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.
Communications Officer II
Parker H. Petit Institute for
Bioengineering and Bioscience
For researchers pursuing the primordial history of oxygen in Earth’s atmosphere, a new study might sour some “Eureka!” moments. A contemporary tool used to trace oxygen by examining ancient rock strata can produce false positives, according to the study, and the wayward results can mask as exhilarating discoveries.
Common molecules called ligands can bias the results of a popular chemical tracer called the chromium (Cr) isotope system, which is used to test sedimentary rock layers for clues about atmospheric oxygen levels during the epoch when the rock formed. Researchers at the Georgia Institute of Technology have demonstrated in the lab that many ligands could have created a signal very similar to that of molecular oxygen.
“There are some geographical locations and ancient situations where measurable signals could have been generated that had nothing to do with how much oxygen was around,” said Chris Reinhard, one of the study’s lead authors. Though the new research may impact how some recent findings are assessed, that doesn’t mean the tool isn’t useful overall.
Rock record tool
“We’re not trying to revolutionize the way the tool is viewed,” said Yuanzhi Tang, who co-led the study. “This is about understanding its possible limitations to make discerning use of it in particular cases.”
Tang and Reinhard, both assistant professors of biogeochemistry in Georgia Tech’s School of Earth and Atmospheric Sciences, published their team’s results in a study on November 17, 2017, in the journal Nature Communications. Their work was funded by the NASA Astrobiology Institute, the NASA Exobiology program, and the Agouron Institute.
“On a global level, the chromium isotope system is still a great indicator of atmospheric oxygen levels through the ages,” Tang said. “The issue we exposed in the lab is more local with isolated samples, especially during eras when there wasn’t much atmospheric oxygen.”
Without a dominant oxygen presence, ligands likely made a great reactive substitute, as the researchers demonstrated in reactions with chromium. Like oxygen, ligands strongly attract electron pairs, which is what characterizes them as a chemical group.
And like reactions with oxygen, reactions with ligands enable metals like chromium to move around more easily in the world. In this case, the researchers were interested in organic ligands, ligands that contain carbon.
They were more apt to match oxygen’s mobility effect on chromium that made it end up as the signals in sedimentary rock that scientists, today, look for as a sign of ancient atmospheric oxygen.
Here’s roughly how the chromium isotope system works, followed by how organic ligands could make for false positives.
The Earth is an enormous chemical laboratory performing reactions in conditions varying from arctic cold to volcanic heat, and from crushing ocean depths to no-pressure upper atmospheres. Winds and waves sweep around materials like turbulent conveyor belts, depositing some in sediments that later turn to stone.
Chromium’s ticket for the rollercoaster ride into sedimentary rock was usually an oxidizing agent that made it more soluble and better able to float, and atmospheric oxygen was an ideal oxidizer. The chemical reaction, which can be found in the study and involved manganese oxide handing off oxygens to chromium, would be a little like adding pontoons to chromium compounds.
For billions of years, Earth’s atmosphere was nearly devoid of O2, but after oxygen began increasing, especially in the last 800 million years, it became the domineering oxidizer. And characteristics of chromium deposits in ancient layers of rock became a great indicator of how much O2 was in the atmosphere.
Today, researchers test deep rock layer samples for the relation between two chromium isotopes, 52Cr, by far the most common Cr isotope, and 53Cr, to get a read on oxygen presence across geological eras.
“You powder the rock up; you dissolve it with acid, and then you measure the ratio of 53Cr to 52Cr in the material by using mass spectrometry,” Reinhard said. “It’s the ratio that matters, and it will be controlled by a range of complex processes, but generally speaking, elevated 53Cr in ocean sediment rock tends to indicate oxygen in the atmosphere.”
By the way, these Cr isotopes are stable and don’t undergo radioactive decay, thus the system does not work the way radiocarbon datingdoes, which relies on the decay of carbon 14.
In the lab, with a small assortment of organic ligands, Tang’s group showed that reactions of chromium with ligands led to 53Cr/52Cr signals that closely mimicked those stemming from oxygen-chromium reactions.
“Ligands have the capability to mobilize chromium as well,” Tang said. “In fact, ligands might be a significant factor in controlling chromium isotope signals in certain rock records.”
Organic ligands were probably around long before Earth’s atmosphere filled up with O2. And today, hundreds of millions of years after the reactions occurred, it’s basically impossible to find out if oxygen or ligands were at work.
