On the topic of safety and DIY tools
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Sebastian Cocioba
Jul 15, 2014, 3:22:51 PM7/15/14
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In light of the current thread regarding the ethics/responsibility of proposing/posting crazy ideas, I would like to share some thoughts that have been troubling me.
As some of you may know, I've been working on a bench top and portable particle delivery system or "gene gun" for some time now. I've done a number of experiments towards optimizing the parameters required for proper DNA delivery and subsequent integration into PLANT cells. Its coming along nicely but still much work to be done. It will ultimately culminate in a formal write-up that will be shared with you all for the sake of peer review and criticisms. The design will be open source and all data sets (raw or otherwise) will be supplied upon request.
That being said I feel uneasy with the notion of openly publishing the procedures for constructing a device which may be dangerous if misused. I know that, like any and all appliances, devices, etc there can be an inherent risk to the operator but this one in particular may pose as not only a hazard but an attractive tool for deliberate self-experimentation to the newer bunch on the list or those aforementioned "bio-punks".
On the other hand this device may be of use to lower budget labs that are interested in biolistic experimentation but cannot afford the PDS-1000/He ($25,000 Bio-Rad) or the cheaper Chinese knock-off ($7000). I've brought the price down to less than $100 for the portable and less than $500 for the bench top using off the shelf parts and minor modifications. That's all fine and dandy but I don't want to hear that someone decided to build my device and shoot some "telomerase" into themselves and ended up seriously hurting themselves, others, animals, etc.
The information on constructing a device similar to mine has been out for decades (PIG particle inflow gun) and are freely accessible articles but the authors are shielded by the implicit disclaimer that their publication is for research purposes only. I, like many of you, am just a private individual doing citizen science. I have no real way of protecting myself from the actions of irresponsible people nor do I have the funds to hire a legal team in case such a scenario unfolds and I am held somehow responsible due to lack of iron clad disclaimer or warnings.
Realistically, due to the large amount of wetlab work, synthesis, lab overhead, etc required to actually make a construct that can utilize mammalian cellular machinery effectively the best case scenario is a non-functional construct entering the soft tissues and just sitting there. I doubt the experimenter would use gold due to price so the next available material is tungsten. This material is a Lewis acid and has DNA nicking properties therefore geno- and cytotoxic. More often than not cells shot with tungsten just die. I've found a work around to the toxicity of the tungsten and will also include that in my write up. This will make such a device even more accessible to the experimenter. That may or may not be a good thing.
Im on the fence whether or not publish the "how-to" for fear of liability and potential misuse. I by no means wish to offend the collective intelligence of the list and know there are plenty of responsible scientists who would benefit from this. I just need some advice on proper disclaimer structure before I seek professional legal counsel if that is even necessary. Anyone can zap themselves with a DIY gel box or spill some ethidium bromide onto their skin, I just don't want to be liable in any way for my device. Its purely for educational and research purposes only.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
As some of you may know, I've been working on a bench top and portable particle delivery system or "gene gun" for some time now. I've done a number of experiments towards optimizing the parameters required for proper DNA delivery and subsequent integration into PLANT cells. Its coming along nicely but still much work to be done. It will ultimately culminate in a formal write-up that will be shared with you all for the sake of peer review and criticisms. The design will be open source and all data sets (raw or otherwise) will be supplied upon request.
That being said I feel uneasy with the notion of openly publishing the procedures for constructing a device which may be dangerous if misused. I know that, like any and all appliances, devices, etc there can be an inherent risk to the operator but this one in particular may pose as not only a hazard but an attractive tool for deliberate self-experimentation to the newer bunch on the list or those aforementioned "bio-punks".
On the other hand this device may be of use to lower budget labs that are interested in biolistic experimentation but cannot afford the PDS-1000/He ($25,000 Bio-Rad) or the cheaper Chinese knock-off ($7000). I've brought the price down to less than $100 for the portable and less than $500 for the bench top using off the shelf parts and minor modifications. That's all fine and dandy but I don't want to hear that someone decided to build my device and shoot some "telomerase" into themselves and ended up seriously hurting themselves, others, animals, etc.
