The role of the cellular economics in the expression of exogenous genes: Towards modularity in synthetic circuit design.

Lead Research Organisation: University of Surrey
Department Name: Microbial & Cellular Sciences

Abstract

One of the goals of synthetic biology is the design and construction of biological systems capable of performing logic computations, that is, to integrate environmental signals to produce desired outputs. This is a very important step towards further developments of the field, such as the construction of synthetic tissues and organs. To achieve that goal, it is required that engineering principles could be applied into biological systems. This proposal focuses in the principle of modularity as a rule of design in biology. Modularity will allow fast and reliable building of complex synthetic genetic circuits. Large circuits could be easily implemented as the sum of well-known modules that keep the same properties that they exhibit when they are isolated, as it happens in electronics. That is a big challenge for synthetic biologists as the modules are rarely independent from each other. This is mainly because all of them compete for the same pool of cellular resources for the expression of their constituent genes.
As a consequence in the limitations of the availability of resources, the cell can be envisioned as a molecular economical market where many genes compete simultaneously for the same transcriptional and translational machineries. These machineries catalyse, respectively, the synthesis of the RNA and the synthesis of the proteins that ultimately perform functions in the cell. The resources available for gene expression are not infinite and, therefore, depending on how the cellular resources are invested, some genes will benefit from larger fractions of the pool while some others will only have access to very small amounts. This asymmetric distribution or resources is consequently reflected in the different relative abundances of the proteins encoded by genes being expressed at the same time. This uneven distribution affects particularly the performance of artificial genetic circuits and, ultimately, compromise the notion of modularity.
In a comparison with computer science, the synthetic circuits would be the software of the system - a set of scripts designed to perform a function -, whereas the cell machinery would be the hardware needed to accomplish the instructions coded in the exogenous DNA. In this project we aim to identify modifications of the hardware increasing the processing capabilities of the cell so that more complex programs can be run using to that end the model system Escherichia coli. We will analyse in a test circuit the effect of modifications in genes involved in the synthesis and function of the RNA polymerase and ribosomes. We will use for this task a circuit that I developed and applied previously to determine the extent of competition in gene expression using fluorescent reporters. Once the relevant genes for resource allocation have been identified, we will develop strains optimized for circuit implementation. These newly evolved strains will be used to implement complex computations based on genetic circuits encoding transcriptional cascades, oscillators and multi-layered logic gates. To understand the behaviour of these complex systems we will generate mathematical models describing each of the circuits operating in conditions where the cell resources are limited. The models will be used to make predictions about circuit performance, and these predictions will be validated experimentally.
With the results of these investigations we aim to bypass the problem of poor circuit performance due to sharing of resources in the cell, a phenomenon that substantially limits the complexity of the circuits that can be built. In addition, we will test the limits of modular design in bacteria. Achieving modular construction of genetic networks will have a great impact in the way that we can design complex processes for making decisions in living organisms. It will help to transform synthetic biology into a real engineering discipline, paving the path for multiple biotechnological applications.

Technical Summary

In this proposal we aim to understand the mechanisms of allocation of transcriptional and translational resources in Escherichia coli looking to optimize the performance of synthetic genetic circuits. We hypothesize that the determinants of how those resources are invested are genetically encoded and, therefore, simple manipulations of the host can greatly improve the dynamic properties of synthetic circuits allowing complex computations.
We propose a combined experimental and theoretical approach where we will determine the role of genes controlling the production and activity of RNA polymerase and ribosomes in the levels of protein production that can be achieved in the cell. We will use to that end a test circuit that I developed previously and measures the coupling in the expression of two fluorescent reporters in single cells. We will test mutants displaying different allocation of resources and we will select those that show and improved capacity for protein production. Once this new strains are characterized, we will use them to implement larger circuits for complex cellular computations. We will first model the behaviour of known synthetic transcriptional cascades, oscillators and multi-layered logic gates under the different conditions given by the newly evolved economies of the selected hosts. We will use for that the parameters provided in the literature and we will add the reactions and conservation laws exclusive of our model. We will validate the theoretical predictions building the circuits and implementing them in the hosts endowed with the new properties. With these experiments we will investigate the limits of modularity in the design and construction of synthetic genetic circuits.
As a result of these investigations the major sources of unaccounted coupling in gene expression will be addressed in the design phase, greatly facilitating the task of engineering large biological networks.

