Team:KU ISTANBUL/Human Practices
Human Practices
We as KU-ISTANBUL team worked on creating a new technique using model organisms that may be used for diagnosis of lesions. Early diagnosis of lesions and tissue changes may make early diagnosis of cancer easier. As if we can achieve lasing from live tissues, every shape change in tissues will create a different lasing than before that can be observable. Also, our technique can be used to pick quality oocytes for in-vitro fertilization easier as quality oocytes will have characteristic lasing properties in comparison to non-quality oocytes. Oocytes can act like natural lasers so there is no need to add new gain-mediums or resonators. Also a part of our Oocyte plan got funded by TUBITAK(Biggest National Science Institute in Turkey) 2209a grant. For tracking tissue shape or stiffness changes, we are planning to insert synthetic dyes which are safe for humans(FDA approved) as gain mediums. To understand the possible safety, ethical and technical problems for our future plans, we decided to talk with IVF center doctors and oncology doctors. We also talked with an internal diseases doctor who also owns a start-up to understand how we can get our project to a start-up level in future and we also wanted to explore what kind of applications we can have in internal diseases as we also plan to use red blood cells to get lasing out of them.
Human Practices
M.D. Eser Uyanık- Internal Diseases Doctor & Co-Founder of Premea(Preventive Medicine App)
We have discussed with Dr. Eser Uyanık in Zoom to understand what kind of applications can be done in internal diseases as we know that red blood cells have high refractive index and if we insert a FDA approved fluorescent dye such as ICG, we can get lasing out of them. He told us that they already can observe what kind of shape changes blood cells have continuously, however it is hard to diagnose cirrhosis earlier and if the patients can’t prove that their livers aren’t functional, they can’t get support from the government for drugs. So we searched about the ICG and apparently it gets destroyed in livers and how fast the liver destroys ICG is a clear indication of how functional the liver is. We proposed this idea to him and he thought that it is a feasible idea and we should work on it. But what excited him the most is the possibility of tracking the changes in tissues for early diagnosis of many diseases.
We asked if inserting approved synthetic dyes will create any safety problems to tissues but he thought that it will be safe but it needs to be tested in cultures before. We also asked about his start-up Premea, which allows patients to directly contact doctors and physicians alongside with direct access to medicines. He talked about the importance of having a team who you trust. He also mentioned how patient you need to be when forming a biotech start-up company. He applied to a TUBITAK BiGG grant to form a company which gave him quite a bit of budget. He also suggested that we should apply to BiGG to form a start-up company in the future.
TUBITAK-BIDEB 2209a
In late 2019, the whole world is affected by the new strain of the coronavirus family. Most of the health care providers infected by the virus. It is a result of the lack of regulations in the primary health care system. Our project aims to strengthen the primary health care service and decrease the burden on the health professionals with the invasive early detection sensor. In the first line, we believed that easy-to-use sensors will be good for the whole world for current situations. In future perspective, the optimized production line will provide us easily manufacturable user friendly sensors for viruses which are transmitted by air-droplet route.
Dr. Randy Schekman - Nobel Laureate in 2013 Physiology or Medicine
Prize motivation: "for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells."[nobelprize.org]
We invited Randy Schekman to our Academy Talks and he joined our Q&A. Our project consists of experiments with Saccharomyces cerevisiae. We needed to learn different aspects of the yeasts’ secretory pathway. He kindly answered our questions related to the overexpression of different organelles(such as peroxisomes) and fluorescent proteins in the yeast. Also we were eager to know more about his Nobel Prize/ more about his project , future advices and experiences as eager scientists. During our talk, he explained everything that we wanted to know in detail and we are really thankful for him. It was a magnificent experience, we hope to see him again in the future!
M.D. Atakan Demir - Oncology, Acıbadem Hospital
We discussed with Dr. Atakan Demir, about our technique’s potential applications on early detection of cancer and cancer cell tracking. We learned how cancer affects tissues specifically and what kind of tracking and detection tools are used right now. He said, tracking tissues at the molecular level can be helpful to detect early changes in people. He also said that we need to narrow down our focus and focus on one of the most common cancer types such as breast cancer or prostate cancer because every tumor type in cancer is different from each other so even focusing on 1 cancer type will be challenging. Also he suggested making genetic tests on people about which cancer is most possible for them to have in the future depending on their family.
