer Science, will serve as co-principal investigator.

“The emphasis on theoretical foundations of data science offers a great opportunity for mathematicians to actively engage with other scientists and help make breakthroughs in this fast-growing interdisciplinary field,” says Tetali. “Our team also recognizes the importance of being the only team, out of the dozen winners of Phase I, to have been selected from the Southeast,” he added.

Faculty from the College of Sciences with expertise in algebraic and convex geometry, applied dynamics, computational and numerical methods, discrete mathematics, quantitative and computational biology, high-dimensional probability, and statistical inference will provide research for TRIAD. Faculty members include School of Biological Sciences Professor Joshua Weitz and School of Mathematics professors Leonid Bunimovich, Sung Ha Kang, Vladimir Koltchinskii, Rachel Kuske, Anton Leykin, Galyna Livshyts, Ionel Popescu and Mayya Zhilova.