Planned Impact

Economic Growth and Development

The Synthetic Biology Roadmap for UK highlights a recent assessment performed by BCC Research. It predicts an increase of one order of magnitude in a period of five years. By 2016 the market will be worth $10.8 bn and will continue growing. The rapid expansion takes place thanks in part to the identification of new niches to develop applications, but also because of technological breakthroughs that could significantly reduce the time and cost of implementation of engineered biological systems. This proposal aims to help keeping the pace of development of the field, filling the current gap in the design of modular synthetic genetic circuits by addressing the question of how resources required for gene expression are allocated in a cell. We envision a broad impact of our work benefiting distinct sectors of society.

Commercial exploitation and industrial partnership

Many biotechnological processes, ranging from large fermentation processes to cellular decision making in synthetic tissues, could be improved if accounting for the findings of the proposal. We will identify companies in the UK with interest in the topic for collaborative endeavours, several of which are accessible in the Surrey area. We have already made contact with the company ReBio (former TMO renewables) that is aware of the problematic issue of resource competition and could adapt our discoveries to its own specific applications in production of metabolites with added value from waste, mainly for synthesis of biopolymers. We expect to obtain results at different stages of the project with potential commercial interest that we will foster through the university technology transfer office. We will increase the impact of this work in industry under the umbrella of the EU program Horizon2020. Bacmine SL (Spain), a company specialized in the synthesis of genetic circuits for tailor made applications, is interested in the concepts detailed in the proposal and willing to test the strains produced.

Improvement to human health

Although the work does not aim to solve a health concern directly, it will improve health indirectly as many applications could be achieved in an affordable way. This research is likely to translate in larger numbers of molecules with pharmacological relevance produced at a lower cost, better synthesis of bioinspired devices and improved environmental quality control.

Public engagement in scientific issues

The development of the field of synthetic biology not only depends on the technical capabilities and scientific achievements. The perception of synthetic biology by society is critical for its success and we will make sure that the ethics and importance of the work are available for the general public, technical specialists and policy makers. The vision of the field highly depends on the implication and knowledge of the audience. For that reason, in this project we also aim to analyse whether all social groups involved share a common vision of the technology, its prospective risks and benefits, and the ethical boundaries that should be set for the targets of the field. We aim to collect sociological data from polls and interviews to assess the perception and elaborate communication strategies targeting different audiences.

Evidence based policy making

With this work we hope to accelerate the development of synthetic biology so that many applications become feasible in a short period of time. To ensure this, we expect a parallel contribution to policy making so that we can anticipate challenges regarding intellectual property of methods, applications and deliverables. In relationship with the previous section, with the public awareness of the approach we also expect to contribute to the implementation of policies according with the demands of society. With the visibility provided by this contribution we also hope to foster the investment in the field from both public and private sources.

Publications

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Jiménez JI (2017) Shedding light on the black box models of the cell. in Microbial biotechnology

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Qian Y (2017) Resource Competition Shapes the Response of Genetic Circuits. in ACS synthetic biology

 
Description In this project we have completed the assessment of the interplay between cell growth and the key resources required for gene expression in the model organism Escherichia coli. For this, we have used theoretical and experimental approaches and we now have a complete model of a cell that can be used to predict the impact of selective interventions in the gene expression machinery and determine strategies aimed at optimising the production of multiple proteins (e.g. as in a pathway) by a more efficient distribution of the resources required for their synthesis. This is a significant improvement compared to previous works, in which similar concepts had been proposed based on phenomenological observations. Our work provides mechanistic insights into the process and allows for direct interventions that could be useful in industrial biotechnology.

