Joshua Watson of Dr. Shaying Zhao’s lab successfully defended his dissertation titled, “Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs.” on Friday, April 14, 2023.
Congratulations Dr. Watson!
Natarajan Kannan, professor in the Department of Biochemistry and Molecular Biology and the Institute of Bioinformatics, leads an internationally recognized program at the interface of bioinformatics and biochemistry. Developing and applying sophisticated statistical and computational tools, he maps the complex relationships connecting sequence, structure, function and regulation in large families of protein kinases. These enzymes turn signals on and off in cells, a critical part of cell communication. Kinases are involved in many diseases and in related drug development studies as anti-cancer and infectious disease targets. He has also developed powerful informatics tools and deep learning models for the classification and evolutionary analysis of glycosyltransferases, a large family of enzymes. He is leveraging new information from these proteins from different cell, tissue, disease types and organisms to develop predictions about how they propagate signals in diseases. And he continues to train the next generation of scientists to apply new computational tools for biological discovery.
research.uga.edu/research-awards/2023/04/05/natarajan-kannan-2/
IOB doctoral student Ehsan Suez has earned a 2023 Outstanding Teaching Assistant Award from the Center for Teaching and Learning for superior teaching skills.
Ruijie (Rachel) Xu of Dr. Liliana Salvador’s lab successfully defended her dissertation, “Using Multi-Omics Data to Study Leptospira sp. Across Multiple Biological Scales” on Friday, April 7th, 2023.
Congratulations Dr. Xu!
April 6, 2023
Thank you to all the students who participated in this year’s University of Georgia Three Minute Thesis (3MT™) Competition.
The competition is open to all currently enrolled UGA master’s and doctoral students, and this year’s 3MT™ drew dozens of submissions from across the university. Several preliminary heats led to the selection of ten finalists, who submitted their presentations for a panel of judges.
The final competition was held Wednesday, April 5, 2023, at the University Chapel and was livestreamed on on Facebook.
This year’s grand prize winner was Karen Gonzalez, a doctoral student in the Institute of Bioinformatics, for her presentation titled “Humans vs Viruses.”
Karen Gonzalez, Grand Prize Winner
The runner-up was Chisom Okoli, a doctoral student in the Department of Nutritional Sciences, for presenting “Equity in Wellness: Development of an eLearning Training to Improve Healthy Beverage Consumption in Black Families of Young Children.”
Chisom Okoli, Runner Up Winner
The people’s choice award, which is given to the contestant who receives the most votes from viewers of the competition, went to Yang Su, a graduate student in the Department of Biochemistry and Molecular Biology, for his presentation of “The Bacteria Glycans: Trojan Horses in Disguise.”
Yang Su, People’s Choice Winner
Three Minute Thesis (3MT™) is an academic competition developed by The University of Queensland (UQ), Australia.
Lambodhar Damodaran of Dr. Justin Bahl’s lab successfully defended his dissertation, “Molecular Epidemiology of Contemporary Seasonal Influenza Epidemics” on Thursday, March 16th, 2023.
Congratulations Dr. Damodaran!
Noah Legall of Dr. Liliana Salvador’s lab successfully defended his dissertation, “Computational techniques for unraveling the genomic variations of Mycobacterium bovis across organizational scales” on Tuesday, March 14th, 2023.
Congratulations Dr. Legall!
(L to R) Leidong Mao, Christine Szymanski and Hitesh Handa
Christine Szymanski, Hitesh Handa and Leidong Mao were selected for their proven ability to invent and innovate
The National Academy of Inventors has selected three University of Georgia faculty as 2023 NAI Senior Members. NAI Senior Members are faculty, scientists and administrators selected for their proven ability to invent and innovate.
The UGA representatives of the 2023 class are Christine Szymanski, Hitesh Handa and Leidong Mao. With their selections, UGA now has 11 Senior Members overall.
“University of Georgia’s innovation and entrepreneurial ecosystem is propelled forward by exactly the kinds of research performed in the labs of our three newest National Academy of Inventors Senior Members,” said Karen Burg, vice president for research. “We are proud of Drs. Handa, Mao and Szymanski not only for their benchwork but also for the efforts they’ve made to apply that work in addressing real-world problems. I congratulate them all on being selected as NAI Senior Members.”
Christine Szymanski
Szymanski is a professor, associate head of the Franklin College of Arts & Sciences Department of Microbiology and member of the Complex Carbohydrate Research Center. She is a leading researcher in the areas of Campylobacter pathogenesis and microbial glycobiology. Her trailblazing efforts have laid the foundation for researchers in this field and are critical for the development of vaccines and therapeutics for animal and human health.
In addition to her research, Szymanski has been named inventor on six U.S.-issued patents, along with many issued foreign patents and numerous pending patents. Her patents have been licensed to seven companies for the development of interventions against bacterial infections. GlycoVaxyn, a specialist vaccine pharmaceutical company, was founded to leverage discoveries she made during her postdoctoral studies. The company was later purchased by GSK (formerly GlaxoSmithKline) for nearly $200 million. In 2013, Szymanski co-founded VaxAlta to develop glycoconjugate vaccines for human and animal health.
Leidong Mao
Mao is a professor of electrical and computer engineering in the College of Engineering. He is a leading researcher in the field of nanoscale engineering, specifically in nanoscale magnetism and its application in biomedical devices.
In 2012, Mao received an NSF CAREER Award and in 2013 the Young Scientist Award from the 13th International Conference of Magnetic Fluids. He has 20 invention disclosures and has been named inventor on five U.S.-issued patents with multiple pending applications. Three of Mao’s patents are licensed to biomedical companies for the development of diagnostic and therapeutic devices. He has also founded his own startup company, FCS Technology, to commercialize his patented discoveries.
Hitesh Handa
Handa is an associate professor in the College of Engineering. His innovative translational research in biocompatible coatings for medical devices led to the development of materials that can decrease the morbidity, mortality and hospitalization costs associated with current medical devices, such as indwelling catheters, by reducing thrombosis and infection.
