Revision as of 16:35, 4 September 2012

Labjournal

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Week 1 (04/30 - 05/06/12)

Start of our WET LAB time.
Generating new competent E.coli KRX cells.
Cultiviation of Xanthomonas campestris B100 and E. coli BL21(DE3). The bacterial strains we got from a working group at our University. After cultivation we isolated the genomic DNA. The DNA was needed as template for PCRs to purify the wanted laccase ORFs.

Monday April 30th

Team Student Academy: We got the chance to organize one part of the first school academy “synthetic biology/ biotechnology” at the CeBiTec of University Bielefeld by arranging experiments for the pupils and by presenting us and the iGEM competition. For the experimental part our general idea was to give them an understanding of principle methods in biotechnology / synthetic biology by using fluorescent proteins. We planned the following experiments:
- Plasmidisolation of RFP/GFP from a liquid culture.
Team Bacterial Laccases:
- Transformation of a plasmid mixture consisting of two different fluorescent proteins (e.g. RFP and GFP) and different antibiotic resistances into E.coli KRX. It will be plated out on LB agar plates without antibiotics and on plates containing one of the two antibiotics, which are present on the plasmids. This way we can demonstrate the effect of antibiotics as selective pressure.
- Sending requests to working groups for different plasmids, which have already worked with laccases and described them in their papers.
- Primerdesign for isolation of laccases from genomic DNA of Xanthomonas campestris B100 and E. coli BL21(DE3). The forward primers were designed with T7 promotor-overhanging ends after prefix and the first 20 bases of the wanted gene. The reverse primers were designed with a HIS-Tag and tweo stop codons before suffix and the last 20 bases of the wanted gene without the stop codon.

Tuesday May 1th

Team Student Academy: Searching for two plasmids with different fluorescent proteins behind and antibiotic resistance in parts registry. Found [http://partsregistry.org/Part:BBa_J04450 BBa_J04450], a Plasmid with RFP and chloramphenicol resistance (but lacI and CAP sensitive), [http://partsregistry.org/Part:BBa_J23100 BBa_J23100], a plasmid with RFP and ampicillin resistance and [http://partsregistry.org/wiki/index.php?title=Part:BBa_I13522 BBa_I13522], a Plasmid with GFP and ampicillin resistance in Kit Plate 2011.

Team Bacterial Laccases: We got answer on our request for a vector with the laccase-ORF CotA from Bacillus pumilus ATCC7061 from the Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomaterials in Switzerland. They promised to send us the plasmid.

Wednesday May 2th

Thursday May 3th

Team Bacterial Laccases:
- After the vector has arrived, we transformed it into the competent E.coli KRX which we have already made competent to have a greater amount of vector. The protocol we used was as followed:
  - The electroporation setup: U= 2,5kV C= 25 µF and R= 400 <math>\omega</math>
  - Since we did not know the efficient of our competent KRX we used two different E.coli volumes for the transformation, 50µL and 100µL. We gave 50µL 10% Gylcerol to the reaction tubes with 1µL of the vector DNA (Bacillus pumilus). After the transformation we plated them into ampicillin plates.
- PCR with the Xanthomonas campestris B100 and E. coli BL21(DE3) genomic DNA to isolate the laccases. Therefore we used the primers Xcc_LAC_FW_T7, Xcc_LAC_RV_HIS, E.coli_LAC_FW_T7 and E.coli_LAC_RV_HIS, which are listed under Materials.
- PCR table

Material	Volume
Buffer (10x Phusion)	10µL
Phusion Polymerase	0,5µL
dNTPs	1µL
Primer Mix	1µL
Template DNA	1µL
DMSO	1,5µL
Water	35µL

- PCR program

Temperature	Time
1) 98°C	30 sec
2) 98°C	15 sec
3) 62°C	45 sec
4) 72°C	1 min
5) 72°C	3 min
6) 12°C

Cycle between step 2 and 4 35 times.

weekly seminar:

Do we want to order strains of Trametes versicolor and Trametes villosa?
Gathering information about signal sequences in yeast
Decision to create a database, so that we can easily number and inscribe our lab results
Decision to arrange a summer school for pupils in their last year before the final exams
Discussion about how to meet a member of the german Bundestag (the german parliament)

Friday May 4th

Team Bacterial Laccases: Colony PCR on the transformed the Bacillus pumilus plasmid. Unfortunately the control with colony PCR didn't work so we just picked some colony for plasmid isolation in the hope that on the AMP plate were no false positives.

@@ Line 37: / Line 37: @@
 ** Transformation of a plasmid mixture consisting of two different fluorescent proteins (e.g. RFP and GFP) and different antibiotic resistances into ''E.coli'' KRX. It will be plated out on LB agar plates without antibiotics and on plates containing one of the two antibiotics, which are present on the plasmids. This way we can demonstrate the effect of antibiotics as selective pressure.
 ** Sending requests to working groups for different plasmids, which have already worked with laccases and described them in their papers.
+** Primerdesign for isolation of laccases from genomic DNA of ''Xanthomonas campestris B100'' and ''E. coli BL21(DE3)''. The forward primers were designed with T7 promotor-overhanging ends after prefix and the first 20 bases of the wanted gene. The reverse primers were designed with a HIS-Tag and tweo stop codons before suffix and the last 20 bases of the wanted gene without the stop codon.
 === Tuesday May 1th ===

Team:Bielefeld-Germany/Labjournal/week1

From 2012.igem.org