Synthetic Biology for engineering plants

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 could be used to reprogram plant development and morphogenesis.
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Open positions
Postdoctoral position to develop freeze-dried cell-free extracts for low cost diagnostics in Africa. (
Closing date 3 April 2018

Postdoctoral Research Coordinator position to manage the Cambridge Synthetic Biology Research Initiative and OpenPlant, see: (
Closing date: 12 Mar 2018
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OpenPlant Handbook 2018
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) - Feb 2018
Download Bakubung Report (3.9 MB, 26 pages) Dec 2017
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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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Research project ideas for 2017-2018
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 2018. These events will provide a showcase for open source technologies that are useful for research and education. The events promote a maker ethos in science and sharing of open source software, open hardware systems such as Arduino and Raspberry Pi, alongside 3D printing technologies and open biological tools. More details can be found at

Tools for macrophotography of liverworts in the field

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Updated information about cameras 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 bryophytes.

Recent Publications

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Loop assembly
Description of Loop assembly, based on a recursive approach to DNA fabrication. Alternate use of two Type IIS restriction endonucleases and corresponding vector sets allows efficient and parallel assembly of large DNA circuits. Plasmids containing standard Level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly provides a simple generalised solution for DNA construction with standardised parts. The cloning system will be provided under an OpenMTA license for unrestricted sharing and open access. bioRxiv Click to download PDF
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Programmed hierarchical patterning of bacterial populations
Hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its importance 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, (2018) Click to download PDF
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Marchantia polymorpha genome published
Publication of characterisation of the Marchantia polymorpha genome - with description of the streamlined genome of this key lower plant, with low regulatory gene counts and evolutionary stepping-stone between algae and higher plants. A great example of selfless community building by John Bowman, Takayuki Kochi, Tom Yamato and many colleagues!
Bowman et al. Cell 171:287–304 (2017). Click to download PDF
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Supplemental material from our group
Analysis of Cambridge isolates of Marchantia polymorpha, Bernardo Pollak, Mihails Delmans and Jim Haseloff. Summary of comparison of Cam-1, Cam-2 and Tak-1 isolates, and transcriptomic analysis of germinating sporelings. Cambridge contribution to Bowman et al. Cell 171:287–304 (2017). 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. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits. Christian R. Boehm, Bernardo Pollak, Nuri Purswani, Nicola Patron, and Jim Haseloff, Cold Spring Harb Perspect Biol 2017. (doi:10.1101/cshperspect.a023887). Click to download PDF
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MarpoDB: An open registry for Marchantia polymorpha genetic parts
MarpoDB is an open source database for Marchantia genes and DNA parts, which has been designed as a tool for a synthetic biology workflow. Among its features are precompiled cross-database querying to InterPro, Pfam signatures and non redundant Viridiplantae BLAST annotations; BLAST querying to Marchantia genes; sequence export in GenBank format; recoding of sequences to the common syntax for type IIS assembly and exchange of DNA parts; and a user interface for gene models and sequence exploration. MarpoDB is a platform for plant synthetic biology experiments in this model system. Mihails Delmans*, Bernardo Pollak* and Jim Haseloff, MarpoDB: An Open Registry for Marchantia polymorpha Genetic Parts, Plant Cell Physiol. 58: e5(1–9) (2016). Click to download PDF.
(Additional resources: GitHub site for the source code and URL for the active database)
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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.

Bioengineering activities in Cambridge

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OpenPlant initiative in Plant Synthetic Biology
BBSRC and EPSRC have funded OpenPlant: a £13.5M research centre for plant synthetic biology, a joint venture between the University of Cambridge and the John Innes Centre and Earlham Institute, Norwich. This initiative promotes open technologies for engineering of plant systems, including development of new standards, techniques and simple chassis. Click here for more details about the initiative at

The OpenPlant Fund offers regular calls for mini-funding across researchers at the University of Cambridge, John Innes Institute and the Earlham Institute. For more details, look here.
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Synthetic Biology Strategic Research Initiative
A strategic research initiative in Synthetic Biology has been established at the University of Cambridge. The website at provides a clearing house for information about synthetic biology research and activities in this field.
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Synthetic Biology Opportunities and Outreach in Cambridge
There are a number of open meetings like Cafe Synthetique, Science Makers and funding opportunities associated associated with the initiative - with a particular focus on building tools and interdisciplinary research across biology, engineering, computing, physical sciences and the humanities. For a directory and information about events in Cambridge, see:
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Biomakespace in Cambridge
Join a group of scientists, engineers, students and curious minds who are developing the new Biomakespace - an innovation space for biology and biological engineering. This will be located in the historic, original Laboratory of Molecular Biology building, supported by the University of Cambridge Synthetic Biology Strategic Research Initiative and other local supporters. For more information see:
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The Biomaker Challenge
OpenPlant, in partnership with the John Innes Centre, Earlham Instituitre and the Cambridge Sensor CDT is funding teams of students and researchers from Biology, Engineering and the Physical Sciences - in an iGEM-like challenge to construct low-cost devices for biology. For more information see: and
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The Cambridge University Synthetic Biology Society, CUSBS, is a new society aiming to spread the word of Synthetic Biology. Founded by the 2015 Cambridge-JIC iGEM team, they are a growing and enthusiastic team of undergraduates taking on practical bioengineering projects. See their website here.
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EUSynBioS: Society for Students and Postdocs in Synthetic Biology
The European Association of Students and Post-docs in Synthetic Biology (EUSynBioS) was founded as a student-led initiative in late 2014. Their goal is to shape and foster a community of young researchers active in the young scientific discipline of synthetic biology within Europe by providing a central resource for interaction and professional development. See the website at: