Episode 7 of ScienceMatters' Season 1 stars Jennifer Leavey. Listen to the podcast here and read the transcript here.
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.
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.
Thesis Advisor:
Dr. Mark Hay
School of Biological Sciences
Georgia Institute of Technology
Committee members:
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
SUMMARY
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.
Event Details
Nolan English
School of Biological Sciences
Advisor: Dr. Matthew Torres (School of Biological Sciences)
Committee Members:
Dr. Melissa Kemp, School of Biomedical Engineering; Georgia Institute of Technology
Dr. Raquel Lieberman, School of Chemistry and Biochemistry; Georgia Institute of Technology
Dr. Peng Qiu, School of Biomedical Engineering; Georgia Institute of Technology
Dr. Christopher Rozell, School of Electrical and Computer Engineering; Georgia Institute of Technology
Abstract:
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality remains limited. Fewer than 4% of all eukaryotic PTMs are reported to have biological despite their ubiquity across the proteome. This percentage continues to decrease as the pace of identification of PTMs surpasses the rate that PTMs are experimentally researched. To bridge the gap between identification and interpretation we have developed SAPH-ire, Structural Analysis of PTM Hotspots, a machine learning based tool for prioritizing PTMs for experimental study by functional potential. In this thesis, I aim to expand SAPH-ire’s functionality to predict potential function and improve its performance in ranking PTMs by functional potential. Here I will first discuss some challenges facing computational PTM research from an informatics perspective. I will then discuss the creation of new resources to address these challenges in four objectives. First, the creation of a new data resource that captures experimental data from mass spectrometry experiments designed to focus on PTMs. Second, the renovation of the SAPH-ire machine learning model to improve model performance and predictive recall. Third, the generation of a new model capable of discerning function from functional potential and structural features. Fourth, the development of a visual interface for SAPH-ire and the data resource that enhance one’s ability to understand the model’s results and drives further study.
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality remains limited. Fewer than 4% of all eukaryotic PTMs are reported to have biological despite their ubiquity across the proteome. This percentage continues to decrease as the pace of identification of PTMs surpasses the rate that PTMs are experimentally researched. To bridge the gap between identification and interpretation we have developed SAPH-ire, Structural Analysis of PTM Hotspots, a machine learning based tool for prioritizing PTMs for experimental study by functional potential. In this thesis, I aim to expand SAPH-ire’s functionality to predict potential function and improve its performance in ranking PTMs by functional potential. Here I will first discuss some challenges facing computational PTM research from an informatics perspective. I will then discuss the creation of new resources to address these challenges in four objectives. First, the creation of a new data resource that captures experimental data from mass spectrometry experiments designed to focus on PTMs. Second, the renovation of the SAPH-ire machine learning model to improve model performance and predictive recall. Third, the generation of a new model capable of discerning function from functional potential and structural features. Fourth, the development of a visual interface for SAPH-ire and the data resource that enhance one’s ability to understand the model’s results and drives further study.
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality remains limited. Fewer than 4% of all eukaryotic PTMs are reported to have biological despite their ubiquity across the proteome. This percentage continues to decrease as the pace of identification of PTMs surpasses the rate that PTMs are experimentally researched. To bridge the gap between identification and interpretation we have developed SAPH-ire, Structural Analysis of PTM Hotspots, a machine learning based tool for prioritizing PTMs for experimental study by functional potential. In this thesis, I aim to expand SAPH-ire’s functionality to predict potential function and improve its performance in ranking PTMs by functional potential. Here I will first discuss some challenges facing computational PTM research from an informatics perspective. I will then discuss the creation of new resources to address these challenges in four objectives. First, the creation of a new data resource that captures experimental data from mass spectrometry experiments designed to focus on PTMs. Second, the renovation of the SAPH-ire machine learning model to improve model performance and predictive recall. Third, the generation of a new model capable of discerning function from functional potential and structural features. Fourth, the development of a visual interface for SAPH-ire and the data resource that enhance one’s ability to understand the model’s results and drives further study.
Event Details
A Frontiers in Science Lecture by Mindy-Millard Stafford, School of Biological Sciences
Recent work from the lab of Mindy Millard-Stafford brings attention to the cognitive effects of dehydration. The findings have garnered immense media attention, from Newsweek and National Public to Men’s Health Magazine. Millard-Stafford discusses her Georgia Tech research leading up to this widely noticed work.
She will discuss: Why is water essential? How much do we need? Is water the most hydrating beverage? Can you drink too much water? And based on one media headline -- Does dehydration make you dumber?
She will reflect on the unexpected media blitz: how it happened and what lessons we might take away from this experience.
Light refreshments will be served after the lecture.
About The Speaker
A member of the Georgia Tech faculty for more than three decades, Mindy Millard-Stafford is a professor in the School of Biological Sciences, where she directs the Exercise Physiology Laboratory.
She is past president of the American College of Sports Medicine and member of the National Academy of Kinesiology.
The goals of her research are to seek nutritional and exercise interventions that can improve human health, well-being, and performance. Her lab is particularly focused on the importance of hydration to delay fatigue and maintain safety during exercise, especially in conditions of heat stress.