Handa has generated 28 invention disclosures, leading to six issued U.S. patents with 25 pending applications in the U.S. and elsewhere. Many of these inventions are licensed to his startup company, Nytricx, and are in preclinical development while seeking additional funding.
NAI Senior Members will be formally inducted at the NAI annual meeting on June 25-27 in Washington, D.C. A full list of NAI Senior members is available on the website.
It’s intended to strengthen public health response to infectious disease threats and support workforce development
The University of Georgia and the Georgia Tech Research Institute (GTRI) in partnership with the Georgia Department of Public Health, have received a five-year, $17 million cooperative agreement from the Centers for Disease Control and Prevention to establish a Pathogen Genomics Center of Excellence.
The center is intended to strengthen public health response to infectious disease threats and support public health workforce development.
The award is part of a $90 million investment by the CDC to build a network of centers in five states. Each Pathogen Genomics Center of Excellence (PGCoE) consists of a health department and one or more academic institutions.
The Georgia Department of Public Health will provide overall leadership and prioritization of center efforts. UGA will be leading the effort to translate new discoveries into usable data and interventions. GTRI will be leading the operations and implementation arm of the Georgia-based center.
Collectively, this work will be focused on transitioning innovations out of academia and into use at public health departments across the United States.
“We really are trying to learn about outbreak epidemiology, those population-scale processes that are impacting disease spread. Patterns of transmission that are really hard to observe,” said Justin Bahl, an associate professor with joint appointments in UGA’s College of Public Health and College of Veterinary Medicine. Bahl will be leading the project at UGA.
Molecular epidemiology uses genomic data to learn how pathogens like the SARS-CoV-2 virus move and infect people within populations. This work is what allows scientists to trace the origins of a virus strain and track its spread as it moves from place to place.
Bahl says that adding pathogen genomic data to traditional epidemiological surveillance could dramatically strengthen the public health workforce’s ability to prevent and mitigate local outbreaks.
“We’re going to be able to work closely with these departments of public health, connect the genetic data from the pathogens to the actual population characteristics. That provides information for those public health practitioners to direct their interventions,” he said.
Researchers from GTRI will support the data management, data analytics and information security needs of the center toward a goal of providing disease information in real-time to public health organizations at the local and state levels.
“We want to support public health departments in getting out ahead of pathogen trends,” said Rebecca Hutchins, chief engineer in GTRI’s Advanced Concepts Laboratory. “With COVID-19, we had to stand up new genomic sequencing and data analytics capabilities. In future infectious disease outbreaks, this center will allow us to pivot from a reactive mode – responding to what the virus is doing – to a more proactive mode aimed at quickly taking preventive measures.”
By facilitating ongoing collaborations, the network will help ensure that academic researchers, public health agencies and others involved in a pandemic response will have systems in place to share crucial information and apply consistent data-gathering techniques. Sampling and sequencing innovations developed at the center will be shared with other centers and public health agencies nationwide.
“The true measure of success for the Georgia-based Pathogen Genomics Center of Excellence will be the increased capabilities of public health departments across the United States to prevent and respond to infectious disease outbreaks,” said Hutchins.
“We have a very strong infectious disease research community here at UGA, especially with pathogen transmission modeling, and a lot of experience with integrating different types of data,” said Bahl. “There are probably not many other places that have the amount of expertise that’s here.”
This work will build on the innovative tools generated from UGA’s interdisciplinary infectious disease research centers, including the Center for Vaccines and Immunology, Center for Influenza Disease Emergence Research, and the Center for Ecology of Infectious Diseases.
“And now we have this center that is focused on taking all this wealth of information that we’ve generated and these new approaches and methodologies, and apply them at the population level, to inform public health response,” said Bahl.
This project, which will establish the Center for Applied Pathogen Epidemiology and Outbreak Response, is the fourth major funding investment the university has received in the past five years.
Bahl is optimistic that this investment in pathogen genomics will create more pathways for data sharing among scientists and practitioners and enhance genomic surveillance nationwide.
“We’re active, and we’re trying to learn more, translate more to the public health labs and be better prepared collectively to respond to these new threats,” said Bahl. “This investment is about trying to strengthen partnerships with public health. We’re part of that effort, building up public health across the board.”
Team members include Tonia Parrott at the Georgia Department of Public Health and Amy Winter, Erin Lipp, Travis Glenn, Magdy Alabady, Liang Liu, Pej Rohani, Susan Sanchez, Mandev Gill and John Drake from UGA. They will be joined by Rebecca Hutchins and True Merrill at GTRI. The network across Georgia also includes researchers from Emory University, Georgia State University and Augusta University Medical College of Georgia.
It’s intended to strengthen public health response to infectious disease threats and support workforce development
The University of Georgia and the Georgia Tech Research Institute (GTRI) in partnership with the Georgia Department of Public Health, have received a five-year, $17 million cooperative agreement from the Centers for Disease Control and Prevention to establish a Pathogen Genomics Center of Excellence.
The center is intended to strengthen public health response to infectious disease threats and support public health workforce development.
The award is part of a $90 million investment by the CDC to build a network of centers in five states. Each Pathogen Genomics Center of Excellence (PGCoE) consists of a health department and one or more academic institutions.
The Georgia Department of Public Health will provide overall leadership and prioritization of center efforts. UGA will be leading the effort to translate new discoveries into usable data and interventions. GTRI will be leading the operations and implementation arm of the Georgia-based center.
Collectively, this work will be focused on transitioning innovations out of academia and into use at public health departments across the United States.
“We really are trying to learn about outbreak epidemiology, those population-scale processes that are impacting disease spread. Patterns of transmission that are really hard to observe,” said Justin Bahl, an associate professor with joint appointments in UGA’s College of Public Health and College of Veterinary Medicine. Bahl will be leading the project at UGA.
