The Krish Roy - GRA Travel Award is a new travel award endowed by Professor Krishnendu Roy with funding provided by the Georgia Research Alliance (GRA). Roy is a Regents’ Professor and the Robert A. Milton Endowed Chair in Biomedical Engineering. He also serves as Director of the NSF Engineering Research Center (ERC) for Cell Manufacturing Technologies (CMaT), the Marcus Center for Cell Therapy Characterization and Manufacturing (MC3M), and the Center for ImmunoEngineering. The award was designed to support to IBB-affiliated undergraduate, graduate, and postdoctoral trainees conducting research in cell manufacturing, drug delivery, immunoengineering, and regenerative medicine.
Ten finalists (pictured left) were selected to receive a stipend to travel to a domestic or international conference or workshop to present their research work.
“The Krish Roy Travel award allowed me to participate in my first conference of my graduate school career." said Parisa Keshavarz-Joud. "I had the opportunity to present a poster on my research at the Physical Virology Gordon Research Conference in January 2023 and interact with experts in the field. This experience broadened my knowledge of the field and helped me in developing new ideas about the next steps of my project.”
Elijah Holland used his award in January to attend the Fibronectin Gordon Research Conference in Ventura, California. In expressing gratitude for the award, Holland shared that he was able to meet leaders in the cell adhesion field and gave his first oral research presentation, titled "Mechanotransduction at Focal Adhesions: Interplay among Force, FAs, and YAP."
Fourth-year ChemE PhD student Hyun Jee Lee plans to use the award to her support her first experience at an international seminar and conference, where she will present her research and connect with other researchers around the world. Lee's research focus is developing microfluidic tools to study cellular and molecular mechanisms in small organisms. "I'm particularly interested in investigating brain activity changes associated with learning in C. elegans." Lee explained. "I'm very grateful to have received the award."
Awardees (pictured from top left to right):
John Cox, Graduate Research Assistant, Chemical and Biomolecular Engineering
Yarelis Gonzalez-Vargas, Graduate Student, Biomedical Engineering
Travis Rotterman, Ph.D., Postdoctoral Fellow, Biological Sciences
Wenting Shi, Graduate Research Assistant, Chemistry and Biochemistry
Kamisha Hill, Graduate Research Assistant, Chemistry and Biochemistry
Paris Keshavarz-Joud, Graduate Research Assistant, Chemistry and Biochemistry
Elijah Holland, Graduate Research Assistant, Mechanical Engineering
Hun Jee Lee, Graduate Student, Chemical Engineering
Maeve Janecka, Undergraduate Student, Chemical and Biomolecular Engineering
Sunny (Chao-yi) Lu, Graduate Research Assistant, Chemical and Biomolecular Engineering
Fermented foods like kimchi have been an integral part of Korean cuisine for thousands of years. Since ancient times, Korean chefs have used onggi — traditional handmade clay jars — to ferment kimchi. Today, most kimchi is made through mass fermentation in glass, steel, or plastic containers, but it has long been claimed that the highest quality kimchi is fermented in onggi.
Kimchi purists now have scientific validation, thanks to recent research from David Hu, professor in the George W. Woodruff School of Mechanical Engineering and the School of Biological Sciences at Georgia Tech, and Soohwan Kim, a second-year Ph.D. student in Hu’s lab.
In a combined experimental and theoretical study, Hu and Kim measured carbon dioxide levels in onggi during kimchi fermentation and developed a mathematical model to show how the gas was generated and moved through the onggi’s porous walls. By bringing the study of fluid mechanics to bear on an ancient technology, their research highlights the work of artisans and provides the missing link for how the traditional earthenware allows for high quality kimchi.
Their research was published in the Journal of the Royal Society Interface.
“We wanted to find the ‘secret sauce’ for how onggi make kimchi taste so good,” Hu said. “So, we measured how the gases evolved while kimchi fermented inside the onggi — something no one had done before.”
The porous structure of these earthenware vessels mimics the loose soil where lactic acid bacteria — known for their healthy probiotic nature — are found. While previous studies have shown that kimchi fermented in onggi has more lactic acid bacteria, no one knew exactly how the phenomenon is connected to the unique material properties of the container.
