For elementary school children, an upcoming field trip is riveting, the one time they find themselves unable to sleep in anticipation. This year, fifth-grade students at Laurel Ridge Elementary School, in Decatur, were bound for a beach on Tybee Island, the easternmost point of the state of Georgia. But some couldn’t go. Thanks to School of Biology Professor Joel E. Kostka and his students, these fifth graders did not have to miss the excitement of a year-end activity.
“We were asked by the organizer of outreach opportunities – Tracy Hammer – to come, because half of the kids in the fifth-grade class could not make it to the beach,” Kostka said. “So we brought the beach to them.”
This clever solution had many positive outcomes. It advanced Hammer’s goal for science education at Laurel Ridge. It taught Georgia Tech researchers how to explain their work to school children. And it opened the eyes of elementary students to the excitement of scientific research.
Hammer is the science, technology, engineering, and mathematics (STEM) coordinator and teacher for gifted students at Laurel Ridge. She has dedicated her career to getting young children excited about mathematics and science. “Part of my mission at school is to expose all of the kids to science in as many ways as I can,” she said. “I refused to have our fifth graders staying behind, missing out on the hands-on experience the other kids were getting. So I decided to bring science to the school.”
Kostka came with graduate students Will A. Overholt, Boryoung Shin, and Xiaoxu Sun and undergraduate biology major Kyle Sexton. At Georgia Tech, one research focus in the Kostka lab is biodegradation of oil in the oceans, including oil spills in the Gulf of Mexico. Kostka and his students study how marine microbes break down oil, how fast the breakdown occurs, and what factors affect the process. Their goal is to learn enough to direct the management and cleanup of contaminated systems, such as the aftermath of the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. The beach they brought to Laurel Ridge resembled those sullied by the environmental disaster.
One of Hammer’s goals is for Laurel Ridge to be STEM certified. The process requires the school to have community and industry partners. To fulfill this requirement, Hammer has been inviting researchers from Georgia Tech, including her husband, School of Biology’s Brian K. Hammer.
According to the Georgia Department of Education, STEM-certified schools offer an integrated curriculum in STEM “that is driven by problem solving, discovery, exploratory project/problem-based learning, and student-centered development of ideas and solutions.”
To doubters, who may think such a program would be too much for elementary-level students, Tracy Hammer would disagree. “I believe we underestimate elementary school children and their abilities and interest levels when it comes to science,” she said. “The more we offer, the more they want to learn, and the more questions they ask.”
The Georgia Tech researchers engaged the fifth-graders in activities they named “Oiled Beach,” designed by Beth Kostka, wife of Joel Kostka, and a teacher Renfroe Middle School, in Decatur. Working in small groups of six to eight members per group, the school children modeled oil spills, counted bacteria, discussed Gulf of Mexico ecosystems, and watched oil-eating bacteria at work.
“The children were really engaged, had fantastic questions,” Overholt said. “They seemed to really enjoy the two hours we spent with them.”
Seeing the students’ thirst for knowledge and ability to learn was an eye-opening experience for Overholt. “The kids were so excited about things that my peers and I take for granted,” he said. “It was very rewarding to see kids so curious about the world around them. I also think it is great practice to talk about our science at the fifth-grade level and still be able to communicate what we do.”
Through these activities led by research scientists, Tracy Hammer moves closer to her goal of getting Laurel Ridge STEM-certified. “When we expose our budding scientists to the world and the possibilities it holds,” she said, “then we can say we are truly doing our jobs as educators.”
She hopes Joel Kostka will return and that other Georgia Tech research groups would visit Laurel Ridge throughout the year.
“I will do it again,” said Joel Kostka. “The kids were very perceptive. I learned that kids as young as those in fifth grade can really understand the oceans and the implications of oil spills. Those kids have a lot to offer.”
Although the “beach” they had did not come with sun and ocean and waves, the children had a great time. “When the others returned from Tybee,” Tracy Hammer said, “the kids who stayed behind were the ones bragging about their experiences.”
Scott Smith
Student Assistant, College of Sciences
Effective July 1, the Georgia Tech College of Sciences has a new unit focused on the life sciences — the School of Biological Sciences.
The new school emerged from a reorganization of the former Schools of Applied Physiology and of Biology. The reorganization was motivated by the College’s strategic goals to enhance the research ecosystem for the basic sciences and mathematics, enrich and diversify educational opportunities for science and mathematics majors, and strengthen the opportunities for creativity and innovation by the College.
“The life sciences are an exciting and fast-moving field, and the issues it addresses are varied but interconnected,” said Rafael L. Bras, provost and executive vice president for Academic Affairs. “The new School of Biological Sciences brings together individuals that span the various aspects of living systems and their study. It will add synergies and create a resilient, flexible, and fast-responding academic unit in a fast-moving field.”
J. Todd Streelman, associate chair for Graduate Studies in the School of Biology, will serve as chair of the new School beginning August 15. Terry W. Snell, professor and chair for the School of Biology, will serve as chair in an interim role until then.
“I am thrilled to be named chair on behalf of my colleagues in the School of Biological Sciences,” Streelman said. “I am excited to continue progress made under Richard [Nichols] and Terry [Snell] to both sustain and propel innovative research and teaching in the life sciences.”
The new school comprises 10 tenure-track faculty, three academic professionals, and four staff members from Applied Physiology as well as 38 tenure-track faculty, six academic professionals, and 18 staff members from Biology. The School of Biological Sciences will administer all the academic programs offered previously by the two schools it replaces.
“The life sciences, including neural systems, are destined to grow and become even more central as we define our research and education programs for the new millennium,” said Paul M. Goldbart, dean of the College of Sciences. “I am grateful to the many members of our community who have stepped up to create a stronger, more coherent base from which to take on exciting challenges presented by the life sciences.”