If not accounted for, ligand reactions can distort small details in rock records about atmospheric oxygen, and they may have already.
Like paleontologists, who catalog ancient animal bones and other fossils, geologists keep massive, digitized archives of rock that they study to learn more about Earth’s ancient geological history. Scientists began testing physical samples of them with the Cr isotope system around 2009 and adding the results to the records.
“Since then, some discrepancies have turned up,” Reinhard said. “Ancient soil layers were showing evidence of oxygen when it probably shouldn’t have been there. Other samples from the same period weren’t showing that signal.”
But some researchers confronted with odd Cr signals have thought they had perhaps stumbled upon a radical find, and they developed explanations for how O2 may have been surprisingly bountiful on the lonesome spot where a particular rock layer formed, while molecular oxygen was scant on the rest of the globe. Others puzzled that atmospheric O2 levels may have risen much earlier than overwhelmingly broad evidence has indicated.
“A lot of that could be chalked up to other chemical processes and not to interactions with oxygen,” Reinhard said.
The study may serve as a cautionary tale about how to view Cr isotope data, especially when they leap off the page.
The study was co-authored by Emily Saad from Georgia Tech, and Noah Planavsky and Xiangli Wang of Yale University. Research was funded by the NASA Astrobiology Institute (grant number NNA15BB03A, the NASA Exobiology program NNX16AL06G, and an Agouron Institute Postdoctoral Fellowship. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of those sponsors.
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.”
A discovery by an international team of researchers from Princeton University, the Georgia Institute of Technology and Humboldt University in Berlin points the way to more widespread use of an advanced technology generally known as organic electronics.
The research, published November 13, 2017, in the journal Nature Materials, focused on organic semiconductors, a class of materials prized for their applications in emerging technologies such as flexible electronics, solar energy conversion, and high-quality color displays for smartphones and televisions. In the short term, the advancement could particularly help with organic light-emitting diodes that operate at high energy to emit colors such as green and blue.
“Organic semiconductors are ideal materials for the fabrication of mechanically flexible devices with energy-saving, low-temperature processes,” said Xin Lin, a doctoral student and a member of the Princeton research team. “One of their major disadvantages has been their relatively poor electrical conductivity. In some applications, this can lead to difficulties and inefficient devices. We are working to improve the electrical properties of organic semiconductors.”
Semiconductors, typically made of silicon, are the foundation of modern electronics because engineers can take advantage of their unique properties to control electrical currents. Among many applications, semiconductor devices are used for computing, signal amplification, and switching. They are used in energy-saving devices such as light-emitting diodes and devices that convert energy such as solar cells.
Essential to these functionalities is a process called doping, in which the semiconductor’s chemical makeup is modified by adding a small amount of chemicals or impurities. By carefully choosing the type and amount of dopant, researchers can alter semiconductors’ electronic structure and electrical behavior in a variety of ways.
In their Nature Materials paper, the researchers have described a new approach for greatly increasing the conductivity of organic semiconductors, formed of carbon-based molecules rather than silicon atoms. The dopant, a ruthenium-containing compound, was a reducing agent, which means it added electrons to the organic semiconductor as part of the doping process. The addition of the electrons was the key to increasing the semiconductor’s conductivity. The compound belongs to a newly-introduced class of dopants called dimeric organometallic dopants. Unlike many other powerful reducing agents, these dopants are stable when exposed to air but still work as strong electron donors both in solution and solid state.
Georgia Tech’s Seth Marder, a Regents Professor in the School of Chemistry and Biochemistry, and Stephen Barlow, a research scientist in the school, led the development of the new dopant. They called the ruthenium compound a “hyper-reducing dopant.”
They said it was unusual, not only in its combination of electron donation strength and air stability but also in its ability to work with a class of organic semiconductors that have previously been very difficult to dope. In studies conducted at Princeton, the researchers found that the new dopant increased the conductivity of these semiconductors by about a million times.
The ruthenium compound was a dimer, meaning it consisted of two identical molecules, or monomers, connected by a chemical bond. As is, the compound proved relatively stable and, when added to these difficult-to-dope semiconductors, it did not react and remained in its equilibrium state. That posed a problem because to increase the conductivity of the organic semiconductor, the ruthenium dimer needed to split and release its two identical monomers.
