I completed my Ph.D in Biochemistry in 2016 at the University of Cambridge, under the guidance of Professor Christopher Howe and Dr Andrew Spicer of Algenuity. Together with collaborators, the Howe lab has pioneered the development of biological solar cells, which are able to produce current as a result of photosynthetic activity in cyanobacteria. I then joined Professor Patricia Harvey’s laboratory to work on the D-factory project, which aims to set up a sustainable CO2 algal biorefinary utilizing the algae Dunaliella. While there I also contributed to a European Commission report ‘food from the oceans’ as part of a high level group of scientific advisors. I have now returned to Chris Howe’s lab as part of the OpenPlant Project. The goal of this project is to create an overexpression system for transgenes that is sensitive to changed in electropotential.
Dr Zhenhua Liu
It has been estimated that plants can produce over 1 million specialized metabolites, but we know less than 0.1 % of their biosynthetic pathways. Creative methods are eminently needed to look under the iceberg of largely untapped biosynthetic pathways. As a post-doc from Anne Osbourn group at John Innes Centre, I am employing multidisciplinary approaches across bioinformatics, genetics, and chemistry, to comprehensively understand how and why plants produce this hallmark of specialized metabolites.
I am currently focusing on plants from the Brassicaceae family and systematically studying the function, evolution and biosynthesis of triterpenes from this family. I am in particular interested in pathways encoded by gene clusters. It holds great potential to mine more and novel biosynthetic pathways efficiently. However, how and why plants have evolved BGCs is still a mystery. We are aiming to gain the first understanding of their assembly, patterns of evolution and common features in a systematic fashion. This knowledge can then be used as a template guiding the research of BGCs in other types of compounds and plant families.
Figure legend: Multidisciplinary approaches to discover new pathways and novel natural compounds. We are using combination of bioinformatics, genetics and chemistry in attempt to decode and recode the largely untapped plant specialized metabolism
Dr Ingo Appelhagen
I am a molecular biologist, with a background in plant transcription factors, flavonoid biosynthesis, natural colours and metabolic engineering.
In Cathie Martin’s lab at the John Innes Centre, we have recently developed novel suspension cultures from engineered tobacco plants, to obtain stable sources of natural colourants. These cultures can produce exceptionally high levels of red to purple anthocyanin pigments, and allow a scalable constitutive year-around production under controlled conditions.
Intense blue colours are rare in nature and difficult to reproduce in pigment formulations, which is the main reason why almost all blue food colourants are synthetic dyes. Our project aims to investigate the structural properties of anthocyanin preparations that confer strong and stable blue colours and to select for anthocyanins with improved stability as reliable natural colourants. Our goal is to extend our plant cell culture approach to develop the first production platform for blue anthocyanin colourants, to replace synthetic food dyes.
Dr Gonzalo Mendoza
I obtained my PhD in Cell Biology from the University of Edinburgh, mentored by Prof. Jean D Beggs. During this time, I was interested in the spliceosome cycle, in the connection between splicing and transcription, and also in how proofreading factors help to prevent error in splicing. I spent a significant amount of time using the auxin-inducible degron to conditionally deplete essential proteins, and finding ways to improve this depletion system to get a faster and more tightly-controlled response.
My desire to embark on plant synthetic biology, while maintaining an interested in splicing and conditional expression systems, lead me to join the Plant Metabolism Group of Prof. Alison Smith in October 2017, to develop riboswitches as molecular tools to control transgene expression in algae, higher plants and other eukaryotes. The ultimate aim of this project is to develop novel inducible systems for metabolic engineering applications or as in vivo sensors of metabolites.
Mr Mihails Delmans
Mihails is a PhD student in the Haseloff Lab, with an Engineering background as an undegraduate. His research topic is the regulation of cell proliferation in Marchantia gemmae. In collaboration with Bernardo Pollak, he has developed an open source gene-centric database platform for managing genome data and synthetic DNA parts for Marchantia. He maintains a strong interest in enginnering approaches to biological problems, and explots his considerable expertise with electronics, optics and 3D printing to build and modify instrumentation for observing Marchantia cell dynamics.