The other academic schools in the College of Sciences include Chemistry and Biochemistry, Earth and Atmospheric Sciences, Mathematics, Physics, and Psychology.
In tough times, humans aren’t the only species that think twice about having children. Consider roundworm strain LSJ2.
Though it can’t think – much less think twice -- about anything, the laboratory worm underwent a surprising mutation that made it prioritize the survival of adults over creating abundant offspring. Researchers noticed the sweeping change in behavior, and the mutation, after LSJ2 had faced hardship for 50 years.
Such so-called life history trade-offs have been described in many living things from mice to elephants, but now, for the first known time, researchers at the Georgia Institute of Technology have pinned some to a specific mutation.
“This is a great hint at how life history trade-offs could be regulated genetically,” said lead researcher Patrick McGrath, an assistant professor in Georgia Tech’s School of Biological Sciences.
The researchers confirmed the link in LSJ2, a strain of the C. elegans species, by duplicating the mutation in another strain, which reproduced the mutation’s effects to a very high degree.
The researchers published their results in the journal PLOS Genetics on Thursday, July 28, 2016. Their work has been funded by the National Institutes of Health and the Ellison Medical Foundation.
Snowball to avalanche
The mutation in the LSJ2 strain amounted to a small deletion in its DNA. As a result, a large protein changed by a meager 10 of its roughly 3,000 amino acids.
But that triggered a huge behavioral overhaul that boosted lifespan and slowed down reproduction. The contrast between the minor genetic tweak and its transformative ramifications might compare well with a toddler knocking loose an avalanche with a snowball.
The new discovery also has a tangential connection to human genetics. The roundworm shares with us the NURF-1 gene, on which the mutation occurred. And an associated human protein is involved in, among other things, reproduction.
Evolve faster, please
All at once, LSJ2 did a lot of peculiar things, and that got the attention of McGrath and his team. And that’s what the lab roundworms are there for.
Since 1951, generations of scientists have been speeding up the evolution of lab-bound C. elegans by forcing the microscopic species of roundworms to adapt to new, mostly stressful, conditions. Then, when researchers have noticed changes, they’ve worked to trace them to the animals’ genes.
McGrath points to a thin, glass slide standing vertically under a light with tubules of fluid connected to it. Inside the slide, is a different lab strain of C. elegans.
“We’re raising those in fluid with gravity pulling them down to see if mutations will give them the ability to swim,” McGrath said.
50 years of bread and water
In the case of LSJ2, researchers came up with a different challenge to accelerate its evolution. They fed it bland food for 50 years.
“It’s a diet of watery soy extract with some beef liver extract,” said Wen Xu, a graduate student who researches with McGrath. Sounds yucky enough to humans, but to the roundworm, it's worse. It equates to a regimen of bread and water.
Mutations eventually took hold to promote LSJ2’s survival in the scanty broth, and they were head-turning.
Fewer kids, less sleep
“The stark thing that we noticed first was the propensity to no longer enter the state called dauer,” McGrath said. It’s a kind of hyper-hibernation. “Dauer is something most C. elegans do to extend their lives, but LSJ2 did not. And it lived longer in spite of it.”
Then the list of anomalies grew, and grew.
“We found that almost everything was affected – when they started reproducing, how many offspring they made, how long they lived,” McGrath said. Some even survived exposure to drugs and heavy metals.
“Eventually we realized that the worms were prioritizing individual survival over reproductive rate.”
Mutation sleuthing
In many species, sex dries up when food is scarce, resulting in fewer progeny to compete for it. In addition, many organisms are well-equipped to manage their energies to survive dearth.
But C. elegans LSJ2 had to mutate into those abilities, and so many mutation-based behavioral changes all at once is uncommon.
“What you usually find is mutations that play narrow, very specific roles,” McGrath said. “They only affect egg laying, or they only affect life span, or they only affect dauer formation."
McGrath and Xu went sleuthing for DNA alterations by mapping quantitative trait loci, which matches up changes in characteristics to genetic changes. They dug in for a long investigation, anticipating multiple suspects among LSJ2’s many mutations.
“There were hundreds of genetic differences between roundworm strain LSJ2 and the one we were comparing it to,” McGrath said.
‘Smoking gun’
The comparison laboratory strain is called N2, and it has led a pampered existence with a diet of E. coli -- optimal food for C. elegans. (Both the E. coli and the roundworms are strains that are not harmful to humans.)
So, N2 hadn’t been pushed to mutate so much. In addition, to avoid confusion in their research results, the researchers reset some of the mutations N2 did happen to undergo.
The comparison led to swift evidence in LSJ2. “Every single time, it pointed us to the same genetic region on the right arm of chromosome 2,” McGrath said. C. elegans has six chromosomes.
“There were only five genes that were candidates. One of the mutations was a smoking gun -- a 60-base-pair deletion just at the end of the NURF-1 gene.”
NURF-1 has the function of remodeling chromatin, which pairs DNA with proteins to wrap them into chromosomes. The resulting configurations strongly influence which genes are expressed. It appears the tiny mutation in the remodeling gene may have led to a massive change in the expression of other genes.
There are missing pieces needed to understand the pathway from the mutated gene to the massive real-life changes, and the researchers are working to fill them in.
Worm whoopy
To confirm the mutation as the trigger of the changes, Xu deployed a CRISPR Cas9 gene editor into N2 worms to make the deletion that LSJ2 had received via mutation, and the results left little doubt.
“It had a lot of the same effects – longer life, dauer formation,” Xu said. “The main difference was the reduction of reproduction rates. It was only about half as much in the comparison worm that got the gene editing.”
By the way, as sex goes, C. elegans are mostly hermaphrodites that produce eggs and their own sperm to fertilize them with. But there are also males that copulate with the hermaphrodites to add new sperm and with it genetic diversity.
