Georgia Tech alumna Megen Wittling is the winner of the ScienceMatters Episode 8 quiz. She is our first winner from outside the Georgia Tech campus. Having graduated last May, she now works in the Food & Drug Administration (FDA), Washington, DC. Her ScienceMatters prize is in the mail!
"I listen to ScienceMatters on my commute to work while I ride the Metro," Wittling says."I have listened to four episode so far, and love it!"
Wittling hails from Johns Creek, Georgia. She graduated with a B.S. degree in Biology, with a minor in Health and Medical Sciences. After graduation, she went for an ORISE Research Fellowship at FDA, while she applies to MD and MD/PhD programs.
As an undergrad, Wittling conducted research in the PARK Lab of the School of Psychology under the guidance of Phillip Ackerman. The lab's research spans cognitive, aging, personality, social, and applied psychology domains.
From there, Wittling moved to the lab of Shuyi Nie, an assistant professor in the School of Biological Sciences and a member of the Parker H. Petit Institute of Bioengineering and Bioscience. A Petit Undergraduate Research Scholar Award made the transfer possible. In the Nie lab, Wittling characterized the role of a protein in the development and migration of certain cells.
At FDA, Wittling works in the Laboratory of Immunobiochemistry, where she studies the response to interferon of bronchial epithelial cells.
The Episode 8 quiz question: What brain waves are associated with deep states of sleep?The answer: Delta waves.
Episode 9 of ScienceMatters is out this week. "The Mathematics of ... Donuts?" stars Dan Margalit, professor in the School of Mathematics.
If you would like to join the ScienceMatters Hall of Fame, enter the answer to this question: According to Episode 9, what group of people can’t tell the difference between a coffee cup and a donut?
Submit your answer by 11 a.m. Monday, October 22, at sciencematters.gatech.edu.
"Even a horse's tail shouts out secrets," says David Hu, who holds joint appointments in the School of Biological Sciences and the School of Mechanical Engineering. For the past few months, Hu had been plagued by a simple question: What's the purpose of a horse's tail? Using biology and engineering, Hu and his team found the answer. Hu is also an adjunct professor in the School of Physics.
By Mallory Rosten, Communications Assistant
Simone Jarvis was sitting in the car when she got a call from Terry Snell, a professor in what is now the Georgia Tech School of Biological Sciences.
It was 2015. She was a high school senior thinking about her future, uncertain, like most of her peers, about the path she would take. Although she had been admitted to Georgia Tech, she was still undecided. When Snell offered her a $1,500 stipend and the opportunity to start research in her first year at Tech, Jarvis took it as a sign.
“It aligned perfectly with what I wanted to do,” Jarvis recalls. “The chance to get into a lab my freshman year definitely swayed my decision toward Tech. It was really exciting.”
What Snell offered was a Fast Track to Research Scholarship. Snell conceived the program while he was school chair, struck by the low uptake of admission offers: of 300 offers, only a third would enroll.
Snell had an epiphany: Research is one of Georgia Tech’s biggest strengths. The opportunity to join research labs as an undergraduate is one of Tech’s most attractive features as a university. What would be more enticing than offering incoming first-year students a chance to jump into research right from the start?
“One of the most compelling things about science is doing science,” Snell says. “If you can start doing science in your first year, without waiting until you’re a junior, it makes the road to a career in science much smoother.”
The program offers the top 30 accepted biology majors a $1,500 stipend if they commit to doing research in their first year. Since the program’s inception, Snell has seen a positive impact on recruitment, in both the quality and number of students that apply.
Jarvis was among the first recipients of Fast Track scholarships. As a first-year student, she joined the lab of renowned marine ecologist and evolutionary biologist Mark Hay.
Jarvis was focused and bright from the start, Hay says. She took over graduate-student duties after just a few weeks in the lab. Now in her fourth year at Tech, Jarvis still works with Hay. The Fast Track scholarship had ignited a passion for the scientific inquiry going on in the Hay Lab.
In 2017, Alexandra Towner also joined the Hay Lab as a Fast Track scholar.
“I’ve always been drawn to oceans,” she says. She loved that Hay’s work encompassed both large concepts about ocean ecosystems but also drilled down to the molecular aspects of interspecies interactions in coral reefs. “It was the best of both worlds,” she says.
“It was nerve wracking,” Towner recalls of the first time she met with Hay. “You don’t know a lot and you’re meeting this incredible professor who has 20,000 citations on Google Scholar. But he sat us down and explained everything in terms we could understand.” This fall, Towner began her second year at the Hay Lab.
Hay wants to help students achieve their dreams. If they want to become scientists, he hopes to place them so they’ll be competitive for graduate schools. If they want to become physicians, he’ll make sure that they understand the scientific method and problem-solving.
