Team:KU ISTANBUL/Notebook



Friday, April 4th

Biolaser project is accepted as main project

Friday, April 11th

Project topic was discussed, Tasks and duties were distributed

Friday, April 18th

Accessible laser sources were searched and discussed

Sunday, April 20th

Project presentation was prepared.

Thursday, April 24th

The team done presentation to instructors and project is developed

Sunday, April 27th

Single-cell biological lasers were investigated. The cells with GFP tagged used as gain medium in vivo and in vitro.

Friday, May 1st

Biolaser articles, arranged and sorted by years, started to be read. Having a natural resonator inside the cell used may be more efficient than using an artificial bead. Although the efficiency issue is open to debate, using a spherical structure produced by the cell itself, since it is difficult to engulf a large inorganic material into a living cell motivated us to work on the tool.

Monday, May 18th

Different sources about the project discussed. Distribution of the proposal tasks was done.

Saturday, June 13th

Özgür Can, a member of our team, presented the following article on our youtube channel:

"Transient inhibition of mTOR in human pluripotent stem cells enables robust formation of

mouse-human chimeric embryos" by Hu et al. Science Advances (2020)

Sunday, June 21st

Administrative and executive decisions have been made for the way the team works.

The Bio-laser project was decided to be the team’s main focus for the iGEM 2020.

Wednesday, July 1st

Randy W. Schekman is an investigator of the Howard Hughes Medical Institute and a Professor of Cell and Developmental Biology in the Department of Molecular and Cell Biology at the University of California at Berkeley. He was awarded the Nobel Prize in Physiology or Medicine in 2013.

He and his colleagues have made a huge contribution to our understanding of responsible genes for intercellular and intracellular transportation. For his great contributions to his field, he is honored with a Nobel Prize in Physiology or Medicine. Aside from being one of the greatest cell biologists, he is deeply passionate about cell biology. We had an one-hour long meeting with him , we explored his journey as a great scientist, asked him some questions and learnt from his experiences.

Sunday, July 5th

“Bio-laser” project was proposed. The overall aim was determined as to create a project that every other future scientist would cite from it.

  • It has offered that, oocytes could be got from KUH Pathology with proper papers and permissions

  • The expression of GFP is an issue. We should try both overexpressing it, use its inner cell membrane proteins, and maybe inside and outside of the organelles. These options will be tried immediately after one another.

The following issues about the planning teams works were agreed on:

  • We will complete the overall plan for both projects in a week (it is a must), and fulfill the protocols and other detailed stuff later in this summer before going into the lab. We should have a detailed plan to execute when we step into the lab, so we can continue smoothly.

  • Weekly meeting schedule is still not decided.

    • A poll must be created in Slack to find optimal spaces.

    • First, days then hours will be decided.

  • New team members will be introduced to the team in meetings.

    • There will be a separate meeting (other than our formal meetings) for this job.

Sunday, June 28th

Ali Doğa Yücel, a member of our team, presented the following article on our youtube channel: "Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations" by López-Igual et al. Nature Biotechnology (2019)

Sunday, July 12th

The ideas for the Biolaser project and its possible applications were discussed. The outcome of the discussions was to create a resonator within the cells. Silicatein covered peroxisomes or cell membrane could work as a resonator. Search for silicon binding proteins and alternative proteins to silicatein has started.

Collaboration with Bilkent-UNAMG iGEM team has helped the team to develop the project for suitable plasmid search.

There are three applications and two methods to apply, details are found in the proposal document.

Sunday, July 19th

Team members are assigned to communicate with other iGEM teams for kits. Planning for the Biolaser project proposal to the team’s mentor Madina Akan was prepared.

Tuesday, July 21st

Some lab-related issues and general iGEM related things were discussed.

It has been communicated with the METU iGEM team and ACIBADEM iGEM team for the library, thus their responses were discussed.

Academy talk with Aubrey de Grey was planned.

Sunday, July 26th

Some lab-related issues and general iGEM related things were discussed.

A mail was sent to the iGEM headquarters about the gene names in the 2018 library list.

The team has collaborated with TuDelft Team and contacted Athens Team. TuDelft team shared their project by a recorded video.

iGEM’s initiative to global session between teams was discussed.

The offer for starting a TEDx talk culture in the Koc University was assessed.

Sedat Nizamoğlu and his research lab shared a thesis presentation about biological lasers.

The planning for the wiki page has started. Wxc or other creator programs that contain Java were possible ways to create the wiki page.

Team project theme mascot 3D and pencil type were drawn.

Bacterial synthetic grid and circuit systems were discussed.

A protein named reflection was found as an alternative silicatein for the Biolaser project. It is a fluorescent protein found in deep-sea creatures such as octopuses etc and soluble in lipids.

The deadline for the FDTD program lectures was determined as next week since its visual interactions could create a simulation for the iGEM project.

The following question was raised during the meeting:

Are there any programs like FDTD but provide data about plasmids in bacteria and how do they work in the expression of specific proteins?