Edward E. Large, Yuehui Zhao and Lijiang Long from Georgia Tech; Shannon Brady and Erik Andersen from Northwestern University, and Rebecca Butcher from the University of Florida coauthored the paper. Research was sponsored by grants from the National Institutes of Health (numbers R21AG050304 and R01GM114170) and by an Ellison Medical Foundation New Scholar in Aging grant.
In ocean expanses where oxygen has vanished, newly discovered bacteria are diminishing additional life molecules. They are helping make virtual dead zones even deader.
It’s natural for bacteria to deplete nitrogen in oxygen minimum zones (OMZs), ocean regions that have no detectable O2. But as climate change progresses, OMZs are ballooning, and that nitrogen depletion is also on the rise, drawing researchers to study it and possible ramifications for the global environment.
Now, a team led by the Georgia Institute of Technology has discovered members of a highly prolific bacteria group known as SAR11 living in the world’s largest oxygen minimum zone. The team has produced unambiguous evidence that the bacteria play a major role in denitrification.
7 questions, 7 answers
The new bacteria impact global nutrient supplies and greenhouse gas cycles. Below are questions and answers that illuminate the discovery and its significance.
The researchers published their findings in the journal Nature on Wednesday, August 3, 2016. They produced genomic and enzyme analyses that pave the way for further study of carbon and nitrogen cycles in oxygen minimum zones.
The research has been funded by the National Science Foundation, the NASA Exobiology Program, the Sloan Foundation and the U.S. Department of Energy.
1. Why does denitrification matter?
While melting ice caps and dying polar bears splash across headlines, climate change is stressing oceans in other ways, too – such as warming and acidifying waters. Loss of ocean oxygen and nitrogen are pieces of that bigger puzzle.
As to nitrogen: Anyone who has picked up a bag of fertilizer knows it as a building block of life.
“It’s an essential nutrient,” said Frank Stewart, an assistant professor at Georgia Tech’s School of Biological Sciences, who headed the team. “Nitrogen is used by all cells for proteins and DNA.”
Taking it away makes it harder for algae and other organisms to grow, or even live. But it doesn’t stop there. Algae absorb carbon dioxide, so, when algae are diminished, that leaves more of that greenhouse gas in the atmosphere.
But it’s not yet clear how heavily this particular loss of CO2 absorption weighs in the global balance.
2. How do these newly discovered bacteria deplete nitrogen?
In OMZs, with O2 gone, the newly discovered strains of SAR11 bacteria (and some other bacteria) respire NO3 (nitrate) instead, the Georgia Tech researchers found. They kick off a chemical chain that leads to nitrogen disappearing out of the ocean.
“They take nitrate, convert it into nitrite (NO2), and that can ultimately be used to produce gaseous nitrogen,” Stewart said. Plain nitrogen, N2, and nitrous oxide, N2O, would result. “Both of those gases have the potential to bubble out of the system and leave the ocean.”
That makes the oxygen-barren waters even less hospitable to life while putting more nitrogen into the air, as well as nitrous oxide, a key greenhouse gas.
The newly discovered members of the SAR11 bacteria clade – clade means a branch of living species -- appear to be the single largest contingent of bacteria in OMZs. That makes them a very significant player in nitrogen loss.
3. Ocean zones with no oxygen? Sounds wild. Did climate change do that?
No. Oxygen minimum zones are natural. The issue is that global warming is making them grow, just like it’s making ice caps shrink.
OMZs form mostly in the tropics, off coastlines where wind pushes surface waters out to sea, allowing deeper waters to rise up. These are full of nutrients and boost the growth of simple aquatic life like algae.
“Eventually, the algae die and sink slowly,” Stewart said. “Bacteria munch on it, and in the process, they breathe oxygen.” There’s so much algae that the bacteria consume oxygen at a dizzying rate, depleting the water of it.
Global warming is causing OMZs to spread because it makes seawater less able to hold oxygen. As OMZs expand, so does the potential for denitrification, tipping global balances of nitrogen, greenhouse gases, and nutrients.
4. I’ve heard of the disease SARS, but what is SAR11?
The two are unrelated.
SARS is caused by a virus and is potentially deadly. SAR11 bacteria are not only harmless to humans; hypothetically, we might starve without them. They’re at the base of an oceanic food chain, which is very important to the global food supply.
“After they eat dissolved organic carbon (dead stuff), then the bacteria are eaten by bigger cells, which are eaten by larger plankton, and so on up the food chain,” Stewart said.
Previously known SAR11 are so incredibly widespread in the ocean, it’s surprising they’re not a household name. They may even comprise the largest number of living organisms on Earth.
Under the microscope, SAR11 bacteria pretty much look the same. “They’re usually short little slightly bent rods,” Stewart said. Until now, SAR11 have been known to require oxygen to live, so finding SAR11 that respire nitrate is new and surprising.
5. Where did the team get these new nitrate breathing SAR11 strains?
Stewart and his team sailed for four days aboard a research vessel from San Diego, California, to an area off the Pacific coast of Mexico’s Calimo state. There, they dropped a carousel of tube-like bottles about four feet long down to the center of the world’s largest OMZ 1,000 feet below.
“The bottoms and tops of the bottles are open,” Stewart said. “When you get to the depth you want, you close them to get your sample.”
The new bacteria don’t have species names yet, but their genomes, which were sequenced in the study, indicate they’re members of the SAR11 bacteria clade.
6. Why is this discovery scientifically significant?
It upends quite justified scientific doubts.
Scientists thought SAR11 wouldn’t have strains that flourish in the harsh OMZ environment, because the SAR11 clade doesn’t have a reputation for being very adaptable. “When their genomes do change, they’re usually very subtle changes,” Stewart said.
Many other bacteria, by contrast, plunk in and out big chunks of their DNA, making them widely adaptable. Also, though researchers had already detected genetic signatures of SAR11 bacteria in OMZs, they didn’t think the bacteria were actually at home there.