About The Frontiers in Science Lecture Series
Lectures in this series are intended to inform, engage, and inspire students, faculty, staff, and the public on developments, breakthroughs, and topics of general interest in the sciences and mathematics. Lecturers tailor their talks for nonexpert audiences.
Event Details
College of Sciences faculty, staff, and students are invited to join Provost Rafael L. Bras and Search Committee Chair Pinar Keskinocak, for a town hall to learn about the dean search process and timeline, and to provide feedback on the characteristics of the ideal candidate.
The international search for the new dean for the College of Sciences will be chaired by Pinar Keskinocak, William W. George Chair, H. Milton Stewart School of Industrial and Systems Engineering; College of Engineering ADVANCE Professor; and Director, Center for Health and Humanitarian Systems. The individual selected by this search committee will also hold the Betsy Middleton and John Clark Sutherland Chair.
Event Details
Episode 2 of ScienceMatters' Season 1 stars Jenny McGuire. The assistant professor in the School of Earth and Atmospheric Sciences and the School of Biological Sciences has a tough commute to her summer research site: An 80-foot drop into Wyoming’s deep, dark Natural Trap Cave. There she collects fossils that she hopes will yield clues about the impact of climate change on animal and human populations.
Follow her journey at sciencematters.gatech.edu.
Enter to win a prize by answering the episode's question:
What small four-legged animals mentioned in Episode 2 help Jenny McGuire collect bones from Natural Trap Cave?
Submit your entry by noon on Friday, Aug. 31, at sciencematters.gatech.edu. Answer and winner will be announced on Monday, Sept. 3.
Congratulations to Vineeth Aljapur, winner of Episode 1 quiz. Aljapur is a first-year student in the Georgia Tech Bioinformatics Graduate Program.
Episode 3 of ScienceMatters' Season 1 stars M.G. Finn. Listen to the podcast and read the transcript here!
Leishmaniasis is a scary parasitic disease; it can rot flesh. Formerly contained in countries near the equator, it has arrived in North America. School of Chemistry and Biochemistry Professor and Chair M.G. Finn explains why it’s so tough to fight this disease. His collaboration with Brazilian researcher Alexandre Marques has raised hopes for a possible vaccine.
Follow the the researchers' journey at sciencematters.gatech.edu.
Enter to win a prize by answering the episode's question:
What sugar molecule mentioned in Episode 3 is the main reason surgeons can’t transplant organs from animals into humans?
Submit your entry by noon on Friday, Sept. 7, at sciencematters.gatech.edu. Answer and winner will be announced on Monday, Sept. 10.
Results of Episode 2 Quiz
Q: What small four-legged animals mentioned in Episode 2 help Jenny McGuire collect bones from Natural Trap Cave?
A: Wood rats, pack rats, or rats
The winner is Pedro Marquez Zacarias. He was listening to ScienceMatters while doing routine data analysis for his research.
A third-year Ph.D. student in the Georgia Tech Quantitative Biosciences Graduate Program, Marquez Zacarias aims to add to the understanding of how biological complexity evolved, particularly multicellularity.
Marquez Zacarias comes from a small town in rural México, an indigenous community called Urapicho, in the state of Michoacán.
They may look a little like space capsules, but nuclear magnetic resonance spectrometers stay planted on the floor and use potent magnetism to explore opaque constellations of molecules.
Three Atlanta area universities jointly launched a nuclear magnetic resonance collaboration called the Atlanta NMR Consortium to optimize the use of this technology that provides insights into relevant chemical samples containing so many compounds that they can otherwise easily elude adequate characterization. The consortium has been operating since July 2018.
Crab pee
Take, for example, crab urine. It’s packed with hundreds to thousands of varying metabolites, and researchers at the Georgia Institute of Technology wanted to nail down one or two of them that triggered a widespread crab behavior. Without access to NMR they may not have found them at all even after an extensive search.
The spectrometer pulled the right two needles out of the haystack, so the researchers could test them on the crabs and confirm that they were initiating the behavior.
Emory University, Georgia State University and Georgia Tech already have NMR technology, but the Atlanta NMR Consortium will enable them to fully exploit it while cost-effectively staying on top of upgrades.
“NMR continues to grow and develop because of technological advances,” said David Lynn, a chemistry professor at Emory University.
That means buying new machines every so often, and one new NMR spectrometer can run into the millions; annual maintenance for one machine can cost tens of thousands of dollars. Thus, reducing costs and maximizing usage makes good sense.
Medicine, geochemistry
The human body, sea-side estuaries, and rock strata present huge collections of compounds. NMR takes inventory of complex samples from such sources via the nuclei of atoms in the molecules.
A nucleus has a spin, which makes it magnetic, and NMR spectrometry’s own powerful magnetism detects spins and pinpoints nuclei to feel out whole molecules. These can be large or small, from mineral compounds with three or four component atoms to protein polymers with tens of thousands of parts.
Researchers in medicine, biochemistry, ecology, geology, food science – the possible list is exhaustive -- turn to NMR to untangle their particular molecular jungles. The consortium wants to leverage that diversity.