Molecular epidemiology uses genomic data to learn how pathogens like the SARS-CoV-2 virus move and infect people within populations. This work is what allows scientists to trace the origins of a virus strain and track its spread as it moves from place to place.
Bahl says that adding pathogen genomic data to traditional epidemiological surveillance could dramatically strengthen the public health workforce’s ability to prevent and mitigate local outbreaks.
“We’re going to be able to work closely with these departments of public health, connect the genetic data from the pathogens to the actual population characteristics. That provides information for those public health practitioners to direct their interventions,” he said.
Researchers from GTRI will support the data management, data analytics and information security needs of the center toward a goal of providing disease information in real-time to public health organizations at the local and state levels.
“We want to support public health departments in getting out ahead of pathogen trends,” said Rebecca Hutchins, chief engineer in GTRI’s Advanced Concepts Laboratory. “With COVID-19, we had to stand up new genomic sequencing and data analytics capabilities. In future infectious disease outbreaks, this center will allow us to pivot from a reactive mode – responding to what the virus is doing – to a more proactive mode aimed at quickly taking preventive measures.”
By facilitating ongoing collaborations, the network will help ensure that academic researchers, public health agencies and others involved in a pandemic response will have systems in place to share crucial information and apply consistent data-gathering techniques. Sampling and sequencing innovations developed at the center will be shared with other centers and public health agencies nationwide.
“The true measure of success for the Georgia-based Pathogen Genomics Center of Excellence will be the increased capabilities of public health departments across the United States to prevent and respond to infectious disease outbreaks,” said Hutchins.
“We have a very strong infectious disease research community here at UGA, especially with pathogen transmission modeling, and a lot of experience with integrating different types of data,” said Bahl. “There are probably not many other places that have the amount of expertise that’s here.”
This work will build on the innovative tools generated from UGA’s interdisciplinary infectious disease research centers, including the Center for Vaccines and Immunology, Center for Influenza Disease Emergence Research, and the Center for Ecology of Infectious Diseases.
“And now we have this center that is focused on taking all this wealth of information that we’ve generated and these new approaches and methodologies, and apply them at the population level, to inform public health response,” said Bahl.
This project, which will establish the Center for Applied Pathogen Epidemiology and Outbreak Response, is the fourth major funding investment the university has received in the past five years.
Bahl is optimistic that this investment in pathogen genomics will create more pathways for data sharing among scientists and practitioners and enhance genomic surveillance nationwide.
“We’re active, and we’re trying to learn more, translate more to the public health labs and be better prepared collectively to respond to these new threats,” said Bahl. “This investment is about trying to strengthen partnerships with public health. We’re part of that effort, building up public health across the board.”
Team members include Tonia Parrott at the Georgia Department of Public Health and Amy Winter, Erin Lipp, Travis Glenn, Magdy Alabady, Liang Liu, Pej Rohani, Susan Sanchez, Mandev Gill and John Drake from UGA. They will be joined by Rebecca Hutchins and True Merrill at GTRI. The network across Georgia also includes researchers from Emory University, Georgia State University and Augusta University Medical College of Georgia.
Jiani Chen of Dr. Justin Bahl’s lab successfully defended her dissertation, “Using computational and statistical strategies to study the evolution and epidemiology of Human Respiratory Syncytial Virus” on Wednesday, November 16, 2022.
Congratulations Dr. Chen!
Michael Francis of Dr. Kaixiong Ye’s lab successfully defended his dissertation, “Nutrigenetics of Polyunsaturated Fatty Acids and Vegetarianism” on Thursday, November 17, 2022.
Congratulations Dr. Francis!
Please join me in congratulating Karen Gonzalez on receiving the American Association of Hispanics in Higher Education (AAHHE) Graduate Student Fellowship 2023!
Please join me in congratulating Lasya Penumarthi on being selected as one of the recipients the George Hugh Boyd Memorial Scholarship for the 2022-2023 academic year.
Holly Bik, assistant professor in the University of Georgia Franklin College of Arts and Science department of marine sciences with a joint appointment in UGA’s Institute of Bioinformatics, has received a grant from the National Science Foundation Faculty Early Career Development Program (CAREER) to study the biodiversity, evolution, and ecology of free-living marine nematodes and their host-associated microbiomes.
The five-year, $1 million CAREER grants, among the most prestigious awarded by the NSF, support early-career faculty who exhibit promise as both researchers and teachers, and whose work has the potential to advance their field and their institution.
Bik’s expertise stands at the interface between biology and computer science, using biological questions and evolutionary hypotheses to drive the development and refinement of –Omic approaches focused on marine microbes.
Her NSF-supported project will represent the first large-scale investigation that collects molecular data across marine habitat gradients, including across salinity levels, water depths, and and gradients of environmental stressors such as pollution and oxygen availability. The study will provide a comparative dataset for the existing body of nematode taxonomic studies to advance knowledge of the structure and function of seafloor marine ecosystems.
“Nematode worms are populous in sediment habitats worldwide, from coastal estuaries to deep-sea methane seeps, though little is known regarding their interactions with sediment geochemistry and bacteria and archaeal members of the community,” Bik said. “We want to better understand how they interact with those microbial communities, as well as utilize new computational frameworks and data visualization tools to advancing the pace of environmental microbiome studies.”
“Dr. Bik is well-recognized by the scientific community for her development and refinement of high-throughput sequencing and novel computational tools to study the ecology and evolution of microbial taxa from diverse environments,” said Daniela Di Iorio, professor and head of the department of marine sciences. “Students have shown a keen interest in learning these advanced computational methods used to study complex biological ecosystems and I am confident that she will continue to provide excellent student research and educational experiences at UGA and beyond, and that this CAREER grant will aid Dr. Bik in achieving those goals.”
