Team:Bielefeld-Germany/Labjournal/week10

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Contents

Week 10 (07/02 - 07/08/12)

weekly seminar

  • Summer school: we will organize a barbecue and drinks, therefore some stuff has to be bought.
  • We now have contact to the first sewage treatment plant.
  • Malak will translate our abstract into english for the CAS conference in munich.

Monday July 2nd

  • Team Student Academy:
    • During the whole week the two presentations for school academy were prepared and the barbecue for the pupils was organized. In the lab the last preparations were made.
  • Team Fungal and Plant Laccases:
    • Sending a request for plasmids containing cDNA sequences of five different laccases from Trametes versicolor and Pycnoporus cinnabarinus from the Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis at Ernst-Moritz-Arndt-University in Greifswald.

Tuesday July 3rd

  • Team Site Directed Mutagenesis:
    • Decided how to insert silent mutations to get rid of the restriction-sites with an eye on the codon-usage of host- and scource-oragnism, using the Kazusa “Codon Usage Database”
    • ecol’s illegal NgoMIV will be deleted by changing ggG to ggA (Glycin) at 2307
    • tthl’s illegal PstI will be deleted by changing caG to caA (Glutamine) at 2796
    • bpul’s illegal XbaI will be deleted by changing ctA to ctT (Leucin) at 2883
    • bpul’s mutation will be deleted by changing Gag (Glutamat) to Aag (Lysin) at 2317
    • xccl’s first illegal PstI will be deleted by changing ctG to ctC (Valine) at 2247
    • xccl’s second illegal PstI will be deleted by changing ctG to ctC (Valine) at 3633

Wednesday July 4th

  • Team Student Academy:
    • Final meeting with all instructors of the student academy to talk about all details.
  • Team Cloning of Bacterial Laccases:
    • After the failed attempts to isolate the laccase genes from Streptomyces lavendulae and Streptomyces griseus we assumed that maybe the sequences from this laccases and the laccase sequences we designed the primers for were to different to get a product (look here for more details). So we used the sequences of the laccase genes we tried to isolate from the Streptomycetes strains and blasted them against an intern database from our university. The results showed that we could use genomic DNA from Streptomyces sp. tuebingen, S.roseochromogenes and Streptomyces sp. goettingen, from which we can get already isolated genomic DNA. Therefore we designed primers for the isolation of the predicted laccase genes from these three strains.

Thursday July 5th

  • Team Shuttle Vector:
    • Some fragments for Gibson Assembly with overlapping DNA sequences were amplified via Phusion-PCR. The fragment 5'AOX1 was amplified with the primer pair pSB1C3-5aox1-f and pSB1C3-5aox1-r. The fragment MF-alpha1 was amplified with the primer pair 5aox1-mfalpha1-f and 5aox1-mfalpha1-r. The fragment 3'AOX1 was amplified with the primer pair his4-3aox1-f and his4-3aox1-r. The fragment pSB1C3 was amplified with the primer pair 3aox1-pSB1C3-f and 3aox1-pSB1C3-r.

Friday July 6th

  • Team Database:
    • FINISHED!! We finished our database. The search statement is now correct. And here it is:
Figure 1: Finally our saerch statement.


Saturday July 7th

  • Team Fungal and Plant Laccases:
    • We received an e-mail from the working group leader Prof. Dr. Bornscheuer (Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis at Ernst-Moritz-Arndt-University in Greifswald (Germany)). He send us a confirmation that the plasmids with the cDNA of four Trametes versicolor-laccases and one laccase of Pycnoporus cinnabarinus were sended to the iGEM Team Bielefeld.

Sunday July 8th

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