Difference between revisions of "Team:Oxford/Engagement"
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| − | <p> | + | <p>Computer with the free software <a href="http://www.async.ece.utah.edu/ibiosim">iBioSim</a> and <a href="https://static.igem.org/mediawiki/2017/9/99/Genetic_Toggle.zip">toggle switch model</a></p></br> |
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| − | <p><ul><li>Protein and DNA paper parts</li><li>A3 paper or whiteboard to draw cell outline</li></ul></p></br> | + | <p><ul><li><a href="https://static.igem.org/mediawiki/2017/f/f3/Bacterial-photography-circuit-cards.pdf">Protein and DNA paper parts</a></li><li>A3 paper or whiteboard to draw cell outline</li></ul></p></br> |
<center><img class="img-responsive" width="400px;" src="https://static.igem.org/mediawiki/2017/2/29/Lesson_plan_img3.jpeg" /> | <center><img class="img-responsive" width="400px;" src="https://static.igem.org/mediawiki/2017/2/29/Lesson_plan_img3.jpeg" /> | ||
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| − | <p><ul><li>Strongly agree and strongly disagree cards</li><li>Case study cards: x10</li><li>Ownership cards: x3</li><li>String and clips or board and blue tac</li></ul></p></br> | + | <p><ul><li>Strongly agree and strongly disagree cards</li><li>Case study cards: x10</li><li>Ownership cards: x3</li><li>String and clips or board and blue tac</li></ul><a href="https://static.igem.org/mediawiki/2017/d/d9/Ethical-washing-line-case-studies.pdf">Link to cards</a></p></br> |
<h3>Activity</h3> | <h3>Activity</h3> | ||
Revision as of 11:46, 1 November 2017
Education and Public Engagement
Introduction
Designing educational activities around synthetic biology is difficult because the field is new and interdisciplinary. Consequently there is a lack of standard principles and definitions, creating an enlarging division of knowledge between the general public and the synthetic biology community; this may foster generalisations and misconceptions. Bidirectional public engagement is necessary to help bridge this gap, and it was therefore a key focus of our summer.
Summer School Engagement
A major reason for the gap between the general public and the scientific community is a lack of exposure to synthetic biology in modern education. To accurately tackle this problem we based our activities on the learning objectives for MIT undergraduates training in synthetic biology (Figure 1). Importantly, we had to ensure that our activities were:
- Not generalised
- True to core synthetic biology
- Encouraging scientific thinking
Although there are some excellent secondary education tools available (e.g. Biobuilder), we found that many of these require extensive access to lab equipment and expensive resources, creating a barrier to use in teaching. Therefore, our designed activities are low cost, require minimal materials and do not assume lab access.
Figure 1: Main outcomes of synthetic biology education and activities we designed to fulfil these
Our Activities
We carried out workshops at 3 different summer schools in Oxford: Northwest Science (students aged 17-18 yrs interested a broad range of sciences), Oriel College summer school (students aged 13-14 yrs interested in medicine) and UNIQ (academically selected state school students aged 17-18 yrs from state schools interested in biochemistry).
To meet these outcomes we designed a variety of activities including: a genetic memory computer lab, a bacterial photography system worksheet, an ethical washing line activity, and a 'Design your own biosensor' activity. These activities have been formatted into lesson plans and printable resources, made publicly available for use by future iGEM teams. Each activity has a set of aims to ensure a directed learning approach.
Aims
- Understand how the genetic toggle switch works as an example of a synthetic biology system
- Interpret a model of the circuit for the toggle switch built in iBioSim
- Understand the importance of modelling in the context of the design test build cycle
Resources
Computer with the free software iBioSim and toggle switch model
Activities
Before starting the simulation explain the toggle switch mechanism (Figure 1) to students e.g. A toggle switch is a circuit that allows switching of 2 stable states, much like turning on and off a computer. The switch is on when cells produce green fluorescent protein output, and is flipped between states by adding different on and off chemicals. The green fluorescence output is maintained even after the on and off chemicals are removed creating genetic memory.
Figure 1: DNA circuit for genetic toggle switch
Run the model in stochastic and deterministic modes, and vary the GFP degradation rate and promoter strength to alter GFP output (Figures 2a – d).
Figure 2: Expected graphs a) Deterministic simulation b) Stochastic simulation c) Decreased GFP degradation rate d) Increased promoter strength
Ask students the following questions:
Look at the graph a, can you see identify when the system is on and off? What happens when you add more on chemical when the system is on?
Peaks. No change.
Compare the deterministic and stochastic models in graphs a and b? Which is better?
The deterministic model is a simplification to ignore output fluctuations due to random collisions of molecules in the cell. The deterministic model is easier to identify trends but the stochastic is more realistic of the noise in a cell.
How could you modify the circuit to get greater output (greater fluorescence)?
Increase promoter strength or decrease degradation rate of GFP modelled by graphs c and d.
Which of these introduces the most time lag?
Decreasing degradation rate.
Aims
- Explain synthetic biology concepts of biobricks and modularity
Resources
- Protein and DNA paper parts
- A3 paper or whiteboard to draw cell outline
Figure 1: Key words
Activity
Before carrying out the activity give a brief overview of the system. The circuit (Figure 3) works by taking an input of light to a light detector, the output of which controls the activity of a colour generator to produce a colour output, therefore allowing the bacterial population to reproduce an image taped to the petri dish by changing colour in the dark regions masked by the image.
Figure 2: DNA circuit for genetic toggle switch
Figure 3: Bacterial photography circuit (a) inputs and outputs and (b) complete circuitry
Students will be given a set of proteins and DNA and challenged piece them together to construct the circuit. This exercise can be used to distinguish key biochemical processes and DNA modules (defined above).
