Seminar Detail

CBCB Seminar

November 4, 2024 3:30 PM

Ammon-Pinizzotto Biopharmaceutical Innovation (BPI) Building
Conference Room 140

Unconventional signals discovered in plasmodesmal targeting: Lessons from machine learning

Jung-Youn Lee, PhD

Professor of Plant Cell Biology
Department of Plant and Soil Sciences
University of Delaware

Abstract: Malfunction in cell-cell communications often leads to detrimental diseases or cancer in humans. Similarly, cell-cell communication is vital to health and survival of plants. In plants, direct communication between adjacent cells occurs through plasmodesmata, membrane-lined cytoplasmic membrane nanopores. Numerous proteins including those derived from microbial pathogens are found to target plasmodesmata to localize there or translocate through, and these activities are critical for normal physiology, development and immunity. However, conventional bioinformatics approaches failed to help identify any conserved domains or motifs shared by those proteins and the question remained unresolved. In collaboration with Dr. Li Liao’s group at UD CIS, we took an approach combining cell and molecular biology and machine learning approaches. This approach was in a way counterintuitive or unconventional because machine learning requires “ground truths” from a wealth of experimentally validated data, which we did not really have. Regardless, we were able to overcome this dilemma using concerted intuition and a few experimental molecular data and supervised, iterative machine learning, eventually discovering unconventional targeting signals. This study showcases how machine learning can uncover subtle biological patterns that elude traditional sequence analysis methods, but also what machine learning requires for a successful learning, particularly in cases with limited training examples. I will discuss the challenges, strategies, and lessons learned from our study as well as the broader implications for predicting protein targeting in complex cellular contexts from a biologist’s perspective.

Short bio: Dr. Jung-Youn Lee is a Professor of Plant Cell Biology in the Department of Plant and Soil Sciences at UD and a resident faculty member of the Delaware Biotechnology Institute, where she is also serving as interim director. She has a joint appointment in Biological Sciences and is an affiliated faculty member of the Chemistry-Biochemistry Interface training program. A biochemist by training and self-taught cell biologist, she studies one of the most challenging biological problems: plasmodesmata. She has trained numerous students and postdoctoral fellows and published her findings in Science, Nature Communications, Nature Plants, The Plant Cell, among other journals. She has served on several editorial boards and is currently serving as a Senior Editor for The Plant Cell. She has served as the President of the Mid-Atlantic section of the American Society of Plant Biologists and as a UD NSF-ADVANCE Faculty Fellow