ViennaXUCL ongoing collaboration

They wanted to engineer yeast to produce spider silk, gelatine and silica proteins which would allow them to design their own hydrogel to grow bacteria on. They would then grow cyanobacteria, which are capable of biomineralizing, on their hydrogel and combine them with other aggregates to build their material.

Summary of our proposal for parnership with Vienna

We presented our project idea: genetically modifying B. subtilis to express both the urease and carbonic anhydrase genes (which are the two main biomineralizing pathways), and combining them with mycelium and other aggregates, which at the time of the meeting remained undefined.

Date	Action
July 2022	Established contact with their team because we were both working on developing a novel biomaterial. In our first meeting we introduced each other’s projects Decided to form a partnership because we were working on similar topics and there was room to influence and contribute to each other’s projects. We brainstormed which track would be the best fit for our projects and put down the same choices.
August 2022	Continued to trouble shoot each other’s projects, both by text and through our fortnightly Microsoft Team meetings. We advised them to autoclave all of the materials they used in their bricks to prevent unwanted fungal growth. They tried this out and agreed that it worked better for them. They suggested using silicon moulds since it they found that it was easier to extract their bricks. This unfortunately did not work for us, because the silicon moulds prevented us from properly packing our material into the mould. In this month, we also brainstormed ideas for our partnership goals. The initial objectives included: We wanted to share each other’s protocols and try to build each other’s materials so we could test their material properties and compare results. We shared our protocols and results with them. They had some internal issues during the month of August so they were not able to start their brick-making process, but they planned to start soon and share their protocols in September. We wrote a survey about biomaterials which we conducted in the UK. Because we wanted to increase our reach, we suggested that their team translate the survey and run it in their local hardware stores. This would be beneficial for both of our projects because we share the same set of stakeholders and their responses would allow us to redefine some sections of our projects. Their team did not have much modelling experience, so we offered to work with them on their modelling, helping them to design a pipeline and then with the coding itself. We offered to attend their internal modelling meetings and guide them in the right direction or even share our code with them so they could adapt it to their project. The BOKU-Vienna team was planning on creating a guide to synthetic biology for high school teachers. Since our team was also thinking of doing educational outreach in schools, we thought that it would be interesting for them to share the guide with us and so we could deliver those lesson plans in schools in the UK. We started working on the Coding with Biology Collaboration with BOKU-Vienna, along with the Cambridge and Sheffield iGEM teams (can read more about it in our Collaborations page).
September 2022	We kept meeting on a fortnightly basis and sharing updates on both of our projects. We continued focusing on common objective development: We kept sharing our updated protocols and the progress that we were making with our bricks. We gave them advice on how we dried our bricks and which proportions of which materials worked best for us. Despite our insistence, they did not share their protocols. We offered our help with the design and testing of their prototypes, but did not receive an affirmative response. They were not able to run the survey because their wet lab work got very busy. Since we were still interested in getting some data, we suggested that they could try to share it in their social media, both the team’s and their personal ones, to get some responses. By the end of September this still had not happened. They never invited us to any of their modelling meetings despite our willingness to help. We eventually stopped offering our services to help them build a model because we did not receive any indication from them that they were interested in this and while we had provided a lot of things, we had not received the same amount of input and commitment from them. We organised an outreach activity in a school in Kent. By the time this happened (21st September), they still had not started writing their synthetic biology guide, so it was not possible for them to share it with us. We created our own workshop; you can read more about it in our Education page.
October 2022	We finished working on our common objective development. Specifically: We are still to receive their protocols. They posted the survey on Facebook on the 5th of October but have yet to receive responses.

Date

Action

July 2022

Established contact with their team because we were both working on developing a novel biomaterial.
In our first meeting we introduced each other’s projects
Decided to form a partnership because we were working on similar topics and there was room to influence and contribute to each other’s projects.
We brainstormed which track would be the best fit for our projects and put down the same choices.

August 2022

Continued to trouble shoot each other’s projects, both by text and through our fortnightly Microsoft Team meetings.