By comparing protein expression profiles in batch cultures and chemostats we now know that the capacity of a cell for gene expression is set by the carbon source used. Rich carbon sources allow for higher protein productions but also promote faster growth, which is detrimental for the expression of recombinant genes, circuits and pathways. This is due to the fact that cells that grow very fast invest most of their resources into making the machinery for continuing growing fast (rRNA and ribosomal proteins). Our results and models explain that lower growth on a rich carbon source allows to spend part of the resources, which would go into ribosomal synthesis during fast growth, into the synthesis of proteins of interest. In addition, during fast growth partial inhibition of transcription allows to increase the number of ribosomes per molecule of mRNA, therefore contributing to mitigate couplings in gene expression due to limited availability of the translational machinery.

In a following step we investigated what are the genes responsible for setting the capacity of the engine used for gene expression. This is determined by the total number of ribosomes and mRNAs. More specifically, it depends on the allocation of RNA polymerases to either mRNA or rRNA synthesis. We have conducted experiments in which part of the rRNAs of E. coli have been removed, and observed that even though total protein synthesis is limited, the cost of making a protein in these strains is lower, possibly due to the RNA polymerase not being limiting. These findings are part of a manuscript in preparation.

In addition, we have developed a new method to mitigate translational couplings between co-expressed genes. This method relies on the use of orthogonal ribosomes. These are ribosomes that can be allocated for the transcription of specific mRNAs due to the engineered complementarity between anticodon sequences in their 16S RNA and certain ribosome binding sites. This system as been further optimized to produce orthogonal ribosomes on demand thanks to a feedback controller, an idea imported from electrical engineering in which we are collaborating with researchers at Warwick University. By using these orthogonal ribosomes we have demonstrated that a partition in the pool of ribosomes can effectively decrease the cost of making proteins and we have demonstrated the potential biotechnological applications of these findings improving production yields of the drug violacein in E. coli. These results have been published in the journal Nature Communications and ACS Synthetic Biology.

We have also validated the case of competition for resources in a more complex genetic circuit composed of a cascade of two transcriptional activators. This has been carried out in collaboration with researchers at MIT and resulted in a publication in ACS Synthetic Biology.

Finally, we have used a method of random mutagenesis followed by high-throughput sequencing of mutants to identify the genes responsible for allocating resources required for protein synthesis. In parallel to this we have generated a model that predicts the cost of making any protein in bacterial cells with information obtained from transcriptomic data. The combination of these two techniques has resulted in the generation of a blueprint of the cost of each protein that is not essential under the culture conditions used. This blueprint is important because it can be used to design mutants with improved allocation of resources for recombinant protein production. These findings have been published in Nature Chemical Biology.
Exploitation Route We have produced a theoretical framework validated experimentally to derive couplings on gene expression due to basic rules. We believe this is significant conceptual advance with broad implications for the scientific community. We have started a collaboration with a company, Ingenza Ltd. with an interest of using our orthogonal ribosomes for different industrial applications.

In addition we have developed a set of methods that could be used for similar purposes in any microbial organism. They are currently being used by researchers developing bioprocesses such as industrial microbial fermentations. Our findings, combined with current state of the art molecular methods for gene editing will enable the generation of streamlined organisms for industrial processes on demand.
Sectors Agriculture, Food and Drink,Chemicals,Creative Economy,Energy,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Newton Advanced Fellowship (Mexico)
Amount £111,000 (GBP)
Funding ID NA160328 
Organisation Newton Fund 
Sector Public
Country United Kingdom
Start 03/2017 
End 03/2020
 
Description UGPN partnering awards
Amount £25,000 (GBP)
Organisation University of Surrey 
Sector Academic/University
Country United Kingdom
Start 09/2017 
End 08/2018
 
Title Orthogonal ribosomes 
Description Method to decrease protein costs by partitioning the pool of ribosomes available in the cell so that one fraction can be specifically allocated to mRNAs of interest. 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2018 
Provided To Others? Yes  
Impact Publication (Nature Communications) computational methods and experimental results publicly available. 
URL https://www.nature.com/articles/s41467-018-02898-6
 
Title Trans-coupling in bacterial gene expression 
Description We have established a method for quantification of the cost of gene expression in bacteria. This method is based on the determination of the intracellular concentration of two fluorescent reporters (one constitutive and one inducible). We have upgraded this system so that now can be used in any bacteria, either using a plasmid or chromosomal integration for delivery of the reporters. 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Provided To Others? No  
Impact We will make public this method in April, during a workshop in biotechnology of soil bacteria for plastic recycling. This workshop is organised under the H2020 project P4SB 'From plastic waste to plastic revenue using Pseudomonas putida synthetic biology' in which my laboratory is also involved. As a result we hope that the method will be implemented in other model organisms for determination of protein production costs. 
 