Bik’s research will use a novel approach that combines traditional light microcopy, environmental DNA sequencing, and single-worm genome sequencing in order to advance scientific knowledge of free-living nematodes and their ecological and evolutionary roles in marine habitats worldwide. The resulting datasets will produce an important baseline of global nematode biodiversity in shallow-water and deep-sea marine habitats, and illuminate “dark areas” in the Nematode Tree of Life – lineages which are currently poorly sampled. The project combines interdisciplinary research themes spanning marine nematode systematics, bioinformatics, and microbial ecology, with a strong integration of computational training and science communication for undergraduate and graduate students across all project aims.
“I’m absolutely thrilled to receive an NSF CAREER award that will advance my lab’s research merging classical nematode taxonomy, microbial ecology, and benthic marine science,” Bik said. “I’m especially excited to incorporate bioinformatics training into graduate and undergraduate curricula at UGA, which will help students develop strong data science skills that will be valuable for their future career paths.”
Image courtesy of Holly Bik.
By: Alan Flurry, UGA- Franklin News
Douda Bensasson, associate professor in the Department of Plant Biology, has pioneered a new understanding that wild plant environments serve as reservoirs for a common fungal pathogen of humans. Her laboratory discovered that old oak trees harbor Candida albicans, which is responsible for potentially lethal yeast bloodstream infections in humans. Scientists thought that this species could only thrive in warm-blooded animals, but she showed that three genetic strains in oaks were more closely related to strains isolated from warm-blooded animals like humans than to other oak strains. The high genetic diversity found in oak strains implies that C. albicans has moved between humans and oaks multiple times and that plants could be the pathogen’s ancestral source. Her work in isolating, characterizing, genome sequencing and analyzing C. albicans has reshaped her field. She has inspired researchers worldwide to explore the evolution of this and potentially other human pathogens in wild plants.
Wayland Yeung of Dr. Natarajan Kannan’s lab has successfully defended his dissertation titled, “Traditional representation learning approaches for protein sequence analysis” on Friday, April 15, 2022. Congratulations Dr. Yeung!
Yuan Feng of Dr. Shaying Zhao’s lab has successfully defended his dissertation, “Canine MHC-I Genotyping and Diversity Landscape” on Wednesday, April 13, 2022. Congratulations Dr. Feng!
Michael Skaro of Dr. Jonathan Arnold’s lab had successfully defended his dissertation, “Applications of machine learning in omics and computer vision” on Monday, April 11, 2022. Congratulations Dr. Skaro!
(L to R) Patricia Yager, Jessica Kissinger, James E. Byers.
Three University of Georgia faculty have been named Fellows of the American Association for the Advancement of Science.
In a tradition stretching back to 1874, these individuals are elected annually by the AAAS Council for their extraordinary achievements leading to the advancement of science. Fellows must have been AAAS members for at least four years.
“Researchers are elected Fellows of the AAAS by their peers in recognition of significant contributions to their field,” said Karen Burg, vice president for research. “As we expand our research and innovation ecosystem, it’s exciting to see our faculty continue to be honored for their superb scholarship. I congratulate all of them on this wonderful achievement.”
The 2021 class of AAAS Fellows includes 564 scientists, engineers and innovators spanning 24 scientific disciplines who are being recognized for their scientifically and socially distinguished achievements. The new Fellows will be honored at the annual AAAS meeting in Philadelphia, Feb. 17-20. Along with the rest of their 2021 class, UGA’s three new Fellows will receive an official certificate and a gold and blue rosette pin whose colors represent science and engineering.
Including these three, 37 faculty at UGA are Fellows of the American Association for the Advancement of Science.
UGA’s 2021 AAAS Fellows are:
James E. Byers: Meigs Distinguished Teaching Professor and associate dean for research and operations in the Odum School of Ecology, Byers was selected for distinguished contributions to the field of ecology, particularly in invasion biology, parasite ecology, ecosystem engineering and range boundaries in marine environments, as well as excellence in teaching.
Jessica Kissinger: Distinguished Research Professor of genetics in the Franklin College of Arts and Sciences, Kissinger was selected for distinguished contributions to the field of the evolution of infectious diseases, particularly for bioinformatics approaches.
Patricia Yager: Professor of marine science in the Franklin College, Yager was selected for outstanding work on climate-driven processes and their impact on marine ecosystems.
To view a list of all AAAS Fellows from UGA, visit the Office of Research website.
Bioinformatics Professor Ying Xu has been elected as a 2022 Institute of Electrical and Electronics Engineers Fellow for contributions to knowledge discovery from biological data.
Xu Tan of Dr. Andrew Paterson’s lab has successfully defended his dissertation, “Comprehensive analysis of resistance gene evolution, structural variation and recent genome rearrangement in plant genomes” on Wednesday, December 15, 2021. Congratulations Dr. Tan!
Research Corporation for Science Advancement and the U.S. Department of Agriculture have awarded a total of $1.25 million to 10 multidisciplinary teams of early career scientists — including Liliana Salvador, Infectious Diseases & Institute of Bioinformatics, University of Georgia — in the first year of the Scialog: Mitigating Zoonotic Threats initiative. Each of the 25 individual awards is $50,000.
Awards will go to 20 early career researchers from a variety of institutions, including two U.S. Department of Agriculture agencies working together at the National Bio and Agro-Defense Facility — the Animal and Plant Health Inspection Service and the Agricultural Research Service. The funded projects, to launch new research in the detection and mitigation of emerging animal-borne infectious diseases, include seven new partnerships between USDA and academic scientists.
Shunhua Han of Dr. Casey Bergman’s lab has successfully defended his dissertation, “Novel computational strategies for the analysis of transposable elements in Drosophila cell culture genomes.” on Friday, November 19, 2021. Congratulations Dr. Han!
Sara Shen of Dr. Art Edison’s lab has successfully defended her dissertation, “Characterization of Mesenchymal Stem Cells Using Metabolomics” on Tuesday, November 16, 2021. Congratulations Dr. Shen!
Yinwen Zhang of Dr. Bob Schmitz’ lab has successfully defended her dissertation, “Origination, Distribution, and Implication of Spontaneous Epialleles” on Friday, November 12, 2021. Congratulations Dr. Zhang!
