iGEM 2016 — Team Linkoping_Sweden

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# Team:Linkoping Sweden/Notebook

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[Team](/Team%3ALinkoping_Sweden/Team)

[Collaborations](/Team%3ALinkoping_Sweden/Collaborations)
[Attributions](/Team%3ALinkoping_Sweden/Attributions)

Project

[Design](/Team%3ALinkoping_Sweden/Design)
[Experiments](/Team%3ALinkoping_Sweden/Experiments)
[Protocols](/Team%3ALinkoping_Sweden/Protocols)
[Results](/Team%3ALinkoping_Sweden/Results)
[Safety](/Team%3ALinkoping_Sweden/Safety)
[Notebook](/Team%3ALinkoping_Sweden/Notebook)
[Economic Viability](/Team%3ALinkoping_Sweden/Economic_Viability)

[Project Description](/Team%3ALinkoping_Sweden/Description)

[CRISPR/Cas9 System](/Team%3ALinkoping_Sweden/Description/CRISPR/Cas9-system)
[Gibson Assembly](/Team%3ALinkoping_Sweden/Description/Gibson_assembly)
[Chlamydomonas Reinhardtii](/Team%3ALinkoping_Sweden/Description/Chlamydomonas_reinhardtii)

[Parts](/Team%3ALinkoping_Sweden/Parts)

[Human Practices](/Team%3ALinkoping_Sweden/Human_Practices)

[Silver](/Team%3ALinkoping_Sweden/HP/Silver)
[Gold](/Team%3ALinkoping_Sweden/HP/Gold)

Labratory work
Project progressionsOther activities
Human practice

March

i Publishing of group members

After a few information meetings held by the principle investigators and the
instructors the 2016’ LiU iGEM Team was set.

Team registration

i Lecture about arsenic poisoning

To find inspiration for our project we had a lecture in arsenic poisoning and
protein aggregation with one of the principal investigators of our project. We
all were very excited about the topic of the lecture but we decided that it
would be difficult to make a iGEM project about it.

April

i Lecture about algae

Further on we had a lecture about algae and why the biodiesel production from
algae is not economically sustainable with the Assistant Professor Johan
Edquist. It did not take long until we all were agreed that we wanted to work
with algae in the 2016’ iGEM project.

i Project design

To make more biomass out of algae we investigated different methods and
promoters, but in an early state is was clear that we wanted to work with
CRISPR/Cas9 and a light inducible promoter called SORLIP.

i Project plan development

When we had a project design we planned the time we had before the Giant
Jamboree, this to be able to make the best we could of the time we had. The
project plan was a draft of this timeline.

May

Applying for sponsorship by Genscript

i Sequence construction

At this state we did research about how to construct the including parts as well
as the BioBricks in total. Also, we started off with design of primers to
different parts.

June

Inventory

i Biobrick design

![](https://static.igem.org/mediawiki/2016/2/24/T--Linkoping_Sweden--BiobrickDesign.jpg)

Finally, our final DNA Construct design was finished. See [Project design](/Team%3ALinkoping_Sweden/Design) for
more information.

Laboratory saftey lecture

i Nordic iGEM conference

![](https://static.igem.org/mediawiki/2016/1/1d/T--Linkoping_Sweden--NIC.png)

The Nordic iGEM Conference, NiC, is a weekend long mini Jamboree held by one of
the Nordic iGEM Teams. This event is hosted by the team who held the best
presentation the previous year according to the NiC jury. The 2016’s conference
was arranged by Stockholm, the capital of Sweden. This was a perfect opportunity
to get to know the Nordic iGEM Teams and to practice our presentation for the
Giant Jamboree. Also, the event offered Workshops, BBQs with biotech students
from five different countries amongst other activities.

