Re: [DIYbio] lacI Repressor in domesticated Coli

Sweet, thanks so much for your insight! That's great news







On Monday, October 29, 2018 at 1:02:29 AM UTC-4, incisive systematics wrote:
Edit .. typo. ... "endogenous lacI represssor is there so no need to add another" is what it should read.

Sent from my iPhone

On Oct 29, 2018, at 12:57 AM, Matt Lawes <ma...@insysx.com> wrote:

Yes the endogenous lacI repressive is there so. I need to add another. You add inducer IPTG to control gene expression from the lac promoter ....the inducer causes the repressor  to fall off  the lacO operator that overlaps the lac promoter. Now RNA Polymerase can come in and transcribe from lac promoter ..... the more IPTG the more expression you get .. kind of linear (sigmoidal with a large linear center).
>matt

Sent from my iPhone

On Oct 29, 2018, at 12:42 AM, Andreas Mega Stuermer <andreas.t...@gmail.com> wrote:

Hi guys, 

I was wondering if it is neccessary to express the lac repressor protein in DH5a and similar strains to be able to use the lac or tac promoter, or if this one is still intact in coli? 
Google is remarkably unhelpful. 

I would think it is still intact? 


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Re: [DIYbio] lacI Repressor in domesticated Coli

Edit .. typo. ... "endogenous lacI represssor is there so no need to add another" is what it should read.

Sent from my iPhone

On Oct 29, 2018, at 12:57 AM, Matt Lawes <matt@insysx.com> wrote:

Yes the endogenous lacI repressive is there so. I need to add another. You add inducer IPTG to control gene expression from the lac promoter ....the inducer causes the repressor  to fall off  the lacO operator that overlaps the lac promoter. Now RNA Polymerase can come in and transcribe from lac promoter ..... the more IPTG the more expression you get .. kind of linear (sigmoidal with a large linear center).
>matt

Sent from my iPhone

On Oct 29, 2018, at 12:42 AM, Andreas Mega Stuermer <andreas.t.stuermer@gmail.com> wrote:

Hi guys, 

I was wondering if it is neccessary to express the lac repressor protein in DH5a and similar strains to be able to use the lac or tac promoter, or if this one is still intact in coli? 
Google is remarkably unhelpful. 

I would think it is still intact? 


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Re: [DIYbio] lacI Repressor in domesticated Coli

Yes the endogenous lacI repressive is there so. I need to add another. You add inducer IPTG to control gene expression from the lac promoter ....the inducer causes the repressor  to fall off  the lacO operator that overlaps the lac promoter. Now RNA Polymerase can come in and transcribe from lac promoter ..... the more IPTG the more expression you get .. kind of linear (sigmoidal with a large linear center).
>matt

Sent from my iPhone

On Oct 29, 2018, at 12:42 AM, Andreas Mega Stuermer <andreas.t.stuermer@gmail.com> wrote:

Hi guys, 

I was wondering if it is neccessary to express the lac repressor protein in DH5a and similar strains to be able to use the lac or tac promoter, or if this one is still intact in coli? 
Google is remarkably unhelpful. 

I would think it is still intact? 


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[DIYbio] lacI Repressor in domesticated Coli

Hi guys, 

I was wondering if it is neccessary to express the lac repressor protein in DH5a and similar strains to be able to use the lac or tac promoter, or if this one is still intact in coli? 
Google is remarkably unhelpful. 

I would think it is still intact? 


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[DIYbio] Meet the Scientist Who Injected Himself with 3.5 Million-Year-Old Bacteria

https://www.youtube.com/watch?v=1EFPuLhawlI


https://curiosity.com/topics/a-russian-scientist-injected-himself-with-35-million-year-old-bacteria-curiosity/


https://motherboard.vice.com/en_us/article/yp3gg7/meet-the-scientist-who-injected-himself-with-35-million-year-old-bacteria


It determines dormancy and life cycle of bacteria. 



