Team:LMU-Munich/Weekly Journal

10-14 September 2012

<p align="justify"> To clean up our Sporobeads from vegetative B. subtilis cells we tried three different methods: French Press, sonification and lysozymes. A significant difference was observed after the treatment with lysozyme! Furthermore the lysozyme did not damage our fusion protein as GFP fluorescence was still obtained in microscopy!</p>

3-7 September 2012

<p align="justify"> All our CotZ-GFP variants were examined with fluorescence microscopy! The brightest spores derived from our P_cotyz-cotZrep-gfp-terminator mutants!</p>

<p align="justify"> Plates of our spores diluted at 10^-2, 10^-4 and 10^-6 from the germination assay show NO GERMINATION for our triple and quadruple mutants, and plenty of germination for the WT168 positive control! We will try plating undiluted mutant spores to see if any germination occurs.</p>

<p align="justify"> A collection of useful tags in Freiburg standard and with RBS included was cloned into pSB1C3. The tags are: 3xFlag, HA, cMyc, 10xHis and Streptavidin.</p>

August

26-31 August 2012

<p align="justify"> Finally, we got our first glowing spores!! After 4 months of hard work we have the first proof that this module works.</p>

<p align="justify"> Jara created quadruple mutants using two variations on past mutants: cwlD::kan + cwlJ::spec + gerD::cat + sleB::mls and gerD::cat + sleB::mls + cwlJ::spec + cwlD::kan. Germination assay was performed on triple and quadruple mutants.</p>

<p align="justify"> The BioBrick [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823019 lacZ] for B. subtilis was shown to be functional in pSB_Bs0K-P_spac in E. coli and B. subtilis. (blue color on plates with IPTG and X-Gal)</p>

<p align="justify"> The genes [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823028 luc+] and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K823029 mKate2], synthesized by GeneArt were successfully cloned into pSB1C3 and sequenced.</p>

20-24 August 2012

<p align="justify"> Double negative loop with lacZa was finished and works qualitatively (Julia).</p>

<p align="justify"> Good and bad news this week. First the good one: Another big step towards the GFP-Sporobeads is done! We have the CotZ constructs in pSB_BS1C! Hopefully it will integrate easily! :D Now the bad one: Finally we could start with the P_cgeA evaluation! But contrary to our expectations this promoter did not show any activity :( </p>

13-17 August 2012

<p align="justify"> Jara and Jenny used last week's double mutants to create triple mutants as follows: cwlD::kan + sleB::mls + cwlJ::spec ; cwlD::kan + sleB::mls + gerD::cat ; cwlD::kan + cwlJ::spec + gerD::cat ; gerD::cat + sleB::mls + cwlJ::spec.</p>

<p align="justify"> ß-glactosiase assay of the Anderson promoters J23100, J23102, J23103, J23106 in pSB_Bs1C-lacZ in B. subtilis. The xylose-inducible promoter with the according repressor (which has a constitutive promoter, RBS and terminator) P_Xyl + XylR was cloned into pSB1C3 and sequenced.</p>

<p align="justify"> At last Bacillus was keen on integrating the pSB_BS3C-luxABCDE-P_cgeA!! And the clean deletions of CotZ and CgeA worked out, too!</p>

6-10 August 2012

<p align="justify"> Jara and Jenny created four double-mutants using resistance-cassettes to knock out germination genes as follows: cwlD::kan + sleB::mls ; gerD::cat + sleB::mls ; gerD::cat + cwlD::kan ; cwlJ::spec + cwlD::kan. We also created the resistance cassette knockout cwlB::kan.</p>

<p align="justify"> Finally, the last PstI site could be removed and pSB_Bs3C-luxABCDE was completed. Also, the double terminator B0014 was cloned into pSB1C3.</p>

<p align="justify"> The final Promoter-CotZ-GFP-Terminator constructs in pSB1C3 are ready!! And Promoter-CgeAmut constructs are finally finished too. </p>

July

30 July - 3 August 2012

<p align="justify"> GFP-Terminator is ready for use and the AgeI site in CgeA is mutated!</p>

23-27 July 2012

<p align="justify"> This week is our Human Practise week! Form 23^rd to 25^th of July we enjoyed the CAS SynBio conference and the visit of 10 iGEM teams! This weekend, high school students participated in our Students Practical Course for three days and developed their ideas for useful Sporobeads! It was a great week! </p>

<p align="justify"> Plate reader measurements of the Bacillus promoters P_liaG, P_liaI and P_lepA finished. Look at Data!</p>

16-20 July 2012

<p align="justify"> Not many of us are working on our modules this week, as we are helping out for CAS SynBio conference and organising the Students Practical Course.</p>

<p align="justify"> Plate reader measurements of the Anderson promoters J23100, J23101, J23102, J23103, J23106, J23107, J23113, J23114, J23115, J23117, J23118 in the Bacillus reporter vector pSB_Bs3C-luxABCDE completed. Look at Data!</p>

<p align="justify"> Cloning of the Anderson promoters J23100, J23102, J23103, J23106 in the reporter vector pSB_Bs1C-lacZ for β-galactosidase assays finished.</p>

9-13 July 2012

<p align="justify"> The vectors pSB_Bs4S-P_Xyl , pSB_Bs1C-lacZ and pSB_Bs4S were succesfully completed and tested by restriction digest as well as red colony color. </p>

