Team:TEC COSTA RICA/Contribution
Contribution
As a team, we have contributed in several areas to improve as well as expand future iGEMers’ project development experience.
01
Counter
The architecture of the counter module itself is novel and one of a kind, allowing a count more efficient than any existing one and permitting its own reset, which furthers its efficiency and gives rise to different counter-reset designs and applications. It harnesses serine recombinases’ potential, building up on previous authors work while giving it a special twist marked by the application of sequential logic.
02
Initiation Module
Offers a great way to prevent the start of the counter module during lab work, an essential requirement for our project but also many other synthetic biology systems that can’t rely on inducible promoters (positive feedback) for this purpose.
03
Overcount Prevention
This regulatory module is a game changer for counter systems, since one of the main deficits that already developed counters have is the lack of discrete counting in the presence of continuous input, which makes characterization and experimental optimization a very exhausting task. Also, since it’s a regulatory module that’s designed to fit all, it can be used for regulation in any other genetic circuit that might need it.
04
Amplify
Along with the counter module, “amplify” allows a theoretically endless amount of resets, making the count virtually infinite. Its design also gives rise to new possibilities for other circuits which could be modified to allow the incorporation of the circuit in order to expand or improve their performance, particularly in the area of genetic editions and metabolic engineering. It’s also a simple way to adapt already existing devices to fulfill sequential logic functions.
05
Killswitch
Although not novel, our killswitch fulfills the highest of standards, by incorporating a multilayered approach to biocontainment, allowing the characterization of many toxins and their synergy along with other biosecurity strategies in the molecular level.
06
Parts & Protocols
The fragments constructed for our characterization, along with a T4 ligase were added to the registry in order to enrich it. The protocols for their characterization, along with new information for some of the parts used were also made accessible.
01
Conceptual Framework
In order to make this knowledge more available, we have organized our research and findings and included them in our conceptual framework. The conceptual framework itself encompassess even more, it’s where we propose a guide for conceptualizing, modeling and representing biological elements, such as genes and proteins along with their interactions among themselves and the environment. The development process for this guideline was complex and time consuming, requiring discussion, research and decision making, because of which we documented the troubleshooting process that it entailed.
02
Software Framework
To make the conceptual framework’s application more tangible, we developed the specification for a software framework, which organises the workflow of the previously conceptualized parts in order to build, assess and manipulate genetic circuits. This makes software development more accessible for researchers and other iGEM teams, while maintaining flexibility in the implementation and optimization. This can be used by iGEMers and scientists to develop their own software proposals.
03
Software Implementation
Our software proposal is an already implemented and user-ready version of our conceptual and software frameworks, through which users can not only develop but also troubleshoot, improve, validate and compare biological circuits targeted for sequentially dependent tasks.
01
In vivo mathematical model
Development of an in vivo mathematical model of serine recombination, which is a breakthrough in modeling since most models were developed from and oriented to in vitro conditions. This along with a particular manipulation of when to express the proteins involved in the process serves as reference for future teams. We made a list of constants or parameters used that will be helpful for future iGEM teams.
02
Gillespie Algorithm
Application of a randomization algorithm to the process of recombination, called the Gillespie Algorithm, which allows to see best-worst case scenarios. By pursuing this approach we confirmed that the stochastic process converges to the deterministic one. It will be helpful reference for iGEM teams to apply this algorithm as well as using our implementation.
03
Bacterial Population Model
Development of a bacterial population model and its respective software tool. This tool will be helpful for iGEM teams to predict how the microorganisms population's growth and quantity will behave in time, in the application that they want. Also, it can give information about the necessary number of initial population of bacteria one would need to do a certain task, if one knows beforehand the total amount of bacteria needed.
04
Decision Trees
Development of a new approach to designing genetic circuits based on decision trees. This new approach can give good information to people about their circuits’ behavior. Also, it can be used to first generate the tree of requirements that represent a problem or process, and, based on that search patterns of the tree that follow the constraints defined, generate biological structures that fulfill them.
