This summer, Joshua Weitz, a professor with the School of Biological Sciences who is also the founding director of the Quantitative Biosciences Interdisciplinary Graduate Program (QBioS), organized a “Hands-On Modeling Virtual Workshop” focusing on epidemics.
The Weitz Group at Georgia Tech has created various models and figures to help explain the spread and epidemiology of Covid-19. Weitz has frequently shared his findings with local and national media outlets.
This year marked the fourth annual “Quantitative Biosciences Hands-On Modeling Workshop”. Due to Covid-19, the summer 2020 event was held virtually. Focused on the basics of epidemic modeling, the workshop was joined by more than 50 online attendees from around the globe.
Weitz delivered two lectures on epidemic theory and the latest Covid-19 research. In addition, ten QBioS students, two post-doctoral scientists from the Weitz group (David Demory and Stephen Beckett), and one external post-doctoral scientist (Bradford Taylor) served as instructors for small group sessions, focusing on the hands-on experience of coding deterministic and stochastic models to predict the spread of epidemics.
The QBioS Ph.D. student organizers collected surveys following the event, which provided feedback on both the content and format of the workshop. Some examples:
“The flow of the workshop is great. Learning introductory concepts to start, the ability to apply some of them with hands-on, and then finishing with applications and extensions. Having many participants from many backgrounds adds a lot to the small group sessions as well.”
“I thought it was a great workshop to get core concepts across. I think the online format was done as best as possible and appreciated the thoughtful instructors.”
Weitz and Pablo Bravo, a second year QBioS Ph.D. student in Quantitative Biosciences, share thoughts on how they ran the virtual workshop — along with ideas and advice for those looking to host similar online workshops:
What were the biggest lessons learned from your summer workshop?
Weitz: The survey results communicated two important lessons. First, positive
responses to the workshop structure reinforce just how critical it is to contextualize modeling in terms of a key biological challenge. Providing a biological scaffold helps to focus student work and keep their interest and attention on the technical material. The second lesson is that there is an adaptation period to hands-on learning online. We intentionally spaced out the coding sessions with a mid-day break and most of the issues appeared in the morning as students and instructors adjusted to their group's dynamic, including debugging code while in different locations, and indeed, countries.
Bravo: One aspect that made the workshop possible was the participation of many members in different roles: coordinators, advertising, lecturers, instructors, IT support. Planning and working early as a team were essential.
What were the biggest challenges you had to overcome?
Bravo: There were two main problems that we had to solve. First, we offered support for three programming languages (MATLAB, Python, R), and given the high number of registrations, the first year QBioS cohort couldn't handle all of them. Members of the QBioS community, current and past members of the Weitz group stepped in and helped us in leading activity groups. It wouldn't have been possible without them!
Also, debugging was an issue. Debugging scripts over video calls was extremely difficult. Attendees were not keen on screen-sharing their code at the beginning, but as they got to know each other, this stopped being an issue. Delay between the video and audio feed remained an issue throughout the whole workshop.
What’s the one takeaway you want to stress to instructors looking to offer similar webinars and online workshops?
Weitz: Overall, we are optimistic about our ability to continue to develop and implement innovative teaching strategies in QBioS — but remain realistic that adjustment periods will be needed to foster an atmosphere conducive to small group learning when groups are dispersed.
Bravo: I think the biggest factor in the success of the workshop is that it was centered around interactive activity sessions, in which five students and an instructor would go through the material and write the scripts together. This promoted both active learning and discussion between the attendees, and also allowed attendees to follow up with questions and comments to their respective instructors — even days after the workshop finalized.
In the wake of the Covid-19 outbreak, universities have quickly shifted their classes online. But opening up research labs, and ongoing scientific experiments to remote possibilities is a much harder task. As colleges potentially reopen, how do labs and research resources factor in? And how do key funding sources factor into that planning? Hear from College of Sciences Dean and Betsy Middleton and John Clark Sutherland Chair Susan Lozier, along with experts from NIH and University of Michigan. Join the virtual seminar at 2 p.m. EDT on July 16.
