Team:Paris Bettencourt/Notebook/Manufacturing

July 27th

Beginning of the manufacturing project! Let's do it!

Goal

The goal of this project is to create an way to grow and distribute our strains in India, easily and for cheap.
Since our genetically engineered strains will be ready only in september, we will not have time to work on it, so we have to find similar strains, that we can study and select with antibiotics.
We chose Saccharomyces cerevisiae mcherry, wich is resistant to geneticin at a concentration of 200µg/mL, and produce RFP.
Basically, we are going to try different ways to distribute the strains and see how well they survived for each process.
In order to do that, we will have to calculate a survival rate so we have to be able to know how many cells we are putting in the beggining, in the recipe we are trying.

Material

  • Glycerol stock of Sc. mcherry
  • YPD broth
  • Agar
  • Geneticin, 100mg/ml
  • Osmosed water
  • Sterile eppendorf tubes
  • Sterile plates and beads

Procedure

  • Make a culture of Sc. mcherry in 10ml of YPD media adding 20µL of geneticin
    • (We did cultures on the 25th of july)
  • Two days later, centrifuge the culture tube
  • Throw the media away and replace it by 10ml of osmosed water
  • Measure the OD, doing the blank with osmosed water
  • If the OD is too high to be measured, make a 10 times dilution and measure the OD of the dilution
  • In the eppendorf tubes, make 10^-1 to 10^-5 dilutions of the yeasts/water solution to plate them on YPDagar+GEN(200)

That is what we did today, and we plated the different dilutions, thanks to the beads.

July 28th

Goal

Our first idea to distribute the yeast was to simply dry them and collect the dry cells, without adding anything.
Today is a first try, to have an idea of how to do it.

Material

  • YPD broth
  • Agar
  • Geneticin, 100mg/ml
  • Osmosed water
  • Glycerol stock of Sc. mcherry
  • Sterile eppendorf tubes
  • Sterile plates and beads

Procedure

  • Centrifuge a culture tube
  • Throw the media away
  • Add 300µL of water to detach the yeasts from the tube easily
  • Spread on aluminium
  • Let it dry for 2 hours in the open air or in the incubator (2 different tests)
  • Scratch the aluminium to detach the dried yeasts
  • Put the powder in 10ml of osmosed water
  • Plate the solution to see if Sc. mcherry survived

Results and discussion


We obtained this powder:

We realised the aluminium was not a good idea:
The yeasts stick to it and it gets destroyed when we scratch.
We have to find another drying paper, more resistant.


July 29th

Result of the OD test made on the 27th of July:

The 10ml solution of Sc. mcherry/water had an OD of 2,557.
100µL of the 10^-4 dilution grew 359 colonies, so:
1 OD = 1,4x10^7 cells/ml
We repeated the very same OD experiment today, for more repetitions.

July 30th

Results of the drying test made on the 28th of July:

Yeasts grew in the plate.
We can check that they produce RFP, it's Sc. mcherry who survived.

Procedure

Today, we are repeating the drying experiment (see July 28th) but drying the yeasts on a plastic dish.
  • Take 100µL of the culture solution of Sc. mcherry to make dilutions (10^-1 to 10^-5)
    • We remind that the culture tube contain 10ml of media.
  • Plate 100µL of each dilutions to deduce the number of cells in the culture tube
  • Centrifuge the culture tube
  • Throw the media away
  • Add 300µL of water to detach the yeasts from the tube easily
  • Spread on aluminium
  • Let it dry for 2 hours
  • Scratch the aluminium to detach the dried yeasts
  • Put the powder in 10ml of osmosed water
  • Take 100µL of the solution to make dilutions (10^-1 to 10^-5)
  • Thanks to the beads, plate 100µL of each dilution


July 31th

Result of the OD test made on the 29th of July:

The 10ml solution of Sc. mcherry/water had an OD of 2,635.
100µL of the 10^-4 dilution grew 205 colonies, so:
1 OD = 7,8x10^6 cells/ml

August 1st

Result of the drying test made on the 30th of July:

100µL of the 10^-5 dilution of the initial 10ml culture solution grew 106 colonies, so we initially dried 1,06x10^9 cells.
100µL of the 10^-4 dilution of the powder mixed with 30ml of osmosed water grew 123 colonies, so 8,4x10^8 cells survived.
We therefore have a survival rate of 79%.

