Synthetic Biology for engineering plant growth

Synthetic Biology is an emerging field that employs engineering principles for constructing genetic systems. The approach is based on the use of well characterised and reusable components, and numerical models for the design of biological circuits.

We have constructed a series of tools for controlling gene misexpression and marking specific cells in growing plants. We are building a new generation of genetic circuits that incorporate intercellular communication, and could be used to generate self-organised behaviour at the cellular scale. These can be used to reprogram plant development and morphogenesis. We have chosen Marchantia polymorpha as a simple model system for understanding and engineering plant growth. This lower plant provides unparalleled benefits in ease of culture, simple genome, haploid genetics, open form of development and rapid growth and regeneration, and is an ideal partner for modern quantitative analytical tools.
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Recent Publications

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OpenMTA: Opening options for material transfer
The Open Material Transfer Agreement enables practical, broader sharing and use of biological materials by biotechnology practitioners. Linda Kahl, Jennifer Molloy, Nicola Patron, Colette Matthewman, Jim Haseloff, David Grewal, Richard Johnson & Drew Endy. Nature Biotechnology doi.org/10.1038/nbt.4263, (2018). Click to download PDF
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Loop assembly: a simple and open system for recursive fabrication of DNA circuits
Loop assembly is based on a recursive use of two Type IIS restriction endonucleases and corresponding vector sets to enable efficient assembly of large DNA circuits. Bernardo Pollak, Ariel Cerda, Mihails Delmans, Simón Álamos, Tomás Moyano, Anthony West, Rodrigo A. Gutiérrez, Nicola Patron, Fernán Federici and Jim Haseloff. New Phytologist, 222: 628-640, (2019). Click to download PDF
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Programmed hierarchical patterning of bacterial populations
Hierarchical induction of gene expression domains plays an important role in biological self-organization. This paper reports a synthetic genetic system implementing population-based AND-logic for programmed autonomous induction of bacterial gene expression domains. Christian R. Boehm, Paul K. Grant & Jim Haseloff. Nature Communications 9:776-786 (2018). Click to download PDF
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Synthetic Botany
Plants modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. Christian R. Boehm, Bernardo Pollak, Nuri Purswani, Nicola Patron, and Jim Haseloff. Cold Spring Harbor Perspectives in Biology: Synthetic Biology 1-19, (2017). Click to download PDF
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Intercellular adhesion promotes clonal mixing in growing bacterial populations
Expression of ag43 adhesin protein in Escherichia coli to generate adhesion between cells, which caused aggregation in liquid culture and cell-stirring and altered micro-colony morphology on solid media. Anton Kan, Ilenne Del Valle, Tim Rudge, Fernán Federici and Jim Haseloff. Journal of The Royal Society Interface. doi.org/10.1098/rsif.2018.0406, (2018). Click to download PDF
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μCube: A Framework for 3D Printable Optomechanics
An assembly standard for the production of 3D printed optical devices -basis of a framework for parametric design of modular mounts for generalised design of modular optical devices following this μCube standard.M Delmans, J Haseloff. Journal of Open Hardware 2:1-9 (2018). Click to download PDF
Synthetic Biology initiatives in Cambridge
The laboratory helps to organise a range of Synthetic Biology themed initiatives that promote interdisciplinary exchange between Biology, Computer Sciences and Engineering in Cambridge though informal meet-ups, forums, project-based training and shared research projects.
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SynBio SRI
http://www.synbio.cam.ac.uk
A clearing house for information about synthetic biology research at the University of Cambridge,
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OpenPlant
https://www.openplant.org
Research centre to promote open technologies for plant Synthetic Biology.
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Biomaker
https://www.biomaker.org
Project funding for construction of low-cost devices for biology. For more information see
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Café Synthetique
http://www.meetup.com/Cambridge-Synthetic-Biology-Meetup
Monthly meeting for networking and building interdisciplinary links.
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Biomakespace
http://biomake.space
An innovation space for biological engineering, located in the historic original MRC-LMB building.
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Cambridge CODE (Centre for Organismal Design and Engineering) project is a new initiative that brings together biologists, engineers, physicists, mathematicians and computer scientists to tackle the challenge of engineering of growing cellular systems, where advanced biology and artificial intelligence techniques can allow the creation of predictive multi-scale models for living systems. and used to guide genome engineering and redesign of organisms. Details of the plant effort can be found at: https://www.plantcode.org
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PhD studentships in Cambridge
The best place to find general information about postgraduate study at the University of Cambridge is the Graduate Admissions site. This includes customised links to potential funding sources for UK and international students. For information about synthetic biology research projects in the Haseloff Lab at the University of Cambridge, click here.
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Open positions
3 month internship as Coordinator for GCRF-funded Biomaker initiative - help assemble and run Biomaker workshops in South Africa, Ghana, Benin, Ethiopia and Egypt. Contact Jim Haseloff (jh295 at cam.ac.uk for more details).
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2019-2020: Research projects
The lab hosts undergraduates for research projects in the Department of Plant Sciences. Students may be taking the third year of their Natural Sciences Tripos (Part II) or fourth year of a Master's Degree in Engineering. Students will have a day-to-day supervisor, and projects are generally customised for the individual, but a list of broad areas of interest can be found here. Please contact Prof. Jim Haseloff for more detailed information.
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Biomaker Challenge
The annual Biomaker Challenge and Open Technology Week will run again in 2019. These events support interdisciplinary training and projects that promote a maker ethos in science and sharing of open source software and hardware systems, graphical programming, 3D printing technologies and open biological tools. More details can be found at www.biomaker.org.

