Revision as of 06:37, 27 September 2013

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Experiment 1: Preparation of growth mediums (MRS and LB) (June 5th, 2013)

10 Agar LB plates

15 Agar MRS plates

Notes:

(1) 18.6g of Agar MRS were weighted to prepare 300ml of medium
(2) 7g of Agar LB were weighted to prepare 200ml of medium
(1) 5g of A-MRS were diluted in 80ml of distilled water
Another 5g and 170ml of distilled water were added
Small lumps were formed in the bottom of the Erlenmeyer flask
(2) 7g of Agar LB were distilled in 100ml of distilled water
Further 100ml of distilled water were added
It wasn’t possible to use a control of the sterilization because there was no autoclave tape
The autoclave began heating up
The autoclave valve was lowered
When the temperature of the autoclave reached 120⁰c, the power was cut to the half
The vapor cycle ended and the temperature decreased
The temperature reached 105⁰c and the valve was opened. The mediums were left inside the autoclave until de laminar flow cabinet was unoccupied
The medium in petri dishes were stored in the refrigerator
The growth mediums in storage were revised, they do not show signs of contamination

17 MRS Agar

9 LB Agar

Experiment 2: Preparation of MRS broth and glycerol stocks (July 8th, 2013)

0.7679g of powder for MRS broth were weighted
15ml of distilled water were measured in a 100ml measuring cylinder
Besides, 200ml were prepared for future use
10.009g of powder for MRS broth were weighted
It was diluted in 100ml of distilled water
Another 100ml of distilled water were added
0.7679g of powder for MRS broth were diluted in 15ml of distilled water
Both flasks were marked with autoclave tape and they were sterilized for 15 minutes at 121⁰c
They cooled down and the autoclave tape confirmed the sterilization
The 200ml broth was stored properly labeled
The 15ml of MRS broth and the 15ml of glycerol were mixed to 100% in the laminar flow cabinet. They were gently shaken until an homogenous mixture was obtained in a falcon tube of 45ml
An aliquot of L. Plantarum was added to the broth and glycerol solution and it was sealed with parafilm
It was left incubating at 37⁰c and 200rpm
After 24 hours the sample was taken out of the incubator to striate it
2500 (x2)ml were placed in 22 eppendorf tubes using a micropipette of 200µl to cultivate and recompile the mixture of L. Plantarum contained in the falcon tube
1 eppendorf tube was centrifuged at 13.4 rpm for 3 minutes
After the centrifugation there was a small pellet left, from which the supernatant was discarded and a solution of MRS broth (500ml) was added
Once the mixture was made, two petri dishes with MRS Agar were striated in the laminar flow cabinet. A third dish was striated fin case of an emergency
The petri dishes were placed facing down in the incubator at 37⁰c and 200 rpm
The remaining samples (21 falcon tubes) were stored in deep freezing
E. Coli K12 was striated in two petri dishes with LB Agar
They were placed in the incubator at 37⁰c.

Experiment 3: Plasmid purification (July 16th, 2013)

An eppendorf tube of 1.5ml with L. Plantarum culture was centrifuged at 12000 rpm for 1 minute two times
The supernatant was discarded and the tube’s content was resuspended with more L. Plantarum culture in MRS broth
The eppendorf tube was centrifuged for 15min at 6000 rpm
The supernatant was discarded
The pellet was resuspended in 250ml resuspension buffer
250ml of Lysis Buffer L7
The tube was gently mixed inverting it 5 times carefully
350ml of precipitation Buffer N4 were added and mixed softly inverting the tube
It was centrifuged at 12000 rpm for 10 minutes
The supernatant was transferred to a spin column inside a washtube
It was centrifuged at 12000 rpm for a minute
The supernatant was discarded and 500 ml of Wash Buffer with ethanol (w10) were added to the column
It was incubated for one minute at room temperature
The column was centrifuged at 12000 rpm for 1 minute
The liquid from the washtube was discarded and the column was placed inside the tube
700ml of Wash Buffer W9 with ethanol were added to the column
The column with the washtube was centrifuged at 12000 rpm for 1 minute
The liquid from the washtube was discarded
The column in the washtube was centrifuged at 12000 rpm for 1 minute
The liquid from the washtube was discarded
The column was placed inside an eppendorf tube of 1.5ml
75ml of preheated TE Buffer were added at the center of the column
The TE Buffer was previously warmed in water bath at 65⁰c-70⁰c for 3 minutes
The column was incubated for 1 minute at room temperature
The column was centrifuged at 12000 rpm for 2 minutes
The eppendorf tube contains the purified plasmid

