January 2015 | Science

[DIYbio] Re: I want to DIY a Stirred-Tank Bioreactor

9:35 PM |

Hi All,

In our first IndieBio SF class we'll have Sensa.io joining us, Greg (who worked out of Biocurious, Counter Culture Labs and most recently Genspace) and the team are really passionate about building an open source bioreactor (they've build several bioreactors previously) and we're really pleased to be able to back him through IndieBio SF. I'm sure he'd welcome your thoughts and help with the open source bioreactor they'll be building to ensure it's as useful as possible to the community!

Feel free to reach out directly to him via Sensa.io!

All the best,

Ryan

On Saturday, January 31, 2015 at 9:28:36 PM UTC-8, Priya Phalak wrote:

If there is anything that depresses me more in this group is cynicism rather than debate, discussions, rebut or even arguments over scientific topics..
people are inclining more towards plotting boundary , limitations of this group they are not doing any good to this group,
"Scratch any cynic and you will find a disappointed idealist... your cynicism wont stop my hunger for wisdom "

hmm no matter how much one may try to show his supremacy in literature, dialects or even as low as spelling ..
this is fkn bio group discuss about bio only.. and your manuals wont stop somebody's passion..

On Wednesday, January 21, 2015 at 7:03:36 PM UTC+5:30, Priya Phalak wrote:
hello group , I am new to DIYBIO .. I want to DIY a stirred-tank bio reactor,
tried going through https://github.com/Bioreactor/ but unable to catch a clue where to start it coz of geeked documentation
hence can some one demystify building bioreactor with simple step by step style document or help me find some other open source DIY Project
and guide me to build a bioreactor by providing every single details to DIY a bioreactor.
kindly provide us the specifications of generic board numbers,specific board numbers , sensors, connectors , hardware etc.,
and also kindly provide us the materials like step by step documents and videos in this regard

with love
Priya Phalak

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[DIYbio] Re: I want to DIY a Stirred-Tank Bioreactor

9:28 PM |

If there is anything that depresses me more in this group is cynicism rather than debate, discussions, rebut or even arguments over scientific topics..

people are inclining more towards plotting boundary , limitations of this group they are not doing any good to this group,

"Scratch any cynic and you will find a disappointed idealist... your cynicism wont stop my hunger for wisdom "

hmm no matter how much one may try to show his supremacy in literature, dialects or even as low as spelling ..

this is fkn bio group discuss about bio only.. and your manuals wont stop somebody's passion..

On Wednesday, January 21, 2015 at 7:03:36 PM UTC+5:30, Priya Phalak wrote:

hello group , I am new to DIYBIO .. I want to DIY a stirred-tank bio reactor,
tried going through https://github.com/Bioreactor/ but unable to catch a clue where to start it coz of geeked documentation
hence can some one demystify building bioreactor with simple step by step style document or help me find some other open source DIY Project
and guide me to build a bioreactor by providing every single details to DIY a bioreactor.
kindly provide us the specifications of generic board numbers,specific board numbers , sensors, connectors , hardware etc.,
and also kindly provide us the materials like step by step documents and videos in this regard

with love
Priya Phalak

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[DIYbio] Re: I want to DIY a Stirred-Tank Bioreactor

9:24 PM |

hello Jonathan Cline,

If there is anything that depresses me more in this group is cynicism rather than debate, discussions, rebut or even arguments over scientific topics..

people are inclining more towards plotting boundary , limitations of this group they are not doing any good to this group,

"Scratch any cynic and you will find a disappointed idealist... your cynicism wont stop my hunger for wisdom "

hmm no matter how much one may try to show his supremacy in literature, dialects or even as low as spelling ..

this is fkn bio group discuss about bio only..

On Wednesday, January 21, 2015 at 7:03:36 PM UTC+5:30, Priya Phalak wrote:

hello group , I am new to DIYBIO .. I want to DIY a stirred-tank bio reactor,
tried going through https://github.com/Bioreactor/ but unable to catch a clue where to start it coz of geeked documentation
hence can some one demystify building bioreactor with simple step by step style document or help me find some other open source DIY Project
and guide me to build a bioreactor by providing every single details to DIY a bioreactor.
kindly provide us the specifications of generic board numbers,specific board numbers , sensors, connectors , hardware etc.,
and also kindly provide us the materials like step by step documents and videos in this regard

with love
Priya Phalak

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[DIYbio] Re: TLR Biosensor

8:49 PM |

hey Simon Rose ,

"synthetic pathogen sensor using human toll " such a cool idea ...

have you seen this Multiplex Automated Genome Engineering (MAGE) project http://wyss.harvard.edu/viewpage/330/

every thing is possible once you have decided to do it ... so keep doing the good work.. tell me more about what you know

about factor VIII ...

and always remember one thing no matter what they say ...

