We established a list of goals to be achieved over the course of the following year as we began this year's endeavour. In addition to these goals, we also wanted to promote synthetic biology as much as we could within the Egyptian community, especially given that there are now just two Egyptian and three African teams competing in iGEM. The absence of fundamental information about synthetic biology and its applications to enhancing quality of life is one of the challenges that African nations must overcome. By sharing this information, we could potentially attract more African participants and introduce them to the field of SynBio. As a result, we distributed a message to undergraduates all around Egypt encouraging them to form multidisciplinary teams and offering to give them a lecture on the iGEM application process. Al-Galala University was one of the universities that showed a lot of interest and requested additional details. In order to educate them the fundamentals of the iGEM competition, we went on an official visit; the specifics of that tour are covered in the human practices. A bright new generation of researchers and synthetic biologists would be created as a result. We tried our best to reach this precise goal throughout the course of the year in a variety of ways, one of which was the SynFair programme, where we host young students and instruct them on the fundamentals of synthetic biology through brief lectures and workshops with quizzes.
However, the SynFair has been running for a few years, and other iGEM teams have taken inspiration from our event and held their own SynFairs with courses and participant competitions. This year, we made the decision to slightly veer from tradition and create a scaled-down version of the iGEM competition for the students. The event this year is now known as "iGEM Camp."
The first move we made was complete the task we started last year. The projects of participants from the previous year would be assessed and graded by eminent tutors from a variety of disciplines, including genetics, research, and synthetic biology. As promised, we forwarded the projects to the judges for examination. After we received their comments, we invited the participants from the previous year back to our location to share the results and recognise the top project.
In addition, we went a step further and invited the top competitors from last year's SynFair to the iGEM camp.
To promote the iGEM competition to school pupils, a two-day iGEM camp was planned. We began the first day by introducing our team members and going into great depth about how we developed our rooster and the procedure for creating a new iGEM team. We then educated them on the various iGEM tracks. A presentation on the components of a wiki page and how they are put together without going into the coding specifics followed. The human practices portion with all of its branches was then explained. We went into great length about the dry lab. To simulate the dynamics of projects' systems, we presented a succinct lecture on mathematical modelling. The need of having clear graphics to depict one's work was discussed in the lecture. The lecture included the importance of graphical representation of one's work in an easily-understandable way. To assist students in plotting their systems, we also demonstrated how to construct ordinary differential equations (ODEs). Python was used throughout the tutorial to plot the equations and provide graphs. In order to fit the equations into experiments, they have also received training in retrieving parameter values and altering them. Another in-depth instruction was available on NUPACK, an online programme that aids in anticipating the secondary structures of the components being employed. Additionally, we instructed them on how to execute thermodynamic simulations and decipher the output, including mean free energy in the before- and after-bound state. The Toehold Switch, which resembles a hairpin, and its target mi-RNA were the objects of the trained model. These workshops exposed them to actual situations, which helped them comprehend crucial transitional steps prior to the wet lab.
Wet lab was our final activity, and we taught the kids about the necessary safety measures. They were instructed on the construction of parts using Synthetic Biology Open Language (SBOLs). We then went over the procedure for assembling pieces by ligating them to one another using restriction enzymes (Digestion & Ligation). The day was over after that.
We asked the pupils to put their knowledge into practice on day two. First, we instructed them to divide into four groups of ten people each. Each team was then further divided into three categories: Wiki, Human Practices, and Scientific. They began by generating ideas for the project in a brainstorming session. The designs and sections of their own wiki pages were then created. The human practices division of each team then arranged who they would meet with and the locations where they would distribute surveys and acquire data. They created their own ODEs for the scientific areas. They put on their lab coats, went into the wet lab, read the pre-written protocols posted on the board, and then followed their designated instructor's instructions to do their own digestion and ligation. Finally, they performed gel electrophoresis on their samples and recorded the results.
Each team gave a ten-minute presentation that included all of their work for the audience to round up the event and was given a participation certificate.
The Egyptian meet-up had participants who were enrolled in iGEM before and ones who plan to join it in the upcoming years, but it also had ones who were interested in synthetic biology and did not know much about the competition. As a result, we started by defining the competition itself to everyone and explaining its tracks and the process of being part of the competition.
Moreover, there was a synthetic biology workshop given by five members of our team: Ahmed Shaalan, Khalid Al-Hela, Ahmed Wael, Hossam Banis, and Mohamed Abo Al-Ghar. The course started with tutorial on building a genetic circuit. The second lecture was about using restriction enzymes and bio-bricks and as our project involves colorimetric detection, a brief introduction to fluorescence and how it started was the topic of the third lecture. We also gave a brief overview of the basics of toe-hold switches. Finally, Khalid Al-Hela gave details about logic gates and their different types and usages.
Ahmed Gamal Matar lectured the audience about Mathematical modeling and its application in synthetic biology. Dr. Mohamed Tarik introduced the viewers to bioinformatics and databases. Finally, Dr. Mohamed Elhadidy described the Galaxy website and how it can be used to detect genetic mutations between variants. It was definitely beneficial for us, and we were grateful for the opportunity to be taught by him that day.