His PhD research combines the construction of new marker genes, expression in Marchantia gemma, quantitative imaging and software analysis in order to map the dynamics of growth in gemmae. He has found evidence of long distance control of cell proliferation which can be deregulated by surgical manipulations.
Dr Philip Carella
I recently completed my PhD in Dr. Robin Cameron’s lab (McMaster University, Canada), where I studied phloem-mediated long-distance immune signalling induced by a bacterial pathogen in Arabidopsis thaliana. Feeling a need to branch out a little, I joined Dr. Sebastian Schornack’s group (Sainsbury Laboratory, University of Cambridge, UK) to study interactions between filamentous microbes and non-vascular early land plants. Our goal is to identify core developmental processes required for the colonization of early land plant tissues by filamentous microbes and to understand how these processes evolved into the defense and symbiotic programs employed by higher plants. Our work will generate transcriptomics data, fluorescent marker lines and microbe inducible promoters for cell biology, and other molecular-genetic tools that will enable the OpenPlant community to explore early land plant biology.
Dr Henry Temple
Dr Bruno Martins
I am a post-doctoral researcher in James Locke's group at the Sainsbury laboratory. I am interested in how cells discriminate between different environmental states, integrate dynamic outputs from different gene circuits, and make decisions. In my current research, I use a combination of theory and time-lapse microscopy experiments to understand the dynamical coupling of the cyanobacterial circadian clock to other networks, in both endogenous and synthetic systems.
Circadian clocks are a class of networks that regulate rhythmic expression in response to daily cycles of sunlight. A large fraction of all genes in the cyanobacterium Synechococcus elongatus are clearly under circadian control. Recently, I studied the coupling of the clock to a circuit that controls expression of the gene psbAI. Genes regulated by the clock typically peak once a day, either at dawn or at dusk. However, under conditions of constant low light, I observed a doubling of the frequency of expression of psbAI, i.e., its expression peaks twice a day. Using genetic and environmental perturbations, I found these dynamics can be modulated: either single-peak or two-peak expression can be generated. Using an iteration of modelling and experiments, I then determined the network design principles underlying the dynamics of frequency doubling.
In electronics, clock signals are essential elements of complex circuits, allowing different components of the circuit to be linked and synchronised. In biology, clocks likely play a similar role. Rational designing of oscillators has been a pursuit of synthetic biology since its inception, but evolution has already endowed natural systems with extremely reliable and robust oscillators in the form of circadian clocks. If we can understand how to harness clocks to generate specific (non-circadian) frequencies, and how to systematically integrate clocks with other pathways, we could gain a powerful tool to enable the construction of more complex synthetic circuits.
Before coming to Cambridge, I did a PhD in Peter Swain's lab at the University of Edinburgh. In my PhD I used mathematical modelling to gain insight into two simple, yet ubiquitous, sensing and transductions mechanisms: allosteric sensing and phosphorylation-dephosphorylation cycles. I studied the input-output dynamics of these mechanisms in terms of the fundamental constraints inherent in their design.
Dr Lukas Müller
I’m interested in the circadian clock and its effect on physiological and agricultural performance in plants. In the OpenPlant project I am investigating the circadian clock in Marchantia polymorpha and analyze the regulation of clock behavior and outputs in this relative of early land plants. In particular, I am focusing on the primary metabolism as an excellent proxy for systemic processes and vegetative growth.
I apply fluorescent imaging tools with computational time-lapse analysis to obtain cell-specific read-outs for the whole plant in real-time. This data is intended to set the stage for both physiological engineering and systems biology approaches.
Part of my project is to engineer fluorescent proteins that are standardised and improved reporters for dynamic changes in gene expression.
Dr Eftychis Frangedakis
Eftychis did his PhD at Oxford University focusing on the evolution of developmental mechanisms in land plants. During his doctoral research he developed a strong interest and fascination for bryophytes. He then moved to the University of Tokyo to work with the least studied group of bryophytes, hornworts. After a short detour in Hong Kong he is now back to the UK working on the development of new synthetic biology tools in Marchantia.