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Ribonucleotides, units of RNA that can become rooted in DNA during processes such as replication and repair, generally are associated with genomic instability, an increase in mutations, and DNA fragility.
Researchers have been aware of the abundance of ribonucleotides for about a decade, and the lab of Francesca Storici at the Georgia Institute of Technology has been at the forefront, researching the relationship between RNA and DNA in genome stability and instability, and DNA modification.
“There is much that is unknown about the phenomenon of ribonucleotides in DNA, andit needs to be uncovered,” says Storici, professor in the School of Biological Sciences and a researcher in the Petit Institute of Bioengineering and Bioscience at Georgia Tech, where her lab’s previous studies have led to the development of new-age tools and techniques, to collect and analyze data and answer some of the questions surrounding ribonucleotides.
“It’s important to establish a framework for better directing future studies to uncover physiological roles of ribonucleotides in DNA,” she says. And that’s exactly what she and her colleagues have done in their latest research paper, “Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine,” published recently in the journal Nature Communications.
Namely, they use the tools and techniques they’ve developed over the past few years to characterize sites of ribonucleotide incorporation in DNA, demonstrating clearly that ribonucleotides in yeast DNA are not randomly distributed but show preferences for being incorporated in specific DNA sequence contexts. “We specifically reveal a bias for ribonucleotide incorporation both in yeast mitochondrial and nuclear DNA,” Storici says.
In a previous study published in January 2015, the lab introduced ribose-seq, a high-throughput sequencing technique that allows researchers to establish a full profile of ribonucleotides embedded in genomic DNA, generating large, complex data sets. In late 2018, the lab published its work on a new bioinformatics toolkit called Ribose-Map, which effectively and efficiently transforms the massive amounts of raw sequencing data obtained from the ribose-seq process into summary datasets and publication-ready results.
For their latest work described in Nature Communications, the team deployed ribose-seq to generate the data and Ribose-Map to analyze it, identifying sites of ribonucleotides in yeast DNA and explore their genome-wide distribution. Consequently, the paper’s four co-lead authors included Sathya Balachander (part of the ribose-seq development team and co-author of that paper, now licensing associate for the Bill Harbert Institute for Innovation and Entrepreneurship/University of Alabama-Birmingham) and Alli Gombolay (lead author of the Ribose-Map study).
Contributing equally as co-lead authors of the new research were Taehwan Yang and Penghao Xu, who, like Gombolay, are Ph.D. students in Storici’s lab (where Balachander was a Ph.D. student and postdoctoral researcher).
The team studied three different yeast species and detected a number of similar patterns. In all three species, the deoxyribonucleotide that is immediately upstream of the ribonucleotide was shown to have the greatest impact on the incorporation of ribonucleotides in DNA. “This rule was not clear before,” Storici says. “The study also highlights hotspots of ribonucleotides in DNA sequences containing di- and tri-nucleotide repeats, showing that specific sequence contexts have higher likelihood of ribonucleotide incorporation in DNA. This might be associated with ribonucleotide physiological/pathological functions that are yet to be discovered.”
The lab is now working toward better understanding of how cells control and benefit from ribonucleotide incorporation in DNA by uncovering the patterns and hotspots of incorporation in yeast cells of different genotypes, as well as cells from other species and organisms.
“Now we are interested to see if the rule that we have discovered for yeast applies to other cell types beyond yeast, like human cells for example, and to what extent,” says Storici. “As long term goal, we aim to determine whether there is a sort of language of ribonucleotide incorporation that cells utilize for regulating different cell metabolic functions.”
In addition to those mentioned, other authors of this multi-institutional study were Fredrik Vannberg (former professor in the School of Biological Sciences at Georgia Tech and former Petit Institute researcher), Gary Newnam (manager of the Storici Lab), Anton Bryksin (director of the Petit Institute’s Molecular Evolution Core), Havva Keskin (former Storici grad student, now a researcher with Omega Bio-tek), Kyung Duk Koh (former member of Storici lab, now a researcher at the University of California-San Francisco), Waleed M. M. El-Sayed (former visiting scholar in the Storici’s lab, now researcher at the National Institute of Oceanography and Fisheries in Egypt), and Sijia Tao, Nicole Bowen, Raymond Schinazi, and Baek Kim from the Emory School of Medicine’s Department of Pediatrics.
