DIYbio

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

Public biobrick:[http://partsregistry.org/Part:BBa_K729016 BBa_K729016: Antifreeze protein, type I from Oceanibulbus indolifex HEL-45]

Sequence: http://www.ebi.ac.uk/ena/data/view/EDQ05862

Planning

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.

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.

For primers, protocols and results,these can be found on the [http://wiki.london.hackspace.org.uk/view/Public_Biobrick#Visualisation_and_interpretation London Hackspace Wiki]

Post-Workshops Some of the work was done after the workshops. Now that the Biohackers had experience of working in an academic laboratory, they paid more attention to reducing contamination and health and safety particularly with regards to Ethidium Bromide.

Result: Analytical Digest of the Public Biobrick

Safety and regulations

To comply with UK/EU regulations on GMOs, we conducted transformation of our ligated plasmid into W3110 E.coli cells at UCL. Making Competent Cells We attempted to make E. coli W3110 cells chemically competent at Hackspace. After long discussion and checking with relevant documents, we concluded that making these cells does not constitute genetic modification and therefore there is no legal restrictions on the creation of this competent strain.