Team:UNIPV-Pavia/Calendar/August/settimana1

From 2010.igem.org

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m (August, 4th)
m (August, 5th)
 
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<table class="menu" border="0" width="100%">
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<td align="center">
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[[Team:UNIPV-Pavia/Calendar/August/settimana1|Week 1]]
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</td>
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<td align="center" style="padding:0; height:20px">
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[[Team:UNIPV-Pavia/Calendar/August/settimana2|Week 2]]
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</td>
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<td align="center">
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[[Team:UNIPV-Pavia/Calendar/August/settimana3|Week 3]]
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</td>
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<td align="center">
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[[Team:UNIPV-Pavia/Calendar/August/settimana4|Week 4]]
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</td>
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</tr>
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</table>
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<br>
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<html><p align="center"><font size="4"><b>AUGUST: WEEK 1</b></font></p></html><hr><br>
<html><p align="center"><font size="4"><b>AUGUST: WEEK 1</b></font></p></html><hr><br>
 +
<html><a name="indice"/></html>
==August, 2nd==
==August, 2nd==
Miniprep and quantification with Nanodrop of:
Miniprep and quantification with Nanodrop of:
Line 32: Line 51:
{|border="1" align="center"
{|border="1" align="center"
|-
|-
-
|'''Part''' || '''Strain'''
+
|'''Part''' || '''Strain''' || '''Culture name'''
|-
|-
-
|rowspan="2"| pAH123 || MC1061
+
|rowspan="2"| pAH123 || MC1061 || MC123
|-
|-
-
|MG1655
+
|MG1655 || MG123
|-
|-
-
|rowspan="2"| <partinfo>BBa_J72009</partinfo> || MC1061
+
|rowspan="2"| <partinfo>BBa_J72008</partinfo> || MC1061 || MC008
|-
|-
-
|MG1655
+
|MG1655 || MG008
|-
|-
-
|<partinfo>BBa_R0062</partinfo> ||rowspan="2"| DH5-alpha
+
|<partinfo>BBa_R0062</partinfo> ||rowspan="2"| DH5-alpha || rowspan="2"|
|-
|-
|<partinfo>BBa_K081009</partinfo>
|<partinfo>BBa_K081009</partinfo>
Line 55: Line 74:
|pAH123 ||rowspan="2"|  Amp 50 ug/ml ||rowspan="2"| 30°C
|pAH123 ||rowspan="2"|  Amp 50 ug/ml ||rowspan="2"| 30°C
|-
|-
-
|<partinfo>BBa_J72009</partinfo>
+
|<partinfo>BBa_J72008</partinfo>
|-
|-
|<partinfo>BBa_R0062</partinfo> || rowspan="2"| Amp 100 ug/ml ||rowspan="2"| 37°C
|<partinfo>BBa_R0062</partinfo> || rowspan="2"| Amp 100 ug/ml ||rowspan="2"| 37°C
Line 89: Line 108:
*Blank (Nothing)
*Blank (Nothing)
-
Gel run of amplified DNA showed for every sample the expected distance between primers of a strain with nothing integrated in attPhi80 site (~XXX bp), but unfortunately we forgot to take a picture of the gel ;(
+
Gel run of amplified DNA showed for every sample the expected distance between primers of a strain with nothing integrated in attPhi80 site (~570 bp), but unfortunately we forgot to take a picture of the gel ;(
 +
 
 +
 
 +
<div align="right"><small>[[#indice|^top]]</small></div>
==August, 4th==
==August, 4th==
-
Glycerol stocks for MC1061 and MG1561 strains transformed with pAH123 or <partinfo>BBa_J72008</partinfo> helper plasmids.
+
Glycerol stocks for MC1061 and MG1655 strains transformed with pAH123 or <partinfo>BBa_J72008</partinfo> helper plasmids.
2 ul of MC1061 bacteria were transferred into 5 ml LB+Amp 50 ug/ml and grown and shaken at 30°C over-day and over-night for re-competentization of the following day.
2 ul of MC1061 bacteria were transferred into 5 ml LB+Amp 50 ug/ml and grown and shaken at 30°C over-day and over-night for re-competentization of the following day.
-
200 ul of cultures was transferred into 100 ml LB+Amp 50 ug/ml and grown and shaken at 30°C for re-competentization.
+
200 ul of MG1655 cultures were transferred into 100 ml LB+Amp 50 ug/ml and grown and shaken at 30°C for re-competentization of today.
-
Cultures left were miniprepped to check again the presence of helper plasmids.
+
All cultures were miniprepped to check again the presence of helper plasmids.
 +
 