Title Repromin 
Description Model that integrates transcriptomic and proteomic data to quantify the theoretical size of the proteome produced by a microorganism. It allows to optimise strains that release proteome size that could be allocated for the recombinant production of proteins of interest. 
Type Of Material Computer model/algorithm 
Year Produced 2020 
Provided To Others? Yes  
Impact The method is described in Lastiri et al., 2020 Natural Chemical Biology (see my portfolio). It has been adopted by other researchers in order to improve bioprocesses such as industrial fermentations. 
URL https://www.nature.com/articles/s41589-020-0593-y
 
Title Trade-off model of gene expression and bacterial physiology 
Description Model developed by our collaborators Declan Bates and Alex Darlington (University of Warwick) capturing the differential allocation of resources for gene expression in bacterial cells in variety of culture conditions. My laboratory has conducted extensive validation of the model. 
Type Of Material Computer model/algorithm 
Year Produced 2018 
Provided To Others? Yes  
Impact The model is being used by other researchers in the field. We are currently upgrading it to include a more accurate description of metabolic processes. 
URL https://www.nature.com/articles/s41467-018-02898-6
 
Description Accurate metrology of RNA levels 
Organisation LGC Ltd
Country Global 
Sector Private 
PI Contribution We design experiments and produce samples later analysed by LGC.
Collaborator Contribution Jim Huggett's team at LGC has brough expertise and in kind goods (reagents, instruments, etc) to accurate measure changes in RNA levels during couplings in gene expression. Understanding the mechanistic determinants of these couplings at the molecular level is critical for the efficient design of genetic circuits. LGC is currently measuring changes in RNA levels with the highest possible accuracy using qPCR and dPCR.
Impact No outputs yet. Multidisciplinary between molecular metrology and synthetic biology.
Start Year 2016
 
Description Bacterial hedging (UNAM-Mexico) 
Organisation National Autonomous University of Mexico
Department Center For Genomics Sciences
Country Mexico 
Sector Academic/University 
PI Contribution Support designing CRISPR interference methods and development of molecular tools and reporter strains.
Collaborator Contribution Computational modelling and analysis of gene expression networks
Impact Grant awarded from the Newton fund (Advanced fellowship) to foster collaborations with Mexico (see further funding for details). Interdisciplinary between systems and synthetic biology. Publications: Lastiri-Pancardo G., Mercado-Hernandez J.S., Kim J., Jimenez J.I. and Utrilla J. A quantitative method for proteome reallocation using minimal regulatory interventions (2019). Under second review in Nature Chem. Biol. Preprint available at https://www.biorxiv.org/content/10.1101/733592v1 Kim J., Darlington A.P., Salvador M., Utrilla J. and Jimenez J.I. Trade-offs between gene expression, growth and phenotypic diversity in microbial populations (2020) Curr. Opin. Biotechnol. 62:29-37
Start Year 2017
 
Description Bioplastics 
Organisation University College Dublin
Department School of Biomolecular and Biomedical Science UCD
Country Ireland 
Sector Academic/University 
PI Contribution In this collaboration we are contributing with materials, mainly engineered strains, that are optimised for biotechnological purposes and tested at UCD for relevant applications.
Collaborator Contribution Our collaborators at UCD Dr Narancic and Prof. O'Connor are experts in bioplastics. They use different culture conditions and analytical methods to determine the polyhydrohyalkanoate and polyhydroxybutyrate production yields of the strains generated in my laboratory.
Impact This collaboration has resulted already in a publication in the journal Microbial Biotechnology (https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.13712).
Start Year 2019
 
