Project Proposal: Developing Cell-Free Genetic Circuits and their Electronic Counterparts as Educational Tools for SynBio Students.
The Idea
There is a notable absence of Synthetic Biology (SynBio) concepts and methods within the STEM courses at Cambridge, particularly in the first two years of study. In addition, the course structures preclude any interdisciplinary student research. The need for a society bridging departmental divides and giving students a platform on which to develop experience in SynBio outside the conventional course structure was clear.
In 2015, CUSBS was established with the aim of increasing understanding and involvement in SynBio within the student body, and to allow students from different backgrounds to share ideas and skills. Through fully-funded biological and hardware projects, CUSBS hopes to give students hands-on experience with SynBio and provide them with valuable independent research skills. Since our establishment, CUSBS has grown from 20 to over 200 members including undergraduates and graduates from the full spectrum of STEM fields.
The focus of the biological project this year is understanding gene regulation by engineering oscillating genetic networks in cell-free TX-TL systems. Generally, the project aims to develop along two parallel “biological” and “physical” branches designed to be mutually informative and complementary. Theoretical design of genetic networks will run alongside the practical realisation of their electronic counterparts, allowing students to gain experience in circuit design, and informing their view on biological systems. Do cells compute information in terms of AND, OR, IF gates? If yes, how do they implement these genetically and molecularly? How are bistable switches, hysteretic systems, all-or-none responses, proportional control mechanisms etc. implemented in living cells? Can we reconstruct simple and complex networks motifs outside of a cell? We will make our work available to other groups in collaboration in order to support novel applications and enable open innovation. Alongside the practical project, invited speakers will develop some of these topics in more detail, present current research, or expand on wider areas of Synthetic Biology.
Who We Are
Stefano Vianello (sdv20), CUSBS Committee, Biological Project Manager, MPhil, Genetics
Lucie Studená (ls679), Biological Project manager, NST Part II Plant Sciences
Michael Casey (mjc259), President, NST Part II Genetics
Stefan Grossfurthner (sg791), Vice President, PhD Candidate, Plant Sciences
Atti English (maoe2), Secretary, NST Part III Chemistry
Ptolemy Jenkins (pj316), Treasurer, NST Part II Physics
Ben Kitching-Morley (bk362), Publicity, NST Part II Physics
Jaza Syed (js2612), Sponsorship, Engineering Part IIa
Will Earley (wje25), Webmaster, PhD Candidate, Systems Biology
Tristan Orchard (tho24), Hardware Project Manager, NST Part II Physics
Souradip Mookerjee (sm2030), Safety, MVST Clinical School
Andrew Tung-Yep (adt40), Social Events, NST Part II Pathology
Our project is practically conducted by the project managers, interested members of the society and the committee. Our members consist of a diverse group of students ranging from Natural Sciences Biology and Physics students to Engineering and PhD students of various years. The particular project group is not constrained, with 27 students having been actively involved so far.
Implementation
Funding will primarily go towards materials (biological and hardware) and Biomakespace membership costs to ensure that students do not have to bear any costs as part of their membership. This is a core aspect of our society, as we aim to make it accessible to all students regardless of financial status. The wet-lab aspects of the project will be run in the newly established Biomakespace with potential support from other labs or Plant Sciences Teaching Laboratory where storage/licenses are not yet available in Biomakespace. Hardware and electronics workshops will be run in the Dyson Centre, Department of Engineering.
A general outline of the steps and activities planned for this year’s biological project is provided below. It is worth stressing that participation in all or any of these steps is not enforced, and completely dependent on student availability, interests, and needs. Ideally, students will attend most sessions/activities.
Biological
- Familiarisation with cell-free transcription- translation (TX-TL) systems
- Generation and introduction of designed plasmids and reporters
- Measurement, study, and parameterisation of oscillatory behaviour
- Optimisation of designed circuits
- Introduction of designed circuits in living cells (e.g. bacterial cultures)
Physical
- Design and construction of simple and complex electronic circuits to be translated in living cells
- Design and construction of common network motifs and feedback control systems (positive, negative, logic gates, hysteresis, switches, etc...)
- Attempts to recapitulate electronically gene-expression behaviours observed in the wild Need your help and input to further develop this branch!
The activities above are best viewed as “sub-modules” or “sub-workshops” to be completed towards the overall realisation of our project. Breaking down the work in this way will allow for easier organisation, hand-over of completed work if people cannot make to the next session, and greater flexibility in project commitment. Each of these modules will be further expanded and accompanied by much more specific task breakdowns. These will be updated as the project progresses through the tasks, and will be detailed case-by-case via our online collaboration platforms (Slack, Trello).
