Sounds Like a Bad Biotech Business Idea or Not? Color Changing Flowers

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Josiah Zayner

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Mar 20, 2015, 2:19:23 PM3/20/15
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I think it is the responsibility of Scientists to question and police and have certain standards when it comes to interacting with the public and selling products online. To this end I tend to be critical and I hope you all can be. Besides being a dick, I think it helps the companies and people proposing ideas to really think about them and have a clear plan to what they are doing.

With projects like the Glowing Plant Project being way behind schedule, how much would it suck if the first 5 or 10 crowdfunded biotech projects failed to deliver anything? It would make us all look bad and makes us look like charlatans when unreasonable things are touted as reasonable.

At SXSW I met Nikolai and RevBIo and I am pretty skeptical of their project(https://www.indiegogo.com/projects/color-changing-flowers) and did not completely understand how they plan to do what they wanted to do so we decided to do a question and answer

You can read the questions and answers here:
http://doitourselfscience.blogspot.com/2015/03/genetically-engineered-color-changing.html

This first round is just to get a general idea of how they plan to do what they are doing. The second round of questions I plan to be more technical and critical.

I encourage you to post technical questions that you want to ask and be critical. I will make sure Nikolai, Kiera and Revolution Bioengineering address them when we do a second round.




Josiah Zayner, Ph.D.
Space Bioengineering Branch
NASA Ames Research Center
Moffett Field, CA 94035

Josiah Zayner

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Mar 20, 2015, 2:23:25 PM3/20/15
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Here is the post:

I am a pretty skeptical person. That is what they taught me during my Ph.D. at UChicago, "Question Everything". That can be good but also bad sometimes (look like a dick for putting down someone's pet project). Anyways, there is company called Revolution Bioengineering that started an Indiegogo campaign up about creating Color Changing Flowers using genetic engineering. Of course I am skeptical. The glowing plant project was supposed to deliver flowers that glow 7 months ago and still there is nothing, yikes!

What I get from their Indiegogo and the answers below is that they are planning to have two products ones that change color once during budding and others that "Change color on Demand"

It just so happens that I met one of the founders at SXSW and asked him if he would do dueling blog posts with me and he agreed. Understand I have never met Nikolai before in my life and this is not preplanned or a publicity stunt. I have not invested in their Indiegogo because I am wary. I gave him this post beforehand so he could write up a response HERE and everyone can see the Scientific basis of the project. If needs be we will then post a second time to allow us both to have rebuttals and ask new questions. In the end we can see if it holds up to scrutiny. I am all about Scientific transparency, if you can claim you can do something you should be able to explain the mechanism of how you plan to do it. I think many of these Science projects people post on Indiegogo or Kickstarter are very vague and lack details. This helps them sell because the public is not usually concerned about that stuff but it makes me wary of over-hype and exaggeration of what is currently possible.



Questions(underlined and bold) and Nikolai/RevBio's Answers(italics)

Color changing is a complicated process, I have worked with engineering bacteria that change color and it takes a long period of time. Visible color change either through chromophores or proteins can take 24 hours and this is usually under special growth conditions such as decreased temperature or optimal nutrient availability. Bacteria are some of the easiest to engineer organisms. Once you take an organism out of a controlled environment or lab how realistic do you think it is to recapitulate the function?

This was something that we considered when we designed this project—Keira and I are two experienced plant synthetic biologists, and it was important for us to do something achievable and not overpromise.  Credibility is a problem in the biotech community.
To that end, we are playing around with the existing anthocyanin pathways—the enzymatic pathways native to petunias that produce the vibrant flower colors.  Petunias are already programmed to produce milliMolar quantities of anthocyanins in flower vacuoles, and we probably can’t do better than that with bioengineering.  (Well, we might be able to with a lot of iterative work, but we don’t have time or money for that right now..)
For the petunia we are crowdfunding to create—the color change on demand—we have an anthocyanin pathway that is broken at a certain early step resulting in a plant with all white flowers.  If we inducibly express the broken enzyme, we get purple/red flowers.
You bring up a very good point about function in real world conditions.  It happens all the time in plant biotechnology that your favorite transgenic works great in a growth chamber, in a laboratory, or in a greenhouse-- but when you take it outside to real world conditions, the trait disappears.  This phenomenon is common knowledge, and part of the reason that the “big guys” do about 6000 unique transformation events, and select the best from that group.  Plant biotechnology is still in the stone age as far as technology goes, and many things are still mysterious enough that it is just a numbers game to get a good plant out of a biotech project.
We don’t have the money or facilities to do 6000 unique transformations, but we will be doing a lot of them and selecting the best responders.


