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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Summer 2017 Biomaker Challenge

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Due to additional late interest, we are opening a second round of Biomaker Challenge applications, with a deadline of July 21st, 2017. Applications can be made online at: http://www.synbio.cam.ac.uk/biomakerchallenge
The Biomaker Challenge provides funds to support DIY construction projects for interdisciplinary teams, based on low-cost sensors and instruments for biology. From colorimeters to microfluidics to cell-free systems and beyond, we’re looking for frugal, open source and DIY approaches to biological experiments. Click here for ideas.

Whether you’re a biologist looking to optimise your protocols and pick up some electronics knowledge; an engineer looking to apply your skills and gain experience of practical biology or you’re just curious and interested to participate, we’re keen to hear from you, and can introduce you to potential partners from other disciplines and institutes.

Participants will receive a
Biomaker Starter Kit and a discretionary budget for additional sensors, components, consumables and 3D-printing worth up to £1000. All teams will exhibit their device at a Biomaker Fayre on October 21st. Primary applicants should be students or staff at the University of Cambridge, John Innes Centre or the Earlham Institute. External team members are welcome. Click here for more information
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PhD studentships in Cambridge for 2017
The UK government recently announced a new programme for PhD studentships, and some of these are filtering through to Cambridge. For information about synthetic biology research projects in the Haseloff Lab at the University of Cambridge, click here. 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.
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New section: Handheld macrophotography
New lightweight consumer cameras have 4K photo modes that allow video-rate capture of bracketed focus sweeps and in-camera or off-camera focus stacks. The addition of specialised optics and lighting allows handheld collection of high resolution extended focus images. More information here.

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Plant Development lectures and practical notes updated for 2017
Resources for an introductory course in plant developmental biology (Natural Sciences Part 1B CDB at the University of Cambridge), with lecture images, notes, key references and details of a practical laboratory exploring the role of auxin patterning in xylogenesis. Click here for more information.

Recent Publications

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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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Artificial symmetry-breaking for morphogenetic engineering of bacterial colonies
This paper describes genetic tools for symmetry-breaking and domain-specific cell regulation in bacterial colonies, with elementary functions to create new colony shapes starting from a single cell. The work includes computational modules for CellModeller that represent these functions and application of these for improved reproducibility and understanding of complex dynamic behaviours. The cover shows fluorescent images of Escherichia coli colonies exhibiting uncommon morphologies. Isaac N. Nuñez, Tamara F. Matute, Ilenne D. Del Valle, Anton Kan, Atri Choksi, Drew Endy, Jim Haseloff, Timothy J. Rudge, and Fernan Federici. ACS Synth. Biol. ((DOI: 10.1021/acssynbio.6b00149) Click to download PDF
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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.
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Cambridge-JIC iGEM2016 team creates Phytobrick library and tools for chloroplast engineering in Chlamydomonas
The team developed a library of new DNA parts for engineering of the plastid genome in the green alga Chlamydomonas, a single-cell model for plants. The DNA parts followed the new Phytobrick standard for plants. They also built transformation and culture devices to make this system more widely accessible. More details of the team and project can be found on their wiki site. The team was sponsored by OpenPlant, the Wellcome Trust - SEB - BBSRC consortium and Cambridge Consultants, and the team was awarded Gold Medal and prize for Plant Synthetic Biology.
Cambridge Consultants are world-leading product developers and technology consultants are sponsoring the Cambridge-JIC iGEM2016 team. They see synthetic biology as a significant new technology with global impact and are now working in this area. For more information about Cambridge Consultant's work in synthetic biology see http://www.cambridgeconsultants.com/core-skills/synthetic-biology.

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 www.openplant.org

The OpenPlant Fund offers regular calls for mini-funding across researchers at the University of Cambridge, John Innes Institute and the Earlham Institute. Next deadline is June 30th, 2017. 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 www.synbio.cam.ac.uk 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: www.meetup.com/Cambridge-Synthetic-Biology-Meetup
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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: http://biomake.space
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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: http://www.synbio.cam.ac.uk/biomakerchallenge and https://www.openplant.org/biomaker-challenge/
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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: http://www.eusynbios.org