Ms Marta Tomaselli

I did my bachelor and master in Biotechnology in Pisa, where I discovered how fascinating plants can be. In the past, I have worked with CRISPR/Cas9 system in two different plant models: Arabidopsis thaliana and Marchantia polymorpha. These were my first experiences related to synthetic biology and they, really, got me involved into it.

In September 2016 I started as an OpenPlant PhD student at the University of Cambridge. In my first year I will do three lab rotations before beginning my final PhD project. During my first rotation in the Haseloff Lab, I have been developing microscopy techniques to image M. polymorpha gemmae. These tools will allow to retain the signal coming from fluorescent proteins in fixed samples and exploit them to achieve a 3D representation of the plant tissue.

For my second rotation, I moved to a different topic, working in the Schornack lab. This project focuses on plant-pathogen interactions: we are looking for pathogen-responsive promoters in M. polymorpha. These sequences can be exploited to generate new reporter lines.

In the future, I would like to continue working with Marchantia and exploit this plant as a model to implement new synthetic circuits. I think that the OpenPlant Community is a great resource for a PhD student, since a lot of different topics are covered by senior researchers to whom you can ask questions and suggestions about your own project.

Dr Susana Sauret-Gueto

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Dr. Susana Sauret-Gueto is an experienced molecular biologist and microscopist, with a scientific background in plant growth and development.

In the OpenPlant Cambridge laboratory, she coordinates the establishment of semiautomated workflows to accelerate the generation and characterisation of genetically engineered Marchantia lines. This requires standardised practices for DNA parts building, as well as appropriate registries to facilitate sharing of resources (DNA parts and transformed plants). Susana is establishing a new facility for robotic liquid-handling around the Echo acoustic liquid handler, and an advanced microscopy facility. The microscopy hub includes a Keyence digital microscope for real-time 3D reconstruction of Marchantia plants, as well as a series of fluorescent microscopes with different resolution capabilities, for example a Leica stereo microscope with fluorescence as well as a Leica SP8 confocal microscope.

The projects being developed along these workflows aim at mapping cell and tissue types throughout Marchantia gemmae development, for basic research questions and synthetic biology approaches. The strategies include the identification of cell types by screening Enhancer Trap lines, a collection of proximal promoters from transcription factors and its screening for specific expression patterns, a high-throughput targeted mutagenesis pipeline using CRISPR/Cas9, and the induction of localised genetic modifications through sector analysis. Susana helps managing and coordinating these interlinked projects working closely with Linda Silvestri, lab Research Technician in charge of Marchantia tissue culture, as well as with the Marchantia team of PhD and postdoc members of the lab. She is specially interested in the sector analysis project in order to dissect gene function and autonomy at the cell and tissue level.

Susana is also the main organiser of the ROC Group (Researchers with OpenPlant Cambridge), which brings together researchers in Cambridge doing Plant Synthetic Biology, both from CU and SLCU, to share common scientific interests, resources and protocols. Researchers work in a variety of plant species, but there are two core subgroups Algae-ROC and Marchantia-ROC. People are very engaged and active, which is making a difference in order to advance projects and pipelines in an efficient and collaborative way.

Mr Louis Wilson

I started as an OpenPlant PhD student at the University of Cambridge in September 2016, where I will complete three rotation projects before selecting my final PhD project. I am interested in all parts of plant biochemistry, but my projects tend to focus on the characterization and manipulation of enzymes and catalytic pathways.

In my first rotation project, I worked with Prof. Alison G Smith in Cambridge on metabolic gene clusters, developing methods for the expression of higher plant clusters in algae and yeast, and the detection of potential clusters endogenous to algae themselves. During this time I wrote a number of computer scripts for cluster detection and began the assembly of a heterologous expression system using a yeast MoClo system from the Dueber Lab.

Now in my second rotation project, I am working with Paul Dupree to study and engineer cell wall-modifying enzymes for improved crops, food and materials. I have been using OpenPlant heterologous expression systems and a transient expression construct from the Lomonossoff lab to assess the stability of glycosyltransferases in vitro, with the aim of finding better enzymes for further study and exploitation. Increasing our understanding of these enzymes may ultimately permit the creation of designer fibres and saccharides, as well as being able to manipulate the properties of plant cell walls.

Ms Linda Silvestri

As the Research Technician for the Haseloff group, I work closely with Susana Sauret-Gueto, Research Lab Manager, to ensure the smooth running of the lab. I am responsible for Marchantia polymorpha tissue culture and am working on the standardisation of existing protocols for the propagation, transformation and short and long term storage solutions, including cryopreservation.

