Difference between revisions of "Team:Aix-Marseille/Notebook2"

Revision as of 15:39, 17 September 2015

Chew fight

CALENDAR

Suspension of 4 BioBricks:

-E0240 -K823005 -K823012 -I20260

Transformation of E.coli (DH5-Alpha) with biobricks E0240, K823005, K823012 and I20260

Observation of transformation results

Plasmid purification of the 4 BioBricks transformed on June 26, using a Promega kit.

Plasmid digestion of the BioBricks:

E0240 => X/P

K283005 => E/S

K823012 =>E/S

I20260 => E/P

Suspension of BioBrick J23119 and transformation into E.coli (TG1)

Observation of transformants.

Digestion of pSB1K3 : E/P + Dpn1

Electrophoresis of the digested backbones, E0240 K823005 and K823012

We got good results => ligation:

K823005 + E0240 + pSB1K3 (Named M1)

K823012 + E0240 + pSB1K3 (Named M2)

I20260 + pSB1K3 (named M3)

Transformation of these ligations and a plasmid from our lab =LismA201 (which is a GFP with promotor, RBS and terminator)

Suspension of BioBricks -I13504 -J23100 -J23118 -J23106 -J23117 -J23103

Transformation of these BioBricks into E.coli (TG1)

Plasmid purification of J23119 => bad results (due to the Macherey-Nagel kit?)

Preparation of E.coli (TG1 and DH5-alpha) competent cells

Observation of transformation results

PCR on recombinant clones => LismA201/M1/M2 and M3

TheBioBrick J23100 was not the BioBrick we wanted we made a little error in the suspension (bad plate)

Transformation of the correct J23100 into E.coli (TG1)

Test with the Macherey-Nagel kit => it works!!

Starters of positive clones verified by PCR and of -I13504 -J23100 -J23118 -J23106 -J23117 -J23103

Plasmid purification of starters from positive clones of M1/M2/M3 and LismA201 and of -I13504 -J23100 -J23118 -J23106 -J23117 -J23103

E/S digestion of -J23118 -J23106 -J23117 and J23103

XP digestion of -I13401 and I13504

Ligations:

J23101 + I13504 + pSB1C3
J23118 + I13504 + pSB1C3
J23106 + I13504 + pSB1C3
J23117 + I13504 + pSB1C3
J23103 + I13504 + pSB1C3
K525998 + I13401 + pSB1C3

Dosage of these purified plamids

Digestion E/P on purification products and electrophoresis to detect positive ligations

Suspension of BioBrick J23100, we did an error when we suspended the previous BioBrick

Ligations:

BBa_K823005 + I13504 + pSB1K3
BBa_J23118 + I13504 + pSB1K3
BBa_K823008 + I 13504 + pSB1K3
BBa_K823013 + I13504 + pSB1K3
BBa_J23103 + I13504 + pSB1K3
BBa_K525998 + I13401 + pSB1K3

Transformation of ligation products

PCR on some M1 clones.

Test of competent cells BL21 and DH5-Alpha with the iGEM test kit.

Digestion E/P of positive clones M1/M2/M3/LismA201 and electrophoresis.

Plasmid purification of J23100, DNA dosage, E/P digestion and electrophoresis

PCR of ligation products

BBa_K823005 + I13504 + pSB1K3
BBa_J23118 + I13504 + pSB1K3
BBa_K823008 + I 13504 + pSB1K3
BBa_K823013 + I13504 + pSB1K3
BBa_J23103 + I13504 + pSB1K3
BBa_K525998 + I13401 + pSB1K3
And PCR M1 relaunch

Starters launched of positive clones

PCR on BBa_K823008 + I 13504 + pSB1K3 and on J23100 + I13504 + pSBK3

Transplanting of:

J23100 + I13504 + pSB1K3
K823008 + I13504 + pSB1K3
I13504 + pSB1C3

Starters of:

BBa_K823008 + I 13504 + pSB1K3
J23100 + I13504 + pSB1K3
M1

Plasmid purification of

BBa_K823005 + I13504 + pSB1K3
BBa_J23118 + I13504 + pSB1K3
BBa_K823013 + I13504 + pSB1K3
BBa_J23103 + I13504 + pSB1K3
BBa_K525998 + I13401 + pSB1K3

Digestion E/P of :

BBa_K823005 + I13504 + pSB1K3
BBa_J23118 + I13504 + pSB1K3
BBa_K823013 + I13504 + pSB1K3
BBa_J23103 + I13504 + pSB1K3
BBa_K525998 + I13401 + pSB1K3
M1/M2/M3/LismA201

M1 has to be done again

Plasmid purification of

J23100 + I13504 + pSB1K3
K823008 + I13504 + pSB1K3
and M1

Digestion E/P of purified plasmids

Electrophoresis and sequencing of positive results

Transformation of J23103 + I13504 + pSB1K3 into E.coli (DH5-Alpha)