 +
Samples were digested with SpeI (it cuts twice) for 3 hours and gel run:
 +
*pAH123 digested: 3580 and 2755 bp
 +
*<partinfo>BBa_J72008</partinfo> digested: 2755 and 2437 bp
 +
 
 +
[[Image:UNIPV10_MG1655_MC1061_helper_screening.jpg|thumb|200px|center|pAH123 and <partinfo>BBa_J72008</partinfo> screening transformed into MG1655 and MC1061]]
 +
 
 +
Samples are positive (right lengths) but unfortunately we got a bad gel run (smearings) so this time we decided to pick two single colonies from each of the plates made on August, 3rd and to inoculate them into 5 ml LB+Amp 50 ug/ml. A total of eight falcon tubes was incubated ON at 30°C, 220 rpm.
 +
 
 +
We planned to screen them (to check the presence of helper plasmids again) and to re-competentize only the positive ones.
 +
 
 +
----
 +
 
 +
[[Image:UNIPV10_plux.jpg|thumb|200px|center|Autoinducibles]]
 +
 
 +
<div align="right"><small>[[#indice|^top]]</small></div>
==August, 5th==
==August, 5th==
 +
Glycerol stock and miniprep of MG1655 and MC1061 cultures incubated for 19 hours at 30°C, 220 rpm.
 +
Miniprep was quantified as follows:
 +
*MG123-1: 27 ng/ul
 +
*MG123-2: 40,2 ng/ul
 +
*MG008-1: 20,5 ng/ul
 +
*MG008-2: 26,5 ng/ul
 +
*MC123-1: 21,4 ng/ul
 +
*MC123-2: 17,4 ng/ul
 +
*MC008-1: 33,3 ng/ul
 +
*MC008-2: 38,1 ng/ul
 +
 +
DIgestion for 1 hour with SpeI.
 +
 +
Gel run on medium agarose gel.
 +
 +
[[Image:UNIPV10_transformed_helper_screening.jpg|thumb|200px|center|pAH123 and <partinfo>BBa_J72008</partinfo> screening (miniprepped from MG1655 and MC1061)]]
 +
 +
This time gel run succeeded, we chose samples
 +
*MG123-1
 +
*MG008-1
 +
*MC123-1
 +
*MC008-1
 +
to be re-competentizied. So they were inoculated into 5 ml LB+Amp 50 ug/ml and grown and shaken ON at 30°C.
 +
----
 +
Sequencing for I20 and I21 arrived from BMR, but all samples were wrong; sites X and S of the vector paired and nothing could ligate. So we started a new ligation cycle dephosphorylating the previously gel-extracted vector <partinfo>pSB1A3</partinfo>.
 +
New ligations:
 +
*I20-new: Pha-10S-1 (X-S) + <partinfo>pSB1A3</partinfo> (X-S, dephosphorylated)
 +
*I21-new: Pha-SS-1 (X-S) + <partinfo>pSB1A3</partinfo> (X-S, dephosphorylated)
 +
and their negative control:
 +
*C-: <partinfo>pSB1A3</partinfo> (X-S, dephosphorylated)
 +
 +
 +
<div align="right"><small>[[#indice|^top]]</small></div>
==August, 6th==
==August, 6th==
 +
Resuspension of linker <partinfo>BBa_K105012</partinfo> from iGEM 2010 Distribution Kit.
 +
 +
Transformation of ligations and resuspended DNA
 +
*I20-new
 +
*I21-new
 +
*C-
 +
*<partinfo>BBa_K105012</partinfo>
 +
into 100ul ''E. coli DH5-alpha''.
 +
 +
They were plated on LB+Amp 100ug/ml agar plates
 +
 +
----
 +
Competentization of colonies selected the previous day:
 +
*MG123 (without '-1' from now on)
 +
*MG008
 +
*MC123
 +
*MC008
 +
 +
<div align="right"><small>[[#indice|^top]]</small></div>
==August, 7th==
==August, 7th==
 +
Plates of transformed cells were stored at +4°C.
 +
 +
<div align="right"><small>[[#indice|^top]]</small></div>
 +
 +
-
==August, 8th==
+
<!-- table previous next week -->
 +
<br><br>
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<table border="0" width="100%" class="menu">
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<tr>
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<td align="left">[[Team:UNIPV-Pavia/Calendar/July/settimana5| Previous week]]</td>
 +
<td align="right">[[Team:UNIPV-Pavia/Calendar/August/settimana2| Next week]]</td>
 +
</tr>
 +
</table>
 +
<!-- fine table previous next week -->
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</td>
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<td width="15%" align="right" valign="top">
-
<td width="20%" valign="top">
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{{UNIPV-Pavia/menu_mesi}}
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<table border="0" width="100%" height="100%">
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</td>
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<tr align="right"><td height="15">
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</tr>
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[[Team:UNIPV-Pavia/Calendar|Calendar]]
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</td></tr>
+
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<tr align="right"><td height="15">
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[[Team:UNIPV-Pavia/Calendar/August|August]]
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</td></tr>
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<tr align="right"><td height="15">
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[[Team:UNIPV-Pavia/Calendar/August/settimana1|week 1]]
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</td></tr>
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<tr align="right"><td height="15">
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[[Team:UNIPV-Pavia/Calendar/August/settimana2|week 2]]
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</td></tr>
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<tr align="right"><td height="15">
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[[Team:UNIPV-Pavia/Calendar/August/settimana3|week 3]]
+
-
</td></tr>
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<tr align="right"><td height="15">
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[[Team:UNIPV-Pavia/Calendar/August/settimana4|week 4]]
+
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</td></tr>
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<tr align="right"><td height="15">
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[[Team:UNIPV-Pavia/Calendar/August/settimana5|week 5]]
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</td></tr>
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</table>
</table>