Blue holes scattered throughout the Gulf of Mexico inspire a team of exploration scientists and divers who set out to uncover the mysteries of these submerged sinkholes. Tune in to watch the episode and hear from Georgia Tech scientists in June, or join the July 14 interactive screening, which will feature live Q&A with the experts!
Read more about the research and experts behind this episode.
- June 24 at 8 p.m. through WPBT South Florida PBS
- June 24 at 8 p.m. through http://changingseas.tv
- June 28 at 9 p.m. through WXEL South Florida PBS
- July 14 at 6 p.m. with live Q&A through Eventbrite (RSVP here)
Reports of large aggregations of fish in the Gulf of Mexico led divers to discover deep holes opening down into the seafloor. These submerged sinkholes and springs, more commonly called blue holes, attract a diversity of marine life in an otherwise ocean desert. A group of scientists and technical divers collaborate to better understand these ecological oases in the sea. The experts begin by exploring Amberjack Hole – a sinkhole located 20 miles off the coast of Sarasota, Florida, that opens at 115 feet below the surface and extends down to over 350 feet.
Do these blue holes connect to mainland Florida? What organisms are found at the bottom of the hole? What effects do these holes have on the surrounding Gulf of Mexico? Join scientists as they search for answers and explore these never before studied environments.
Major funding for this program was provided by the Batchelor Foundation, encouraging people to preserve and protect America’s underwater resources. And by the Arthur Vining Davis Foundations, strengthening America’s future through education. Additional funding was provided by The William J. and Tina Rosenberg Foundation. And by the Do Unto Others Trust.
Learn more: changingseas.tv
Event Details
Blue holes scattered throughout the Gulf of Mexico inspire a team of exploration scientists and divers who set out to uncover the mysteries of these submerged sinkholes. Tune in to watch the episode and hear from Georgia Tech scientists in June, or join the July 14 interactive screening, which will feature live Q&A with the experts!
Read more about the research and experts behind this episode.
- June 24 at 8 p.m. through WPBT South Florida PBS
- June 24 at 8 p.m. through http://changingseas.tv
- June 28 at 9 p.m. through WXEL South Florida PBS
- July 14 at 6 p.m. with live Q&A through Eventbrite (RSVP here)
Reports of large aggregations of fish in the Gulf of Mexico led divers to discover deep holes opening down into the seafloor. These submerged sinkholes and springs, more commonly called blue holes, attract a diversity of marine life in an otherwise ocean desert. A group of scientists and technical divers collaborate to better understand these ecological oases in the sea. The experts begin by exploring Amberjack Hole – a sinkhole located 20 miles off the coast of Sarasota, Florida, that opens at 115 feet below the surface and extends down to over 350 feet.
Do these blue holes connect to mainland Florida? What organisms are found at the bottom of the hole? What effects do these holes have on the surrounding Gulf of Mexico? Join scientists as they search for answers and explore these never before studied environments.
Major funding for this program was provided by the Batchelor Foundation, encouraging people to preserve and protect America’s underwater resources. And by the Arthur Vining Davis Foundations, strengthening America’s future through education. Additional funding was provided by The William J. and Tina Rosenberg Foundation. And by the Do Unto Others Trust.
Learn more: changingseas.tv
Event Details
Visit the AbSciCon 2022 website to learn more about the event.
About the Event
AbSciCon, the conference brings the astrobiology community together every two years to share research, collaborate, and plan for the future, will be held 15-20 May 2022. NASA and the American Geophysical Union decided to move the 2021 conference to these new dates to facilitate a robust gathering of scientists in Atlanta and in an online capacity. Origins and Exploration: From Stars to Cells is the theme.