First, Kim obtained a traditional, handmade onggi jar from an artisan in his hometown in Jeju, South Korea, a region famous for onggi. Back at Georgia Tech, Hu and Kim first tested the permeability of the onggi by observing how water evaporated through the container over time.
Next, they installed carbon dioxide and pressure sensors into both the onggi and a typical, hermetically sealed glass jar. They prepared their own salted cabbage and placed it in both containers. They then used the sensors to measure and compare the change in carbon dioxide — a signature of fermentation.
Hu and Kim also developed a mathematical model based on the porosity of the onggi. The model allowed them to infer the generation rate of carbon dioxide, since the onggi lets carbon dioxide out gradually.
They concluded that the onggi’s porous walls permitted the carbon dioxide to escape the container, which accelerated the speed of fermentation. The onggi’s porosity also functioned as a “safety valve,” resulting in a slower increase in carbon dioxide levels than the glass jar while blocking the entry of external particles. Their data revealed that the carbon dioxide level in onggi was less than half of that in glass containers.
They also found that the beneficial bacteria in the onggi-made kimchi proliferated 26% more than in the glass counterpart. In the glass jar, the lactic acid bacteria became suffocated by their own carbon dioxide in the closed glass container. It turns out that, because the onggi releases carbon dioxide in small rates, the lactic acid bacteria are happier and reproduce more.
“Onggi were designed without modern knowledge of chemistry, microbiology, or fluid mechanics, but they work remarkably well,” Kim said. “It’s very interesting to get these new insights into ancient technology through the lens of fluid dynamics.”
Onggi’s semiporous nature is unique compared to other forms of earthenware. A clay container that leaks, but only slightly, is not easy to make. Terra cotta containers, for example, quickly leak water.
“It's amazing that, for thousands of years, people have been building these special containers out of dirt, but in many ways, they are very high tech,” Hu said. “We discovered that the right amount of porosity enables kimchi to ferment faster, and these onggi provide that.”
Kim said that some artisans still use ancient methods when making onggi, but their numbers are decreasing. Now, the market is flooded with inauthentic versions of the vessels.
“We hope this study draws attention to this traditional artisan work and inspires energy-efficient methods for fermenting and storing foods,” he said. “Also, the onggi are quite beautiful.”
Citation: Kim Soohwan and Hu David L. Onggi’s permeability to carbon dioxide accelerates kimchi fermentation. J. R. Soc. Interface. 2023.
DOI: https://doi.org/10.1098/rsif.2023.0034
This material was supported by the Woodruff Faculty fellowship and the NSF Physics of Living Systems student network.
The Krish Roy - GRA Travel Award is a new travel award endowed by Professor Krishnendu Roy with funding provided by the Georgia Research Alliance (GRA). Roy is a Regents’ Professor and the Robert A. Milton Endowed Chair in Biomedical Engineering. He also serves as Director of the NSF Engineering Research Center (ERC) for Cell Manufacturing Technologies (CMaT), the Marcus Center for Cell Therapy Characterization and Manufacturing (MC3M), and the Center for ImmunoEngineering. The award was designed to support to IBB-affiliated undergraduate, graduate, and postdoctoral trainees conducting research in cell manufacturing, drug delivery, immunoengineering, and regenerative medicine.
Ten finalists (pictured left) were selected to receive a stipend to travel to a domestic or international conference or workshop to present their research work.
“The Krish Roy Travel award allowed me to participate in my first conference of my graduate school career." said Parisa Keshavarz-Joud. "I had the opportunity to present a poster on my research at the Physical Virology Gordon Research Conference in January 2023 and interact with experts in the field. This experience broadened my knowledge of the field and helped me in developing new ideas about the next steps of my project.”
Elijah Holland used his award in January to attend the Fibronectin Gordon Research Conference in Ventura, California. In expressing gratitude for the award, Holland shared that he was able to meet leaders in the cell adhesion field and gave his first oral research presentation, titled "Mechanotransduction at Focal Adhesions: Interplay among Force, FAs, and YAP."