Discussion and new goal

The powder we obtained with the drying method stick to everything, because of static electricity and therefore, it is not very easy to distribute and manipulate.
Consequently, we are looking fo other solutions...

Our second idea was to cook a homemade powder with edible ingredients easily found in India.
We found a recipe that inspired us here: http://www.instructables.com/id/Stop-Paying-for-Yeast-Make-Your-Own/
We decided to compare the initial recipe to our modifications, so we made for different tests :
  • Test 1, original recipe: wheat flour, sugar and ginger
    • Since the project is designed for rice fermentation and rice is cheaper than wheat, we wanted to try with rice flour.
  • Test 2: rice flour, sugar and ginger
    • Ginger can be expensive so maybe we can avoid using it...
  • Test 3: rice flour, sugar
    • And maybe we can also avoid using sugar
  • Test 4: only rice flour

Material

  • Culture of Sc. mcherry
  • Potatoes
  • Flour (wheat and rice)
  • Cornmeal
  • Sugar
  • Ginger
  • Plate of YPDagar+Gen(200)
  • Osmosed water
  • Sterile eppendorf tubes
  • Sterile beads

Procedure

  • Cook some potatoes
  • Save the cooking water, wait till it's not too hot and mix 20ml of it with the yeasts
  • Add 20ml of flour (rice or wheat depending on the recipe), 40ml of mashed potatoes
  • Depending on the recipe add 20ml of sugar and a teaspoon of ginger
  • Add 80ml of cornmeal
  • Let it dry for 1 day
  • Mill the paste to obtain a powder
  • Plate the powder obtained to see how many Sc. M Cherry survived



August 3rd

Continuing the experiment we began on the 4th of August


After almost two days of drying, we obtained a very hard paste that we milled.
After milling, we had this nice yellow powder you can see on the picture

We put 100mg of each powder in 10ml of osmosed water, made dilutions,
and plated the solutions in YPDagar+GEN(200) plates.



August 4th

Goal

While doing the recipe with the potatoes, we realise it wasn't easy to do and it took a lot of time and a lot of ingredients.
We decided to reduce the number of ingredients, using only water and rice flour.

Procedure

  • Mix the yeasts with one cup of osmosed water
  • Add 2 cups of rice flour
  • Knead till you get a nice paste
At this point, we tought the paste could be shaped, instead of being milled in a powder.
  • Shape it in little cubes
  • Let it dry for few hours

Result


The result is a small solid cube, very easy to give away.

Several cubes can be packed together.

We tought it could be a good media of distribution.

We plated small amount of the cubes dissolved in water.



August 5th

Results of the potato powder:

Survival rate:
  • Wheat flour, sugar and ginger: 6,9%
  • Rice flour, sugar and ginger: 9,5%
  • Rice flour, sugar: 5,7%
  • Rice flour: 1,9%
We can see that the more ingredients we put, the more the yeasts survived.

August 6th

Results of the cube test:


The survival rate is about 7%.

After staying 5hours in the water, the survival rate reached 737%.



August 7th

Goal

Now that we are at ease with the process, we are trying the very same process with lactococcus lactis. We chose MG 13.63, containing the plasmid PSIP411, resistant to erythromycin at a concentration of 10µL/mL, to study it's survival rate. We will name this strain G1513. We also have to correlate the OD of a solution of G1513 to the number of alive cells inside.

August 10th

Results of the OD test for G1513:

1 OD = 6,0x10^4 cells/ml

Procedure

Making new cubes containing Sc. M Cherry and G1513 to calculate the survival rate.

August 11th

Goal

While waiting for the cubes results, we are thinking about the next step: finding a media to grow the strains, easy to give to the population and to use afterward. The perfect media would be an edible one, that we could incorporate to the cube, instead of the water.

Procedure

We tried 2 different medium: potato juice and potato juice with rice flour.

For the potato juice:
  • Heat 3 potatoes in 750ml of water
  • Let the water boil (sterilisation)
  • Save the water and stock it in a bottle
  • Put 10ml of this potatoe water in a culture tube
  • Add 20μL of geneticin (100mg/ml)
  • Inoculate with Sc. M Cherry
  • Put in the incubator at 30°C for 2 days

For the mix potato juice with rice flour:
  • Put 5ml of the potatoe water made previously in a culture tube
  • Inoculate with Sc. M Cherry
  • Add 20μL of geneticin (100mg/ml)
  • Add 5ml of rice flour
  • Put in the incubator at 30°C for 2 days

August 12th

Results of the cube tests

The yeasts survived well: 42%.
Seven days later, we plated again cubes from this test, and obtained a survival rate of 21%.
But strangely, the number of cells in the plates of M17 glucose with erythromycin, which are supposed to be G1513, is the same as in the plates with YPD and geneticin, selecting the yeasts.
Therefore, we checked the production of RFP, since Sc. M Cherry produces RFP but not G1513.
Unfortunately, we came to the conclusion that the cells in the M17 plates were yeasts. Actually, Sc. M Cherry resist to erythromycin and is therefore growing in the plate.

