Team:Patras/Contribution
Contribution
Life is not accumulation, it is about contribution.
- All
- Overview
- Build upon Oxford Nanopore
- Novel Variants
- Audio Description
- Sustainable Development Goals
- Sign Language
Our contributions to the iGEM community were one of our main goals. In our project, we used existing tools, and our vision is to set us as an example for future iGEM teams to build upon our workflow for research. Our team is proposing the "MinION" device of Oxford Nanopore, a device for DNA and RNA sequencing that can be easily adjusted by future teams too. To make sequencing and its applications more understood for future teams, we decided to make a comprehensive workflow for the identification & functional characterization of PGx variants based not only on rare and novel variants-polymorphisms acquired by our experiments but also on common polymorphisms from older pharmacogenetic studies. This will allow future teams to propose the proper adjustment of drug dosage, giving them even the opportunity to fill it with novel polymorphisms. Thus it could be an invention in order to make it viable for further development after the iGEM competition to make their ambitious ideas come to full fruition. Lastly, our team has gone to great lengths to include visually impaired people in our project. We documented the measures we took to achieve this goal so future teams can do the same!
Build upon Oxford Nanopore
To fulfill our goal of finding a portable, real-time device for DNA sequencing, we investigated the Oxford Nanopore Company. The company developed innovative and portable devices for sequencing with a lot of advantages compared to existing tools for sequencing. After research, "MinION device" was suitable for conducting our experiments. Using this device, Pharmacogenomics can be more accessible to everyone. It is more inexpensive for a physician to acquire a portable device to perform sequencing than to look for a physical laboratory or to create one in his place, which has proven difficult for someone settled in a remote area.
This sequencing tool gives us the opportunity to sequence everywhere with low cost and real-time data saving. Moreover, its applications include detection of the rare/novel variants by whole-genome analysis, which is project PGasus' main goal. Minion's results have been engineered into gene constructs encoding CYP2D6 & CYP2C19 enzymes, and they have been characterized as harmful or benign and compared against in silico prediction scores. Finally, it helped us develop a comprehensive workflow for the identification & functional characterization of PGx variants.
Novel Variants
After our team set up the goal to functionally characterize novel variants, we would like to investigate how we could apply our results to the community of medicine. To do so, we spent approximately a year reading primary research articles, conducting site-directed mutagenesis and consulting professionals in the field. Although we successfully identified novel variants’ effects on eukaryotic cells for our project, we found this searching process time consuming, energy-draining, and sometimes frustrating. Meanwhile, from 2016 to 2020, we noticed that 26 iGEM teams selected the diagnostic track per year, and only Team Patras occupied Pharmacogenomics. Considering these situations, after conducting all the right steps and processes regarding the approval of the detected novel variants, lab technicians in diagnostic labs, for starters and later doctors in clinics, will have the prospect to also consider these variants before prescribing a drug to a patient by adjusting its dose. We have to admit that even if it is a long-term procedure, it can lead to the enrichment of the already existing pharmacogenetic panels with new variants. Thus, the faster this process of improving the services provided by pharmacogenomic platforms occurs, the less likely it is that a patient will not have a proper dose adjustment due to a novel variant he may have in his genome.
In summary, we gave information about characterizing various mutations to propose the proper adjustment of drug dosage. We presented all the novel and rare variants being detected and, at the same time, the already reported variants according to the genomic databases. Thus, this information could be used by future iGEM teams and scientists in the field in order to be further checked and compared with the detected common variants and guidelines. Taken together, especially rare and novel variants account for a considerable percentage of the whole population; the determination of their effects on drug response and adverse effects would be essential for the improvement of personalized medicine. This will be used by anyone who could perform a sequencing analysis in order to make the process even more effortless.
A wiki guide to include audio description
Trying to make our project as accessible as possible, we researched on how to include Audio Descriptions on our site. Audio Description involves the accessibility of the visual text for people who are blind, have low vision, or who are otherwise visually impaired. It is a narration service that attempts to describe what the sighted person takes for granted. We want to make Synthetic Biology accessible to everyone by eliminating this barrier. Thus, we propose everyone follow the instructions to give the opportunity to have access to every site.
First of all, it is necessary to install the Google extension “Read Aloud” and then to select the pin which is near to the name of the extension on the toolbar. After that, the “Read Aloud” extension will appear. If you want to check it, you have to search 2021.igem.org/Team:Patras and the audio description starts. Furthermore, there are different settings you can regulate. The voice could be set as female or male and the speed and the pitch of the voice could be regulated, too. There is the chance to highlight the text during audio description. You can find more information in Diversity and Inclusivity wiki page.