PCR on transformants of J23103 + I13504 + pSB1K3

Starters of positive clones

Digestion E/P of

J23100 + I13504 + pSB1C3
J23101 + I13504 + pSB1C3
J23118 + I13504 + pSB1C3
J23106 + I13504 + pSB1C3
J23117 + I13504 + pSB1C3
J23103 + I13504 + pSB1C3
K525998 + I13401 + pSB1C3

Plasmid purification of two J23103 + I13504 + pSB1C3 starters

Digestion E/P of the two J23103 + I13504 + pSB1C3 purified plasmids

Ligation in pSB1C3

Transformation into E.coli (DH5-Alpha) of:

J23100 + I13504 + pSB1C3
J23101 + I13504 + pSB1C3
J23118 + I13504 + pSB1C3
J23106 + I13504 + pSB1C3
J23117 + I13504 + pSB1C3
J23103 + I13504 + pSB1C3
K525998 + I13401 + pSB1C3

PCR on many transformants:

J23100 + I13504 + pSB1C3
J23101 + I13504 + pSB1C3
J23118 + I13504 + pSB1C3
J23106 + I13504 + pSB1C3
J23117 + I13504 + pSB1C3
J23103 + I13504 + pSB1C3
K525998 + I13401 + pSB1C3

Electrophoresis of the PCR products from July 20th

Starters on positive clones

Transformation of J23117 + I13504 + pSB1C3 because it was negative

PCR of J23117 + I13504 + pSB1C3

Starters on positive clones

The sequences are bad we have to do it again except for M3 which was the only good one

Starter of I13504 to make a stock of positive control

Plasmid purification of

J23100 + I13504 + pSB1C3
J23101 + I13504 + pSB1C3
J23118 + I13504 + pSB1C3
J23106 + I13504 + pSB1C3
J23103 + I13504 + pSB1C3
K525998 + I13401 + pSB1C3

Digestion E/P and electrophoresis to see if the insertion is good

We took the wrong BioBrick!!!

Transformation of the right I13504 into E.coli (TG1), two starter cultures launched

DNA purification of I13504. Digestion X/P of I13504

Digestion E/S of J23100, K823005, J23118, K823008, K823013

Ligation:

BBa_J23100 + I13504 + pSB1C3
BBa_K823005 + I13504 + pSB1C3
BBa_J23118 + I13504 + pSB1C3
BBa_K823013 + I13504 + pSB1C3
BBa_J23103 + I13504 + pSB1C3
BBa_K525998 + I13401 + pSB1C3

But we did not get enough pSB1C3 only BBa_J23100 + I13504 + pSB1C3

BBa_K823005 + I13504 + pSB1C3 could be launched

Transformation of BBa_J23100 + I13504 + pSB1C3

BBa_K823005 + I13504 + pSB1C3 into E.coli (TG1)

PCR of BBa_J23100 + I13504 + pSB1C3 and BBa_K823005 + I13504 + pSB1C3

Preparation of pSB1C3 Backbone with a digestion E/P of BBa_K525998 electrophoresis and gel purification of the highest band

Ligation:

BBa_J23118 + I13504 + pSB1C3
BBa_K823013 + I13504 + pSB1C3
BBa_J23103 + I13504 + pSB1C3
BBa_K525998 + I13401 + pSB1C3

Transformation into E.coli (TG1)

BBa_J23118 + I13504 + pSB1C3

BBa_K823013 + I13504 + pSB1C3

BBa_J23103 + I13504 + pSB1C3

BBa_K525998 + I13401 + pSB1C3

M1/M2

PCR on a green colony seen in the “magic box” => no positive results

Thermal shock forgot for the transformations, we have to do it again!!

PCR of J23100 + I13504 + pSB1C3 and BBa_K823005 + I13504 + pSB1C3

Starters launched on positive results

Transformation into E.coli (TG1)

BBa_J23118 + I13504 + pSB1C3
BBa_K823013 + I13504 + pSB1C3
BBa_J23103 + I13504 + pSB1C3
BBa_K525998 + I13401 + pSB1C3
M1/M2

Plasmid purification of J23100 + I13504 + pSB1C3

E/P digestion of J23100 + I13504 + pSB1C3 and electrophoresis to see the insertion of the BioBrick

Preparation of starters to use the TECAN, a plate reader we use to mesure GFP

We learned how to use the TECAN

PCR on M1, M2, BBa_K823013 + I13504 + pSB1C3, BBa_K823013 + I13504 + pSB1C3

Transformation of BBa_K823005 + I13504 + pSB1C3 into E.coli (TG1)

Ligation overnight:

BBa_J23118 + I13504 + pSB1C3
BBa_K823013 + I13504 + pSB1C3
BBa_J23103 + I13504 + pSB1C3
BBa_K525998 + I13401 + pSB1C3

Transformation of ligation products:

BBa_J23118 + I13504 + pSB1C3
BBa_K823013 + I13504 + pSB1C3
BBa_J23103 + I13504 + pSB1C3
BBa_K525998 + I13401 + pSB1C3

PCR on the only clone of BBa_K823005 + I13504 + pSB1C3 we got => positive result=> starter launched

Plasmid purification of BBa_K823005 + I13504 + pSB1C3 and E/P digestion to see the right insertion of the insert

PCR on green colonies on “the magic box”

PCR of BBa_K823005 + I13504 + pSB1C3 done again because of bad results

Starter launched on positive results

Starter of BBa_K823013 + I13504 + pSB1C3 and on BBa_K823008 + I13504 + pSB1C3 launched

J23100 + I13504 + pSB1C3 good sequencing!!!