Fourth-year ChemE PhD student Hyun Jee Lee plans to use the award to her support her first experience at an international seminar and conference, where she will present her research and connect with other researchers around the world. Lee's research focus is developing microfluidic tools to study cellular and molecular mechanisms in small organisms. "I'm particularly interested in investigating brain activity changes associated with learning in C. elegans." Lee explained. "I'm very grateful to have received the award."
Awardees (pictured from top left to right):
John Cox, Graduate Research Assistant, Chemical and Biomolecular Engineering
Yarelis Gonzalez-Vargas, Graduate Student, Biomedical Engineering
Travis Rotterman, Ph.D., Postdoctoral Fellow, Biological Sciences
Wenting Shi, Graduate Research Assistant, Chemistry and Biochemistry
Kamisha Hill, Graduate Research Assistant, Chemistry and Biochemistry
Paris Keshavarz-Joud, Graduate Research Assistant, Chemistry and Biochemistry
Elijah Holland, Graduate Research Assistant, Mechanical Engineering
Hun Jee Lee, Graduate Student, Chemical Engineering
Maeve Janecka, Undergraduate Student, Chemical and Biomolecular Engineering
Sunny (Chao-yi) Lu, Graduate Research Assistant, Chemical and Biomolecular Engineering
Fermented foods like kimchi have been an integral part of Korean cuisine for thousands of years. Since ancient times, Korean chefs have used onggi — traditional handmade clay jars — to ferment kimchi. Today, most kimchi is made through mass fermentation in glass, steel, or plastic containers, but it has long been claimed that the highest quality kimchi is fermented in onggi.
Kimchi purists now have scientific validation, thanks to recent research from David Hu, professor in the George W. Woodruff School of Mechanical Engineering and the School of Biological Sciences at Georgia Tech, and Soohwan Kim, a second-year Ph.D. student in Hu’s lab.
In a combined experimental and theoretical study, Hu and Kim measured carbon dioxide levels in onggi during kimchi fermentation and developed a mathematical model to show how the gas was generated and moved through the onggi’s porous walls. By bringing the study of fluid mechanics to bear on an ancient technology, their research highlights the work of artisans and provides the missing link for how the traditional earthenware allows for high quality kimchi.
Their research was published in the Journal of the Royal Society Interface.
“We wanted to find the ‘secret sauce’ for how onggi make kimchi taste so good,” Hu said. “So, we measured how the gases evolved while kimchi fermented inside the onggi — something no one had done before.”
The porous structure of these earthenware vessels mimics the loose soil where lactic acid bacteria — known for their healthy probiotic nature — are found. While previous studies have shown that kimchi fermented in onggi has more lactic acid bacteria, no one knew exactly how the phenomenon is connected to the unique material properties of the container.
First, Kim obtained a traditional, handmade onggi jar from an artisan in his hometown in Jeju, South Korea, a region famous for onggi. Back at Georgia Tech, Hu and Kim first tested the permeability of the onggi by observing how water evaporated through the container over time.
Next, they installed carbon dioxide and pressure sensors into both the onggi and a typical, hermetically sealed glass jar. They prepared their own salted cabbage and placed it in both containers. They then used the sensors to measure and compare the change in carbon dioxide — a signature of fermentation.
Hu and Kim also developed a mathematical model based on the porosity of the onggi. The model allowed them to infer the generation rate of carbon dioxide, since the onggi lets carbon dioxide out gradually.
They concluded that the onggi’s porous walls permitted the carbon dioxide to escape the container, which accelerated the speed of fermentation. The onggi’s porosity also functioned as a “safety valve,” resulting in a slower increase in carbon dioxide levels than the glass jar while blocking the entry of external particles. Their data revealed that the carbon dioxide level in onggi was less than half of that in glass containers.
They also found that the beneficial bacteria in the onggi-made kimchi proliferated 26% more than in the glass counterpart. In the glass jar, the lactic acid bacteria became suffocated by their own carbon dioxide in the closed glass container. It turns out that, because the onggi releases carbon dioxide in small rates, the lactic acid bacteria are happier and reproduce more.
“Onggi were designed without modern knowledge of chemistry, microbiology, or fluid mechanics, but they work remarkably well,” Kim said. “It’s very interesting to get these new insights into ancient technology through the lens of fluid dynamics.”