The information on constructing a device similar to mine has been out for decades (PIG particle inflow gun) and are freely accessible articles but the authors are shielded by the implicit disclaimer that their publication is for research purposes only. I, like many of you, am just a private individual doing citizen science. I have no real way of protecting myself from the actions of irresponsible people nor do I have the funds to hire a legal team in case such a scenario unfolds and I am held somehow responsible due to lack of iron clad disclaimer or warnings.
Realistically, due to the large amount of wetlab work, synthesis, lab overhead, etc required to actually make a construct that can utilize mammalian cellular machinery effectively the best case scenario is a non-functional construct entering the soft tissues and just sitting there. I doubt the experimenter would use gold due to price so the next available material is tungsten. This material is a Lewis acid and has DNA nicking properties therefore geno- and cytotoxic. More often than not cells shot with tungsten just die. I've found a work around to the toxicity of the tungsten and will also include that in my write up. This will make such a device even more accessible to the experimenter. That may or may not be a good thing.
Im on the fence whether or not publish the "how-to" for fear of liability and potential misuse. I by no means wish to offend the collective intelligence of the list and know there are plenty of responsible scientists who would benefit from this. I just need some advice on proper disclaimer structure before I seek professional legal counsel if that is even necessary. Anyone can zap themselves with a DIY gel box or spill some ethidium bromide onto their skin, I just don't want to be liable in any way for my device. Its purely for educational and research purposes only.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Matt Harbowy
Jul 15, 2014, 4:05:32 PM7/15/14
to diy...@googlegroups.com
One way that you can cover yourself against those liabilities is by using an umbrella insurance policy. These are typically attached to other policies and can be quite reasonable (~$500/yr or less) and cover large amounts ($1m). I don't believe it provides complete coverage in all circumstances- you should also carry insurance for your corporation, as well, and a commercial umbrella policy can supplement that coverage. There may be gaps. But this is a good simple step that should be taken- it covers things like libel or slander, which can be crippling to defend if you are on the right side of the law.
Once you have (and maintain) coverage, I would expect that this would free you up to feel more comfortable in a "research use only" disclosure statement. In my observation, it's not the ironclad ness of the disclaimer, but whether you have engaged and networked with the right sort of advisers and have sought the guidance of people who have experienced the harm.
As a corporation, you should be able to buy that kind of coverage as an institution and cover all your employees and deduct it on your taxes.
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Sebastian Cocioba
Jul 15, 2014, 4:21:56 PM7/15/14
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Thank you very much for the detailed insight. Ill dig into that more in due time. Im curious how things like liability will affect the progress of open source hardware especially when it comes to more potentially dangerous contraptions. All these avenues for law suits would really put a damper on free and open communication when it comes to DIY tools. Kinda ruins the spirit...
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
From: Matt Harbowy
Sent: 7/15/2014 4:05 PM
To: diy...@googlegroups.com
Subject: Re: [DIYbio] On the topic of safety and DIY tools
Nathan McCorkle
Jul 15, 2014, 5:25:21 PM7/15/14
to diybio
On Tue, Jul 15, 2014 at 12:22 PM, Sebastian Cocioba <scoc...@gmail.com> wrote:
> That being said I feel uneasy with the notion of openly publishing the
> procedures for constructing a device which may be dangerous if misused.
I feel the same way about my DNA synthesis research, there are a lot
> That being said I feel uneasy with the notion of openly publishing the
> procedures for constructing a device which may be dangerous if misused.
of people that are concerned with this sort of thing. There's also
ITAR/trade-restrictions, which is vaguely written regarding DNA-tech
that I bet the Govt. could make a good case against
publishers/info-distributors if they wanted.
My plan currently is, once my process is working, that I'd just setup
a web store. That way sequences submitted for synthesis could be
screened with existing recommendations (checking against a list of
harmful organisms basically), which should at least make it harder for
nefarious activity to ensue (until someone makes a
controllable/directable polymerase with the synthecons).
I think you could do the same... have folks send you their organism
and DNA, and transform it for them, then ship the transformants back.
You could find trustworthy contacts in other countries that would
provide the same service too, if you wanted the world at-large to
benefit.