Experiment 4: Preparation of mediums for lactobacillus and E. Coli (July 17th, 2013)

15.3 g of MRS were weighted for 300 ml, the 2% (0.306 g.) of the MRS was used to do agar-agar
The autoclave started to heat
8.75 g of LB agar were weighted to dilute in 500 ml of distilled water
0.5005 g of LB broth were weighted to be diluted in 250 ml of distilled water
The 3 mediums were introduced in the autoclave
After 54 minutes the sterilization was complete
0.750 g of Kanamycin sulfate were measured and they were diluted in 15 ml of distilled water
1.5 g of Ampicillium sodium were weighted and diluted in 15 ml
The mediums were collocated in the laminar flow cabinet to pour into the petri dishes and striate
The mediums never solidified
2% more of agar was added in the LB broth and the mediums were placed in the autoclave
The mediums were collocated in the laminar flow cabinet to be poured into the petri dishes and striate
But the mediums didn’t solidified

Experiment 5: Preparation of MRS agar mediums (July 19th, 2013)

The mediums didn’t solidify, because the agar added wasn’t enough
10.2 g of MRS broth were measured and 2 g of agar-agar were added
The pH of the mediums was 6.6
A stock of HCl at 10% was added until the pH reached 6.4
The mediums were sterilized with the autoclave for 15 minutes at 121°C
40 ml of MRS agar were mixed with 40 µl of kanamycin and poured into 2 petri dishes
6 petri dishes were made with only MRS agar
2 control petri dishes with MRS agar were striated with L. Plantarum with 1.5 ml of glycerol stock
The petri dishes were incubated at 37°C for 2 hours

Experiment 6: Growth of E. Coli (July 21st, 2013)

No growth was discernible in the petri dishes with E. Coli, which were left incubating. This attributed to the use of an E. Coli sample, which was in refrigeration since 2011
The LB Agar medium was heated in an electric stove for approximately 10 minutes
A new sample of lyophilized E. Coli sample was opened and a representative sample was extracted to be rehydrated with LB broth
Liquid LB agar was poured into 2 petri dishes and they were left to solidify
Both dishes were striated with the rehydrated E. Coli
Both dishes were left incubating, after being sealed, during 24 hours at 37⁰c

Experiment 7: Glycerol stocks reactivation (July 22nd, 2013)

No discernible growth was observed in the L. Plantarum plates after a 72 hours incubation period. After consulting an external source, it was determined that this was due to glycerol stocks used, which weren’t reactivated
Two stocks of glycerol were reactivated with MRS broth
10 ml of MRS broth were added to a 1 ml stock in a falcon tube
The second stock was poured into another falcon tube, the result was 1.5 ml of stock with 15 ml of MRS broth
Both falcon tubes were sealed and left incubating at 37⁰c

Experiment 8: Overnight growth of E. Coli in LB broth (July 22nd, 2013)

5 ml of LB broth were poured into 2 falcon tubes each
An E. Coli colony was added to each tube with broth
Both tubes were sealed and left incubating at 37⁰c

Experiment 9: Preparation of mediums for lactobacillus and E. Coli (July 23rd, 2013)

15.3 g of MRS and 6 g of bacto agar were weighted to be diluted in 300 ml
17.5 g of LB agar were weighted to prepare 500 ml
The MRS and LB agar were autoclaved
1 ml of E. Coli was inoculated in 100 ml of LB agar in a flask of 250 ml
5 g of LB broth were weighted
It was autoclaved for 15 minutes at 121⁰c