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Re: [DIYbio] was: glowing plant - Open Source chloroplast engineering

Gene gun has the advantage that you can shoot it into leaf tissue and then regenerate it. 

Electroporation of protoplasts may be possible but they are easy to burst

On Sat, Oct 27, 2018, 10:25 John Griessen <john@industromatic.com> wrote:
On 10/26/18 7:57 PM, Andreas "Mega" Stuermer wrote:
> First project: creating the empty vector, SciHouse in Florida will store the vector in bulk and share with anyone interested (open
> source)

How do you do transformation?  Is electroporation used?  I'd like more beta testers of my electroporator.
So far, the folks that have gotten one have never used it on live cells.  Kind of slows the project momentum...

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Re: [DIYbio] was: glowing plant - Open Source chloroplast engineering

On 10/26/18 7:57 PM, Andreas "Mega" Stuermer wrote:
> First project: creating the empty vector, SciHouse in Florida will store the vector in bulk and share with anyone interested (open
> source)

How do you do transformation? Is electroporation used? I'd like more beta testers of my electroporator.
So far, the folks that have gotten one have never used it on live cells. Kind of slows the project momentum...

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Re: [DIYbio] was: glowing plant - Open Source chloroplast engineering

Now that's interesting, I swear I saw it glow. It was the first generation (bioglow) before they called it gleaux. 

If you can send it to my friend in Florida, that would be cool. He might try to grow it on spectinomycin, which was their selection marker. Maybe they didn't delete it

I will check if we can grow it in the museum's biolab or if that requires months of approval. We might be lucky because we already had approval to put gfp and lux into tobacco. 



On Sat, Oct 27, 2018, 01:49 Nathan McCorkle <nmz787@gmail.com> wrote:
I have seed from my gleaux plant, a bunch that dropped into the pot
that it was planted in have sprouted so I know they're viable. I never
saw the original glow, nor these... and they don't show up with a 30
second dSLR exposure image. I had been working to setup my laptop to
remotely trigger my camera to take a series of images and then add a
bunch of images together to try stack the brightness... but I got
caught up with other things and then my laptop went through 3 weeks of
failed ubuntu upgrade attempts before I got it straightened out again
recently.

Anyway, if you think you could use some seed, how many would you want?
On Fri, Oct 26, 2018 at 5:57 PM Andreas "Mega" Stuermer
<andreas.t.stuermer@gmail.com> wrote:
>
> Hi guys,
>
> I am currently re-visiting the idea of chloroplast engineering. Chloroplast engineering yields loads of proteins, and is only maternally inherited (containment bonus). Antibiotic selection marker will be removable with Cre-Lox, and should happen with low frequency by iself too.
>
> First project: creating the empty vector, SciHouse in Florida will store the vector in bulk and share with anyone interested (open source)
> Second project: putting the lux operon in, just because. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015461 *
> I have seen one of these plants, and they were visibly glowing to the naked eye (but weak). Note that that was way before the Silicon Valley glowing plant cowboy project.
>
> *Unfortunately they stopped selling them in the United States for no apparent reason (maybe they didnt't get enough customers).
>
> Not sure if I should start with weeping willow or tobacco. I've been routinely working with tobacco and can share my protocols with our US collaborators so they can do the tissue culture there. Tobacco is pretty lame though.
>
> Anyways, just wanted to see if anyone would be willing to chime in, synthesis is expected to cost around 500$. Attached the file. Addition of lux will just be one PCR step
>
>
>
>
> --
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Re: [DIYbio] was: glowing plant - Open Source chloroplast engineering

I have seed from my gleaux plant, a bunch that dropped into the pot
that it was planted in have sprouted so I know they're viable. I never
saw the original glow, nor these... and they don't show up with a 30
second dSLR exposure image. I had been working to setup my laptop to
remotely trigger my camera to take a series of images and then add a
bunch of images together to try stack the brightness... but I got
caught up with other things and then my laptop went through 3 weeks of
failed ubuntu upgrade attempts before I got it straightened out again
recently.