Do you have an exact plan of what you are going to modify and if so can you tell us?

In our color-change-on-demand petunias [anthocyanin 2]AN2 is the broken enzyme.  This is actually not an enzyme in the anthocyanin pathway, but instead a transcriptional activator of that whole pigment pathway.  Without it, the pigment-producing genes are not transcribed.
We are linking expression of AN2 to an ethanol-inducible transcriptional activator.  In our prototype flower, we have AN2 linked to a dexamethasone-inducible transcriptional activator, and that clearly works in a robust way.
https://www.youtube.com/watch?v=hOlO1Cu6E9I
However, we could never distribute a flower that requires dexamethasone to the public.  Or maybe we could, but very few people have Dex laying around their house that they can apply to their flowers, thus the changeover to the ethanol system.
We talk an awful lot about “petunia circadia” and “continuous color change”.  This is a different project, and will be more technically challenging, and is thus listed as a stretch goal on the campaign, not the main goal.
To make Petunia circadia we will be changing the pH within the flower vacuoles.  



I am a little bit confused, will the actual flowers that are growing change color or only new buds about to flower?

Color-change-on-demand : new buds
Petunia circadia : developed flowers
The color-change-on-demand flowers will typically bloom all white.  If you water them with a beer, or spray a flower bud with a beer (we present these beer applications as a possibility, we will need to test the resulting flowers to see what works and what doesn’t) the new flowers will bloom purple.
Once a petunia flower is open, the small molecule building blocks used to make anthocyanins will have been diverted for other uses.  Anthocyanins are also astonishingly stable molecules.  The flowers are locked into being that color, whether they are white or purple.
Petunia flowers last for about 5 days before they senesce, but petunias are prolific bloomers, and will continuously put out new blooms.  So you could change over the entire plant’s flower colors on a one week time scale.  



I assume you are basing your work off of: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456866/ which seems reasonable but it is not mentioned in the paper how quickly the fading occurs, any idea?

This is for the petunia circadia.  I mentioned that that is a more ambitious project, and there is a lot of testing we would have to do along the path to creating this flower.  That paper you linked to demonstrates the pH change you can achieve through a knockout (roughly 0.5 pH units) and the corresponding color change of the flower.  That pH-color change phenomenon is described several different ways using several different mechanisms by that laboratory.
Circadian promoters form plants are likewise well described and used in synthetic systems (check out luciferase linked to a circadian promoter in arabidopsis here: https://www.youtube.com/watch?v=hOlO1Cu6E9I )
Linking pH change in the vacuole to a circadian promoter will be the challenge.  Will we be doing proton channel expression on a circadian promoter, or doing RNAi knockdowns of a channel on a circadian promoter?  Will the protein lifetime of a proton pump on the plant vacuole exceed the 12 hour timeline of a circadian expression system?  Will we need to stabilize/destabilize proteins/RNAs to get this to work?  There are many unknowns in this project and a lot more testing, measuring, and fiddling required to get petunia circadia to work.  This is definitely higher risk science than color-change on demand, but is still a totally reasonable and doable project.


Do you think any of these engineered processes will affect the normal growth and metabolism properties of the petunias?  

In all cases we will be having a selectable marker in our plants that will be constitutively expressed.  This will place a metabolic burden on the plants that their non-transformed cousins won’t have.  All the clever things we are adding to make the flowers change color will be expressed only using a flower-specific promoter—so metabolic burden will be limited to the reproductive organs, not the photosynthetic tissues.
With all the varieties of plants out there which have been developed with conventional breeding that have one or two genes knocked/overexpressed and still have vigorous growth habits, I don’t think it won’t be too hard to get a robustly-growing petunia out of this. 



Heather Dewey-Hagborg

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Mar 20, 2015, 4:27:42 PM3/20/15
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thanks for doing this - really helpful in parsing out facts from hype.
One question I have is whether they will be openly publishing their research from this project ie. will it be accessible in some way to the community?