Ligation overnight BBa_J23101 + I13504 + pSB1C3

Transformation of J23101 + I13504 + pSB1C3 into E.coli (TG1)

BBa_K823008 + I13504 + pSB1C3 prepared to send for sequencing

PCR on J23101 + I13504 + pSB1C3

Starter of positive clones

Ligation J23103 + I13504 + pSB1C3

Transformation of J23101 + I13504 + pSB1C3 into E.coli (TG1)

Plasmid purification of J23101 + I13504 + pSB1C3 starters

J23101 + I13504 + pSB1C3 prepared to send for sequencing

Starter of BBa_K823013 + I13504 + pSB1C3 launched => preparation for sequencing

Isolation of BBa_K823008 + I13504 + pSB1C3

X/P digestion of I13504

Ligation BBa_K823008 + I13504 + pSB1C3

Transformation BBa_K823008 + I13504 + pSB1C3 into E.coli (TG1)

BBa_K823005 + I13504 + pSB1C3 has the right sequence!

Ligation J23103 + I13504 + pSB1C3

Transformation of J23103 + I13504 + pSB1C3 into E.coli (TG1)

Send for sequencing BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3

Plasmid purification of BBa_K823013 + I13504 + pSB1C3

PCR screening colonies of J23119 + I13504 + pSB1C3

BBa_K823013 + I13504 + pSB1C3 send for sequencing

Starter launched on positive clones from the PCR done on August 16

Plasmid purification and digestion E/P to check the insertion => wrong results

Try again on the same clone

Ligations: BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3

BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3 and J23100 + I13504 + pSB1C3 send for sequencing

J23103 + I13504 + pSB1C3 has a good sequencing result

J23119 + I13504 + pSB1C3 send for sequencing

BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3 => good sequencing result

Transformation of ligation products of J23119 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3

PCR on J23119 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3

Transformation of J23119 + I13504 + pSB1C3 and K823013 + I13504 + pSB1C3 into E.coli (DH5-Alpha)

First try of construction of a box to observe GFP called “magic-box”. First try with coomasie blue as light filter, public lab spectrometer, yellow filter and a webcam

J23119 + I13504 + pSB1C3 (obtained the August 24th) send for sequencing

Construction of the magic-box without the public lab spectrometer

Coomasie blue concentration determination and first assay with the magic box

Sequencing results of J23119 + I13504 + pSB1C3 => bad

K823013 + I13504 + pSB1C3 clone 5 => good

K823013 + I13504 + pSB1C3 clone 2 => bad

Isolation of K525998 + I13401 + pSB1C3, K823008 + I13504 + pSB1C3, J23119 + I13504 + pSB1K3 and K823013 + I13504 + pSB1K3

E/P digestion of J23119 + I13504 + pSB1K3

Ligation overnight:

J23119 + I13504 + pSB1C3

tarter launched on another J23119 + I13504 + pSB1C3 clone

Measure of fluorescent intensity with different bacterial OD

Determination of the medium that will be use => LB or PBS1X

Colony PCR and electrophoresis of “08”, “15”, “12-02” and “30-02” to check the size of the insert. Positive results for “15”, “12-02” and “13-02” (expected size) but negative result for “08” (several sizes observed). Starters of “08”, “15”, “12-02” and “30-02”.

Plasmid purification (miniprep) of “05”, “09” and “10”. Problem encountered: genomic DNA contamination.

E/P digestion and electrophoresis to check the size of the insert of “05”, “09”, and “10”.

Miniprep of “08”, “15”, 12-02”, “30-02”. E/P digestion and electrophoresis to check the size of the insert of “08”, “15”, 12-02”, “30-02”. Positive results for “15”, “12-02”, “30-02” (expected size) and negative result for “08” (unexpected size).

Comment: constructs “12-02” and “30-02” have to be compared with the single “12” and “30” to check if “02” was added.

Colony PCR and electrophoresis to check the size of the insert of “08”. Negative result

Electrophoresis of “12”, “12-02”, “30” and “30-02”. No result (no DNA observed on the agarose gel)

Construction of “09-02”, “10-02” and “13-02”: E/S digestion of “09”, “10” and “13”. X/P digestion of “02”. Ligation into pSB1A3, transformation into TG1. Positive results for “09-02” and “13-02” (1 colony on the plate). Negative result for “10-02” (no colony on the plate).

