Team:University College London/HumanPractice/DIYbio/Workshops


Revision as of 22:48, 26 September 2012 by Zcbths3 (Talk | contribs)



Overview | Concept | DIYbio | Workshops | Exhibition | Evaluation | Conclusion

Public biobrick:BBa_K729016: Antifreeze protein, type I from Oceanibulbus indolifex HEL-45


Prior to the wetlab workshops, we visited the Hackspace on several occasions to prepare for the wetlab sessions. This included a short introduction to synthetic biology and our project, a large health and safety discussion, and primer a design workshop. From our early interactions with the citizen scientists, we found that they have done many PCRs and gels before. Some of these have been successful. However, they have not attempted cloning before due to the lack of licensing and UK regulations. What they wanted from this collaboration is to visit our lab to see how we conduct the experiments in an academic institution and also to be able to perform all the steps in the cloning process. Hence, in the UCL workshop schedule we attempted to fit all the experiments in three days.

Selecting genes to PCR from Oceanibulbus Indolifex Which genes to PCR? The Biohackers looked at the list of genes in the Oceanibulbus Indolifex genome database and selected genes which they think would be useful when transformed into E.coli. There were a number of potential candidates including metal binding proteins, arsenic reductase, mercuric reductase and antifreeze. The list was then shortened to antifreeze and mercuric reductase. Antifreeze was chosen because a relatively easy assay was found that can characterize the gene and mercuric reductase due to its useful ability to detoxify mercury.

Hackspace Workshop 29th-31st

Hackspace Wetlab Workshop schedule

In the Hackspace, we worked with the Biohackers on making competent E.coli (W3110) cells in the lab. This was an exciting experience, as we had to make a DIY incubator/shaker ourselves. We had help from many people in the Hackspace from sawing wood to circuit building. For PCR, we autoclaved our boxes of tubes and tips using their makeshift autoclave pressure cooker and then they were put in the oven to dry.

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UCL Workshops 3rd-5th September

Original UCL Wetlab Workshop schedule

In the beginning of September, we held a three day workshop in UCL's teaching laboratory for the citizen scientists. We had an ambitious plan for the workshops, from genomic DNA extraction to ligation and transformation. This was a packed schedule. However, after day one, we quickly realised that it would be a much better learning experience for the Biohackers if the pace was slowed down. The amount of practical experience between these citizen scientists also varied. We allowed much longer time intervals between the practicals to answer the Biohackers questions and to show them proper techniques we use in the laboratory.

Unfortunately, the first genomic DNA extraction was unsuccessful and some items delayed. However, the participants remarked how exciting and insightful they found the trouble-shooting that ensued.

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All protocols and results of the collaboration can be found on the London Hackspace wiki (1)

Result: Analytical Digest of the Public Biobrick

Analytical digest public biobrick.jpg Five colonies were picked from the ligation plates. After inoculation in LB + chloramphenicol overnight, these were minipreped and analytical digest was performed. All samples in lanes labelled one were digested once with Eco RI and samples labelled two are digested with EcoRI and Pst I. Colonies C and D clearly have the antifreeze insert. Lanes C2 and D2 show bands around 2000bp for the CMP plasmid backbone and around 400bp for the 435bp antifreeze region amplified by the primers. Therefore we have the biobrick!

Safety and regulations

Legality of making competent cell protocol at London Hackspace