Princeton’s Lin, the study’s lead author, said the researchers looked for different ways to break up the ruthenium dimer and activate the doping. Eventually, he and Berthold Wegner, a visiting graduate student from the group of Norbert Koch at Humboldt University, took a hint from how photosynthetic systems work. They irradiated the system with ultraviolet light, which excited molecules in the semiconductor and initiated the reaction. Under exposure to the light, the dimers were able to dope the semiconductor, leading to a roughly 100,000 times increase in the conductivity.
After that, the researchers made an interesting observation.
“Once the light was turned off, one might naively expect the reverse reaction to occur and the increased conductivity to disappear,” said Georgia Tech’s Marder, who is also associate director of the Center for Organic Photonics and Electronics (COPE) at Georgia Tech. “However, this was not the case.”
The researchers found that the ruthenium monomers remained isolated in the semiconductor, increasing conductivity, even though thermodynamics should have returned the molecules to their original configuration as dimers. Antoine Kahn, a Princeton professor who led the research team, said the physical layout of the molecules inside the doped semiconductor provides a likely answer to this puzzle. The hypothesis is that the monomers are scattered in the semiconductor in such a way that it was very difficult for them to return to their original configuration and re-form the ruthenium dimer. To recombine, he said, the monomers would have to have faced in the correct orientation, but in the mixture, they remained askew. So, even though thermodynamics showed that dimers should reform, most never snapped back together.
“The question is why aren’t these things moving back together into equilibrium,” said Kahn, who is Stephen C. Macaleer '63 Professor in Engineering and Applied Science. “The answer is they are kinetically trapped.”
In fact, the researchers observed the doped semiconductor for over a year and found very little decrease in the electrical conductivity. Also, by observing the material in light-emitting diodes fabricated by the group of Barry Rand, an assistant professor of electrical engineering at Princeton and the Andlinger Center for Energy and the Environment, the researchers discovered that doping was continuously re-activated by the light produced by the device.
“The light activates the system more, which leads to more light production and more activation until the system is fully activated, said Marder, who is Georgia Power Chair in Energy Efficiency. “This alone is a novel and surprising observation.”
The paper was co-authored by Kyung Min Lee, Michael A. Fusella, and Fengyu Zhang, of Princeton, and Karttikay Moudgil of Georgia Tech. Research was funded by the National Science Foundation (grants DMR-1506097, DMR-1305247), the Department of Energy’s Energy Efficiency & Renewable Energy Solid-State Lighting program (award DE-EE0006672) and the DoE’s Office of Basic Energy Sciences, Division of Materials Sciences and Engineering (award DE-SC0012458), the Deutsche Forschungsgemeinschaft (project SFB 951) and the Helmholtz Energy-Alliance Hybrid Photovoltaics project.
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.”
Calvin Runnels plans to spend his life learning, and learning about life. That’s what the biochemistry major wrote in his personal statement when he applied for the Rhodes Scholarship this year.
“I cannot say for sure where exactly in the field my interests will take me — evolutionary biology, medicinal chemistry, biophysics,” he noted. “I know myself too well to claim that any of these subjects would fail to fascinate and invigorate me the way research and learning always does.”
In Spring 2018, Runnels, a native of Baton Rouge, Louisiana, will graduate with a bachelor's degree in biochemistry after only three years at Georgia Tech. And next fall, he will begin postgraduate study at the University of Oxford — the sixth student in Tech history to be named a Rhodes Scholar.
Runnels works in the lab of Loren Williams, professor in the School of Chemistry and Biochemistry. Under the guidance of Williams, graduate student Nicholas Kovacs, lab manager Jessica Bowman, and others in the lab, he is studying the origins of protein folding.
“Calvin is considered by my lab members and by me to be among the brightest and most promising undergraduate students in our program,” Williams stated in his Rhodes Scholar recommendation letter for Runnels. “He ranks in my view alongside a young John Rinn. John began his research career in my laboratory and is now a highly successful member of the University of Colorado faculty. Calvin, like John, is bound to do great things.”
Runnels’ research investigates the primitive protein and RNA folding structures fossilized in the ribosome, which may provide insight into the origins of life.
“The really cool thing about our research is that in the Williams lab, we think that the secrets of the origins of life are encoded in everyone’s cells,” Runnels said. “Every organism that exists has a little fossil record of the history of the molecules that are most important to life on Earth. That fossil record is called the ribosome, which is a little machine in your cells that makes protein.”