05
Markov Model
Application of a Markov Model approach to sequential logic that gives information about the probability of the entire process to work as intended. It is a great example and future reference for sequential circuits created by our software.
01
Potential Users Feedback
In addition to be in an abstract category like foundational advance, our project has an enormous potential with a wide plasticity, which makes clustering it for potential users a complex task, so we decided to consult professionals from different areas, to get feedback on what they thought of the project in a positive and negative way and how they would see different uses according to their experience and the way they could be applied on their own projects and investigations. This not only promoted a dialogue that allowed the improvement of the project and the consideration of aspects that were not initially visualized, but also extended the coverage of possible implementations of our genetic circuit, framework and software. Also, we believe this approach can be used by future teams who have abstract projects and/or believe in having a closer relationship with users. This creates a basis to understand what a user might actually look for in an application or product and thus make the necessary modifications to convert our idea into a functional reality. It also involved a large group of teachers and researchers from different universities who had never before become familiar with the iGEM initiative or related projects, so this highlights our interest in increasing the reach of synthetic biology in the country and thus seeking the support needed to continue scientific development.
02
Biosafety & Ethical considerations
The search for ways to mitigate the impact of man on the planet, to repay it the benefits that has given to us as growing professionals and human beings or simply to try to find solutions based on what it is already around us, is part of the task in which not only dedicated or enthusiastic scientists should be involved, but it must be a whole network of circular support. Environmental and moral concerns should be involved from the process of having an idea, making this idea a creation, to each of its ramifications and resulting coincidences. Our main values considered in order to cover all the potential risks and keep them in mind are: integrity, responsibility, balance, accountability, commitment, perseverance and innovation; all of them with the intention of having under control not only the specific project parts and their interactions but also the whole range of applications.
03
Biocontainment
Using the collaborative component and knowledge of different interested teams, we developed a biocontainment round table along with the MSU team to highlight the importance of biosecurity and biosafety in project development in iGEM. This activity is important not only to discuss the methods used for biocontainment of the potential results of synbio projects such as those developed in iGEM, but also to be able to educate the participating population to take part on the consideration of possible risks involved in its development and implementation regardless of the scale at which it is carried out, considering the characteristics of their projects and applications they aspire to or visualize.
Synbio Clubs
An inspirational tool for new potential iGEMers
In Costa Rica only 4 teams have participated in iGEM, including ourselves. As the most recent team in our country and based on our experience as one of the teams with the most participants so far, we know how difficult it can be to recruit participants, not because of unwillingness, but because of lack of information. Hence, we consider it vital not only to tell our experience as a team, but also to spread the word and motivate others about the possibility to participate, making it a point to evidence that they do not have to be experts in synbio to be able to develop projects of high value. With synbio clubs we encourage the search for interdisciplinarity, creativity and interest in having a positive and responsible impact not only in science, but also in society and the environment that provides us the problems and elements with which we are going to work to generate a range of possible solutions.
Shipping Policies in Costa Rica
An inspirational tool for new potential iGEMers
Following After iGEM’s initiative, we assumed the task of consulting, registering and analyzing the different procedures and their limitations of our country for the entry of certain reagents, equipment, genetic parts and microorganisms necessary to work in the synbio world. It is relevant to establish a guide for other future teams and stakeholders and, in addition, to establish possible routes to simplify and cover permissions to accelerate scientific development, which, in our case as a developing country of Latin America, means having to make visible the potential we already possess.
Participation in various events
Medsci Week
Virtual event on science and technology applied in the field of medicine in which we presented our project to the general public, organized by the CAS and EMBS student chapters of the ITCR IEEE.
Jornadas de Bioinformática Clínica (Conference on Clinical Bioinformatics)
An open and prestigious event organized by the Technical Council of Clinical Bioinformatics in which we presented our project alongside high-level experts in several projects whose intersection was found in the use of bioinformatics for possible clinical applications.