Resuspension of biobrick “11” and new try for the “05” and the “08” received from IDT. E/P digestion and ligation into pSB1C3. Transformation into TG1. Positive result for “11” (several colonies on the plate) but not for “05” and “08” (no colony on the plate)

Colony PCR and electrophoresis to check the size of the insert of « 11 », “09-02” and “13-02”. Uncertain results (problems: DNA is not observed on the agarose gel). “13-02” seems good: starter of “13-02”.

New try with new oligos for the colony PCR and electrophoresis of « 08 ». No result (no DNA observed on the agarose gel).

New try with new volumes for resuspension of the biobrick “05” received from IDT. E/P digestion and ligation into pSB1C3. Transformation into TG1. Negative result (no colony on the plate).

New try to construct “09-02”, “10-02” and “13-02”. E/S digestion of “09”, “10” and “13”. X/P digestion of “02”. Ligation overnight into pSB1A3, transformation into TG1 (07/31). Positive result for “13-02” (several colonies on the plate. Negative result for “09-02” and “10-02” (no colony on the plate).

E/P digestion to check the size of the insert of “30”, “30-02”, “12”, “12-02”. Results seems good for “12” and “12-02”: send for sequencing. Negative results for “30”, “30-02” (unexpected sizes).

Miniprep of « 13-02 ». E/P digestion and electrophoresis to check the size of the insert. Positive result (expected size).

Colony PCR and electrophoresis to check the size of the insert of “13-02”. Negative result (unexpected size).

Transformation of “09-02”, “10-02” and “13-02” into TG1.

pSB1C3 backbone was running out. New backbone done: E/P digestion on measurement biobricks, electrophoresis and purification of the digested plasmid by gel extraction and PCR clean up.

Problem encountered: no DNA observed on the agarose gel.

Colony PCR and electrophoresis to check the size of the insert of “09-02”, “10-02” and “13-02”. Positive results (expected sizes). Starters of “09-02”, “10-02” and “13-02.

New try for making pSB1C3 backbone: E/P digestion of measurement biobricks, electrophoresis and purification of the digested plasmid by gel extraction and PCR clean up.

Resuspension of the biobrick “07” (cotA) received from IDT. E/P digestion and ligation into pSB1A3, transformation into TG1

Colony PCR and electrophoresis to check the size of the insert on “07” => we got a positive clone, starter of this clone launched

Plasmid purification of “13-02” “09-02” “10-02”

E/P digestion of “05” and “11” and ligation “05” + pSB1K3 and “11” + pSB1K3

Transformation of ligation products into E.coli (TG1)

PCR on “07” and “08” => seems to be unclean with the Q5 high fidelity DNA amplification

X/P digestion of “15”

Overnight ligation “12”+”02”+pSB1A3 and “01”+”15”+pSB1T3

“30-02” and “08” got bad results in sequencing

Transformation of ”01-15” and “12-02” into E.coli (TG1)

Plasmid purification of “09-02” “07” “13-02” “09-02” “10-02” => low concentration of “09-02” but we got good result for “13-02”

Transformation of “12-02” and “01-15” into TG1

PCR clean up “07” “08” “24” ==> low plasmid concentration of “07” and “08” to do again.

Colony PCR of “05” “11” “12-02” “01-15” => good but only for “12-02”

PCR clean up of “08” and “07” → PCR products contaminated → PCR clean up

Transformation of “10-02” and “09-02”→ Wrong size starter relaunched

Ligation “09-02” and “10-02” into pSB1A3 and “01-15” into pSB1T3

Colony PCR of “05” and “01-15” --> no results on this PCR

Transformation of “09-02” “10-02” “01-15” into E.coli (TG1)

Ligation “05” + pSB1K3 and “11” + pSB1K3

Plasmid purification of “12-02” --> Bad results with electrophoresis

For “05” “07” “08” “11” → PCR with Q5 high fidelity polymerase and “PCR clean up”

Preparation of BL21 competent cells

Colony PCR of “01-15” → No results => Ligation with the digestion product “01-15” relaunched

For “05” “07” “08” “11” : Digestion E/S + Ligation pSB1C3 + Transformation into TG1

For “30” : Digestion E/P + Ligation into pSB1K3

For “01-15” : Ligation into pSB1T3

PCR clean up of “28”

Colony PCR of “09-02” “10-02” “05” “07” “08” “11”

Preparation of TG1 competent cells

We used the wrong “02” Biobrick we have to do everything again with the good one → Colony PCR of the “new” “02” → size = ok

Transformation of “30” “01-01” “02” into TG1

Preparation of the backbone pSB1A3

Ligation of “05” “08” “07” “11” into pSB1A3

Colony PCR of “30” “21-17” “23-17” “01-15”

For “35” et “36” : Digestion E/S + ligation into pSB1A3 + transformation into TG1

