Team:UNIPV-Pavia/Calendar/July/settimana1

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<html><p align="center"><font size="4"><b>JULY: WEEK 1</b></font></p></html><hr><br>
 
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[[Team:UNIPV-Pavia/Calendar/July/settimana1|Week 1]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana2|Week 2]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana3|Week 3]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana4|Week 4]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana5|Week 5]]
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<html><p align="center"><font size="4"><b>JULY: WEEK 1</b></font></p></html><hr><br>
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==June, 28th==
==June, 28th==
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||MG1655 || ''E. coli'' wild type strain||LB, 37°C
||MG1655 || ''E. coli'' wild type strain||LB, 37°C
|}
|}
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<div align="right"><small>[[#indice|^top]]</small></div>
==June, 29th==
==June, 29th==
-
All cultures were grown. From I7-1, I7-2, I8-1, I8-2, I9-1, I9-2, I10-1 and I10-2 5ul were aliquoted and diluted in 500ul LB+Amp for a <font size =4>[[Team:UNIPV-Pavia/Material Methods/Measurements/Tecan/test1|preliminary TECAN test]]</font>.  
+
All cultures were grown. From I7-1, I7-2, I8-1, I8-2, I9-1, I9-2, I10-1 and I10-2 5ul were aliquoted and diluted in 500ul LB+Amp for a preliminary TECAN test.  
Cultures were MiniPrepped with the following quantifications (NanoDrop):
Cultures were MiniPrepped with the following quantifications (NanoDrop):
{| border='1' align='center'
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Digestion was performed at 37°C for 3 hours. Digestions were gel run. For I9 and I10 clones all colonie were correct, while for I7 and I8 extra bands could be observed. Since preliminar results of TECAN test didn't provide encouraging results, we decided to select other 3 colonies both for I7 and I8 and to repeat the screening, while I9 and I10 were correct at this screening, so we chose I9-1 and I10-1 as definitive I9 and I10 parts. I9 and I10 will be further screened next week.
+
Digestion was performed at 37°C for 3 hours. Digestions were gel run. For I9 and I10 clones all colonies were correct, while for I7 and I8 extra bands could be observed. Since preliminar results of TECAN test didn't provide encouraging results, we decided to select other 3 colonies both for I7 and I8 and to repeat the screening, while I9 and I10 were correct at this screening, so we chose I9-1 and I10-1 as definitive I9 and I10 parts. I9 and I10 will be further screened next week.
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PhaP-1 and PhaP-2 were prepared or sequencing: 13,8 ul (2x quantity) of PhaP-1 and 14,7ul (1x quantity) oh PhaP-2 were dryed at 65°C and setn to BMR genomics for sequencing service.
+
PhaP-1 and PhaP-2 were prepared or sequencing: 13,8 ul (2x quantity) of PhaP-1 and 14,7ul (1x quantity) of PhaP-2 were dryed at 65°C and sent to BMR genomics for sequencing service.
-
All strains received from Yale Univesity were on blotting paper disks, that were placed on an LB agar plates (with/without antiobiotic, see growth conditions), resuspended wih 80ul LB and then streaked. After plate streaking, disks were transferred in falcon tubes containing liquid LB.
+
All strains received from Yale Univesity were on blotting paper disks, that were placed on an LB agar plates (with/without antiobiotic, see growth conditions), resuspended with 80ul LB and then streaked. After plate streaking, disks were transferred in falcon tubes containing liquid LB.
* '''BT340''' was streaked on LB+Amp (50ng/ml) agar plates and from here on LB+Amp (100ng/ml) agar plates. The paper disk was then transferred in liquid LB+Amp (100ng/ml).  
* '''BT340''' was streaked on LB+Amp (50ng/ml) agar plates and from here on LB+Amp (100ng/ml) agar plates. The paper disk was then transferred in liquid LB+Amp (100ng/ml).  
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* '''BW25142''' was streaked on LB agar plates. The paper disk was then transferred in liquid LB.
* '''BW25142''' was streaked on LB agar plates. The paper disk was then transferred in liquid LB.
* '''BW25141''' was streaked on LB agar plates. The paper disk was then transferred in liquid LB.
* '''BW25141''' was streaked on LB agar plates. The paper disk was then transferred in liquid LB.
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<div align="right"><small>[[#indice|^top]]</small></div>
==June, 30th==
==June, 30th==
CGSC strains streaked the previous day:
CGSC strains streaked the previous day:
-
*1
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*BT340/pCP20 grew on both LB+Amp at 50ug/ml and 100 ug/ml
 +
 
