Chemostat

[GabiM]

Hello,

I’m using chi.bio for the first time and the goal is to use it as a chemostat. However, after reading the manual and the references recommended in the site, I couldn’t figure out how to use it as a chemostat. In the original paper, it is said that: “the OD control algorithm can easily be reprogrammed to provide constant input/output pump rates to provide a chemostat setup”. So, I’m guessing I’ll have to make a custom program?
So far, I was able to install and assemble it and perform a growth curve wth it. I’ve assembled the pumps but I don’t know how to setup it to work. I’ve tried to use the User Interface, altering rate parameters in the stir/pumping section, but it did not work. Then, from the information I collected, the chi.bio’s default program is the turbidostat mode and accoding to the manual, the manual control of the pumps 1 and 2 is disabled. So, probably this is why I can get it to work.

What are the necessary configurations to use it as a chemostat and how do I make those configurations? Please, can you guide me trhough it?

Thanks,
Gabi

[harrison]

Hello,

Using the device, you could just start an experiment then NOT turn on turbidostat mode, and instead permanently activate the in/out pumps at some fixed rate.
The turbidostat mode indeed does disable the punps – but for your sake you don’t need the OD control – hence you can do exactly as you did for a growth curve, and once it is running activate the pumps to whatever rate you want.
Make sure the outflow pump is much faster than the inflow so that it cannot overflow the reactor..!

[GabiM]

I’m not sure I know how to do that. Here’s what I’m thinking. Please let me know if it’s correct.
The turbidostat mode is not the dafault. To activate it I have to click on “switch” in the OD regulation section and then the OD will be maintained at a certain value os my choice, right? Why you don’t recomend it?
For activation of the pumps, shoud I just set a new rate and then it will immediately work?

[harrison]

Apologies for not being clear. What I suggest is start experiment. then DON’T click switch to activate OD control – since that is not a chemostat, but rather a turbidostat. Instead, once the experiment is started, go to the pump control section and enter a rate for each one and manually switch on the pumps. Then the system will run with constant inflow/pump rate (i.e. a chemostat).

Does this make sense?

[GabiM]

Hi Harrison.

I managed to get the pumps working. Now I understand a little better how it works. All the questions above about how to turn it on and the fact that the pumps works periodically are settled now.

I’m advancing slowly and now I’ve got new issues. Te first one is how I can make the pumps run continuously? I’ve been testing the pump rates to find the best dilution rate for my experiment. I wat to achieve 10 ml per hour, considering a 10 mL culture in the tube that goes into the reactor. So far, it seems that I will have to use a very small rate and I noticed that after a while, the medium is no longer added to the tube in the reactor. It seems that the pump does not have strenght enough to push the small volume into the tube. This happend with a 0.01 rate. What can I do to solve this?

Earlier, you mentioned that the outflow pump shold have a rate higher than the inflow rate. How much higher is enough? 2 times, 5 times, 10 times?

[harrison]

– TO fix the flow rate thing, have a look at the user guide about this troubleshooting challenge – probably best method is to add a one way check valve to inflow media line.
– 5 times higher probably ideal. Or you could set it to do something like keep same rate as inflow then every ~10 minutes do a bigger pump out… But this would require some programming in python

[GabiM]

Hi Harrison.

Thanks for the replies!

Regarding reply #1900, your explanation was very helpful and confirmed what I observed yesterday testing this. Initially, I was envisioning a continuous inflow and outflow of media, similar to our lab’s peristaltic pump-based chemostat and that’s why I may have understand it wrong.

For reply #1902, thank you for the suggestions. I will try the tape solution first. If that proves ineffective, I will explore the valve option, although importing items to Brazil can be challenging.
I am also considering adjusting the pump period through code modification. As a programming beginner, I believe the following steps are necessary:
1) conect the putty
2) set de date and hour
3) move to chi bio folder (cd chibio)
4) confirm that the app.py file that contains the code is in that folder with ls command
5) open this file with an text editor (nano app.py)
6) in the PumpModulation function, go to the line #789 and change the value from 1.05 to 10.05 (or whatever time i want to)
7) save the file (crtl + 0 in nano)
8) run the command bash cb.sh to start using it

1) Connect via PuTTY.
2) Set the date and time.
3) Navigate to the Chi.bio directory (cd chibio).
4) Verify the presence of app.py using ls.
5) Open app.py with nano (text editor).
6) In the PumpModulation function, change the value on line 789 from 1.05 to 10.05 (or the desired value).
7) Save the file (Ctrl+O in nano).
8) Execute bash cb.sh to restart the application.

Please let me know if these steps are correct or if you have any recommendations.

Thanks again,
Gabriella

[harrison]

Hello,
You could try that with the pump, but I am not sure it is the best idea. Why do you need to slow things down?
It sounds as if it would work though, you can easily test it in a dry run etc before actually tryhing in an experiment

[GabiM]

Hi!

Because I need a slower dilution rate. I get approximately 14 mL per hour and I need 5 mL per hour. Since I’m using the slowest pump rate (0.001), I thought I needed to increase the period of the pump.

I did change the cycle to 10 minutes, but it didn’t work. I’ve notice that if I increase the cycle time, the volume added to the tube is higher too. So it does not get smaller.

[harrison]

hmm. that may not work since the main loop of the experiment turns the pumps on and off each time it iterates (60 seconds). What you could instead do is put some logic check around the part in pumpmodulation which turns them on, and (for example) check if experiment cycle modulo 10 is 1 (or whatever) and if so turn it on, if not leave it off. This way you would let pumpmodulation run on the same timer but 9 out of 10 times it would do nothing.

[GabiM]

Hi Harrison.

Thanks for the tip. I’ll try to do that.

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