Research News
Supercomputer-powered 3D imaging of roots helps develop climate change-adapted plants
Composite artwork of a photograph and a reconstructed 3D model of the same maize root.
November 3, 2021
The shoots of plants get all the glory, with their fruit and flowers and visible structure. But it’s the portion that lies below the soil — the branching, reaching arms of roots and hairs pulling up water and nutrients — that has deep implications for the future, according to plant physiologist and computer scientist Alexander Bucksch of the University of Georgia.
The ability to grow enough food to support the population despite a changing climate, and soil’s ability to fix carbon from the atmosphere, are critical to human and other species’ survival. The solutions, Bucksch believes, lie in the quality of roots.
“When there is a problem in the world, humans can move. But what does the plant do?” said Bucksch. “It says, ‘Let’s alter our genome to survive.’ It evolves.”
Until recently, farmers and plant breeders didn’t have a good way to gather information about the root system of plants or make decisions about the optimal seeds to grow deep roots.
In a paper published in Plant Physiology, Bucksch and colleagues introduce Digital Imaging of Root Traits, or DIRT/3D, an image-based 3D root phenotyping platform that can measure 18 architecture traits from mature field-grown maize root crowns.
The system reliably computed all traits, including the distance between whorls and the number, angles and diameters of nodal roots for 12 contrasting maize genotypes with an 84% agreement when compared to manual measurements. The research is supported by the U.S. National Science Foundation.
Scientists who use DIRT/3D to image roots will soon be able to upload their data to a service called PlantIT that can perform the same analyses that Bucksch and his collaborators describe in their paper. PlantIT provides information on a wide range of traits from young nodal root length to root system eccentricity. These data let researchers and breeders compare the root systems of plants from similar or different seeds.
The framework is made possible by massive number-crunching capabilities behind the scenes provided by the Texas Advanced Computing Center.
Gerald Schoenknecht, a program director in NSF’s Division of Integrative Organismal Systems, added, “This is a great example how the interdisciplinary application of high-performance computing on plant physiology enables new experimental approaches and provides new biological insights.”
— NSF Public Affairs, Researchnews@nsf.gov
Tuesday, October 5, 2021 – 10:22am
By:Alan Flurry
Sugars in our bodies, and in nearly all living organisms, are synthesized and built by a large family of proteins called Glycosyltransferases (GTs) that adopt unique three-dimensional structures and folds to perform a diverse array of cellular functions. Understanding the structure and fold of these proteins is an important first step towards characterizing their functions, which is critical for developing effective glycovaccines and for improving crop yields and sustainable biofuels through the synthetic design of glycoproteins with desirable functional properties.
However, despite significant efforts in the structural characterization of GTs, mapping the full functional and fold landscape remains a challenge because of the large and diverse nature of these proteins and the cost and time associated with their structural characterization.
To address this challenge, an inter-disciplinary team of UGA researchers have leveraged recent advances in deep learning to predict and classify GT folds from primary sequences with high accuracy. Deep learning is a branch of artificial intelligence (AI) that uses interconnected artificial neural networks to automatically find patterns in large datasets.
The methods are designed to mimic the learning process of the human brain and are widely used in a range of applications from marketing to self-driving cars. However, their application in biology is only being realized, thanks to the massive amounts of biological data generated from gene sequencing studies.
“With over a half million GT sequences available, investigating the relationships connecting primary sequence, fold and function is a problem well poised for the application of deep learning methods” said Natarajan Kannan, professor of biochemistry and molecular biology and the Institute of Bioinformatics in the Franklin College of Arts and Sciences who led the research team.
Their work, published in the journal Nature Communications, reports the development of an “interpretable” deep learning model for predicting GT fold and function from primary sequences.
“One unique aspect of our model is that it is simple and interpretable, meaning that the neural network can be tracked by identifying the neurons that get activated during the learning process, which, in turn, helps in the biological interpretation of the prediction and classification process,” said Sheng Li, assistant professor of computer science and co-author on the study. “This is conceptually different from most existing deep learning models that operate as a “black box.”
“By predicting GTs that can adopt novel folds, this study provides a range of structural templates along with their crucial functional features for the design and synthesis of novel GTs for various applications,” said Kannan, who received a Maximizing Investigator Research Award, or MIRA, from the National Institute of General Medical Sciences in March 2021.
“This method promises to be a valuable tool for the glycobiology community and marks a significant milestone towards leveraging the full potential of GTs in biomedicine and other industries. It’s one great advantage to receiving the NIGMS award, which provides us with the flexibility to move in new and exciting directions,” he said.
The award and the new study help support interdisciplinary graduate training in the Institute of Bioinformatics and the department of computer science, as well build new synergies with campus-wide AI initiatives at UGA.
Image: Figure 2 from the study. Dots represent 2D UMAP projection of features for individual sequences.
Chronicles Tagging:
Researchers all over the world will have access to the University of Georgia’s expertise in nuclear magnetic resonance, or NMR, thanks to a new infrastructure funded by a $40 million grant from the National Science Foundation.
The Network for Advanced Nuclear Magnetic Resonance, or NAN, will allow researchers to access ultra-high field nuclear magnetic resonance spectrometers to study the structure, dynamics and interactions of biological systems and small molecules. The project is led by the University of Connecticut School of Medicine in partnership with UGA and the University of Wisconsin.
“This is much more than just a new expensive instrument—it’s an entirely different way of thinking about doing NMR,” said Art Edison, co-principal investigator and Georgia Research Alliance Eminent Scholar. “Once we started to think in those terms, a lot of ideas emerged. For example, we want to create an easy way for scientists to discover what is available to them, even if they aren’t NMR experts themselves. We also realized that everyone has the same problems dealing with data: saving it, processing it, analyzing it and depositing it into public databases. Centralizing this would be much more efficient.”