Runnels said the ribosome evolves similarly to the way a tree grows.
“If you cut down a tree you can see [in the rings] the history of when that tree was a lot smaller and younger. You can peel away the layers and trace the history to the way it looked at the very beginning,” he explained. “The ribosome is very similar in that the core of the ribosome is evolutionarily the most ancient part, and as it evolved over time new little pieces of protein and pieces of RNA accreted onto its surface, and it grew up into the modern ribosome.”
Runnels studies the core protein and RNA molecules in the ribosome and what their interactions tell us about the very earliest interactions of biopolymers on Earth.
Choosing Georgia Tech
Like many new Tech students, Runnels started as an undecided engineering major.
“I mostly came to Georgia Tech because I liked the way it felt. When I was here on my scholarship weekend I felt very welcome. I felt like people really liked it here. So, I came here on a feeling, more than on what I wanted to study,” he said.
In high school, he enjoyed chemistry and he was good at it, but he didn’t see himself being a scientist or chemist because his experience at working in labs had been less than positive.
One of the first things Runnels did as a first-year student was to go on a Tech Trek to Banff National Park in Alberta, Canada, with his cohort of Stamps President’s Scholars. He met his research professor Loren Williams on that trip, and he was inspired and fascinated by their conversation.
“That sums up my relationship with science and learning in general,” he said. “I think it’s all about what can inspire you and what can motivate you to dive into a topic that you didn’t know anything about. Many of my favorite scientists didn’t study just one thing.”
At Tech, Runnels has been equally accomplished outside the research lab. He served as representative for the School of Chemistry and Biochemistry in the undergraduate Student Government Association (SGA), as well as co-chair of SGA’s Cultural and Diversity Affairs Committee. He is a linear algebra teaching assistant, Beckman Coulter Petit Undergraduate Research Scholar, Stamps President’s Scholar (Randolph Whitfield Scholarship), member of the Honors Program, Georgia Tech Student Ambassador, Diversity and Inclusion Fellow, member of the Omicron Delta Kappa honor society, recipient of the Georgia Tech Campus Life and Community Scholarship, and was a semifinalist for Mr. Georgia Tech this year. He is a transgender male, and served as the student co-chair of the campus LGBTQIA Action Team.
How does he manage this high level of activity and commitment?
Stephanie Ray, associate dean of students and director of Student Diversity Programs, addressed the question in her letter of recommendation for Runnels.
“In addition to his accomplishments in the classroom and laboratory, Runnels was able to find balance in his life, and he was able to excel as a well-rounded student. At Georgia Tech balancing school and extracurricular activities is not always unproblematic, but Runnels found the key,” Ray said. “Calvin has spent a great deal of time at Tech learning about himself and learning about others. As a result, Calvin is very committed to improving the human condition.”
The Rhodes Scholarship, established in 1902 and named for the British mining magnate and South African politician Cecil John Rhodes, is an international postgraduate award for students to study at the University of Oxford. It is considered one of the world’s most prestigious scholarships, with 32 American students chosen for 2018. Runnels will be at Oxford for two to three years, depending on his course of study.
Runnels said being named a Rhodes Scholar is a tremendous honor and came as a shock. He said he is trying to keep its meaning in perspective.
“What I think it means, and the way I’m trying to frame it in my mind, is that I don’t want to view getting this scholarship as my peak accomplishment of my life,” he said. “I want to think of it as an affirmation of the things I have done so far and also as a call to duty to make a difference in the world and try to do great things from here on.”
Runnels is the sixth Tech student to win a Rhodes Scholarship. Previous Rhodes Scholars include S. Alton Newton (1951); Will Roper (2002); Jeremy Farris (2004); Joy Buolamwini (2012); and Melissa McCoy (2013).
Genetic mutation may drive evolution, but not all by itself. Physics can be a powerful co-pilot, sometimes even setting the course.
In a new study, physicists and evolutionary biologists at the Georgia Institute of Technology have shown how physical stress may have significantly advanced the evolutionary path from single-cell to multicellular organisms. In experiments with clusters of yeast cells called snowflake yeast, forces in the clusters’ physical structures pushed the snowflakes to evolve.
