Difference between revisions of "Team:Lethbridge/HP/Gold Integrated"

Our gold and integrated practices were two large components of our project this year as we took into consideration what our user groups needed and how we could ensure we were providing a safe tool. Based on our conversations with educators and members of the DIY biology community, we decided to focus on education as an application of our cell-free system. To ensure our system would be safe and available for people to use around the world, we explored the regulations surrounding synthetic biology and cell-free systems. We also discovered a potential dual-use of our system and came up with a solution to this using software.

Education Kit

Taking into account the suggestions we received from the interviews we conducted with educators, we have developed a simple experiment that aligns with the Alberta Biology 30 curriculum [1]. Members of the University of Lethbridge iGEM community have previously looked at how the principles of iGEM aligns with the Alberta curriculum [2]. Derek Masterman, a high school teacher, suggested we use physical indicators to ensure students understand that the processes are separate. To validate the occurrence of transcription, the fluorescence capability of the RNA Mango aptamer was employed. Translation is confirmed based upon the chemical reaction between salicylic acid and the protein BMST1 (Paris Bettencourt 2014  BBa_K1403009 ) to produce a wintergreen scent.

During the development of this experiment, we received feedback from students on the Lethbridge High School iGEM Team (pictured below), Keith Aiken (an education student and member of the Lethbridge iGEM team), and Patrick Shackleford (a biology teacher from Winston Churchill High School). The high school students suggested the inclusion of figure captions to avoid student confusion. Keith sent us the current Alberta curriculum guidelines for us to base our learning objectives off of. Our modules were sent to Patrick and he confirmed that they are aligned with what is currently taught as part of the Biology curriculum (pictured below).

In addition to the transcription and translation protocol, we also developed a biosafety module. We designed this module in response to conversations with the Public Health Agency of Canada. They recommended that students need to understand how to interact with microorganisms at an early age to ensure lab safety and proper procedure in the future. Using Next vivo as a protein expression system the students could mimic working with a microorganism while getting the same results as working directly with a living cells. Additionally, our Next vivo system was designed to be safe for use anywhere as cell-free systems lack the ability to propagate and thus lowers the biosafety risk. Combining our transcription and translation protocols, biosafety module, and Next vivo system together would provide teachers an ideal tool to teach their students the principles of synthetic biology, protein synthesis, and proper laboratory techniques. With that, we are happy to announce the creation of the Next vivo Education kit!

Student's Guide	Teacher's Guide	Biosafety Module

We are currently developing more experiments that can utilize our cell-free Next vivo system. Further development is required to fully align our Education kit experiments with STEAM (Science, Technology, Engineering, Arts, and Mathematics) initiatives to complement the Lethbridge High School iGEM Team's proposal. Additional development toward introductory and intermediate level kits to suit the DIY Biology community based on their feedback have also been a priority for our team.

Professional Development

Within education, Professional Development (PD) days are defined as a variety of specialized training sessions to help administrators and teachers improve their ability to teach [3]. To better integrate synthetic biology concepts within the existing Alberta curriculum, the teachers we spoke with suggested that training sessions during PD days would be an effective way to ensure that teachers understand the concepts to effectively teach students. Our team paired up with SynBridge, a makerspace located in the University of Lethbridge, to begin the process of hosting these workshops. Our team will work on designing these workshops, with SynBridge providing the space to host them and acting as a resource for teachers after our iGEM season has ended.

We met with Emily Wilton, the coordinator for SynBridge, to discuss the design of the PD Day workshops and the content taught. Emily told us that they would like to provide the workshops free of charge or at a subsidized rate for the schools, which helps to accommodate the limited teaching budgets schools have. Initial experimental designs and We would also work on the design of experiments to teach, while keeping in contact with teachers to ensure they would meet the curriculum needs.

When we discussed our plans with the Winston Churchill Science Department, the best direction to have the PD days instilled was discussed. They suggested forming a collaborative community. In Alberta, a collaborative community is defined as a group of teachers being able to focus on any one school related topic and is open for any teacher to join. Moving forward in this direction, this would also allow these PD days to be open to the whole school district in Lethbridge.