We advised them to autoclave all of the materials they used in their bricks to prevent unwanted fungal growth. They tried this out and agreed that it worked better for them.
They suggested using silicon moulds since it they found that it was easier to extract their bricks. This unfortunately did not work for us, because the silicon moulds prevented us from properly packing our material into the mould.

In this month, we also brainstormed ideas for our partnership goals. The initial objectives included:

We wanted to share each other’s protocols and try to build each other’s materials so we could test their material properties and compare results.
We shared our protocols and results with them. They had some internal issues during the month of August so they were not able to start their brick-making process, but they planned to start soon and share their protocols in September.

We wrote a survey about biomaterials which we conducted in the UK. Because we wanted to increase our reach, we suggested that their team translate the survey and run it in their local hardware stores. This would be beneficial for both of our projects because we share the same set of stakeholders and their responses would allow us to redefine some sections of our projects.

Their team did not have much modelling experience, so we offered to work with them on their modelling, helping them to design a pipeline and then with the coding itself.
We offered to attend their internal modelling meetings and guide them in the right direction or even share our code with them so they could adapt it to their project.

The BOKU-Vienna team was planning on creating a guide to synthetic biology for high school teachers. Since our team was also thinking of doing educational outreach in schools, we thought that it would be interesting for them to share the guide with us and so we could deliver those lesson plans in schools in the UK.
We started working on the Coding with Biology Collaboration with BOKU-Vienna, along with the Cambridge and Sheffield iGEM teams (can read more about it in our Collaborations page).

September 2022

We kept meeting on a fortnightly basis and sharing updates on both of our projects.
We continued focusing on common objective development:

We kept sharing our updated protocols and the progress that we were making with our bricks. We gave them advice on how we dried our bricks and which proportions of which materials worked best for us.
Despite our insistence, they did not share their protocols. We offered our help with the design and testing of their prototypes, but did not receive an affirmative response.

They were not able to run the survey because their wet lab work got very busy. Since we were still interested in getting some data, we suggested that they could try to share it in their social media, both the team’s and their personal ones, to get some responses.
By the end of September this still had not happened.

They never invited us to any of their modelling meetings despite our willingness to help. We eventually stopped offering our services to help them build a model because we did not receive any indication from them that they were interested in this and while we had provided a lot of things, we had not received the same amount of input and commitment from them.

We organised an outreach activity in a school in Kent. By the time this happened (21st September), they still had not started writing their synthetic biology guide, so it was not possible for them to share it with us. We created our own workshop; you can read more about it in our Education page.

October 2022

We finished working on our common objective development. Specifically:

We are still to receive their protocols.

They posted the survey on Facebook on the 5th of October but have yet to receive responses.

Date	Action
August 2022	We established first contact in mid-August and met on the 15th of August for the first time. We established the following common goals: They were planning on developing bricks as part of their proof of concept, but had not yet started, so we decided to set up another meeting when they had done some brick development to share protocols and our experiences with the process. We shared our biomaterial survey with them and asked if they could run it in the US. We thought that it would be interesting to see how stakeholders from different parts of the world felt towards biomaterials and what the different concerns were. Both of our teams were working on making bacteria express the urease enzyme, which meant that we could collaborate and trouble-shoot any issues relating to urease activity assays.
September 2022	We met on a fortnightly basis and remained in contact through Instagram. We then focused on common objective development: They shared their protocols with USAFA and we shared ours with them. We set up a meeting with their entire team to discuss brick building and issues that we had both encountered and how we had overcome them. They gave us some feedback on our protocols. They sent the survey around a received a couple of responses. We asked them if it would be possible to go to their local hardware store and run it there or post a flier so people could scan a QR code. We had a discussion about the urease enzyme and how we had both worked to incorporate it into our bacteria. They told us that at the beginning of their project they had run a urease assay, but had decided not to keep going that way. We were at that point designing our own urease assay, so they sent us the protocol they used so that we could compare it with ours and perhaps integrate some aspects into ours.
October 2022	We finished working on our common objective development. Specifically: We implemented the feedback that they gave us on our protocols: One of their comments asked about characterisation of the moulds that we used. Based on this feedback, we decided to include a section on our Engineering Success page about the different moulds that we have used and developed and the advantages and disadvantages of each. They also asked about the different drying conditions that we used. For this reason, we decided to address how and why we had used different drying procedures (leave on bench, shaking incubator, incubate no shake…) for our bricks to investigate which protocol worked best for each composition. We addressed this in our Engineering Success page We provided feedback of our own about their protocols, in particular: We asked about why they chose to pour their bacteria over the material, rather than creating material that already has their modified organism integrated within. We asked about more details of their drying techniques, since they found that bench drying worked quite well for them, while we found than when our bricks were left outside to dry, they would take too long to solidify and would often turn moudly. Further discussion with their team about this particular aspect led us to conclude that the differences in our drying experiences, might be related to the differences in weather conditions between London (humid) and Colorado (dry, desert-like). They run our biomaterials survey and received a couple of responses, which have been included in our Human Practices page. Since Wiki Freeze season came around in October, we decided to establish a new point of partnership: checking each other’s wiki pages drafts. This is the ultimate form of influencing each other’s projects, since judges will only consider the work that is documented in our wikis.

