Improved large serine integrases for Synthetic Biology
Lead Research Organisation:
University of Glasgow
Department Name: College of Medical, Veterinary, Life Sci
Abstract
Studentship strategic priority area:Synthetic Biology
Keywords:Biocomputing, memory, switches, site-specific recombination, microfluidics
Large serine integrases are used to build biological computing systems that can process information, record the order of signals, and count events in living cells. These biocomputing systems take advantage of the directionality of large serine integrases to store binary information in the form of 1s and 0s in the sequence of DNA. Many of the integrases that we have tested display less than ideal levels of directionality. This PhD project will use directed evolution approaches to generate an orthogonal set of recombinases with improved directionality. This set of optimized recombinases will then be linked together to create binary counters that will count to larger numbers, paving the way to practical uses. In association with Julien Reboud from the School of Engineering, microfluidics devices will be built that allow exquisitely controlled delivery of chemical signals. These will be used to characterise responses of counters at the single cell level.
Ada Scarrott will first get a thorough grounding in modern techniques in Molecular Biology and Synthetic Biology, creating libraries of mutants in integrase and its gp3. She will select mutants from these libraries that have improved directionality. This will lead to new techniques for isolating previously unknown recombination directionality factors (proteins that switch the directionality of integrases). This will add new orthogonal integrase-RDF pairs to our toolkit and increase the data storage potential of these systems. Ada will then learn techniques for culturing and monitoring cells in microfluidic systems so that the behaviour of recombinase based biological switches can be monitored in real time.
The outcome of this studentship will be improved tools for biological computing, memory and recording events, as well as improved microfluidic methods for monitoring bacterial responses to changes in conditions.
Keywords:Biocomputing, memory, switches, site-specific recombination, microfluidics
Large serine integrases are used to build biological computing systems that can process information, record the order of signals, and count events in living cells. These biocomputing systems take advantage of the directionality of large serine integrases to store binary information in the form of 1s and 0s in the sequence of DNA. Many of the integrases that we have tested display less than ideal levels of directionality. This PhD project will use directed evolution approaches to generate an orthogonal set of recombinases with improved directionality. This set of optimized recombinases will then be linked together to create binary counters that will count to larger numbers, paving the way to practical uses. In association with Julien Reboud from the School of Engineering, microfluidics devices will be built that allow exquisitely controlled delivery of chemical signals. These will be used to characterise responses of counters at the single cell level.
Ada Scarrott will first get a thorough grounding in modern techniques in Molecular Biology and Synthetic Biology, creating libraries of mutants in integrase and its gp3. She will select mutants from these libraries that have improved directionality. This will lead to new techniques for isolating previously unknown recombination directionality factors (proteins that switch the directionality of integrases). This will add new orthogonal integrase-RDF pairs to our toolkit and increase the data storage potential of these systems. Ada will then learn techniques for culturing and monitoring cells in microfluidic systems so that the behaviour of recombinase based biological switches can be monitored in real time.
The outcome of this studentship will be improved tools for biological computing, memory and recording events, as well as improved microfluidic methods for monitoring bacterial responses to changes in conditions.
Organisations
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| EP/N509668/1 | 01/10/2016 | 30/09/2021 | |||
| 1954248 | Studentship | EP/N509668/1 | 01/10/2017 | 16/02/2022 | Ada Scarrott |
| Description | Bichemistry Society Conference Bursary |
| Amount | £200 (GBP) |
| Organisation | Biochemical Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2019 |
| End | 11/2019 |
| Description | Internal Seminar University of Glasgow |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | As part of a seminar programme run in my institute, I gave a 30 minute presentation of my PhD work so far, followed by questioning. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster Presentation (Netherlands, Bristol) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I have attended two conferences at which I presented a poster of my work. One being 'DNA transactions', in the Netherlands, a conference about DNA recombination and associated proteins. The other conference was the Biochemical Society's 'SynBio' conference in Bristol. At both conferences I presented a poster to engage other participants with my work. |
| Year(s) Of Engagement Activity | 2018,2019 |
| Description | Poster and Flash Talk at EMBL Heidelberg |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I attended the EMBL Synthetic Biology conference in Heidelberg. At the conference I presented a poster, as well as a flash talk to engage the audience with my work. |
| Year(s) Of Engagement Activity | 2019 |
| Description | School Visit - Glasgow |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | As STEM ambassador I visited a school group, ages 15 - 16 to go through possible scientific careers with them. This involved a brief talk about my PhD project, talking about the roles of lab workers and then an experiment to show the kind of work done in labs. |
| Year(s) Of Engagement Activity | 2018,2019 |
| Description | Video of work |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | As part of an "Impact in 60 seconds' competition, I made a short video explaining my work. This was then shared via social media, to engage the general public, as well as publically shown at a university based Impact day. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://youtu.be/ocgN738HTqE |