“The evolution of multicellularity is as much a matter of physics as it is biology,” said biologist Will Ratcliff, an assistant professor in Georgia Tech’s School of Biological Sciences.
The bigger they are…
Like the first ancestors of multicellular organisms, in this study the snowflake yeast found itself in a conundrum: As it got bigger, physical stresses tore it into smaller pieces. So, how to sustain the growth needed to evolve into a complex multicellular organism?
In the lab, those shear forces played right into evolution’s hands, laying down a track to direct yeast evolution toward bigger, tougher snowflakes.
“In just eight weeks, the snowflake yeast evolved larger, more robust bodies by figuring out soft matter physics that took humans hundreds of years to learn,” said Peter Yunker, an assistant professor in Georgia Tech’s School of Physics. He and Ratcliff collaborated on the research that documented the evolution and measured the physical properties of mutated snowflake yeast.
They published their results on November 27, 2017, in the journal Nature Physics. The work was funded by the NASA Exobiology program, the National Science Foundation, and a Packard Foundation Fellowship to Ratcliff.
Questions and answers
Here are some questions and answers to illuminate the study and its significance.
But first, some background: Baker’s yeast, which was used in these experiments, is usually a single-cell organism. Yeast cells with a well-known mutation stick together in groups called snowflakes.
That was not the focus of the experiments, but the yeast snowflakes were the starting point in this study on the evolution of multicellularity.
Why is this study significant?
Such a cell cluster like a yeast snowflake is not a well-integrated multicellular organism yet. To make it to even simple multicellularity like that of some algae is a very long evolutionary haul.
“It’s a journey of a thousand steps,” Ratcliff said. “The key change is for this group of cells not to evolve as a gang of single cells but as one multicellular individual.”
In this work, the researchers showed how snowflake yeast took first steps in that direction by evolving more resilient multicellular bodies that sustained growth. The process was mainly driven by physical forces, as the simple snowflakes did not have complex inner biological workings that were capable of being the main drivers.
“This is an amazing example of multicellular adaptation around physical constraints well before the evolution of a cellular developmental program,” Yunker said.
How does this evolution via physical stress work?
“Yeast snowflakes grew by adding cells end to end to form branches kind of like those of a bush,” Yunker said. “But the branches crowded each other, and the stresses that result made some break off.”
The breakage chopped down the size of individual yeast snowflakes, but after multiple generations, the snowflakes evolved to reduce the crowding of branches by elongating its individual cells.
As a result, the overall snowflakes were less stressed and could grow larger and more robust.
In addition, Georgia Tech researchers discovered that physics made the snowflakes basically have babies. Specifically, the pieces that broke off became propagules that grew into snowflakes of their own.
This reproduction was created by physical force and not by a biological program. Ratcliff published a separate study about the reproduction aspect on October 23, 2017, in the journal Philosophical Transactions of the Royal Society B.
“Physics does a lot for multicellularity,” Ratcliff said. “It also gives it a lifecycle.” Lifecycle refers to birth, growth, reproduction, and death.
“A consensus is forming that for something to really evolve to multicellularity, very early on, a multicellular lifecycle has to develop.”
How did the experiments select for these specific adaptations?
Ratcliff and Yunker streamlined evolution in the lab by creating a consistent selection regime for the yeast snowflakes to evolve in. In this case, they selected for snowflakes that were best at sinking.
The snowflakes that sank better were heavier, because they grew larger than others in the manner described above, giving them more mass. “The clusters that evolved to grow bigger were therefore also heavier,” Ratcliff said.
This experimental selection setup befitted natural evolution, which also had to select for size to arrive at complex multicellular bodies, which are much, much larger than single cells.
Mutation of branches is genetic. Is physics really so important here?
That’s correct: Random genetic mutations resulted in the better, longer branches in some yeast snowflakes giving them a cumulative weight advantage.
But the propagation of the superior snowflake mutations was the result of physical stresses not breaking the snowflakes until they had grown larger.
The pieces that eventually did break off, due purely to physical force, were the propagules. Some of them carried mutations forward that made the new snowflakes even better at sinking.
And that was a critical step in the multicellular evolution.
How was stress corroborated as the cause of snowflakes splitting apart?
The researchers put the material properties of the snowflakes to the test under an atomic force microscope. “We squished the clusters and measured how much force and energy you needed to break them,” Yunker said.