"Positive anything is better than negative nothing."

On Sunday, February 1, 2015 at 1:22:54 AM UTC+5:30, Simon Rose wrote:

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

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Re: [DIYbio] $50 camera good for microscopy with machine vision code included

5:01 PM |

The camera comes with software from Canon for controlling it via USB.

There is also an SDK if you want to design your own interface.

There is also Magic Lantern that adds features to the software in the camera. It is FOSS. If is is anything like CHDK (for the PowerShot cameras), it would give you the ability to run programs inside the camera itself. If not, you could add that capability.

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On Sat, Jan 31, 2015 at 9:03 AM, John Griessen <john@industromatic.com> wrote:

On 01/31/2015 09:54 AM, Simon Quellen Field wrote:

When controlled by my computer, I find the Canon to be quite suited to microphotography.

What's the software? Sounds good... FOS SW preferred...

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[DIYbio] Re: DIY Turbidostat

5:00 PM |

Hi everyone,

thanks to JT first for his amazing project and sharing it as well as the content around it. Just to compelete this thread here a few links of more turbidostat and chemostat systems that were built by the Dunham and the Klavin lab:

DIY Turbidostat Array:
https://depts.washington.edu/soslab/turbidostat/pmwiki/pmwiki.php
DIY Chemostat Array:
http://dunham.gs.washington.edu/DunhamLabMinistats.pdf

I find these projects really inspiring especially as considering this patent solves the problems of biofilms/ dilution resistant strains! https://www.google.de/patents/WO2003004656A9?dq=mutzel&ei=im-mVI2uK4e-PK6OgMgO&cl=en
So by using two culture vessels and transfering the culture from one to the other vessel and cleaning out the one that is not in use - you can actually grow ou bugs for unlimited generations. So basically you can adapt bugs to grow on any waste media by just waiting until they are adapted (talking it easy).

I am currently planning to built a low cost model of the Evolinator and optionally combing it with another vessel. We will see :). However, I intend to culture anaerob archeae that grow really slow (doubling time 4h) so I will start with the normal Evolvinator set up under a DIY anaerobic chamber. Does anybody has experience with anaerobes? Are they suitable for such an automated culturing endeavor?

Cheers and thanks for feedback

Johann

Am Freitag, 28. Oktober 2011 04:19:41 UTC+2 schrieb Jt:

Hello,

New to the DIYBio group.

I have created a turbidostat that I would like to share with the
community. In brief, it uses an Arduino to control a peristaltic pump
based on OD readings, includes temperature control as well as an
aquarium pump for aeration. Additionally, I have a version that
forgoes the pump and relies on air pressure and valves to move fluid
through the system. The system currently uses the Arduino Ethernet
Shield and HTML interface to control it, though an interface over
serial could be easily written for anyone who wants to go into the
code.

Besides the Arduino code, I have CAD drawings for the housings,
EAGLE .brd and .sch files for the additional "Turbidostat Shield" I
made that contains the electrical components, as well as the parts
list. I haven't created the How-To yet because I'm not sure where the
best place to publish the designs are and what the demand is from the
community. I read that there was an open source turbidostat project on
DIYbio, but cannot find its current progress.

In any case, the device is relatively cheap (especially depending on
what you have on hand and where you want to cut corners), and I think
it would be helpful the community.

Any direction would be greatly appreciated.

jt

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[DIYbio] Re: DIY Turbidostat

4:16 PM |

Hi jt,

thanks again for sharing your amazing project and also linking to the other turbidostats and chemostat systems from the dunham and kalvin lab. You mentioned in your Evolvinator that for anaerobic samples one could just flush the system with an anoxic gas. I don't think this will work especially working with oxygen atolerant anaerobes. I was thinking about building your system under a diy anaerobic chamber (there are lot of diy projects for those out).

Do you have any idea, papers, literature that could help me in cultivating Archeae in turbidostat system (does it make sense with an doubling time of 4h) ? Also for your problem with the formation of biofilms : there has been a patent out to solve that. They seem to use a combination of two culture vessels - changing vessels frequently to kill of biofilm producers and dilution resistant strains. Since you used yout system at Ginko Bioworks you can not really use it for commercial interest as it is patented but mabe there is a clever design around.

I think a DIY turbidostat - especially one that enables growing bugs for thousands of generation - would be powerful in changing substrate affinities and cleaning up waste streams.

On Friday, October 28, 2011 at 5:13:03 PM UTC+2, Jt wrote:

Awesome. Thank you Cathal, Jonathan, and John.

openwetware and github seem like the right combination.