Event Details
Research opportunities that opened up to Georgia Tech students during their undergraduate years expand significantly when students continue their work as graduate or doctoral students.
Georgia Tech College of Sciences encourages that work with the annual presentation of Larry S. O’Hara Graduate Fellowships, given to outstanding doctoral students who are scheduled to graduate in the calendar year following their nominations.
This year four students were chosen as the winners of the O’Hara Graduate Fellowships:
Yuchen He
Mathematics
Advisor: Sung Ha Kang
Research Area: Lattice Indentification and Separation
Suttipong (Jay) Suttapitugsakul
Chemistry
Advisor: Ronghu Wu
Research Area: Analysis of glycoproteins on the cell surface
Deborah Ferguson
Physics
Advisor: Deirdre Shoemaker
Research Area: Binary coalescences as probes of strong-field gravity
Hyeonsoo (Harris) Jeong
Biology
Advisor: Soojin Yi
Research Area: Genomic landscape of methylation islands in hymenopteran insects
Congratulations to the O’Hara Fellowship winners!
Research opportunities that opened up to Georgia Tech students during their undergraduate years expand significantly when students continue their work as graduate or doctoral students.
Georgia Tech College of Sciences encourages that work with the annual presentation of Larry S. O’Hara Graduate Fellowships, given to outstanding doctoral students who are scheduled to graduate in the calendar year following their nominations.
This year four students were chosen as the winners of the O’Hara Graduate Fellowships:
Yuchen He
Mathematics
Advisor: Sung Ha Kang
Research Area: Lattice Indentification and Separation
Suttipong (Jay) Suttapitugsakul
Chemistry
Advisor: Ronghu Wu
Research Area: Analysis of glycoproteins on the cell surface
Deborah Ferguson
Physics
Advisor: Deirdre Shoemaker
Research Area: Binary coalescences as probes of strong-field gravity
Hyeonsoo (Harris) Jeong
Biology
Advisor: Soojin Yi
Research Area: Genomic landscape of methylation islands in hymenopteran insects
Congratulations to the O’Hara Fellowship winners!
The 2020 WST Distinguished Lecture with Abigail Stewart, orginally scheduled for April 9, has been postponed. Please visit cos.gatech.edu for further updates.
RSVP: If you'd like to attend this free event, please email: mary.fox@gatech.edu
Please join the College of Sciences and the Center for the Study of Women, Science, and Technology for the 2020 WST Distinguished Lecture with Professor Abigail Stewart, who will speak on "Creating an Inclusive Culture: Recruiting and Retaining the Faculty We Need."
Everyone is welcome to attend and enjoy a reception following the lecture!
About Abigail J. Stewart
Dr. Abigail J. Stewart is the Sandra Schwartz Tangri Distinguished University Professor of Psychology and Women's Studies at the University of Michigan. She served as director of the University of Michigan ADVANCE Program, 2001-2016, before which she held a number of other administrative positions. She holds degrees from Wesleyan University, London School of Economics, and Harvard University. Her current research focuses on academic and life experiences related to race, class and gender, and on political attitudes and activision.
Dr. Stewart's recent book, with Virginia Valian, is called An Inclusive Academy: Achieving Diversity and Excellence (MIT Press, 2018):
How colleges and universities can live up to their ideals of diversity, and why inclusivity and excellence go hand in hand.
Most colleges and universities embrace the ideals of diversity and inclusion, but many fall short, especially in the hiring, retention, and advancement of faculty who would more fully represent our diverse world—in particular women and people of color. In this book, Abigail Stewart and Virginia Valian argue that diversity and excellence go hand in hand and provide guidance for achieving both.
Stewart and Valian, themselves senior academics, support their argument with comprehensive data from a range of disciplines. They show why merit is often overlooked; they offer statistics and examples of individual experiences of exclusion, such as being left out of crucial meetings; and they outline institutional practices that keep exclusion invisible, including reliance on proxies for excellence, such as prestige, that disadvantage outstanding candidates who are not members of the white male majority.
