Team:Thessaloniki/Attributions

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Attributions

Overview

This page is dedicated to everyone that believed in our team and assisted us on our long iGEM journey. We could not be more grateful and inspired by the consistent support we received from our PIs, Advisors and Mentors.

Summary

Our project design at its main core was an initiative of the undergraduate students consisting the team. The brainstorming sessions started in March of 2019 and until May we had decided the main idea and started working on the project. The team entered the lab in June of the same year. The wet lab team received proper lab training from executive personnel from the lab we worked during our project.

As mentioned above, to its greatest extent, our project was accomplished based on work done by our team members during the iGEM season and all its details are presented in our wiki page. Generally, the project design was done by our team members, mainly based on bibliography, while the parts that our PIs and advisors had helped us are stated below. Further support from the scientific community is stated in the Integrated Human Practices tab.

All the experiments were conducted by our team members, under the surveillance of experienced lab staff. The lab support provided by the Ph.D. candidates working at the same lab, was in the form of demonstrations and advises. They also helped us familiarize with the lab devices used in the experiments.

In parallel, the code used for the computational model is a mix of custom code and code from packages found in the bibliography. In each case, in the Model parts of the wiki, it is clearly noted when custom or not custom code is used. The primary supporter for the model was our advisor Konstantinos Kozalakis, whose role was advisory.

Although the main fundraising activity was conducted by our team members, we had also support from our Principal Investigator, Dr. Aivaliotis and our advisor Dr. Vizirianakis Ioannis. Regarding the final presentation we had been couched by Dr. Kappas. For the Human Practices, we had valuable support from the Department of Medicine, from local media, from our PIs and Advisors and from the TShop marketing group. As for the wiki, we had some initial guidance from Christos Perchanidis, an undergraduate student from the Department of Informatics AUTh.

Our Team

Platon Megagiannis, undergraduate student at the School of Medicine of Aristotle University of Thessaloniki. Platon as a part of the wet lab team proposed the initial idea for the project development and organized and designed the experiments conducted in the lab. He also assisted in our dry lab work, by running DSD simulations for our DNA circuit.

Sofia Moysiadou, undergraduate student at the School of Biology of Aristotle University of Thessaloniki. Sophia as a part of the wet lab team worked in the lab and was responsible for ordering materials and communicating with the suppliers. She also contributed to our fundraising efforts and organized our Human Practices and Public Engagement events.

Kyriaki Karava, undergraduate student at the School of Biology of Aristotle University of Thessaloniki. Kyriaki as a part of the wet lab team worked in the lab and was responsible for the design of the part characterization and improvement experiments. Kyriaki was also involved in our Human Practices and Public Engagement events.

Ioannis Maliouris, undergraduate student at the School of Informatics of Aristotle University of Thessaloniki. Ioannis, as a part of the dry lab team, constructed our whole wiki page.

Aliki Athanasiadou, undergraduate student at the Department of Physics of Aristotle University of Thessaloniki. Aliki, as a part of the dry lab team, worked on running Molecular Dynamic simulations for the Protein-DNA reaction. Aliki was responsible for the fundraising process. She also worked on Human Practices development and participated in our Public Engagement and Outreach events.

Charalampos Malathounis, undergraduate student at the Department of Chemical Engineering of Aristotle University of Thessaloniki. Charalampos, as a part of the dry lab team, was responsible for the design and development of our Genetic Algorithm, for the DSD simulations and the evaluation of our experimental results based on our model predictions. He also worked on the molecular dynamics simulations.

Apostolos-Stephanos Ioannidis, undergraduate student at the School of Pharmacy of Aristotle University of Thessaloniki. Apostolos, as a part of the wet lab team, worked in the lab and contributed in all the experiments conducted. He also participated in our fundraising efforts and was involved in our Human Practices and Public Engagement events.

Kristine Chanagian, undergraduate student at the Department of Biomedical Sciences of Alexander Technological Educational Institute of Thessaloniki. Kristine, as a part of the wet lab team, worked in the lab and contributed in all the experiments conducted. She also participated in our Human Practices and Public Engagement events.