Goal

We need a chemical that will allow us to select G1513 and kill Sc. M Cherry.
After some researchs, we found out that cycloheximide could be helpful and ordered it. While waiting for this chemical, we can't work with G1513.

August 13th

Results of the media test

Nothing grew on the potato juice media.
We had the idea of adding sugar, to see if it changes something.
The potato juice/rice flour media strongly smells yeasts. We therefore admit the yeast grew in this media but decided that the aspect wasn't very attractive and the smell so so bad that indian population would be disgusted and won't use it.

August 17th

Procedure

Making new cubes with Sc. M Cherry alone, G1513 alone, and a mix of both strains.
Measuring the OD and plating to count the cells

Results of the media test

With sugar, we can see there are cells growing in the potato juice.
It's a very small growth compared to the one in YPD but it's still a growth.
We will work more precisely on this media, trying to deduce the influence of the concentration in potato and in sugar.

August 18th

Results of the OD test

For Sc. M Cherry:
1 OD = 3,8x10^6 cells/ml
For G1513:
1 OD = 1,1x10^8 cells/ml

August 19th

Results of the cube test

  • Sc. M Cherry alone: 39%
  • Sc. M Cherry in the mix: 26%
  • G1513 alone: 1,8%
We kept samples of the mix in the fridge to be able to study it later, when we will have the cycloheximide.

August 20th

Procedure

Making more cubes with Sc. M Cherry alone, G1513 alone, and a mix of both.
Making more OD correlations.

August 24th

Procedure

Making more cubes...

Results of the OD test

For Sc. M Cherry:
1 OD = 3,1x10^6 cells/ml
For G1513:
Nothing... It seems that the colony used was dead so the cubes will not contained any G1513.

Results of the cube test

  • Sc. M Cherry alone: 92%
  • Sc. M Cherry in the mix (but dead G1513): 96%
  • G1513 alone: Nothing

August 25th

Results of the OD test

For Sc. M Cherry:
1 OD = 2,6x10^6 cells/mL
For G1513:
Nothing... We used cells from the previous culture, wich was dead, so it seems normal.

August 26th

Results of the cube test

  • Sc. M Cherry alone: 122% et 162%

  • Sc. M Cherry in the mix (but dead G1513): 178% et 217%

  • G1513 alone: Nothing


    • August 27th

    Goal

    We want to find a media that could be use in India to grow the yeasts and the Lactococcus lactis for cheap.

    Procedure

    • Make 3 different potato juice solutions: low, medium and high concentration in potatoes
    • For each one of these solutions, make samples with different concentration of sugar
    • Inoculate the strains separetely in these media, with the appropriate antibiotics
    • Put 150μL of the solutions in a Tecan plate well and add 50μL of oil
    • Put in the Tecan at 30°C, measuring the OD every 15minutes, for 2 days

    August 28th

    Goal

    We want to see how the strains in the cubes react when put in the idli.

    Procedure

    ???????????????

    August 31th

    Results of the media test

    It's a fail, the OD was too high so we can't really see the growth.
    We did it again, diluting the media and strain 200times in osmosed water.

    Results of the idli test

    ????????????????????????????

    September 2nd

    Results of the second media test

    It's a fail, there was almost only water in the well so nothing grew.
    We will do it again, asking for a real protocol to some experts.

    September 4th

    Procedure

    Trying the new method for the Tecan test.
    This time, we did an overnight culture for each media and each strain, that we diluted 200times (till we get an OD smaller than 0,01)

    September 7th

    Results of the Tecan test

    Third fail, because one parameter was changed and we didn't noticed: the Tecan measured the OD for only few hours, not enough to see the growth...

    September 8th

    Procedure

    We made fresh new culture of Sc. M Cherry and G1513, that we used today to make lots of new cubes and OD test. We planned on making many cubes to plate one each day and follow the survival rate during the week.

    September 9th



    September 10th