Perhaps most important, Stewart and Valian provide practical advice for overcoming obstacles to inclusion. This advice is based on their experiences at their own universities, their consultations with faculty and administrators at many other institutions, and data on institutional change. Stewart and Valian offer recommendations for changing structures and practices so that people become successful in ways that benefit everyone. They describe better ways of searching for job candidates; evaluating candidates for hiring, tenure, and promotion; helping faculty succeed; and broadening rewards and recognition.
Event Details
Passionate about learning, discovery, and all things science? Check out more than 100 family friendly events at the 2020 Atlanta Science Festival, which will be held March 6-21 around Georgia Tech and the greater Atlanta area.
The annual two-week festival celebrates local science and technology, reaching 50,000 children and adults each year. Georgia Tech is one of the founding members of the Atlanta Science Festival and hosts and sponsors several Atlanta Science Festival events.
This year, festivities kick off on March 6 with 2100: A Climate Odyssey at Georgia Tech's Ferst Center for the Arts. This interactive and immersive, family friendly experience will be followed by a conversation with environmental scientists and meteorologists including The Weather Channel’s Carl Parker and Kim Cobb, Georgia Power Chair, ADVANCE Professor in the College of Sciences, Director of the Global Change Program, and professor in the School of Earth and Atmospheric Sciences. Friends of Georgia Tech can use discount code "HALF" to purchase $10 tickets.
Opening weekend also features one of the most unique experiences in music performance. On March 7, The Guthman Musical Instrument Competition Concert will showcase nine global finalists playing unique instruments created for the competition. It's free and open to the public.
New this year as part of the Guthman event is the Music, Art, and Technology Fair, hosted by the Georgia Tech School of Music and Cycling ’74. It's a unique opportunity to share projects at the intersection of art and technology in a hands-on, interactive, science-fair format.
The GVU Center at Georgia Tech (formerly the Graphics, Visualization and Usability Center) has created interactive graphics to explore the two-week festival and find specific events connected to Georgia Tech.
2020 Atlanta Science Festival events taking place on the Georgia Tech campus; sponsored or presented by Georgia Tech units; and featuring Georgia Tech faculty, students, or staff include:
- Friday, March 6, 8:00pm to 9:30pm, 2100: A Climate Odyssey
2100: A Climate Odyssey will transport you to the year 2100, when life is a little different due to climate change As a major storm hits Atlanta in this immersive theatrical experience, we will peer into the future and discover how we can work together to mitigate disaster. 5% of proceeds will be donated to the Captain Planet Foundation to empower positive change for the earth.
- Saturday, March 7, 9:30am to 11:30am, Science in Little 5 Points: The Science of Kombucha
Kombucha is tangy and tasty, but did you know that it gets that way through the hard work of millions of microbes? Join Jennifer Leavey, Ph.D., from Georgia Tech and Lupa Irie, N.D. of Lupa’s Kitchen for a hands-on, interactive demonstration of kombucha fermentation—including samples! - Saturday, March 7, 12:00pm to 3:00pm, STEAM at Tech Day
Fun for the entire family at STEAM at Tech Day! Join us for a day of hands-on, engaging, and full-filled STEAM learning. Middle and high school students will participate in a 3-hour intensive STEAM workshop and 2nd through 5th grade students will rotate between three STEAM activities. Parents and guardians will hear from experts in the field of Artificial Intelligence about what’s next in education to help develop their future scientists and engineers. - Saturday, March 7, 4:00pm to 7:00pm, Guthman Music, Art & Technology Fair
Get a sneak peek at what goes into the latest in music technology by visiting our music, art and technology fair, just before the Georgia Tech Guthman Musical Instrument Competition. See musicians, artists, engineers, and makers showcase their latest work at this hands-on, interactive showcase. - Saturday, March 7, 7:00pm to 9:00 pm, Guthman Musical Instrument Competition
A music, engineering, and tech mashup, the Georgia Tech Guthman Musical Instrument Competition is an annual event aimed at identifying the world's next generation of musical instruments and unveiling the best new ideas in musicality, design, engineering, and impact.