Participating in CUSBS projects is intended to be an extremely rewarding and enriching activity as we foster a culture of interdisciplinary cross-over and reciprocal learning. This year we are lucky to have members from all areas of science (biology, physics, engineering, medicine, mathematics, HPS), and all levels of expertise (from first year undergraduates to masters and postgraduates). The amount of learning a student can expect is strictly dependent on them, their interests, their participation and their engagement with others. In that sense, we want to accommodate students’ busy schedules by making our framework as flexible as possible.
Scientific Skills:
- Experience with bacterial transcription- translation cell-free systems and bacterial cultures
- Experience with recombinant DNA technology: plasmid design, PCR, plasmid delivery
- Experience with fluorescent reporters, fluorescence imaging and quantification
- Working with primary literature and reviews
- Experience with electronics, circuit design (theoretical + practical)
- Theoretical understanding of gene regulatory networks and motifs, feedback loops, basic control theory
Transferable skills
- Working in research teams
- Cooperation with students of different backgrounds
- Networking
- Creativity, original thought and independent research
- Possibility of joining project sub-committee
Those undergraduate members doing NST Part IB CDB or Part II Genetics (and hopefully many others) will find this project as a very useful opportunity to further develop or strengthen topics mentioned during lectures. We strongly encourage members to contact us and let us know what technique/topic/area they would like us to focus on in the future, and member feedback is an essential part of the project planning process
Benefits and outcomes
As part of the biological project, CUSBS is running electronics workshops aimed at the investigation of simple and complex circuit dynamics, and their implementation in biological systems. This series of workshops is developing quickly, with each session being accompanied by written teaching resources summarising and expanding on the topics covered. Examples of learning resources already made by team members include a summary sheet of electronic components, an in-depth guide about transistors, and an introduction to operational amplifiers. By the end of the project CUSBS aims to have established a consolidated 6-months electronics syllabus and series of workshops able to introduce students without a physical/engineering background to principles of circuit design, and students from non-biological fields to topics of natural sciences. For the moment the documents are only available to society members, but all will be compiled as a single piece of work and made freely available on the society’s website or other appropriate public platforms. We welcome any other student society, school, or university initiative to make use of our syllabus and improve it/modify based on individual needs. We believe this holds an important potential for outreach by introducing anyone to basic principles of interdisciplinarity and complementarity between STEM fields.
On the biological side of the project, CUSBS is working towards the establishment of a tested, robust transcription-translation cell-free system for the in vitro testing of synthetic genetic circuits. By the end of the project we are expecting to have developed a reliable experimental platform and protocol that could be used by any other group interested in such system, which will be published on an appropriate platform. Specifically, we are envisaging to establish a collaboration with University’s iTeams whereby our established transcription-translation systems would be used as a testing platform for independent projects and novel applications. This will expose a whole generation of undergraduates to the potential innovations available in synthetic biology. As for the electronics workshop, every meeting is documented and freely available to members, a compiled version of all the documents will be published by the end of the academic year. Accordingly, this year’s biological project will not only produce teaching resources for the bio-hacking community, but also establish an experimental precedent that will undoubtedly help any other group wanting to start working with translation transcription systems, or external initiatives in need of such a system to quickly test projects and ideas.
Budget
Consumables
Lab gloves 20 box medium £45.00
1.5 mL microcentrifuge tubes with caps 1500 £42.15
96-well Plate with caps 10 £41.91
384 well plate 3 £15.24
96-well strip plates 5 £38.23
Pipette Tips (P2) 10 muL 10 boxes £108.72
Pipette Tips (P10) 10 muL 10 boxes £108.72
Pipette Tips (P200) 200muL 10 boxes £50.00
Pipette Tips (P1000) 1000muL 10 boxes £50.00
Falcon tubes (50mL) 100 £73.72
Falcon tubes (15mL) 100 £52.79
Reagents
QIAprep (Qiagen) miniprep kit 1 £68.00
PCR purification kit Invitrogen 1 £85.60
Antibiotics (depending on plasmids used) £70.00
HPLC H2O £63.58
Ethanol (96-100%) 1 tank (2.5L) £60.00
isopropanol 1 £5.00
Restriction enzymes for ligation £200.00
DNA constructs from commercial sources £300.00
Synthetic Biology Speakers (3 per term)
Lecture room hire 6 £450.00
Refreshments 6 £180.00
BioMakespace (£10 pppm)
Makespace membership (2 terms) (£10/month) 27 £1,620.00
Administration
AGM Refreshments 1 £30.00
Freshers Fair Stall (standard with electricity) 1 £58.00
Website 1 £5.00
Expenses Total £3,821.65