Dr Francisco Navarro
Francisco J. Navarro's work focuses on the function of small RNA (sRNA) molecules and their use as regulatory elements in synthetic gene circuits. sRNA molecules most likely evolved as a defense mechanism against viruses and retro-transposons, and were co-opted for fine-tuning of gene expression. Their small size and predictable targeting rules make them perfect tools for regulating gene expression in synthetic gene circuits. This project is carried out in the green alga Chlamydomonas reinhardtii, which is amenable to genetic manipulation and a model organism for key plant processes, such as photosynthesis. With an sRNA pathway that resembles that of higher plants, Chlamydomonas allows the testing of proof-of-principle small RNA-based genetic devices before extrapolating to other plant species.
Francisco completed his PhD in the laboratory of Prof. Jose Manuel Siverio (University of La Laguna, Spain), studying nitrate assimilation in Hansenula polymorpha, a methylotrophic yeast with important biotechnological applications. This was followed by a postdoc in the laboratory of Sir Paul Nurse, first at The Rockefeller University, USA, and then at the London Research Institute, on cell size control and regulation of gene expression by RNA-binding proteins. Through systematic screening of a gene deletion collection of the fission yeast Schizosaccharomyces pombe, he identified a set of novel genes involved in the coordination between cell growth and cell cycle progression. In 2015, he joined the laboratory of Sir David Baulcombe in the Department of Plant Sciences, University of Cambridge.
Francisco’s research interests concern questions regarding global regulation of gene expression and limits of cell growth. These questions are relevant to synthetic biology because synthetic gene circuits are embedded into the cell’s own gene network, and so their activities are not insulated from global cell regulation. He believes that microorganisms, like Chlamydomonas, will continue to be useful research models to uncover new exciting biology, and contribute to the advancement of synthetic biology. The fast growth of unicellular algae, in addition to a range of recently developed tools and resources, are making these organisms an interesting chassis for synthetic biology, with industrial applications in the biopharming sector.
He is also a collaborator of Café Synthetique, an informal monthly meetup with public talks that brings together the Cambridge synthetic biology community
Dr Noam Chayut
I am interested in the interface between applied plant breeding and plant metabolism. In my master’s thesis we used classical breeding of passionfruit with the goal of releasing new varieties, now used by farmers. In my PhD thesis we studied carotenoid metabolism in melons and established a molecular marker now used routinely by melon breeders. More importantly, we suggested a novel non-transgenic path toward pro-vitamin A carotenoid biofortification of food crops. The objective of the current OpenPlant project is to develop pre-breeding lines of beetroot for the production of L-DOPA.
L-DOPA is used to treat Parkinson’s symptoms; however, the current costs of chemical synthesis make it unavailable for deprived populations worldwide. In addition, there is a growing demand for ‘natural’ or plant sourced pharmaceutical substances in the first world. L- DOPA, a product of tyrosine hydroxylation, is an intermediate metabolite in biosynthesis of violet and yellow betalain pigments, in Beta vulgaris (table beet). L-DOPA natural steady state levels are very low, usually undetectable. We intend to block the turnover of L-Dopa in beetroot to allow its accumulation to levels that could enable low-tech accessible production in a plant system.
Current data indicate two betalain metabolic genes that, if repressed, may boost L-Dopa accumulation. Therefore, we aim to inhibit the activity of L-DOPA-dioxygenase, and L-DOPA-cyclase in beetroot. Currently, as proof of concept, we silence both genes in hairy roots system. We adopted three complementary strategies to meet the overarching objective of L-DOPA production in beet: a) Classical genetics; b) targeted genetic mutagenesis; and c) random mutagenesis. Yellow beet, mutated in L-DOPA-cyclase exists and can be crossed with “blotchy” red beet, which probably has lower L-DOPA-dioxygenase activity. Impairing L-DOPA-dioxygenase activity in yellow beet is carried out by both the targeted mutagenesis technology CRISPR/Cas9 and the random, yet more assured, EMS mutagenesis approach.
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
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
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.