Experiment 10: Preparation of TE buffer (July 25th, 2013)

6.05 g of TRIS were weighted and diluted in 60 ml of distilled water
9.3041 g of EDTA were weighted and diluted I 60 ml of distilled water
The TRIS’ pH was 10.29, therefore HCl was added until the pH reached 8.3
The EDTA’s pH was 3.25, therefore NaOH crystals were added until the pH reached 7.79
They were sealed and autoclaved for 15 minutes at 121⁰c

Experiment 11: Preparation of competent E. Coli cells (July 26th, 2013)

A falcon tube was prepared with 50 ml of CaCl2 0.1M
Another falcon tube was prepared with CaCl2 0.1M/ 15% glycerol
4 eppendorf tubes of 1.5 ml were filled
- 2 of them with 1.5 ml each of E. Coli culture in LB broth (1)
- 2 of them with 1.5 ml each of E. Coli culture in LB broth (2)
The 4 tubes were left in ice for 10 minutes
The 4 tubes were centrifuged for 3 minutes at 6000 rpm and the supernatant was discarded
1.5 ml of the aforementioned culture were added to each tube
The tubes were centrifuged for 3 minutes at 6000 rpm
The supernatant was discarded
The pellet was gently resuspended with 1.2 ml CaCl2 0.1M for each tube
The 4 tubes were incubated in ice for 20 minutes
The tubes were centrifuged again for 3 minutes at 6000 rpm
The supernatant was discarded
The pellets were resuspended with 0.6 ml of CaCl2 0.1M/ 15% glycerol each
They were poured into micro-tubes (300ml/tube), sealed and frozen at -80⁰c

Experiment 12: L. Plantarum plasmid purification (July 26th, 2013)

1.5 ml of L. Plantarum culture in MRS broth were poured into 2 eppendorf tubes, 1.5 ml each
Both tubes were centrifuged for 4 minutes at 12000 rpm
The supernatant was discarded and another 1.5 ml of culture were added
Both tubes were centrifuged for 4 minutes at 12000 rpm
The supernatant was discarded
250 ml of resuspension buffer (R3) were added and the pellets were resuspended until the mixture was homogenous
The tubes were incubated at room temperature for 15 minutes
250 ml of Lysis buffer (L7) were added to each tube. They were gently mixed
The tubes were incubated at room temperature for 5 minutes
350 ml of precipitation buffer (N4) were added
Both tubes were vigorously mixed until a homogenous mixture was obtained
The tubes were centrifuged at 12000 rpm for 10 minutes
The supernatant was poured into a spin column in a wash tube of 2 ml
The columns were centrifuged at 12000 rpm for 1 minute
The supernatant was discarded and the column was placed in the new washtube
500 ml of wash buffer (W10) with ethanol were added to the column
The columns were incubated for 1 minute at room temperature
The columns were centrifuged at 12000 rpm for 1 minute
The liquid that went through the columns was discarded
700 ml of wash buffer (W9) were added
The columns were centrifuged at 12000 rpm for 1 minute
The liquid that went through the columns was discarded
The columns were centrifuged at 12000 rpm for 1 minute
The liquid that went through the columns and the washtube was discarded
The columns were placed in eppendorf tubes of 1.5 ml
70 ml of TE buffer (previously heated at 65⁰c for 3 minutes) were added in the center of each column
The columns were incubated at room temperature for 1 minute
The columns were centrifuged at 12000 rpm for 2 minutes
The eppendorf tubes contain the purified plasmids
The columns were removed, the eppendorf tubes were sealed and they were refrigerated at 4⁰c until the next day

Experiment 13: Electrophoresis gel for L. Plantarum (July 27th, 2013)