Wiki design

Project description on the Wiki webpage

i First day at the laboratory

![](https://static.igem.org/mediawiki/2016/a/a0/T--Linkoping_Sweden--FirstLab.jpg)

In the waiting for ordered primers, vector and such, we prepared TAP and LB
medium, agar plates etc.

i LiU iGEM Team Kick-off

![](https://static.igem.org/mediawiki/2016/1/1a/T--Linkoping_Sweden--Kickoff.jpg)

When the group members were chosen and the project design was finished we
started the summer with a kick-off at Robert Forchheimer, the founder of LiU
iGEM. We had a lovely meal outside and some of us took a swim in the swimming
pool. We listened to music, played games and had a fantastic evening.

i Made the cover of the local newspaper "Östgöta Correspondenten"

![](https://static.igem.org/mediawiki/2016/6/63/T--Linkoping_Sweden--Corren.jpg)

We made the cover of the local newspaper, *Östgöta correspondenten* called *Corren*.
This Newspaper is delivered to households each morning within the providence
Östergötland. The article was mainly about the concept of iGEM and the project
of the year. The focus laid at making more biomass out of *C. reinhardtii* and the
contributing work to minimize the greenhouse effect.

i New project approach

Publishing of interviews with interesting personalities on FB

![](https://static.igem.org/mediawiki/2016/3/34/T--Linkoping_Sweden--NewApproach.jpg)

With the laboratory deadline getting closer, we were still out of luck when it
came to results. We decided that it was time to make a change regarding how we
executed our project to reach our goals. The project idea remained the same, but
the approach changed. Instead of using the traditional digest-ligation method to
construct the parts, we went ahead with a different method called Gibson
Assembly. This Assembly enables the creation of a construction of up to six
parts in just one reaction. Our hope was restored!

i All firms at the list of potantial sponsor of the project this year must be contacted

We started off early with finding potential sponsors and listed them on an
internal document. Further on we contacted them one by one at the same time we
investigated firms to build on our list with. At this deadline we had to been in
contact with all of the firms at our list to be able to focus fully on our lab
activities. Our search for sponsors continued though.

July

i First transformation and Chlamydomonas reinhartii cultivation

Publishing of Donor Website

![](https://static.igem.org/mediawiki/2016/e/e0/T--Linkoping_Sweden--FirstTransformation.jpg)

We used the iGEM Competent Cell Test Kit in order to control the transformation
efficacy of our heat competent cells (E. Coli Xl1-blue). Our goal was to
introduce the [DNA
construct](https://2016.igem.org/Team%3ALinkoping_Sweden/Design) into the algae *C. reinhardtii*, which is why the first
cultivation was started early. We wanted to optimize the cultivation conditions
for the algae.

i Birth of Miss Mona

![](https://static.igem.org/mediawiki/2016/3/3b/T--Linkoping_Sweden--MsMona.jpg)

After inactivation of the gene coding for starch in a baby Mona our team mascot
evolved into Miss Mona. This young single-celled lady alga is a specie called *C.
reinhardtii*, the algae we use in our project experiments. Her mainly diet is
Swedish bulk confectionary and she is currently single. Miss Mona was created both
as a tradition for the Liu iGEM team, as well as a part of the Human Practice.
She has been attending to all exhibitions and presentations of the year.

i First PCR and gel electrophoresis

![](https://static.igem.org/mediawiki/2016/9/93/T--Linkoping_Sweden--FirstPCR.jpg)

The first PCR-reaction was made and we amplified one of the desired sequences to
[our construct](https://2016.igem.org/Team%3ALinkoping_Sweden/Design),
the Cas9 sequence, from an existing BioBrick. Verification of the product was
made according to fragment size through gel electrophoresis.

Interwied by LiU Nytt

First digest and ligation

i NärCon convention

![](https://static.igem.org/mediawiki/2016/2/2d/T--Linkoping_Sweden--Notebook-Narcon.jpg)

NärCon is a Play and CosPlay Festival where the team worked as representatives
for Linköping University in order to inform about the university as well as iGEM
and our project. This CosPlay convention attracted over 8500 visitors and lasted
for four days, LiU iGEM was of course active during all that time!

August

i First Chlamydomonas reinhartii cultivation in darkness

![](https://static.igem.org/mediawiki/2016/a/af/T--Linkoping_Sweden--Darkness.jpg)

As the [DNA construct](https://2016.igem.org/Team%3ALinkoping_Sweden/Design) was designed with the light inducible promotor, a test culture in darkness was grown in order to study the optimal parameters such as temperature, TAP medium etc. in these conditions.

Visit at local company

i First draft: team wiki and final report

i Was on the SVT News

It is important to start off with things early. Our iGEM project is possible to
have as a course within synthetic biology, if you have the qualifications
needed. As a final exam for this course we all write a scientific report about
our project of the year. At this state we had both a first draft for the final
report but also our Team Wiki.