<p align="justify"> We started with the clean deletions of CgeA and CotZ this week, seems like it will take for ever if you judge from the protocoll length... What took even longer is the pSB_BS3C-luxABCDE-P_cgeA, but it is finished now!</p>

2-6 July 2012

<p align="justify"> Clean deletions of germination genes sleB and cwlB from PCR accomplished. DNA purified and frozen to be later transformed with Bacillus.</p>

<p align="justify"> β-galactosidase assays of the promoters P_liaG, P_liaI and P_veg are finished. Look at Data!</p>

<p align="justify"> Cloning of the Anderson promoters J23100, J23101, J23102, J23103, J23106, J23107, J23113, J23114, J23115, J23117, J23118 in pSB1C3 finished.</p>

<p align="justify"> Our first plate reader experiments with P_cotyz and P_cotv are running! Like expected they both show activity in the late stationary phase, thus during sporulation!</p>

June

25-29 June 2012

<p align="justify"> pSB_BS3C-luxABCDE-P_cotyz and pSB_BS3C-luxABCDE-P_cotv integrated into the B. subtilis genome! Bad luck, we found an additional AgeI site in cgeA, seems like this is the reason why we could not fuse gfp to it... Mutagenesis primers are designed and ordered!</p>

18-22 June 2012

<p align="justify"> CotZ and GFP constructs are finished, now we can try to fuse them together!</p>

11-15 June 2012

<p align="justify"> Clean deletions of germination genes cwlD, cwlJ, and gerD from PCR accomplished. DNA purified and frozen to be later transformed with Bacillus.</p>

4-8 June 2012

<p align="justify"> Still working on the Promoter-Gene and now GFP-Terminator constructs!</p>

May

28-1 June 2012

<p align="justify"> GFP in BioBrick standard is readyyyy!</p>

21-25 May 2012

<p align="justify"> pSB_BS3C-luxABCDE-P_cotyz and pSB_BS3C-luxABCDE-P_cotv are ready for transformation into Bacillus! </p>

<p align="justify"> Promoters P_liaG, P_liaI, P_veg and P_lepA are now in the vector pSB1C3 as BioBrick standard for the registry. BioBricks are BBa_K823000, BBa_K823001, BBa_K823002, BBa_K823003.</p>

<p align="justify"> The Anderson promoters J23100, J23101, J23102, J23103, J23106, J23107, J23113, J23114, J23115, J23117, J23118 are now in the Bacillus reporter vector pSB_Bs3C-luxABCDE for measuring their activity as luminescence.</p>

<p align="justify"> The Bacillus promoters P_liaG, P_liaI and P_lepA are in the Bacillus reporter vector pSB_Bs3C-luxABCDE.</p>

14-18 May 2012

<p align="justify"> Combining the BioBricks and integrating them into different vectors works good! But still there are constructs missing, we'll keep on working! The fusion of the up and down fragment of CotZ finally works!</p>

7-11 May 2012

<p align="justify"> The last weeks we tried to fuse the up and down fragment of our spore crust gene together for its clean deletion. For CgeA we have the first fused fragments! CotZ needs a little more attention :)</p>

<p align="justify"> Cloning of P_liaG, P_liaI and P_veg in vector pSB_Bs1C-lacZ finished.</p>

April

30 April-4 Mai 2012

<p align="justify"> We have the first essential BioBricks for this module: pSB1C3-CotZ, pSB1C3-P_cotV, pSB1C3-P_cotYZ, pSB1C3-P_cgeA, pSB1C3-CgeA! Still working on the pSB1C3-GFP.</p>

23-27 April 2012

<p align="justify"> pSB_Bs3C-luxABCDE with still one PstI site was created with RFP in the multile cloning site to have a vector for promoter measurments. edit: This PstI site was removed later and only that backbone is submitted to the registry.</p>

16-20 April 2012

<p align="justify"> The Sporobead team starts the work in the lab!</p>

<p align="justify"> The cloning of the reporter vector pSB_Bs1C-lacZ was finished.</p>

9-13 April 2012

<p align="justify"> Jara created the single mutant cwlD::kan.</p>

2-6 April 2012

<p align="justify"> Jara successfully created our first single knockouts of germination genes using a resistance cassettes: sleB::mls, gerD::cat and cwlJ::spec. Jara tried knocking out cwlB using the kan resistance cassette. Mutants of cwlB::kan grew very poorly.</p>

<p align="justify"> With pSB_Bs0K-P_spac our first vector for our Bacillus BioBrick Box was completed.</p>

March

26-30 March 2012

<p align="justify"> Jara tried knocking out cwlB using the tet resistance cassette. Mutants of cwlB::tet grew very poorly.</p>

19-23 March 2012

<p align="justify"> We decided which genes to knock out for the germination stop. Based on the work of [http://www.ncbi.nlm.nih.gov/pubmed/19554258 J. Kim and W. Schumann (2009)], we decided to knock out genes cwlB, gerD, cwlJ, and sleB. From the research of [http://www.ncbi.nlm.nih.gov/pubmed/11466293 B. Setlow et al (2001)], we also chose cwlD.</p>

12-16 March 2012

5-9 March 2012

February

27 February - 2 March 2012

20-24 February 2012

Team fully formed!

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