We received word from our college that we had a visit from a newly opened institute, Al Galala University, and they showed interest in iGEM and wanted a brief session about the competition as they wanted to inquire about the process of joining the iGEM universe.
We saw this as a great opportunity to spread the knowledge about iGEM and make it more popular in our local area. We immediately joined them and listened to what they needed. We had to give a very brief introduction about the competition. We mainly spoke about the broad lines of the competition and gave detailed history of our previous achievements at iGEM.
They showed great interest in the competition as a whole but required more detailed information. So, we decided to arrange a future meeting where the center of discussion would be iGEM and how to build a team, enroll in the competition, what tracks are available, and how to fulfill medal criteria.
Our team had a visit to El Galala University, responding to the university’s request when they visited our college. The day kicked off with a welcome speech and they expressed their full interest in research & in iGEM competition specifically. Then, they gave us a tour in the university. The tour ended with heading to a lecture hall in which our lectures were to be given.
For the first lecture, our colleague Yasser Al-Bedewi gave a brief introduction to iGEM and the history of the competition with our team’s previous achievements starting since 2017; he also explained the team building process and how to choose your new team members. Afterwards, another colleague, Mohamed Hasouna, started presenting a brief overview of iGEM tracks and fields; he explained the human practices, scientific, and media parts of the competition. For a closure, he discussed the full medal criteria for the future iGEMers. Mohamed Mattar started with a lecture about mathematical modeling that proved very challenging to the students, but they all got it in the end and did some modeling themselves. Finally, Dr. Mohamed Tarek gave a brief introduction to bioinformatics and synthetic biology.
A Synthetic Biology and Genetic Circuits Workshop was held in collaboration with the AUC Biology Association, where we gave various lectures and workshops regarding SynBio and how to enter the iGEM competition.
Lectures and workshops were taught via Zoom meetings, where the attendees were divided into 2 groups; one group was given theoretical lectures while the other group was given practical workshops, with shifting between the 2 groups in between.
The lectures that were presented in workshops include:
1- An introduction to the iGEM competition; one of the team members explained the timeline of the competition and how to apply for iGEM. We also explained how to start recruiting new members of the team and what skills and knowledge they are required to have and the ones that they will gain along their journey in iGEM.
2- After which, an introduction to synthetic biology and bioinformatics was given to the attendees to explain the basic concepts of SynBio.
3- Following this session, the attendants were divided into two groups, alternating between several theoretical lectures and practical workshops.
4- The lectures given included the following:
a) A lecture on genetic circuits and restriction enzymes, where we explained the meaning of what is called ‘BioBricks’ that are the building block of these circuits and that can be extracted via processing DNA plasmids using various restriction enzymes.
b) We also gave a lecture on the integration of one of the concepts of engineering called logic gates into the science of synthetic biology, where various genetic parts can perform different functions similar to that of logic gates.
c) Another lecture was given regarding the application of mathematical modeling in the field of biology and how to apply differential and ordinary equations to the chemical reactions that occur on the cellular level.
5- As for the practical workshops, they included the following:
a) We gave a session on how to use Synthetic Biology Open Language (SBOL) to generate a different design of genetic circuits that can be used in the construction of various genetic parts. In addition, we also gave a session on how to use the Benchling website to build your plasmid for your SynBio Project.
b) Moreover, a session regarding vaccine design was also given during the event to help the attendant learn more about the process of vaccine production and about the new types of vaccines that were developed using synthetic biology.
c) Thirdly, we gave a session on how to perform molecular visualization of proteins using the software called PyMOL which is a free, open-source software tool that can be used to visualize the structure of different proteins and manipulate them freely according to the aim of your work.
d) The final workshop included a tutorial on how to use the online tool called NUPACK, which is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems.
All of the workshops were held in an interactive manner, where the participants contributed actively and shared in the training process. In addition, it was an open discussion session, where questions were allowed to be freely expressed by anyone who found any trouble with the proposed academic or practical materials.
To spread awareness about Phenylketonuria to the public, we decided to make a small guide for mothers of children with PKU to understand the disease. The guidebook has a brief definition of the disorder, with how it is inherited from parents to children. Moreover, it discusses the current diagnostic methods and management of the disease. Lastly, we sealed with the red flags and when a mother should seek medical advice and some delicious recipes that fit the dietary plan of a child with phenylketonuria. Such a guidebook would help mothers better understand the disease, when to worry, and how to support their children psychologically and medically by following strict dietary plans. We decided to make this guidebook as our surveys' results for public awareness of PKU were negative and most of the people had no idea about the disorder and how to manage it. The guidebook is now available in different languages and as a hard and soft versions for anyone to gain access to. Over the course of our human practices work, we distributed the guidebook to mothers everywhere we went. They showed gratitude and gave us positive feedbacks about it on our e-mail.
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