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Keira Havens

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Mar 20, 2015, 7:27:18 PM3/20/15
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Hey Heather, 
I'm one of the cofounders at RevBio.  All of this research is already publicly available - we've just put them together in a new way using the literature that is already available.  None of this is brand new research, we're working with the academic scientists that have discovered these things to make the current flower. 
Happy to answer any more questions!
Keira

Idan Efroni

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Mar 21, 2015, 6:33:47 PM3/21/15
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Actually, their plan sounds pretty solid in terms of the science. This project is miles away from the Glowing Plants, in which the technical problems were obvious to anyone with plant biotech experience. I just hope that when they fail to deliver the lightbulb plants (and with the hype set so high, they most likely will), it will not be a problem for the whole field.

However, the main problem with the on-demand color changing is that the alcohol-inducible AlcR/AlcA system is patented and owned by Syngenta. How are they going to deal with that?

scoc...@gmail.com

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Mar 21, 2015, 8:33:09 PM3/21/15
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I've always had difficulty with determining patent expiration reliably.

https://patentscope.wipo.int/search/docservicepdf_pct/id00000000591879?download

This is the patent in question taken from the Syngenta website. They ask for some initial signing fee plus $50,000 for first commercial event. The date of publication is 1997 but filing is 1996 and priority is 1995. Why can't patents just clearly state expiration dates and have a simple patent search tool that uses the patent number and spits out an exact expiration date?

There are some really neat patents expiring in the next few years (or expired already) including the phosphomannose isomerase gene usage, bar, etc. that I am eagerly awaiting for.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

From: Idan Efroni
Sent: ‎3/‎21/‎2015 6:33 PM
To: diy...@googlegroups.com
Subject: [DIYbio] Re: Sounds Like a Bad Biotech Business Idea or Not? ColorChanging Flowers

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Idan Efroni

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Mar 21, 2015, 9:29:28 PM3/21/15
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The original Alc patent was filled in 1993, so it has probably expired already, but there is this:  https://www.google.com/patents/EP2665832A1

I'm not sure if and how it applies, but it is definitely an issue the guys at RevBio want to check.

Keira Havens

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Mar 22, 2015, 8:56:20 AM3/22/15
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Sebastian is right about the expiry of the patent, but we've also been talking with IP holders throughout this whole process. It makes it longer and more complicated, but we think it's better to have all the stakeholders on the same page. So, we have no formal agreements with anyone, but we're working through the process - hope that gives you a little more insight. 

Nikolai Braun

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Mar 22, 2015, 10:46:56 AM3/22/15
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Hey all--
  We are 100% aware of the Alc patent issues, and have had conversations with Syngenta about this.  I can't say anything else, other than we are on top of it.

-Nikolai

Mega [Andreas Stuermer]

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Mar 24, 2015, 6:12:20 PM3/24/15
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Hi, to come in a bit late but still,
I am not sure. But anthocyanin modification has been done, think of the blue carnation. Inducing it by alcohol can be done definitely.
I don't know how they wanna change the colour - expressing new enzymes may have inertia as you say. But there may  also be ways to shift colours of plant pigments by oxidation state - H2O2 or something similar. And this doesn't take hours. So I'd say worst outcome is still a success... A plant that changes colour when watered with ethanol. Nice product, I'd totally buy if I wouldn't get in prison here in Europe for owning it.

Cathal Garvey

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Mar 24, 2015, 6:19:26 PM3/24/15
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> I am not sure. But anthocyanin modification has been done, think of
> the blue carnation. Inducing it by alcohol can be done definitely.

Not only has Anthocyanin mod been done by others, there's a detail that
Keira and Nikolai leave out a lot, which is that *they've done dynamic
plant colour modification in the past*. They were on that (DARPA
funded?) project to make "bomb detecting plants" and have some amusing,
if not list-safe, anecdotes to share on the subject.

So, if you could back a team to make colour-changing plants, you
literally can't find a team more likely to deliver, because they're
possibly the only people to have done it before.

Cue Keira and Nikolai chipping in to tone down my rhetoric, I expect. :)

> A plant that changes colour when watered with ethanol.
> Nice product, I'd totally buy if I wouldn't get in prison here in
> Europe for owning it.

Crazy thing; the Moondust Carnation (The "blue" carnation) is actually
cleared for release in the EU, meaning you can legally own a Moondust
Carnation and keep one in your garden. The reason you can't buy one is
because the manufacturers are just plain stupid and only sell cut
flowers grown in Brazil.