Edison teamed with colleagues at UConn and UW to develop the concept for NAN, which has three primary goals: to provide institutional researchers across the country easy access to the most powerful instruments, simplify the discovery and use of NMR resources, and foster good data stewardship. It will allow researchers across the U.S. to expand their own biomedical research study findings and collectively contribute any new scientific insights to the evolving NAN knowledge bases.
Researchers will be able to visit or deliver their samples for analysis using state-of-the-art 1.1 GHz instruments located in Athens, Georgia, and Madison, Wisconsin. Both instruments, as well as the large number of existing instruments at all three locations, will be linked to a central hub based at UConn Health in Farmington, Connecticut, that will assist discovery and scheduling, host knowledge bases with information on optimal experiment design, and securely archive the collected data.
“This new infrastructure, along with the network of scientists to support it, will advance research in biological sciences across the country through innovative experimentation and new biological insights,” said NSF Assistant Director for Biological Sciences Joanne Tornow.
The network will be led by UConn’s Jeffrey C. Hoch, along with Edison and co-principal investigators Katherine Henzler-Wildman and Chad Rienstra from the University of Wisconsin.
“Thanks to NSF’s funding, our new network will empower researchers to have open access to the latest advanced NMR technology with the necessary computational power to fuel future discoveries,” said Hoch, professor of molecular biology and biophysics at UConn School of Medicine. “Any researcher nationwide with a laptop will be able to make use of these powerful NMR instruments, methods and online data bank.”
NAN’s central hub at UConn has a computational resource that brings NMR processing and software into one location, and they’ll also be in charge of the primary database where people will deposit NMR data. UGA provides expertise in metabolomics and protein structural biology, especially with complex carbohydrate modifications—areas that were pioneered by Jim Prestegard, emeritus professor and GRA Eminent Scholar at the university’s Complex Carbohydrate Research Center. Edison is a member at the CCRC as well as the Institute of Bioinformatics.
“We are building two knowledge bases for NAN in these areas, and these will be designed to make it easier for non-experts to use our NMR resources to solve important problems,” said Edison, professor of biochemistry and molecular biology and genetics in the Franklin College of Arts and Sciences. “This is not going to be easy, but will have great impact.”
Edison’s field is metabolomics, and the overall goal is to measure metabolites in biological systems like human disease, plants and microbes. NAN will benefit collaborations across campus in areas like cell manufacturing, dog and cat health and nutrition, carbon cycling in the ocean, and basic biology of microbes. There is also potential for facilitating drug discovery by learning the shape and dynamics of proteins and carbohydrates, according to Edison. All of these areas are central to research in precision medicine.
“The University of Georgia’s partnership in this significant national project underscores our commitment to advancing discovery in a range of critically important fields,” said S. Jack Hu, the university’s senior vice president for academic affairs and provost. “We thank Georgia Research Alliance Eminent Scholar Dr. Art Edison for his national leadership on this project.”
UGA will also play an important role in connecting NAN with HBCUs.
“We have several strong relationships with HBCUs that we will build on to use NAN to help underrepresented students have more advanced NMR resources available for their research,” Edison said.
This grant award is part of NSF’s Mid-Scale Research Infrastructure II program, an NSF-wide effort to meet the research community’s needs for modern research infrastructure to support science and engineering research. More information about the Mid-Scale Research Infrastructure-2 program supporting the Network for Advanced NMR project can be found at nsf.gov.
Source: UGA Columns, JUN 16, 2021, https://news.uga.edu/uga-part-of-40m-grant-for-nmr-network/?utm_source=digital-issue&utm_medium=email&utm_campaign=columns-20210628
(Photo by Dorothy Kozlowski)
University of Georgia faculty member Natarajan Kannan is a recipient of a highly prestigious Maximizing Investigator Research Award, or MIRA, from the National Institute of General Medical Sciences. The MIRA award is intended to provide investigators with greater stability and flexibility in funding to enhance scientific productivity and make important scientific breakthroughs. The program funds research by the nation’s most highly talented and promising investigators.
Kannan, professor of biochemistry and molecular biology in the Franklin College of Arts and Sciences and the Institute of Bioinformatics, will use the $2 million award over a period of five years to map the complex relationships connecting sequence and function in biomedically important gene families such as protein kinases.
A large family of enzymes, protein kinases function as molecular switches in most living organisms by turning “on” and “off” cellular signals at the right place and time. Abnormal functioning of these proteins in our cells is causally associated with diseases such as cancer, diabetes and neurological disorders. This project will answer fundamental questions related to protein kinase functions in disease and normal states and develop new tools to predict disease phenotypes from genotypes. In so doing the project will accelerate the targeting of these proteins for drug discovery and personalized medicine. The MIRA award also provides the flexibility to extend the specialized tools and approaches developed for the study of kinases to other gene families such as glycosyltransferases, which is a major area of focus in the Complex Carbohydrate Research Center at UGA.
Predicting disease phenotypes from genotypes is a grand challenge in biology and personalized medicine. Kannan’s evolutionary systems biology group is focused on addressing this challenge using a combination of computational and experimental approaches that incorporate techniques from diverse disciplines including biochemistry, bioinformatics, cell biology and computer science.
“Professor Kannan’s work is so impactful because he is not afraid to tackle the big questions. Furthermore, he freely shares his unique expertise in collaborations that help make for new discoveries in other labs as well,” said Christopher West, professor and head of the department of biochemistry and molecular biology. “He previously received a National Science Foundation CAREER award and the UGA Creative Research Medal in Natural Sciences and Engineering, and the NIH MIRA award is a further tribute to his outstanding contributions. We are lucky to have Professor Kannan as part of our scientific community.”
“We have made important contributions towards uncovering the functional impact of natural and disease variants in biomedically important gene families, and our success is attributable to the interdisciplinary team of highly motivated and talented students, fellows and research scientists working towards a common research goal,” said Kannan. “We are also fortunate to be part of a strong network of national and international collaborators and a highly collaborative research environment at UGA.”
Dr. Walter Lorenz joint publication: Fc γ receptor IIIa/CD16a processing correlates with the expression of glycan-related genes in human natural killer cells.