To give a full story, I work for Ginkgo BioWorks and have developed
this device for our own inhouse bug testing/polishing. Though the
current iteration is probably a little more sophisticated than a lot
of hobbyists would want to get into, there are pared down versions
which are totally within grasp. We don't have any intention of selling
the device so we want to open source it to kick start all the diy
bioers out there. So I don't know if I'll go through the lengths of
making it Sparkfun/Ponoko purchasable myself, but take Jonathan's
advice of setting it free. Also, a UBW is most definitely in the
works, which I am happy to share as well.

Look forward to the openwetware How-To and please continue posting any
suggestions you have!

jt

Also to respond to your question Cathal: a IR LED and photodiode pair
work perfectly well to measure OD and can be more accurate than a lot
of common laboratory cuvette readers, especially if you can get the
optics down (super cheap too).

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[DIYbio] Re: TLR Biosensor

12:10 PM |

Feedback and suggestions would be welcome

On Saturday, January 31, 2015 at 7:52:54 PM UTC, Simon Rose wrote:

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

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[DIYbio] Re: TLR Biosensor

12:07 PM |

ps, I won't be doing this in a biohacklab but in a university lab under supervision. I've just seen the post about recombinant factor 8 by the way. Sterile techniques, if required should be no problem

On Saturday, January 31, 2015 at 7:52:54 PM UTC, Simon Rose wrote:

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

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[DIYbio] TLR Biosensor

11:52 AM |

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

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Re: [DIYbio] Re: Synbio and DIYbio referenced in World Economic Forum Global Risks 2015 report

9:55 AM |

This argument would hold more water for me if there weren't already a
multi-billion voluntarily labelled and anti-GMO market: Organic food.
And plenty of people who subscribe to it entirely, creating a control group.

All of which is irrelevant, because GE foods are already extensively tested.

The "control group" in this case is also anti-everything, including
vaccines and antibiotics, and are currently suffering from a serious
measles problem. The confounding factors involved in treating nutters as
a "natural experiment" are significant and difficult to account for.
They're also fond of letting unlicensed people jab them with hot
needles, realign their spinal column, and feed them dilute "mystery
medicine" or mercury-laced ayurveda, so you really can't tell if a
difference between groups is due to your chosen factor or something else.

Maybe this is radical of me to suggest, but there's this thing called
the "scientific method" which is fairly good at establishing whether
stuff is safe or not, and applying it in this case might be a good
approach. Oh wait, people have. Extensively. Repeatedly. Ad nauseum.

On 31/01/15 05:52, Jonathan Cline wrote:
>
>
> On Wednesday, January 28, 2015 at 11:55:12 AM UTC-8, Cory Geesaman wrote:
>
> Personally I'm for GMO labels and having a viable market for non-GMO
> foods - if only to ensure we have something to fall back on ...
> Paranoia does serve a legitimate evolutionary purpose in a large
> number of situations - it's almost always good to have a portion of
> the population that doesn't do things the same way as everyone else
> and if paranoia of GMO spurs that it is worth keeping.
>
>
>
> Well said. Also, studies always need good control groups. If labels
> exist then there will be groups which are inclusive or exclusive for
> certain ingredients. Now if only microbiome studies could include
> pure vegans as a separate experimental group, that would be really
> something. When I have asked PI's about this, usually "lack of
> funding" is cited as the excuse.
>
>
>
> ## Jonathan Cline
> ## jcline@ieee.org
> ## Mobile: +1-805-617-0223
> ########################
>
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peerio.com: Use email or phone. Uses above miniLock key.

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Re: [DIYbio] $50 camera good for microscopy with machine vision code included

9:03 AM |

On 01/31/2015 09:54 AM, Simon Quellen Field wrote:
> When controlled by my computer, I find the Canon to be quite suited to microphotography.

What's the software? Sounds good... FOS SW preferred...

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[DIYbio] Re: help me setup DIY-BIO home Lab to produce Recombinant Factor VIII

8:25 AM |

Pichia pastoris is a species of methylotrophic yeast... "study up", OK?

On Saturday, January 17, 2015 at 7:31:14 AM UTC+5:30, Sunil Phani wrote:

can someone please help me setup DIY-BIO home Lab to perform mammalian cell culture to produce Recombinant Factor VIII protein with mammalian cells(CHO, HKE 293, HEL, etc) and kindly provide me recombinant dna protocols for identification, isolation , extraction, insertion and expansion .my requirement is to prepare pilot project in small scale DIY-BIO lab which can further be scaled.
if possible provide me vectors, cell line and seedstock. i am new to DIY-BIO hence i need helping hands of veterans like you ppl .. your help be highly appreciated

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Re: [DIYbio] $50 camera good for microscopy with machine vision code included

7:54 AM |

The software might be nice, but the Canon has higher resolution, lower noise, higher video speeds, and a larger sensor.