For “37” “38” : Digestion E/P + Ligation into pSB1K3 + transformation into “supercompetent” cells

Plasmid purification of “02” --> Low concentration of plasmid, starter relaunched

For “02” : Digestion X/P

For “13” : Digestion E/S

Ligation of “35-02” “36-02” “12-02” “13-02” into pSB1A3

PCR on “09” et “10” to remove the stop codon

Transformation of “05” “07” “08” “11” into “supercompetent” cells

Colony PCR on “05” “07” “08” “21-17” “11” “35” “36” “37” “38”

Transformation of “12-02” “13-02” “35-02” “36-02” “36-02” into TG1

PCR clean up of “35” “36”

Digestion E/S of “12” “35” “36” “16” “13”

For “12-02” “13-02” “35-02” “36-02” : Ligation into pSB1A3 + transformation in TG1

For “01-15” : Ligation into pSB1T3 + transformation into TG1

For “16-17” : Ligation into pSB1C3 + transformation into TG1

Colony PCR on “38” “05” “07” “36” ”08” “11”

For “39” “30” : Digestion E/P + Ligation into pSB1K3

Colony PCR on “12-02” “13-02” “39” “36-02” “23-17” “35-02”

Plasmid purification of “36” “38” “07” “05” “35” “11” “37” --> Verification ok for “36” “38” “35” “37”

Colony PCR on “05” “07” “08” “11” “16-17” “21-17” “05” “07” “08” “11” “16-17” “21-17” --> Bad results for all

Plasmid purification of “38” “05” “11” “08” “39” “12-02” “13-02” “35-02” “23-17” “35” “01-15” “16-17” “21-17” --> Problem with the ladder, we cannot read the gel

For “38” “39” “08” “05” : Digestion E/S

For “12” “13” “39” “35” “35-02” “13-02” “12-02” : Digestion X/P

For “38-12” “38-13” “39-02” “38-39” “08-02” “36” “05-02”: Ligation into pSB1A3

For “01-3502” “01-1302” “01-1202” “01-35” : Ligation into pSB1T3

For “21-17” “22-17” : Ligation into pSB1C3

==> Transformation for all ligation products into TG1

Colony PCR of “07” “05” “08” “11” with “pool” technic

Colony PCR of “11” “7” => starters launched on positive clones

Plasmid verification of “05” “07” “08” “11” and “16-17”

“07” and “08” have to be relaunched

Colony PCR on transformants from August 17 => Starters on positive clones launched and the constructions “01-3502” and “38-39” have to be rebuilt

Preparation of the backbone pSB1A3

Ligation of “01-1302” “01-1202” “01-35” into pSB1T3

Starters launched of “05” and “11”

Preparation of the backbone pSB1A3

Sequencing results “12-02” “13-02” “35-02” “01-15” are ok

“08” is bad and “05” couldn’t be sequenced

Plasmid purification of “30” “38-13” “39-02” “08-02” “05-02” “38-12” “11” “07” “16-17”

“38-13” “39-02” “16-17” “38-12” send for sequencing

“30” “08-02” “05-02” “11” “07” are bad we cannot use its

Colony PCR of “05-02” “01-1302”

Plasmid purification of “05” and “11” and of 2 starters to make some backbones (pSB1A3 and pSB1T3)

The digestion to prepare pSB1T3 is bad, starter relaunched

Ligation of “38-39” “11-02” into pSB1A3

“38-11” into pSB1C3

“01-1202” “05-02” “01-36” “01-1302” “01-3502” “01-35” “21-17” “22-17” into pSB1K3

Transformation of previous ligation products into DH5-Alpha for “21-17” and “22-17”, into TG1 for “11-02” “38-11” “05-02” and “38-39” and into BL21 for “01-1202” “01-36” “01-1302” “01-3502” and “01-35”

“38-13” “39-02” “11” and “38-12” sent for sequencing

Sequencing result of “05” => bad

Transformation of “18-17” “19-17” “20-17” and “23-17” into DH5-Alpha

Colony PCR of “07”

Digestion E/S fof “16” “38” “11” “22”, X/P for “17” “39” “02” “11” “35”

Ligation of “16-17” “22-17” + pSB1C3 “38-39” “11-02” “38-11” + pSB1A3

“01-35” “05” “07” “08” “30” + pSB1K3

Transformation of “30” “08” “07” “05” into C2987 (“supercompetent” cells)

Transformation of “38-39” “11-02” “38-11” and “01-35” into TG1

Plasmid purification of “01-1202” “01-3502” “05” “01-1302” “07” and of pSBT3 to get some backbone.

Colony PCR of “08” “01-3502” “01-1202” “01-1302” “01-36”

We got many bad results today so bad luck, but we got some good results also.

Colony PCR of “38-39” “38-11” “11-02” “01-35”

Starters launched of positive clones

Transformation of overnight ligation produtcs (“16-17” and “22-17” from August 21)

Plasmid purification to make some pSB1A3 and pSB1T3

First protein expression test, we maybe succeed to express our first laccase

Colony PCR of “16-17” and “22-17” launched overnight => green colonies!!

