Cancel the Cancer2012.igem.org/files/poster/Fatih-Medical.pdf · helping hand to the high school...
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INTRODUCTION RESULTS HUMAN PRACTICES ACHIEVEMENTS To detect the tumor cell, we identified a target protein which is the Epithelial Cell Adhesion Molecule (EpCAM) presenting on their cell membrane. Therefore, we have worked on specific antibodies of this target molecule, CD215, which is planned to be presented on our “binding docks”, OmpAs. In the inner cell domain of the docks, there are two separate subparts of TEV protease which we aim to use as signal trigger. Another protein we have designed is the anchor- inducer protein complex which is fixed together with TEV cleavage site, is considered to be that trigger. In the course of the binding to the EpCAM, TEV protease subparts assemble into a fully active protease which begins to cleave the anchor- inducer complex. The inducer, LasR, proceeds to the pLas promoter afterwards in order to enhance the transcription of AHL-2, the major component of intercommunication of bacteria in our design. After LasR proceeds to the pLas promoter in order to induce the promoter by the synergic effect with AHL-1 (3OC12HSL), which is generated constitutively, pLas promoter starts to produce AHL-2 (3OC6HSL) which is planned to activate nearby bacteria to amplify the detection signal via producing fluorescent proteins. To do this, we want to transform these cells with quorum sensing receiver device based on Lux promoter system. The receiver device that produces LuxR constitutively, becomes activated by the AHL-2 diffusion and begins the signal amplification The Secret Book of Fatih-Medical This year, our team decided to design a pocket notebook of short and concrete abstracts of iGEM projects. As a result of intensive work, the notebook is prepared with short project overviews, comments about them and empty pages which are ready for you to take notes during the event. Moreover, there will be surprise presents in our both oral and poster presentations and our great lottery will take place. Helping the Youngsters Last year, we performed lots of speeches in various high schools in order to spread SynBio and iGEM into the younger ages and to inspire them to attend iGEM. Ahmet Ulusoy College formed a high school team, AUC Turkey, which have won the iGEMers prize this year in iGEM HS, has showed a great hard-working performance in the laboratory and we were happy to help them about their project as their advisors. Kermes It is a traditional event in Turkish culture which aims to help a charity or a group of people by buying some food or souvenirs etc. without troubling their price. This year, we used this opportunity to introduce iGEM and SynBio spirit. This also helped us to overcome our expenses which are taken place during the Jamboree. Survey We are doing a lot of human practices, inspire people or performing long speeches about synthetic biology; but how well are we sure about the feedback of these events? Are they really effective and beneficial? To measure this, we decided to prepare a survey which aims to show how people reacts to outreach performances about SynBio and iGEM and how well they have learnt about them so far. You can get the full results in our wiki page. More… We have done additional outreach from introducing presentation in different places and towards different audiences to make meeting with specialists and to discuss the future of SynBio and its applications onto the real life. You can check them out in our wiki page We attended iGEM 2012 Regional Jamboree Europe with a new project, completed our Judging form and prepared a wiki page fully presents it. We performed an oral and poster presentation at the Jamboree. We have successfully added 13 new BioBricks to the Registry which three of them are well- characterized and documented. These parts have found working properly and as expected. We submitted and posted three of our parts as favorites to the iGEM HQ. Especially, the results of BBa_K772100 show that our part is synthesized and it functions correctly. We have collaborated with Freiburg and Frankfurt iGEM teams by helping each other in project ideas or human practices. We did five different human practices activities including a pocket notebook that introduces all of iGEM teams of this year, a traditional event called “kermes” that had inspired many of our fellow students, a survey that shows how people reacts when they heard SynBio and a helping hand to the high school iGEM team, AUC Turkey. Cancer Cancel the TEV (N term) C215 OmpA AHL Lux R Reporter Protein Chloride ions Chlor Channel Holin Endolysin Ahmet Altınışık * Ayşe demirci * Bora Vergül * Burak Yasin Avcı * Büşra Nur Aydın * Esma Ölmez * Fatma Betül Çevik * Maral Amangurbanova * Mesut Yiğit * Muhammed Enes Gürses * Muhammed Hasar * Mustafa Hakyemezoğlu * Mustafa Semih Elitok * Nazym Bashkenova * Ömür Celal Kazaz * Ozan Sami Bayrak Eyüp Üçtepe * Gökhan Nas * Fazilet Yılmaz * Burak Yılmaz * Muradiye Acar ADVISORS UNDERGRADUATES Cancer is one of the most common death causes nowadays. According to the latest research of the World Health Organization, 19.8% of all deaths in Europe and 13.8% of those all over the world are due to cancer. Today, blood screening tests for cancer are expensive and time consuming while the number of patients is constantly increasing. Moreover, once a patient shows symptoms and gets diagnosed cancer, the disease mostly is advanced and it becomes more difficult to fight against it. We had the envision of a simple routine blood test for the early diagnosis of cancer in the future which offers a cheap and rapid opportunity to diagnose the disease in very early stages even if the patient does not show any symptoms. In order to put our idea in practice, we designed a system in E.coli which detects Circulating Tumor Cells (CTC). CTCs derive from the primary tumor, permeate through the bloodstream or lymphatic system and are finally responsible from the development of metastasis. On their surface there are EpCAM (Epithelial Cell Adhesion Molecule) antigens which are our main target. EpCAM is a pan-epithelial differentiation antigen which is overexpressed on almost all CTCs and tumor cells. Our system is built on 3 modules: Sherlocoli detects CTCs via C215 anti-EpCAM antibodies fixed on its outer cell wall, DJcoli ensures the enrichment of the detection signal by the means of quorum sensing mechanism and finally in Dracoli, light exposure induces the destruction of our genetically modified bacterium. Cloning: Our parts