University of Cambridge

Dr Stephen Rowden

profile-Stephen.jpg

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 Gonzalo Mendoza

Gonzalo.png

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

P1010114.jpg

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 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

Lukas Portrait-1-2.jpg

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

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

LinkedIn | Twitter

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

LinkedIn | Twitter

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 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.

Dr Thomas Meany

I am jointly hosted by the labs of Lisa Hall (Chemical Engineering and Biotechnology) and Jim Haseloff (Plant Science) as an interdisciplinary fellow part funded through OpenPlant. My background training is as a physicist, with a specific emphasis on optics and microfabrication. I undertook a PhD in Macquarie University (Sydney, Australia) where I developed microphotonic circuits using a 3D laser printing technique. My postdoctoral research continued in Toshiba’s Cambridge Research Labs where I worked on advanced manufacturing techniques for semiconductor quantum dots.

As a part of OpenPlant I am passionate about using optical analytical tools to study the production of secondary metabolites in specialised plant tissues. Specifically, the oil bodies of the Liverwort, Marchantia polymorpha, are potentially rich reservoirs of bio-active compounds. Using Raman microscopy, a label-free, non-destructive spectroscopy technique it is possible to study metabolic processes in real-time. As this is non-destructive it can be performed in situ and therefore both spatial and temporal information can be obtained. My hope is to correlate this data with information available using other approaches such as Matrix Assisted Laser Deposition Ionisation Mass Spectroscopy (MALDI), Gas Chromatography Mass Spectrometry (GC-MS), fluorescence microscopy and other high resolution analytical approaches. In future this could be then adapted to studies of transgenic plant species as an additional tool to study metabolic pathways. Additional model species can also be explored, for instance Nicotiana benthamiana, and potentially crop plants. I am keen to engage with teams operating in the area of natural product chemistry, metabolic engineering or teams focused on alternative analytical approaches.

Photo: Prototype microfluidic rapid 3D printed circuit fabricated during the Bio-Hackathon.

Photo: Prototype microfluidic rapid 3D printed circuit fabricated during the Bio-Hackathon.

Working with the Cambridge University Technology and Enterprise club (CUTEC), I organised the UK’s first Bio-Hackathon, hosted in the Department of Plant Science (Cambridge) during the week of 21-25 June 2016. This was possible with thanks, in part, to a grant provided by the University of Cambridge Synthetic Biology Strategic Research Initiative. This event brought together a diverse interdisciplinary group of 50 participants from across the UK and the world. Teams focused on “bioware” by incorporating hardware, software and wet lab tools. One team developed a 3D printed microfluidic prototyping tool, another built a comparison software tool for DNA synthesis pricing. The winning team built a tool called “Alpha-Brick” which is a drag and drop tool for assembling bio-bricks and plugs directly into Transcriptic (a cloud laboratory) allowing immediate order of an assembled part.

Mr Bernardo Pollak 

Bernardo Pollak is a 4th year PhD candidate at the University of Cambridge in Prof. Haseloff’s laboratory. As part of his PhD, he has been developing DNA assembly systems, methods for quantitative characterisation of gene expression and tools for precise manipulation of gene expression for engineering of morphogenesis in Marchantia.

Before joining the Haseloff group, he obtained his undergrad degree in Biochemistry after coursing one year of Civil Engineering in Pontificia Universidad Católica de Chile. During his undergrad thesis, he gathered support and led the first team from Chile to participate in iGEM in 2012. He has been interested in marine luminescent bacteria, isolating environmental strains and performing directed evolution experiments to obtain optimised lux reporters. As part of his luminescence work, he produced a bioluminescent dress featured in Wired as part of a collaboration with Anton Kan, former member of the Haseloff lab, and Victoria Geany from the Royal College of Arts.