 +
*BW5328/pAH123 did not grow in LB+Amp at 50ug/ml, LB+Amp at 100 ug/ml (also the liquid culture containing the disk appeared clear)
 +
 
 +
*MG1655, MC1061, BW25142 and BW25141 grew on LB plates.
 +
 
 +
We requested another disk for BW5328/pAH123 to CGSC, while the working strains plates were stored at +4°C.
-
*2
 
Inoculum of cultures for a TECAN test. From glycerol stocks: I7-1, I7-2, I8-1, I8-2 (all tese 4 colonies were not correct! we want to see if any fluorescence is observed in order to understamd if there is any unexpected GFP production), I9-1, I9-2, I10-1, I10-2. For these cultures 8ul of glycerol stock were inoculated in 2 ml Lb+Amp.
Inoculum of cultures for a TECAN test. From glycerol stocks: I7-1, I7-2, I8-1, I8-2 (all tese 4 colonies were not correct! we want to see if any fluorescence is observed in order to understamd if there is any unexpected GFP production), I9-1, I9-2, I10-1, I10-2. For these cultures 8ul of glycerol stock were inoculated in 2 ml Lb+Amp.
-
Other three colonies were peaked from I7 and I8 plates.  
+
Other three colonies were picked from I7 and I8 plates.  
{| border='1' align='center'
{| border='1' align='center'
|| I7-3 || 5 ml LB+ Amp, grown ON 37°C 220 rpm
|| I7-3 || 5 ml LB+ Amp, grown ON 37°C 220 rpm
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All cultures were incubated ON, 37°C 220 rpm.
All cultures were incubated ON, 37°C 220 rpm.
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<div align="right"><small>[[#indice|^top]]</small></div>
==July, 1st==
==July, 1st==
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<font size='4'>[[Team:UNIPV-Pavia/Material Methods/Measurements/Tecan/test2|First TECAN test]]
 