“The physical measurement indicated closely the size the clusters would attain before they broke off a branch due to stress,” Ratcliff said.
Coauthors of this study were Shane Jacobeen, Jennifer Pentz, Elyes Graba, and Colin G. Brandys of Georgia Tech. The research was funded by the NASA Exobiology program (grant #NNX15AR33G), the National Science Foundation (grant #IOS-1656549), and a Packard Foundation Fellowship. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of those sponsors.
If you are serious about a career in astrobiology research, the NASA-supported Astrobiology Graduate Conference (AbGradCon) is a must-attend meeting. The next one takes place at Georgia Tech on June 4-8, 2018. Apply now to participate. Application deadline is Feb. 5, 2018.
AbGradCon offers a unique setting for graduate students and early-career scientists interested in astrobiology research to share, collaborate, and network. Organized and attended by only graduate students, postdoctoral researchers, and select undergraduates, the meeting is an ideal venue to form bonds, share ideas, and candidly discuss the issues that will help shape the future of the field.
For a preview, go to this YouTube video.
Each meeting location is selected by attendees of the previous year. Georgia Tech offers a unique venue. Attendees will gather in a vibrant campus in the middle of Atlanta, one of the most tech-savvy cities in the U.S.
In addition to a scientific program, plans for AbGradCon 2018 include outreach events at local venues in midtown Atlanta and an educational field trip. Participants can also attend the popular Astrobiology Proposal Writing Workshop, which will take place on June 1-4, 2018.
Georgia Tech is home to the most rapidly growing community of astrobiology researchers in the U.S. From Earth and planetary scientists, to chemists and biologists, the astrobiology community at Georgia Tech, is closely aligned with the NASA Astrobiology Program and the NASA Astrobiology Institute. They seek to answer the full spectrum of the basic astrobiology questions: How did life begin? Where else could life exist?
“We are very excited to welcome early-career astrobiology researchers from all over the U.S. and beyond,” says George Tan, a Ph.D. student in the School of Chemistry and Biochemistry and AbGradCon 2018 conference chair. “We are working very hard to ensure a productive and memorable conference.”
At Georgia Tech, the following postdocs and Ph.D. students are the organizers of AbGradCon 2018:
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
Outside Georgia Tech, the following are co-organizers of AbGradCon 2018:
Thomas Campbell, St. Louis University
Nicole Chase, Portland State University
Theresa Fisher, Arizona State University
Ben Intoy, University of Minnesota
Jonathan Jackson, Pennsylvania State University
Lin Jin, Boston University
Jay Kroll, University of Colorado, Boulder
Megan Krusor, University of California, Davis
Graham Lau, University of Colorado, Boulder
Mike Lee, University of Southern California
Julia McGonigle, University of Colorado, Boulder
Brett McGuire, National Radio Astronomy Observatory
Shahrzad Motamedi, University of Utah
Rebecca Rapf, University of Colorado, Boulder
Katie Rempfert, University of Colorado, Boulder
Harrison Smith, Arizona State University
Kamil Stelmach, George Mason University
Jennifer Thweatt, Pennsylvania State University
As recently announced by Chancellor Steve Wrigley, all colleges and universities in the University System of Georgia (USG), as well as the system office, will be participating in a Comprehensive Administrative Review (CAR). Beginning Dec. 11, Georgia Tech will begin implementing the CAR among its staff.
“The CAR process provides an opportunity for employees to provide input on how we can improve administrative processes to enhance our ability to deliver on our teaching, research and service mission,” said President G.P. “Bud” Peterson.
When this systemwide initiative was announced last spring, Chancellor Wrigley stated that the project would be focused on creating efficiencies, streamlining processes, and finding ways to more effectively utilize USG resources. The USG is working with Huron Consulting to perform this review.
Administrative functions across the USG have been identified, and staff within each function will be selected to participate in a series of reviews as detailed below. Because the CAR initiative will focus only on nonteaching activities and roles, faculty will generally not be involved in the process.
Opportunity Identification Survey
Starting next week, an Opportunity Identification Survey will be conducted with supervisors, managers, and select groups — approximately 1,100 individuals. The goal of the Opportunity Identification Survey is to collect information on functions and processes that work well and those that present an opportunity for improved administrative effectiveness, efficiency, and best practices.
The Opportunity Identification Survey is voluntary and should take 15 minutes to complete.