Tools for macrophotography of liverworts in the field

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Lunularia cruciata liverwort plant photographed in situ, using a Panasonic GX80 camera, Olympus 60mm macro lens, 10mm extension tube and Raynox DCR-250 macro lens adapter. Technical details at: https://www.hackster.io/jim-haseloff
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Jim's hints: camera systems suitable for field work and documentation of small plants in the field. Camera setup and modification for high-speed, handheld focus stacking - including a comparison of the new Olympus TG-5 camera, modification of the Panasonic GX80 camera, and choice of a tripod that is well-suited for macrophotography of small plants, like bryophytes. More technical information at: https://www.hackster.io/jim-haseloff/

OpenPlant Handbook

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An introduction to OpenPlant, objectives, work programme and summary of recent progress. The Handbook also contains thumbnail sketches of OpenPlant researchers.
Download PDF version of Handbook (15 MB, 170 pages)
Download Bakubung Report Capacity Building for the Bioeconomy in Africa (3.9 MB, 26 pages)
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A transatlantic perspective on 20 emerging issues in biological engineering
Identification of 20 issues considered to be emerging, to have potential global impact, and to be relatively unknown outside the field of biological engineering. Wintle BC, Boehm CR, Rhodes C, Molloy JC, Millett P, Adam L, Breitling R, Carlson R, Casagrande R, Dando M, Doubleday R, Drexler E, Edwards B, Ellis T, Evans NG, Hammond R, Haseloff J, Kahl L, Kuiken T, Lichman BR, Matthewman CA, Napier JA, ÓhÉigeartaigh SS, Patron NJ, Perello E, Shapira P, Tait J, Takano E, Sutherland WJ. eLife doi: 10.7554/eLife.30247, (2017). Click to download paper
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Lab publications
Find a list of published papers and patent applications from the lab compiled here. These can be downloaded directly as PDFs.
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Teaching materials
Updated and new reference materials, including lecture notes, slides and PDFs can be found for courses on Origins of Agriculture (NST PMS 1B), Plant Development (NST CDB 1B) and Synthetic Biology (NST PS 2), taught by Jim Haseloff at the University of Cambridge.
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Images of liverworts in the field
See photo galleries of plants from the Australian Bryophyte Workshop in the Flinders Ranges
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Microscopy image galleries
Navigate to the Imaging index page to find different galleries of microscopy images. These include a wide range of historic plant samples that have been collected at the Department of Plant Sciences in Cambridge, where conventional cytological stains are often highly fluorescent and reveal new features when imaged using modern multispectral confocal laser scanning microscopes.