Caltech Young Investigators Lecture

Abstract: How living organisms generate spatial patterns of gene expression is an area of particular interest to synthetic biologists for applications from biomaterials to regenerative medicine. In this talk, I introduce my research into the theory and practice of multicellular gene expression patterning using tools from signal processing and dynamical systems. First I discuss patterning atop spatially varying inputs, focusing on a framework that represents cellular networks as spatial filters that amplify or attenuate spatial frequency components in the input. I challenge the notion that instability—which may be difficult to engineer biologically—is necessary for spontaneous patterning. Next I discuss my work with synthetic biologists to bring theory into practice, specifically an experimental testbed where physical communication among living cells is substituted with light inputs calculated in silico based on real-time gene expression levels. The setup achieves spontaneous checkerboard patterning in quantitative agreement with mathematical predictions. I conclude by encouraging further work that applies engineering theory and techniques to biological systems, both natural and synthetic.

Bio: Melinda Liu Perkins is a postdoctoral fellow with Justin Crocker and Eileen Furlong at the European Molecular Biology Laboratory in Heidelberg, Germany, where she aims to bring analytical tools from engineering theory into the biological community. Her current research combines mathematical modeling and synthetic biology to investigate how genes turn on and off in developing fruit fly embryos. She is particularly interested in how the dynamics of protein binding to DNA and subsequent activation or repression of single genes affect entire genetic networks, from transient to steady-state behavior. Prior to joining EMBL in 2020, Mindy completed her Ph.D. in Electrical Engineering at the University of California, Berkeley, advised by Murat Arcak. She received the department's Leon O. Chua Award for achievement in nonlinear science in recognition of her doctoral work in biological patterning.

Please contact Diana Bohler for the Zoom link.

This talk is part of the Caltech Young Investigators Lecture Series, sponsored by the Division of Engineering and Applied Science.