An overview of our technology stack
We're excited to bring you this months update - we are getting closer and closer to shipping every day. We've also got an update on the bombardments which have been very intensive this month and most of our teams focus. This months video covers the whole technology stack we've developed to make the plants brighter. Finally we've got an update on shipping dates and our funding situation.
Gene gun bombardments of the full working construct are our main focus right now and we are running three bombardments a week at the moment. The idea is that by making many lines we increase the chances that one of them gets inserted somewhere really good. Potentially multiple lines also allow us to cross them with each other to further increase copy number (we are considering mixing up the lines when we ship seeds so you guys can play with breeding them yourselves to get your own brightest strains - would any of you be up for that?).
The following photos show the relative progress of a plate's worth of tissues from each of the last four weeks. Week 4 is the oldest! It's interesting to see the progress.
We have tried taking a long exposure image of the oldest plate to see if it glows, but no luck so far so probably none of these incorporate the full construct correctly yet. That's something to look out for in a future backer update!
The TAXA infrastructure
Now that we are in the final stage of preparing the seeds we've covered all the key pieces of technology in the backer updates so we thought we would do an overview of the whole tech infrastructure we are using to make the plants brighter. We are excited about this system because while it took a long time to get working we think we've really cracked a process for making the plants brighter - there's a really long way to go to reach our long term goals, but as long as we can stay funded we can make the plants brighter. We are calling this infrastructure TAXA and want to make it available to other collaborators with other syn bio plant ideas.
Our vision is a world where bio-engineering is as easy and commonplace as mobile application development is today. Game-changing technologies, like genetic engineering, should not be the exclusive preserve of large corporations and a wealthy elite. Democratizing the tools of creation enables anyone, anywhere, to genetically engineer plants and will unleash a wave of creativity to power an environment where ultimately what we create is limited only by our imagination. So if you have a cool idea and want to use this technology to make your own GMO plant get in touch with us at http://www.taxa.com.
Here's a video overview explaining how it works:
The TAXA platform has been specifically designed to make our plants brighter as quickly and cheaply as possible. The platform has four pillars, or components, as shown in this chart:
Optimizing proteins in plants is hard, slow work; it can be significantly more efficient to first optimize your target proteins in bacteria, like E. coli. The key limitation here is the assay, of course, but with glowing plants that is easy (how bright are the colony's!). We have two systems that allow us to perform protein engineering on the entire pathway:
- Directed Evolution: we mutagenize the plasmid randomly and then screen for variations which improve performance. This is faster and cheaper than the saturation scan but produces more false positives which improve the genes in E. Coli but don't translate into plants (eg through codon optimization for bacteria)
- Saturation Scan: We step through each codon in the pathway and substituted the other 19 possible amino acids that could be inserted at that point. We've tested this on pathways up to 2,000 amino acids long. Hits generated with this method are more likely to translate into higher performance in plants, but the process is more expensive than directed evolution because we use custom sequences of DNA libraries.
We've automated most of the process for doing this and hope to have a fully automated system working shortly.
Automated DNA Assembly System
We've automated our DNA assembly system which means no more nights in the lab working on cloning and we can build many different combinations of genes really fast and at low cost. We've now built a whole library of standardized parts, including promoters, terminators and selectable markers that allow us to rapidly and affordably design and assemble many combinations of our target pathway genes for testing in vivo. Currently all of our parts are in the Golden Braid assembly system.
Transient experiments are designed to enable us to test a DNA construct quickly and without the expense of a stable transformation. This allows a relatively large number of constructs to be tested quickly and affordably. Again the key bottleneck here is the assay. Currently we have systems setup for the following plant tissues (gives you a hint what varieties of plant we are working on!):
- Callus: Arabidopsis, N. tabacum, Rose
- Seedlings: Arabidopsis, N. tabacum, Petunia
- Leaf tissue: N. tabacum
- Petal tissue: Rose, Petunia
- Epidermis: Onion
We generally use the biolistic method for stable transformation, though we do have agro-bacterium methods available in order to prototype more quickly (which is the version we've demoed previously). While the biolistic method is slower and more expensive to generate a single plant, it's key advantage is that - if care is chosen with DNA parts used - the final product is immediately free for sale and distribution in the United States without requiring regulatory review. This saves years and millions of dollars from the budget for getting the product to market and made this whole kickstarter possible.
Strategy for sustainable improvements
The diagram below illustrates the strategy which we hope to use to create a brighter plant and reach our long term goals of sustainable lighting. Essentially we want to sell the plant (and seeds) and use the proceeds from that to invest back in the infrastructure we just described. This should allow us to make a brighter plant, which we can then sell for increased cashflow which we can then reinvest back in the infrastructure and new version of the plant, until we reach our goals.
Now that we are in the bombardment phase we can give a clearer view of shipping dates. Because of the system we described above we have many versions of the plant in development and expect to ship them progressively over time. We expect later versions to have improved luminosity over time. The timeline below shows our expected shipping dates for each version.
A note on the notation in the above timeline. AtFluc plants are the ones which require a substrate, Lux plants are autoluminescent (our real goal). T1 plants are the first generation plants, which result directly from the bombardment/transformation. Typically they have the genes inserted into just one chromosome, so the first thing we do is cross the plant with itself to generate the T2 seeds. Mendelian genetics tells us that 25% of these plants have copies of the genes on both chromosomes, this is known as a homozygous line. The great thing about a homozygous line is that the offspring are guaranteed to carry the gene, and these are the seeds we will ship (the T3 seeds, for third generation). As you can see from the chart this is a relatively slow process as each generation we have to take the plant through a full life cycle from seed to seed and that isn't something which can be radically accelerated (not with today's technology anyway!).
Here's a picture of the T2 seeds from the first AtFluc plants, you can see we've harvested a lot of seeds. Underneath are some of the seeds growing on controlled media to test for presence of selectable markers etc.
Given we have so many versions in development (construct and species!), it's a little tricky to figure out when to ship. I expect some of you will want the earliest version, and some will want to wait a few months for an improved version. Let us know your thoughts in the comments below.
Update on Funding
We know some of you are frustrated by the delays, but we are working as hard as possible to get the seeds to you as fast as we can. We got a comment from one of our backers earlier this month asking how we were still going on the project after so long and we just wanted to address that. We have already spent the Kickstarter funds on the project, however as you may recall we were funded by Y Combinator last summer and were able to successfully raise a small seed round from some awesome angel investors - this round would not have been possible without your amazing support for the Kickstarter, so thank you for that. As a result we still have enough money in the bank to deliver on all the milestones outlined in the timeline above and get your seeds to you.
That's all for now, looking forward to connecting again in a month or so.
The Glowing Plant team