But first, the students he chooses must be driven to do research. “I want them invested in the question,” Hay says. “I want research to be a way of life for them, not just a job. Everyone starts off knowing how to do science as a little kid – you’re curious and explore. That’s what I’m still doing, and that’s what I want my students to do.”
“It was nerve wracking. You don’t know a lot and you’re meeting this incredible professor who has 20,000 citations on Google Scholar. But he sat us down and explained everything in terms we could understand.”
FIELD WORK IN FRENCH POLYNESIA
Jarvis and Towner are innately curious. Which is why this past summer, Hay took them on a trip to Moorea, an island in French Polynesia where he conducts field work. They stayed in the University of California Berkeley's research station, with researchers from various institutions.
In Moorea, Jarvis and Towner spent many hours every day seven feet deep underwater. “We would wake up early, watch the sun rise over the reef, and go out to the water” Jarvis recalls, “We were so exhausted by the end of the day that we would just eat, watch the sun set, and fall asleep.”
The field work gave them a chance to see the genesis of the samples they had been studying in the lab to answer questions about the survival of coral reefs. “Across the world, algae is coming in and taking over coral reefs. We wanted to know if this is making corals more susceptible to disease,” Towner says.
For Towner, the experience was life-changing.
“One day, we did a dive on the reef 30 feet deep. It’s just coral as far as the eye can see,” Towner says. “And you have this moment where you hope that if you have kids they’re able to see something similar. We’re in this incredible time where we’re able to see these incredible things and do this work. My eyes welled up down there.”
“One day, we did a dive on the reef 30 feet deep. It’s just coral as far as the eye can see. And you have this moment where you hope that if you have kids they’re able to see something similar....My eyes welled up down there.”
FIRST OF A KIND
Although Georgia Tech has many programs to encourage research for undergraduates, the Fast Track Scholarship was the first for first-year students. Recipients must use the award within their first two semesters at Tech. Pre-existing awards URSA and PURA are for continuing students.
Recently the College of Sciences, inspired by the success of Fast Track, established the Early Research Award for science and mathematics majors. Awardees have up to their first four semesters at Tech to get into research.
For any prospective biology major offered the scholarship, Jarvis offers this advice: “Take it. It’ll set you on a course that you couldn’t have imagined when you applied to Tech.”
The students are what make Fast Track Scholarship so rewarding, Hay says. “I can only do so much with my hands, but if I look out at what my past students are doing – there are 100 or more – I feel prouder than I would’ve been if I just did it all myself. They’re part of my academic family, my lineage. That’s what we're supposed to do as scientists – allow others to flourish and replace us.”
Editor's Note: Mallory Rosten wrote this story from the reporting notes of A. Maureen Rouhi.
Georgia Tech Ph.D. candidate Chinar Patil is the winner of the ScienceMatters Episode 7 quiz. Unlike most podcast consumers, Patil reads the transcripts, while getting coffee in the morning. "It's a good way to start the day," he says.
ScienceMatters is a great way for "the Georgia Tech community to see what others are doing," Patil says. "We are all specialists in our fields, but it is useful to read or hear about other work in laymen's terms."
Patil hails from the city of Nashik, in the state of Maharastra, in India. He came to Georgia Tech as a Ph.D. student in 2012. He will defend his thesis, and hopes to be a Ph.D. graduate, in December.
Patil has been working with Todd Streelman, who is a professor in and the chair of the School of Biological Sciences. Streelman's research uses cichlid fish from Lake Malawi to study the relationship between genotype and phenotype in wild vertebrates. The lake is known as the site of evolutionary radiations among certain groups of animals, including cichlid fish.The Streelman Lab has pioneered genomic and molecular biology approaches in this natural system to solve problems that are difficult to address using traditional model organisms.
In Streelman's lab, Patil has been studying the evolutionary genomics of cichlid fish from Lake Malawi. "I sequence genomes from various cichlid species and try to understand the genetic basis of the differences between species and make some inferences about their evolutionary history," he says.
The Episode 7 quiz question: What is the name of the song that Jennifer Leavey says sounds like a love song but is actually about bacteria living together in biofilms?
The answer: Stuck on You
Episode 8 of ScienceMatters is out this week. "When People Age and Memory Fails" stars Audrey Duarte, associate professor in the School of Psychology.
If you would like to join the ScienceMatters Hall of Fame, enter the answer to this question: According to Episode 8, what brain waves are associated with deep states of sleep?
Submit your answer by 11 a.m. Monday, October 15, at sciencematters.gatech.edu.
We cannot fully understand DNA, its properties, functions and threats without a bioinformatics approach to study it. Researchers at the School of Biological Sciences of Georgia Tech with PhD student Alli Gombolay, Dr. Fredrik Vannberg and Dr. Francesca Storici have developed a bioinformatics toolkit that precisely maps sites of ribonucleotides present in genomic DNA.
