Research projects in the Haseloff Laboratory
Synthetic Biology is an emerging field that employs engineering principles to construct new genetic systems. The approach is based on the use of well characterised and reusable DNA components, and numerical models for the design of biological circuits. The approach shows great potential for the engineering of multicellular systems, and plants are the obvious first target for this type of approach. Plants possess indeterminate and modular body plans, have a wide spectrum of biosynthetic activities, can be genetically manipulated, and are used globally for low cost bioproduction at up to gigatonne scale.

We are using two experimental systems as testbeds for engineering cellular growth and metabolism. First, close packed microbial cell populations provide surrogates for plant tissues. Further, the liverwort Marchantia polymorpha is a descendant of the earliest terrestrial plants, which is characterised by morphological simplicity, a highly streamlined genome, and a growing set of techniques for facile genetic manipulation, culture and microscopy. Marchantia is providing a new platform for Synthetic Biology and the reprogramming of plant development and physiology.

Work in the Haseloff lab (http://www.haseloff-lab.org) focuses on the interplay between genetics and plant cell growth, and the way that these interactions can be engineered to give rise to self-organisation and emergent behaviour. We are developing new synthetic biology tools for visualising, manipulating and modelling genetic interactions and morphogenesis. A number of research topics are available for rotation projects or a full programme of PhD work:
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Synthetic self-organising genetic circuits in microbes
Synthetic Biology provides a conceptual and practical framework for the systematic engineering of multicellular systems. We have used populations of microbial cells, which exhibit little or no intrinsic coordination of growth, as a models to study physical and genetic interactions in multicellular systems. These very simple systems can be genetically programmed to possess specific intercellular communication and feedback. Dynamic behaviour can be visualised in fixed grids of microbes using non-invasive quantitative microscopy. Large-scale cellular biophysical models demonstrate that local instabilities can generate self-organised behaviour in these systems. We now wish to use hormone-based signalling systems to build synthetic plant-like patterning systems in microbes.
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A simple plant testbed and modular DNA parts
Marchantia polymorpha is a liverwort, descendant of the first terrestrial plants that evolved 500 million years ago. It has a highly simplified body plan, a streamlined genome with all of the genetic mechanisms found in higher plants, and is easy to culture and transform. The plant develops from single-cell spores and undergoes morphogenesis under the microscope. Marchantia is a new testbed for reprogramming of plant development and physiology. As part of the part of the OpenPlant initiative (www.openplant.org), we have established a common syntax for plant DNA parts (Phytobricks), are characterising collections of IP-free DNA parts, and developing techniques for genome-scale DNA editing in this simple plant system. Technical projects are available to characterise DNA parts, including the development of high resolution quantitative microscopy and image processing methods.
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Developmental markers and mutants in Marchantia.
We have established Agrobacterium T-DNA based enhancer trap screens, based on GAL4 and HAP1, respectively. In addition we are constructing a library of promoters from the entire collection of Marchantia transcription factors. These can be used to generate new plant lines which are precisely marked with multispectral fluorescent protein markers. In addition, CRISPR/Cas9 tools can be used to rapidly generate specific gene knock outs. The time course of plant cell proliferation, differentiation and organogenesis can be followed by 3D confocal microscopy. In particular, we are following the development of specialised oil cells and air chambers. The simple genetic architecture and experimental accessibility of Marchantia allows facile study of regulatory systems in situ.
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Hormonal control of cell proliferation and plant morphogenesis
Plant meristems maintain a balance between cells that proliferate and those that are allowed to differentiate. This balance is crucial for proper morphogenesis. Auxins, cytokinins and gibberellins regulate cell division and elongation in plant tissues. Hormonal regulation systems are highly simplified in Marchantia, compared to higher plants. A range of projects are available where targeted expression of genes that regulate auxin, cytokinin and gibberellin levels can be used to alter hormones in situ. The aim of these experiments is to develop generic strategies for engineering growth in Marchantia and other plants. 
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Chloroplast engineering
Chloroplasts are major sites for metabolic flux and biosynthesis in plants. There may be 10-100 chloroplasts in each cell, and each plastid contains many copies (10-100) of the relatively small chloroplast genome (121 Kb in Marchantia). Chloroplast transformation has been used for the introduction of various genes and can result in hyperproduction, with the relevant enzyme or antigen sometimes accumulating to a level of more than 50% of total soluble protein. Plastids retain prokaryote-like mechanisms for gene expression and regulation. In addition, liverwort plastids do not show evidence of the RNA editing found widely in the plastids of more advanced plants. This allows easy refactoring of genetic circuits that may have been tested in microbial systems.
Current approaches to chloroplast transformation rely on biolistic delivery of foreign DNA which contains the gene(s) of interest, a selectable marker and regions of homology to the plastid genome. High levels of homologous recombination in the plastid result in integration of the foreign sequence. Repeated rounds of growth and selection are required to establish the transformant, requiring out-competition of the untransformed DNAs during replication within the targeted plastid, and the establishment of a homogenous chloroplast population within the transformed cells. Projects are available for work on the construction of a synthetic chloroplast genome, and establishment of genome transfer and chloroplast engineering techniques in Marchantia.
Background information
PhD projects in these areas are interdisciplinary, can be tailored to suit a range of interests, and provide an opportunity to work with software models, synthetic DNA circuits and Marchantia, a simple test bed for engineering multicellular systems. Students will have direct access to modern scientific tools, including confocal microscopes, low light fluorescent imaging and molecular biology equipment, plant and algal growth facilities and computational resources for modelling multicellular growth. Candidates would be part of the OpenPlant initiative (www.openplant.org), and have an opportunity to participate in other synthetic biology initiatives in Cambridge (www.synbio.cam.ac.uk). Background information, including downloadable articles and technical information, is available from our web site (http://www.haseloff-lab.org), and more specific questions can be sent directly to Jim Haseloff (jh295@cam.ac.uk).