Share this project

Done

Share this project

Done
Create GLOWING PLANTS using synthetic biology and Genome Compiler's software - the first step in creating sustainable natural lighting
Create GLOWING PLANTS using synthetic biology and Genome Compiler's software - the first step in creating sustainable natural lighting
8,433 backers pledged $484,013 to help bring this project to life.

An overview of our technology stack

Posted by Antony Evans (Creator)
33 likes

Hello Backers,

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.

Bombardments

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.

Week 1
Week 1
Week 2
Week 2
Week 3
Week 3
Week 4
Week 4

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:

Overview of TAXA infrastructure
Overview of TAXA infrastructure

Protein Engineering  

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 

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 

Stable Transformation 

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.

Virtuous cycle for sustainable improvement in plant luminosity
Virtuous cycle for sustainable improvement in plant luminosity

Shipping dates

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.

Timelines for shipping Glowing Plants
Timelines for shipping Glowing Plants

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.

T2 AtFluc seeds
T2 AtFluc seeds

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

Bryan Rathouz, Sergio Araya, and 31 more people like this update.

Comments

Only backers can post comments. Log In
    1. Antony Evans Creator on

      Thomas: don't worry about change of address, we haven't sent out the survey yet to avoid this problem. We'll send it out and confirm right before we ship.

    2. Thomas Murphy on

      also willing to wait

    3. Thomas Murphy on

      Wondering how to get a hold of you to notify a change of address?

    4. Missing avatar

      Matt Harouff on

      I am willing to wait as long as it takes for you to develop the brightest glowing, largest leaved plants possible. Please continue, and keep up the good work!

    5. Kim Sannes on

      I am happy with your progress and can wait for an even better and brighter plant.

    6. Antony Evans Creator on

      Brian: Just to be clear Kickstarter backers will always get first shot at lines we develop. You'll either get them as your backer reward or as an add-on. But yes, always before they are shipped to others.

    7. Jerry Bocci on

      I'm just as fascinated by the process you guys are developing, as I am excited to get the seeds. I can definitely wait this one out!

    8. Brian Roush on

      While I don't mind waiting for the Lux version, and one that meets the goals of what we all pledged for in the original campaign, I must say I'm a bit put off by offering seeds for sale to non-kickstarter backers at this point. I'd ask that kickstarter backers always get first shot at purchasing future lines of seeds that are produced, as that was the incentive to back. Not only were we investing in the science and goals of the project, but also to be first to benefit from it. So, I understand that more working money may be required to continue work on brighter lines without interruption, but it sounds as though there's enough money to get the fully developed Lux version. My preference is to open the option for backers to buy each currently available line of seeds, then open for outside sales 2-3 months later.

    9. Jordon on

      Just keep working away! I'll wait as long as needed.

    10. Michael Littell on

      Whats a little longer for a better glow. A few more months wont hurt

    11. Missing avatar

      Alana Sussman on

      I'm happy to wait for improved luminosity! Can't rush breakthroughs!

    12. Whyemm Ess on

      This is an awesome project! I'm willing to wait longer for the improved plants. Also, I would have to say no to mixing the lines myself. I don't have a good enough understanding to attempt to help you guys with that, sorry. I prefer exercising my patience and waiting around. Thanks for the update!

    13. Missing avatar

      Eric Clifford on

      I like the idea of being able to put some extra money up to get an early version, while waiting longer for a brighter plant.

    14. Antony Evans Creator on

      Thanks for all the support backers!

    15. Missing avatar

      kmarti11 on

      I love your guys' updates!! This is by far my favorite project I've kickstarted, mostly because of your in-depth and science rich posts. Keep them coming, I'll wait for years if it means brighter and better plants!

    16. charles on

      Thanks for the update... as a backer I wouldn't mind waiting a few months longer to get the new and improved seeds. Good things come to those who wait. Getting excited about the new improvements.

    17. Nick on

      Take as long as you need. I funded this project because I wanted to support progress in the scientific field.

    18. Luke E. on

      I will wait as long as necessary for the glowing-est plants possible. I'm here because of the awesome science you folks are doing, and I'm in for the long haul.

    19. Graham on

      In for a day, in for a decade. I will wait for the brightest plants possible. Good luck.

    20. Missing avatar

      Michal Todorovic on

      I'm happy to wait indefinitely for the brightest plants you guys want to work on for us. I backed this more to make it happen than to have some glowing plants myself.

    21. JeanTheBean on

      My view of shipping dates is: Like you said, it's not as if you can make the early-generation plants grow faster. I knew when I signed on that this could take time -- "some" time or a whole lot of time. I'm happy to wait as long as needed to get a nice, bright plant. Watching the development is half the fun!

    22. James Kiser on

      Waiting and getting a better plant is preferable to me. I'm really not worried about the extra time, so long as it gets here eventually. The work you have done is quite impressive.

    23. Eric Gustafson on

      I agree with other backers.. this is one of those projects you want to wait for a mature product high luminance plant and honestly watching them progress is my reward .. the seeds will just be the "cherry" on the ice cream sundae ..