“As we go in different directions, we will benefit from a cohesive community of people who know how to use NMR for a wide range of problems,” said Anant Paravastu, an associate professor in Georgia Tech’s School of Chemical and Biomolecular Engineering.
“The most important goal for us is the sharing of our expertise,” said Markus Germann, a professor of chemistry at Georgia State.
Consortium members will benefit the most from the pooled NMR resources, but non-partners can also book access. Read more about the Atlanta NMR Consortium here on Georgia Tech’s College of Sciences website
Mention “peat moss,” and many people will conjure up the curly brown plant material that gardeners use. “Oh, the thing you get at Home Depot” – is a common reaction Joel Kostka receives when he mentions that he studies peat moss. His response: “Peat moss is a really cool plant that’s important to the global carbon cycle.”
Joel Kostka is a professor in the School of Biological Sciences and the School of Earth and Atmospheric Sciences at Georgia Tech. The National Science Foundation has just awarded him and three co-principal investigators a $1.15 million, three-year grant to study the microbes in peat moss. The goal is to understand the microbiome’s role in nutrient uptake and the methane dynamics of wetlands and the impact of climate change on these activities.
Kostka’s collaborators are Jennifer Glass, an assistant professor in the Georgia Tech School of Earth and Atmospheric Sciences; Xavier Mayali, a research scientist at Lawrence Livermore National Laboratory; and David Weston, a staff scientist at Oak Ridge National Laboratory.
“It has been shown that microbes that live with peat moss help them to grow better by aiding their uptake of carbon and major nutrients such as nitrogen,” Kostka says. “This project will explore which microbes help to keep peat moss plants healthy, how plants and microbes interact, and how these relationships will be affected by climate change?”
Peat moss, also called Sphagnum, carpets the surface of peatlands. This type of wetland locks up huge amounts of carbon in the form of thick, peat soil deposits. When peat is broken down by microbes, greenhouse gases – methane and carbon dioxide – are produced. Methane is of particular interest, because when released to the atmosphere, it has a warming potential that is 21 times that of carbon dioxide.
Scientists hypothesize that environmental warming could cause peatlands to release a lot more methane, which in turn would accelerate climate change.
“Our project is fundamental science. We’re trying to figure out how the microbes help the plants grow better.”
Lots of evidence suggest that peatlands will produce more methane as the environment warms up. “Methanogens [methane-producing bacteria] don’t like the cold,” Kostka says. “The warmer it gets, the better they are in producing methane.”
Methane in peatlands bubbles up to the peat moss layer. Methane-consuming microbes in peat moss eat some of the gas released. In effect, microbes in peat moss comprise a biofilter that reduces the amount of methane reaching the atmosphere.
However, “we hypothesize that the methane-eating microbes in peat moss may crash as the climate gets warmer,” Kostka says. That sets up a double-whammy scenario: As the climate gets warmer, microbes in peatlands produce more methane, while other microbes in peat moss become less able to consume the greenhouse gas. “We could get an explosion of methane much more than we can predict,” Kostka says.
Information about plant microbiomes is scant. Most plants whose microbiomes are being studied are crops, like corn and soybeans. “Few studies are available on plants that are environmentally important but not so economically important,” Kostka says. “A lot of our work is to build better models for how these wetlands respond to climate change.”
“Few studies are available on plants that are environmentally important but not so economically important. A lot of our work is to build better models for how these wetlands respond to climate change.”
Georgia Tech’s Glass will study the geochemical aspects of the peat moss microbiome. She will measure how fast peat moss microbes fix nitrogen and consume methane. She will also identify the trace nutrients available to peat moss in the wetland.
“Because these peatlands receive most of their nutrient input from precipitation, they contain extremely low concentrations of some bioessential trace metals,” Glass says. “We're interested in testing how trace nutrient availability impacts the growth of methane-cycling microbes exposed to warming temperatures.”
At Lawrence Livermore National Laboratory, Mayali will use NanoSims, an imaging mass spectrometer, to identify what microbes are eating the methane or fixing nitrogen. He will incubate microbe samples with substrates – methane, carbon dioxide, and nitrogen – enriched in rare isotopes such as carbon-13 instead of the normally abundant carbon-12. Analysis by NanoSims creates isotope maps that enables detailed tracing of who did what.
“Our instrument is able to not only track who is eating the methane or fixing nitrogen from the air, but more importantly, how much and where it ultimately ends up, for example into the Sphagnum plant versus being kept by the microbes,” Mayali says.
Meanwhile, at Oak Ridge National Laboratory, Weston will use genetically characterized peat moss and microbial members to construct synthetic communities to test how host moss genes influence microbiome assembly and functioning. “Peat moss microbiomes are extremely complex with thousands of members with diverse metabolic capabilities,” Weston says.
“To help determine the role of specific community member interactions,” Weston adds, “we will decompose the field system into simplified synthetic communities where community changes and nutrients can be accurately measured and subjected to precise environmental manipulations.”
“We can engineer wetlands to encourage the growth of peat moss, but that’s not our goal,” Kostka says. “Our project is fundamental science. We’re trying to figure out how the microbes help the plants grow better.”
Pages