Onggi’s semiporous nature is unique compared to other forms of earthenware. A clay container that leaks, but only slightly, is not easy to make. Terra cotta containers, for example, quickly leak water.
“It's amazing that, for thousands of years, people have been building these special containers out of dirt, but in many ways, they are very high tech,” Hu said. “We discovered that the right amount of porosity enables kimchi to ferment faster, and these onggi provide that.”
Kim said that some artisans still use ancient methods when making onggi, but their numbers are decreasing. Now, the market is flooded with inauthentic versions of the vessels.
“We hope this study draws attention to this traditional artisan work and inspires energy-efficient methods for fermenting and storing foods,” he said. “Also, the onggi are quite beautiful.”
Citation: Kim Soohwan and Hu David L. Onggi’s permeability to carbon dioxide accelerates kimchi fermentation. J. R. Soc. Interface. 2023.
DOI: https://doi.org/10.1098/rsif.2023.0034
This material was supported by the Woodruff Faculty fellowship and the NSF Physics of Living Systems student network.
Event Details
For the past 10 years, there’s only been one place in Atlanta where you can touch a brain, see a science fashion show, watch scientists give improv performances, and more — and that’s at the Atlanta Science Festival.
And during that time, the faculty and students of STEMcomm have become a festival staple.
STEMcomm, which stands for Science, Technology, Engineering, and Math (STEM) communication, is a course in Georgia Tech’s Vertically Integrated Projects (VIP) program. Established in 2016 by three faculty in the College of Sciences, the course uses science communication to create outreach events for the Atlanta Science Festival — and popular-science content to share on social media and online publications.
“I feel like there is a gulf in the world between people who do science and the general public,” says Jennifer Leavey, a principal academic professional in the School of Biological Sciences, the College’s assistant dean for Faculty Mentoring, and one of the founders of the course. “There is very little crosstalk there.”
The goal of STEMcomm is to bridge that gap and connect with an at-times overlooked audience: adults.
“When it comes to science, I think in general, there’s not a lot of new learning once you get beyond school-age. Teachers do a great job of engaging children with science, but for adults, I mean, there's not a lot there,” Leavey added. “I think there’s a real space for people with science knowledge to help bring that conversation more into the mainstream.”
Visit the College of Sciences website to hear how the faculty and students of STEMcomm are bringing science to Atlanta.
For the past 10 years, there’s only been one place in Atlanta where you can touch a brain, see a science fashion show, watch scientists give improv performances, and more — and that’s at the Atlanta Science Festival.
And during that time, the faculty and students of STEMcomm have become a festival staple.
STEMcomm, which stands for Science, Technology, Engineering, and Math (STEM) communication, is a course in Georgia Tech’s Vertically Integrated Projects (VIP) program. Established in 2016 by three faculty in the College of Sciences, the course uses science communication to create outreach events for the Atlanta Science Festival — and popular-science content to share on social media and online publications.
“I feel like there is a gulf in the world between people who do science and the general public,” says Jennifer Leavey, a principal academic professional in the School of Biological Sciences, the College’s assistant dean for Faculty Mentoring, and one of the founders of the course. “There is very little crosstalk there.”
The goal of STEMcomm is to bridge that gap and connect with an at-times overlooked audience: adults.
“When it comes to science, I think in general, there’s not a lot of new learning once you get beyond school-age. Teachers do a great job of engaging children with science, but for adults, I mean, there's not a lot there,” Leavey added. “I think there’s a real space for people with science knowledge to help bring that conversation more into the mainstream.”
Visit the College of Sciences website to hear how the faculty and students of STEMcomm are bringing science to Atlanta.
John Wallingford, PhD
University of Texas at Austin
Body Sculpting: How the embryo constructs itself
The fascinating thing about embryos is that they construct themselves. Indeed, it is the behavior of the individual cells within that directs dictates the construction of our tissues and organs, and defects in these behaviors are a key cause of human birth defects, which kill more than twice as many children as pediatric cancer. Thus, understanding the cell biology of developing embryos is a crucial challenge in biology. For the last two decades, our lab has used in vivo imaging, biomechanics, and proteomics to understand the collective cell behaviors that elongate the body axis in vertebrate embryos. In this talk, I’ll discuss our recent work illuminating the nexus between tissue-specific developmental signaling systems that govern cell movements and the ubiquitous cell biological machinery that executes them. The talk will focus on the interplay of Planar Cell Polarity signaling, actomyosin contraction, and cadherin-based cell-cell adhesion.