In order to reach more people for presenting the team’ project and Academy Talks, social media coverage was increased.

Tuesday, July 28th

As usual, some lab-related issues and general iGEM related things were discussed.

Aubrey de Grey was the team’s guest speaker. It went wonderfully.

2018 iGEM part library was found. Silicatein protein wasn’t there, but reflectin exists.

Available cell type, plasmids, and promoters were evaluated.

Wednesday, July 29th

Zeliş Nergiz, a member of our team, presented the following article: "Molecular digital data storage using DNA" by Ceze et al. Nature Reviews Genetics (2019)

Tuesday, August 4th

Dr. Ünal is Assistant Professor of Genetics, Genomics and Development at UC Berkeley.We had an one-hour long meeting with her and talked about her experiences.

Saturday, August 8th

Mısra Taşçı, a member of our team, presented the following article: on our youtube channel "Optoacoustic effect is responsible for laser-induced cochlear responses" by Kallweit et al. Scientific Reports (2016)

Tuesday, August 11th

Random scatter lasers became our main search of interest after meeting with Sedat Nizamoğlu. The team learned a lot from him about how to build, sustain, and control a laser.

Membrane coating with reflectine and silicatein proteins, cell-based lasing could be achieved.

This meeting with Sedat Nizamoğlu became a good opportunity for the wiki page.

SimBiology and Wholecell were investigated in order to simulate experiments. Wholecell was a cell structure/chemistry simulating program that has different perimeters and options to perform an experiment.

Saturday, August 22nd

Dr. Yıldız is Associate Professor of Physics at UC Berkeley. His laboratory at Berkeley combines molecular biology and biophysical techniques to understand mechanisms that underlie the cellular organization and motility. We had a meeting with him on our youtube channel. He shared his experiences with us.

Sunday, August 23rd

Q&A meeting with the iGEM judges was arranged for the better understanding of the criteria that needs to be satisfied.

Research groups and companies who conduct single-cell tracking or can benefit from new bio-laser projects were investigated for the behalf of human practices. Aselsan,TUBITAK, and Havelsan were determined as good candidates in Turkey for that.

Saturday, August 29th

Oktay Göcenler, a member of our team, presented the following article on our youtube channel: "New codons for efficient production of unnatural proteins in a semisynthetic organism" by Fischer et al. (2020)

Sunday, September 6th

General discussions about the gold medal criteria, wiki page designs were made.

Diatoms were proposed from a team member and it took interest since they have cellular symmetry. Additionally, lasing of the red blood cells was discussed.

Tuesday, September 8th

Meeting with Alexander Zagajewski was held in order to get help about FDTD simulations. Future meetings were scheduled as he became an advisor of the team.

The concept of the wiki page, logo design was discussed in order to satisfy the gold medal criteria. Wiki pages of the other teams were investigated and certain parts for the our wiki page were determined. These parts were assigned to the members of the team.

A survey was prepared for PhD students and postdoctoral researchers who use lasers and imaging techniques.

Tuesday, September 15th

Reflectin like protein family was discussed whether if they were used before and had a successive expression technique that they were attached to the cell wall.E coli and S. cerevisiae experiment planning became nearly to the end. Gene orders were listed.

Choice of the fluorescence proteins was discussed. Other research labs that could provide us some of them were contacted.

SEM(ZEISS EVO LS15 SCANNING ELECTRON MICROSCOPE) became accessible to our use after the agreement with the Koç University Surface Science and Technology Center (KUYTAM).

Sunday, September 20th

After the mentorship meeting, the team started to talk about wiki, materials, methods, and mathematical calculations of the concentrations/ density optimizations of our experimental data. One of the mentors told us that V-Cell can be a good simulation program.

For the Mathematical equations and data, a team member was assigned to handle the bioinformatic part and supplementary data was found.

The crucial modeling part was discussed.

Preparations for Team Promotion Video were discussed.

  • The deadline is in 25.09.2020

  • Do not use copyright materials

  • Try to show the project and present it into the world

iGEM has some examples of these videos.

Hasan Demirci’s UNIV101 presentation and the people who listened to him as spreading the iGEM culture and our team were added to the Human practices parts.

Thursday, September 22nd

Meeting with Dr. Eser Uyanık

Tuesday, September 29th

We had a meeting with Burak V. Kabasakal and prepared two videos about structural biology on our YouTube channel.

Friday, October 2nd

We met with Ayşe Koca Çaydaşı on Yeast

Wednesday, September30th

Meeting with Hülya Azaklı

Sunday,October 3rd

Meeting with Dr. Hafez El Sayyed

Sunday,October 4th

Meeting with Atakan Demir

Saturday, October 17th

Meeting with iGEM Athens

Meeting with Dr. Hafez El Sayyed

Sunday, October 18th

First draft of Presentation Video & Wiki design

Monday, October 19th

Meeting with Dr. Yakın and Dr. Simopoulou