This work will enable and facilitate the high-throughput screenings of Marchantia lines, such as the Enhancer Trap lines; a project on which several lab members collaborate. A summer student joined us for 8 weeks to work on this project and I helped with her supervision and provided laboratory training.

Dr Orr Yarkoni

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I’ve been involved in Synthetic Biology for better part of the last decade. My PhD work at Newcastle University focused on facilitating bio-electronic interface via engineered pathways as part of a larger collaborative grant to create a bio-robotic hybrid device. My more recent work at the University of Cambridge was on developing a field-use whole-cell Arsenic Biosensor for deployment in South Asia (www.arsenicbiosensor.org).

I’m relatively new at working with plants and the opportunity to reengineer the Marchantia polymorpha plastid as part of the Open Plant initiative is a great point of transition into this sphere. The main focus of my contribution to Open Plant is to reconstruct the entire 121kb plastid genome in a way that makes it easier to manipulate, facilitating future work on plastid transformation in M. polymorpha and, in time, other plants. I am also working together with Haydn King from the Ajioka Lab on creating a codon optimised reporter toolkit for use in the M. polymorpha plastid, consisting of a 13 fluorescent reporters across a wide spectrum ranging from near UV to near infrared. The codon optimisation platform should also become a useful tool for future work on plastid manipulation, in Marchantia and beyond.

I worked with Jim Ajioka and Jonathan Openshaw on a science/arts collaborative project that came to be known as Syn City. The idea was to create dynamic, living sculptures using modified E. coli such that all the “paint” was living. Jonathan designed 3D printed structures of which we made moulds to cast Agar with an integrated 3D printed mesh skeleton. The modified bacteria could then be deposited on the structure, which developed colour over time. www.syncity.co.uk.

Dr Aytug Tuncel

I am applying the genome editing tools to generate novel, commercially or nutritionally valuable glucans in model crop species. The primary objective of my OpenPlant project is to generate potatoes that contain digestion-resistant starches with two major nutritional benefits: reduced calorie intake from consumption of chips, crisps and other potato-based foods and increased supply of complex carbohydrates to the microbiota of the lower gut that reduces risk of several diseases including colorectal cancer and type II diabetes.

More specifically, the project involves knocking out the gene(s) of starch branching enzymes I and/or II using crispr-CAS9 method thereby increasing the ratio of amylose to amylopectin (linear to branched starch chains) in tubers without significantly compromising the starch yield. The engineered starch will be less accessible to starch degrading enzymes, thus more resistant to digestion.

Dr Benjamin Lichman

Plants are incredible chemical factories, capable of producing a host of complex molecules that synthetic chemists struggle to produce. These compounds are produced by plants to interact with their environment, but they also have great significance for humans, as we use them for fragrances, agrichemicals and medicines. My general research interests are understanding how plants produce these valuable compounds, and how these pathways have evolved. This knowledge can then be used to produce natural products and novel chemicals in microbial or plant based platforms.

I am currently working with catnip and catmint (Nepeta cataria and N. mussinii), plants famous for their intoxicating effect on cats. The origin of this activity is the nepetalactones, a group of volatile compounds from the iridoid family of natural products. Along with their role as feline attractants, nepetalactones have also been reported to have both insect pheromone and insect repellent properties, in some cases having activities superior to DEET. The biosynthetic origin of these compounds is currently unknown. We have been using transcriptomics and proteomics to discover enzymes in the Nepeta nepetalactone biosynthesis pathway.

This work is being performed in the context of a wider chemical and genetic investigation into the mint family (Lamiaceae), a large plant family of economic importance in which Nepeta resides. I am working closely with the Mint Genome Project (funded by the NSF) to understand the evolution and regulation of natural product biosynthesis across the entire plant family. By placing newly discovered Nepeta enzymes in a detailed phylogenetic context we hope to understand the evolutionary origin of nepetalactone biosynthesis in Nepeta, and ultimately use it as a case-study for natural product evolution.

I am currently undertaking training in molecular evolution and phylogenetics with the aim of taking the principles of evolution into synthetic biology. I hope that this will reveal new methods of optimising and editing synthetic biology systems and devices.

Figure 1. Nepetalactone biosynthesis pathway in Nepeta. We are attempting to discover the enzymes that catalyse the formation of all different nepetalactone isomers. We are also attempting to understand how these enzymes have evolved. In the background is Nepeta mussinii.

Dr Eva Thuenemann

Plants can be used as a production platform for high-value products such as vaccines, enzymes and metabolites, thereby providing a potentially fast and cost-effective alternative to other cell culture techniques. Developed within the Lomonossoff group, HyperTrans (HT) is a technology for rapid, high-level transient expression of proteins in plants. One key application of HT in the Lomonossoff group has been the production of virus-like particles for use as vaccines, scaffolds for nanotechnology and in fundamental research of virus assembly.

