Team:Stockholm/27 August 2010

From 2010.igem.org

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(New page: {{Stockholm/Top2}} __TOC__ == Hassan == added some text, animation is a little slower now. <html> <embed src="https://static.igem.org/mediawiki/2010/2/28/Test_SU_vitiligo_animation_0_6_2.sw...)
 
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== Hassan ==
== Hassan ==
-
added some text, animation is a little slower now.
+
added some text, animation is also a little slower now, a border added.
 +
 
 +
other things to be changed now are:
 +
* a darker color for after pigmentation.
 +
* colors need to be changed for proteins and genes.
 +
* a more proper timing for after pigmentation.
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==Andreas==
 +
===Troubleshooting of SOD&sdot;His fusion fail===
 +
====Restreak results====
 +
''From 26/8''
 +
 +
All restreaked clones (pSB1K3.SOD&sdot;His 1 & 2 and pSB1K3.His&sdot;SOD 1 & 3) were able to grow on both Cm 25 and Km 50. This raises the question whether our plasmid actually carries resistance to both Km and Cm. To test this further, new restreaks were made, where colonies from the Cm 25 plate were streaked on a new Km 50, and vice versa. Also, pSB1K3.RFP, pSB1C3.RFP and untransformed Top10 cells were streaked.
 +
*'''Amp 100 plate'''
 +
**pSB1K3.SOD&sdot;His 1 from Km 50 plate
 +
**pSB1K3.His&sdot;SOD 1 from Km 50 plate
 +
**Top10
 +
**pSB1K3.RFP
 +
**pSB1C3.RFP
 +
*'''Cm 25 plate'''
 +
**pSB1K3.SOD&sdot;His 1 from Km 50 plate
 +
**pSB1K3.His&sdot;SOD 1 from Km 50 plate
 +
**Top10
 +
**pSB1K3.RFP
 +
**pSB1C3.RFP
 +
*'''Km 50 plate'''
 +
**pSB1K3.SOD&sdot;His 1 from Cm 25 plate
 +
**pSB1K3.His&sdot;SOD 1 from Cm 25 plate
 +
**Top10
 +
**pSB1K3.RFP
 +
**pSB1C3.RFP
 +
 +
===Transfer of SOD into pMA.His (pMA.SOD&sdot;His)===
 +
A new strategy attempted for fusing SOD to His. This time SOD will be transfered to pMA carrying the His-tag, thereby avoiding cloning/excising the small tag from its vector.
 +
====Strategy====
 +
*pMA.SOD&sdot;His
 +
**SOD digested with EcoRI and AgeI
 +
**pMA.His digested with EcoRI and NgoMIV
 +
*pMA.His&sdot;SOD
 +
**SOD digested with NgoMIV and PstI
 +
**pMA.His digested with AgeI and PstI
 +
====Digestion====
 +
[pMA.His]=85.67 ng/&mu;l<br />
 +
[pSB1C3.SOD]=105.5 ng/&mu;l
 +
 +
{|border="1" cellpadding="1" cellspacing="0"
 +
!&nbsp;
 +
!pMA.His
 +
!pSB1C3.SOD
 +
|-
 +
|10X FD buffer
 +
|align="center"|2
 +
|align="center"|2
 +
|-
 +
|DNA (1 &mu;g)
 +
|align="center"|11.7
 +
|align="center"|9.5
 +
|-
 +
|dH<sub>2</sub>O
 +
|align="center"|4.3
 +
|align="center"|6.5
 +
|-
 +
|FD EcoRI
 +
|align="center"|1
 +
|align="center"|1
 +
|-
 +
|NgoMIV
 +
|align="center"|1
 +
|align="center"|0
 +
|-
 +
|FD AgeI
 +
|align="center"|0
 +
|align="center"|1
 +
|-
 +
|&nbsp;
 +
!20
 +
!20
 +
|}
 +
 +
'''Incubation'''
 +
*'''FastDigest enzymes:''' 37 &deg;C, 30 min
 +
*'''NgoMIV:''' 37 &deg;C, 2 h
 +
 +
=====Gel verification=====
 +
[[image:Gelver_dig_SOD_27aug.png|150px|right|thumb|'''Gel verification of SOD digested with EcoRI and AgeI.'''<br />3 &mu;l &lambda;; 3 &mu;l sample.<br />&lambda;=O'GeneRuler 1 kb DNA ladder.]]