    24. Richmund Fries on

      I would definitely rather wait longer for a brighter plant. Honestly I think you guys are doing great time wise. This is a lengthy process. There isn't much that can be done when your constraints are biological. Like you said, we don't have the technology to speed that up (yet).

      You guys asked if we would like to play with breeding ourselves; personally, as much as I love you guys and what you're doing, I'd rather leave the science to you guys :)

    25. Missing avatar

      Edmond Overbey on

      I would prefer to get the most mature product you develop. Lux is preferred.

    26. Jasen Torres on

      I would kick in another pledge to get multiple brighter plants....seeds
      and i would wait to get the brightest you can get.

    27. Joe Ibershoff on

      I agree, the brighter the better. I would love to get seeds from multiple lines and then cross-breed them in hopes of further improvements, but only if all the lines I get are fairly bright. I'd hate to get a few semi-bright lines (when brighter were available) and then breed them, only to have bad luck and wind up with worse results in my next generation.

    28. Missing avatar

      Paul LeBlond on

      I'm glad you'll be able to continue your research beyond where we were able to get with the Kickstarter alone. I'd be excited to fund/subscribe to each new batch of seeds and see the progress in person, and perhaps try breeding across batches.

    29. John Edmondson on

      The brighter the better. I'll wait 5 more years if I have to.

    30. Antony Evans Creator on

      Wendy: yes, understood about your daughter, she can have one of the earlier versions if she wants them sooner.

    31. Antony Evans Creator on

      Desmond: yes, of course we'll confirm shipping addresses before we ship.

    32. Missing avatar

      Mpitaji on

      I invested in this campaign because I wanted to support this kind of development. In this case, the reward of seeds in its current form are not a priority to me. I love the progress, and fully recognize that this was a long term 'investment' for me. I would be happy to 'subscribe' to keep your cash flow up, and my reward could be your current version of the 'product'? But really, seeing the work progress is quite a reward for me. Keep up the good work!

    33. Desmond Gholar on

      I can wait for better glowing plants. Also before shipping out, will you guys do a double check on shipping addresses?

    34. Jonathan43551
      Superbacker
      on

      I would be happy to pay an add-on fee to get multiple versions.

    35. Timothy Roller
      Superbacker
      on

      More glowy for me, please!

    36. Missing avatar

      Shalev NessAiver on

      I'd love to try breeding stronger strains. Also willing to wait for the brightest plants. Keep it up!

    37. Missing avatar

      Chuck Lunney on

      I'm willing to wait for a stable, complete plant system. But the idea of getting iterative updated plants, as they become available is intriguing - even for a cost.

    38. Diana Viola on

      I'd rather wait for a better plant instead of rushing to have one that is a bit subpar. �� So I can wait, just make it worth it!!

    39. Missing avatar

      Jesse Soileau on

      1. Take all the time necessary to put out a quality plant. I think that releasing a subpar organism will be more damaging than a few irritated impatient people.

      2. I would be happy with mixed lots of seeds as long as they were packaged separately, clearly labeled and had a detailed information packet to assist in creating a comprehensive breeding plan.

    40. Wendy Balelo on

      I'm patient and can wait, but my daughter is not. I ft or these as a gift for her based on the original timeline, and she was willing to wait for a while, but she's been waiting so long that college s luck up us. She wants them sooner than later.

    41. Steven R Black II on

      Michael Denny, there's not any IPO on these genes.

      Remember, we voted for this to be an open project.

      Now for the research and such, that may be a different story. ;)

    42. Arpa Aghamalian on

      Like most others so far, I can wait for the brightest autoluminescent variety. Keep the updates and progress coming.

    43. Steven R Black II on

      I'm all for waiting three or four generations to get the best homozygous hybrid of the bunch .

      I still don't have an appropriate facility to grow them, and have no need to have them any sooner than when they are GOOD and ready.

    44. Antony Evans Creator on

      Guys: thanks for all the supportive comments. I think we will try to make each version available for a small add-on fee for those who want to see them all and track progress. With regards funding the SEC hasn't implemented the full jobs act so we can't sell shares publicly which is a pity, but for sure if the rules ever do get implemented or there's an IPO (way in the future!) Kickstarter backers will be first in line.

    45. Samuel Harvey on

      Best & brightest, take your time!

    46. Missing avatar

      Amy Hyler-Essig on

      I'm all for waiting until the best, brightest result, and the happiest plant possible! Thanks for the continued updates :)

    47. Ricardo Bortolon on

      Also prefer to wait for the later generations!

    48. Missing avatar

      Michael Denny on

      I'd prefer to wait until later generations, I understand how complicated this all seems to be, I'm just glad your making progress and have funding to keep going! If you ever become a public company can you give your original backers access to buy IPO shares or better yet warrants! :) just a thought.

      Someone also mentioned add to your funding below, I'd be up for that as well.

    49. Missing avatar

      Paul Wheeler on

      I'd love to have the brightest possible plant, I'm fine with waiting, no rush :)

    50. David MacDonald on

      I will wait as long as necessary for a bright, stable, healthy plant.