These facts put Stewart and his team under a heavy burden of proof.
7. How did the scientists answer the doubts?
They flushed out the genomes of 15 individual new bacteria strains they had captured as intact single cells. Surprisingly, the researchers found the blueprints for an enzyme, nitrate reductase, which could allow the bacteria to breathe nitrate in place of oxygen.
Since the novel bacteria have not yet been grown in the lab, the researchers inserted their nitrate reduction gene sequences into E. coli bacteria to see if they would use the DNA to produce the enzyme and if the enzyme would then work.
It did.
“Not all studies that do this kind of genome-based analysis take that extra step,” Stewart said with a long exhale. But it nailed nagging doubts.
The thorough analyses produced a critical dataset for science to build upon. More research will be needed to find out what adaptations allow SAR11 bacteria to exist under such harsh conditions.
The following researchers coauthored the study: Despina Tsementzi, Jieying Wu, Luis M. Rodriguez-R, Andrew S. Burns, Piyush Ranjan, Cory C. Padilla, Neha Sarode, Jennifer B. Glass and Konstantinos T. Konstantinidis from Georgia Tech; Samuel Deutsch, Sangeeta Nath, Rex R. Malmstrom and Tanja Woyke from the U.S. Department of Energy; Benjamin K. Stone from Bowdoin College; Laura A. Bristow from the Max Planck Institute; Bo Thamdrup and Morten Larsen from the University of Southern Denmark.
The research was funded by the National Science Foundation (grants 1151698 and 1416673), the NASA Exobiology Program (grant NNX14AJ87G), the Sloan Foundation (RC944), and the U.S. Department of Energy’s Community Science Program. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the sponsoring agencies.
It’s called mental imbalance for a reason. Sanity hangs, in part, in the gentle balance of chemicals strung together within regions of the brain in an intricate matrix.
In schizophrenia, the matrix is sharply jarred, debilitating the mind and triggering hallucinations. Now, researchers at the Georgia Institute of Technology have created an interactive model of that matrix to fast-track research and treatment of the tormenting disorder.
Working memory disruptions paralyze the mental coherence of schizophrenia sufferers, yet there is a stark lack of medical treatment for it. Researchers Zhen Qi and Eberhard Voit hope their new, very accurate computational simulator built around this symptom will help change that to curb anquish for many patients.
Learn more about the simulator, which puts this brain dysfunction into a virtual setting.
For more than 10 years, the Center for GIS has been working with the Dian Fossey Gorilla Fund International on visualization, analysis, and management of their mountain gorilla ranging data. What started with a series of static maps has evolved into a fusion of cutting-edge, multidimensional interactive visualization and analytic tools available online and in-house at the DFGFI’s Karisoke Research Center in Musanze, Rwanda.
Recently, associate director of the Center for GIS, Tony Giarrusso, traveled to Karisoke to assemble and install the “Virtual Virungas” exhibit as part of a 50th anniversary retrospective of Dian Fossey, the pioneer of mountain gorilla field research in Rwanda. Funded by a Smithgall-Watts grant from the School of Biology, the “Virtual Virungas” is an immersive, four-dimensional visualization of mountain gorilla habit and ranging data, projected onto a bed of sand and operated through a variety of high-tech controls and input. Created by CGIS and IMAGINE Lab researchers, Matt Swarts, Noah Posner, and Giarrusso, the "Virtual Virungas" sandbox uses historic mountain gorilla ranging data plus satellite imagery, topographic maps, and other geo-referenced, spatio-temporal data to show how the gorilla groups have ranged during different periods of time. Visitors can even modify what is shown on the sand through their mobile phones or computers. Exhibit tours for local secondary school and university students, conservation officials and tourists are conducted during weekdays by Karisoke staff members.
Initial reviews of the exhibit have been outstanding. Karisoke Director of IT, Jules Abiyingoma, recently gave four tours to local high school students and said this about his and their experiences with the virtual sandbox: “This sand box technology is amazing! I had four demos yesterday for four different schools and it all went smoothly. Everyone loved it and the students did not want to leave that section. They asked so many questions about gorillas, the park and the technology itself. Ironically they were so quiet during the previous sections of the tour and when they reached the sand box, they came to life! And started asking even questions related to previous sections. It's as if the sandbox awakes them from a deep sleep!”
In addition to installing the virtual sandbox, Mr. Giarrusso held GIS training sessions for Karisoke staff members, which included an MS GIS student from the MS GIS program at the National University of Rwanda in Butare, Rwanda. Topics covered included geocoding animal observation data, analyzing animal movements, and basic computer practices.
Mr. Giarrusso was also fortunate enough to obtain a tourist permit to visit the mountain gorillas. He visited the group, Isabukuru, one of the DFGFI mountain gorilla research groups he has mapped, and was able to see more than 10 mountain gorillas in the wild, including a set of identical twins born in early 2016. It was an experience he said he will never forget and hopes to repeat again. He expects to return to Karisoke in 2017 to update the virtual sandbox and conduct a weeklong, more formal GIS training session for Karisoke staff.
Nine graduate students will make up the inaugural Fall 2016 class of the College of Sciences’ interdisciplinary Ph.D. program in Quantitative Biosciences (QBioS). QBioS was established in 2015 by more than 50 participating program faculty in the College of Sciences. It is directed by School of Biological Sciences Professor Joshua S. Weitz.
“QBioS faculty will train Ph.D. students to identify and solve foundational and applied problems in the biological sciences and prepare them for research challenges at scales spanning molecules to ecosystems,” Weitz says.
The QBioS program supports the College’s strategic goal to enhance the research ecosystem and provide new training opportunities. It is Georgia Tech’s third interdisciplinary Ph.D. focusing on life sciences, following the successful models for Bioengineering and Bioinformatics. As in these other programs, QBioS Ph.D. students can select a thesis advisor from the entire program faculty, irrespective of school. In this way, QBioS continues a tradition of fostering innovative, interdisciplinary research and education at Georgia Tech.