Talk for the Mathematics School of the University of Costa Rica
We were invited to give a talk on our project and the general involvement of mathematics in the iGEM competition by the professors of the Mathematics School of the University of Costa Rica in order to promote the involvement of students of this area in the competition and biology related areas in general.
Equal access to labs
Nonetheless, we also want to shed light to a problem that existed way before the pandemic. The access to education was not equal before the pandemic, access to lab being very limited in several parts of the world and lacking from many career curriculums.
Virtual labs & Interactives
We believe all students deserve the opportunity to learn about these spaces, tools and protocols with ease, and this is the reason behind the development of our virtual labs and interactives, which portray scientific knowledge and experiences in a comprehensible, dynamic and graphic way. These also include less renowned topics regarding synthetic biology in many cases referencing iGEM in order to interest more people in the competition and spread the word even further. Finally, to be able to be a content developer for Labxchange was the cherry on top of the cake, since it fulfilled our diffusion and democratization goals to an extent we could’ve never imagined.
01
Impact
New applications were suggested as well, having the distinct element of being an integral representation of our possible users and their various backgrounds. The integration of our human practices in our implementation itself opened doors for the scientific community, specially the scientists we interviewed, to explore a previously unknown way thinking. We believe our short introduction to sequential logic will be the key for harnessing sequential logic’s potential as implied by our follow-up meetings with our users.
02
Improving on past projects
As part of our implementation we also analyzed different iGEM 2020 team projects in order to improve them by applying our circuit and framework on a case by case basis. Based on our systems and the areas of application that we chose to demonstrate the utility of our technologies, we looked on over eight iGEM 2020 projects: iGEM Hong Kong-City U, iGEM Nottingham, iGEM BIT-China, iGEM DeNovocastrians, iGEM NAU-China, iGEM UNI-Lausanne, iGEM UM Macau and iGEM Hannover.
01
User Driven Mindset
Establishing this mindset from the beginning of the project and having it as its core has made our solution really meet the needs of our users and extend the positive impact on the scientific community. We invite other iGEM teams to follow this line of work in their own projects and highlight the key role of involving designers early in the project to succeed in this area.
02
Storytelling
Due to the characteristics of our project, we knew that its effective communication would not be easy, so we have created a narrative through our project, which has facilitated the communication and interaction of the team both internally and with users. Our documentation serves as good reference for other teams to build on this area and develop their own stories.
03
Communication
As an interdisciplinary team, we know scientific communication is complicated for both people who are not in STEM, or in a different field, but also for scientists to develop. Therefore, the two previous points unite on the integral communication of the project. For this, design has been applied in every sense with a functional interest in mind: our desire is for our content to not be just pretty, but to precisely be able to communicate what we mean and who we are in an efficient and easy to understand manner. This is applied throughout the entire project, from the wiki and its content, to the management of the brand in social networks and the video-presentations used throughout the competition. For this endeavour we used other iGEM teams’ wikis and content as reference and inspiration, and in turn, we hope ours can serve the same purpose.
04
Holistic Approach
Involvement of social sciences
As scientists we are required to think about the ethical consequences of our developments; as a team we decided to go even further taking advantage of our team member’s involvement in the social sciences to bring them into the competition. Making use of social sciences’ research principles and perspective a huge impact can be made in understanding and involving public opinion as we establish in the content developed in order to make this perspective accessible for other teams to follow our example without being experts.
05
Intellectual Property & Regulation
In our country, Costa Rica, we have the great responsibility to preserve the biological resources we have, and this complicates the bureaucracy to carry out research processes related to the synthetic biology area. This motivated us to investigate the current biotechnological legal frameworks in our country, the bodies responsible for ensuring compliance, the necessary permissions and requirements, among other aspects based on the previous research carried out for the same purpose in Mexico by the UANL team and Ohio state's team in 2020. This can serve as future reference for other teams who wish to do this research, and for Costa Rican scientists to refer to when needed.