Team:UNIPV-Pavia/Calendar/August/settimana2

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(Difference between revisions)
(→August, 9th)
(→August, 10th)
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==August, 10th==
==August, 10th==
 +
==August, 10th==
 +
 +
Glycerol stock was prepared for:
 +
 +
* linker
 +
*  I22-1
 +
*  I22-2
 +
*  I22-3
 +
*  I23-1
 +
*  I23-2
 +
*  I23-3
 +
*  I8-5 D
 +
*  I8-5 E
 +
*  I8-5 F
 +
 +
and are stored at -80°C.
 +
 +
 +
----
 +
 +
Cultures were diluted (5ul in 2ml LB+antibiotic) for TECAN test:
 +
 +
{| border='1' align='center'
 +
|I8-5 D|| I8-5 E|| I8-5 F
 +
|-
 +
|I74C5|| I84C5 ||I104C5
 +
|-
 +
|I124C5|| Rbs32|| A2
 +
|}
 +
 +
----
 +
 +
MiniPrep was performed for following cultures (using our new NucleoSpin kit, that we prepared yesterday! :) ):
 +
 +
{| align='center' border='1'
 +
|'''Culture'''|| '''Quantification'''
 +
|-
 +
|I20-1 || 16,5 ng/ul
 +
|-
 +
|I20-2|| 8,9 ng/ul
 +
|-
 +
|I20-3|| 19,3 ng/ul
 +
|-
 +
|I20-4||12,5 ng/ul
 +
|-
 +
|I20-5 ||22,4 ng/ul
 +
|-
 +
|I20-6 ||12,3 ng/ul
 +
|-
 +
|I20-7 || 4,1 ng/ul
 +
|-
 +
|I20-8||15,7 ng/ul
 +
|-
 +
|I20-9||14,4 ng/ul
 +
|-
 +
|I20-10|| 17,5 ng/ul
 +
|-
 +
|I20-11 || 24,5 ng/ul
 +
|-
 +
|I20-12||21,2 ng/ul
 +
|-
 +
|I21-1||22,2 ng/ul
 +
|-
 +
|I21-2||24,6 ng/ul
 +
|-
 +
|I21-3||14,2 ng/ul
 +
|-
 +
|I21-4||12,4 ng/ul
 +
|-
 +
|I21-5||19,4 ng/ul
 +
|-
 +
|I21-6||17,0 ng/ul
 +
|-
 +
|I21-7||14,5 ng/ul
 +
|-
 +
|I21-8 ||23,1 ng/ul
 +
|-
 +
|I21-9 ||18,9 ng/ul
 +
|-
 +
|I21-10 ||16,4 ng/ul
 +
|-
 +
|I21-11 || 13,3 ng/ul
 +
|-
 +
|I21-12 ||15,5 ng/ul
 +
|-
 +
|I21-13 || 33,5 ng/ul
 +
|-
 +
|I21-14 || 22,2 ng/ul
 +
|-
 +
|I21-15 || 21,1 ng/ul
 +
|-
 +
|I21-16 ||23,8 ng/ul
 +
|-
 +
|I21-17 || 20,6 ng/ul
 +
|-
 +
|I22-1 || 117,0 ng/ul
 +
|-
 +
|I22-2 || 100,4 ng/ul
 +
|-
 +
|I22-3|| 281,3 ng/ul
 +
|-
 +
|I23-1 || 55,2 ng/ul
 +
|-
 +
|I23-2 || 47,1 ng/ul
 +
|-
 +
|I23-3 || 84,8 ng/ul
 +
|-
 +
|I15-1|| 80,7 ng/ul
 +
|-
 +
|Ent4C5|| 27,6 ng/ul
 +
|-
 +
|rbs34 || 50,4 ng/ul
 +
|-
 +
|linker (<partinfo>BBa_K105012</partinfo>) || 39,3 ng/ul
 +
|-
 +
|plux||45,1 ng/ul
 +
|}
 +
 +
Digestion of:
 +
 +
{| border="1" align='center'
 +
|  ''Culture''    ||  ''Kind''  ||  ''Final reaction volume (ul) '' ||  ''DNA (ul)''  ||  ''H20 (ul)''  ||  ''Enzyme 1''  ||  ''Enzyme 2'' ||  ''Buffer H''
 +
|-
 +
|    I20-1  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-2  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-3  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-4  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-5  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-6  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-7  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-8  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-9  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-10  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-11||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I20-12  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-1  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-2  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-3  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-4  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-5  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-6  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-7  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-8  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-9  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-10  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-11 ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-12  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-13  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-14  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-15  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-16  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I21-17  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I22-1  ||  Insert/Screening || 25 ||  17  ||  3,5  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I22-2  ||  Insert/Screening || 25 ||  20,5  ||  0  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I22-3  ||  Insert/Screening || 25 ||  7,1  || 13,4  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I23-1  ||  Insert/Screening || 25 ||  10  || 10,5  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I23-2  ||  Insert/Screening || 25 ||  10  ||  10,5 ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|    I23-3  ||  Insert/Screening || 25 ||  10  || 10,5  ||      1 XbaI  || 1 PstI  || 2,5
 +
|-
 +
|  I15-1  ||  insert || 25 || 20,5  ||  0  ||      1EcoRI  || 1 PstI  || 2,5
 +
|-
 +
|  Entero4C5  ||  Vector || 25 ||  20,5  ||  0  ||      1 EcoRI  || 1 PstI  || 2,5
 +
|-
 +
|  <partinfo>BBa_B0034</partinfo>  ||  Insert || 25 ||  20,5  ||  0  ||      1 SpeI  || 1 PstI  || 2,5
 +
|-
 +
| <partinfo>BBa_K105012</partinfo>  || Insert || 25 ||  20,5  ||  0  ||      1 SpeI  || 1 PstI  || 2,5
 +
|-
 +
|  <partinfo>BBa_R0062</partinfo> ||  Insert || 25 ||  20,5  ||  0  ||      1 SpeI  || 1 PstI  || 2,5
 +
|-
 +
| PhaP 10-S  ||  Insert || 30+10° ||  26  ||  0 +7 ||      1+1 XbaI  || 1+1 SpeI  || 3+1
 +
|-
 +
| PhaP S-S ||  Insert || 30 ||  26  ||  0  +7 ||      1+1 XbaI  || 1+1 SpeI  || 3+1
 +
|-
 +
|  pSB1A2 ||  Insert || 25 ||  14  ||  6,5  ||      1XbaI  || 1 SpeI  || 2,5
 +
|}
 +
 +
 +
°(after '+' added after 2 hours and incubated for further 2 hours)
==August, 11th==
==August, 11th==