The United Nations' 17 Sustainable Development Goals
The 2030 Agenda for Sustainable Development, adopted by all United Nations Member States in 2015, provides a shared blueprint for peace and prosperity for people and the planet, now and into the future. At its heart are the 17 Sustainable Development Goals (SDGs), which are an urgent call for action by all countries - developed and developing - in a global partnership. The iGEM competition has already adopted these 17 UN's goals, understanding the need for international cooperation to create a better future.
Understanding this need, we have the idea of creating an informative video about Sustainable Development Goals through iGEM projects because we did a survey, and most people didn't know much information about them and their applications. Thus, we created a video in which many iGEM teams share their project and the sustainable development goals they aim to achieve to show what amazing things can be achieved by synthetic biology. In the "SDGs" video, every team explained their project, especially the problem they struggle to solve through synthetic biology and what goals they want to achieve by developing this iGEM project. After that, we made a compilation of all these amazing ideas. Such an innovative idea to spread Sustainable Development Goals and its importance!
iGEM Teams together could leave their footprint in the real world and show people how useful it is to use synthetic biology to solve real problems. Undoubtedly there are many ways in which one can improve the world we live in. In our video, iGEM Teams explored the 17 most promising actions that could have the most impact on our planet by 2030. From ending world poverty and taking action on climate change to gender equality, clean water, and sanitation for all, the power of ordinary people working collectively to improve our world can indeed have extraordinary outcome. Let's make it happen.
Particularly, SDG 17 reads, "Strengthen the means of implementation and revitalize the Global Partnership for Sustainable Development." It recognizes multi-stakeholder partnerships as important vehicles for mobilizing and sharing knowledge, expertise, technologies, and financial resources to support sustainable development goals in all countries, particularly developing countries. So, we adopted all the aforementioned goals, following the example that the iGEM Competition set, and tried to implement them into our project. Starting with the 17th goal, we set the ideals of cooperation and partnership as our fundamental values since the beginning of our journey. To be more specific, we collaborated not only with many iGEM teams for collaboration activities but also cooperated with iGEM Thessaloniki and did partnership all over the year in many different fields. You can find more on the partnership page.
Firstly, we should underline that SDG number 3 is a keystone of Project PGasus! Every one of our moves was in the direction of "ensuring healthy lives and promoting well-being for all ages" by reducing drugs' side effects. Our work's global impact is easily understandable, taking into consideration that these drugs are widely administered against cardiovascular, psychiatric, or other common diseases.
Furthermore, the 5th SDG is a goal that wants to "achieve gender equality and empower all women and girls." Investing and supporting gender equality is the only way for any scientific team that wants to succeed. History has shown that several women have succeeded in various scientific fields, such as J. Dudna & E.M. Charpentier, awarded the Nobel prize in Chemistry 2020. Our composition proves that human gender equality plays a vital role in our life as 10 out of our 19 members are women. In addition, we organized the Rosalind Chronicles collaboration, a Bulletin Board to honor the contribution of Women in STEM on a larger scale. This activity aimed to inspire and broaden women's horizons, empowered them to believe in themselves, aim higher, and excel in any field of science they put their minds into, no matter their gender.
Sustainable economic growth - SDG number 8 - could also be achieved via Project PGasus. The Ministry of Health and other relevant government agencies can make the PGasus project available to public hospitals and laboratories in metropolitan areas and remote ones, taking advantage of its portability. The time needed for sequencing is decreased through our system, while the cost is remarkably reduced compared to existing methods. Promoting sustained, inclusive, and sustainable economic growth, full and productive employment, and decent work for all has always been a great challenge for us. Still, we made it as we managed to propose a way to save money for the patients and the public health systems by reducing the side effects of drugs and hospitalization rates.
As far as the 10th goal is concerned, reducing inequalities, our team made a significant effort to achieve it. We would like to ensure no one is left behind, so we try as much as possible to create a diagnostic system that is not very expensive and understandable by most doctors.
iGEM Patras 2021 team highlighted the efforts and projects of previous iGEM teams, gave practical and theoretical supplies to future generations, and supported 5 of the sustainable development goals established by the United Nations to be remarkable in the history of the iGEM competition.
Sign Language
As we are also describing in our Inclusion Page we tried to make science, and especially Synthetic Biology, accessible to everyone, by including the international sign language into our iGEM Videos. Since, our team is one of the first that made this huge step towards everyone’s inclusion in SynBio, we totally recommend that future teams add this type of content into their Competition videos. We are pleased that we contributed to make biology understandable to hearing impaired people and we hope that our actions will have a positive impact.
