Background

There is a paucity of systematic synthetic biology teaching, in particular on an undergraduate level, and often even in institutions that participate in the iGEM competitions. The principal reasons for this are: 1) interdisciplinarity and thus difficulty in application of knowledge from an unfamiliar field, as well as in arranging inter-departmental expertise and 2) requirement to select and characterise necessary biological, electronic and digital resources for successful creation or emulation of synthetic biology devices.

We aim to lower the barrier to entry for teaching synthetic biology by developing and providing experimental kits, BioBuilder-style, that allow introduction of the principles and approaches of synthetic biology through student-driven and open-ended inquiry. We envision that the kits may constitute an intenstive, 2-week long practical synthetic biology introductory course (for example, for prospective iGEM team participants) or a term-long module for the first year undergraduates.

All of the protocols from this project will be available free-of-charge with no restrictions imposed on non-commercial re-use and modification, and the parts themselves will be free of intellectual property rights.

Kit 1: Basic genetic modification

The purpose of this kit is to introduce a basic set of techniques to manipulate and investigate bacteria. The set of activities it contains is essential for all subsequent experiments, and it comprises:

• transformation of bacteria with a plasmid based on DNA2.0’s pJ401 expressing licensed green fluorescent protein (GFP) from jellyfish Aequorea victoria under constitutive promoter from the BIOFAB collection (Mutalik V.K. et al., 2013);

• introduction of a red fluorescent protein (RFP) from coral Obelia sp. (Aglyamova G.V. et al., 2011) in place of the GFP or, alternatively, swapping of antibiotic resistance genes on the plasmid using Gibson assembly (Gibson D. et al., 2011);

•quantification of transformation efficiency, measurement of bacterial growth and fluorescence output in two different bacterial strains (TG2 and DH10 or DH5α).

An extended version of this kit will add parts allowing for other modes of characterisation of the performance of a genetic device: β–galactosidase (by enzymatic reaction) and alcohol acetyltransferase I (by odor) genes.

Bacterial transformation protocol optimised by NCBE, based on the transformation and storage solution of Chung C.T. et al., 1989. This protocol is a single-step, 15 minute incubation procedure and requires no micropipettes, recovery times and uses microwaveable bacterial media. It is a part of the 18-reactions, £65 kit that NCBE currently provides to secondary schools. The same protocol is the basis for transformations in the undergraduate kits.

FundingThis work is a part of the ‘UNIGEMS’ project, funded by the European Comission’s Maria Skłodowska–Curie Research Fellowship in the 7th Framework Programme. Consumables used in the undergraduate workshop ‘Practical synthetic biology’ at the University of Reading, as well as course evaluation, were funded by the ‘Practical teaching aid’ grant from Society of General Microbiology. We hwould also like to acknowledge kind software support from SnapGene.com.

ContactNCBE, University of Reading2 Earley GateReading RG6 6AUT: +44 118 987 37 43

Onlinej.bryk@reading.ac.uk@jarekbrykwww.ncbe.reading.ac.uk/synbiopracticalsyntheticbiology.net

Images from the ‘Practical synthetic biology’ workshop run at the University of Reading in June 2013. Thirty four students with backgrounds in biology, pharmacy, food sciences, cybernetics and systems engineering participated in a week–long course running experiments from Kits 1 and 2, building logic gates and switches with electronic engineering components, and using computer modelling software GEC (Pedersen M. and Phillips A., 2009) to simulate bacterial patterning system (Basu S. et al., 2005).

Kit 2: Manipulating gene expression

The second kit builds on the skills developed in the first set of experiments and introduces manipulation of gene activity. For both GFP and RFP–based constructs from the first kit, we will provide parts to modify the production of the fluorescent protein:

• a set of 3–5 constitutive promoters from the BIOFAB collection (Mutalik V.K. et al., 2013);

• a set of 3 inducible promoters, induced by arabinose, anhydrotetracycline and lactose;

• a negatively regulated promoter from bacteriophage λ.

Investigation of the performance of these devices may be performed as a competition to produce the most protein (requiring investigation of protein content in a bacterial culture) or as analysis of influence of protein production rate on bacterial growth.

Kit 3: Biological computation and bacterial communication

We envision the third kit being used alongside electronic engineering components (i.e. breadboards, resistors, diodes) to construct various logic gates and switches to emphasize the standardised nature and interoperatibility of the parts used by engineers. This experience can be then directly contrasted with the effort and performance of biological logic gates. The kit will provide parts necessary to construct OR and AND gates and their negative counterparts (NOR and NAND gates), based on data from Tamsir A. et al. (2010) and Anderson J.C. et al. (2007).

Finally, we will provide parts that allow development of bacterial communication system based on quorum sensing genes from Vibrio sp., as described in the band–detecting system developed by Basu S. et al. (2005). We will combine this experiment with computer modelling using the GEC software (Pedersen M. and Phillips A., 2009), allowing for simulation of the bacterial patterns in silico.

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Practical kits to facilitateundergraduate teaching of synthetic biology

Jarek Bryk, John Schollar and Dean MaddenNational Centre for Biotechnology Education, University of Reading, UKemail: j.bryk@reading.ac.uk twitter: @jarekbryk