Labjournal

Week1 Week2 Week3 Week4 Week5 Week6 Week7 Week8 Week9 Week10 Week11 Week12 Week13 Week14 Week15 Week16 Week17 Week18 Week19 Week20 Week21

Week 2 (05/07 - 05/13/12)

weekly seminar:

• Found our first sponsors: [http://corporate.evonik.com/en/Pages/default.aspx Evonik], [http://www.biocircle.com/en-ca/ BioCircle] and [http://www.merckgroup.com/en/index.html Merck], now treaties have to be created and signed
• Julia is working on the database
• Decision to organize waver sell to fill up our petty cash
• Gabi and Isabel are designing a poster for the waver sell
• For our human practices we wanted to find a sociology student, willing to think about bioethics, but failed
• Our video is nearly done, is cutted and only needs be underlain with music

• Team Modeling: Looking for suitable Software and enzymkinetics to model the degradation of our substrates with the different laccases. Finding the Michaelis-Menten kinetics and matlab.

Monday May 7th

• Team Student Academy: First transformation of [http://partsregistry.org/Part:BBa_J04450 BBa_J04450] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_I13522 BBa_I13522] and plating on selective agar.
  • Electroporation setup: U= 2,5 kV C= 25 µF and R= 400 Ω

• Result: We got little colonies. There weren’t any green colonies and only some pale red fluorescent colonies.

Team Bacterial Laccases:

• More PCRs of laccase genes CopA from Xanthomonas campestris B100 and CueO from E. coli BL21(DE3) with the isolated genomic DNA as template and Xcc_LAC_FW_T7 / Xcc_LAC_RV_HIS and B.pumi_LAC_FW_T7 / B. pumi_LAC_RV_HIS primer pairs.
• Since we wanted to characterize laccases from different bacteria we had to order the bacterial strains which weren't available at the University Bielefeld from [http://www.dsmz.de/|DSMZ]. Below is a list of the ordered strains and the laccases we want to isolate from this strains.

• [http://www.ncbi.nlm.nih.gov/protein/46197298 Laccase] from [http://www.dsmz.de/catalogues/details/culture/DSM-7039.html?tx_dsmzresources_pi5%5BreturnPid%5D=304|Thermus thermophilus HB27]

• [http://www.ncbi.nlm.nih.gov/protein/10174701 Lbh1] from [http://www.dsmz.de/catalogues/details/culture/DSM-18197.html?tx_dsmzresources_pi5%5BreturnPid%5D=304|Bacillus halodurans C-125]

• [http://www.dsmz.de/catalogues/details/culture/DSM-40069.html?tx_dsmzresources_pi5%5BreturnPid%5D=304|S. lavendulae sp. Lavendulae ATCC 14158]

• [http://www.ncbi.nlm.nih.gov/protein/182434812 EpoA] from [http://www.dsmz.de/catalogues/details/culture/DSM-40236.html?tx_dsmzresources_pi5%5BreturnPid%5D=304|Streptomyces griseus ATCC 10137]

Tuesday May 8th

• Team Student Academy: Repetition of the transformation didn’t change the result. We made a liquid culture of [http://partsregistry.org/Part:BBa_J04450 BBa_J04450], but it did not fluoresce. Searching for mistakes and alternatives. Maybe competent cells are not that good and in case of RFP the lacI sensitivity could be the problem.
• Team Bacterial Laccases: After some empty agarose gels we finally isolated laccase gene CotA from Bacillus pumilus ATCC7061 as a PCR product. As template we used the plasmid we got from the Swiss working group.

Wednesday May 9th

Thursday May 10th

• Team Student Academy Testing the competent cells by transformation of pUC19. The transformation did not work that good, so that we produced new ones.

• Team Bacterial Laccases PCR on Thermus thermophilus genomic DNA. First we dissolved some of the lyophilized powder in water and for opeing the cells we boiled them for a few minutes. The primers we used were T.thermo_LAC_FW_T7 and T.thermo_LAC_RV_HIS to get the laccase. Finally with aditional DMSO and GC-buffer we had a product of the GC-rich laccase.