Latest revision as of 16:58, 24 October 2010


AUGUST: WEEK 1



August, 2nd

Miniprep and quantification with Nanodrop of:

  • I20-1: 98,2 ng/ul
  • I20-2: 63,6 ng/ul
  • I20-3: 41,5 ng/ul
  • I21-1: 45 ng/ul
  • I21-2: 45 ng/ul
  • I21-3: 54 ng/ul

These samples were prepared and sent (400ng) to BMR Genomics for sequencing.


The following parts were resuspended from iGEM 2010 Distribution Kit:

  • <partinfo>BBa_R0062</partinfo> (Plate 1, Well 6O)
  • <partinfo>BBa_K081009</partinfo> (Plate 2, Well 10N)

both in vector <partinfo>pSB1A2</partinfo>.

Transformation (1ul) of the following parts (resuspended/already miniprepped):

Part Strain Culture name
pAH123 MC1061 MC123
MG1655 MG123
<partinfo>BBa_J72008</partinfo> MC1061 MC008
MG1655 MG008
<partinfo>BBa_R0062</partinfo> DH5-alpha
<partinfo>BBa_K081009</partinfo>

Transformed cells were plated on proper LB+Amp agar plates and grown ON at right temperature:

Part Plate resistance Temperature
pAH123 Amp 50 ug/ml 30°C
<partinfo>BBa_J72008</partinfo>
<partinfo>BBa_R0062</partinfo> Amp 100 ug/ml 37°C
<partinfo>BBa_K081009</partinfo>

August, 3rd

Check for plates grown ON: all plates showed colonies.

<partinfo>BBa_R0062</partinfo> plate
<partinfo>BBa_K081009</partinfo> plate

A single colony was picked from <partinfo>BBa_R0062</partinfo> and <partinfo>BBa_K081009</partinfo> plates and inoculated in 1 ml LB+Amp 100 ug/ml and incubated 37°C, 220 rmp for glycerol stock. Cultures left were refilled to 5 ml of proper medium and incubated ON at 37°C, 220 rpm for further screening.

Since plates left showed small colonies they were let grow until late afternoon; than some colonies were picked from each plate and inoculated into a 5 ml LB+Amp 50 ug/ml falcon. Falcon tubes were incubated and shaken ON at 30°C.