-
</font>
 
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-
 
All cultures incubated yesterday night were diluted 1:100 (10ul in 1ml fresh LB+Amp) and let grown for further 3 hours at 37°C 220 rpm. Also I7-3,4 and 5 and I8-3, 4 and 5 were prepared for TECAN test (10ul were diluted in 1ml LB+Amp). After dilution, static OD was measured for these cultures and a proper dilution was perfeormed, in order to start from the desired OD of 0.02, according to the formula:
All cultures incubated yesterday night were diluted 1:100 (10ul in 1ml fresh LB+Amp) and let grown for further 3 hours at 37°C 220 rpm. Also I7-3,4 and 5 and I8-3, 4 and 5 were prepared for TECAN test (10ul were diluted in 1ml LB+Amp). After dilution, static OD was measured for these cultures and a proper dilution was perfeormed, in order to start from the desired OD of 0.02, according to the formula:
-
[[Image:Unipv_formula_diluizione_OD.jpg|300px|thumb|center]]
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<img src="https://static.igem.org/mediawiki/2010/3/35/Unipv_formula_diluizione_OD.jpg" alt="Dilution formula" title="Dilution formula"/>
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After dilution, 3 aliquotes each of 200ul were transferred in a 96-wells plate and incubated in TECAN multi-well plate reader. Cultures were incubated at 37°C and a kinetic cycle was performed:
After dilution, 3 aliquotes each of 200ul were transferred in a 96-wells plate and incubated in TECAN multi-well plate reader. Cultures were incubated at 37°C and a kinetic cycle was performed:
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|-
|-
|| BW23141 BUP || 1ml LB
|| BW23141 BUP || 1ml LB
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|-
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|| BT340/pCP20 || 1ml LB+Amp100+Cm12.5
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|-
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|| BT340/pCP20 BUP || 1ml LB+Amp100+Cm12.5
|}
|}
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As reported in the table above, BT340/pCP20 was inoculated in LB+Amp(100 ug/ml)+Cm(12.5 ug/ml) to validate the second selection marker of pCP20 and it grew as expected.
Other parts were received from Anderson Lab. in stab form.
Other parts were received from Anderson Lab. in stab form.
 +
{| border='1' align='center'
{| border='1' align='center'
||'''Part''' || '''Description''' || '''Growt condition'''
||'''Part''' || '''Description''' || '''Growt condition'''
|-
|-
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||<partinfo>BBa_J72007</partinfo>|| BamHI methyltransferase encoding CRIM plasmid || Streaked on LB+Amp (50ng/ml) agar plate
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||<partinfo>BBa_J72007</partinfo>|| BamHI methyltransferase encoding CRIM plasmid || Streaked on LB+Amp(100ng/ml)+Cm(12,5 ng/ml) agar plate
|-  
|-  
-
||<partinfo>BBa_J72008</partinfo> || phi80 integration helper plasmid pInt80-649 || Streaked on LB+Amp(100ng/ml)+Cm(12,5 ng/ml) agar plate and on LB+Cm (34 ng/ml) agar plate
+
||<partinfo>BBa_J72008</partinfo> || phi80 integration helper plasmid pInt80-649 || Streaked on LB+Amp (50ng/ml) agar plate and on LB+Cm (34 ng/ml) agar plate
|-
|-
-
||<partinfo>BBa_J72013</partinfo> || BglII methyltransferase encoding CRIM plasmid  || Streaked on LB+Cm (34ng/ml) agar plate
+
||<partinfo>BBa_J72013</partinfo> || BglII methyltransferase encoding CRIM plasmid  || Streaked on LB+Amp (50ng/ml) agar plate and LB+Cm (34ng/ml) agar plate
|}
|}
-
Plates were incubated at 37°C ON.
+
Plates were incubated at 37°C ON (except BBa_J72008 that was grown at 30°C).
 +
 
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<div align="right"><small>[[#indice|^top]]</small></div>
==July, 2nd==
==July, 2nd==
TECAN test provided encouraging results, showing that I7-3, I7-5, I8-4 and I8-5 produced GFP. Also I9-1, I9-2, I10-1 and I10-2 confirmed the preliminar results of the precious test, in fact GFP production was observe. At a preliminary analysis, it seems that GFP production is correlated to the srength of the promoter regulating luxI production!! :)
TECAN test provided encouraging results, showing that I7-3, I7-5, I8-4 and I8-5 produced GFP. Also I9-1, I9-2, I10-1 and I10-2 confirmed the preliminar results of the precious test, in fact GFP production was observe. At a preliminary analysis, it seems that GFP production is correlated to the srength of the promoter regulating luxI production!! :)
-
Other culture (I7-1, I7-2, I7-4, I8-1, I8-2, I8-3) did not produce GFP, se they were thrown away.
+
Other culture (I7-1, I7-2, I7-4, I8-1, I8-2, I8-3) did not produce GFP, so they were thrown away.
A furhter screening were performed on I7-3, I7-5, I8-4, I8-5, I9-1 and I10-1.
A furhter screening were performed on I7-3, I7-5, I8-4, I8-5, I9-1 and I10-1.
-
For this reason, MiniPro was performed for the following colonies, with the following quantiications:
+
For this reason, MiniPrep was performed for the following colonies, with the following quantiications:
{| border='1' align='center'
{| border='1' align='center'
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Inoculum of <partinfo>BBa_J72007</partinfo> and <partinfo>BBa_J72013</partinfo> from LB agar plates: one colony from each plte in 1ml LB+Cm (34) at 37°C 220 rpm for 7 hours. Glycero, stock was prepared for each culture.  
+
Inoculum of <partinfo>BBa_J72007</partinfo> and <partinfo>BBa_J72013</partinfo> from LB agar plates: one colony from each plate in 1ml LB+Cm (34) at 37°C 220 rpm for 7 hours. A glycerol stock was prepared for each culture.  
Inoculum of <partinfo>BBa_J72008</partinfo> from LB agar plate (one colony in 3ml LB+Amp 50), grown at 30°C 220 rpm overnight.
Inoculum of <partinfo>BBa_J72008</partinfo> from LB agar plate (one colony in 3ml LB+Amp 50), grown at 30°C 220 rpm overnight.
 +
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<div align="right"><small>[[#indice|^top]]</small></div>
==July, 3rd==
==July, 3rd==
Glycerol stock for <partinfo>BBa_J72008</partinfo> was prepared.
Glycerol stock for <partinfo>BBa_J72008</partinfo> was prepared.
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[[Team:UNIPV-Pavia/Calendar|Calendar]]
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<td align="left">[[Team:UNIPV-Pavia/Calendar/June/settimana4| Previous week]]</td>
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<td align="right">[[Team:UNIPV-Pavia/Calendar/July/settimana2| Next week]]</td>
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[[Team:UNIPV-Pavia/Calendar/June|June]]
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[[Team:UNIPV-Pavia/Calendar/July|July]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana1|week 1]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana2|week 2]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana3|week 3]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana4|week 4]]
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[[Team:UNIPV-Pavia/Calendar/July/settimana4|week 5]]
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{{UNIPV-Pavia/menu_mesi}}
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Latest revision as of 16:52, 24 October 2010