- Tuesday, March 10, 9:00am to 3:30pm, Project Change: STEM Teachers @ Tech Day
Teachers! Are you looking for a way to move beyond the standards and integrate STEM connections into your curriculum? Do you thirst for more knowledge to better connect and communicate to your class of future scientists, technologists, engineers and mathematicians? Join us for Project Change: STEM Teacher @Tech Day. This innovative professional learning opportunity will allow teachers to engage and tour cutting-edge labs and research centers, with the goal of increasing their understanding of current, real-world applications of their content. - Tuesday, March 10, 5:00pm to 6:30pm, The Astronomy of Star Wars
One with the Force are you? Join us for this all-ages dress up sci-fi adventure where we'll lead a discussion on the worlds and aliens of the Star Wars films and compare them with the planets and life in our solar system, as well as extra-solar planets. Along the way, we'll enjoy video clips inspired by Star Wars and other sci-fi favorites. Young Jedi and Padawan alike are encouraged to attend in their favorite sci-fi attire. - Tuesday, March 10, 7:00pm to 8:00pm, Playing Mother Nature: A Night of Simulating Earth Science Phenomena!
Ever wonder how weather systems are formed in the atmosphere? Or perhaps you would like to know how an earthquake develops? How does Earth's terrain evolve over long periods of time? If you have any interest in Earth Science, this event is for you!
- Wednesday, March 11, 7:30pm to 9:15pm, Cannabis Time with Dr. Pete
Did you know? George Washington grew hemp at his home in Mount Vernon. Cannabis is being seen in a whole new light as states and nations change laws and attitudes about the plant. Come learn about the relevant technical, medical, legal, and economic issues from Georgia Tech engineering professor, local comedian, and cannabis researcher Pete Ludovice, Ph.D.
- Thursday, March 12, 7:30pm to 10:00pm, Sober Science Speakeasy
Join us for an evening soiree that will tickle your tastebuds and wake up your sense of wonder. In our throwback to the 1920s in 2020, you enjoy live prohibition-era jazz music and exotic drinks! Learn about the science of boba, butterfly peaflower tea and kombucha, foams and emulsions, nitrogen cold brew and more with Jennifer Leavey, Ph.D. - Thursday, March 12, 7:30pm to 9:30pm, Science Riot
Take some scientists, teach them the basics of comedy writing, and put them onstage for a live audience performance. Real Science. Real Experts. Real Funny.
- Saturday, March 14, 9:00am to 2:00pm, 8th Annual Latino College & STEM Fair
We invite you to our 8th Annual Latino College and STEM Fair at Georgia Tech! Come join us for bilingual workshops, fun hands-on activities for the entire family, a college fair, and inspirational conversations with Latino college students, parents, professors, and other STEM professionals. - Saturday, March 14, 11:00am to 2:00pm, Investigating the Nanoscale
How do scientists and engineers make and see nanoscale objects? What does your hair or an insect’s eye look like under a scanning electron microscope? Through hands-on demos, learn what makes the nanoscale different, how harnessing it has led to improvements in products you use every day, and about future applications you can only imagine. Take a cleanroom tour and bring a sample (not wet and not greater than an inch in diameter) to scan with our tabletop SEM. - Saturday, March 14, 3:00pm to 5:00pm, Petri Dish Picassos
Bacteria art — is it crazy, awesome, or both? Come learn about professional artists that use bacteria to make living artwork and learn how to become a petri dish Picasso yourself! Participants will be provided with agar plates, paints, and tools commonly used to “paint” with bacteria. You will get to take home your own petri dish masterpiece!
- Wednesday, March 18, 7:30pm to 9:30pm, Science Improv
It's improv comedy with a science twist! Come see experienced improv actors and professional scientists take the stage together to put on a unique entertaining and educational experience. The audience will provide scientific suggestions to drive the performance, and you're sure to have a great time and come away having learned something too! Comedy improvisation has never been geekier.
More information about the festival: Atlanta Science Festival
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