Anyway, if you think you could use some seed, how many would you want?
On Fri, Oct 26, 2018 at 5:57 PM Andreas "Mega" Stuermer
<andreas.t.stuermer@gmail.com> wrote:
>
> Hi guys,
>
> I am currently re-visiting the idea of chloroplast engineering. Chloroplast engineering yields loads of proteins, and is only maternally inherited (containment bonus). Antibiotic selection marker will be removable with Cre-Lox, and should happen with low frequency by iself too.
>
> First project: creating the empty vector, SciHouse in Florida will store the vector in bulk and share with anyone interested (open source)
> Second project: putting the lux operon in, just because. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015461 *
> I have seen one of these plants, and they were visibly glowing to the naked eye (but weak). Note that that was way before the Silicon Valley glowing plant cowboy project.
>
> *Unfortunately they stopped selling them in the United States for no apparent reason (maybe they didnt't get enough customers).
>
> Not sure if I should start with weeping willow or tobacco. I've been routinely working with tobacco and can share my protocols with our US collaborators so they can do the tissue culture there. Tobacco is pretty lame though.
>
> Anyways, just wanted to see if anyone would be willing to chime in, synthesis is expected to cost around 500$. Attached the file. Addition of lux will just be one PCR step
>
>
>
>
> --
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-Nathan

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[DIYbio] was: glowing plant - Open Source chloroplast engineering

Hi guys, 

I am currently re-visiting the idea of chloroplast engineering. Chloroplast engineering yields loads of proteins, and is only maternally inherited (containment bonus). Antibiotic selection marker will be removable with Cre-Lox, and should happen with low frequency by iself too. 

First project: creating the empty vector, SciHouse in Florida will store the vector in bulk and share with anyone interested (open source) 
Second project: putting the lux operon in, just because. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015461 *
I have seen one of these plants, and they were visibly glowing to the naked eye (but weak). Note that that was way before the Silicon Valley glowing plant cowboy project. 

*Unfortunately they stopped selling them in the United States for no apparent reason (maybe they didnt't get enough customers).  

Not sure if I should start with weeping willow or tobacco. I've been routinely working with tobacco and can share my protocols with our US collaborators so they can do the tissue culture there. Tobacco is pretty lame though. 

Anyways, just wanted to see if anyone would be willing to chime in, synthesis is expected to cost around 500$. Attached the file. Addition of lux will just be one PCR step 




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[DIYbio] Re: Climate change solutions?

Recently had a conversation about how nice it would be to have decaffeinated (+ ideally de-theobrominated, do-theophyllinated, but those are highly related molecules) chocolate. Someone mentioned that the ideal way to decaffeinate coffee beans right now is using CO2, and I remembered this topic. Could CO2 be used to decaf chocolate beans?


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Re: [DIYbio] Re: Climate change solutions?

We set out to make a diamond using atmospheric carbon dioxide. Turns out that's really hard.  
Diamonds are hard? Whodathunkit? :-)
 
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On Mon, Oct 22, 2018 at 6:17 PM Tito <titojankowski@gmail.com> wrote:
You're totally spot on here, Cathal. Cookbooks for peanuts. Cookbooks for carbon.

More uses of carbon dioxide would change the game. Right now it's treated as a nearly worthless burden ($40/ton) that civilization has to bury underground or turn away from. The IPCC modeled a tax of up to $27,000 per ton of carbon dioxide by 2100 though!

Our team wanted to explore high-value uses of carbon. We set out to make a diamond using atmospheric carbon dioxide. Turns out that's really hard. So we made a decorative planter out of air instead: http://airminers.org

Tito

On Tuesday, October 2, 2018 at 11:59:32 PM UTC-7, Cathal Garvey wrote:
Thinking-emoji-face.. When the USDA wanted to make peanuts a thing, they created cookbooks of things you could do with peanuts. It worked.