Date

Action

August 2022

We established first contact in mid-August and met on the 15th of August for the first time.
We established the following common goals:

They were planning on developing bricks as part of their proof of concept, but had not yet started, so we decided to set up another meeting when they had done some brick development to share protocols and our experiences with the process.

We shared our biomaterial survey with them and asked if they could run it in the US. We thought that it would be interesting to see how stakeholders from different parts of the world felt towards biomaterials and what the different concerns were.

Both of our teams were working on making bacteria express the urease enzyme, which meant that we could collaborate and trouble-shoot any issues relating to urease activity assays.

September 2022

We met on a fortnightly basis and remained in contact through Instagram.
We then focused on common objective development:

They shared their protocols with USAFA and we shared ours with them. We set up a meeting with their entire team to discuss brick building and issues that we had both encountered and how we had overcome them.
They gave us some feedback on our protocols.

They sent the survey around a received a couple of responses. We asked them if it would be possible to go to their local hardware store and run it there or post a flier so people could scan a QR code.

We had a discussion about the urease enzyme and how we had both worked to incorporate it into our bacteria.
They told us that at the beginning of their project they had run a urease assay, but had decided not to keep going that way. We were at that point designing our own urease assay, so they sent us the protocol they used so that we could compare it with ours and perhaps integrate some aspects into ours.

October 2022

We finished working on our common objective development. Specifically:

We implemented the feedback that they gave us on our protocols:

One of their comments asked about characterisation of the moulds that we used. Based on this feedback, we decided to include a section on our Engineering Success page about the different moulds that we have used and developed and the advantages and disadvantages of each.
They also asked about the different drying conditions that we used. For this reason, we decided to address how and why we had used different drying procedures (leave on bench, shaking incubator, incubate no shake…) for our bricks to investigate which protocol worked best for each composition. We addressed this in our Engineering Success page

We provided feedback of our own about their protocols, in particular:

We asked about why they chose to pour their bacteria over the material, rather than creating material that already has their modified organism integrated within.
We asked about more details of their drying techniques, since they found that bench drying worked quite well for them, while we found than when our bricks were left outside to dry, they would take too long to solidify and would often turn moudly. Further discussion with their team about this particular aspect led us to conclude that the differences in our drying experiences, might be related to the differences in weather conditions between London (humid) and Colorado (dry, desert-like).

They run our biomaterials survey and received a couple of responses, which have been included in our Human Practices page.

Since Wiki Freeze season came around in October, we decided to establish a new point of partnership: checking each other’s wiki pages drafts. This is the ultimate form of influencing each other’s projects, since judges will only consider the work that is documented in our wikis.

Partnership

An overview of our partnership activities

ViennaXUCL ongoing collaboration

Summary of Vienna's project

Summary of our proposal for parnership with Vienna

UCLXVienna detailed timeline

UCLXUSAFA detailed timeline