That won't matter if all you need is 50 micron (or even 1 micron) resolution. But I've been getting close to 0.2 micron resolution using a Canon T3i (a fairly old camera) and a homemade microscope (I also use an excellent phase-contrast research microscope and get similar resolution but with much less aberration).

When controlled by my computer, I find the Canon to be quite suited to microphotography. You look at the computer monitor, and click on the shutter icon to take the picture. It's pretty friendly.

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On Sat, Jan 31, 2015 at 5:42 AM, John Griessen <john@industromatic.com> wrote:

I was telling Nathan how flex circuits like are used in LCD screens for desktops of a few years ago
are a commodity process of making layers with 50 micron width and space between and might be
repurposed to fabbing microfluidics inexpensively. I took a flatbed scanner photo of the flex circuit
that could not get down to its resolution, and emailed that, and
offered to send him a piece to look at under a microscope,
since I did not have any good digital camera for microscope photos.

I was saying how I'd take the lens off of a Canon powershot for that, but it still has a crummy user interface
for microphotography, which triggered him telling me about this:

https://www.kickstarter.com/projects/botthoughts/openmv-cam-embedded-machine-vision

It's got a perfect user interface for microphotography -- python programmed machine vision
programs that can recognize features in a scene. Just add a little problem-specific
development and you have a cell counter program. Well, add that not-yet-existing, accurate and inexpensive
plastic molded microgrid to drop on your samples then top with a cover slip, *then*
hit the go button of the counting program...

John

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Re: [DIYbio] Re: help me setup DIY-BIO home Lab to produce Recombinant Factor VIII

6:57 AM |

there is nothing to get alarmed about mammalian cell culture until it's being used up on human beings ...

No, that TOTALLY doesn't sound like the beginnings of a Bio-weapon lab.

On Sat, Jan 31, 2015 at 7:08 AM, Sunil Phani <consultsunilphani@gmail.com> wrote:

hello friends,
i respect your gathered concerns and there is nothing to get alarmed about mammalian cell culture until it's being used up on human beings ...
and i thoroughly understand the intention behind cautioning me.. i am actually feeling very encouraged and will be continue to pursue my passion ....
now i am actually looking into adaptable approaches to produce Recombinant Factor VIII using pichia pastoris is a species of methylotrophic yeast.
Pichia is widely used for protein expression using recombinant DNA techniques.
i sincerely believe that you ppl and Diybio will continuously advise me in this regard and guide me to accomplish my goal rather than plotting the scopes of Diybio

"If your actions inspire others to dream more, learn more, do more and become more, you are a leader...."

and in my view Diybio is a leader and savant ppl like you made this group a leader in all aspects ...

friends pls through some light on pichia pastoris and its pros and cons

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Re: [DIYbio] Re: help me setup DIY-BIO home Lab to produce Recombinant Factor VIII

6:33 AM |

On 01/31/2015 08:08 AM, Sunil Phani wrote:
> nothing to get alarmed about mammalian cell culture until it's being used up on human beings ...

It's just that "it" could be used on YOU accidentally as you do lab technique...
and then consider side effects of disease spread risk from your lab cultures, etc.

So, "study up" is all they are saying.

I don't think anyone was alarmed. But...

They care about you even though they don't know you.

They worry when you say non-chalantly, "nothing to get alarmed about mammalian cell culture"...

They worry comparing your non-spell checked emails to all the long sequences of exacting detail
needed to do mammalian cell culture, and worry that "It might not work out..." as Bob Allen,
a good horse trainer says fairly often to his students...

So, "study up", OK?

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[DIYbio] Re: help me setup DIY-BIO home Lab to produce Recombinant Factor VIII

6:08 AM |

hello friends,
i respect your gathered concerns and there is nothing to get alarmed about mammalian cell culture until it's being used up on human beings ...

and i thoroughly understand the intention behind cautioning me.. i am actually feeling very encouraged and will be continue to pursue my passion ....

now i am actually looking into adaptable approaches to produce Recombinant Factor VIII using pichia pastoris is a species of methylotrophic yeast.

Pichia is widely used for protein expression using recombinant DNA techniques.

i sincerely believe that you ppl and Diybio will continuously advise me in this regard and guide me to accomplish my goal rather than plotting the scopes of Diybio

"If your actions inspire others to dream more, learn more, do more and become more, you are a leader...."

and in my view Diybio is a leader and savant ppl like you made this group a leader in all aspects ...

friends pls through some light on pichia pastoris and its pros and cons

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