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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
Click here to see introductory videos

Click here to find information for class revision exercise: Synthetic yeast genome papers.
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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. Advent of Synthetic Biology

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Click here to download PDF version of the lecture handout.

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.

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Lecture 2: Genetic circuits and genome scale DNA engineering
6. BioBricks, standardisation and social engineering
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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Click here to download PDF version of the lecture handout.

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.
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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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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.
Paper-based synthetic gene networks. Pardee, K. et al., 2014. Cell, 159(4), pp.940–954.
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.

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Lecture 4: Self-organisation and 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.
Plant synthetic biology. Liu, W. & Stewart, C.N., 2015. Trends in Plant Science, 20(5), pp.309–317.
Systems and synthetic biology approaches to cell division. Mashaghi, A. & Dekker, C., 2014. Systems and Synthetic Biology, pp.1–6.
Coordination of plant cell division and expansion in a simple morphogenetic system. Dupuy, L., Mackenzie, J. & Haseloff, J., 2010. Proceedings of the National Academy of Sciences of the United States of America, 107(6), pp.2711–2716.
Synthetic biology in plastids. Scharff, L.B. & Bock, R., 2014. Plant Journal, 78(5), pp.783–798.
Synthetic Botany. Boehm, C.R., Pollak, R. Purswani, N. Patron, N. and Haseloff, J. 2017. Cold Spring Harb Perspect Biol doi:10.1101/cshperspect.a023887.
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
Synthetic Biology: Integrated Gene Circuits, N. Nandagopal and M. B. Elowitz
Synthetic Biology Moving into the Clinic, W. C. Ruder et al.
Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World P. Schwille
Synthetic Biology: Regulating Industry Uses of New Biotechnologies, B. Erickson et al.

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