Three fully-funded, four-year PhD studentships are available from the University of Cambridge in association with OpenPlant, a UK Synthetic Biology Research Centre creating open technologies for plant synthetic biology.

Synthetic Biology takes an engineering approach to reprogramming biological systems and while early efforts in the field have been directed at microbes, the engineering of plant systems provides even greater potential benefits. OpenPlant labs are therefore working on foundational technologies that will be made openly available as a toolbox for plant synthetic biology as well as applying these tools to trait engineering in many aspects of plant biology from metabolism to development.

Studentships will run alongside the University’s Doctoral Training Programme (DTP), which includes training in statistics and Systems biology (SysMIC), and two rotation projects in OpenPlant labs in the first year. The final three years will be spent in an OpenPlant lab working on a project related to plant synthetic biology. See below for some examples of potential projects.

The studentships will start in October 2016 and cover a stipend at the standard Research Council rate (£14,057 per annum for 2015-2016), research costs and tuition fees at the UK/EU rate for four years. UK and EEA students who meet the UK residency requirements are eligible.

Update for EU students: One of the three studentship is now able to support a stipend for EU students who do not meet the residency criteria above. The other two studentships will only cover fees for such applicants as detailed in research council criteria. Applicants applying for fees-only support would need to provide evidence of financial support for living costs for the full duration of the PhD.

For informal enquiries, please contact OpenPlant Coordinator Dr Jenny Molloy (jcm80@cam.ac.uk).

To apply

Please send the following as email attachments to jcm80@cam.ac.uk

  1. A cover letter, outlining your interest in this research area and any relevant experience that you have in the field. Please explain what makes you suitable for this position.
  2. Your CV (maximum two pages).
  3. Two academic references.

Please include “OpenPlant Studentship” in the subject line.

Deadline

Closing date for applications is 20 May 2016. Shortlisted candidates will be asked to go through the formal University application process, and interviews will take place in early June.

OpenPlant Group Leaders in Cambridge

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Examples of potential PhD projects:

[x_accordion_item title="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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[x_accordion_item title="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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[x_accordion_item title="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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[x_accordion_item title="Hormonal control of cell proliferation and plant shape."]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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[x_accordion_item title="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

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