More specifically, we would like to thank:

  • Erik Winfree, Professor at Caltech, for providing us with material regarding the choice of DNA sequences for our circuit and for answering our questions over the python package KinDA.

  • James Parkin, Graduate Student Murray's lab Caltech, for answering a plethora of questions about the python package piperine.

  • RGCC for providing us with computational resources for running our Genetic Algorithm and especially Mr Nikos Karanikolas for his support on the technical issues that occured.

  • Konstantinos Kozalakis, PhD student at Physics Department of Aristotle University of Thessaloniki, for the constant support on the work of our dry lab and for his contribution on the construction of the electrochemical assay.

  • Arampatzis Asteris, Ballhysa Eugene, Giannitsis Charis and Theocharis Thanasis, as former iGEM participants for providing their expertise on iGEM competition throughout our whole iGEM Journey.

  • Lioulia Elisavet, PhD Candidate at the Department of Genetics Development and Molecular Biology of the School of Biology of Aristotle University of Thessaloniki, for providing immediate assistance on every problem concerning our lab work.

  • Dimitris Stamatis, M.Sc. student NKUA, for his constant support and advice over using Desmond and AMBER and for helping us evaluate the results.

  • Aristotle University of Thessaloniki (AUTh) High Performance Computing Infrastructure and Resources and especially Mrs Alexandra Charalampidou for the constant support over the use of Parallel computing software and for providing us the resources for the Molecular Dynamics simulations.

  • Dr. Antigoni Malousi, Laboratory Assistant on Bioinformatics in the School of Medicine AUTh, for providing us immediate assistance in every question concerning Transcription Factors and for bringing us in contact with some enterprises and laboratories that helped us improve our project.

  • Dr. Aggeli Amalia, Associate Professor on Biomedical Engineering in the Department of Chemical Engineering, AUTh, for registering us to the competition and for her support as the former PI of our team.

  • Dr. Ilias Kappas, Assistant Professor at School of Biology AUTh, for vouching for us in order to have access in the computational resources of Aristotle University of Thessaloniki High Performance Computing Infrastructure and Resources. Also he helped us improve our final presentation for the Giant Jamboree.

  • Dr. Maria Touraki, Assistant Professor at School of Biology AUTh, for providing us with essential laboratory expendables and valuable feedback on our laboratory techniques.

  • Antonios Kolocouris, Associate Professor at the Department of Pharmaceutical Chemistry NKUA, for providing assistance concerning Molecular Dynamics, AMBER and Desmond. Additionally Dr Kolocouris referred us to his lab members for further questions and constant advise.

  • Dr. Zacharias Skouras, Professor at School of Biology AUTh, for providing us with laboratory space for our dry lab team to work for the iGEM season.

  • The lab of Pharmaceutical Technology AUTh, which is under the surveillance of the Associate Professor Dr. Fatouros Dimitrios, for providing us with a spectrofluorometer.

  • The lab of Pharmacognosy-Pharmacology AUTh, which is under the surveillance of the Associate Professor Dr Papadopoulou Lefkothea, for providing us with a Nano-Drop and a Plate-Reader device.

  • The lab of Genetics Development and Molecular Biology AUTh, which is under the surveillance of the Associate Professor Assistant Professor Dr Dafou Dimitra, for allowing us work in the laboratory for the iGEM season.

  • Evita Kouteliou, Professional Graphic Designer, for helping us design our promotion material and banners used in our Human Practises and Public Engagement events.

  • Tshop Marketing group and especially Ms Tatiana Tourna and Ms Fotini Gallou for the production of our “iGEM Box” video and for the support on organizing our Outreach events.

  • Real Creation Studios and especially Theodoros Tziatzios, for the creation of the animated video presentation of our project.

  • Christos Perchanidis, Undergraduate student of the School of Informatics AUTh, for designing our project’s logo and providing us with the initial design of the home page of our wiki.