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Category: News

Listing of news from the Institute of Bioinformatics at University of Georgia

Shunhua Han Successfully Defends Dissertation

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!

IOB Faculty News | Alexander Bucksch, NSF Research News: Adapting plant roots to a hotter planet could help ease pressure on food supply

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.

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

Dr. Kannan: New UGA study maps the structural diversity of sugar building enzymes using AI

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 studyDots represent 2D UMAP projection of features for individual sequences.

 

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UGA’s Art Edison is co-principal investigator of $40M NSF grant for NMR network

Science & Technology

UGA part of $40M grant for NMR network

GRA Eminent Scholar Arthur Edison in the NMR Facility at the CCRC. (Photo by Andrew Davis Tucker/UGA)

UGA’s Art Edison is co-principal investigator for the NSF-funded project

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

Kannan receives $2M NIH MIRA award

University of Georgia faculty member Natarajan Kannan

(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.”

 

 

Glenn named new Institute of Bioinformatics Director

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.”