Ph.D. Candidate Wins Podcast Episode 7 Quiz

October 15, 2018 | Atlanta, GA

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.

For More Information Contact

maureen.rouhi@cos.gatech.edu

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

October 8, 2018 | Atlanta, GA

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

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky874/5112988

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.).

Postdoctoral Researcher Wins Podcast Episode 6 Quiz

October 4, 2018 | Atlanta, GA

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."

Chen hails from Taipei, in Taiwan. She came to Georgia Tech in 2016, joining the labs of Matthew Herron and Frank Rosenzweig, in the School of Biological Sciences. 

"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.

For More Information Contact

maureen.rouhi@cos.gatech.edu

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

Leavey uses popular culture to convey scientific concepts

October 1, 2018 | Atlanta, GA

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.

For More Information Contact

maureen.rouhi@cos.gatech.edu

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

First of 12 stories about Women at Georgia Tech

October 8, 2018 | Atlanta, GA

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 More Information Contact

maureen.rouhi@cos.gatech.edu

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

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.

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

Date/Time:

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

Date/Time:

The winners’ revolutionary discoveries represent a major breakthrough, have saved many lives

October 2, 2018 | Atlanta, GA

The 2018 Nobel Prize in Physiology or Medicine was awarded jointly to James P. Allison and Tasuku Honjo for their discovery of cancer therapy by putting the brakes on the immune system. Allison is a professor at the University of Texas MD Anderson Cancer Center, in Houston. Honjo is a professor at Kyoto University.

The 2018 winners “found ways to alert immune cells to recognize cancer cells as non-self and destroy them,” says Francesca Storici, a professor in the School of Biological Sciences and a member of the Parker H. Petit Institute for Bioengineering and Bioscience (IBB). Working with both healthy and cancer cells, she studies what happens inside cells and the DNA damage that occurs with cancer. “Research in this direction has the potential to save many lives not only from cancer but possibly also from many other cell degenerative disorders,” Storici says.

The immune system is well-designed to attack cells that the body considers foreign. The system is tightly regulated to avoid attacking our own normal healthy cells. “This year's winners are long-time students of the mechanisms underlying this regulatory aspect of immune function,” says John McDonald, a professor in the School of Biological Sciences whose lab uses an integrated systems approach to the study of cancer. He directs the Integrated Cancer Research Center at Georgia Tech and is a member of IBB. 

Most cancer cells are sufficiently mutated to be viewed as “foreign.” But they often escape attack by shrouding themselves with proteins that block the immune response. By developing strategies to inhibit these blocking mechanisms, McDonald says, the Nobel Prize winners “unleashed the natural anti-cancer properties of the immune system.”

Specifically, Allison and Honjo unraveled the mechanisms that inhibit T-cells, the major immune system components that attack foreign cells, says Fredrik Vannberg, an assistant professor in the School of Biological Sciences and IBB member.

Their basic science discovery led to what is now known as immune checkpoint therapy, which works by reversing T-cell inhibition and allowing the body’s own immune system to destroy cancer cells. Immune checkpoint therapy has saved the lives of many late-stage cancer patients, Vannberg says.

However, not every patient benefits from any particular therapy. Research at Georgia Tech aims to provide additional tools to find the treatment that suits the patient. For example, McDonald and Vannberg collaborate in using genomic profiling to help predict which specific therapy will lead to the best clinical outcome for a given cancer patient.

Toward this goal, last year they offered to cancer researchers – for free – a new program that predicts cancer drug effectiveness via machine learning and raw genetic data. They hoped to attract other researchers who will share their cancer and computer expertise and data to improve upon the program and save more lives together.

“The hope is that – by exploiting these new discoveries alone and in combination with other novel strategies to target treatment to tumors – cancer will soon be transformed from a lethal to a manageable chronic disease,” McDonald says.

For More Information Contact

maureen.rouhi@cos.gatech.edu

A. Maureen Rouhi, Ph.D.
Director of Communications
College of Sciences

Graduate Student Wins Podcast Episode 5 Quiz

September 26, 2018 | Atlanta, GA

Once again, a Georgia Tech student ends up winning a ScienceMatters quiz because of the desire to take a homework break.

For Episode 4, it was Allie Caughman hearing the winning quiz detail during a study break. For Episode 5's quiz, Sachin Sarath Yadav Kothandaraman's need to relax a little resulted in the graduate student joining the ScienceMatters Hall of Fame.

"I heard this particular episode while I was taking a break from my assignments," Kothandaraman says. But it wasn't the first time he listened to the podcast. "I started listening to ScienceMatters after my classmate shared it with me. I've been hooked since."

Kothandaraman is from Chennai, India, where he received a bachelor's degree in biotechnology from Anna University. He is in his first year in the Georgia Tech Bioinformatics Graduate Program.

Continue here to the full story.

For More Information Contact

renay.san@cos.gatech.edu

Renay San Miguel
Communications Officer
College of Sciences

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