Of the nine new students, four are from overseas and one is a Georgia Tech alumnus; five will be based in the School of Biological Sciences, three in the School of Physics, and one in the School of Mathematics.
Shlomi Cohen earned a B.S. in Mechanical Engineering from the Technion-Israel Institute of Technology, in Haifa. Cohen followed his wife to Atlanta after she had been accepted to the Industrial and Systems Engineering Ph.D. program at Tech, and he soon applied for his own doctorate.
Cohen says QBioS is a natural choice for him, despite his engineering background. “I have been interested in biosciences for as long as I can remember,” Cohen says. In fact, he adds, he chose to study mechanical engineering at Technion because they offered a biosciences specialization.
“I look forward to obtaining knowledge and experience that will allow me to gain a set of professional tools to handle real scientific problems and achieve a better understanding of the amazing world around us.” Cohen will be based in the School of Physics during his time in the program.
Nolan Joseph English comes to QBioS with a B.S. in Chemical Engineering from Howard University, in Washington, D.C. English says he was drawn to Tech for its “incredibly strong focus on computer science and interdisciplinary studies that pervade both the culture and research.” That Tech is his father’s alma mater also played a role in his decision.
“The QBioS program allows one to experience many aspects of computational biology – such as systems biology, bioinformatics, and bioengineering – while building a strong core of computational capability and understanding,” English says. “This strong core is what I desire most and is something truly unique to Georgia Tech.”
What most excites English about QBioS is the prospect of learning “how to translate an in silico knowledge base into an in vivo actualization of concept.” For this reason, he says, “I am keenly interested in learning about modeling techniques at the transcriptome and genome levels.” English will be based in the School of Biological Sciences.
Elma Kajtaz earned her bachelor’s degree in behavioral sciences from the University of Sarajevo, in Bosnia-Herzegovina. No longer a stranger to Georgia Tech, Kajtaz had previously worked and studied in the former School of Applied Physiology, now the School of Biological Sciences, with Professor T. Richard Nichols. That research opportunity is what drew Kajtaz initially to Georgia Tech.
“The interdisciplinary and quantitative approach to behavior and physiology emphasized by the QBioS program is perfectly aligned with my research philosophy and interests,” Kajatz says. “I am looking forward to learning and working alongside faculty and researchers from different disciplines to contribute to our understanding of biological systems.” Kajtaz will be based in the School of Biological Sciences.
Alexander Bo-Ping Lee received his bachelor’s degree in mathematical biology at Harvey Mudd College, in Claremont, California. A paper on ant rafts by School of Biological Sciences Associate Professor David Hu intrigued Lee and sparked his interest in attending the QBioS program. Lee is most excited to be a teaching assistant during his time in the program and hopes to become a professor one day, in line with his love of teaching. Lee will be based in the School of Physics.
Joy Elizabeth Putney received her B.S. in Biology and Physics-Engineering from Washington and Lee University, in Lexington, Virginia. She was drawn to QBioS by her love of research that uses quantitative techniques to study biology.
“Life is full of examples of complex systems, from the molecular to the ecological scales, and most complex systems can be best understood using quantitative techniques,” Putney says. She’s excited to start research, taking advantage of the program’s rotation-based structure to gain experience in multiple labs. “This will give me the best opportunity to find a place where I can do research that aligns with my passions,” she says. Putney will be based in the School of Biological Sciences.
Putney may work government or industry after completing the program, but that is a long way in the future. “I hope that Georgia Tech will point me in the right direction,” she says, “even if it ends up being something completely different from what I thought or expected.”
Pedro Márquez-Zacarías has a bachelor’s degree in biomedical sciences from the School of Medicine at the National Autonomous University of Mexico, in Mexico City.
“Georgia Tech is a very prestigious university where science and technology are at the frontiers of knowledge” Márquez-Zacarías says. “I like how students and professors from different fields join efforts to tackle complex problems in the most diverse fields of science.”
Márquez-Zacarías is excited to be part of the diverse and collaborative groups of scientist in the QBioS program. “I can’t imagine a better program for my doctoral degree,” he says. He looks forward to collaborating with various research groups and learning cutting-edge techniques to study how nature works. Márquez-Zacarías will be based in the School of Biological Sciences.
Stephen Anthony Thomas is no stranger to Georgia Tech, where he earned bachelor’s and master’s degrees in electrical engineering. But it is mathematics where Thomas finds his passion.
The QBioS program offers “a great chance to apply a subject I love – mathematics – to areas that can make a real difference to society,” he says.
A potential research focus for Thomas is mathematical modeling for epidemiology. “It’s exciting to be able to work not only at Georgia Tech,” he says, “but also through partnerships with Emory University on critical problems, such as countering antibiotic resistance in bacterial infections.” Thomas will be based in the School of Mathematics.
Hector Augusto Velasco-Perez received his bachelor’s degree in physics from the Faculty of Sciences in the National Autonomous University of Mexico, also in Mexico City. “I was looking for a graduate program and a place that could combine theory and practice, physics and biology, pen and paper, and high-performance computing with GPUs [graphics-processing units],” he says. “I wanted my work to be something that someone can use, something that I can point at – big or small – and say, ‘Look, I did that!’.”
QBioS fits the bill, and Velasco-Perez looks forward to working in a diverse community. The QBioS program “is a perfect opportunity for new ideas to be created,” he says. Velasco-Perez will be based in the School of Physics.
Seyed Alireza Zamani-Dahaj received his master’s degree in physics from McMaster University, in Hamilton, Ontario, Canada. He was drawn to QBioS by the wide range of classes and the multiple labs doing interesting research. “Being among the first class of the QBioS Program is very exciting,” Zamani-Dehaj says. He will be based in the School of Biological Sciences.