Event Details
Justin Meyer, PhD
University of California, San Diego
Coevolution between phage and bacteria drives the evolution of key innovations, new species, and biological complexity
Coevolution is predicted to be a creative force in the evolution of life, possibly contributing to the evolution of phenomena such as diversity, novelty, and complexity. One key mechanism by which coevolution promotes the emergence of these phenomena is by causing fitness landscapes to fluctuate, inducing continual evolutionary change, and causing exploration of new adaptations. For this talk, I will discuss several experimental studies on bacteria and phages that demonstrate the role coevolution plays in driving the evolution of key innovations, speciation, and the formation of complex ecological networks. The studies include quantification of how fitness landscapes change during coevolution by leveraging high-throughput gene editing-phenotyping technologies.
Event Details
There are times when John McDonald, emeritus professor in the School of Biological Sciences and founding director of Georgia Tech’s Integrated Cancer Research Center, is asked to share his special insight into cancer.
“Over the years, I’ve gotten calls from non-scientist friends and others who have been diagnosed with cancer, and they call me to get more details on what’s going on, and what options are available,” said McDonald, also a former chief scientific officer with the Atlanta-based Ovarian Cancer Institute.
That’s the primary motivation why McDonald wrote A Patient's Guide to Cancer: Understanding the Causes and Treatments of a Complex Disease, which was published by Raven Press LLC (Atlanta) and is now available at Amazon or Barnes and Noble in paperback and ebook editions. The book describes in non-technical language the processes that cause cancer, and details on how recent advances and experimental treatments are offering hope for patients and their families.
A book for the proactive patient
McDonald said he couldn’t go into detail for every type of cancer, but provides a generally applicable background for the disease. For those who want more information, he provides links to other resources, including videos, that provide more detail on specific types of cancer. “There’s not much out there in one place for patients who want to understand the underlying causes of cancer, and the spectrum of therapies currently available,” he said.
McDonald, who was honored in January by the Georgia Center for Oncology Research and Education (CORE) as one of “Today’s Innovators,” also didn’t want A Patient’s Guide to Cancer to be a lengthy book, and it checks in at only 86 pages.
McDonald believes that when patients talk to their physicians about cancer treatments, they should ideally have a basic understanding of the underlying cause of their cancer, as well as a general awareness of the range of therapies currently available, and what may be coming down the road in the future.
“My book is specifically designed to provide newly diagnosed cancer patients who are not scientists with this kind of background information, empowering them to play a more informed role in the selection of appropriate treatments for their disease”.
The current experimental treatment landscape; McDonald’s 2023 research goals
McDonald’s own cancer research has led to two related startup companies, co-founded with School of Biological Sciences colleagues.
McDonald is working with postdoctoral researcher Nick Housley on using nanoparticles to deliver powerful drugs to cancer cells while sparing healthy tissue. The other company, founded in collaboration with Jeffrey Skolnick, Regents' Professor, Mary and Maisie Gibson Chair & Georgia Research Alliance Eminent Scholar in Computational Systems Biology, uses machine learning to create personalized diagnostic tools for ovarian cancer.
He and his lab team are also preparing to submit a research paper that builds off their 2021 study on gene network interactions that could provide new chemotherapy targets for breast cancer. That paper focuses on the three major subtypes of breast cancer. McDonald and his colleagues will also soon submit another study detailing genetic changes that happen with the onset and progression of ovarian cancer.
When it comes to current experimental treatments, McDonald says he’s especially excited about the potential of cancer immunotherapy, which uses the body’s own immune system to fight cancer cells. But he writes in A Patient’s Guide to Cancer that because these drugs are also delivered systemically, healthy tissues can also be affected, potentially leading to autoimmunity or the self-destruction of our normal cells.
“In the future, I believe many of the negative side-effects currently associated with the system-wide delivery of cancer drugs will be averted by the use of nanoparticles designed to target therapies specifically to tumors”.
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