His concerns were about carrying the project out of the lab to the hospitals in the future as it needs huge financial support and work to do in the lab. He said “This project is only a hobby if you plan to do it just for a year, if you want to make this project feasible, you have to work on it for years and need to find financial support.” I explained to him we as a team want to continue on this project for years and make it turn into a start-up and he said he would love to help without any financial expectation for himself. He said he can help on getting an ethical board acceptance for using live human tissues in the future, and he can provide these cells from hospitals after the approval in the future. He also said that he can help on the marketing part as he is experienced on that part too. Lastly, he said he wants to join our team and work with us, and we said that we would love to have him in our team.
Neolife
After we talked with Dr. Demir, we searched for centers which do genetic liability tests for cancer. We found an oncology center which we thought does these kinds of tests. We called neolife to get more information about how their system works. They generally work with “Doctor Demand Forms” which a doctor demands a genetic test for the patient if the patient has cancer in his/her family. After that the only thing they do is to get blood samples. They work with “Genetiks” a test company which does many genetic tests and they send the blood samples to that company.
Genetiks
After we talked with an oncology center, we decided to call “Genetiks”. They work with genes that are related to cancer and mostly people who have cancer in their families do these kinds of tests. The only sample you need to give is a blood sample and for cancer they have 2 main different tests for different patients. The first test analyses 275 genes and finds which cancer types the person who did the test might have in the future. If possible, they also do tests to that person’s relatives who have cancer. For patients who have breast cancer in their family and only want to check breast cancer, They do BRCA1 and BRCA2 tests. These tests check for these 2 tumor suppressor genes. The possibility of having cancer if that person has problems in these genes is %80.
Hülya Azaklı - Genetiks
After we talked with Genetiks on the phone, we discussed with Hülya Azaklı from Genetiks on a zoom call. She told us about how the tests are done and she also said that we should focus on 1 cancer type such as breast cancer or hematologic cancer types. She said that Genetiks is open to R&D work and collaborations in the future and they have a department named “Helix” for R&D. She told us that if someone who has mutations on genes such as BRCA1, BRCA2 or TP53 has a kid, after the kid is 18, tracking systems such as ours could be used in the future. She also told us that if there are people who are under 50 and have cancer, genetic tests can be done to understand the risks.
Prof. Dr. Kayhan Yakın-IVF Expert
By doing some research, our team thought that our technique could be used to choose quality oocytes. To support our idea, we reached out to Dr. Kayhan, who is an IVF expert, to discuss whether our technique is necessary to the field. He shared some insights about the process in general and mentioned the problems they usually face off. Then, we shared an overview of our project and discussed what can be done. We talked about the ethical concerns and possible obstacles since doing research on a patient's oocyte is not allowed and animal oocyte studies require some expertise.
Asst. Prof. Mara Simopoulou-IVF Expert
After our team talked with Dr. Kayhan Yakın, we decided to take a second opinion on the application of our technique on oocytes, we arranged a meeting with Dr Mara Simopoulou who is an expert in IVF. iGEM Athens helped us get in contact with Dr. Simopoulou. The meeting started with her introduction about the concept of egg collection and fertilization. After that brief introduction, she also explained the usage of lasers in IVF treatments. After we shared the overview of our project, she said that our project can be used while choosing the best quality eggs in Ovarian Stimulations. She explained the criteria for good quality eggs in treatments. The technique can show the cause of the problems in the cases of unexplained fertilizations. After that informative meeting, we will arrange another meeting for our further studies.
Integrated Human Practices
After we talked with Dr. Eser Uyanık, we thought that we should focus on tissue lasing more in our future plan. We searched for ways to get lasing out of the tissues and tracking their changes. What we found is a technique called “random lasing” in which you don’t need any resonator. Also we thought that inserting safe synthetic dyes is feasible after we talked with Dr. Uyanık and we decided to add new experiments to our proof-of-concept model species: E.coli and Yeast. We will include random-lasing experiments for both of the species in our future experiments. He also said that we can apply BiGG, a start-up grant in Turkey, so we took our notes about it and after we do some proof of concept work on lab, we will apply for the BiGG grant.
After we talked with Dr. Atakan Demir, we decided to narrow down our focus on the cancer side application to prostate and breast cancer. We also decided to contact with companies who can do “genetic liability tests” for cancer. We also made sure that we are working on something that will be good for the world. However, we need to take it out of the lab to the patients in the future and to do that we decided to collaborate with someone experienced such as Dr. Demir after his kind offer.