Yuriy Fazylov
Jul 15, 2014, 5:26:42 PM7/15/14
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Less than $100? When do we get to see it?
Sebastian Cocioba
Jul 15, 2014, 6:21:21 PM7/15/14
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When there is enough data to support reliable function. Last thing I want to do is publish a haphazardly written article to the list and get torn a new one. More importantly I would like to finish at least the preliminary debugging of the device so anyone interested can hit the ground running. All this pending a decent way to cover my ass in case of a disastrous liability claim. I wish we lived in a world where people can just share their knowledge and inventions and not have to worry about silly shit like some asshole hurting themselves, deliberately or not, and suing you for damages...and winning. Lets not even talk about selling the damn thing as a kit for those who want it pre-built and ready to rock....complete with open source gfp transient expression vector.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Dakota Hamill
Jul 15, 2014, 7:10:00 PM7/15/14
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Don't let fear run your decision making process. I understand the concern, but even in the super rare instance that someone did seek damages against you, they'd have to have a solid case which showed you purposefully intended harm or were so negligent in the design that injury was imminent. I doubt any judge or jury would hold you accountable for something that is clearly intended for use in a specific niche of the sciences. I'm sure a disclaimer / user agreement prior to downloading plans would also give you added protection. I understand that you want to prepare for the worst, and hope for the best, but I hope that doesn't keep you from showing off your hard work and design, or selling completed units.
I guess there are asshole's everywhere, but I'd like to think the # of potential ones that would download an open design to a gene gun for transformation wouldn't be the type of person to sue someone.
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Yuriy Fazylov
Jul 15, 2014, 8:04:31 PM7/15/14
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shamrock
Jul 15, 2014, 8:54:01 PM7/15/14
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Here's an idea that might work-patent it and grant licenses at no or minimal charge and with an iron clad provision that you can't be sued. Any "unauthorized use" would be infringement and you might escape liability. I'm not a lawyer so I don't know if this is a viable defense. I would put talking to an attorney high on the to-do list. Applying for a patent sounds counter to open source but if I was faced with the possibility of being sued (which I am on a daily basis) I would do everything possible to protect myself and install as many firewalls as possible.
Simon Quellen Field
Jul 15, 2014, 8:59:43 PM7/15/14
to diybio
1. You are not liable if someone misuses information you provide. You can freely teach people how to sharpen knives without worrying about criminal charges against you when they kill someone with a sharp knife. Likewise, they would not win a civil lawsuit for damages against you, unless you had an incompetent lawyer.
2. Anyone can sue anyone for anything. You are always at some risk that way, whether you publish or not. The risk is small, since there is no money to be made by suing you.
3. If you want to publish anonymously, that is easy to arrange.
4. You can give exact details about how to replicate work you have done, without worrying about any legal repercussions other than the frivolous lawsuits we are all susceptible to just for breathing. I write novels that give precise details about how to get away with murder, and I am not prohibited from doing so, nor would I lose a lawsuit if someone used my methods in real life.
5. I presume you live in New York, from your signature. In the U.S. we have this concept of constitutionally protected free speech.
6. You aren't selling a product that is defective. You are providing information. What someone does with that information is their problem. You can even sell a product that when used according to directions is designed to kill someone, and the most you will have to do is fill out some paperwork to sell your pistol.
You don't have to be a lawyer. As a citizen, you are supposed to know this stuff. Ignorance of it is not an excuse in a court of law.
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Matt Harbowy
Jul 15, 2014, 9:15:39 PM7/15/14
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Sebastian Cocioba
Jul 15, 2014, 10:11:10 PM7/15/14
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Pardon the language earlier. Just irked by the thought of a few trolls ruining my day with a left field lawsuit. I hope you didn't think that was directed at anyone in particular. I mean no quarrel nor disrespect and if it came off as such I humble apologize.