Description Cascade (MIT) 
Organisation Massachusetts Institute of Technology
Department Department of Mechanical Engineering
Country United States 
Sector Academic/University 
PI Contribution Development of molecular tools and reporter strains.
Collaborator Contribution Mathematical modelling.
Impact Manuscript accepted in ACS Synthetic Biology: https://pubs.acs.org/doi/abs/10.1021/acssynbio.6b00361
Start Year 2015
 
Description NCSU - erythromycin 
Organisation North Carolina State University
Country United States 
Sector Academic/University 
PI Contribution Use of molecular and computational methods for improving erythromycin biosynthesis.
Collaborator Contribution Applications in biocatalysis including the biosynthesis of macrolide antibiotics. Implementation of analytical methods.
Impact No outputs produced yet.
Start Year 2017
 
Description Othogonal ribosomes 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution We are using the platform we have developed to determine protein costs associated to the translation performed by orthogonal ribosomes. We are also conducting the experimental validation of a mathematical trade-off model of the whole bacterial cell developed by our colleagues at Warwick.
Collaborator Contribution Colleagues at UEA have provided plasmid constructs encoding subunits of orthogonal ribosomes. Partners at Warwick have derived a computational model of the whole cell accounting for ribosomal partitions and their effect in couplings in protein production.
Impact Publications resulting from this collaboration: Kim J., Darlington A.P., Salvador M., Utrilla J. and Jimenez J.I. Trade-offs between gene expression, growth and phenotypic diversity in microbial populations (2020) Curr. Opin. Biotechnol. 62:29-37 Darlington A.P., Kim J., Jimenez J.I. and Bates D.G. Engineering translational allocation controllers: Mechanistic models, design guidelines, and potential biological implementations. (2018) ACS Synth. Biol. 7:2485-2496 Darlington A.P., Kim J., Jimenez J.I. and Bates D.G. Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. (2018) Nature Comm. 9:695
Start Year 2016
 
Description Othogonal ribosomes 
Organisation University of Warwick
Department School of Life Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We are using the platform we have developed to determine protein costs associated to the translation performed by orthogonal ribosomes. We are also conducting the experimental validation of a mathematical trade-off model of the whole bacterial cell developed by our colleagues at Warwick.
Collaborator Contribution Colleagues at UEA have provided plasmid constructs encoding subunits of orthogonal ribosomes. Partners at Warwick have derived a computational model of the whole cell accounting for ribosomal partitions and their effect in couplings in protein production.
Impact Publications resulting from this collaboration: Kim J., Darlington A.P., Salvador M., Utrilla J. and Jimenez J.I. Trade-offs between gene expression, growth and phenotypic diversity in microbial populations (2020) Curr. Opin. Biotechnol. 62:29-37 Darlington A.P., Kim J., Jimenez J.I. and Bates D.G. Engineering translational allocation controllers: Mechanistic models, design guidelines, and potential biological implementations. (2018) ACS Synth. Biol. 7:2485-2496 Darlington A.P., Kim J., Jimenez J.I. and Bates D.G. Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. (2018) Nature Comm. 9:695
Start Year 2016
 
Description Ribosomal inheritance at the single cell level 
Organisation National Physical Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution Produce genetic constructs labelling ribosomes with fluorescent reporters.
Collaborator Contribution Provide expertise in single cell imaging in flow cells and image integration. Computational models to study inheritance of cell traits (cell cycle duration, size, number of ribosomes).
Impact None yet. Physics, Systems Biology, Synthetic Biology, Microbiology
Start Year 2017
 
Description Ribosomal inheritance at the single cell level 
Organisation University of Surrey
Department Institute of Sound Recording
Country United Kingdom 
Sector Academic/University 
PI Contribution Produce genetic constructs labelling ribosomes with fluorescent reporters.
Collaborator Contribution Provide expertise in single cell imaging in flow cells and image integration. Computational models to study inheritance of cell traits (cell cycle duration, size, number of ribosomes).
Impact None yet. Physics, Systems Biology, Synthetic Biology, Microbiology
Start Year 2017
 
