Contribution

Our team's participation in the iGEM Global Competition aimed to maximize our impact within the iGEM community and the broader scientific community, particularly in the field of Synthetic Biology. By setting these goals, we successfully achieved our objective through various contributions to our project, e-PHAESTUS.

Genes of GshFss and PPKTe

The genes of GshFss and PPKTe as optimized for IDT synthesis (a long-time partner of iGEM) and made to comply with the Type IIS cloning standard are the contribution of our Wet Lab Team to the iGEM Community.

These genes are outlined and described in their part pages, giving future iGEM teams a headstart in understanding glutathione production and how it can be optimized. In addition, the ways to express them are outlined and detailed in this Wiki and allow for a reproduction of our experiments. We hope that this knowledge will be the basis for further exploration of glutathione production.

For a comprehensive list of parts please see the Parts table at Basic Parts page.

Python Script: 'calculate_B_factors.py'

Our team developed a powerful Python-based tool to streamline the analysis of protein structures by calculating B-factors for specific regions of interest. This script parses PDB files to extract and average residue B-factors, providing insights into protein flexibility and dynamics. Additionally, it leverages data from CSV files containing loop information to efficiently compute average B-factors for defined loops, which are often critical in understanding protein functionality. The results are automatically exported in a user-friendly CSV format, facilitating visualization and interpretation.

This Python script serves as a versatile resource for iGEM teams and researchers engaged in structural biology, protein engineering, or synthetic biology projects. By automating the B-factor analysis process, our script eliminates the need for manual calculations and empowers teams to focus on the broader implications of their work. We believe that sharing this tool will enable teams to accelerate their research and deepen their understanding of protein dynamics across various projects.

Python Script: 'calculate_loopdepth.py'

We have also developed a Python script that calculates the spatial depth of protein loops relative to the protein's center of mass. This script parses PDB files to extract atomic coordinates and computes the center of mass, offering critical insights into the protein’s structural arrangement. By cross-referencing loop data from CSV files, the tool estimates the depth of each loop, helping researchers understand how deeply loops are embedded within the protein’s 3D structure. The results are saved in an intuitive CSV format for easy integration into further analyses.

This script is designed to empower iGEM teams and other research groups to explore protein structure-function relationships more effectively. By automating the computation of loop depths, our tool provides valuable spatial insights that can be applied in protein design, molecular docking studies, or enzyme engineering. Sharing this resource reflects our commitment to advancing fellow researchers' work and accelerating breakthroughs in synthetic biology.

Through our initiatives, we made a concerted effort to engage individuals from diverse age groups, social backgrounds, and fields of knowledge. Tailoring our materials to suit our audience maximized benefits for both our team and the participants. Some of our most noteworthy actions are highlighted below, while you can find more details on our Human Practices page and Education page.

Education Initiatives

DaProtein Code: The Survival Code

Students from various grades in primary and secondary education successfully participated in the first escape room created by our team as part of the Athens Science Festival. By solving a mystery, younger students absorbed new knowledge about Biology, while older students were encouraged to recall concepts learned in previous years. Alongside this creative approach to knowledge-sharing, parents and guardians had the opportunity to learn about the iGEM competition, our initiatives, and our team's participation in the event.

Biomunch

This initiative offers the perfect combination of fun and education regarding our team's project. Participants can learn about our broader concept this year, which focuses on the binding of metals found in electronic devices. The goal of the game is to "consume" all the metals without coming into contact with the electronic devices.

2nd National Competition of Riddles in Synthetic Biology

This year, our team successfully reached out to groups from across Greece, who expressed interest in participating in the Synthetic Biology Riddles Competition. Through a series of challenging topics, each team showcased their knowledge, with the top-performing teams awarded at a special event. This event highlighted both our team and the iGEM competition, with attendance exceeding all expectations.

Integrated Human Practices

Through our communication with companies operating within Greece, we secured significant support during the development and advancement of our project. Engaging with companies, communicating scientific concepts, and exchanging ideas contribute to the iGEM community's influence in the industrial sector and help build trusting relationships between both sides. With businesses supporting the ambitious ideas developed by young participants in the competition, the iGEM initiative gains wider public recognition, allowing projects to grow in scope and potentially leading to the implementation of ideas at both pilot and mass production levels.

Collaborations

iGEM Athens x iGEM Leuven

Following a joint initiative between our teams aimed at communicating science to the general public and due to the shared focus of both projects, we developed a questionnaire inviting participants to answer a series of questions about electronic waste. Despite a small sample size of responses, the teams gathered valuable data for each project, which can also be utilized by the iGEM community and teams interested in similar topics in the future.

Social Media

Social media serves as the most effective and accessible platform for communicating and disseminating ideas to the public. Through quizzes, engaging posts on various platforms, podcasts, and vidcasts, our team has connected with individuals from diverse social and age backgrounds. By leveraging both visual and auditory mediums, we effectively shared our perspectives and ideas, reinforcing the values of scientific inquiry.