Revision as of 15:02, 10 August 2010
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Week 1

Week 2

Week 3

Week 4


AUGUST: WEEK 2


August, 9th

Phasins plates showed very few colonies (12 for I20-new and 17 for I21-new): they were all picked and let grow in LB+Amp 100ug/ml. In the evening we made glycerol stocks and re-filled the tubes for the screening of the following day:

I20-new:I21-1I21-2I21-3I21-4I21-5I21-6I21-7I21-8I21-9I21-10I21-11I21-12
I21-new:I20-1I20-2I20-3I20-4I20-5I20-6I20-7I20-8I20-9I20-10I20-11I20-12I20-13I20-14I20-15I20-16I20-17

In order not to loose our time we decided to perform again the PCR-amplification/modification of <partinfo>BBa_K208001</partinfo> in case of a negative screening. Than we gel-ran and gel-extracted right amplicons. PCR was performed with:

  • 10_F and S_R primers
  • S_F and S_R primers
PCR results: PhaP 10-S and PhaP S-S

The image shows results of our PCR: both amplicons are positive, so we purified cut DNA, obtaining the following quantifications:

  • PhaP 10-S: 16,8 ng/ul
  • PhaP S-S: 17,1 ng/ul

Tomorrow we will proceed to digest this part, in order to have an alternative if all clones of I20 and I21 are negative.

In the afternoon, we inoculated all parts we will need tomorrow.

Part Medium Task
<partinfo>BBa_B0034</partinfo> 5ml LB+Amp Ligation
I15-1 5ml LB+Amp Ligation
Linker 5ml LB+Amp Ligation
pSB4C5 5ml LB+Cm 12,5 Ligation
I22-1 5ml LB+ Amp (picked from colony) Ligation/Screening/Glycerol stock
I22-2 5ml LB+ Amp (picked from colony) Ligation/Screening/Glycerol stock
I22-3 5ml LB+ Amp (picked from colony) Ligation/Screening/Glycerol stock
I23-1 5ml LB+ Amp (picked from colony) Screening/Glycerol stock
I23-2 5ml LB+ Amp (picked from colony) Screening/Glycerol stock
I23-3 5ml LB+ Amp (picked from colony) Screening/Glycerol stock
<partinfo>BBa_r0062</partinfo> 5ml LB+ Amp Ligation
I7_4C5-2 1ml LB+ Cm12,5 Tecan Test
I8_4C5-2 1ml LB+ Cm12,5 Tecan Test
I10_4C5-1 1ml LB+ Cm12,5 Tecan Test
I12_4C5-1 1ml LB+ Cm12,5 Tecan Test
A2(=<partinfo>BBa_J23100</partinfo>+GFP) 1ml LB+ Amp Tecan Test
<partinfo>BBa_B0032</partinfo> 1ml LB+ Amp Tecan Test
I8-5 D 1ml LB+ Amp (picked from colony) Tecan Test/Glycerol stock
I8-5 E 1ml LB+ Amp (picked from colony) Tecan Test/Glycerol stock
I8-5 F 1ml LB+ Amp (picked from colony) Tecan Test/Glycerol stock

Check of LB+Cm 6 ug/ml agar plates. We let grow at 30°C:

  • MG1655 in LB
  • MC1061 in LB
  • MG123/008 in LB+Amp 50 ug/ml
  • MC123/008 in LB+Amp 50 ug/ml
  • F2620-4C5 (positive control)

Than we streaked cultures on a seven-sector divided plate, and we let grow it ON at 30°C. Since 6 ug/ml is a very low concentration, we wanted to check if actually nothing (except F2620-4C5) grow on these plates.