 +
*Dig.SOD E+N (SOD)
 +
 +
1% agarose, 100 V, 45 min
 +
 +
'''Results'''<br />
 +
Gel shows successful digestion: no undigested plasmid and a band corresponding well to the expected SOD size (492 bp).
 +
 +
====Gel extraction====
 +
Remaining 22 &mu;l SOD sample run on 1 % agarose gel, 100 V. SOD DNA band excised (240 mg gel; "Extr. Dig SOD E+A") and saved in -20 &deg;C until tomorrow.
 +
 +
===Isolation of CPPs from N-CPP cluster===
 +
====Gel verification====
 +
[[image:Gelver_CPPcluster_PCR_27aug.png|180px|right|thumb|'''Gel verification of CPP cluster PCR.'''<br />3 &mu;l &lambda;; 3 &mu;l sample.<br />&lambda;=O'GeneRuler 1 kb DNA ladder.]]
 +
Gel verification of Nina's CPP cluster PCR
 +
 +
1.5 % agarose, 100 V, 25 min<br />
 +
'''Expected band:''' 379 bp
 +
 +
====Gel extraction====
 +
&asymp; 35 &mu;l sample. CPP cluster band excised (220 mg gel; "Extr. N-CPP clust") and saved in -20 &deg;C.
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
== Mimmi ==
 +
 +
 +
=== MITF-M ===
 +
 +
==== re-digest and ligate ====
 +
 +
{|
 +
| colspan="5" |
 +
! colspan="2" | Conditions
 +
|-
 +
! Mix
 +
| (µl)
 +
| rowspan="7" width="100" |
 +
|
 +
| rowspan="5" width="100" |
 +
! time
 +
! &deg;C
 +
|-
 +
| DNA
 +
| 10
 +
| align="center" | DNA = pSB1C3.RFP
 +
| 10m
 +
| 37
 +
|-
 +
| sH<sub>2</sub>O
 +
| 15
 +
| align="center" | +
 +
| 20m
 +
| 65
 +
|-
 +
| 10x buffer
 +
| 3
 +
| align="center" | MITF-M
 +
| oo
 +
| 10
 +
|-
 +
| EcoRI
 +
| 1
 +
|
 +
|
 +
|
 +
|-
 +
| SpeI
 +
| 1
 +
| ( [pSB1C3]=50ng/µl, [MITF-M]=160ng/µl )
 +
|-
 +
| align="right" | tot
 +
| 30µl
 +
|
 +
|
 +
|
 +
|}
 +
 +
 +
*Ligate
 +
 +
{|
 +
! Mix
 +
| (µl)
 +
| rowspan="7" width="100" |
 +
! colspan="2" | Conditions
 +
|-
 +
| cut pSB1C3
 +
| 3
 +
! time
 +
! &deg;C
 +
|-
 +
| cut MITF-M
 +
| 3
 +
| 10m
 +
| 22
 +
|-
 +
| 5x buffer
 +
| 4
 +
| oo
 +
| 4
 +
|-
 +
| T4 ligase
 +
| 1
 +
| rowspan="3" colspan="2" |
 +
|-
 +
| sH<sub>2</sub>O
 +
| 9
 +
|-
 +
| align="right" | tot
 +
| 20µl
 +
|}
 +
 +
==== Transformation ====
 +
 +
*Follow original protocol
 +
 +
=== pEX.RFP & CPPn ===
 +
 +
==== Gel ====
 +
 +
[[Image:2010-08-27_pEX_+_CPPn.jpg|200px|thumb|left|]]
 +
{|
 +
! well
 +
! sample
 +
|-
 +
| 1
 +
| 1kb ladder
 +
|-
 +
| 3
 +
| pEX.RFP 1
 +
|-
 +
| 4
 +
| pEX.RFP 2
 +
|-
 +
| 5
 +
| pEX.RFP 3
 +
|-
 +
| 6
 +
| pEX.RFP 4
 +
|-
 +
| 7
 +
| pEX blank
 +
|-
 +
| 8
 +
| Transportan10
 +
|-
 +
| 9
 +
| TAT (dowdy's)
 +
|-
 +
| 10
 +
| LMWP
 +
|-
 +
| 11
 +
| 50bp ladder
 +
|}
 +
 +
 +
 +
==== pEX.RFP plasmid mini prep ====
 +
 +
*PEX_VR binds perfectly to a region in RFP and pEX_VF binds with two mismatches to a region in RFP, so 4 different bands could be expected:
 +
**1272bp
 +
**1124bp
 +
**1010bp
 +
**862bp
 +
*Two clear bands and one faint band obtained in the colony-PCR in the right sizes.
 +
 +
 +
==== CPPn culture  and glycerol stock ====
 +
 +
*Pick one colony from the transformation plate and add 7ml LB with Amp
 +
 +
*1600µl culture in pre-sterile glycerol
 +
 +
*Leave the rest of the culture ON for plasmid prep
 +
 +
{{Stockholm/Footer}}