After building the basic circuit extend the exercise with the following discussion points:
The natural function of the receptor in E coli is to respond to extracellular salt concentration (osmoregulation). How could this receptor be modified to be light responsive?
The receptor sequence is modified to contain the sequence from a light receptor from the photosynthetic single celled organism cyanobacterium to encode a recombinant receptor protein with the extracellular region from the cyanobacterium of the protein is light responsive, but the intracellular region from the E. coli receptor conserved to activate its cognate transcription factor.
In this model the proteins are already present in the cell. How is this simplification from the real cell system and why is this simplification valid?
The proteins need to be expressed by the cell so the genes would be present. These would be on plasmids expressed all the time (constitutively). Only the Beta galactosidase gene is regulated in this system therefore it is only relevant to include its DNA to interpret the circuit.
The transcription factor is phosphorylated. What do you think is the function of this modification and how does it occur?
Phosphorylation is the covalent addition of a phosphate group to an -OH containing amino acid on the protein. This changes the binding surface and/or structure of the transcription factor allowing it to make new protein-protein or protein-DNA interactions that can change the outcome of a cell signalling pathway, allowing it to act as a switch in cell signalling. Phosphorylation is by enzymes (kinases) using the phosphate from ATP. Dephosphorylation is by separate enzymes (phosphatases). The relative activity of these enzymes can in turn be regulated to fine tune activity of a cell signalling pathway.
How could you modify the circuit?
Change the promoter strength and RBS strength to tune the output intensity, and change the degradation rate of the proteins to change the timing of colour output production.
Aims
- Stimulate an ethical discussion around use and ownership of synthetic biology.
Resources
- Strongly agree and strongly disagree cards
- Case study cards: x10
- Ownership cards: x3
- String and clips or board and blue tac
Activity
Students are given a set of cards of case studies of current and potential applications of synthetic biology applications and asked to rank them on a scale of agreement to disagreement on the ethics of each application on a piece of string. Similarly, students will rank who they think should own the synthetic biology devices.
Aims
- Explain key features of expression vectors and their function in molecular cloning.
- Explain concepts of modularity and biobrick parts in synthetic biology.
- Highlight the design aspect of synthetic biology.
Resources
- Worksheet and pens
- Scrap paper
Activity
Work with student groups to identify and explain the key features of an E. coli expression vector (Figure 4) before asking them to design their own simple biosensor part including promoter, ribosome binding site and up to 2 protein coding genes. Promoter regulation and sensitivity, ribosome binding site strength and proteins can be varied. The worksheet can be used as a template for the activity.
Figure 1: Annotated key features of expression vector
Image 1: Zoë C and John giving a presentation at the Northwest Science school at Corpus Christi College
Image 2: Chun, Jei, Alissa, Helen and Sumaera at the UNIQ summer school
Improvement through Feedback
Student feedback allowed us to refine our activities after each summer school session (Table 1). For example, we converted the TinkerCell computer based bacterial photography system activity into a paper based game so computer access was no longer needed, and we also developed a formalised ethical washing line workshop after finding students disengaged by an unstructured ethical discussion. In addition to workshops, Zoe F gave a university style lecture about synthetic biology and our project to students at the Northwest Science school.
| School | Positives | Problems | Modifications |
|---|---|---|---|
| Northwest School |
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| Oriel |
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| UNIQ |
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Curiosity Carnival
The Curiosity Carnival is an Oxford wide festival for researchers to share their research in innovative ways, as a part of the European Researchers' Night (NIGHT). The Oxford team were thrilled to be accepted in having an activities stand at this event. Our stand was in the centre of the city and attracted a diverse audience of more than 4500 members of the public, from young children to other researchers.
Image 3: Kushal, Angela, Sumera and Zoe C at the Curiosity Carnival
Our stand involved:
- Poster display outlining facts about Chagas disease and our diagnostic solution
- ‘Find-cruzi’ game to highlight the difficulty of identifying the parasite by microscopy of a blood smear
- ‘E. coli pong’ game to explain transformation
- Competition to design a biosensor from magnets on a white board
- Voting on ethical scenarios
Image 4: Sumaera demonstrating our ‘E. coli - pong’ activity
iGEM UK Meet-ups
Engaging with other teams to share ideas and techniques is a vital component of iGEM: we were grateful to be able to attend the UK meet up jointly organised by the University of Westminster, UCL, and Warwick during which we gave Jamboree style poster and powerpoint presentation to other teams, providing invaluable preparation for Boston. The event was lots of fun and we appreciated the opportunity to meet, network and form collaborations with other UK teams.
Image 5: Our excellent speakers (Arthur and John) pose with Tom cruzi (complete with his own little tie) before they go in to give our presentation at the Shard
Image 6: UCL held a fantastic set of debates about synthetic biology, and our team members were very successful - here's Zoe F with their winning team, who argued in favour of using genetically modified organs
Image 6: At Westminster, Arthur talks through our poster with members of the UCL team
Social Media
We have worked hard to develop a solid and consistent social media presence across three platforms during our project. Our Instagram account has included regular updates on what the team was getting up to inside and outside of the lab, helping to promote a more well-rounded image of scientists, and also participating in tags such as #femalesinstem to display the gender diversity in our team. We have a high level of engagement for our Instagram posts, regularly reaching a variety of accounts including Oxford colleges, scientific institutions, and the general public. Our Twitter account keeps abreast of the important instagram and facebook posts, and is also key to engaging with other iGEM teams. The Oxford iGEM Facebook page has the biggest following of all our accounts, with over 1000 followers, and displays a range of posts from ‘Meet the Team’ to information about our outreach events and human practices. We have made sure to advertise any outreach we have been involved in across all platforms, such as the Curiosity Carnival and the UNIQ summer schools.