The big whoop im worried about is the fact that the device I've designed can go well beyond 1500psi (1100 required for chloroplast bombardment) thus in essence becoming a tungsten shotgun of sorts. Not something I would play around with without care. The whip cream, trojok wooden gun and others dont have the pressure capabilities, sterile vacuum chamber, control features, lack of need for compressed air tanks, etc which make this prototype a competitive variant to the retail PDS-1000. Its a high pressure apparatus and I haven't tested the upper limits and assessed overall safety yet. Basically I need to push it beyond its spec to see the stresses it can handle before catastrophic failure within reason and set a physical upper limit well within tolerances. Schedule ratings for piping be damned, I've seen schedule 80 pipes burst well below their rating. Either way I don't want to make it seem like my crappy gene gun is the best thing since sliced bread, just that I need to do more testing since its not reliable enough yet. Particle spread, nozzle design, size and amount of micro carrier needed, pH conditions, pressure optimization since pressures expressed by the bio-rad device do not directly convert to absolute particle velocity and impact force but relative to rupture disk rating, reproducibility, SAFETY, and of course stable transformation capabilities. All this is required of any decent particle delivery system and so I set my device to the same standard. All this takes time.
You could manage to place a drop of tungsten or gold with some bound plasmid on the tip of a super soaker, pump it to the max, and fire at a leaf and you can get some results though reproducibility and consistency will be severely lacking (tried it before). There are plenty of examples of DIY gene guns, some more complex than others, few if any have been able to transform chloroplasts. That's my goal and that's what my device will be capable of doing in its final form.
The big whoop im worried about is the fact that the device I've designed can go well beyond 1500psi (1100 required for chloroplast bombardment) thus in essence becoming a tungsten shotgun of sorts. Not something I would play around with without care. The whip cream, trojok wooden gun and others dont have the pressure capabilities, sterile vacuum chamber, control features, lack of need for compressed air tanks, etc which make this prototype a competitive variant to the retail PDS-1000. Its a high pressure apparatus and I haven't tested the upper limits and assessed overall safety yet. Basically I need to push it beyond its spec to see the stresses it can handle before catastrophic failure within reason and set a physical upper limit well within tolerances. Schedule ratings for piping be damned, I've seen schedule 80 pipes burst well below their rating. Either way I don't want to make it seem like my crappy gene gun is the best thing since sliced bread, just that I need to do more testing since its not reliable enough yet. Particle spread, nozzle design, size and amount of micro carrier needed, pH conditions, pressure optimization since pressures expressed by the bio-rad device do not directly convert to absolute particle velocity and impact force but relative to rupture disk rating, reproducibility, SAFETY, and of course stable transformation capabilities. All this is required of any decent particle delivery system and so I set my device to the same standard. All this takes time.
You could manage to place a drop of tungsten or gold with some bound plasmid on the tip of a super soaker, pump it to the max, and fire at a leaf and you can get some results though reproducibility and consistency will be severely lacking (tried it before). There are plenty of examples of DIY gene guns, some more complex than others, few if any have been able to transform chloroplasts. That's my goal and that's what my device will be capable of doing in its final form.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
whats with the colorful language? I believe my question was pretty simple. The answer should in tern be just as simple.
When there is enough data to support reliable function. Last thing I want to do is publish a haphazardly written article to the list and get torn a new one. More importantly I would like to finish at least the preliminary debugging of the device so anyone interested can hit the ground running. All this pending a decent way to cover my ass in case of a disastrous liability claim. I wish we lived in a world where people can just share their knowledge and inventions and not have to worry about silly shit like some asshole hurting themselves, deliberately or not, and suing you for damages...and winning. Lets not even talk about selling the damn thing as a kit for those who want it pre-built and ready to rock....complete with open source gfp transient expression vector.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Less than $100? When do we get to see it?
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Dakota Hamill
Jul 15, 2014, 11:29:52 PM7/15/14
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You seem to be very knowledgeable in the plant biotech field and have always posted well thought out things, so I have no doubt you will have a nice finished product. I'm interested to see what you've dreamed up.
The real question is, can you compete with the mustache of the kid in the video Yuriy posted?
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Sebastian Cocioba
Jul 15, 2014, 11:43:36 PM7/15/14
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Truly, that is one thing I may never be able to compete with. That thing is legend. I digress...thanks all for the deep insight, thoughtful ideas, and kind words. I hope my finished device won't disappoint.
