Team:UNIPV-Pavia/Calendar/August/week1

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UNIPV TEAM 2011

March
M T W T F S S
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7 8 9 10 11 12 13
14 15 16 17 18 19 20
21 22 23 24 25 26 27
28 29 30 31    

April
M T W T F S S
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4 5 6 7 8 9 10
11 12 13 14 15 16 17
18 19 20 21 22 23 24
25 26 27 28 29 30

May
M T W T F S S
            1
2 3 4 5 6 7 8
9 10 11 12 13 14 15
16 17 18 19 20 21 22
23 24 25 26 27 28 29
30 31

June
M T W T F S S
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6 7 8 9 10 11 12
13 14 15 16 17 18 19
20 21 22 23 24 25 26
27 28 29 30

July
M T W T F S S
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4 5 6 7 8 9 10
11 12 13 14 15 16 17
18 19 20 21 22 23 24
25 26 27 28 29 30 31

August
M T W T F S S
1 2 3 4 5 6 7
8 9 10 11 12 13 14
15 16 17 18 19 20 21
22 23 24 25 26 27 28
29 30 31

September
M T W T F S S
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5 6 7 8 9 10 11
12 13 14 15 16 17 18
19 20 21 22 23 24 25
26 27 28 29 30

October
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3 4 5 6 7 8 9
10 11 12 13 14 15 16
17 18 19 20 21 22 23
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31

AUGUST: WEEK 1

August, 1st

Two colonies for E28-AGAIN and E41-AGAIN plates were picked and inoculated in LB + Cm12.5; J101-31, J101-E5 and J101-E7 plasmids were extracted:

Plasmid DNA (ng/μl)
J101-31 38
J101-E5 14.5
J101-E7 14

These plasmids were digested with EcoRI and SpeI restriction enzymes and screened by gel-electrophoresis; a medium-size agarose gel was then prepared.
MGZ1 competent cells were prepared according to protocol. They were put in 22 100 μl test-tubes.
Gel electrophoresis was performed:

Medium size gel

Insert lengths were all correct so J101-31, J101-E5, J101-E7 were transformed from MiniPrepped DNA in MGZ1 competent cells.


E37-2, E38-1, E39-1, E40-2 and E42-1 were inoculated in 5 ml LB + Cm12.5 and grown ON for plasmid extraction.

August, 2nd

MGZ1 J101-31, J101-E5 and J101-E7 plates were all grown; one colony was picked from each of them and inoculated in LB + Cm12.5. Plasmids harboring E28-AGAIN-1, E28-AGAIN-2, E41-AGAIN-1, E28-AGAIN-2, E37-2, E38-1, E39-1, E40-2 and E42-1 were extracted with MiniPrep kit from ON saturated cultures; purified DNA was quantified with NanoDrop Spectrophotometer:

Plasmid DNA (ng/μl)
E28AGAIN-1 21.4
E28AGAIN-2 21.0
E41AGAIN-1 33.7
E41AGAIN-2 27.7
E37-2 18.5
E38-1 26.0
E39-1 21.6
E40-2 19.9
E42-1 25.1

Digestions of E28AGAIN-1, E28AGAIN-2, E41AGAIN-1 and E42AGAIN-2 were performed for screening; a 5x mix was prepared and for each sample the volumes specified in the table below were used:

DNA (μl) H2O (μl) Enzyme 1 (μl) Enzyme 2 (μl) Buffer H (μl) Final Volume (μl)
5 16.5 0.5 EcoRI 0.5 PstI 2.5 25

A small-size agarose gel was prepared for gel electrophoresis.
TOP10 competent cells, harboring BBa_T9002 construct, were co-transformed with ENTERO4C5 to confer resistance to Cloramphenicol (12.5 mg/ml) and plated on LB agar + Amp + Cm 12.5 plates.
In the afternoon gel electrophoresis was performed:

Small size gel

Unfortunately insert length was correct only for E28-AGAIN-1 so we ligated again E41:

Ligation Name Vector Vector volume (μl) Insert Insert volume (μl) Buffer (μl) T4 Ligase (μl)
E41N E36 (S-P) 4 E3-1 (X-P) 4 1 1

Glycerol stocks were prepared according to the protocol for J101-31, J101-E5 and J101-E7.
E37-2, E38-1, E39-1, E40-2, E42-1 and E28-AGAIN-1 DNA was sent to BMR genomics for sequencing.
5 μl of E37-2, E38.1, E39-1, E40-2 and ENTERO4C5 were inoculated in 1 ml M9 + Cm12.5 for a preliminary test on the autoinducer inactivation enzyme A (AiiA) enzyme.

