iGEM 2020 — Team KU_ISTANBUL

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# Team:KU ISTANBUL/Notebook

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# [KU ISTANBUL](https://2020.igem.org/Team%3AKU_ISTANBUL)

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* [Hardware](https://2020.igem.org/Team%3AKU_ISTANBUL/Hardware)
* [Human Practices](https://2020.igem.org/Team%3AKU_ISTANBUL/Human_Practices)
  + [Education](https://2020.igem.org/Team%3AKU_ISTANBUL/Education)* [Notebook](https://2020.igem.org/Team%3AKU_ISTANBUL/Notebook)
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# 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

## KU ISTANBUL

![](https://static.igem.org/mediawiki/2020/f/ff/T--KU_ISTANBUL--LogoFinal.png)

#### Adress:

Koç University
Rumelifeneri Road 34450
Sarıyer, Istanbul / Turkey

Email:
kuigem2020@gmail.com

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# Team:KU ISTANBUL/Engineering

KU ISTANBUL WIKI - Template

# [KU ISTANBUL](https://2020.igem.org/Team%3AKU_ISTANBUL)

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* [Hardware](https://2020.igem.org/Team%3AKU_ISTANBUL/Hardware)
* [Human Practices](https://2020.igem.org/Team%3AKU_ISTANBUL/Human_Practices)
  + [Education](https://2020.igem.org/Team%3AKU_ISTANBUL/Education)* [Notebook](https://2020.igem.org/Team%3AKU_ISTANBUL/Notebook)
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# Engineering

**Disclaimer: We are not going to do lab work this year**

**A. Introduction to Experiments**

**Reflectin Proteins**

Cephalopods (octopuses, squids, cuttlefish, etc.) often have an adaptation
of demonstrating camouflage as a result of adaptive transparency. Some of
the cephalopod species can vanish from the environment with their optical
adaptation capabilities. Cephalopods owe these camouflage skills to their
ability to change optical properties by how light is transmitted, absorbed,
and reflected by their skin [1]. Specifically, reflectivity on their
tissues are achieved by stacking flat, insoluble, structural platelets by
alternating layers of high and low refractive index in iridocytes [2].
These alternate arrangements, called Bragg reflectors, create a thin-film
interference pattern which is the reason for reflection of incident light
from the tissue [1]. In aquatic animals, reflector platelets generally
consist of purine crystals, particularly guanine and hypoxanthine; however,
cephalopod reflector platelets contain reflectin proteins instead of these
purine crystals. Reflectin proteins found in cephalopods are responsible
for transparency abilities by employing structural coloration and
iridescence [3, 4].

Optical characterization of these proteins is an important effort for
studies involving reflectin proteins. However, it is hard to characterize
the refractive index of these proteins since there are multiple Bragg
stacks with unknown variation in spacings, refractive indices, and
orientations in a typical tissue of a chalepod. Hence,the results of
different studies can vary greatly although the refractive index of these
proteins are generally found higher than ~1.40, up to ~1.62 [1, 2, 4]. High
refractive index of reflectin proteins allows possible use in biotechnology
as a novel biomaterial which can be used to design a resonator from
proteins to create fully biological lasers.

We will be using following reflectin proteins:

* Reflectin A1 obtained from Loligo pealeii

![](https://static.igem.org/mediawiki/2020/c/c2/T--KU_ISTANBUL--engineer1.png)

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# Team:KU ISTANBUL/Experiments

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# [KU ISTANBUL](https://2020.igem.org/Team%3AKU_ISTANBUL)

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## KU ISTANBUL

![](https://static.igem.org/mediawiki/2020/f/ff/T--KU_ISTANBUL--LogoFinal.png)

#### Adress:

Koç University
Rumelifeneri Road 34450
Sarıyer, Istanbul / Turkey

Email:
kuigem2020@gmail.com

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# Team:KU ISTANBUL/Results

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* [Hardware](https://2020.igem.org/Team%3AKU_ISTANBUL/Hardware)
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# Results

**Results of Our Computational Models**

We have created computational models of our biological resonators and
performed finite difference time domain simulations using Lumerical FDTD.
Details of our models can be found in the modelling page.

We have determined the minimum sizes of cells for each model geometry in an
experiment where we would cover the cell with proteins with a
high-refractive index. We have taken the experimentally achievable
refractive index limit as 1.7 since there are some experimental results in
the literature in which researchers can measure the refractive index of
reflectins in different media [1-4 ].

First of all, as a general remark we can see that we need higher refractive
index materials to build a resonator as the resonator size gets smaller.
This correlation becomes even more drastic in the size limit of below 5 µm
for structures that have spherical symmetry.

When we analyze the spherical models, we can see that one can obtain
whispering gallery modes from the resonators with diameters 10 µm, 9 µm and
8 µm if these resonators were built from a material with refractive index
around 1.7. Resonance peaks of these cavities are very clear as can be seen
in Figures 1-4, 8-11, 15-18. Also heatmaps belonging to these modes are
given in Figures 5-7, 12-14, 19-21.

If we look at Figures 22-25, 26-28, we can see that the refractive index
limit for clear resonance peaks rose up, from 1.7 to 1.8 or 1.9; as we are
decreasing the diameter of the cavity, the cavity can no longer sustain the
whispering gallery modes. They start appearing at higher refractive
indices, and they are again very sharp at higher indices. Heatmaps
belonging to these modes are given in Figures 26-28, 33-35.

We can realize that we can no longer see sharp resonance peaks in a cavity
with 1.9 refractive index membrane for 4-5 µm diameters as can be seen in
Figures 36-37, 41-42. Although the resonance occurs for higher refractive
index around 1.9-2.0, we can see these resonance modes in Figures 38-40,
43-44.

As we are analyzing even smaller cavities of diameters 1-3 µm, it is very
clear that we can not observe whispering gallery modes in these cavities if
they were built with a material of refractive index smaller than 2.0. We
have performed simulations with higher refractive index materials just for
these small cavities, and we have found that one can observe resonance
modes if these cavities are built with higher refractive index materials
around 2.25-2.5. Resonance peaks obtained for these modes can be seen in
Figure 45-48.