@@ Line 167: / Line 167: @@
 ----
 '''Experiment 10: Preparation of TE buffer (July 25th, 2013)'''
+*6.05 g of TRIS were weighted and diluted in 60 ml of distilled water
+*9.3041 g of EDTA were weighted and diluted I 60 ml of distilled water
+*The TRIS’ pH was 10.29, therefore HCl was added until the pH reached 8.3
+*The EDTA’s pH was 3.25, therefore NaOH crystals were added  until the pH reached 7.79
+*They were sealed and autoclaved for 15 minutes at 121⁰c
+----
+'''Experiment 11: Preparation of competent E. Coli cells (July 26th, 2013)'''
+*A falcon tube was prepared with 50 ml of CaCl2 0.1M
+*Another falcon tube was prepared with CaCl2 0.1M/ 15% glycerol
+*4 eppendorf tubes of 1.5 ml were filled
+**2 of them with 1.5 ml each of E. Coli culture in LB broth (1)
+**2 of them with 1.5 ml each of E. Coli culture in LB broth (2)
+*The 4 tubes were left in ice for 10 minutes
+*The 4 tubes were centrifuged for 3 minutes at 6000 rpm and the supernatant was discarded
+*1.5 ml of the aforementioned culture were added to each tube
+*The tubes were centrifuged for 3 minutes at 6000 rpm
+*The supernatant was discarded
+*The pellet was gently resuspended with 1.2 ml CaCl2 0.1M for each tube
+*The 4 tubes were incubated in ice for 20 minutes
+*The tubes were centrifuged again for 3 minutes at 6000 rpm
+*The supernatant was discarded
+*The pellets were resuspended with 0.6 ml of CaCl2 0.1M/ 15% glycerol each
+*They were poured into micro-tubes (300ml/tube), sealed and frozen at -80⁰c
+----
+'''Experiment 12: L. Plantarum plasmid purification (July 26th, 2013)'''
+*1.5 ml of L. Plantarum culture in MRS broth were poured into 2 eppendorf tubes, 1.5 ml each
+*Both tubes were centrifuged for 4 minutes at 12000 rpm
+*The supernatant was discarded and another 1.5 ml of culture were added
+*Both tubes were centrifuged for 4 minutes at 12000 rpm
+*The supernatant was discarded
+*250 ml of resuspension buffer (R3) were added and the pellets were resuspended until the mixture was homogenous
+*The tubes were incubated at room temperature for 15 minutes
+*250 ml of Lysis buffer (L7) were added to each tube. They were gently mixed
+*The tubes were incubated at room temperature for 5 minutes
+*350 ml of precipitation buffer (N4) were added
+*Both tubes were vigorously mixed until a homogenous mixture was obtained
+*The tubes were centrifuged at 12000 rpm for 10 minutes
+*The supernatant was poured into a spin column in a wash tube of 2 ml
+*The columns were centrifuged at 12000 rpm for 1 minute
+*The supernatant was discarded and the column was placed in the new washtube
+*500 ml of wash buffer (W10) with ethanol were added to the column
+*The columns were incubated for 1 minute at room temperature
+*The columns were centrifuged at 12000 rpm for 1 minute
+*The liquid that went through the columns was discarded
+*700 ml of wash buffer (W9) were added
+*The columns were centrifuged at 12000 rpm for 1 minute
+*The liquid that went through the columns was discarded
+*The columns were centrifuged at 12000 rpm for 1 minute
+*The liquid that went through the columns and the washtube was discarded
+*The columns were placed in eppendorf tubes of 1.5 ml
+*70 ml of TE buffer (previously heated at 65⁰c for 3 minutes) were added in the center of each column
+*The columns were incubated at room temperature for 1 minute
+*The columns were centrifuged at 12000 rpm for 2 minutes
+*The eppendorf tubes contain the purified plasmids
+*The columns were removed, the eppendorf tubes were sealed and they were refrigerated at 4⁰c until the next day
+----
+'''Experiment 13: Electrophoresis gel for L. Plantarum (July 27th, 2013)'''

Team:BIOINT Mexico/Lab work

From 2013.igem.org

Revision as of 06:37, 27 September 2013

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Lab work