Until then, here is a neat article from one of my favorite journals Plant Methods that may be of interest to those itching to build their own, albeit low pressure, gene gun for transient assays.
http://www.plantmethods.com/content/pdf/1746-4811-8-27.pdf
It was the first gene gun I've built a handful of months ago. Works fine for transient assays. Did some modifications to make it less cumbersome which I will include in my write up. Nothing fancy. It just works. The super soaker variant was my all time favorite though the swinnex filter holders are a bit hard to come by used and pricey new ($80/10pack) its the 13 (12.5mm) ones. If anyone has questions regarding this gene gun in particular, let me know. Ive hit some pitfalls along the path toward building and debugging this guy that may save you some time and teflon-tape frustrations.
Until then, here is a neat article from one of my favorite journals Plant Methods that may be of interest to those itching to build their own, albeit low pressure, gene gun for transient assays.
http://www.plantmethods.com/content/pdf/1746-4811-8-27.pdf
It was the first gene gun I've built a handful of months ago. Works fine for transient assays. Did some modifications to make it less cumbersome which I will include in my write up. Nothing fancy. It just works. The super soaker variant was my all time favorite though the swinnex filter holders are a bit hard to come by used and pricey new ($80/10pack) its the 13 (12.5mm) ones. If anyone has questions regarding this gene gun in particular, let me know. Ive hit some pitfalls along the path toward building and debugging this guy that may save you some time and teflon-tape frustrations.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
Destiny Z
Jul 16, 2014, 11:21:58 AM7/16/14
to diy...@googlegroups.com
There is always the option of creative commons license. They are free, and you could define the usage of your gene gun without restricting use or exchange of ideas.
https://creativecommons.org/
https://creativecommons.org/
Yuriy Fazylov
Jul 18, 2014, 1:41:27 AM7/18/14
to diy...@googlegroups.com
Good to know it's not directed at anyone. This coming after I asked you for an expression vector from you and you just happening to mention it. No need to hide what you mean.
Still I am curious about what could do 1500 psi and cost less than $100. I walked through a hardware store just out of curiosity :)
I wasn't wrong to ask you for the vector either. Did I noticed a plan for gene repository here? Nice.
Sebastian Cocioba
Jul 18, 2014, 6:23:27 AM7/18/14
to diy...@googlegroups.com
That is a gross misinterpretation of my post, yuriy. How you could
possibly link my off-list denial of giving you a vector I've made from
scratch for free or otherwise which contains novel, patentable,
elements not found in prior art which I kindly explained to my on-list
post of my rant about someone wanting to do self-experimentation may
hurt themselves because they think its a good idea to use said gene gun
inappropriately is beyond me. How are the two related? Why are you so
upset and snarky? Do you plan on self-experimentation?
Its quite difficult to convince someone that a rant wasn't intended in
any way towards them but come on now. What did I say that made you
think it had anything to do with you? Im sorry you are upset that I
didn't just hand you months of hard work and heavy financial burden
regardless of compensations offered. I don't think its fair to hold
that against me and twist my words. :( I mean no quarrel, friend and am
happy to help with any and all questions verbosely regarding your
project as I've done previously but I can't just hand out freebies if I
could support myself with them otherwise. Its a moral dilemma and right
now im too broke to throw such plasmid into the public domain yet.
Please refrain from posting personal issues on the list. Its not fair
to anyone. I would have preferred you just contact me in person and
discuss the issues at hand and not be publicly salty about them. I
don't know how else to convince you that you were, in no way, the
target nor even the after thought of my colorfully worded rant about
bio-punk grinders. Hope we can still maintain a positive, professional
relationship and set this issue aside. Peace, love, science.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D From: Yuriy Fazylov
Sent: 7/18/2014 1:42 AM
To: diy...@googlegroups.com
Subject: [DIYbio] Re: On the topic of safety and DIY tools
possibly link my off-list denial of giving you a vector I've made from
scratch for free or otherwise which contains novel, patentable,
elements not found in prior art which I kindly explained to my on-list
post of my rant about someone wanting to do self-experimentation may
hurt themselves because they think its a good idea to use said gene gun
inappropriately is beyond me. How are the two related? Why are you so
upset and snarky? Do you plan on self-experimentation?
