DIY Biorreactor at Nature Biotechnology

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Markos

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Jul 12, 2018, 12:50:12 PM7/12/18
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https://www.nature.com/articles/nbt.4151

Dakota Hamill

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Jul 12, 2018, 12:57:40 PM7/12/18
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Open source reactor paywalled article REE

On Thu, Jul 12, 2018, 12:50 PM Markos <mar...@c2o.pro.br> wrote:
https://www.nature.com/articles/nbt.4151

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Scott

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Jul 12, 2018, 1:06:20 PM7/12/18
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Markos

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Jul 12, 2018, 2:26:46 PM7/12/18
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Marnia Johnston

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Jul 12, 2018, 2:45:54 PM7/12/18
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Ah, brilliant, Thanks Markos!

On Thu, Jul 12, 2018 at 11:26 AM, Markos <mar...@c2o.pro.br> wrote:
Em 12-07-2018 13:57, Dakota Hamill escreveu:
Open source reactor paywalled article REE

On Thu, Jul 12, 2018, 12:50 PM Markos <mar...@c2o.pro.br> wrote:
https://www.nature.com/articles/nbt.4151

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Jonathan Cline

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Jul 20, 2018, 2:13:58 PM7/20/18
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Great paper, some skepticism is in order.  

Not sure how this differs from similar systems prototyped at MIT in ~2005 (which were abandoned as dead-ends, I believe).

"Thermistors and heaters attached to a machined aluminum tube" with given (and very ideal looking) graph of temp oscillation 30C-40C over 14 hrs vs. room temp with period 30 mins, for a culture in "40 mL autoclavable borosilicate glass vials".  The heating system seems questionable.  No active cooling (except if provided by fan, which also operates for stirring).

"the hardware design enables rapid, cost-effective scaling and customization"  The design certainly is not cost-effective.   "Individual sleeves cost ~$25".  In terms of scalability, it is not scalable, N cultures must scale with N hardware devices (appears to be 16), N pumps, N flow tubes, etc.  (All flow tubes needing replacement.)  N is further reduced (divided by constant X) for the biofilm elimination protocol. The concept to "monitor hundreds of cultures in real time" will require some M arduino's which also scale linearly.  Power requirements will create problems once N > some small number. 

"With daily replacement of used vials, four Smart Sleeves could be used to passage a culture, biofilm-free, for an indefinite period of time"  ... which means a minimum run-time cost of $x*(N-y) per day.   (Some part of that cost may be reduced by autoclaving, better if the design used more glass)

"LED/photodiode sensor pairs perform OD900 readings." Biofilm, condensation, etc will obscure the optics.

The interesting part of the paper is the "Millifluidic device w/ integrated pneumatic valves"  (approx 14 cm in size) "by adhering a silicone rubber membrane between two clear sheets of laser-etched plastic, each patterned with desired channel geometries and aligned" "that overcomes biofilm formation during long-term continuous growth experiments" ...  yet that device is not detailed in this paper.  No discussion of where the pneumatics is sourced from.  The device is perhaps these papers from 2000 and 2003, which are not novel in 2018,   1) Unger, M.A., Chou, H.P., Thorsen, T., Scherer, A. & Quake, S.R. Monolithic microfabricated valves and pumps by multilayer soft lithography. Science 288, 113–116 (2000);  2) Grover, W. H., Skelley, A. M., Liu, C. N., Lagally, E. T. & Mathies, R. A. Monolithic membrane valves and diaphragm pumps for practical large-scale integration into glass microfluidic devices. Sensors Actuators, B Chem. 89, 315–323 (2003).





No mechanism for reading pH. 



On Thursday, July 12, 2018 at 9:50:12 AM UTC-7, Markos wrote:
https://www.nature.com/articles/nbt.4151



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John Griessen

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Jul 20, 2018, 4:05:28 PM7/20/18
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On 07/20/2018 01:13 PM, Jonathan Cline wrote:
> "LED/photodiode sensor pairs perform OD900 readings." Biofilm, condensation, etc will obscure the optics.

How do you know that? They probably stir often enough to avoid condensation problems and
their code probably keeps track of when bio-film is starting and ask for a
transfer of contents to a clear bioreactor tube and sleeve.

It's all very efficient as soon as it saves a person from having to do inhuman tasks on
an hourly basis 24x7.

Sleeves are just suggestions. They say their aim is to promote using 3DP for custom
sleeves. A custom sleeve could be made
with lots of insulation for incubation without big power draws.

By the time it gets to be stacks of 16 sleeve modules 10 high 2 deep with an aisle
between, there will be some evolution to take care of your concerns.

Ravasz

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Jul 21, 2018, 6:29:56 AM7/21/18
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Hi there,

We are just developing a prototype photobioreactor for growing algae on Mars. I read this discussion with great interest.

With regards to the paper, I agree with some points raised by Jonathan. For instance I am also surprised the design has no cooler. I'd reckon this could be overcome by installing a heat sink for each vial and using a peltier system to regulate temperature instead as the vials are fairly small.

I agree with John, most biofilm formation is avoided by regularly pumping cultures into new vials. They even test this and find that passage every 8 hours eliminates the problem entirely, as shown in Figure 5b.
With regards to the millifluidic device, it is outlined in supplementary figure S11, on page 25 of the supplementary materials. I'm not sure I fully understand it, but my excuse is being a biologist. Still, it does seem to rely on a silicone membrane that either allows or obstructs flow.  It looks like they manufacture the pneumatics themselves as outlined in the S11 figure legends.

For me personally, I would need to redesign several parts to make it adaptable for algae: I would need to fit in a lighting system instead of the aluminium housing, and replace the stir bar with a gas bubbler. Seems like too much hassle, but I do like some of the concepts developed, especially the complex fluidics that can be taken advantage of by other designs.

Mate

Jonathan Cline

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Jul 22, 2018, 4:02:19 AM7/22/18
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The aluminum sleeves for the vials are the heat sink.  If vials or sleeves are insulated, the result would be thermal runaway, inability to cool.  As it is, the temp control is dependent on room conditions.  This also results in another limitation in scaling the system larger than as presented (16 sample tubes).  

A continually flowing system should be superior to the paper's method of allocating 4 tubes per culture for liquid transfer simply to eliminate biofilms.


On Saturday, July 21, 2018 at 3:29:56 AM UTC-7, Ravasz wrote:
Hi there,

We are just developing a prototype photobioreactor for growing algae on Mars. I read this discussion with great interest.

With regards to the paper, I agree with some points raised by Jonathan. For instance I am also surprised the design has no cooler. I'd reckon this could be overcome by installing a heat sink for each vial and using a peltier system to regulate temperature instead as the vials are fairly small.

I agree with John, most biofilm formation is avoided by regularly pumping cultures into new vials. They even test this and find that passage every 8 hours eliminates the problem entirely, as shown in Figure 5b.
With regards to the millifluidic device, it is outlined in supplementary figure S11, on page 25 of the supplementary materials. I'm not sure I fully understand it, but my excuse is being a biologist. Still, it does seem to rely on a silicone membrane that either allows or obstructs flow.  It looks like they manufacture the pneumatics themselves as outlined in the S11 figure legends.

For me personally, I would need to redesign several parts to make it adaptable for algae: I would need to fit in a lighting system instead of the aluminium housing, and replace the stir bar with a gas bubbler. Seems like too much hassle, but I do like some of the concepts developed, especially the complex fluidics that can be taken advantage of by other designs.

Mate

 


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