With our motivations to pursue Enzocrete set, and the background research done to validate our motivations through reference to news articles, journal articles and governmental reports, we arrived at the stage where we needed expert advice to drive our wet and dry labs. The seven correspondences we had all combined to inform our design-build-test-learn cycle by complementing the literature review by enabling us to make multiple design and organisational decisions.
A meeting with a previous iGEM team that has worked on MICP had provided us with advice on potential pitfalls to avoid and organisational decisions that needed to be taken to ensure that. From the wet-lab side of things we received technical advice on plasmid choice, best sources for enzymes, reemphasis on the problem with toxic by-products like ammonia as well as testing methods for the MICP product. On dry lab side, we sought advice and took inspiration from alternate implementations of the robotic systems as well as gain understanding the logistics scaling up of how our systems would look like. Below are detailed descriptions these correspondences.
Associate Professor of Microbiology and Immunology, LSU Health, Shreveport.
We reached out to Doctor McGee to inquire about possible collaboration. Not only through ongoing advice about his field of expertise but also we were interested in the acquisition of a plasmid he designed on which we could more easily introduce synthetic products and modifications. Unfortunately this opportunity was halted due to extensive regulatory requirements at UNSW for the import of modified organisms. Despite this however he contributed several ideas that were useful for avenues of research.
He provided advice that expanded on his paper, suggesting that the Nix Transporter was a possible option for our Urease as it has proven efficiency increases. Ultimately we decided not to pursue this possible avenue, mainly to reduce the number of introduced elements to minimise uncertainties.
Senior Lecturer, School of Biotech & Biomolecular Science, UNSW.
During our research into the MICP pathways the strongest Urease identified was those from Helicobacter Pylori strains, but our supervisor warned us of the difficulties in obtaining and working with an infectious disease. One of our team knew that Dr Rodriguez was working on H. pylori Urease and so we reached out to ask for information about obtaining and handling the bacterium.
Dr Rodriguez was incredibly helpful in this regard, identifying the Urease and confirming its effectiveness from her studies. She also recognised the difficulties in working with this bacteria and offered to train team members and provide materials for the growth and extraction of the relevant genes. Through further investigation and communication she offered an alternative solution to reduce the input required and allow us to prioritise the E. coli implementation by providing us the extracted genomic DNA. This allowed us to accelerate our work on this pathway, an ultimately invaluable contribution.
Nuclear Magnetic Resonance Facility, UNSW Sydney, Chemistry.
During the initial research into MICP we identified a potential future hazard if this system was implemented, the ammonia by product. Ammonia pollution has significant effects on the environment, massively increasing eutrophication potential. To ensure we are act in a responsible manner and do not ignore long-term detrimental effects. We then resolved to investigate this issue which led us to Dr Rawal.
Aditya Rawal delivered a comprehensive elucidation on the environmental detriments stemming from the cement manufacturing process, particularly focusing on the issue of ammonia pollution. He proposed an innovative solution through ammonia capture, suggesting that the captured ammonia could be repurposed for agricultural applications, thereby not only addressing the pollution issue but also creating a potential resource for other industries. Furthermore, Dr Rawal shared his expertise on the essential testing procedures for cement and concrete to ascertain their strength and functionality. This pivotal input ensures that the developed solutions transition from theoretical concepts to practical, functional products capable of real-world application. His insights significantly enriched the project by ensuring that the environmental solutions conceived are not confined to the laboratory but are robust and practical for industrial application.
Civil Engineering Program coordinator and Sustainable Infrastructure Research Group coordinator, UNSW Canberra, Civil Engineering.
Denitrification became a critical process for us to include for the environmental sustainability of MICP usage for construction. The ammonia produced by and required for efficient enzymatic pathways cannot be allowed to enter the waterways. During our research we determined that incorporation of denitrification pathways into the main Enzocrete chassis would be the most efficient, so we reached out to Dr Al-Deen.
Dr Safat Al-Deen provided significant insights towards denitrification. He elaborated on the potential of MICP in large-scale biocementation endeavour but as a enhancement to the traditional techniques rather than a standalone solution. Dr. Al-Deen emphasized that when employing MICP, mitigation of the adverse effects associated with ammonia is a priority for large scale adoption. His insights validate the necessity for advancing denitrification methods, but also inspired us to create a powerful and integrated MICP bacteria that could economically and effectively replace traditional methods.