Latest revision as of 11:02, 26 October 2010

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Contents


Hassan

added some text, animation is also a little slower now, a border added.

other things to be changed now are:

  • a darker color for after pigmentation.
  • colors need to be changed for proteins and genes.
  • a more proper timing for after pigmentation.

Andreas

Troubleshooting of SOD⋅His fusion fail

Restreak results

From 26/8

All restreaked clones (pSB1K3.SOD⋅His 1 & 2 and pSB1K3.His⋅SOD 1 & 3) were able to grow on both Cm 25 and Km 50. This raises the question whether our plasmid actually carries resistance to both Km and Cm. To test this further, new restreaks were made, where colonies from the Cm 25 plate were streaked on a new Km 50, and vice versa. Also, pSB1K3.RFP, pSB1C3.RFP and untransformed Top10 cells were streaked.

  • Amp 100 plate
    • pSB1K3.SOD⋅His 1 from Km 50 plate
    • pSB1K3.His⋅SOD 1 from Km 50 plate
    • Top10
    • pSB1K3.RFP
    • pSB1C3.RFP
  • Cm 25 plate
    • pSB1K3.SOD⋅His 1 from Km 50 plate
    • pSB1K3.His⋅SOD 1 from Km 50 plate
    • Top10
    • pSB1K3.RFP
    • pSB1C3.RFP
  • Km 50 plate
    • pSB1K3.SOD⋅His 1 from Cm 25 plate
    • pSB1K3.His⋅SOD 1 from Cm 25 plate
    • Top10
    • pSB1K3.RFP
    • pSB1C3.RFP

Transfer of SOD into pMA.His (pMA.SOD⋅His)

A new strategy attempted for fusing SOD to His. This time SOD will be transfered to pMA carrying the His-tag, thereby avoiding cloning/excising the small tag from its vector.

Strategy

  • pMA.SOD⋅His
    • SOD digested with EcoRI and AgeI
    • pMA.His digested with EcoRI and NgoMIV
  • pMA.His⋅SOD
    • SOD digested with NgoMIV and PstI
    • pMA.His digested with AgeI and PstI

Digestion

[pMA.His]=85.67 ng/μl
[pSB1C3.SOD]=105.5 ng/μl

  pMA.His pSB1C3.SOD
10X FD buffer 2 2
DNA (1 μg) 11.7 9.5
dH2O 4.3 6.5
FD EcoRI 1 1
NgoMIV 1 0
FD AgeI 0 1
  20 20

Incubation

  • FastDigest enzymes: 37 °C, 30 min
  • NgoMIV: 37 °C, 2 h
Gel verification
Gel verification of SOD digested with EcoRI and AgeI.
3 μl λ; 3 μl sample.
λ=O'GeneRuler 1 kb DNA ladder.
  • Dig.SOD E+N (SOD)

1% agarose, 100 V, 45 min

Results
Gel shows successful digestion: no undigested plasmid and a band corresponding well to the expected SOD size (492 bp).

Gel extraction

Remaining 22 μl SOD sample run on 1 % agarose gel, 100 V. SOD DNA band excised (240 mg gel; "Extr. Dig SOD E+A") and saved in -20 °C until tomorrow.

Isolation of CPPs from N-CPP cluster

Gel verification

Gel verification of CPP cluster PCR.
3 μl λ; 3 μl sample.
λ=O'GeneRuler 1 kb DNA ladder.

Gel verification of Nina's CPP cluster PCR

1.5 % agarose, 100 V, 25 min
Expected band: 379 bp

Gel extraction

≈ 35 μl sample. CPP cluster band excised (220 mg gel; "Extr. N-CPP clust") and saved in -20 °C.



















Mimmi

MITF-M

re-digest and ligate

Conditions
Mix (µl) time °C
DNA 10 DNA = pSB1C3.RFP 10m 37
sH2O 15 + 20m 65
10x buffer 3 MITF-M oo 10
EcoRI 1
SpeI 1 ( [pSB1C3]=50ng/µl, [MITF-M]=160ng/µl )
tot 30µl


  • Ligate
Mix (µl) Conditions
cut pSB1C3 3 time °C
cut MITF-M 3 10m 22
5x buffer 4 oo 4
T4 ligase 1
sH2O 9
tot 20µl

Transformation

  • Follow original protocol

pEX.RFP & CPPn

Gel

2010-08-27 pEX + CPPn.jpg
well sample
1 1kb ladder
3 pEX.RFP 1
4 pEX.RFP 2
5 pEX.RFP 3
6 pEX.RFP 4
7 pEX blank
8 Transportan10
9 TAT (dowdy's)
10 LMWP
11 50bp ladder


pEX.RFP plasmid mini prep

  • PEX_VR binds perfectly to a region in RFP and pEX_VF binds with two mismatches to a region in RFP, so 4 different bands could be expected:
    • 1272bp
    • 1124bp
    • 1010bp
    • 862bp
  • Two clear bands and one faint band obtained in the colony-PCR in the right sizes.


CPPn culture and glycerol stock

  • Pick one colony from the transformation plate and add 7ml LB with Amp
  • 1600µl culture in pre-sterile glycerol
  • Leave the rest of the culture ON for plasmid prep





The Faculty of Science at Stockholm University Swedish Vitiligo association (Svenska Vitiligoförbundet) Geneious Fermentas/ Sigma-Aldrich/

Retrieved from "http://2010.igem.org/Team:Stockholm/27_August_2010"