“We warmly welcome our new graduate students in QBioS,” says College of Sciences Dean Paul M. Goldbart. “We look forward to their unique contributions to the College’s tradition of forging new paths of discovery.”
Scott Smith
Student Assistant
College of Sciences
Benjamin Franklin famously wrote, “In this world, nothing can be said to be certain, except death and taxes.”
In addition to being a founding father of the United States, Franklin also was a scientist, so he’d probably be interested in the Bioinformatics Graduate Program at the Georgia Institute of Technology, where another kind of certainty has been in play.
For the last five years every graduate of the program found the work they wanted – a 100-percent job placement rate. Well, almost. It turns out, there’s a tiny wrinkle in that impeccable run of success, according to program director King Jordan.
“It’s a lofty claim, to be sure, that we’ve been at 100 percent for years,” says Jordan, researcher at the Petit Institute for Bioengineering and Bioscience and associate professor in the School of Biological Sciences. “But there is one person we know for sure that isn’t working right now. He isn’t sure what he wants to do yet. That’s why he isn’t employed.”
Yet.
For now, 99-plus percent will do. It’s a high success rate, 10 years in the making, since Jordan arrived at Georgia Tech to help develop the bioinformatics curriculum and grow the program.
“The program didn’t have the best record at the time; some of our graduating students were struggling to find employment,” says Jordan, who came to Georgia Tech from the National Center for Biotechnology Information at NIH.
Jordan and his colleagues revamped the curriculum, emphasizing active learning and practical skills. “We made the program more project oriented,” he says.
One of the first courses, and part of the core curriculum, is programming for bioinformatics. It’s taught largely by Ph.D. students and is a fundamental first-step, designed to bring everyone up to the same speed on the primary tool of the trade – the computer.
“Bioinformatics lies at the intersection of biology and computer science,” Jordan says. “So we have a diverse cross-section of students. At one end are straight biologists, like me. At the other end, we have the programmers.”
Students are given coding assignments every week, and every assignment is grounded in the actual analysis of data.
The computational genomics course takes data analysis up to another level. Students are charged with analyzing sets of genomic sequences from microbial pathogens for the Centers for Disease Control and Prevention (CDC).
The relationship between the CDC and the Bioinformatics Graduate Program has had far-reaching impact. Jordan and a team of graduate students worked closely with CDC to develop computational tools for microbial genome analysis that helped trace the source of listeria outbreaks in Colorado and an E. coli outbreak in Europe.
“Students are producing products and technology that is being used by the CDC to address real world public health challenges,” says Jordan, whose team developed and teaches the course in collaboration with the CDC.
The tools needed for a course like computational genomics keep changing, so students are expected to stay abreast of an ever-shifting technological landscape, which is moving the science briskly forward. Think about it. The Human Genome Project, completed in 2003, took 10 years and $3 billion to sequence one genome – something that can be done in a day for about a thousand dollars now.
“If I teach you how to use program X today, by next year it will probably be obsolete,” Jordan says.
Consequently, students are presented with the project goals and the different technical options, and then asked to evaluate which computer programs (which tools, which options) to use in their analysis.
“Mostly, they wind up using a combination of programs,” Jordan says. “It’s cliché, but it’s like teaching them how to fish, how to acquire and evaluate the technology to complete the project.”
While the Georgia Tech curriculum and deep-dive project experience has been an obvious selling point for the job seekers, the market for their services has expanded as well.
“There’s more demand in the market than we can meet,” says Jordan.
The Georgia Tech Bioinformatics Program is trying to help meet the demand by adding more students – this fall’s incoming class of 52 students (40 master’s, 12 PhD) is the biggest in the program’s history, and as usual, they come from a range of backgrounds.
So, what are all of these students doing after they graduate?
For one thing, they’re working in university and research institute labs. Biology is becoming a ‘big data’ science as biologists are generating massive data sets in the era of high-throughput experimentation techniques. Consequently, biologists today need people who are competent in the skills and tools used to analyze those huge data sets.
“The technological revolution in DNA sequencing, which has vastly outpaced increases in computing speed over the last decade, is fundamentally transforming biological sciences in nearly all disciplines,” explains Jung Choi, associate professor in the School of Biological Sciences, and director of the Professional Science Masters (M.S.) track in the bioinformatics program. Jordan directs the Ph.D. track.
“The explosion of big data in biological sciences created a shortfall in people trained to manage and make sense of the data in the context of biology,” Choi adds. “Bioinformatics, genomics, and computational biology are among the most rapidly advancing fields. In a research setting, our students learn how to evaluate and adapt the best new tools and methods that emerge every year.”
Bioinformatics grads are finding their way into government labs – once again, the CDC has come up big, hiring seven bioinformatics grads from the past two classes. And they’re also going into the private sector.
“Within biotech are two big sectors that are frequent employers of our graduates,” says Jordan. “The pharmaceutical industry and the agriculture industry.”
Then there is another route some students are choosing as a result of the research-intensive nature of the bioinformatics program. About a quarter of the Master’s students choose to continue their education and enter Ph.D. programs.
“M.S. students can go right away to pharmaceutical companies and make big bucks, but some who are exposed to research are becoming passionate about that, so they decide to go on and pursue the Ph.D.,” Jordan says. “That’s what I call an unanticipated benefit of our revamped focus.”
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The College of Sciences has selected the 2016 recipients of the Cullen-Peck Fellowships in the College of Sciences: Tamara Bogdanovic, an assistant professor in the School of Physics; Andrew V. Newman, an associate professor in the School of Earth and Atmospheric Sciences, Frank J. Stewart, an assistant professor in the School of Biological Sciences, and Lewis A. Wheaton, an associate professor in the School of Biological Sciences.