We have some industrial processes already that use supercritical CO2. Perhaps if we devised more uses, especially ones that would be awesome but are uneconomical because of the cost of CO2, we could help create demand for high-volume CO2?

No uses that do not involve full recovery/recycling of CO2, please..

One obvious sink for the CO2 is, of course, greenhouses. CO2 is a Greenhouse Gas after all :)

On 3 October 2018 00:01:06 GMT+01:00, Tito <titoja...@gmail.com> wrote:
Agreed, Patrik, burying fossil fuels sounds like a plan, I know a place right down the street that sells liquid fuel!

And yes, smokestack is way more energetically efficient than sucking it straight from the air, carbon dioxide at industrial smokestack "can be as much as 10−25 volume percent or more of the flue gas". The main limitation seems to be that the uses of concentrated carbon dioxide are limited.

Tito

On Friday, September 21, 2018 at 10:39:38 PM UTC-7, Patrik D'haeseleer wrote:
The biggest problem with carbon capture and sequestration (CCS) is that the efficiencies go down dramatically the more diluted the carbon is. So capturing CO2 at a smokestack is way more efficient than sucking it straight from the air. 

By extrapolation, by far the most efficient form of carbon capture and sequestration would be to capture the carbon in its purest form. That is, take coal and other fossil fuels, and bury them underground!

Patrik


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Re: [DIYbio] Re: Climate change solutions?

You're totally spot on here, Cathal. Cookbooks for peanuts. Cookbooks for carbon.

More uses of carbon dioxide would change the game. Right now it's treated as a nearly worthless burden ($40/ton) that civilization has to bury underground or turn away from. The IPCC modeled a tax of up to $27,000 per ton of carbon dioxide by 2100 though!

Our team wanted to explore high-value uses of carbon. We set out to make a diamond using atmospheric carbon dioxide. Turns out that's really hard. So we made a decorative planter out of air instead: http://airminers.org

Tito

On Tuesday, October 2, 2018 at 11:59:32 PM UTC-7, Cathal Garvey wrote:
Thinking-emoji-face.. When the USDA wanted to make peanuts a thing, they created cookbooks of things you could do with peanuts. It worked.

We have some industrial processes already that use supercritical CO2. Perhaps if we devised more uses, especially ones that would be awesome but are uneconomical because of the cost of CO2, we could help create demand for high-volume CO2?

No uses that do not involve full recovery/recycling of CO2, please..

One obvious sink for the CO2 is, of course, greenhouses. CO2 is a Greenhouse Gas after all :)

On 3 October 2018 00:01:06 GMT+01:00, Tito <titoja...@gmail.com> wrote:
Agreed, Patrik, burying fossil fuels sounds like a plan, I know a place right down the street that sells liquid fuel!

And yes, smokestack is way more energetically efficient than sucking it straight from the air, carbon dioxide at industrial smokestack "can be as much as 10−25 volume percent or more of the flue gas". The main limitation seems to be that the uses of concentrated carbon dioxide are limited.

Tito

On Friday, September 21, 2018 at 10:39:38 PM UTC-7, Patrik D'haeseleer wrote:
The biggest problem with carbon capture and sequestration (CCS) is that the efficiencies go down dramatically the more diluted the carbon is. So capturing CO2 at a smokestack is way more efficient than sucking it straight from the air. 

By extrapolation, by far the most efficient form of carbon capture and sequestration would be to capture the carbon in its purest form. That is, take coal and other fossil fuels, and bury them underground!

Patrik


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Re: [DIYbio] Re: Surface Plasmon Resonance

Here is a good paper on SPR as a biosensor: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481982/

Contingent to my application with this device is the ability to test tens of things at once or more, meaning I can't use a single or even small set of probes. Plus as you may know, it is virtually impossible to attach probes to a specific protein in a raw lysate without also tagging a million other things. But SPR is a great way to find specific things in complex solutions label free using antibodies, etc.

On Saturday, October 20, 2018 at 2:56:21 AM UTC-4, Skyler Gordon wrote:
I've never heard of SPR being used on liquids.