Description 5th UK-Corea Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Near 50 delegates from the UK and Korea attended a symposium to foster collaborations. As a result of the presentation there was active discussion and I stablished links with a Korean institute interested in my research. In addition, this facilitated the exchange of ideas with the CEO of a UK-based SME an we are currently working together in a grant proposal for antibody engineering.
Year(s) Of Engagement Activity 2015
 
Description CNB-KRIBB Symposium on Microbial Cell Factories 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to an event aimed at fostering collaborations between the Spanish National Centre for Biotechnology and KRIBB a Corean research institute. There were near 100 participants all of them researchers at different stages. The presentation had a good reception and as a consequence I was invited to take part in an European consortium that resulted in the submission of a grant application currently under review.
Year(s) Of Engagement Activity 2015
 
Description Complex Systems - Aston 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Invited seminar to discuss modelling approaches and experimental work in complex systems. Extensive discussion at the end about potential collaborations.
Year(s) Of Engagement Activity 2017
 
Description Conference SBUK2017 Manchester 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We presented a poster and a short oral talk at SBUK2017 held in Manchester. This is the largest conference in the UK specific for Synthetic Biology. Resulting from this activity we got requests for further information from policymakers, collaborations from academics and support from other researchers to follow-up this research. We also received numerous requests of UG and PGR students to join the laboratory.
Year(s) Of Engagement Activity 2017
URL http://synbiochem.co.uk/uncategorised/synthetic-biology-uk-2017/
 
Description Edinburgh 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Keynote talk for the Institute of Quantitative Biology, Biochemistry & Biotechnology (IQB3) organised by the PhD students and postdocs in the institute. 50 academics and postgraduate researchers attended. This was a day visit that involved 1 to 1 discussions with several students and group leaders. Different opportunities for collaboration were discussed.
Year(s) Of Engagement Activity 2020
 
Description Gordon Research Conference in Synthetic Biology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited as a keynote speaker to the Gordon Research Conference in Synthetic Biology 2019 taking place in New Hampshire (USA). The talk was well received and led to discussion and follow-up interactions with researchers in the field. I was also approached by the editor of a journal that is currently assessing one of the manuscripts in which my lab has been involved.
Year(s) Of Engagement Activity 2019
URL https://www.grc.org/synthetic-biology-conference/2019
 
Description Imperial College 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I was invited to give a seminar for the Bioengineering Dpt at Imperial College. The audience were academics exclusively. Opportunities for collaboration resulted from the discussion.
Year(s) Of Engagement Activity 2017
 
Description Industry day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation for industrial partners collaborating in taught postgraduate programmes at Imperial College. The day involved discussions with industrial researchers to explore future collaborations.
Year(s) Of Engagement Activity 2020
 
Description Ingenza 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact Visit to the company Ingenza (Edinburgh) to give a presentation on research relevant for the company. This was a day visit involving conversations to the different departmental leads.
Year(s) Of Engagement Activity 2019
 
Description Keynote talk at the International Workshop on Control Engineering and Synthetic Biology (UK) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to give a keynote presentation at the Control Engineering and Synthetic Biology conference that took place at the University of Oxford in September 2019. The conference had nearly 200 attendees and there was stimulating discussion after the presentation.
Year(s) Of Engagement Activity 2019
URL http://sysos.eng.ox.ac.uk/wiki/index.php/SynBioControl2019
 
Description Promotion of research activities in social media 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Our research activities are periodically highlighted in the Facebook and Twitter accounts of the laboratory. We use them for outreach and engagement with the general public, but we have noticed our updates are also very popular among undergraduate and college students. Since we have started doing this we have experience a significant increase in the applications received from undergraduates and college students to conduct final year projects, PhDs and placements in the lab.
Year(s) Of Engagement Activity 2015,2016
 
Description SB7.0 conference Singapore 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact PDRA Juhyun Kim presented research outcomes in the international conference SB7.0 held in Singapore. This is one of the largest and most prestigious conferences in the field with near 1,000 attendees from all over the world.
Year(s) Of Engagement Activity 2017
URL http://sb7.info
 