have been cloned and confirmed significantly which can be seen in the images below. The length of the parts overlaps with their predicted base pairs. Sequencing: After cloning, we have performed gene sequencing of our favorite part, BBa_K772100, and found fully correct which indicates our gene is cloned exactly what it should have been. Data is shown below. Characterization: Later on, we decided to isolate the EpCAM binding docks which are coded with BBa_K772100, the part that has been cloned correctly, by carrying out the Co- Immunoprecipitation (Co-IP) assay. We were able to do that; because the part had been designed for this purpose before. After isolating the proteins, we performed an SDS-PAGE to see whether our proteins had been actually synthesized and whether they work as it is expected. The data demonstrates that our binding docks are fully and significantly produced. (The bands at the below represent our parts; BBa_K772001, BBa_772002, respectively.) Moreover, the band seen in the above picture proofs that our designed proteins bind to the EpCAM antigen as it is expected. Among all the other mechanisms, the projects should propose a system that ensures the public and environment safeties. The more synthetic systems we establish, the more genetically modified organisms rise throughout the world and cause many problems. In our model, we designed a light-driven and easy-to-control self- destruction device in E.coli with aim of inducing self-lysis after the detection has been done. To do this, we planned to use halorhodopsin ion channel which can be activated with the emission of light. In the course of activation, this channel accepts chloride ions presenting in the media into the cell and decreases the pH level in the bacterium. Chloride ions are planned to enhance with the Pgad promoter, which is inducible with these ions. Therefore, we want to start the transcription of downstream genes which is considered as lysis device or reporter, just by using light. Esra Gündüz * Hüsamettin Erdamar * Kadir Demircan * Mehmet Gündüz INSTRUCTORS
Transcript of Cancel the Cancer2012.igem.org/files/poster/Fatih-Medical.pdf · helping hand to the high school...
INTRODUCTION
RESULTS
HUMAN PRACTICES
ACHIEVEMENTS
To detect the tumor cell, we identified a target protein which is the Epithelial Cell Adhesion Molecule (EpCAM) presenting on their cell membrane. Therefore, we have worked on specific antibodies of this target molecule, CD215, which is planned to be presented on our “binding docks”, OmpAs. In the inner cell domain of the docks, there are two separate subparts of TEV protease which we aim to use as signal trigger. Another protein we have designed is the anchor-inducer protein complex which is fixed together with TEV cleavage site, is considered to be that trigger.
In the course of the binding to the EpCAM, TEV protease subparts assemble into a fully active protease which begins to cleave the anchor-inducer complex. The inducer, LasR, proceeds to the pLas promoter afterwards in order to enhance the transcription of AHL-2, the major component of intercommunication of bacteria in our design.
After LasR proceeds to the pLas promoter in order to induce the promoter by the synergic effect with AHL-1 (3OC12HSL), which is generated constitutively, pLas promoter starts to produce AHL-2 (3OC6HSL) which is planned to activate nearby bacteria to amplify the detection signal via producing fluorescent proteins. To do this, we want to transform these cells with quorum sensing receiver device based on Lux promoter system. The receiver device that produces LuxR constitutively, becomes activated by the AHL-2 diffusion and begins the signal amplification
The Secret Book of Fatih-Medical This year, our team decided to design a pocket notebook of short and concrete abstracts of iGEM projects. As a result of intensive work, the notebook is prepared with short project overviews, comments about them and empty pages which are ready for you to take notes during the event. Moreover, there will be surprise presents in our both oral and poster presentations and our great lottery will take place. Helping the Youngsters Last year, we performed lots of speeches in various high schools in order to spread SynBio and iGEM into the younger ages and to inspire them to attend iGEM. Ahmet Ulusoy College formed a high school team, AUC Turkey, which have won the iGEMers prize this year in iGEM HS, has showed a great hard-working performance in the laboratory and we were happy to help them about their project as their advisors. Kermes It is a traditional event in Turkish culture which aims to help a charity or a group of people by buying some food or souvenirs etc. without troubling their price. This year, we used this opportunity to introduce iGEM and SynBio spirit. This also helped us to overcome our expenses which are taken place during the Jamboree. Survey We are doing a lot of human practices, inspire people or performing long speeches about synthetic biology; but how well are we sure about the feedback of these events? Are they really effective and beneficial? To measure this, we decided to prepare a survey which aims to show how people reacts to outreach performances about SynBio and iGEM and how well they have learnt about them so far. You can get the full results in our wiki page. More… We have done additional outreach from introducing presentation in different places and towards different audiences to make meeting with specialists and to discuss the future of SynBio and its applications onto the real life. You can check them out in our wiki page
We attended iGEM 2012 Regional Jamboree Europe with a new project, completed our Judging form and prepared a wiki page fully presents it. We performed an oral and poster presentation at the Jamboree. We have successfully added 13 new BioBricks to the Registry which three of them are well- characterized and documented. These parts have found working properly and as expected. We submitted and posted three of our parts as favorites to the iGEM HQ. Especially, the results of BBa_K772100 show that our part is synthesized and it functions correctly. We have collaborated with Freiburg and Frankfurt iGEM teams by helping each other in project ideas or human practices. We did five different human practices activities including a pocket notebook that introduces all of iGEM teams of this year, a traditional event called “kermes” that had inspired many of our fellow students, a survey that shows how people reacts when they heard SynBio and a helping hand to the high school iGEM team, AUC Turkey.