DNA, the blue print of life, which we know to be made of deoxyribonucleotides, contains many scattered ribonucleotides (ribonucleoside monophosphates, or rNMPs) embedded in its sequence. rNMPs in DNA alter DNA structure and properties, and often are sites of mutation and strand breakage. Specific high-throughput sequencing techniques have been recently developed to mark the presence of the rNMPs in genomic DNA. The discovery of hotspot sites and particular patterns of rNMP presence in genomic DNA requires the analysis of large sets of sequencing data. Currently, computational methods to study rNMPs embedded in DNA are highly customized and are not designed as platform-independent, automated pipelines that allow for fast, scalable analyses. Alli Gombolay, a PhD student in the bioinformatics program in the group of Dr. Francesca Storici, in collaboration with Dr. Fredrik Vannberg, designed and tested the scripts of the Ribose-Map software. By accommodating data from each technique available for rNMP mapping, Ribose-Map is a unique pipeline to standardize the analysis of rNMPs embedded in DNA, increasing the reproducibility of rNMP-capture experiments and enabling a head-to-head comparison of these techniques. Ribose-Map transforms raw sequencing data into summary datasets and publication-ready visualizations of results.
The Storici’s lab recently set up a molecular biology technique, ribose-seq, to build genomic libraries of rNMP sites by directly capturing DNA sequences containing an rNMP. “We can build ribose-seq libraries form any DNA of interest, and now, with Ribose-Map, we can also analyze the sequencing data from ribose-seq or other techniques in a straightforward and efficient manner” says Storici.
The Ribose-Map pipeline standardizes and speeds up the analyses of sequencing data obtained from libraries of rNMP sites. It will help the scientific community in the efforts to uncover rNMP spectra, biomarkers and sites of potential distortion or fragility in any type of DNA source, bacterial, fungus, plant or animal cells, from healthy or diseased cells.
The study is just published as an article in the journal Nucleic Acids Res (Monday October 1, 2018):
Gombolay, A. L., Vannberg, F. O. and Storici, F. Ribose-Map: a bioinformatics toolkit to map ribonucleotides embedded in genomic DNA, Nucleic Acids Res, Oct 1 2018, doi: 10.1093/nar/gky874
This project was supported by the National Institute of Health grants (R01ES026243-01 to F.S. and R01EB025022-01 to F.O.V.), the Parker H. Petit Institute for Bioengineering and Bioscience at the Georgia Institute of Technology grant (12456H2 to F.S.), the Howard Hughes Medical Institute Faculty Scholar grant (55108574 to F.S.).
Georgia Tech postdoctoral researcher Kimberly Chen has ended up winning a ScienceMatters quiz after relaxing at home one evening last week.
"I've listened to a few other episodes of the podcast," Chen says. "It's a great way to get to know the exciting research happening at Georgia Tech."
"I am broadly interested in the evolution of complexity," Chen says. "For my Ph.D in Indiana University Blomington, I studied the evolution of non-coding RNAs that regulate bacterial development."
In Georgia Tech, Chen's research aims to find answers to a major question in evolutionary biology: How did the transition from single cells to multicellular organisms take place. She is especially examining the genetic mechanisms underlying this transition.
Chen and her colleagues are using experimental evolution to generate de novo multicellularity in a unicellular alga that's under pressure from predation."I am using both genomic and genetic approaches to understand the genetic basis of the evolved multicellular phenotypes," she says.
You can get a flavor of her research area from this YouTube video of her talk, "Genetics Underlying De Novo Origins of Multicellularity in Response to Predation," at the 2018 Georgia Tech Astrobiology Colloquium.
The Episode 6 quiz question: According to Episode 6, what animal did Simon Sponberg study when he was an undergraduate in Lewis and Clark College, in Oregon?
The answer: Gecko
Episode 7 of ScienceMatters is out this week. "Sneaking Science into Punk Rock" stars Jennifer Leavey, principal academic professional in the School of Biological Sciences, director of the Georgia Tech Urban Honey Bee Project, and integrated science curriculum coordinator for the College of Sciences. But when she straps on a guitar, Leavey becomes Leucine Zipper, leader of the rock band Zinc Fingers.
If you would like to join the ScienceMatters Hall of Fame, enter the answer to this question: In Episode 7, what is the name of the song that Jennifer Leavey says sounds like a love song but is actually about bacteria living together in biofilms?
Submit your answer by 11 a.m. Monday, October 8, at sciencematters.gatech.edu.