Description Seminar Bellerbys Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Seminar to secondary school students to foster the interest in Synthetic Biology.
Year(s) Of Engagement Activity 2018
 
Description Seminar Dpt. Bioengineering Imperial College London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Seminar in the Dpt. of Bioengineering of Imperial College London. 30-40 academics attended and sparked questions and follow-up interactions which may result in future collaborations with other experts in the area, mainly theoretical scientists.
Year(s) Of Engagement Activity 2017
 
Description Seminar Natural History Museum 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I was invited to give a seminar by colleagues at the Dpt. of Life Sciences at NHM. The talk was well-attended and there was stimulating discussion in the Q&A session. The feedback from several of the attendees (to the organisers) was good and there has been a follow-up trying to engage in a collaboration.
Year(s) Of Engagement Activity 2018
 
Description Seminar at Bellerbys Cambridge 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Invited seminar for high school students at Bellerbys Cambridge. Students were very engaged and asked many questions. Some got interested and requested further info for potential internships in academic labs with related interests. I was requested to participate again for another branch of the same school.
Year(s) Of Engagement Activity 2017
 
Description Seminar for Bellerbys Brighton 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Following up a previous successful interaction with Bellerbys I was asked to repeat the presentation for another branch of the high school (Brighton) visiting Surrey. Students were again engaged with the talk and we also had a stimulating discussion.
Year(s) Of Engagement Activity 2018
 
Description Seminar to Life Sciences Dpt (Imperial College) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Seminar given to the Dpt of Life Science of Imperial College London. Most of the attendees were faculty members and there was a number of PhD students and postdoctoral researcher. The seminar was well received and since then there have been conversations about future collaborations.
Year(s) Of Engagement Activity 2019
 
Description Seminar to UNAM - Mexico 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Online presentation to the 'Centro de Ciencias Genómicas' at UNAM. The seminar was attended by mainly academics and postgraduate researchers and included discussion. The seminar was the result of an ongoing collaboration with researchers in that institute.
Year(s) Of Engagement Activity 2020
 
Description Synthetic Biology 2016 (Edinburgh) - Juhyun 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited presentation of team member Juhyun Kim in the SB-UK 2016 conference (Edinburgh). November.
Year(s) Of Engagement Activity 2016
URL https://www.biochemistry.org/Events/tabid/379/MeetingNo/SA186/view/Conference/Default.aspx
 
Description Synthetic Biology Congress UK 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invitation as keynote speaker in a conference organised in London. There was extensive discussion in the Q&A section at the end and during the rest of the conference, specially with colleagues in the US.
Year(s) Of Engagement Activity 2018
URL https://www.oxfordglobal.co.uk/syntheticbiology-congress/
 
Description UCL Synthetic Biology showcase 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to present research in this project in the Synthetic Biology showcase workshop organised by UCL. There were numerous questions and allowed to establish links with developers of molecular methods for orthogonal translation.
Year(s) Of Engagement Activity 2017
URL https://www.ucl.ac.uk/biosciences/biosciences-events-publication/2016-2017/synthetic-biology-showcas...
 
Description UCL seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Seminar for the Biochemical Engineering Dpt at UCL.
Year(s) Of Engagement Activity 2016
 
Description UK-Argentina workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Near 100 delegates from UK and Argentina took part in this event. There was very active discussion and as a result I was invited to give similar seminars in other institutions. The presentation was highlighted in social media including the twitter account of Technology Transfer Network.
Year(s) Of Engagement Activity 2015
 
Description Warwick seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Seminar to the School of Biological Sciences at the University of Warwick.
Year(s) Of Engagement Activity 2016
 
Description Warwick visit and seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I was invited to give a presentation at the Warwick Integrative Synthetic Biology Centre. In the seminar room there was a mixed audience of near 50 established academics, post and undergraduate researchers that showed interest in my research and provided me with helpful feedback. I also had the chance to visit the facilities of the institute and meet with some of its members. Since this event took place I have exchanged ideas with some of the academics with the intention of starting collaborations. In addition, I have also been invited to the official launch of the institute taking place in April.
Year(s) Of Engagement Activity 2016