JULY: WEEK 1



June, 28th

Inoculum from glycerol stock for I7-1, I7-2, I8-1, I8-2, I9-1, I9-2, I10-1 and I10-2 in 5ml LB+Amp. Cultures were grown ON at 37°C 220rpm.

Inoculum of PhaP-1 and PhaP-2 in 5ml LB+Kan and ON growth at 37°C 220rpm.

We received strains and plasmid from CGSC (Yale University)

Culture name description growth conditions that will be used
BT340 pCP20 plasmid LB+Amp LC 30°C,LB+Amp HC 30°C
BW23473 E. coli pir+ strainLB, 37°C
BW23474 E. coli pir116 strainLB, 37°C
BW25141 E. coli pir+ strainLB, 37°C
BW25142 E. coli pir116 strainLB, 37°C
BW5328 /pAH123 helper plasmid LB+Amp LC 30°C,LB+Amp HC 30°C
MC1061 E. coli strain for integrationLB, 37°C
MG1655 E. coli wild type strainLB, 37°C

June, 29th

All cultures were grown. From I7-1, I7-2, I8-1, I8-2, I9-1, I9-2, I10-1 and I10-2 5ul were aliquoted and diluted in 500ul LB+Amp for a preliminary TECAN test. Cultures were MiniPrepped with the following quantifications (NanoDrop):

Culture name quantification
I7-1 83,3 ng/ul
I7-2 104 ng/ul
I8-1 123,8 ng/ul
I8-2 103,7 ng/ul
I9-1 117,8 ng/ul
I9-2 110,4 ng/ul
I10-1 98,8 ng/ul
I10-2 93,6 ng/ul
PhaP-1 29,1 ng/ul
PhaP-2 13,6 ng/ul

All cultures, except PhaP-1 and PhaP-2 were digested. Digestion of:

Culture Kind Final reaction volume (ul) DNA (ul) H20 (ul) Enzyme 1 Enzyme 2 Buffer H
I7-1 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5
I7-2 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5
I8-1 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5
I8-2 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5
I9-1 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5
I9-2 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5
I10-1 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5
I10-2 Screening 25 2 19,5 0,5 EcoRI 0,5 PstI 2,5

Digestion was performed at 37°C for 3 hours. Digestions were gel run. For I9 and I10 clones all colonies were correct, while for I7 and I8 extra bands could be observed. Since preliminar results of TECAN test didn't provide encouraging results, we decided to select other 3 colonies both for I7 and I8 and to repeat the screening, while I9 and I10 were correct at this screening, so we chose I9-1 and I10-1 as definitive I9 and I10 parts. I9 and I10 will be further screened next week.



TECAN TEST



Screening of I7, I8, I9, I10


PhaP-1 and PhaP-2 were prepared or sequencing: 13,8 ul (2x quantity) of PhaP-1 and 14,7ul (1x quantity) of PhaP-2 were dryed at 65°C and sent to BMR genomics for sequencing service.