![](https://static.igem.org/mediawiki/2016/d/d0/T--Linkoping_Sweden--SVT.jpg)

*Sweden's Television*, SVT, is the national public TV broadcaster of
Sweden. They made a reportage about our project in particular, but we also
informed about iGEM in general.

i First Gibson assembly

![](https://static.igem.org/mediawiki/2016/1/10/T--Linkoping_Sweden--FirstGibson.jpg)

We made the first attempt to assemble our final [DNA construct](https://2016.igem.org/Team%3ALinkoping_Sweden/Design) with the method Gibson Assembly, which was totally new for us.

Gibson assembly is an exonuclease-based method to assembly multiple DNA fragments in correct order. The method was invented in 2009 by Daniel G. Gibson, of the J. Craig Venter Institute. The assembly reaction is carried out in one single reaction-tube, all at once, at 50° Celsius for 15-60 minutes. The process involves three different enzymatic actions. A 5’ exonuclease creates overhangs, enabling matched fragments to anneal. Then a DNA polymerase fills gap between the annealed strands and the 5´ end. Finally, a DNA ligase seals the gaps between the filled in gap and the annealed strands.

For more information, see [Gibson Assembly](/Team%3ALinkoping_Sweden/Description/Gibson_assembly)

Using this method, we constructed three different parts, see [results](/Team%3ALinkoping_Sweden/Results).

Track selection (title and abstract)

Hajk (promoted iGEM for new students at Linköping University)

Registration Giant Jamboree

September

Prepairing for Boston

i First electroporation

Project presentation for the LiU Authorities

![](https://static.igem.org/mediawiki/2016/4/45/T--Linkoping_Sweden--FirstElectro.jpg)

After the second Gibson Assembly we succeeded to bring together a variant of our
final DNA construct. This allowed us to try out the electroporation of this
fragment into the algae *C. reinhardtii*. Confocal microscopy was used to
detect fragment-positive colonies for yellow fluorescent protein (YFP), while
the YFP was inserted to the final DNA construct instead of the Hygromycin B
cassette.

Second draft: Team Wiki

i Kalas (Exhibition fornew students at Linköping University)

![](https://static.igem.org/mediawiki/2016/0/01/T--Linkoping_Sweden--Kalas.jpg)

Kalas is a great fair that mainly refers to the new students from all programs
at Linkoping´s University. With 8000 students visiting, Kalas is the largest
event for new students in Sweden. We were on site to reach out to all students
about our project and arouse an interest for iGEM and our student organization
as well as synthetic biology. It was an excellent opportunity to recruit
interest from a wide set of skills for future project and engagement. LiU iGEM
had our own table and was giving handouts to the visitors and exchanged some
words about iGEM.

Final Saftey Form

Publishing project ethics on the Team Wiki

Second draft: Final Report

Printing of team poster

Laboratory freeze

Preparing presentation for Boston

October

i Holding presentation about igem and the project of the year for a course in gene techology at LiU

We held a presentation for a course in gene technology at the University. The
presentation was a preview of the presentation that we are about to have on the
Giant Jamboree. We also promoted iGEM and the yearly LiU iGEM project, many
found a great interest in taking part in this synthetic biology project and
signed up for a future membership.

Finishing Team Wiki

i Study visit at Ångströmhuset

![](https://static.igem.org/mediawiki/2016/8/85/T--Linkoping_Sweden--Angstrom.jpg)

The major part of our team attended to the study visit at Ångströmhuset, where
the university have their electron microscope. The building is named after the
Swedish physicist Anders Ångström and is located a short distance from the
centre of the university. The location as well as the placement on solid ground
is to minimize disruption of the measurements. We learned a lot about the
function and the applications of electron microscopy, but also how difficult it
can be to receive trust-worthy data from measurements we use daily.

Releasing video about our project

Wiki freeze

Deadline: Final Report

i Flying to Boston

![](https://static.igem.org/mediawiki/2016/8/8e/T--Linkoping_Sweden--Flight.jpg)

October 26th the LiU iGEM Team takes the morning flight to Amsterdam, and from
there directly to Boston, USA.

i Giant Jamboree

![](https://static.igem.org/mediawiki/2016/7/71/T--Linkoping_Sweden--Jamboree.jpg)

The whole Team really are looking forward to be part of the Giant Jamboree 2016.

LiU iGEM is proudly sponsored by

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LiU iGEM

Kårallen, Linköpings Universitet

581 83 Linköping

liuigemgroup@gmail.com

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