Usually SPR uses Infra-Red (IR-SPR) and anything that IR will bounce off of should give you a signal that represents that material. If your sample is negative without bonding and positive with, it sounds possible.

That being said, if you're bonding something to a molecule that will result in IR-SPR signal, youre really just adding a probe anyways... I'd suggest just using some sort of probe.

-SG
On Fri, Oct 19, 2018 at 3:18 PM Jacob Palumbo <palumb...@gmail.com> wrote:
Sorry to necrobump a clearly dead thread, but I am actually specifically in need of this literally right now. In regards to Josiah's question, I'll run validation tests (can test lysozyme and various cancer biomarkers) in exchange for the spec and design files.

Let me know ASAP, thanks.

On Wednesday, January 28, 2015 at 2:01:23 PM UTC-5, Josiah Zayner wrote:
If Daniel responds to this thread I have a question about the Kickstarter.

Have you done any experiments to validate your instrument by showing it provides measurements similar to what is seen for commercial grade instruments in literature?




On Friday, January 23, 2015 at 12:14:23 PM UTC-8, Daniel Glenn wrote:

I was wondering if their would be interest in an affordable surface plasmon resonance bio-assay sensor?


Surface plasmon resonance can be used as a method to detect antibody-antigen (and other) reactions directly with an optoelectronic sensor. Biacore and others make very expensive instruments that read 96-well plates, but I'm talking about something that reads samples one at a time and doesn't cost $33,000+.


It can be used to perform the same type of assays that occur in Western blot and ELISA without attaching tags, because the probe molecule is immobilized chemically on the surface of the optics with chemistry. Would those type of assays be useful to the general DIYbio community?


Do you think that there would be interest in such a device for the more general citizen-science community if test kits for things like Salmonella or Dengue that anyone with reasonable skills and training could use were developed?


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Re: [DIYbio] Re: Surface Plasmon Resonance

I've never heard of SPR being used on liquids.

Usually SPR uses Infra-Red (IR-SPR) and anything that IR will bounce off of should give you a signal that represents that material. If your sample is negative without bonding and positive with, it sounds possible.

That being said, if you're bonding something to a molecule that will result in IR-SPR signal, youre really just adding a probe anyways... I'd suggest just using some sort of probe.

-SG

On Fri, Oct 19, 2018 at 3:18 PM Jacob Palumbo <palumbojacob@gmail.com> wrote:
Sorry to necrobump a clearly dead thread, but I am actually specifically in need of this literally right now. In regards to Josiah's question, I'll run validation tests (can test lysozyme and various cancer biomarkers) in exchange for the spec and design files.

Let me know ASAP, thanks.

On Wednesday, January 28, 2015 at 2:01:23 PM UTC-5, Josiah Zayner wrote:
If Daniel responds to this thread I have a question about the Kickstarter.

Have you done any experiments to validate your instrument by showing it provides measurements similar to what is seen for commercial grade instruments in literature?




On Friday, January 23, 2015 at 12:14:23 PM UTC-8, Daniel Glenn wrote:

I was wondering if their would be interest in an affordable surface plasmon resonance bio-assay sensor?


Surface plasmon resonance can be used as a method to detect antibody-antigen (and other) reactions directly with an optoelectronic sensor. Biacore and others make very expensive instruments that read 96-well plates, but I'm talking about something that reads samples one at a time and doesn't cost $33,000+.


It can be used to perform the same type of assays that occur in Western blot and ELISA without attaching tags, because the probe molecule is immobilized chemically on the surface of the optics with chemistry. Would those type of assays be useful to the general DIYbio community?


Do you think that there would be interest in such a device for the more general citizen-science community if test kits for things like Salmonella or Dengue that anyone with reasonable skills and training could use were developed?


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[DIYbio] Re: Surface Plasmon Resonance

Sorry to necrobump a clearly dead thread, but I am actually specifically in need of this literally right now. In regards to Josiah's question, I'll run validation tests (can test lysozyme and various cancer biomarkers) in exchange for the spec and design files.