All strains received from Yale Univesity were on blotting paper disks, that were placed on an LB agar plates (with/without antiobiotic, see growth conditions), resuspended with 80ul LB and then streaked. After plate streaking, disks were transferred in falcon tubes containing liquid LB.

  • BT340 was streaked on LB+Amp (50ng/ml) agar plates and from here on LB+Amp (100ng/ml) agar plates. The paper disk was then transferred in liquid LB+Amp (100ng/ml).
  • BW5328 was streaked on LB+Amp (50ng/ml) agar plates and from here on LB+Amp (100ng/ml) agar plates. The paper disk was then transferred in liquid LB+Amp (100ng/ml).
  • MG1655 was streaked on LB agar plates. The paper disk was then transferred in liquid LB.
  • MC1061 was streaked on LB agar plates. The paper disk was then transferred in liquid LB.
  • BW25142 was streaked on LB agar plates. The paper disk was then transferred in liquid LB.
  • BW25141 was streaked on LB agar plates. The paper disk was then transferred in liquid LB.

June, 30th

CGSC strains streaked the previous day:

  • BT340/pCP20 grew on both LB+Amp at 50ug/ml and 100 ug/ml
  • BW5328/pAH123 did not grow in LB+Amp at 50ug/ml, LB+Amp at 100 ug/ml (also the liquid culture containing the disk appeared clear)
  • MG1655, MC1061, BW25142 and BW25141 grew on LB plates.

We requested another disk for BW5328/pAH123 to CGSC, while the working strains plates were stored at +4°C.


Inoculum of cultures for a TECAN test. From glycerol stocks: I7-1, I7-2, I8-1, I8-2 (all tese 4 colonies were not correct! we want to see if any fluorescence is observed in order to understamd if there is any unexpected GFP production), I9-1, I9-2, I10-1, I10-2. For these cultures 8ul of glycerol stock were inoculated in 2 ml Lb+Amp. Other three colonies were picked from I7 and I8 plates.

I7-3 5 ml LB+ Amp, grown ON 37°C 220 rpm
I7-4 5 ml LB+ Amp, grown ON 37°C 220 rpm
I7-5 5 ml LB+ Amp, grown ON 37°C 220 rpm
I8-3 5 ml LB+ Amp, grown ON 37°C 220 rpm
I8-4 5 ml LB+ Amp, grown ON 37°C 220 rpm
I8-5 5 ml LB+ Amp, grown ON 37°C 220 rpm

All cultures were incubated ON, 37°C 220 rpm.

July, 1st

All cultures incubated yesterday night were diluted 1:100 (10ul in 1ml fresh LB+Amp) and let grown for further 3 hours at 37°C 220 rpm. Also I7-3,4 and 5 and I8-3, 4 and 5 were prepared for TECAN test (10ul were diluted in 1ml LB+Amp). After dilution, static OD was measured for these cultures and a proper dilution was perfeormed, in order to start from the desired OD of 0.02, according to the formula:


Dilution formula

After dilution, 3 aliquotes each of 200ul were transferred in a 96-wells plate and incubated in TECAN multi-well plate reader. Cultures were incubated at 37°C and a kinetic cycle was performed:

  • Duration: 20h
  • Kinetic cycle: 5 minutes
  • Every 5 minutes:
    • 15 s shaking (3mm, linear)
    • 10 s wait
    • OD600 measurement
    • GFP measurement

I7-3, I7-4, I7-5, I8-3, I8-4 and I8-5 cultures were prepared in 5ml LB+Amp, so the remaining cultures not used for TECAN test were pelletted at 4000 rpm for 10 minutes, supernatant was discarded and pelletes were stored at 4°C for tomorrow MiniPrep of cultures that provided promising results at TECAN test.