To read the full article please click HERE.
Travis Glenn, professor of environmental health science in the College of Public Health, has been appointed the new director of the university’s Institute of Bioinformatics. Taking over Jan. 1, Glenn said he is honored to step into this new role and eager to see what lies ahead for IOB in the coming months.
“The future of bioinformatics and computational biology is strong at UGA,” Glenn said. “There is an ever-growing need for faculty and students to be able to manipulate and analyze large datasets.”
Glenn, whose research areas include comparative and environmental genomics, molecular ecology, infectious disease and vectors, has already established a set of goals for the institute.
“First, I would like to expand partnerships across UGA, including the Georgia Informatics Institute, Health Informatics Institute and other interdisciplinary programs,” Glenn said. “Second, we need to enhance training and outreach at UGA via workshops, short and modularized courses, training cohorts, and undergraduate and graduate programs. Finally, I would love to expand research productivity by facilitating partnerships, training, shared resources and recruitment of qualified students and faculty.”
Established in 2002, IOB emerged from a recognition that all life sciences and biotechnology investigators were analyzing vast quantities of data. It has facilitated cutting-edge interdisciplinary research in bioinformatics and computational biology and their applications. The importance of a program like IOB is not lost on Glenn.
“The IOB fosters a community at UGA for all who use computational tools to solve biological problems,” he said. “We advocate for shared resources and interdisciplinary research, teaching and programs. We facilitate coordination and coherence to create a whole that is greater than the sum of the individual parts. I am honored to have the opportunity to work with and for the bioinformatics community at UGA.”
“Advancing technologies in ‘omics’ fields and other areas have produced a deluge of biological data, making the field of bioinformatics indispensable,” said David Lee, vice president for research. “Thanks to the vision of its previous leaders, Ying Xu and Jessie Kissinger, the Institute of Bioinformatics is facilitating studies from plants to animals, including humans, and providing the next generation of life scientists with the necessary skills. I am confident that Travis will continue in their footsteps and provide outstanding leadership for the IOB, a point of pride for UGA, for many years to come.”
Liang-Chin Huang, Wayland Yeung, Ye Wang, Huimin Cheng, Aarya Venkat, Sheng Li, Ping Ma, Khaled Rasheed & Natarajan Kannan
BMC Bioinformatics volume 21, Article number: 520 (2020)
David Montgomery
Graduate Student, Institute of Bioinformatics
Woods Research Lab
Complex Carbohydrate Research Center
IOB graduate student, David Montgomery, will give a online seminar on:
Title: “Finally, a New Approach to Annotating and Finding Carbohydrates in the PDB “
Date: Friday, August 14th, 2020 at 1:30pm
To register please follow the link below:
Webinar @ the Society for Glycobiology
Date: AUG 14th, 2020
Time: starting at 1:30PM
Dr. Jessica Kissinger receives a Fulbright Global Scholar Award to work with Makerere University in Kampala, Uganda.
Congratulations Dr. Kissinger!
Congrats to Xiao Qiu and Michael Skaro for receiving 2020 Innovative and Interdisciplinary Research Grants from the graduate school and to Michael Francis for the 2020 Communication of Research and Scholarship Grant.
Thank you for representing IOB with your applications!
To download a PDF of this news letter click HERE
David Montgomery: COVID-19 collaboration submitted to PLOS Pathogens. The title is: “Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry”.
New York Times
NPR
CGTN
Dr. Alexander Bucksch (is the tenth presenter in the IPPN online webinar.
Title: Computers, Roots & Big Data from the Field: Can new methods identify uncharacterized phenomena in existing data?
To join this webinar on the 10th of April 2020, go on time to Join Zoom Meeting https://zoom.us/j/734731883 Meeting ID: 734 731 883
Dial by your location – Meeting ID: 734 731 883. Find your local number: https://zoom.us/u/abyh97W3SI
IOB faculty member, Dr. Justin Bahl, was recently interviewed on NPR to discuss mutational patterns of the coronavirus. Please see the links below details.
On April 10th 2020 the IPPN – ‘Imaging for phenotyping’-working group will have its 10th online webinar at 10:00 AM Eastern Time (US and Canada) and at 16.00 PM Central European Summer Time.
NB: To enable you to interact now all conferences/ international travels are cancelled because of Corona. The aim of these IPPN webinars is to easily share new research results with everybody interested world-wide.
The 10th presenter is Dr. Alexander Bucksch (University of Georgia) / moderator: Rick van de Zedde (WUR)
To join this webinar on the 10th of April 2020, go on time to Join Zoom Meeting https://zoom.us/j/734731883 Meeting ID: 734 731 883
Dial by your location – Meeting ID: 734 731 883. Find your local number: https://zoom.us/u/abyh97W3SI
Title: Computers, Roots & Big Data from the Field: Can new methods identify uncharacterized phenomena in existing data?
Abstract: The use of mathematical and computational methods in the plant sciences enables two new major areas: The discovery of uncharacterized phenomena in existing phenotyping data and detailing phenotypic measurements beyond the manually achievable. Therefore, plant phenotyping is able to set new breeding targets for rapid increases of grain yields or improved plant functions such as carbon sequestration to lower atmospheric CO2 concentrations. However, the opportunities to phenotype discovery are buried in large amounts of collected phenotyping data that often is only analyzed for one experimental purpose. The computational plant science lab at the University of Georgia makes use of the increased data volume and physical resolution of imaging data to quantify root architecture. In particular, the coupling of high-performance computing with image acquisition systems holds the potential to discover uncharacterized phenotypes that were previously “invisible” to phenotyping researcher. In part, the invisible phenotypes can be attributed to the time-consuming manual evaluation of root phenotypes that resulted in a low coverage of the phenotypic variation. This IPPN webinar will highlight the mathematical challenges in phenotyping root architecture associated with the low coverage phenotypic variation. As a response to these challenges, we introduce computational advances developed at UGA to quantify variation root phenotypes on the population level. Furthermore, the webinar will give a preview of 3D imaging and high-performance computing technologies that will further detail the observed variation of phenotypes from the field.