MC1061 transformed with pAH123
MC1061 transformed with <partinfo>BBa_J72008</partinfo>
MG1655 transformed with pAH123
MG1655 transformed with <partinfo>BBa_J72008</partinfo>

PCR from the following colonies (this is a test for the efficiency of our primers synthesized to check attPhi80 E. coli genomic integration and it will be our negative control for future screenings):

  • MC1061-1
  • MC1061-2
  • MG1655-1
  • MG1655-2
  • Blank (Nothing)

Gel run of amplified DNA showed for every sample the expected distance between primers of a strain with nothing integrated in attPhi80 site (~570 bp), but unfortunately we forgot to take a picture of the gel ;(


August, 4th

Glycerol stocks for MC1061 and MG1655 strains transformed with pAH123 or <partinfo>BBa_J72008</partinfo> helper plasmids.

2 ul of MC1061 bacteria were transferred into 5 ml LB+Amp 50 ug/ml and grown and shaken at 30°C over-day and over-night for re-competentization of the following day.

200 ul of MG1655 cultures were transferred into 100 ml LB+Amp 50 ug/ml and grown and shaken at 30°C for re-competentization of today.

All cultures were miniprepped to check again the presence of helper plasmids.

Samples were digested with SpeI (it cuts twice) for 3 hours and gel run:

  • pAH123 digested: 3580 and 2755 bp
  • <partinfo>BBa_J72008</partinfo> digested: 2755 and 2437 bp
pAH123 and <partinfo>BBa_J72008</partinfo> screening transformed into MG1655 and MC1061

Samples are positive (right lengths) but unfortunately we got a bad gel run (smearings) so this time we decided to pick two single colonies from each of the plates made on August, 3rd and to inoculate them into 5 ml LB+Amp 50 ug/ml. A total of eight falcon tubes was incubated ON at 30°C, 220 rpm.

We planned to screen them (to check the presence of helper plasmids again) and to re-competentize only the positive ones.


Autoinducibles

August, 5th

Glycerol stock and miniprep of MG1655 and MC1061 cultures incubated for 19 hours at 30°C, 220 rpm. Miniprep was quantified as follows:

  • MG123-1: 27 ng/ul
  • MG123-2: 40,2 ng/ul
  • MG008-1: 20,5 ng/ul
  • MG008-2: 26,5 ng/ul
  • MC123-1: 21,4 ng/ul
  • MC123-2: 17,4 ng/ul
  • MC008-1: 33,3 ng/ul
  • MC008-2: 38,1 ng/ul

DIgestion for 1 hour with SpeI.

Gel run on medium agarose gel.

pAH123 and <partinfo>BBa_J72008</partinfo> screening (miniprepped from MG1655 and MC1061)

This time gel run succeeded, we chose samples

  • MG123-1
  • MG008-1
  • MC123-1
  • MC008-1

to be re-competentizied. So they were inoculated into 5 ml LB+Amp 50 ug/ml and grown and shaken ON at 30°C.


Sequencing for I20 and I21 arrived from BMR, but all samples were wrong; sites X and S of the vector paired and nothing could ligate. So we started a new ligation cycle dephosphorylating the previously gel-extracted vector <partinfo>pSB1A3</partinfo>. New ligations:

  • I20-new: Pha-10S-1 (X-S) + <partinfo>pSB1A3</partinfo> (X-S, dephosphorylated)
  • I21-new: Pha-SS-1 (X-S) + <partinfo>pSB1A3</partinfo> (X-S, dephosphorylated)

and their negative control:

  • C-: <partinfo>pSB1A3</partinfo> (X-S, dephosphorylated)


August, 6th

Resuspension of linker <partinfo>BBa_K105012</partinfo> from iGEM 2010 Distribution Kit.

Transformation of ligations and resuspended DNA

  • I20-new
  • I21-new
  • C-
  • <partinfo>BBa_K105012</partinfo>

into 100ul E. coli DH5-alpha.

They were plated on LB+Amp 100ug/ml agar plates


Competentization of colonies selected the previous day:

  • MG123 (without '-1' from now on)
  • MG008
  • MC123
  • MC008

August, 7th

Plates of transformed cells were stored at +4°C.