Of the plates incubated yesterday, a colony was picked and grown in 1ml LB (+ antibiotic) for 6 hours at 37°C 220 rpm:

Culture name Growth condition
MG1655 1ml LB
MG1655 BUP (backup) 1ml LB
MC1061 1ml LB
MC1061 BUP 1ml LB
BW23142 1ml LB
BW23142 BUP 1ml LB
BW23141 1ml LB
BW23141 BUP 1ml LB
BT340/pCP20 1ml LB+Amp100+Cm12.5
BT340/pCP20 BUP 1ml LB+Amp100+Cm12.5

As reported in the table above, BT340/pCP20 was inoculated in LB+Amp(100 ug/ml)+Cm(12.5 ug/ml) to validate the second selection marker of pCP20 and it grew as expected.

Other parts were received from Anderson Lab. in stab form.


Part Description Growt condition
<partinfo>BBa_J72007</partinfo> BamHI methyltransferase encoding CRIM plasmid Streaked on LB+Amp(100ng/ml)+Cm(12,5 ng/ml) agar plate
<partinfo>BBa_J72008</partinfo> phi80 integration helper plasmid pInt80-649 Streaked on LB+Amp (50ng/ml) agar plate and on LB+Cm (34 ng/ml) agar plate
<partinfo>BBa_J72013</partinfo> BglII methyltransferase encoding CRIM plasmid Streaked on LB+Amp (50ng/ml) agar plate and LB+Cm (34ng/ml) agar plate

Plates were incubated at 37°C ON (except BBa_J72008 that was grown at 30°C).

July, 2nd

TECAN test provided encouraging results, showing that I7-3, I7-5, I8-4 and I8-5 produced GFP. Also I9-1, I9-2, I10-1 and I10-2 confirmed the preliminar results of the precious test, in fact GFP production was observe. At a preliminary analysis, it seems that GFP production is correlated to the srength of the promoter regulating luxI production!! :) Other culture (I7-1, I7-2, I7-4, I8-1, I8-2, I8-3) did not produce GFP, so they were thrown away. A furhter screening were performed on I7-3, I7-5, I8-4, I8-5, I9-1 and I10-1.

For this reason, MiniPrep was performed for the following colonies, with the following quantiications:

I7-3 107,7 ng/ul
I7-5 55,4 ng/ul
I8-4 94,5 ng/ul
I8-5 118,3 ng/ul

I7-3, I7-5, I8-4 and I8-5 were digested with EcorI and PstI. All colonies were digested with NheI-PstI (2 NheI sites are present in the BBa_J23xx promoter, so this digestion shows if the promoter has been ligated.)


Digestion of:

Culture Kind Final reaction volume (ul) DNA (ul) H20 (ul) Enzyme 1 Enzyme 2 Buffer H
I7-3 Screening 25 2 18,5 1 EcoRI 1 PstI 2,5
I7-5 Screening 25 2 18,5 1 EcoRI 1 PstI 2,5
I8-4 Screening 25 2 18,5 1 EcoRI 1 PstI 2,5
I8-5 Screening 25 2 18,5 1 EcoRI 1 PstI 2,5
I7-3 Screening 25 2 18,5 1 NheI 1 PstI 2,5
I7-5 Screening 25 2 18,5 1 NheI 1 PstI 2,5
I8-4 Screening 25 2 18,5 1 NheI 1 PstI 2,5
I8-5 Screening 25 2 18,5 1 NheI 1 PstI 2,5
I9-1 Screening 25 2 18,5 1 NheI 1 PstI 2,5
I10-1 Screening 25 2 18,5 1 NheI 1 PstI 2,5

Digestions were incubated at 37°C for 3 hours and gel run.

Screening of new colonies of I7 and I8. New screening for I9, I10

This time all the clones are OK :)

We choose the following colonies:

Colony chosen ligation name
I7-3 I7
I8-5 I8
I9-1 I9
I10-1 I10


Inoculum of <partinfo>BBa_J72007</partinfo> and <partinfo>BBa_J72013</partinfo> from LB agar plates: one colony from each plate in 1ml LB+Cm (34) at 37°C 220 rpm for 7 hours. A glycerol stock was prepared for each culture.

Inoculum of <partinfo>BBa_J72008</partinfo> from LB agar plate (one colony in 3ml LB+Amp 50), grown at 30°C 220 rpm overnight.

July, 3rd

Glycerol stock for <partinfo>BBa_J72008</partinfo> was prepared.