I have a Molecular Engineering PhD from the University of Washington with a Data Science Certificate. I specialized in synthetic biology with a thesis on engineering and understanding plant promoters.
I screened for new plant constitutive promoters (promoters that are on in all the tissues at all times) and used them to build genetic logic gates.
By introducing 2 unique gRNA target sequences into the constitutive promoters, they can be independently targeted by dCas9-guided repressors, such a system works as a logic NOR gate.
By analyzing hundreds of publicly available RNAseq datasets across multiple plant species I was able to identify sets of evolutionary related promoters and track their expression pattern and promoter architecture over evolutionary time.
I am passionate about using concise figures to tell scientific stories. Apart from the figures in the manuscripts, I also build interactve and animated figures you can check out below!
I used Machine Learning to predict protein function and stability by using primary sequence as inputs and flow cytometry measurements as outputs
Constitutive promoters (promoters that are on in all tissues at all times) are useful tools to introduce novel traits like insect resistance in the whole plant.
There aren't that many well characterized plant constitutive promoters available, and reusing promoter parts can lead to instability.
Leveraging publicly available RNA-seq atlases for A. thaliana I identified the most stably expressing natural promoters available and cloned them for testing.
We identified multiple promoters that expresses both in N. benthamiana and A. thaliana and several of which appears to be constitutively expressed in A. thaliana. We then used a few of these promoters to build logic NOR gates.
NOR Logic Gate |
|||
| Input1 | Input2 | Output | |
|---|---|---|---|
| 0 | 0 | 1 | |
| 0 | 1 | 0 | |
| 1 | 0 | 0 | |
| 1 | 1 | 0 | |
Main core promoter types in plants include TATA, Y-patch, and Coreless promoters. TATA promoters tend to be conditionally expressed while Coreless promoters tend to be constitutive.
Do changes in core promoter types correlate with changes in expression pattern?
We leveraged RNA-seq atlases for 15 plant species to evaluate expression uniformity for each promoter, and identified orthologous genes across species (i.e. evolutionarily related). We can then track changes in expression uniformity and core promoter type of related promoters across evolution.
We found unexpected trends for expression pattern for Coreless promoter in monocots (see animation). We also found that changes in core promoter types do no explain changes in expression pattern.
Check out my music project PoPoPoltergeist 👻
More to come ...
