Shannon Johnson Dissertation Defense

February 10, 2022
11:00am ET

Dissertation Title: Simultaneous, Large Multi-Gene Delivery for Implementation of Fluorescent Reporter Spatial Multiplexing to Image Signaling Pathways


In order to study intricate, multifaceted biological systems, one must be able to measure numerous cellular activities in real-time. Today, many intracellular, genetically encoded sensors provide a readout in living cells using fluorescent proteins. Spectral multiplexing has been attempted by engineering sensors to each have a unique spectrum that does not overlap with other sensors to allow for simultaneous recording of multiple signals in a single physiological cascade.  However, the problem with spectral multiplexing is the large degree of spectral overlap from the broad shape of the sensor’s spectrum that leads to a blended signal masking which data belongs to which molecule.  This dissertation describes the concept of spatial multiplexing to circumvent the limitations of spectral multiplexing, the challenges of designing a system to deliver multiple reporters simultaneously in culture, and the attempt to teach resilience in developing tools for understanding the nervous system in a 14-week course.  

By fusing a fluorescent reporter to a pair of self-assembling peptides or a self-assembling RNA-protein pair, reporters could be stably clustered within cells at random points, distant enough to be resolved by a microscope, but close enough to spatially sample the relevant biology. These clusters, called signaling reporter islands (SiRIs), can be modularly designed and permit a set of fluorescent reporters to be efficiently adapted for simultaneous measurement of multiple points in a signaling pathway within single cells.  SiRIs for indicators of second messengers and kinases were created to image up to five signals at once in a single living neuron.  This introduces the need to express multiple genes in the same cell, but the probability of multiple plasmids entering the same cell for simultaneous expression is lowered as the number of plasmids increases.  Therefore, means of expressing multiple SiRI genes in a single plasmid backbone were evaluated.  Lastly, a record is shared of the process used to develop and implement a digital learning experience for teaching the place of failure in research and development.

Committee members: 

Ed Boyden, PhD
Professor of Media Arts and Sciences

Simmie Foster, MD, PhD
Instructor at the Harvard Medical School
and Boston’s Children Hospital

Shuguang Zhang, PhD
Principal Research Scientist
in Media Arts and Sciences

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