Individual Final Project

StromataLight Screen

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Abstract

A stromatalite is a tower structure created by microbial biofilm communities as they grow up and are mineralized underneath. In the ancient past this was the dominant visible form of life on shore lines. My idea is to engineer a combination of a tubular bioreactor and bacterial community that will grow a synthetic stromatalite with a programable pattern of colored fluorescent stripes. By placing multiple reactor tubes with different programming next to each other you will have a simple display that can display images and text.

To implement this the idea is to engineer two varieties of bacteria, the paint bacteria and the glue bacteria so that

  • The two varieties need to sense each other to trigger biofilm formation
  • The glue bacteria emits biofilm protein (curlin) with calcium bonding areas engineered as rapidly as possible once it detects a drop in oxygen and the presence of the paint.
  • The paint bacteria has a timing circuit so that it turns on and off the generation of fluoresent proteins as different layers/generations are formed and it grows up layer by layer.
  • The paint bacteria need to have some way to program or control the timeing of their fluoresence without doing new genetic edits. (I am not sure how I would implement this yet. Maybe just delegating the timing to the bioreactor, so that it feeds in a consumable/decaying trigger for the paint bacteria to produce fluorescent protein at the correct point?)

The bioreactor will be a transparent glass tube with drop feeding and air supply hoses attached.

  • Delivers nutrient and calcium by a slow drip from the top.
  • There is no stirring or emptying of the drip so the tube gradually fills with liquid.

The gradual filling of the bioreactor will create pressure on the bacterial community to grow towards the top of the tube and the calcium mineralization and the surrounding tube should give the biofilm enough rigidity to support the futher growth up. This similar to the selection pressure that celluose producing bacteria like K. Xylinus experience and resolve by rapdily creating thick mats of celluose.

Placing a series of these tube bioreactors next to each with these communities will create a simple programmable “screen” that grows up from the bottom of the tubes and forms a message or picture when it reaches the time. The goal would be to able to grow a 10cm tall display in 3-5 days and have the images persist once full growth is reached.

This is a development proof of concept to explore growing programmable macroscopic layered objects with consortia that form a simplified and optimized version of that consortia that form natural biofilms. Once developed the basic idea could be extended to provide base for biological environmental sensors that keep a persistent record of their detections via the colors or properties of different layers like tree rings.

Project Aims

Aim 1 - Experimental Aim

The first aim of my final project is to bioengineer two different e. coli to operate in a consortia. One will be the curlin, csgA factory and will produce large amounts of csgA. The other will be a csgB factory and a color sensor.

I will use golden gate assembly and igem DNA plasmids . I will also modify the csgA protein to bind to calcium ions using alphafold and boltz to explore proteins modifications to csgA to bind to calcium for minerialization.

List igem entries + 1 modified igem entry for csgA.

What I expect to see and verify

  • Paint bacteria
    • Color changing of binder e. coli under arbodsis
    • Measure response to dose or arbasose
  • Glue bacteria
    • Do a detergent SDS assay without calcium to verify cration of curlin fibers
    • Verify doing an assay of of calcium binding csgA in glue e. coli by combining with calcium filtering out protein and comparing sodium carbonate preciptation to calcium and base e coli only controls.
  • Consortia
    • Verify that consortia mixed together forms visual accumulations amyloid fibers (visual or congo red)
    • Do calcium absorbtion test again on consortia
    • Repeat color changing test

if all of this works then we know the basic bio engineering worked and we have a viable consortia.

Aim 2 - Developmental Aim

Once the basic biological components work they need to be optimized and calibrated. Develop optimized growth techniques and bioreactors that can grow 10cm tall samples of biomineralized biofilm in 1 week.

Aim 3 - Build Stromatalight Screen

  • Build multiple bioreactor tubes
  • Perform ALE selecting for height and speed (aiming for 10cm in a few days)
  • Make a StromataLight screen PoC
  • Run and record “Hello World” demo on the screen
  • Document and release for others to use

Background

Experimental Design

Other Material