Starters launched of positive results

Plasmid purification of “22”-17” “16-17” and ‘01-35” => all results are good!!!!

Digestion E/S for “38” and X/P for “39”, ligation overnight into pSB1A3

Transformation of “30” “08” “07” “11” “05” into TG1

Plasmid purification of “16-17” “01-1302” “01-1202” “22-17” “01-3502”

Colony PCR of “05” “07” “08” “11” => no positive results!

Q5 PCR of “05” “07” “08” “11” “30” => positive results

“05” and “01-35” sent for sequencing

Transformation of “05” “07” “08” “11” “30” into TG1

Plasmid purification of “01-36” “19-17” “18-17” “23-17” “20-17” => good results

“01-1202” “01-1302” “01-3502” sent for sequencing

Sequencing results of “01-35” “38-12” “38-13” “39-02” => good results “05” “11” => bad results

Starters launched of “39” “01-1302” “01-1202” “01-3502” “01-15” “13-02” “12-02” “38”

Protein expression => the cytochrome c and the laccase are expressed.

Isolation and starter launched of “32”

Plasmid purification of “39” “01-1302” “01-1202” “01-3502” “01-15” “13-02” “12-02” “38” “16-17”=> no results!

Ligation of “40” “41” “42” “43” “44” “45” “46” “47” “48” “22-17” + pSB1C3

“30” + pSB1K3

Transformation of “30” “40” “45” “48” into TG1

Transformations didn’t work! => “40” “45” “48” relaunched

Sequencing results “01-1302” => without promoter

“01-1202” and “01-3502” are good

Colony PCR of “40” “45” “48”

Starters launched of “18-17” “19-17” “20-17” “21-17” “22-17” “23-17” “32” “33” “01-24” each in triplicate

Stock of backbone pSB1C3 done

Preparation of SDS-PAGE, of solutions and of the column to make the protein purification

Digestion E/P of “22-17” “43” “44” “47” and digestion X/P of “1302” “3902”

Ligation “43” “44” “47” into pSB1C3

“013002” into pSB1K3

“01-3902” “01-1302” into pSB1C3

Colony PCR of “40” “45” “48” all clones are positive, starters launched

Protein purification of “01-3502” “01-1202”

SDS-PAGE of “01-3502” “01-1202”

01-3502 purified and pure!!!! We got our first protein which is a laccase from E.coli

Starters launched of “38” “13-02” “01-36” “01-15” “01-3502” “01-1202” “37” “35-02” “12-02” “35” “36” “01-35” “39” “40” “45” “48”

Plasmid purification of “01-36” “40” “39” “48” “45” “37” “36” “01-1202” “01-36” “01-15” “35-02” “35” “38” “13-02” “12-02” “01-3502” “01-35”

Protein expression of 01-3502 and 01-1202

Colony PCR of “01-15” beause we have doubt concerning colonies => all colonies were positive

Ligation of “43” “44” “47” “03002” “01-1302” “013902” into pSB1C3

Transformation of “43” “44” “47” “013002” into C2987 and “01-1302” “01-3902” “3813-02” “3812-02” into TG1

Verification digestion on “40” “38” “01-15” “48” “45” “01-36” “01-1202” “01-36” “37”

Plasmid purification of “01-1202”

Colony PCR of “3812-02” “3813-02” “01-3902” “01-1302” starters launched on positive results

No colony for “43” “44” “47” “013002”

Preparation of the backbone pSB1C3

Transformation of “013002” “41” “44” “47” into C2987

Plasmid purification of “45” “01-36” “381302” “38” “01-1202” “3812-02” “3813-02”

Colony PCR of “47” “01-3002” “43” “44” => almost everything is positive!!! Great day!

Plasmid purification (miniprep) of “44” “47” “43” “38” “01-1302” “01-1202” “01-3002” “45”

“01-1302” “01-36” “3813-02” seems good so they are send for sequencing.

Construction : Digestion E/S of “38” “01-36” “01-35” “01” and Digestion X/P of “44” “47” “43” “48” “44” “45” “1302” “3813-02” “39-02” “40” “3812-02”

Starter launched on “01-1202” “01-3002” for production and on “0136” for miniprep

Ligation in pSB1C3 of “0136-02” “01-381302” “01-381202” “01-3902” “01-1302” “38-3902” “0136-40” “0136-45” “0136-48” “0135-43” “0135-44” “0135-47”

Transformation of “01-3002” in BL21, of pSB4K5 and pSB3T5 in TG1 and transformation of ligation product in TG1

Purification of “01-1202” (1) and (2):

Induction by IPTG

Storing the cells at -80°C

Colony PCR of “013002” “013002” => all results are positive

Production of “01-1202” : Sonication of cells, centrifugation 10 min at 4500 rpm, ultracentrifugation 45 min at 4500 rpm, solubilizing membrane in Triton 1% during 2h and incubation overnight.