Jennifer Leavey is a principal academic professional in the School of Biological Science. She also serves College of Sciences as the coordinator of the Integrated Science Curriculum and director of Georgia Tech Urban Honeybee Project.
The Georgia Tech Urban Honey Bee Project is an interdisciplinary educational initiative to recruit and retain students in STEM careers through the study of how urban habitats affect honey bee health and how technology can be used to study bees.
Leavey is also the faculty director of the Science and Math Research Training (SMaRT) and Scientific Health and Related Professions (SHaRP) Living Learning Communities of the College of Sciences.These communities aim to create lasting connections among College of Sciences majors who are interested in research (SMaRT) or intend to pursue additional education and training health-rleated fields.
In Episode 7 of ScienceMatters, Leavey shares her long-lasting passion for both science and rock music. By day, she’s an academic professional; but when she straps on a guitar , she mutates to Leucine Zipper, leader of the rock band Zinc Fingers.
For a change of pace, ScienceMatters samples the band’s science-inspired songs. Leavey shares how the band uses music and other media to make science concepts fun and accessible.
Take a listen at sciencematters.gatech.edu.
Enter to win a prize by answering the question for Episode 7:
In episode 7, what is the name of the song that Jennifer Leavey says sounds like a love song but is actually about bacteria living together in biofilms?
Submit your entry by 11 AM on Monday, Oct. 8, at sciencematters.gatech.edu. Answer and winner will be announced shortly after the quiz closes.
Jennifer Leavey is the integrated science curriculum coordinator for the College of Sciences. She also directs the Georgia Tech Urban Honey Bee Project, an interdisciplinary initiative designed to recruit and retain STEM students by studying how urban habitats affect honey bee health and how technology can be used to study bees.
“Most of the programs I work on relate to encouraging undergraduates to become more engaged in studying science,” Leavey said. “The Georgia Tech Urban Honey Bee Project sprouted out of the idea that if something is authentic, it doesn’t matter what discipline students are in or what class they’re taking, they’ll become interested in it.”
Learn more about Jennifer Leavey's activities, including leading a science rock band, in the full story by Victor Rogers.
For those about to rock, ready your eardrums, because an unholy alliance of science and rock has come to a head. The debut album, Atomic Anarchy, from Leucine Zipper & the Zinc Fingers dropped on streaming services Sept. 1st. School of Biological Sciences Jennifer Leavey and School of Chemistry and Biochemistry Michael Evans play lead guitar and bass, respectively.
In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology in the School of Biological Sciences Deanna Beatty will defend her dissertation Effects of Macroalgal Versus Coral Reef Dominance on Coral Survival, Chemical Defense, and Microbiomes.
Dr. Mark Hay
School of Biological Sciences
Georgia Institute of Technology
Dr. Frank Stewart
School of Biological Sciences
Georgia Institute of Technology
Dr. Julia Kubanek
School of Biological Sciences
Georgia Institute of Technology
Dr. Danielle Dixson
School of Marine Science and Policy
University of Delaware
Dr. Kim Ritchie
School of Science and Mathematics
University of South Carolina Beaufort
Coral reefs are among the earth’s most biodiverse and productive ecosystems, but are undergoing precipitous decline due to coral bleaching and disease following thermal stress events, which are increasing in frequency and spatial scale. These effects are exacerbated by local stressors such as overfishing and pollution, collectively causing an increasing number of reefs to shift from coral to macroalgal dominance. These stressors can harm or kill corals through diverse mechanisms, including alterations in how corals interact with microorganisms. By employing a variety of field sampling and field experimental approaches, I investigated consequences of local protection from fishing and coral versus macroalgal dominance of the benthos on coral survival, chemical defense, and microbiomes within paired algal dominated fished areas and coral dominated marine protected areas (MPAs) in Fiji. I demonstrate that i) coral larvae from a macroalgal dominated area exhibited higher pre-settlement mortality and reduced settlement compared to those from a coral dominated area, ii) juveniles planted into a coral dominated MPA survived better than those planted into a macroalgal dominated fished area and differential survival depended on whether macroalgae were immediately adjacent to juvenile coral, iii) corals possess chemical defenses toward the thermally-regulated coral bleaching pathogen Vibrio coralliilyticus, but this defense is compromised by elevated temperature, iv) for a bleaching susceptible but ecologically important acroporid coral, anti-pathogen chemical defense is compromised when coral resides within macroalgal dominated reefs and this effect can be influenced by both the current and historic state of the reef. Effects on coral survival and chemical defense for individuals residing within coral versus macroalgal dominated areas largely coincided with nuanced differences in coral microbiomes (e.g., in microbiome variability and specific indicator bacterial taxa) but not with major shifts in microbiome composition. These findings have implications for reef conservation and for understanding how coral-microbe interactions will respond to the pressures of global change.