August, 3rd

T9002-ENTERO4C5 plate was grown and a colony was picked and inoculated in LB + Amp + Cm12.5; E41N ligation was transformed in 100 μl of MGZ1 competent cells and plated on a LB + Cm12.5 plate.
34 LB agar + Cm12.5 plates were prepared according to protocols.
E37-2, E38.1, E39-1, E40-2 and ENTERO4C5 cultures were diluted 1:100 in a final volume of 5 ml of M9 + Cm12.5 for the preliminary test; a 1000 x 75 ng/μl atc stock was prepared.
After 3 hours cultures were induced with 5 μl of atc (75 ng/ml final concentration); after 4 hours 2.5 μl of 2mM 3OC6-HSL (1:2000 dilution) were added (final 3OC6-HSL concentration 1μM) and the experiment started (t = 0 h).
250 μl samples were taken at t = 0 h, t = 1 h, and t = 4 h; O.D. at 600 nm was measured:

E37 E38 E39 E40 ENTERO4C5
t = 0 h 0.12 0.11 0.13 0.10 0.11
t = 1 h 0.22 0.15 0.21 0.28 0.19
t = 4 h 0.47 0.60 0.53 0.37 0.53

Then samples were centrifuged at 13.000 rpm; finally the supernatant was collected and stored at -20°C.
Glycerol stock for T9002-ENTERO4C5 was prepared.
Two 5 μl inocula of E32, E33, E34, E35, J101-E5, J101-31, J101-E6, J101-E7 and ENTERO4C5 were prepared in 1 ml of M9 + Cm12.5 for a preliminary test on TetR repressible promoter.

August, 4th

E41N plate was grown; three colonies were picked (E41N-1, E41N-2, E41N-3) and inoculated in LB + Cm12.5.
E32-1, E33-1, E34-1, E35-1, J101-E5-1, J101-31-1, J101-E6-1, J101-E7-1, E32-2, E33-2, E34-2, E35-2, J101-E5-2, J101-31-2, J101-E6-2, J101-E7-2, ENTERO4C5-1 and ENTERO4C5-2 were diluted 1:500 in a final volume of 1 ml. After 2 hours and 30 minutes inducible cultures were supplemented with anhydrotetracyclin (atc) at final concentrations of: 1 ng/ml, 10 ng/ml, 50 ng/ml, 100 ng/ml. Moreover uninduced cultures were supplemented with ddH2O.
ENTERO-RBS and T9002-ENTERO4C5 were inoculated in 1 ml of Cm12.5 for preliminary AiiA test (with supernatants collected on August, 3rd).

August, 5th

ENTERO-RBS and T9002-ENTERO4C5 cultures were diluted 1:500 in a final volume of 1 ml and 10 ml of M9 + Cm12.5 respectively; they were grown for six hours. Plasmid purification was performed for E41N-1, E41N-2 and E41N-3:

Plasmid DNA (ng/μl)
E41N-1 62.3
E41N-2 17.3
E41N-3 43.9

Screening digestion with EcoRI and PstI restriction enzymes was carried out:

Plasmid DNA (μl) H2O (μl) Enzyme 1 (μl) Enzyme 2 (μl) Buffer H (μl) Final Volume (μl)
E41N-1 2.5 19 0.5 EcoRI 0.5 Pstl 2.5 25
E41N-2 8.5 13 0.5 EcoRI 0.5 Pstl 2.5 25
E41N-2 3.5 18 0.5 EcoRI 0.5 Pstl 2.5 25

3OC6-HSL was diluted to known concentrations in order to induce T9002-ENTERO4C5 biosensor and obtain a reference curve for the measurements on E37, E38, E39, E40 and ENTERO4C5 supernatants.
A small-size agarose gel was prepared; in the afternoon gel electrophoresis was carried out:

Small size gel

Only E41N-1 showed the correct band, so we decided to keep it. E41N-2 and E41N-3 glycerol stocks were thrown.
TECAN test on E37, E38, E39, E40 and ENTERO4C5 supernatants was carried out; as supernatants were not diluted enough it was not possible to precisely measure 3OC6-HSL concentration as the biosensor (T9002-ENTERO4C5) worked in the saturation zone.