Preparation of SDS Page 15% and a western blot with products of yesterday => results are not good so we have to resart the production

Culture of “01-1202” and “01-3002” in anaerobic condition, cells were centrifuged 10 min at 4500 rpm and pellet were stored at -20°C

A western blot was done → Production of Cytochrome, monomer in the membrane and dimer in the cytoplasm

The next step is to purify “01-1202” and “01-3002” and start a culture on 01-3502 in anaerobic condition

@@ Line 532: / Line 532: @@
 Transformation BBa_K823008 + I13504 + pSB1C3 into <i>E.coli</i> (TG1)
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo31">July 8</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo31">August 12</button>
    <div id="demo31" class="collapse">
-ONET company presented our project to the Executive office.
+<p>BBa_K823005 + I13504 + pSB1C3 has the right sequence!</p>
+<p>Ligation J23103 + I13504 + pSB1C3</p>
+<p>Transformation of J23103 + I13504 + pSB1C3 into <i>E.coli</i> (TG1)</p>
+<p>Send for sequencing BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3</p>
+<p>Plasmid purification of BBa_K823013 + I13504 + pSB1C3</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo32">July 9</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo32">August 16</button>
    <div id="demo32" class="collapse">
-Positive answer from ONET: it sponsored our project with 7000 euros !
+PCR screening colonies of J23119 + I13504 + pSB1C3
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo33">July 10</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo33">August 17</button>
    <div id="demo33" class="collapse">
-Resuspension of the biobrick “12” (cyt C Shewanella) received from IDT, ligation into pSB1C3, transformation into DH5-alpha.
+<p>BBa_K823013 + I13504 + pSB1C3 send for sequencing</p>
+<p>Starter launched on positive clones from the PCR done on August 16</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo34">July 15</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo34">August 18</button>
    <div id="demo34" class="collapse">
-<p>Colony PCR on BL21 strain to amplify the 3 parts of ccm operon. Oligos were too concentrated and inhibited the reaction.</p>
+<p>Plasmid purification and digestion E/P to check the insertion => wrong results </p>
-<p>Colony PCR and electrophoresis to check the size of the biobrick “12” (cytochrome c Shewanella). Positive result.</p>
+<p>Try again on the same clone</p>
-<p>Resuspension of biobricks “05”, “08”, “30”, “11” received from IDT. E/P digestion, ligation into pSB1C3, transformation into E.coli (TG1). Negative result (no colony on the plate).</p>
+<p>Ligations: BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width:110px;" data-target="#demo35">July 16</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width:110px;" data-target="#demo35">August 19</button>
    <div id="demo35" class="collapse">
-<p>Second try to resuspend the biobricks “05”, “08”, “30”, “11” received from IDT and resuspension of the biobrick “13” received from IDT. E/P digestion, ligation into pSB1C3, transformation into E.Coli (TG1). Positive result (several colonies on the plate).</p>
+<p>BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3 and J23100 + I13504 + pSB1C3 send for sequencing</p>
-<p>Second try for Colony PCR on DH5-alpha strain to amplify the 3 parts of ccm operon with diluted oligos at 1/10. Positive result except for part 1: there are some contaminants due to nonspecific hybridization.</p>
-<p>Reception of oligos from SIGMA to amplify the laccase of E.coli and T.thermophilus.</p>
+<p>J23103 + I13504 + pSB1C3 has a good sequencing result</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo36">July 17</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo36">August 20</button>
    <div id="demo36" class="collapse">
-<p>Third try for colony PCR on DH5-alpha to amplify part 1 of ccm operon. The Tm changed from 55 to 60°C. Positive result.</p>
+J23119 + I13504 + pSB1C3 send for sequencing
-<p>Colony PCR and electrophoresis to check the size of the biobricks “05”, “08”, “30”, “11” and “13”. Positive results except for “08” et “11”.</p>
-<p>Starters of “05”, “13”, “30”.</p>
-<p>Plasmid purification (miniprep) of the biobrick “12”, E/P digestion to check the size of the insert. Positive result.</p>
-<p>High fidelity DNA amplification of biobricks “09” and “10” by PCR with the Q5 polymerase in order to remove the codon-STOP. PCR clean up. Negative result (nonspecific amplification).</p>
-<p>Reception of the biobrick “15” from IDT.</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo37">July 20</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo37">August 23</button>
    <div id="demo37" class="collapse">
-<p>Colony PCR and electrophoresis to check the size of the biobricks “08” and “11”. Positive result for “08” but not for “11”. Starter of “08”.</p>
+<p>BBa_K823008 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3 => good sequencing result</p>
-<p>New DH5-alpha competent cells done.</p>
