Education & Certifications

  • Master of Science, Stanford University, BIOE-MS (2021)
  • BS, Massachusetts Institute of Technology, Computer Science and Molecular Biology (2018)

Contact

Additional Info

  • Mail Code: 4245

Lab Affiliations

All Publications

  • A genetic and microscopy toolkit for manipulating and monitoring regeneration in Macrostomum lignano. Cell reports Hall, R. N., Li, H., Chai, C., Vermeulen, S., Bigasin, R. R., Song, E. S., Sarkar, S. R., Gibson, J., Prakash, M., Fire, A. Z., Wang, B. 2024; 43 (11): 114892

    Abstract

    Live imaging of regenerative processes can reveal how animals restore their bodies after injury through a cascade of dynamic cellular events. Here, we present a comprehensive toolkit for live imaging of tissue regeneration in the flatworm Macrostomum lignano, including a high-throughput cloning pipeline, targeted cellular ablation, and advanced microscopy solutions. Using tissue-specific reporter expression, we examine how various structures regenerate. Enabled by a custom luminescence/fluorescence microscope, we overcome intense stress-induced autofluorescence to demonstrate genetic cellular ablation and reveal the limited regenerative capacity of neurons and their essential role during wound healing, contrasting muscle cells' rapid regeneration after ablation. Finally, we build an open-source tracking microscope to continuously image freely moving animals throughout the week-long process of regeneration, quantifying kinetics of wound healing, nerve cord repair, body regeneration, growth, and behavioral recovery. Our findings suggest that nerve cord reconnection is highly robust and proceeds independently of regeneration.

    View details for DOI 10.1016/j.celrep.2024.114892

    View details for PubMedID 39427313

  • Feedforward growth rate control mitigates gene activation burden. Nature communications Barajas, C., Huang, H., Gibson, J., Sandoval, L., Del Vecchio, D. 2022; 13 (1): 7054

    Abstract

    Heterologous gene activation causes non-physiological burden on cellular resources that cells are unable to adjust to. Here, we introduce a feedforward controller that actuates growth rate upon activation of a gene of interest (GOI) to compensate for such a burden. The controller achieves this by activating a modified SpoT enzyme (SpoTH) with sole hydrolysis activity, which lowers ppGpp level and thus increases growth rate. An inducible RelA+ expression cassette further allows to precisely set the basal level of ppGpp, and thus nominal growth rate, in any bacterial strain. Without the controller, activation of the GOI decreased growth rate by more than 50%. With the controller, we could activate the GOI to the same level without growth rate defect. A cell strain armed with the controller in co-culture enabled persistent population-level activation of a GOI, which could not be achieved by a strain devoid of the controller. The feedforward controller is a tunable, modular, and portable tool that allows dynamic gene activation without growth rate defects for bacterial synthetic biology applications.

    View details for DOI 10.1038/s41467-022-34647-1

    View details for PubMedID 36396941