After we Talked with Hülya Azaklı, we thought that we can collaborate with Genetiks in the future for genetic liability tests for cancer. This meeting also confirmed that we need to focus on one type of cancer in order to advance in our project.
After we talked with Dr. Kayhan Yakın, we thought that we can work on not just oocytes but embryos. He proposed that rather than focusing on quality oocyte selection, focusing on the embryo selection would be more helpful to the field since picking the best embryo is more challenging and more important for IVF cycles. However, he mentioned that quality oocyte selections are being made by technicians and he added that there is a room for human mistake during this process. He said that we cannot add any material to the oocytes such as fluorescent proteins or synthetic dyes. Our solution to this problem is visualizing the whispering gallery modes (WGM) even before insertion of gain medium since these modes are the prerequisite for obtaining lasing from a resonator. If we can obtain WGM on oocytes and embryos, we can confidently say that we can obtain lasing from these structures.
After we talked with Dr. Simopoulou, we decided to narrow our focus on Oocytes. We decided to focus on characterizing oocytes and trying to create a correlation between oocyte quality and their morphology. After we learned that our study can help to create stimulation protocols depending on oocyte morphology we decided to focus on that in the future.
Genoks 21 Genetic Cancer Risk Panel
Public Engagement & Science Communication
Academy Talks
We invited Randy Schekman, Elçin Ünal, Aubrey de Grey and Ahmet Yıldız to our Academy talks series where we did and livestreamed our Q&A’s with outstanding scientists and we also took questions from the audience. Our team believes that science communication and public engagement are a crucial part of science. In a country where there is almost no scientific communications, our team wanted to start a culture that will be continued by the next generation.
We shared our livestream links in our instagram and twitter accounts. Also for Aubrey de Grey, we shared our livestream link on Reddit and it got 123 upvotes!
Dr. Randy Schekman-Nobel Laureate in 2013 Physiology or Medicine
Prize motivation: "for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells."[nobelprize.org]
Dr. Elçin Ünal-Berkeley University
Elçin Ünal is an assistant professor at UC Berkeley, Molecular & Cell Biology department. She works on the regulatory mechanisms and principles of meiotic differentiation. She is one of the most inspiring and enthusiastic biologists that come out of Turkey. We were greatly honoured and thrilled to have her with our team.
Dr. Aubrey de Grey-Gerontologist
Aubrey de Grey is an English gerontologist and a science author. He is known for the book “Ending Aging” that he co-authored. He is one of the pioneers of his field. Aside from being a great scientist, he is a public figure about the aging issue. Over the years, he gave one Ted, six Tedx and two Google talks. His vision of life is intriguing and must be taken seriously. We were greatly honoured to have him as a guest.
Assoc. Prof. Ahmet Yıldız
Ahmet Yıldız is an Associate Professor at University of California, Berkeley. He is a member of the physics department. However, he has made great contributions to the transport within cells and cell motility. He is an interdisciplinary genius and we are honoured to have him with us.
Journal Clubs
Sharing science and knowledge is crucial to make progress. Every member of our team is aware of this fact. Therefore, we decided to make a concept which a team member shares an interesting article/topic about she or he has an interest in with the rest of the team. This is a great concept since our team members started to learn about science presentation with this way, and shared their visions about the topic they are presenting with the rest of the team. After each presentation, our team members asked their questions to the presenter and had a discussion about the article/topic. By this way, our team members were able to experience different opinions and visions about the same topic. Here is the list of Journal Club presentations that have been made, and links of some of them. We live-streamed our journal clubs on youtube so other people can practice reading articles and join our discussions.
Presentations
Translation of Plasmids 101-Addgene
We as KU_ISTANBUL iGEM Team thought that the current Turkish Synthetic Biology sources are limited or expensive. So we decided to translate a great free guide “Plasmids-101 written by Addgene team. We picked some chapters which we thought are suitable for high school students from Addgene’s free e-book Plasmids-101 and translated it to Turkish. We picked the parts that can be suitable for high-school students to understand synthetic biology and didn’t include the parts that have too much detail for high-school students. We shared the pdf for non-commercial use with students from different schools and we discussed about synthetic biology in Burak Bora Hiigh School via zoom and we said them they can ask their questions about the book by communicating us with e-mail.
Burak Bora High School Presentation
