Ellis:Research

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Latest Update: Dec 2014


Research in the Ellis Lab focuses on advancing our understanding of nature through genome engineering and accelerating biotechnology through the use of synthetic biology. Projects are either foundational work, applied work or a nice mix of both.

Current Projects

Synthetic Yeast Chromosome XI
Project Type: Foundational and Applied
Project Members: Ben Blount, Rob McKiernan, Maureen Driessen, Dejana Jovicevic
Collaborators: Jef Boeke (NYU), Yizhi Cai & Al Elfick (Edinburgh), Steve Oliver (Cam), Paul Freemont, Sc2.0 Consortium
Sc2.0 is a high-profile, international project to do the first full synthesis of a eukaryotic cell genome, the model yeast species Saccharomyces cerevisiae. Led by Prof Jef Boeke at NYU, USA, an international consortium is now established to re-synthesis and make to design changes to all 16 yeast chromosomes. Our group is leading the UK effort in the consortium, aiming to design, synthesise and assemble the complete 666 kbp chromosome XI. During construction we will investigate genome design and topological effects such as nuclear structures and how these can be used to optimise gene expression in metabolic engineering.

Synthetic Biology with engineered modular regulation
Project Type: Foundational and Applied
Project Members: Ben Blount, Tim Weenink, Robert Chen
TAL effectors and CRISPRi are a relatively new forms of DNA-binding protein that have a programmable DNA-recognition code. This means that they can be re-engineered repeatedly to bind to custom DNA sequences. We have now shown that modular TAL-effectors can be customised to be orthogonal repressors (TALORS) for yeast promoters - effectively acting as independent wires in logic systems. This offers a route to scalable logic systems in yeast synthetic biology. We are now looking to improve on this technology to generate a range of custom-built transcription factors which we can apply to advanced logic networks such as oscillators and memory systems.

Investigating device-chassis interactions
Project Type: Foundational
Project Members: Francesa Ceroni, Olivier Borkowski, Arinbjorn Kolbeinsson
Collaborators: Guy-Bart Stan, Rhys Algar, Richard Murray (Caltech)
Most gene devices demonstrated in synthetic biology have been high-expression strength regulatory networks hosted on mid-to-high copy number plasmids in E.coli. Despite being relatively simple and small, these devices are thought to be close to the maximum tolerated by the host cell - if they were any larger they would impinge on the host cell's own mechanisms. In this project, we are trying to quantify the threshold for gene device cloning into the E.coli chassis by examining a standard synthetic networks expressed at a variety of different strengths in plasmid systems of varying copy number. The intention is to define a quantitative standard for inserting gene devices into chassis cells and build a predictive model to aid future design of cells with predictable growth rates.

Combinatorial modular assembly of gene networks and pathways
Project Type: Foundational and Applied
Project Members: Arturo Casini, Ali Raza Awan, Carlos Bricio, Simon Arsene
Collaborators: Geoff Baldwin, Sphere Fluidics
The availability of gene synthesis is increasing rapidly, yet there is no straightforward lab-bench method to arrange modular gene units into larger assemblies with pre-defined positions. In this project we will demonstrate a new method to rapidly assemble gene units in a pre-defined order and showcase the technique to combinatorially assemble diverse synthesis pathways and gene regulatory networks using standardized parts. As well as demonstrating a rapid new assembly technique, the project will yield synthetic cells with high production of high-value therapeutic molecules which can be screened with interesting new microfluidic technologies.

Engineering thermophilic synthetic biology
Project Type: Foundational and Applied
Project Members: Elena Martinez-Klimova, Ben Reeve, Alex Esin
Collaborators: David Leak, Tobias Warnecke
Engineering new function into well-characterised cells is one of the major goals of synthetic biology, but one phenotype almost impossible to add to cells like E.coli is thermostability. Instead, our lab is kick-starting synthetic biology in a Geobacillus species thermophile by developing standard measurement protocols with aerobic and anaerobic fluorescent proteins and charactersing libraries of standard, synthetic parts. We will use these to improve and diversify existing biofuel production pathways to generate high-yields and new products.

Engineering materials from bacteria
Project Type: Applied
Project Members: Ben Reeve, Michael Florea, Charlie Gilbert, Olivier Borkowski
Collaborators: Textiles Futures Research Centre
The materials of the future will be manufactured by biology put programmed by synthetic biology to have diverse functions. We are working with bacteria that overproduce carbohydrate material polymers and functionalising this material as it is made in order to give it new properties. We are also working on programming the polymerisation of protein-based materials with enzymatic and sensing functions built in.

Pattern Formation
Project Type: Foundational
Project Members: Georgios Pothoulakis
Collaborators: The Leverhulme Trust
Differentiation of genetically-equivalent cells allows single-cell cultures to diversify into patterns or achieve division of labour for tasks. In lab yeast, we are adding genes from ancestral strains that grow in a filamentous form when stressed and placing these under control of tunable, inducible promoters so that we can switch yeast colony growth from standard to branched fractal patterns.

Therapeutic Synthetic Biology
Project Type: Applied
Project Members: Will Shaw, Marios Koutsakos, Despoina Paschou
Collaborators: Sophie Helaine, AstraZeneca
shhh... these are secret projects ;)

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