“The fellowships recognize exciting research accomplishments by College of Sciences faculty at the associate professor or advanced assistant professor level,” says College of Sciences Dean Paul M. Goldbart. “The goal is to help recipients take their research programs in new directions.”
The fellowships are made possible by a generous gift to the College of Sciences from alumni Frank H. Cullen (B.S. in Mathematics with Honors 1973, M.S. in Operations Research 1975, Ph.D. Engineering 1984) and Libby Peck (B.S. in Applied Mathematics 1975, M.S. in Industrial Engineering 1976).
“We in the College of Sciences are grateful for the generosity of alumni who encourage our faculty to take intellectual risks in their research,” Goldbart says. “The Cullen-Peck fellowships help ensure that our research is pushing the frontiers of knowledge. Congratulations to the 2016 Cullen-Peck fellows, and thank you for all you do for the Georgia Tech community.”
Tamara Bogdanovic is a theoretical astrophysicist whose research interests include the ins and outs of some of the most massive black holes in the universe. Her group investigates observational signatures associated with supermassive black holes interacting with gas and stars in galactic nuclei.
Recently her group offered a plausible solution to a puzzle: Why is the center of the Milky Way galaxy full of young stars but has very few old ones? Scientists suspect that remnants of old stars are present but are too faint to be detected by telescopes. The theory is that old stars have been dimmed by repeated collisions with the accretion disk – a disk-like structure of diffuse material – that at some point in the past orbited a supermassive black hole in the center of our galaxy.
Computer simulations using models of red giant stars suggest that such collisions could have inflicted significant damage to old stars, making them invisible, only if the accretion disk was sufficiently dense and massive. The study, published in The Astrophysical Journal, is the first to run computer simulations on the theory, which was introduced in 2014.
“The generous support of the Cullen-Peck fellowship will allow us to foray into unexplored aspects of the interaction of matter and radiation in the deep gravitational wells of black holes,” Bogdanovic says. She hopes to be able to make more accurate theoretical predictions about the signatures of accreting supermassive black holes in distant galaxies, which can be confirmed by observations.
Trained as a geophysicist, Andrew V. Newman studies the active deformation and failure of Earth's rigid outer layer in areas of frequent seismic and volcanic activity. And he wants to understand their impact on society.
Of particular interest are megathrust faults, which are responsible for the largest, and some of the deadliest, earthquakes. For example, using a small network of seismometers and Global Positioning System (GPS) sensors, Newman’s team mapped a segment of a megathrust fault in Costa Rica that was locked, loaded, and ready for failure. They reported the discovery in the Journal of Geophysical Research in June 2012. Three months later, the earthquake occurred.
Newman’s group again measured the GPS sites and reported in Nature Geoscience that the anticipated earthquake occurred directly in the locked region and with approximately the magnitude the team estimated was possible. Such pre-event imaging and discovery of dangerous megathrust loading is rare because most such earthquakes occur underwater, where GPS doesn’t work. Likewise, these zones are more concerning, because they generate dangerous tsunami waves.
With the support from the Cullen-Peck fellowship, Newman plans to “explore new and low-cost methodologies for making observations of precise ground deformation on the seafloor.” In the journal Nature, Newman had argued that such tools are needed to explore 90% of the active plate boundaries to both better understand dynamics of tectonic plate interaction and to illuminate the risk associated with their geologic hazards, including tsunami generation and underwater volcanism.
Frank J. Stewart explores the genetic diversity of marine microorganisms in hopes of answering two fundamental questions: How do ecological and evolutionary processes create and structure genetic diversity? How is this genetic diversity linked to the diverse biogeochemical functions of microorganisms in nature? In particular, his group is interested in how oxygen loss affects the diversity and metabolism of marine microbes.
In early August 2016, Stewart and others reported in the journal Nature the discovery of new bacterial strains that thrive in oxygen-poor parts of the ocean. The new strains breath nitrogen-containing nutrients in place of oxygen. Their metabolism thus helps deplete nitrogen from the oceans, making the oxygen-poor zones even more uninhabitable, as well as kick-starting metabolic processes that generate nitrous oxide, a potent greenhouse gas.
The zinger is that climate change is causing oxygen-poor zones to expand, meaning these new strains will play an increasingly larger role in shaping ocean chemistry.
Stewart will use the award to advance a project to analyze whole-genome gene expression data (transcriptomes) from single bacterial cells. Single-cell transcriptomics has been used to study eukaryotic cells, he says, but has been difficult when applied to bacterial cells. With collaborators David A. Weitz and Peter R. Girguis, at Harvard University, Stewart is optimizing methods to recover bacterial transcriptomes from single cells.
If the method works, Stewart says, “it could enhance understanding of microbial ecology and diversity in all of the environments our lab studies, including those in the open ocean and those in the guts of animals.”
Research in the laboratory of Lewis A. Wheaton aims to understand how healthy people plan and execute complex tasks, such as kicking a ball or using tools. At present, he is focused on understanding motor skill development across many populations and the neurophysiological relationships between motor development and lexical (vocabulary) development in pediatric populations. The goal is to reveal couplings of language and motor imitation.
Another focus area is motor skill development after traumatic amputation. Wheaton would like to understand how central neural networks for motor learning are affected after amputation and what role they play in the use of prostheses.
The award will help set up new human neuroimaging studies to identify functional and neuroanatomical changes related to motor learning, Wheaton says. “It will also partially fund a student who is expanding this work to develop better therapeutic approaches for patients with neurological injury and disease.”
How did life on Earth originate from simple molecules? This question is one of the deepest, most fundamental questions of science, and it remains unanswered.
In Georgia Tech’s College of Sciences, scientists are trying to decipher the origin of life. Among them is Loren D. Williams, a professor in the School of Chemistry and Biochemistry and a member of the Parker H. Petit Institute of Bioengineering and Biosciences.
