Throughout our iGEM journey as a team we learned a lot from our instructors, experts, farmers, politicians and fellow students. We are excited to share this newly acquired knowledge with the wide iGEM community through our project. With this page we want to provide a general overview of the contributions made during our work on RhyzUp. We hope that future iGEM teams that want to address the issue of drought will find inspiration and benefit from our project.

icon Wet Lab

Parts:

Our final construct consists of a two-plasmid biofilm overexpression system, composed of a variety of parts. To achieve an increase in the biofilm produced in our bacteria, we have implemented both an enzyme-upregulation and an enzyme-downregulation module, coupled together in a positive feedback loop system. Through a tight sensing system and a kill switch we limit the spread of our genetic circuit in the environment. All composite parts we used can be found under Parts.

Our contribution consists of:

  • The pXut xylose-sensing promoter and its inducer protein XutR
  • Mutations of the diguanylate cyclase (DGC) enzyme of Pseudomonas sp. IsoF: PisoF R240A and PisoF R196A
  • Improved existing part - the WspR mutation
  • A sgRNA that targets the phosphodiesterase (PDE) enzyme
  • A collection of composite parts that build a feedback loop
  • CcdB toxin tests
  • Inducible rhamnose promoter tests
  • A final construct with two Level 2 plasmids

Moreover, having conducted most of our tests in Pseudomonas species IsoF, we provide future teams with a collection of protocols adjusted specifically for the use of this strain which had not previously been used by iGEM teams Protocol.

icon Dry Lab

Model

Our Model page can be used as a guide for planning a similar flux balance analysis (FBA) with a focus on biofilm production. It explains how to design and implement in silico experiments in an adapted model. The FBA explanation example, the code, and references are particularly useful for future teams to get started with constructing a model. This further enhances the collective knowledge of iGEM.

Our team struggled to find information on how to model a soil environment for our FBA, prompting us to develop our own design. Future iGEM teams are encouraged to use our source code, our script for automated condition implementation in FBA and in particular our settings for different soil and rhizosphere conditions.

All files in our repository are provided for use in educational, research, or non-profit projects, with proper attribution, and are not to be used for commercial purposes without prior permission.

Wiki:

We made an effort to code as clearly as possible, and to comment on crucial parts of our code, so that future teams can use it as a guide on how to get from the template to a finished wiki. Custom features such as the “flipping cards” (see Team page) and “scrollable timeline” (see Notebook) could be of interest to future wikis as well.

icon Human Practices

How Agricultural Practices Relate to Sustainable Development

Our subpage “Sustainable Development” in the Human Practices page contains a lot of information on sustainability and agriculture. By extracting information from our interviews with agrometeorology experts, farmers, plant protection experts and several other stakeholders and additionally conducting a lot of research, we provide a solid basis of understanding threats to agriculture.

This is useful for any future iGEM-Team that competes in the “Agriculture” village.
Topics that were specifically researched include:

  • Drought as a threat to agriculture: Switzerland and Ethiopia
  • Sustainability issues of fertilizers: Algal blooms
  • Sustainability issues of pesticides: Human health and ecology
  • Sustainability issues of current irrigation systems

GMOs in Agriculture: Swiss Legislation, Consumer Perception, Criticism

During our interviews with stakeholders from NGOs critical of applications of gene technology in agriculture, consumer behavior experts, and ethicists, we built a good understanding of the current debate around GMOs in Switzerland. In the chapter “Ethics, Law, Politics and Consumer Perception” in the “Integrated Human Practices”, a lot of this knowledge is summarized. We explored how current Swiss legislation of GMOs affects the implementation of our project in the “Regulation” chapter of the “Entrepreneurship and Implementation” subpage of our wiki, where we collected a lot of information on Swiss law regarding applications of gene technology.

Both chapters are of special use for any future iGEM team that plans on gaining a good understanding of GMO legislation in Switzerland. Also, it is of good use for future teams that try to follow the topic in the course of time.

A question that we specifically addressed was the question of how microorganisms and more specifically genetically engineered microorganisms used in agriculture are regulated in Switzerland.
This can also be found in the “Regulation” chapter of the “Entrepreneurship and Implementation” subpage.

Scavenger Hunt through Zurich – Protocol

For the Swiss iGEM meetup we organized for the EPFL Lausanne, the University of Lausanne, the ETH Zürich, and our own University of Zurich team, we planned a scavenger hunt through Zurich. During this scavenger hunt, any number of groups compete by solving six riddles that lead them to historic locations all around Zurich.
The protocol for the scavenger hunt is uploaded to our wiki and can easily be adapted for anyone interested in playing the game. Besides the document containing all riddles, there is a document with the solutions to the riddles.

We hope that some iGEMers will partake in our scavenger hunt if they were to visit Zurich. We can totally recommend it, it was a lot of fun!