Virus-like particles (VLPs) consist of viral structural proteins which assemble into a particle resembling the virus but devoid of the viral genome and therefore unable to replicate. Different VLPs consisting of multiple copies of one, two or four different structural proteins have been successfully produced using the HT system and shown to be morphologically and immunologically representative of the virus. In recent years, a number of emerging diseases have been caused by enveloped viruses such as Zika virus and Chikungunya virus. Such complex virus structures can make the development of efficient vaccines and diagnostic reagents difficult and costly. In my OpenPlant project, we are working on developing strategies for the production of enveloped VLPs in plants. I am also working on modifying a large non-enveloped VLP to allow accommodation of cargo proteins on the inside of the particle.

In addition to my research project, I was involved in the planning stages for the new John Innes Centre spin-out, Leaf Systems International Ltd, which opened on the Norwich Research Park in January 2017 and will enable translation of research to indsutry through scale-up of plant-based production of proteins and metabolites.

I have also participated in various outreach activities, such as a TV interview for regional news, the Great British Bioscience Festival, JIC’s Speed Science event as well as a work experience day for school children, amongst others.

Dr Michael Stephenson

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I am a chemist, with a background in natural product total synthesis, medicinal chemistry, and pharmacy. In the Osbourn group we are interested in plant secondary metabolites, and this places us at the very interface between biology and chemistry. I bring expertise in small organic molecule extraction, purification, and structural characterisation. This strengthens the group’s ability to functionally characterise biosynthetic enzymes; something which is important for many areas of research within the Osbourn lab. As such, I am involved in a number of different projects.

My main focus is on the application of transient expression in Nicotiana benthamiana towards the preparative production of high value triterpenes. I have been heavily involved in platform and method development, improving both the efficiency and scalability of procedures used within the group. I have also demonstrated the preparative utility of this platform by producing triterpenes on the gram scale.

As a medicinal chemist I am interested in applying these techniques to engineer chemical diversity, and to explore the structure activity relationships of bioactive triterpenes. I have been involved in isolating and characterising several novel triterpenes structures arising from co-expression of ‘un-natural’ combinations of biosynthetic enzymes. In addition, I have solved the structure of a number of novel and usual triterpene scaffolds, produced by oxidosqualene cyclases under investigation within the group. It would seem that despite the huge number of unique triterpene scaffolds already reported from many decades of natural product isolation, there is still a wealth of novel chemistry to be discovered, and that its discovery can be accelerated by utilising synergy between bioinformatives, synthetic biology, and chemistry.

In addition to my research, I also take a keen interest in public engagement. I have been involved in several outreach events where we attempt to present concepts in synthetic biology and chemistry in an assessable and ‘hands on’ way.    

Dr Ivan Reyna-Llorens

My research involves using synthetic biology and evolution for improving agricultural traits, more specifically to improve photosynthesis. As the world population continues to expand, it is predicted that crop yields will have to increase by 50% over the next 35 years. Traditional breeding programs cannot keep pace with this current population growth rate. Plant biomass is produced by carbon dioxide (CO2) fixed by the enzyme Rubisco during photosynthesis.

This process known as C3 photosynthesis can be very inefficient as Rubisco also interacts with Oxygen (O2) in a wasteful process known as photorespiration. In order to increase yields, photorespiration should be reduced considerably. Fortunately, some plants have evolved such mechanism already. C4 photosynthesis results from a series of anatomical and biochemical modifications in the leaf that lead to photosynthesis being compartmentalized between mesophyll and bundle sheath cells. This division of labour generates a CO2 enriched environment where photorespiration is effectively abolished. C4 plants therefore produce more yield and use water and nitrogen more efficiently. The fact that C4 photosynthesis has evolved independently in more than 60 lineages allows us to think it is possible to engineer C4 photosynthesis in C3 plants. In order to engineer this trait, cell specific genetic circuits need to be developed. Unfortunately there is a limited number of genetic parts driving cell specificity in leaves. My main objective in OpenPlant is to generate a library of leaf specific motifs that can be used to drive the expression of both nuclear and plastid encoded genes in specific compartments and specific cells of leaves.

Together with colleagues in the Department of Plant Sciences, Department of Chemistry and the Depart­ment of Physics I am part of an OpenPlant fund project that aims to use microfluidics for high-throughput analysis of genetic parts. We hope to generate a whole toolbox of parts that are useful to rewire different traits.