For Williams, part of the answer has to come from the ribosome. This gigantic molecular machine comprising ribonucleic acids (RNA) and proteins enables a key distinction of life: translation of genetic information to proteins.
How did translation begin? Work in Williams' lab suggests that translation is the product of molecular symbiosis, that ancestors of RNA and protein were molecular symbionts, and that life arose from the coevolution of proteins and RNA. That startling notion challenges the popular “RNA world” hypothesis of the origin of life. That world posits a time when life was based only on RNA, RNA-catalyzed transformations, and RNA-based genetic material; proteins, the ribosome, and translation appeared later.
At the meeting of the American Chemical Society in Philadelphia, Williams makes the case that the early history of the ribosome is also the history of the origin of life.
Williams and his coworkers base their conclusions on meticulous analysis of the “fossil record” in all ribosomes. As trees imprint events in their rings, or ice cores suspend time by preserving matter in frozen columns, ribosomes are time machines, Williams says, one “that allows us to look at the behaviors of ancient molecules 3.8 billion years ago.”
Crystal structures indicate that the modern ribosome grew by accretion, Williams says. By peeling away the layers deposited in the ribosome over almost 4 billion years, Williams and coworkers reached inside the so-called common core, which is the common denominator and oldest part of biology. Deep inside is the peptidyl transferase center, which links amino acids through peptide bonds “This part of the ribosome originates in chemistry,” Williams says. “It is pre-biology.”
If two amino acids are located within the peptidyl transferase center, they will easily form a peptide bond. “But as soon as you do that in the absence of the ribosome, the ends of the amino acids come together, forming a cyclic structure,” Williams says. Polymers cannot form. But if the ends are kept apart, by the primitive ribosome, a chain of peptide bonds could grow into a polymer.
As it happens, a feature of the ancient ribosome is a hole in the middle, foreshadowing the tunnel through which proteins leave modern ribosomes after they are made. “We think that an original function of the ribosome was not to catalyze peptide bond formation but to keep amino acids from forming cyclic structures and thereby form longer peptides,” Williams says.
The tunnel through which all proteins pass is a constant in the evolution of the ribosome. By examining crystal structures and mapping how modern ribosomes grew from the common core, Williams gleaned that ribosomes evolved to make this tunnel long and rigid.
Why? Williams suggests that without a long tunnel, a synthesized protein would fold at once, become active, and start eating the ribosome’s structure. “The tunnel is saying to the protein, no you cannot become functional yet.”
Ribosome crystal structures suggest something else: When early ribosomes made small peptides that were not capable of folding, some of these peptides stuck to and accreted on the ribosome. “We think the ribosome started making peptides in the first place to give itself greater stability,” Williams says. In making peptides that became bound to the ribosome like scaffolding, the ribosome became bigger and more stable.
As evidence, Williams presents the protein fossils in ribosomes. The oldest ones are frozen random coils “That’s the first thing we think the ribosome made. They got stuck, they didn’t fold. They don’t look like modern proteins.”
Next are isolated beta hairpins. “Nowhere else in biology will you see isolated beta hairpins without other protein around it,” Williams notes. “Only in the core of the ribosome do you see beta hairpins surrounded by RNA.” These isolated beta hairpins are the most ancient folded proteins in biology, he says.
Then come more modern proteins, made of beta sheets and alpha helices, with hydrophobic exteriors and hydrophilic interiors and the ability to fold to globular forms.
“Our results show that protein folding from random-coil peptides to functional polymeric domains was an emergent property of the interactions of ribosomal RNA and peptides,” Williams says. “The ribosome is the cradle of protein evolution.”
Along with Nicholas V. Hud, a professor at the School of Chemistry and Biochemistry and the director of the Center for Chemical Evolution, Williams and other origin-of-life researchers in Georgia Tech propose that chemical evolution—driven by assembly and other processes that increase stability—gradually converted to biological evolution, involving genes, enzymes, and ribosomes.
“We believe that chemical evolution was driven by assembly,” Williams says. “In biology, things that are assembled live longer chemically than those that are not. A folded protein is chemically stable. Unfold it, and it falls apart.” So it was in chemical evolution. Things that could assemble existed longer than those that couldn’t.
“If you had a molecule that could assemble and make peptides that bound to it, and they co-assemble, all of a sudden you have something better,” Williams says. “We think the reason proteins came into biology was that they stabilized the ribosome and protected it from degradation. The ribosome was looking out for itself. It was an evolutionary process by the ribosome, for the ribosome, and of the ribosome.
“We have the historical record or molecules. These things are preserved in the ribosome, we can see them. There is a molecular record of the origin of life.”
Figure Caption
The evolution of the ribosome, illustrating growth of the large (LSU) and small (SSU) subunits, first as separate units and eventually as parts of a whole.
In Phase 1, ancestral RNAs form stem loops and minihelices. In Phase 2, LSU, which has a short tunnel, condenses short, nonspecific, peptide-like oligomers. Some of these oligomers bind back onto the ribosome and stabilize it. At this point, SSU may have a single-stranded RNA-binding function. In Phase 3, the subunits associate, mediated by the expansion of tRNA from a minihelix to its modern L-shape. The tunnel elongates. In Phase 4, the two subunits associate and they evolve together. The ribosome is a noncoding diffusive ribozyme in which proto-mRNA and the SSU act as positioning cofactors, producing peptide-like oligomers, some of which form beta-hairpins. In Phase 5, the ribosome expands to an energy-driven, translocating, decoding machine. Phase 6 marks completion of the common core with a proteinized surface (the proteins are omitted for clarity). mRNA is shown in light green. The A-site tRNA is magenta, the P-site tRNA is cyan, and the E-site tRNA is dark green.
Adapted from A. S. Petrov et al., 2015, Proc. Natl. Acad. Sci. U.S.A. 112:15396–15401. Courtesy of Loren Williams.
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