Its quite difficult to convince someone that a rant wasn't intended in
any way towards them but come on now. What did I say that made you
think it had anything to do with you? Im sorry you are upset that I
didn't just hand you months of hard work and heavy financial burden
regardless of compensations offered. I don't think its fair to hold
that against me and twist my words. :( I mean no quarrel, friend and am
happy to help with any and all questions verbosely regarding your
project as I've done previously but I can't just hand out freebies if I
could support myself with them otherwise. Its a moral dilemma and right
now im too broke to throw such plasmid into the public domain yet.
Please refrain from posting personal issues on the list. Its not fair
to anyone. I would have preferred you just contact me in person and
discuss the issues at hand and not be publicly salty about them. I
don't know how else to convince you that you were, in no way, the
target nor even the after thought of my colorfully worded rant about
bio-punk grinders. Hope we can still maintain a positive, professional
relationship and set this issue aside. Peace, love, science.
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Sent: 7/18/2014 1:42 AM
To: diy...@googlegroups.com
Subject: [DIYbio] Re: On the topic of safety and DIY tools
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Yuriy Fazylov
Jul 18, 2014, 10:59:19 PM7/18/14
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You know what? You are right. I didn’t realize that you mentioned your expression vector in a context of making a kit for gene delivery or a patent on plasmid.
-Why are you so upset and snarky?
My one liners were snarky?
-Why are you so upset and snarky?
My one liners were snarky?
Accept my apology and understand that it was difficult to judge a character when he is cool - composed and then flips a switch when he notices you are on the scene asking questions. Understand where the confusion got me. All I did after that was recognize a pattern with you mentioning your expression vector.
I had no further interest in your vector after you mentioned how painstaking it was to construct the first time you explained it. Your work is your brainchild. I get that. Don’t think that I am bitter about it. I wouldn't even share details of my work if I didn't have to rely on advice from others from time to time.
-“publicly salty” what is that? I am afraid I am not familiar with that phrase. Attempts at tracking down the meaning gave me nothing other than cryptography.
-Do you plan on self-experimentation?
Question built on assumptions but I did work you up to those assumptions so that deserves an answer. Not that I would reserve to self-experimentation but I believe that an inventor should have that freedom. My personal interests are with plants. Most you can do with that for self-experimentation is using its extracts or cook it for dinner. Self-experimentation with a DIY biolistics gun or any such delivery system would be a stupid way to go. There are always other modes of gene delivery and they are getting better.
I had no further interest in your vector after you mentioned how painstaking it was to construct the first time you explained it. Your work is your brainchild. I get that. Don’t think that I am bitter about it. I wouldn't even share details of my work if I didn't have to rely on advice from others from time to time.
-“publicly salty” what is that? I am afraid I am not familiar with that phrase. Attempts at tracking down the meaning gave me nothing other than cryptography.
-Do you plan on self-experimentation?
Question built on assumptions but I did work you up to those assumptions so that deserves an answer. Not that I would reserve to self-experimentation but I believe that an inventor should have that freedom. My personal interests are with plants. Most you can do with that for self-experimentation is using its extracts or cook it for dinner. Self-experimentation with a DIY biolistics gun or any such delivery system would be a stupid way to go. There are always other modes of gene delivery and they are getting better.
Thanks for the lengthy reply. I had to ask myself, what deserved this kind of reply?
A thought just occurred as I was wrapping this up.
I am paraphrasing but -bacterial and cp expression is similar. I think I understand why you are targeting cp.
A thought just occurred as I was wrapping this up.
I am paraphrasing but -bacterial and cp expression is similar. I think I understand why you are targeting cp.
Sebastian Cocioba
Jul 18, 2014, 11:24:39 PM7/18/14
to diy...@googlegroups.com
Thanks for understanding and truly sorry for the confusion. I can get worked up about silly things and seem hostile. I put my foot in my mouth and for that I am sorry.