Cancer Cancel the
TEV (N term)
C215
OmpA
AHL
Lux R
Reporter Protein
Chloride ions
Chlor Channel
Holin
Endolysin
Ahmet Altınışık * Ayşe demirci * Bora Vergül * Burak Yasin Avcı * Büşra Nur Aydın * Esma Ölmez * Fatma Betül Çevik * Maral Amangurbanova * Mesut Yiğit * Muhammed Enes Gürses * Muhammed Hasar * Mustafa Hakyemezoğlu * Mustafa Semih Elitok * Nazym Bashkenova * Ömür Celal Kazaz * Ozan Sami Bayrak
Eyüp Üçtepe * Gökhan Nas * Fazilet Yılmaz * Burak Yılmaz * Muradiye Acar
ADVISORS
UNDERGRADUATES
Cancer is one of the most common death causes nowadays. According to the latest research of the World Health Organization, 19.8% of all deaths in Europe and 13.8% of those all over the world are due to cancer. Today, blood screening tests for cancer are expensive and time consuming while the number of patients is constantly increasing. Moreover, once a patient shows symptoms and gets diagnosed cancer, the disease mostly is advanced and it becomes more difficult to fight against it. We had the envision of a simple routine blood test for the early diagnosis of cancer in the future which offers a cheap and rapid opportunity to diagnose the disease in very early stages even if the patient does not show any symptoms. In order to put our idea in practice, we designed a system in E.coli which detects Circulating Tumor Cells (CTC). CTCs derive from the primary tumor, permeate through the bloodstream or lymphatic system and are finally responsible from the development of metastasis. On their surface there are EpCAM (Epithelial Cell Adhesion Molecule) antigens which are our main target. EpCAM is a pan-epithelial differentiation antigen which is overexpressed on almost all CTCs and tumor cells. Our system is built on 3 modules: Sherlocoli detects CTCs via C215 anti-EpCAM antibodies fixed on its outer cell wall, DJcoli ensures the enrichment of the detection signal by the means of quorum sensing mechanism and finally in Dracoli, light exposure induces the destruction of our genetically modified bacterium.
Cloning: Our parts have been cloned and confirmed significantly which can be seen in the images below. The length of the parts overlaps with their predicted base pairs. Sequencing: After cloning, we have performed gene sequencing of our favorite part, BBa_K772100, and found fully correct which indicates our gene is cloned exactly what it should have been. Data is shown below. Characterization: Later on, we decided to isolate the EpCAM binding docks which are coded with BBa_K772100, the part that has been cloned correctly, by carrying out the Co-Immunoprecipitation (Co-IP) assay. We were able to do that; because the part had been designed for this purpose before. After isolating the proteins, we performed an SDS-PAGE to see whether our proteins had been actually synthesized and whether they work as it is expected. The data demonstrates that our binding docks are fully and significantly produced. (The bands at the below represent our parts; BBa_K772001, BBa_772002, respectively.) Moreover, the band seen in the above picture proofs that our designed proteins bind to the EpCAM antigen as it is expected.
Among all the other mechanisms, the projects should propose a system that ensures the public and environment safeties. The more synthetic systems we establish, the more genetically modified organisms rise throughout the world and cause many problems. In our model, we designed a light-driven and easy-to-control self-destruction device in E.coli with aim of inducing self-lysis after the detection has been done. To do this, we planned to use halorhodopsin ion channel which can be activated with the emission of light. In the course of activation, this channel accepts chloride ions presenting in the media into the cell and decreases the pH level in the bacterium. Chloride ions are planned to enhance with the Pgad promoter, which is inducible with these ions. Therefore, we want to start the transcription of downstream genes which is considered as lysis device or reporter, just by using light.
Esra Gündüz * Hüsamettin Erdamar * Kadir Demircan * Mehmet Gündüz INSTRUCTORS
