Team:Stockholm/26 August 2010

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Revision as of 23:22, 29 August 2010

Hassan

[http://string.embl.de/version_8_3/newstring_cgi/show_network_section.pl?identifiers=9606.ENSP00000347190%250D9606.ENSP00000270142%250D9606.ENSP00000368424%250D9606.ENSP00000353940%250D9606.ENSP00000295600%250D9606.ENSP00000241052%250D9606.ENSP00000360157%250D9606.ENSP00000373571%250D9606.ENSP00000267082%250D9606.ENSP00000281043%250D9606.ENSP00000343052%250D9606.ENSP00000364094%250D9606.ENSP00000257880&channel1=off&channel2=off&channel3=off&channel4=off&channel5=off&channel6=on&channel7=on&custom_limit=0&interactive=yes&network_flavor=actions&required_score=700&targetmode=proteins] [http://string.embl.de/version_8_3/newstring_cgi/show_network_section.pl?identifiers=9606.ENSP00000347190%250D9606.ENSP00000270142%250D9606.ENSP00000368424%250D9606.ENSP00000353940%250D9606.ENSP00000295600%250D9606.ENSP00000241052%250D9606.ENSP00000360157%250D9606.ENSP00000302777%250D9606.ENSP00000373571%250D9606.ENSP00000354130%250D9606.ENSP00000370171%250D9606.ENSP00000267082%250D9606.ENSP00000281043%250D9606.ENSP00000343052%250D9606.ENSP00000364094%250D9606.ENSP00000257880&channel1=off&channel2=off&channel3=off&channel4=off&channel5=on&channel6=on&channel7=on&custom_limit=0&interactive=yes&network_flavor=actions&required_score=700&targetmode=proteins]

Andreas

Assembly of SOD/yCCS⋅His constructs into pSB1K3

Sequencing results

From 23/8 BLAST results of

pSB1K3.SOD⋅His 1 (pK-SH1)
pSB1K3.SOD⋅His 2 (pK-SH2)
pSB1K3.yCCS⋅His 2 (pK-yH2)
pSB1K3.yCCS⋅His 3 (pK-yH3)

sequences revealed that no His tag was present. In fact, although SOD and yCCS were digested with AgeI for the assembly, the insertion found between SpeI and PstI had not been removed, indicating that SOD and yCCS hadn't even been properly digested; this makes it even more puzzling how the picked clones have been to grow on Km 50 plates, as the SOD and yCCS source plasmid was pSB1C3.

The only reasonable explanation is that SOD and yCCS have been digested only by EcoRI. After enzyme inactivation, however, PstI (which cannot be heat-inactivated) has digested the genes, making them complementary for insertion into pSB1K3 target vector.

Troubleshooting

Two controls were prepared to identify the problems with SOD/yCCS⋅His cloning:

Gel verification of all samples digested with AgeI and EcoRI
- Dig. pSB1K3.yCCS E+A (yCCS)
- Dig. pSB1K3.SOD E+A (SOD)
- Dig. pMA.His E+A (pMA)
Plating of sequenced clones onto both Cm 25 and Km 50 plates, to verify the vector resistance.

Gel verification

Gel verification of samples digested with EcoRI and AgeI.
1 kb λ = O'GeneRuler 1 kb DNA ladder.
50 bp λ = GeneRuler 50 bp DNA ladder.

1 % agarose, 110 V, 40 min

Results
Fairly poor digestion of yCCS and SOD. Unclear for pMA.His, since the His fragment is too small to appear on the gel.

Transfer of RFP cassette into pEX

Transformation results

From 25/8

Good yield of both red and white colonies. Four red clones picked for colony PCR verification. PCR performed by Mimmi.

Tranfer of MITF into pSB1C3

Continued from 25/8

MITF taken over by Mimmi.

Amplification of N-CPPs

PCRs prepared from N-CPP cluster plasmid to isolate our three N-CPPs.

N-Tra10
- Fwd: pSB-VF2
- Rev: pSB-VR
N-TAT
- Fwd: pEXf
- Rev: pEXr
N-LMWP
- Fwd: pGexf
- Rev: pGexr

Procedures according to the standard colony PCR protocol. Elongation time 0:45.

@@ Line 8: / Line 8: @@
 ==Andreas==
+===Assembly of SOD/yCCS⋅His constructs into pSB1K3===
+====Sequencing results====
+''From 23/8''
+BLAST results of
+<blockquote>pSB1K3.SOD&sdot;His 1 (pK-SH1)<br />
+pSB1K3.SOD&sdot;His 2 (pK-SH2)<br />
+pSB1K3.yCCS&sdot;His 2 (pK-yH2)<br />
+pSB1K3.yCCS&sdot;His 3 (pK-yH3)<br /></blockquote>
+sequences revealed that no His tag was present. In fact, although SOD and yCCS were digested with AgeI for the assembly, the insertion found between SpeI and PstI had not been removed, indicating that SOD and yCCS hadn't even been properly digested; this makes it even more puzzling how the picked clones have been to grow on Km 50 plates, as the SOD and yCCS source plasmid was pSB1C3.
+The only reasonable explanation is that SOD and yCCS have been digested only by EcoRI. After enzyme inactivation, however, PstI (which cannot be heat-inactivated) has digested the genes, making them complementary for insertion into pSB1K3 target vector.
+====Troubleshooting====
+Two controls were prepared to identify the problems with SOD/yCCS&sdot;His cloning:
+#Gel verification of all samples digested with AgeI and EcoRI
+#*Dig. pSB1K3.yCCS E+A (yCCS)
+#*Dig. pSB1K3.SOD E+A (SOD)
+#*Dig. pMA.His E+A (pMA)
+#Plating of sequenced clones onto both Cm 25 and Km 50 plates, to verify the vector resistance.
+=====Gel verification=====
+[[image:Gelver_dig_E+A_26aug.png|200px|thumb|right|'''Gel verification of samples digested with EcoRI and AgeI.'''<br />1 kb &lambda; = O'GeneRuler 1 kb DNA ladder.<br />50 bp &lambda; = GeneRuler 50 bp DNA ladder.]]
+% agarose, 110 V, 40 min
+'''Results'''<br />
+Fairly poor digestion of yCCS and SOD. Unclear for pMA.His, since the His fragment is too small to appear on the gel.
+===Transfer of RFP cassette into pEX===
+====Transformation results====
+''From 25/8''
+Good yield of both red and white colonies. Four red clones picked for colony PCR verification. PCR performed by Mimmi.
+===Tranfer of MITF into pSB1C3===
+''Continued from 25/8''
+MITF taken over by Mimmi.
+===Amplification of N-CPPs===
+PCRs prepared from N-CPP cluster plasmid to isolate our three N-CPPs.
+*'''N-Tra10'''
+**Fwd: pSB-VF2
+**Rev: pSB-VR
+*'''N-TAT'''
+**Fwd: pEXf
+**Rev: pEXr
+*'''N-LMWP'''
+**Fwd: pGexf
+**Rev: pGexr
+Procedures according to the standard colony PCR protocol. Elongation time 0:45.