An email will be sent on Dec. 11 to those who have been selected to participate in the survey. The survey is open from Dec. 11 to 20.
Focus Groups and Interviews
In support of the Opportunity Identification Survey, Huron Consulting will conduct on-site focus groups and interviews beginning Jan. 8, 2018.
In mid-January, approximately 3,600 staff employees at Tech will be asked to participate in the Activity Assessment to better understand how resources are allocated to perform the various administrative functions.
Those selected to participate should expect to receive an email on Jan. 16, 2018, with more details related to the assessment. The assessment is open from Jan. 16 to 30.
Participation in the assessment is mandatory for the selected individuals and should take, on average, 30 minutes to complete. In addition, supervisors and managers will be asked to review and validate the assessment submissions between Feb. 5 and Feb. 13, 2018.
Huron Consulting will prepare a draft report containing key findings and recommendations to deliver to Georgia Tech’s leadership, as well as the USG, in Spring 2018. A final report will be generated once all 28 institutions have completed this process in 2019.
Visit the USG Comprehensive Administrative Review website for more information on the systemwide project. Questions about Georgia Tech’s participation in this process may be forwarded to firstname.lastname@example.org.
The Association for Women in Mathematics (AWM) has named Georgia Tech student Libby Taylor the recipient of the 2018 Alice T. Schafer Mathematics Prize. She will receive a B.S. in Mathematics from Georgia Tech in spring 2018, only two years after she graduated from Wheeler High School, in Marietta, Georgia.
Taylor’s advanced mathematical abilities have been evident since high school, according to School of Mathematics Emeritus Professor Tom Morley. As a high-school junior, Taylor took Morley’s third-year-college course Combinatorial Game Theory, and she led the team that applied the theory in interesting ways to Gomoku, the classic five-in-a-row game from China. Taylor’s work, Morley says, “showed mathematical maturity way beyond her age or educational background.”
As an undergrad at Georgia Tech, Taylor has been taking graduate-level courses and conducting original mathematics research. Hard working and highly motivated, she regularly attends research seminars, reads math books and papers voraciously, and eagerly gives talks at workshops and conferences in the U.S. and overseas. She learns as much as she can from discussions with graduate students, postdocs, and professors.
Professors describe Taylor as a strong, talented student with staggering potential, who is fearless in learning new topics, asks insightful questions, and is quick to pick up sophisticated ideas. Already she has six preprints published, one manuscript in preparation, and a chapter in a book about categorical representation theory called “Soergel Bimodules.”
“I have been continually impressed by her mathematical intellect, her initiative, and her ability to absorb mathematics,” says School of Mathematics Assistant Professor Jennifer Hom. “I look forward to seeing what Libby’s future holds.”
“The friendly atmosphere in the Georgia Tech School of Mathematics contributed greatly to my mathematical development,” Taylor says. “It has always been easy to find professors willing to help answer questions, suggest further reading, and discuss mathematical ideas with me. This environment is not present everywhere; this is something special about Georgia Tech.”
Taylor specifically credits her research mentors, Baker and School of Mathematics Professor William T. “Tom” Trotter, both of whom began advising Taylor on research projects when she was still in high school. “Their mentorship gave me a significant head start in my mathematical education and research,” Taylor says.
The Alice T. Schafer Mathematics Prize is named after the former president and founding member of AWM who contributed greatly to women in mathematics. The prize recognizes excellence in mathematics by an undergraduate woman.
Each year, AWM names a winner, a runner-up, and at least two honorable mentions. Among them are the following with Georgia Tech connections:
- Samantha Petti, 2015 runner-up and now a Ph.D. student at Georgia Tech
- Megan Bernstein, 2010 honorable mention and now a postdoctoral fellow at Georgia Tech
- Nicole Larsen, 2009 runner-up when she was an undergrad at Georgia Tech and now a research fellow at the Kavli Institute for Cosmological Physics at the University of Chicago
- Josephine Yu, 2003 runner-up and now an associate professor at Georgia Tech
AWM will recognize the 2018 winner, runner-up, and honorable mentions on Jan. 10, 2018, at the 2018 Joint Mathematics Meeting, in San Diego, Calif.
“This achievement has validated the work I have put into my education over the past few years,” Taylor says. “The accomplishments of past recipients motivate me to continue working hard to live up to their examples.”