I’m a microscopy enthusiast completing my Postdoc at the Stowers Institute in Kansas City, MO, where you’ll find me diving into the world of planaria, exploring the biological question of regeneration, the related questions of data organization and visualization in the Sánchez Alvarado Lab.
As a Ph.D. student in the Peifer Lab, I was interested in how cells coordinate adhesion among neighbors with individual cytoskeletal rearrangements to allow highly dynamic tissue rearrangements required in normal development and homeostasis. Specifically, I worked in Drosophila embryos using light microscopy to understand regulation of the actin cytoskeleton by a suite of proteins which modulate actin filament assembly and architecture to produce both cell movement and protrusions required by the cell for probing the local environment. It sounds interesting, but is even more interesting to look at though live confocal microscopy. Check it out here.
After spending time looking at how cells interact in the context of large developmental events with light microscopy, I naturally became interested in wound healing and regeneration and the other side of microscopy, electron microscopy. Planaria are excellent models for regeneration, as they are able to regrow missing organs and reestablish their full body plan in two weeks after being cut in any orientation and in many pieces*. From a new gut to a new brain, to new skin, planarians are incredibly competent at regrowing themselves. This regeneration process is carried out by stem cells, called neoblasts. I’m interested in where these neoblasts are, who their neighbors are, and how we can identify and visualize them using 3D electron microscopy (3D EM).
In order to responsibly make sense of and reuse big data that comes from 3D EM, we need to make sure that folks (1) understand the planarian anatomy (at a sliding scale from histology to EM) and (2) can use and repurpose any organizational and didactic system we use to teach and organize planarian anatomy. To do this we generated the Planarian Anatomy Ontology(PLANA) which defines planarian anatomy terms but, importantly, connects each term and puts it in relationship, or a context, to other terms. For example the ontology can tell you what a neoblast is and which papers from 2005-2019 use that term, but it also can tell the categorical, spatial and temporal relationships it has to other terms. For example, a neoblast is a stem cell (categorical relationship) and starts existing at stage 5 of embryogenesis (temporal relationship). This type of anatomical data organization is a tool that other big data can use as long as it’s related to the planarian anatomy. You can explore PLANA here. And you can read about it here.
*1/279th of worm is the smallest documented piece that can regenerate, determined by Morgan in 1898. (This is about 10,000 cells)
Nights and weekends give the right side of my brain a chance to stretch, making art.