The main reason Im targeting the chloroplast is simple and two-part:
1. There are many more chloroplasts that would express my transgene than the one nucleus per cell. In a plant, chloroplasts express the bulk of all the proteins in a plant cell including the large subunit of RuBisCo. Lots of potential to bring your gene to the top of the total soluble protein list in terms of overall quantity.
2. Since the chloroplast (cp) is of prokaryotic ancestry, it can be manipulated as a bacterium which is simpler than a higher organism. Expression in bacteria involve far fewer "moving parts" than the myriad components of a eukaryotic expression scenario. Bacteria, including the plant chloroplast, can express a long chain of genes with just a single promoter which makes circuit design simpler in a few ways.
Its a worthwhile endeavor, albeit quite difficult, to transform the chloroplast and the technology to do so is fairly young so there is plenty of room for new discoveries, better ways to skin said cat, etc.
If you need private consultation regarding your project, since im aware of its sensitive nature, feel free to contact me off-list. I'd be happy to give you more info and not bore everyone else with pages and pages of my plant biotech ramblings. :)
The main reason Im targeting the chloroplast is simple and two-part:
1. There are many more chloroplasts that would express my transgene than the one nucleus per cell. In a plant, chloroplasts express the bulk of all the proteins in a plant cell including the large subunit of RuBisCo. Lots of potential to bring your gene to the top of the total soluble protein list in terms of overall quantity.
2. Since the chloroplast (cp) is of prokaryotic ancestry, it can be manipulated as a bacterium which is simpler than a higher organism. Expression in bacteria involve far fewer "moving parts" than the myriad components of a eukaryotic expression scenario. Bacteria, including the plant chloroplast, can express a long chain of genes with just a single promoter which makes circuit design simpler in a few ways.
Its a worthwhile endeavor, albeit quite difficult, to transform the chloroplast and the technology to do so is fairly young so there is plenty of room for new discoveries, better ways to skin said cat, etc.
If you need private consultation regarding your project, since im aware of its sensitive nature, feel free to contact me off-list. I'd be happy to give you more info and not bore everyone else with pages and pages of my plant biotech ramblings. :)
Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D
From: Yuriy Fazylov
Sent: 7/18/2014 10:59 PM
To: diy...@googlegroups.com
Subject: Re: [DIYbio] Re: On the topic of safety and DIY tools
Yuriy Fazylov
Jul 19, 2014, 1:37:16 AM7/19/14
to diy...@googlegroups.com
-it's alright even though it's mostly my fault.
-Regarding #1 & 2 Quantity yes, what about quality? If what you say is true about them being more bacteria-like, don't you run the risk of lack in solubility due to lack in glycosylation?
-My private matter is not so private anymore. I am running a fundraiser, on experiment.com. Not doing a good job of it I am afraid. Someone told me lack in detail is doing me in. Plus a video would help. You and anyone interested is welcome to poke holes in it. For example gene expression stability always seems to be on your mind. I haven't thought of it yet.
Bore anyone else with plant biotech? If I wouldn't be as volatile, I'd moderate a group devoted to that in DIY bio.
On Friday, July 18, 2014 11:24:39 PM UTC-4, Sebastian wrote:
> Thanks for understanding and truly sorry for the confusion. I can get worked up about silly things and seem hostile. I put my foot in my mouth and for that I am sorry.
>
>
> The main reason Im targeting the chloroplast is simple and two-part:
>
> 1. There are many more chloroplasts that would express my transgene than the one nucleus per cell. In a plant, chloroplasts express the bulk of all the proteins in a plant cell including the large subunit of RuBisCo. Lots of potential to bring your gene to the top of the total soluble protein list in terms of overall quantity.
>
>
> 2. Since the chloroplast (cp) is of prokaryotic ancestry, it can be manipulated as a bacterium which is simpler than a higher organism. Expression in bacteria involve far fewer "moving parts" than the myriad components of a eukaryotic expression scenario. Bacteria, including the plant chloroplast, can express a long chain of genes with just a single promoter which makes circuit design simpler in a few ways.
>
>
> Its a worthwhile endeavor, albeit quite difficult, to transform the chloroplast and the technology to do so is fairly young so there is plenty of room for new discoveries, better ways to skin said cat, etc.