The Common Flowers project that featured in Grow Your Own in Science
Gallery used plant tissue culture methods to grow cuttings from Moondust
Carnations into plantlets, with the intention of creating rooted
cuttings that would be released into the wild to crosspollinate with
other carnations, etcetera. I gather they're doing this on the
Continent, though all the ones we tried to raise in Science Gallery
succumbed to fungal contamination. :)
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Mega [Andreas Stuermer]

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Mar 24, 2015, 6:46:15 PM3/24/15
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Crazy thing; the Moondust Carnation (The "blue" carnation) is actually
cleared for release in the EU, meaning you can legally own a Moondust
Carnation and keep one in your garden. The reason you can't buy one is
because the manufacturers are just plain stupid and only sell cut
flowers grown in Brazil.

We had them in the Ars Electronica,

I was told though that import into the EU is only legal as cut flowers, cut before the pollen matures so it won't be able to propagate.
Either way, planting it in the garden in Austria is illegal anyways because the total ban on "genes" lead by the media and executed by the politicians.

There also are different Moondust/moonaqua/... versions, AFAIK only two are permited to import into EU (which are more violet than blue). There are really blue ones (the newer varieities) but they have not been cleared for the EU, but you can buy in Asia.

Tissue culturing in the lab is next-to-impossible as they seem to be heavily contaminated with fungal spores (a strategy to avoid propagation? just kidding. but maybe not), plus you rather take fresh leaves than mature ones that have been shipped etc...

Cathal Garvey

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Mar 24, 2015, 6:51:51 PM3/24/15
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> Tissue culturing in the lab is next-to-impossible as they seem to be
> heavily contaminated with fungal spores

If you've got the right antifungals, I doubt it would be a serious
problem. Fungal spores are all over everything but culturing wild
samples is still doable. There are plenty of tricks for this that can
minimise the need for antifungals in the first place, too, like peeling
buds to expose sterile meristematic tissue; that was hard with cut
flowers because there aren't any juicy buds left, but maybe very fresh
cut flowers would have unopened flowers that would be ideal, if you get
them in time.

> I was told though that import into the EU is only legal as cut
> flowers, cut before the pollen matures so it won't be able to
> propagate.

This may very well be true. The people to ask are the common flowers
peeps, I imagine they've done their research given that they're planning
to cultivate without licenses and then release them! :)
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Mega [Andreas Stuermer]

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Mar 24, 2015, 7:53:26 PM3/24/15
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The cultures with the antifungal mix was as contaminated as the non-antifungal. Both were treated with bleach and ethanol. So the antufungal stuff (I don't mention the name of it, because I don't wanna talk bad about products publicly :P ) was totally useless

scoc...@gmail.com

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Mar 25, 2015, 2:18:52 AM3/25/15
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Did you guys add a drop of dish soap to break surface tension and get the bleach through the cracks? Did you shake, vortex, agitate the tissue? Did you then rinse a few times with distilled sterile water under laminar flow air? Decontamination is a tricky bit but a bit of creativity helps tremendously. :)


Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

From: Mega [Andreas Stuermer]
Sent: ‎3/‎24/‎2015 7:53 PM
To: diy...@googlegroups.com
Subject: Re: [DIYbio] Re: Sounds Like a Bad Biotech Business Idea or Not?Color Changing Flowers

The cultures with the antifungal mix was as contaminated as the non-antifungal. Both were treated with bleach and ethanol. So the antufungal stuff (I don't mention the name of it, because I don't wanna talk bad about products publicly :P ) was totally useless

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Mega [Andreas Stuermer]

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Mar 25, 2015, 6:29:37 AM3/25/15
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The soap would have been a good idea!! We just disinfected it like the leader of the AEC biolab always does with tobacco plus a second time with longer exposure to the disinfectants.

David Murphy

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Mar 25, 2015, 7:24:07 AM3/25/15
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Minor note, there are existing colour changing flowers. :

http://www.hydrangeashydrangeas.com/colorchange.html

On Wed, Mar 25, 2015 at 10:29 AM, Mega [Andreas Stuermer] <masters...@gmail.com> wrote:
The soap would have been a good idea!! We just disinfected it like the leader of the AEC biolab always does with tobacco plus a second time with longer exposure to the disinfectants.

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Mega [Andreas Stuermer]

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Mar 26, 2015, 8:41:42 AM3/26/15
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Protocols said adding Tween20, but that seemed to make it worse. Our chlorine cleanser already contained detergents I was told... The lab leader (who clearly is much more experienced in plant tissue culture than me) assumed contamination from deep inside, because it was time delayed. It wouldn't make sense if the bleach would have gotten inside, because it would have killed the plant tissue too...
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