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Genomics, Epigenetics & Synthetic Biology
Part II Plant Sciences Module L1
Synthetic Biology: Prof. Jim Haseloff
Supplementary material:
Click here to find relevant papers as downloadable PDFs
Click here to find sample essay questions
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Lecture 1: Genetic modification in agriculture and the advent of Synthetic Biology
1. Origins of agriculture
2. Selection and breeding of new crop varieties
3. Industrialisation of agriculture
4. Genetic modification (GM) for plant improvement
5. Genome editing

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Origin and emergence of the sweet dessert watermelon, Citrullus lanatus. Paris, H.S., 2015. Annals of Botany 116(2), pp.133–148.
Genetics and geography of wild cereal domestication in the near east. Salamini, F. et al., 2002. Nature Reviews Genetics 3(6), pp.429–441.
GM plants: Questions and answers. Royal Society, 2016. p.40.
Global status of commercialised Biotech/GM crops: 2016, ISAAA Brief No. 52, 2016.
The new frontier of genome engineering with CRISPR-Cas9. Doudna, JA & Charpentier, E. Science 346, 1077.
CRISPR, the disrupter. Ledford, H. 2015. Nature 522, 20-24.
Riding the CRISPR wave. Ledford, H. 2016. Nature 531, 156-159.
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Dominguez, AA; Lim, WA & Qi, LS. 2016 Nature Reviews Molecular Cell Biology 17, 5-15.

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Lecture 2: Synthetic Biology and genome scale DNA engineering
6. Advent of Synthetic Biology
7. Type IIS assembly and common syntax
8. Smart DNA registries and software tools
9. Chromosome engineering
10. Reprogramming metabolic pathways in plants
11. Implementing plant pathways in microbes

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DNA assembly for synthetic biology: from parts to pathways and beyond. Ellis, T., Adie, T. & Baldwin, G.S., 2011. Integrative biology : quantitative biosciences from nano to macro, 3(2), pp.109–118.
Synthetic Biology: Integrated Gene Circuits. Nandagopal, N. & Elowitz, M.B., 2011. Science, 333(6047), pp.1244–1248.
Design and synthesis of a minimal bacterial genome. Hutchison, C.A. et al., 2016. Science, 351(6280), p.6253-6253.
Engineered biosynthesis of natural products in heterologous hosts. Luo, Y. et al., 2015. Chem. Soc. Rev., 44, pp.5265–5290.
Recent applications of synthetic biology tools for yeast metabolic engineering. Jensen, M.K. & Keasling, J.D., 2015. FEMS Yeast Research, 15(1), pp.1–10.
The discovery of artemisinin (qinghaosu) and gifts from Chinese medicine. Tu, Y., 2011. Nature Medicine, 17(10), pp.1217–1220.
Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Paddon, C.J. & Keasling, J.D., 2014. Nature Reviews Microbiology, 12(5), pp.355–367.

Extended information about yeast genome engineering (2017 Class exercise)
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Lecture 3: Engineered logic and the control of gene expression
12. Cell autonomous genetic logic
13. Microbial test systems
14. Feedback regulation: toggle switches
15. Transcription networks: Genetic oscillators
16. In vitro systems for rapid testing
17. Complex circuit design

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Click here to download PDF version of the lecture handout.

Using movies to analyse gene circuit dynamics in single cells. Locke, J.C.W. & Elowitz, M.B., 2009. Nature Reviews Microbiology, 7(5), pp.383–92.
Engineered gene circuits. Hasty, J., McMillen, D. & Collins, J.J., 2002. Nature, 420(6912), pp.224–230.
Synthetic biology: applications come of age. Khalil, A.S.S. & Collins, J.J.J., 2010. Nature Reviews Genetics, 11(5), pp.367–379.
Implementation of cell-free biological networks at steady state. Niederholtmeyer, H., Stepanova, V. & Maerkl, S.J., 2013. Proceedings of the National Academy of Sciences of the United States of America, 110(40), pp.15985–90.
Rapid cell-free forward engineering of novel genetic ring oscillators. Niederholtmeyer, H. et al., 2015. eLife, 4(2015), pp.1–18.
Synchronous long-term oscillations in a synthetic gene circuit. Laurent Potvin-Trottier, Nathan D. Lord, Glenn Vinnicombe and Johan Paulsson. 2016 Nature 538: 514–517.
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Lecture 4: Reprogramming of multicellular systems
18. Organisation of natural microbial populations
19. Natural cell-cell signalling systems
20. Cellular coupling of genetic circuits
21. Physical coupling of cell populations
22. Organisation of plant cell divisions
23. Simple plant systems
24. Multiscale modelling
25. Prospects for plant engineering

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Click here to download PDF version of the lecture handout.

Artificial cell-cell communication as an emerging tool in synthetic biology applications. Hennig, S., Rödel, G. & Ostermann, K., 2015. Journal of Biological Engineering, 9(1), p.13.
A synchronized quorum of genetic clocks. Tsimring, L. et al., 2010. Nature, 463(7279), pp.326–330.
Engineering quantitative trait variation for crop improvement by genome editing. Rodriguez-Leal, D; Lemmon, ZH; Man, J; Bartlett, ME and Lippman, ZB. 2017. Cell 171, 470-480.
Engineering secondary cell wall deposition in plants. Yang, F; Mitra, P; Zhang, L; Verhertbruggen, Y; Kim, JS; Sun, L; Zheng, K; Tang, K; Auer, M; Scheller, HV and Locque, D. 2013. Plant Biotech. J. 11: 325-335.
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Easy introductions to CRISPR-Cas9 editing technologies.

CRISPR, the disrupter. Ledford, H. 2015. Nature 522, 20-24.
Riding the CRISPR wave. Ledford, H. 2016. Nature 531, 156-159.
Extract from a special Synthetic Biology edition of Science

The Allure of Synthetic Biology; The Life Hacker; Algae’s Second Try; A Lab of Their Own; Visions of Synthetic Biology
REVIEWS
Synthetic Biology: Integrated Gene Circuits, N. Nandagopal and M. B. Elowitz
Synthetic Biology Moving into the Clinic, W. C. Ruder et al.
PERSPECTIVE
Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World P. Schwille
POLICY FORUM
Synthetic Biology: Regulating Industry Uses of New Biotechnologies, B. Erickson et al.

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