Week 1 HW: Final Project Ideas

What would you like to biomanufacture and why?

I’d like to biomanufacture pigments and pigmented fungal materials for artworks and designed objects, with the aim 2 of making genetically modified colorful mycelium furniture. I’d like to completely replace my art materials with waste-stream, home-scale biomanufacturing processes as a philosophical and conceptual exercise and performance art piece. It’s a kind of extreme zero-waste experiment.

I’d like to start by creating a palette of bioinks and then move on to creating colorful living mycelium materials. I’d like to start by designing a simple pigment plasmid framework by compiling a toolkit (IE a spreadsheet) of chassis-categorized promoters and terminators tailored to my personal organism collection and the ChiTownbio collection that we’ve been assembling and caretaking. I’ll eventually work with all of them, so I’d like to set this up just ahead of time so I can iterate quickly and help my students design more efficiently. I’d like to use the same or similar pigment-assembling enzymes across each chassis organism to get foundational data on pigment production and accumulation within each chassis, and on its subsequent morphology across its cycle and/or environmental morphology changes. I’d particularly like to focus on its expression in Fungi across the two major phyla. I’d like to do some microscopy to see how vacuole formation influences pigment accumulation in the tissue. I suspect that, as in plants, water-soluble pigments may accumulate in vacuoles; I’m considering starting with betacyanin, as it’s a lovely magenta, highly reactive to oxygen, and quite water-soluble. I suspect that, at the scale of mycelial tissue, color variation will relate to water distribution and oxygen exposure. I suspect that on the scale of a single fungal cell, the pigment may accumulate in and around vacuoles due to osmosis.

Fungal vacuoles are very dynamic. Unlike plant cell vacuoles, which are centralized, fungal vacuoles form and dissipate in response to the cell’s environment. In the case of some Ascomycetes fungi like yeast, they can form complex spiral structures. I think it would be sick to get a high-quality time-lapse or photograph of pigment production and accumulation within the cell. I imagine that metabolites expressed in basidiomycetous fungi, when there is a mild excess of water in the living system under common commercial and hobbyist growth conditions, may also include the GOI pigment due to osmosis.

What living system could make it? →

I have experience with and active cultures of cyanobacteria, Lactobacillus bacteria, yeast, and various basidiomycete fungi. I’ll start with yeast just to get something done.
I’ll end with my Cinnabar Polypore because I like its liquid culture morphology, membrane strength, and existing pigments. As a reach goal, I’d like to put a pigment gene in Ganoderma multiplidieum / b/c it’s the species I have in bulk and is fairly standard in myco biofabrication.

How could automation help you make it? →

I’d love to automate the DNA Assembly workflow with the Opentron system in the lab. That seems like an automation that could be easily adapted to most of our projects. What would it take to make it at a meaningful scale? Once I’ve got the plasmids in culture, it’s just a matter of setting up a couple of bioreactors to start fermenting bulk synthetic bio pigment, and Liquid culture. If my Cinnabar Polypore is of any relevant indication, the pigment should express in the petri dish and in the mycelium liquid culture I estimate that it would take a month and a half to grow out the Agrobacterium-mediated gene transfer process for the modification of the basidiomycete fungi. From there it would probably take a generous 6 weeks to fully colonize 1 L of basidiomycete liquid culture, I could of course and probably will, grow more of that in that timeframe. After that, it would take about 2 months to grow bulk material.
I’m not going to calculate how many volumes I’m going to produce; I’m just going to produce as much as I have the bandwidth for. Classic artist style. This is my core art practice for the next year or so.