+<p>Transformation of ligation products of J23119 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo38">July 21</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo38">August 22</button>
    <div id="demo38" class="collapse">
-<p>Second try for high fidelity DNA amplification of biobricks “09” and “10” by PCR with the Q5 polymerase in order to remove the codon-STOP (the new synthesized biobricks are called respectively “35” and “36”). PCR clean up. Negative result (non-specific amplification). An electrophoresis was done on the total PCR product and was extracted and purified by PCR clean up.</p>
+PCR on J23119 + I13504 + pSB1C3 and BBa_K823013 + I13504 + pSB1C3
-<p>Miniprep of “08”. E/P digestion to check the size of the insert. Negative result (unexpected size).</p>
-<p>Resuspension of biobrick “15” received from IDT. E/P digestion, ligation into pSB1C3, transformation into E.coli (DH5-alpha). Negative result (no colony on the plate).
-<p>New TG1 competent cells done.</p>
-<p>Transformation efficiency test with the transformation efficiency kit of iGEM on the new DH5-alpha competent cells. Positive result (the DH5-alpha cells are competent enough to be transformed with our constructions).</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo39">July 22</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo39">August 24</button>
    <div id="demo39" class="collapse">
-<p>Colony PCR and electrophoresis to check the size of the biobricks “05” and “13”. Positive result. Starters of « 05 » and « 13 ».</p>
+<p>Transformation of J23119 + I13504 + pSB1C3 and K823013 + I13504 + pSB1C3  into <i>E.coli</i> (DH5-Alpha)</p>
-<p>SLIC reaction to ligate the 3 parts of ccm operon into the pSB1C3 plasmid. Transformation into E.coli (TG1). Negative result (no colony on the plate). </p>
-<p>SLIC reaction to ligate the new biobricks “35” and “36” into pSB1C3. Transformation into E.coli (TG1). Negative result (no colony on the plate).</p>
+<p>First try of construction of a box to observe GFP called “magic-box”. First try with coomasie blue as light filter, public lab spectrometer, yellow filter and a webcam</p>
-<p>Transformation efficiency test with the transformation efficiency kit of iGEM on the new TG1 competent cells. Positive result (the TG1 cells are competent enough to be transformed with our constructions)</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo40">July 23</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo40">August 25</button>
    <div id="demo40" class="collapse">
-<p>Miniprep of “05” and “13” and E/P digestion to check the size of the insert. </p>
+<p>J23119 + I13504 + pSB1C3 (obtained the August 24th)  send for sequencing </p>
-<p>New try to transform “08” into pSB1C3 into DH5-alpha.</p>
-<p>Resuspension of biobricks “09” and “10” from the registry, transformation into TG1.</p>
+<p>Construction of the magic-box without the public lab spectrometer</p>
-<p>Construction of “30-02”, “12-02” : E/X digestion of “30” and “12”, S/P digestion of “02”, ligation into pSB1A3, transformation into TG1. Negative result (no colony on the plate).</p>
+<p>Coomasie blue concentration determination and first assay with the magic box</p>
-<p>New try for the SLIC reaction (ccm operon), “35” and “36”. Negative result (no colony on the plate).</p>
    </div>
-   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo41">July 24</button>
+   <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo41">August 26</button>
    <div id="demo41" class="collapse">
-<p>New try with different volumes for resuspension of biobricks “15” and “08” received from IDT. E/P digestion, ligation into pSB1C3, transformation into E.coli (TG1). Positive result (several colonies on the plate).</p>
+<p>Sequencing results of J23119 + I13504 + pSB1C3 => bad</p>
-<p>Colony PCR and electrophoresis to check the size of the biobricks”08”, “09”, “10”,”12-02”, “30-02”, “32” and “34”. Positive result for “09” and “10” (expected size). Starters of « 09 » and « 10 ».</p>
+<p>K823013 + I13504 + pSB1C3 clone 5 => good </p>
-<p>Negative result for “32”, “34”, “12-02”, “30-02” (No colony on the plate) and for “08” (unexpected size).<
+<p>K823013 + I13504 + pSB1C3 clone 2 => bad</p>
-<p>New try to construct “30-02”, “12-02”: E/X digestion of “30” and “12”, S/P digestion of “02”, ligation into pSB1A3, transformation into TG1. Positive result (several colonies on the plate).
+<p>Isolation of K525998 + I13401 + pSB1C3, K823008 + I13504 + pSB1C3, J23119 + I13504 + pSB1K3 and K823013 + I13504 + pSB1K3</p>
+<p>E/P digestion of J23119 + I13504 + pSB1K3</p>
+<p>Ligation overnight:</p>
+ <p>J23119 + I13504 + pSB1C3 </p>
+<p>tarter launched on another  J23119 + I13504 + pSB1C3 clone</p>
+<p>Measure of fluorescent intensity with different bacterial OD</p>
+<p>Determination of the medium that will be use => LB or PBS1X</p>
    </div>
    <button type="button" class="btn btn-info" data-toggle="collapse" style="width: 110px;" data-target="#demo42">July 27</button>

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