Let me know ASAP, thanks.

On Wednesday, January 28, 2015 at 2:01:23 PM UTC-5, Josiah Zayner wrote:
If Daniel responds to this thread I have a question about the Kickstarter.

Have you done any experiments to validate your instrument by showing it provides measurements similar to what is seen for commercial grade instruments in literature?




On Friday, January 23, 2015 at 12:14:23 PM UTC-8, Daniel Glenn wrote:

I was wondering if their would be interest in an affordable surface plasmon resonance bio-assay sensor?


Surface plasmon resonance can be used as a method to detect antibody-antigen (and other) reactions directly with an optoelectronic sensor. Biacore and others make very expensive instruments that read 96-well plates, but I'm talking about something that reads samples one at a time and doesn't cost $33,000+.


It can be used to perform the same type of assays that occur in Western blot and ELISA without attaching tags, because the probe molecule is immobilized chemically on the surface of the optics with chemistry. Would those type of assays be useful to the general DIYbio community?


Do you think that there would be interest in such a device for the more general citizen-science community if test kits for things like Salmonella or Dengue that anyone with reasonable skills and training could use were developed?


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[DIYbio] Re: Oxalobacter formigenes probiotic suppliers? was: (Re)Becoming Human: what happened the day I replaced 99% of the genes in my body

https://www.atcc.org/products/all/35274.aspx#documentation

I found this-- I'm probably going to order it and see.  I've seen some brief mentions that O.f. supplementation doesn't reduce oxalate content in urine, but that seems like a fragment of a bigger story.  Any other anecdotes or success stories here? I'm one month oxalate-reduced and feeling a little better, but not much.

On Tuesday, September 30, 2014 at 4:50:05 PM UTC-4, Nathan McCorkle wrote:
The article mentions Oxalobacter formigenes being present in significant percentage in the Hadza, and that this is something that western microbiomes pretty much lack.

I tried googling oxalobacter probiotic, but didn't get very far. Is this something that doesn't exist? If it does, can someone post a link here? I've got a friend with kidney stones who has been living with them due to lack of western healthcare insurance.

The role of Oxalobacter formigenes colonization in calcium oxalate stone disease.




On Tue, Sep 30, 2014 at 1:21 PM, Nathan McCorkle <nmz...@gmail.com> wrote:

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Re: [DIYbio] Spider Beer Overview: Making Yeast Produce Black Widow Silk

On Sat, Oct 13, 2018 at 7:41 AM <djwrister@gmail.com> wrote:

That's pretty cool!  It looks like they're still in development though, since they don't offer any actual products for sale.  Hopefully we won't have to wait too long.

-Dan 

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[DIYbio] FW: Announcing the Launch of the OpenMTA



Von: BioBricks Foundation <contact@biobricks.org>
Antworten an: BioBricks Foundation <contact@biobricks.org>


Announcing the Launch of the OpenMTA

The OpenMTA is a new, easy-to-use legal tool enabling open exchange of biological materials

We are pleased to share with you the publication of the OpenMTA in Nature Biotechnology at https://rdcu.be/81zc

The OpenMTA is a Material Transfer Agreement designed to support openness, sharing, and innovation in biology and biotechnology. Material Transfer Agreements provide the legal frameworks within which research organizations define the terms and conditions for sharing their materials - everything from DNA molecules to plant seeds to patient samples.
 
Use of the OpenMTA allows redistribution and commercial use of materials, while respecting rights of creators and promoting safe practices. It promotes access for researchers and individuals working in less privileged institutions and world regions. The new standardized framework also eases the administrative burden for technology transfer offices, negating the need to negotiate unique terms for individual transfers of widely-used material.
 
We invite you to become a signatory, and to encourage the research organization, company, or community lab in which you work to become a signatory, to the OpenMTA Master Agreement. Please visit https://biobricks.org/openmta to learn more and sign on today.

Find Out More
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