Building a Open Source Microfludic Device For Analysis of Plant Protoplasts

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This blog is an experiment in open science. I am a postdoctoral researcher in Prof. Julian Hibberd's lab at the University of Cambridge, and moonlight as a editor for the PLOS Synthetic Biology Community. In my day job I work as part of a team that is seeking to understand an adaptation possessed by high yielding crops like maize, with the aim that we may one day be able to use this knowledge to boost yields of species such as rice. Our lab is part of a couple of international consortia pursuing this goal including the C4 rice project and the 3to4project.

Our research is focused on identifying DNA regulatory elements which limit gene activity to specific regions of a leaf in order to aid the design of synthetic circuits. Conventional approaches involve the fusion of a reporter (often the E. coli uidA gene) to a promoter that is being tested. This reporter is then inserted into plants, and the regions where the promoter is active are visualized by staining (see Kajala et al. for an example).   

Plan for chip to sort protoplasts courtesy of Dr. Sara Abalde-Cela

The problem with these methods is that they are slow and low throughput. With genomic technologies starting to provide vast numbers of candidate promoters, novel methods are required to screen them. I am a molecular biologist, and so is my colleague Ivan Reyna-Llorens who works with me on this topic. We realized that to tackle the problem we needed to bring together a team of experts from different disciplines, so we managed to convince Christian Boehm, Dr. Sara Abalde-Cela, Dr. Paul Bennett to join us. The result was a proposal to use a combination of plant protoplasting, differential fluorescence analysis and microfludics to sort cells based on fluorescence intensity. 

We recently received funding from the Cambridge Strategic Research Initiative for Synthetic Biology to develop this device. This came with the stipulation that all outcomes are open source. Additionally, as my fellow colleague Richard Smith-Unna has been encouraging Cambridge scientists to start implementing open practices in their research, I though this project was an excellent opportunity to learn how to do science openly (hence the blog).

Funding for the project lasts for six months, and we will start in January 2016. We are very excited, and if this pilot project is successful we hope to utilize the device to tackle a range of additional problems. In the spirit of open science we will be reporting regularly and making all our data available online in public repositories. Additionally we recognize science is a collective effort, so we will be keen to hear from anyone who has any bright ideas or novel applications for our device that might be interested in getting involved, comments are welcome.