Bio: Alexander Bucksch received his PhD from the Delft University of Technology in the Netherlands in 2011, where he developed the first algorithm to measure complete tree crowns from laser scanned trees. He then moved as a PostDoc to the Georgia Institute of Technology where he was jointly appointed between the School of Biology and the School of Interactive Computing and began to work on root phenotyping. In 2016, Dr. Bucksch joined the faculty of UGA as an Assistant Professor with joint appointment in the Department of Plant Biology, the Warnell School of Forestry and Natural Resources and the Institute of Bioinformatics. He leads the computational plant science lab which combines computer vision and shape analysis to analyze the topological and geometrical characteristics of plant architecture. The lab is best known for DIRT (Digital Imaging of Root Traits, http://dirt.cyverse.org<http://dirt.cyverse.org/>), which is the world’s largest root phenotyping platform with over 620 users in over 40 countries. Dr. Bucksch is a founding member of the Georgia Informatics Institutes and the Plant Phenomics and Robotics Center at the University of Georgia. He received the 2020 Early Career Award from the North American Plant Phenotyping Network and the NSF CAREER award in 2019 to quantify and simulate the phenotypic spectrum of roots that he presents today.
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To join this webinar on the 10th of April 2020, go on time to
Join Zoom Meeting https://zoom.us/j/734731883 – Meeting ID: 734 731 883
Dial-in by phone by your location – Meeting ID: 734 731 883. Find your local number: https://zoom.us/u/abyh97W3SI
More info about the IPPN Imaging for Phenotyping working group can be found here: https://www.plant-phenotyping.org/ippn_wg_imaging
Earlier recorded webinars can be found here: https://www.plant-phenotyping.org/Imaging-Workgroup-Webinars
UGA’s Institute of Bioinformatics explored Collective Behavior while practicing social distancing, holding its spring symposium online March 20. The decision to go online was an easy one, according to Jonathan Arnold, professor of genetics and co-chair of the event. He’d been following the spread of the coronavirus closely and anticipated that the university might shut down, so early in March he and co-chairs Travis Glenn and Natarajan Kannan decided to take the symposium online. Arnold said the decision relieved the anxiety of their speakers, who would have had to travel from Maryland, California, Texas, Massachusetts, Arizona and Glasgow, Scotland. “It’s also fun,” he said. “It’s a new way of doing things that allows us to reach more people.” The original plan was to host 150 people, but 407 “showed up.” That included students from the country of Jordan, where one of Arnold’s former students is now a professor. “The university is still doing business,” Arnold said. “We just have to find new ways of making it happen that recognize the need for social distancing.”
To view the original article click here.
We are sending a quick updated to the IOB community about the upcoming IOB Symposium scheduled to be held at the University of Georgia Conference Center & Hotel.
The IOB Leadership Team has assessed the Novel Coronavirus situation and out an abundance of caution for everyone’s health & safety, the IOB has adopted a on-line only model for the 2020 Symposium.
Monumental Media will be assisting the IOB in a high-quality virtual broadcast of the Collective Symposium. In addition to the presentations, we will work to include some specific online activities and virtual interactions.
The IOB Symposium is FREE to attend and no additional registration is required. The broadcast will begin with introductions at 9AM, on MARCH 20th via the link below.
Any additional Symposium details, including the event agenda, will be available on the IOB website & sent to registrants via email prior to the event.
The Collective Behavior Symposium is supported by a State-of-the-Art Conference Grant from the Office of the Senior Vice President for Academic Affairs and Provost.
FYI: It is recommended for attendees to test their internet connection prior to the beginning of the broadcast.
You may test your connection by visiting the Monumental Media link above.
Please follow the link(s) below to view each publication:
Name: Michael Francis Year: Third-year PhD Major: Bioinformatics
Name: Sohyun Bang Year: First-year PhD Major: Integrated Life Sciences
Submission: The Music of Life – Musical Composition
Prize: $350
Commentary: In their entry “Music of Life”, Michael Francis and Sohyun Bang take the code of living things and re-codify it as musical notation. That is, they turn a DNA sequence into a song. Using the Python programming language and music production software Ableton Live, Michael and Sohyun transform the sterile string of As, Cs, Gs, and Ts (letters that represent the nucleotides that make up DNA) into an auditory experience reminiscent of the compositions of the 1960s foremost minimalist Steve Reich. Our judges were delighted by their playful artistic choices, like extracting the DNA sequence from AVPR1A, the gene associated with musical ability. To complement the song, the entrants offer another video wherein they explain their creative process, which could serve as a helpful starting point for other researchers who are interested in sonifying their own data. Written by contest judge Ariel Ackerly
To view original announcement please click: HERE
Dr. Kannan receives new NIH funding to develop cutting edge informatics tools for mining the druggable genome. His group will develop a data analytics framework for mining understudied “dark” kinases in collaboration with Dr. Kochut (CS, UGA).
Brigitte Hofmeister successfully defended her dissertation, “Stability of trans-generational and intra-organismal epiallele inheritance in plants” on July 15, 2019.
Congratulations Dr. Hofmeister!
PhD Students Ruijie Xu and Lambodhar Damodaran have been awarded Interdisciplinary Disease Ecology Across Scales (IDEAS) Fellowships which will fund their research beginning in August 2020. Congratulations Ruijie and Lambo! http://ideas.ecology.uga.edu/application/
PhD students Ruijie Xu and Jiani Chen have been awarded scholarships to attend the 2019 Summer Institute in Statistical Genetics at the University of Washington from July 10-18. Congratulations Rachel and Jiani! https://www.biostat.washington.edu/suminst/sisg
PhD student Dave Montgomery has been accepted into the Glycoscience Training Program at the Complex Carbohydrate Research Center. Congratulations Dave! http://glycomics.ccrc.uga.edu/gtp/