The teachers are planning on visiting SynBridge facilities on April 9th, 2018 and plan on using this visit to move forward with the development of more synthetic biology initiatives in their curriculum. We plan on this being a long-term initiative to be continued on after our season has ended.

Regulation Research

To understand if synthetic biology products and cell-free systems were regulated around the world, we researched relevant legislation. Table 1 is an overview of the regulations that we could find that are implemented in the four legal systems used as was suggested to us by Ian Andrews . Figure 1 is a map of the world to show which countries fall under one of the four legal systems mentioned. We concluded that some legal systems have more established regulations for the use of products derived using biotechnology. Most countries have in place some form of assessments to ensure that any products produced will not have detrimental effects on the environment and human health. As the use of biotechnology grows, we envision that more protocols and legislation will be enacted on the international level to have a more standardized way of regulating products and how they can be used within the different legal systems.

Table 1 - Overview of regulations related to the implementation of biotechnology and organismal based devices in society by legal system [5-41].

We looked further into the regulations of biotechnology products in Canada and the United and tried to find any piece of legislation that mentioned the regulation of cell-free systems. Within Canada and the United States they do not regulate the methodology of how products are made; they focus on the end product. While we could not find any specific mention of "cell-free", Ian was able to clarify within our interview as to why we were unable to find any direct mentions. However, the piece of legislation that we could find that was the most associated with our project is the Assisted Human Reproduction Act in Canada as it prohibits transplanting human-based materials into non-human life forms. From our research, we have been able to determine that cell-free systems are indirectly regulated by existing legislation. Moving forwards with the rapid growth of the biotechnology industry as a whole, it will be pertinent that those involved with the scientific community work with law-makers to develop regulations that are comprehensive enough to capture the growth of the industry to the best of their abilities.

Table 2 abbreviations
• HC: Health Canada
• EC: Environment Canada
• CFIA: Canadian Food Inspection Agency
• PMRA: Pest Management Regulatory Agency
• PHAC: Public Health Agency of Canada
• FDA: Federal Food and Drug Agency
• EPA: Environmental Protection Agency
• APHIS: Animal and Plant Health Inspection Service

Biocontainment

In all living organisms each amino acid is encoded by a three nucleotide codon. Changing which codon corresponds to which amino acid has been of scientific interest for many years but has proved difficult as changing one would require changing them throughout the genome, a non-trivial task. As such, the implications of large-scale genetic recoding has never been a concern of biosecurity.

Our cell-free system is quite amenable to recoding as the tRNA anticodon can be altered prior to expression changing what amino acid is coded by each codon (see Biocontainment section in Design). As such we hoped to use this feature to make our Next vivo safe for use outside of laboratories. Changing the tRNA anticodons results in a modified codon table that can be used for encoding DNA or RNA message as an input. By altering our system to only read a modified code, it prevents environmental sequences from contaminating our system modified inputs from being transferred to living organisms and/or modified inputs from being transferred to living organisms [42]. This prevents accidental environmental contamination being introduced by our system. From the research we conducted within environmental regulations, our system becomes more in-line with current regulations and their aim to ensure that synthetic biology produced products do not have a detrimental effect on the environment.

This season we explored the possibilities of how to generate modified sequences. We developed a codon reassignment tool that allows further research into creating safe orthogonal systems. However, this lead us to consider the dual-use implications of this kind of technology for society, particularly DNA synthesis companies. These companies rely on BLAST to detect any harmful sequences sent in DNA synthesis orders. If modified codon tables were used instead of the standard codon table, the companies would not be able to identify harmful sequences. This gap within the current bioinformatic workflow is an issue with no solution being actively pursued by concerned parties. We have come up with a software suite as a solution to this problem and have been in contact with multiple companies for them to test if they could detect a harmful sequence. It was suggested to us in our biosecurity interviews that this may not have been an issue that DNA Synthesis Companies have had to deal with before. We felt it was in the best interest of the synthesis companies to inform them of what we found.

Achievements