Arvind Ramanathan, Casey Stone, Rafael Vescovi & Abraham Stroka.
Dr Arvind Ramanathan leads a group of scientists including Casey Stone, Rafael Vescovi & Abraham Stroka at the Argonne national laboratory, situated in the US. They have established collaborative efforts with scientists in Brazil to develop a comprehensive lab automation system called WEI, which combines lab automation robots including the OT2 and integrates them under a unified control system with a graphical interface. They did not, however, include the xArm6 or thermocycler in their system.
When we initially reached out to the Argonne team, our integrated system was in its early stages of development, and we had not yet included the xArm6. We sought their guidance on establishing the first robot to robot connection. Additionally, we observed significant similarities between their published research and our project goals, prompting us to confirm that they hadn't already achieved our intended objectives.
Since their group works internally in the field of lab automation, they have an internal interest in progress in this field.
Initially, the Argonne team offered us access to WEI to allow us to expand on their system. However, after attempting to implement it, we encountered challenges that led us to transition to our own system. Throughout our collaboration, the team emphasized the critical importance of comprehensive documentation. Especially ensuring that other research teams could replicate the system successfully, allowing progress in the field.
CSIRO BioFoundry Facility Manager and Adrian Marsh, LIMS Head Engineer.
We aimed to get a better understanding of real-world applications of laboratory automation systems, and CSIRO is a high-level part of this field, so we sought out their expertise. Their role as internal stakeholder means that their approaches towards the implementation of automated systems directly impacts the workflow of associated projects. In doing so, we gained an enhanced conceptualisation into the feasibility of large-scale incorporation of automated systems in an industrial context. Additionally, conversing with individuals in charge of automated systems provided us with insights to holistically analyse the potential challenges involved in designing, implementing and maintaining automated systems with a high-throughput pipeline in mind.
The extent of software upkeep and debugging was not as significant as we have expected it to be for an upscale industrial setting. The team of select, experienced individuals associated with software maintenance are those associated with its implementation and/or those with expertise in the system. When adapting a different team’s program, the most important part of documentation are the clear steps the program performs. Correspondingly, it is crucial that the physical and chemical conditions (I.e. concentration, mixing speed) associated with the automated reactions are explicitly stated to ensure generalisability of usage to a broader collective.
Exeter 2020 iGEM team members.
We reached out to Anna and Pazzy through their Professor and iGEM coordinator Dr Love. Their team was the most recent one to investigate MICP aplications and while our overall goals were different, their experience and knowledge could be very useful for our project.
Our pathways and end goals being different meant that the technical details that could be transferred to our project were unfortunately minimal, as things like assays and experimental data are very enzymatically specific, they had several ideas around the administration and communication aspects that we could put into practise.
During their project their two separate groups; Biological and Engineering, became disjointed from each other and began operating independently. This led to miscommunication, repetition and conflicting ideas about the direction of the project. They remedied this through group presentations and better internal communication. Acting on this we maintained weekly whole group meetings regardless of the subgroup meetings so to ensure that all aspects of the project was understood be the members.
They also gave advice on the interuniversity areas of this competition, they worked with their contemporary UNSW team for a seminar. While we were not able to act on these recommendations, they demonstrated new pathways and reminded us to explore more areas than the biology aspect.
Our initial community outreach primarily focused on ensuring that our guiding values were compatible with our current direction and that our proposals were feasible. This meant that we primarily relied on institutions and research papers during this initial period. Once these aspects were confirmed, we had to reflect on and consider the direction our human practices should take. Given the nature of our chosen project, the end product became the point of comparison necessary for in-depth discussions with non-academic stakeholders, especially commercial or governmental entities. Consequently, we prioritized the academic community as the main focus of our outreach to obtain and integrate their ideas and feedback. This information would then serve as the foundation for broadening our scope to include a more extensive range of stakeholders. The work conducted on the ammonia problem and research into BioFoundry applications illustrates how the initially narrow scope allowed for the rapid implementation of feedback and subsequent expansion toward broad community engagement.