Transformation at 30°C of 100 ul of MG13/008 and MC123/008 competent cells to check their efficiency. We used 1 ul (~4 ng) of RING, F2620-4C5, Nothing (water) and plated on proper LB agar plates:

  • RING: Cm 34 ug/ml
  • F2620-4C5 (positive control): Cm 12,5 ug/ml
  • Nothing (negative control): Cm 12,5 ug/ml

Both RING and F2620-4C5 should survive, but we had a problem so that MC008 transformed with RING couldn't be plated. We will check it another time. We let grow plates ON, 30°C.

August, 10th

August, 10th

Glycerol stock was prepared for:

  • linker
  • I22-1
  • I22-2
  • I22-3
  • I23-1
  • I23-2
  • I23-3
  • I8-5 D
  • I8-5 E
  • I8-5 F

and are stored at -80°C.


Cultures were diluted (5ul in 2ml LB+antibiotic) for TECAN test:

I8-5 D I8-5 E I8-5 F
I74C5 I84C5 I104C5
I124C5 Rbs32 A2

MiniPrep was performed for following cultures (using our new NucleoSpin kit, that we prepared yesterday! :) ):

Culture Quantification
I20-1 16,5 ng/ul
I20-2 8,9 ng/ul
I20-3 19,3 ng/ul
I20-412,5 ng/ul
I20-5 22,4 ng/ul
I20-6 12,3 ng/ul
I20-7 4,1 ng/ul
I20-815,7 ng/ul
I20-914,4 ng/ul
I20-10 17,5 ng/ul
I20-11 24,5 ng/ul
I20-1221,2 ng/ul
I21-122,2 ng/ul
I21-224,6 ng/ul
I21-314,2 ng/ul
I21-412,4 ng/ul
I21-519,4 ng/ul
I21-617,0 ng/ul
I21-714,5 ng/ul
I21-8 23,1 ng/ul
I21-9 18,9 ng/ul
I21-10 16,4 ng/ul
I21-11 13,3 ng/ul
I21-12 15,5 ng/ul
I21-13 33,5 ng/ul
I21-14 22,2 ng/ul
I21-15 21,1 ng/ul
I21-16 23,8 ng/ul
I21-17 20,6 ng/ul
I22-1 117,0 ng/ul
I22-2 100,4 ng/ul
I22-3 281,3 ng/ul
I23-1 55,2 ng/ul
I23-2 47,1 ng/ul
I23-3 84,8 ng/ul
I15-1 80,7 ng/ul
Ent4C5 27,6 ng/ul
rbs34 50,4 ng/ul
linker (<partinfo>BBa_K105012</partinfo>) 39,3 ng/ul
plux45,1 ng/ul

Digestion of:

Culture Kind Final reaction volume (ul) DNA (ul) H20 (ul) Enzyme 1 Enzyme 2 Buffer H
I20-1 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-2 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-3 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-4 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-5 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-6 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-7 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-8 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-9 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-10 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-11 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I20-12 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-1 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-2 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-3 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-4 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-5 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-6 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-7 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-8 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-9 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-10 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-11 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-12 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-13 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-14 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-15 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-16 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I21-17 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I22-1 Insert/Screening 25 17 3,5 1 XbaI 1 PstI 2,5
I22-2 Insert/Screening 25 20,5 0 1 XbaI 1 PstI 2,5
I22-3 Insert/Screening 25 7,1 13,4 1 XbaI 1 PstI 2,5
I23-1 Insert/Screening 25 10 10,5 1 XbaI 1 PstI 2,5
I23-2 Insert/Screening 25 10 10,5 1 XbaI 1 PstI 2,5
I23-3 Insert/Screening 25 10 10,5 1 XbaI 1 PstI 2,5
I15-1 insert 25 20,5 0 1EcoRI 1 PstI 2,5
Entero4C5 Vector 25 20,5 0 1 EcoRI 1 PstI 2,5
<partinfo>BBa_B0034</partinfo> Insert 25 20,5 0 1 SpeI 1 PstI 2,5
<partinfo>BBa_K105012</partinfo> Insert 25 20,5 0 1 SpeI 1 PstI 2,5
<partinfo>BBa_R0062</partinfo> Insert 25 20,5 0 1 SpeI 1 PstI 2,5
PhaP 10-S Insert 30+10° 26 0 +7 1+1 XbaI 1+1 SpeI 3+1
PhaP S-S Insert 30 26 0 +7 1+1 XbaI 1+1 SpeI 3+1
pSB1A2 Insert 25 14 6,5 1XbaI 1 SpeI 2,5


°(after '+' added after 2 hours and incubated for further 2 hours)

August, 11th

August, 12th

August, 13th

August, 14th

August, 15th



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