>
> If you need private consultation regarding your project, since im aware of its sensitive nature, feel free to contact me off-list. I'd be happy to give you more info and not bore everyone else with pages and pages of my plant biotech ramblings. :)
>
>
> Sebastian S. Cocioba
> CEO & Founder
> New York Botanics, LLC
> Plant Biotech R&D
>
>
>
-Regarding #1 & 2 Quantity yes, what about quality? If what you say is true about them being more bacteria-like, don't you run the risk of lack in solubility due to lack in glycosylation?
-My private matter is not so private anymore. I am running a fundraiser, on experiment.com. Not doing a good job of it I am afraid. Someone told me lack in detail is doing me in. Plus a video would help. You and anyone interested is welcome to poke holes in it. For example gene expression stability always seems to be on your mind. I haven't thought of it yet.
Bore anyone else with plant biotech? If I wouldn't be as volatile, I'd moderate a group devoted to that in DIY bio.
On Friday, July 18, 2014 11:24:39 PM UTC-4, Sebastian wrote:
> Thanks for understanding and truly sorry for the confusion. I can get worked up about silly things and seem hostile. I put my foot in my mouth and for that I am sorry.
>
>
> The main reason Im targeting the chloroplast is simple and two-part:
>
> 1. There are many more chloroplasts that would express my transgene than the one nucleus per cell. In a plant, chloroplasts express the bulk of all the proteins in a plant cell including the large subunit of RuBisCo. Lots of potential to bring your gene to the top of the total soluble protein list in terms of overall quantity.
>
>
> 2. Since the chloroplast (cp) is of prokaryotic ancestry, it can be manipulated as a bacterium which is simpler than a higher organism. Expression in bacteria involve far fewer "moving parts" than the myriad components of a eukaryotic expression scenario. Bacteria, including the plant chloroplast, can express a long chain of genes with just a single promoter which makes circuit design simpler in a few ways.
>
>
> Its a worthwhile endeavor, albeit quite difficult, to transform the chloroplast and the technology to do so is fairly young so there is plenty of room for new discoveries, better ways to skin said cat, etc.
>
> If you need private consultation regarding your project, since im aware of its sensitive nature, feel free to contact me off-list. I'd be happy to give you more info and not bore everyone else with pages and pages of my plant biotech ramblings. :)
>
>
> Sebastian S. Cocioba
> CEO & Founder
> New York Botanics, LLC
> Plant Biotech R&D
>
>
>
Nathan McCorkle
Jul 19, 2014, 4:45:58 AM7/19/14
to diybio
On Fri, Jul 18, 2014 at 10:37 PM, Yuriy Fazylov <yuriy...@gmail.com> wrote:
> Bore anyone else with plant biotech? If I wouldn't be as volatile, I'd moderate a group devoted to that in DIY bio.
Please no, there isn't nearly enough conversation here to require
> Bore anyone else with plant biotech? If I wouldn't be as volatile, I'd moderate a group devoted to that in DIY bio.
/another/ mailing list.
Brian Degger
Jul 19, 2014, 5:17:33 AM7/19/14
to diy...@googlegroups.com
Please 'bore' us with more plant Biotech, you don't need another list. I learn stuff I find usefull here but weren't looking for.
I haven't seen any email backlashes against biological specialties on this list. If there ever is....then it's worth considering a specialist list.
Cheers
B
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Cathal Garvey
Jul 19, 2014, 7:02:16 AM7/19/14
to diy...@googlegroups.com
Your email formatting is confusing. Are you talking about your own
fundraiser, or someone elses'? Either way, link please?
--
T: @onetruecathal, @IndieBBDNA
P: +353876363185
W: http://indiebiotech.com
fundraiser, or someone elses'? Either way, link please?
T: @onetruecathal, @IndieBBDNA
P: +353876363185
W: http://indiebiotech.com
Josiah Zayner
Jul 20, 2014, 12:58:34 PM7/20/14
to diy...@googlegroups.com
Best line of the month "Publicly salty, does that have to do with cryptography?" hahaha. That is a great play on words even if it was unintentional.
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