Like the true team manager she is, Charlotte was able to set us up with some Bacillus plasmids from iGEM Groningen. While the plasmids were transported from Groningen to Leiden, Laurens was busy
Like the true team manager she is, Charlotte was able to set us up with some Bacillus plasmids from iGEM Groningen. While the plasmids were transported from Groningen to Leiden, Laurens was busy
trying
trying
−
to let <em>E.coli</em> produce colours and Carli and Tim set the record for the longest measurement, using the FACS-machine for over four hours. Each activity was carefully supervised by our
+
to let <em>E. coli</em> produce colours and Carli and Tim set the record for the longest measurement, using the FACS-machine for over four hours. Each activity was carefully supervised by our
Science
Science
manager, Marjolein, who lies awake at night to think about all the problems we could not fix ourselves.<br>
manager, Marjolein, who lies awake at night to think about all the problems we could not fix ourselves.<br>
Revision as of 18:35, 15 October 2018
Although the mobile version has the same content, this wiki is best viewed on larger screens
Newsletter
To keep our followers updated on our continual iGEM endeavours, we send out monthly newsletters. In these newsletters we wrote about the events we visited, what we were doing in the lab and how all other iGEM requirements such as Human
Practices were
coming along. Below, you can read all our previously send newsletters. Also, you can register for future newsletters here.
July
iGEM Leiden 2018
Dear reader, thank you for subscribing to our monthly newsletter. Via this platform we will keep you up to date on our project: Fifty Shades of Stress!
Meet the team!
Our team (from left to right): Marijke Grundeken - PR, Lotte Weel - Ethics, Daphne van den Homberg - Secretary, Chiel van Amstel - Programming, Carli Koster - PR, Laurens ter Haar - Wiki, Maaike de
Jong - Treasurer, Marjolein Crooijmans - Science, Jazzy
de Waard - Fundraising, Tim de Jong - Fundraising, Charlotte de Ceuninck - Chairwoman, Mees Fox - Events and Germaine Aalderink - Lab (absent)
Fifty Shades of Stress
Antibacterial resistance leads to thousands of deaths annually. Meanwhile, only a handful of new antibiotics have been found in the last three decades. Therefore iGEM Leiden 2018 is looking into
designing an innovative and colourful screening platform
to detect bacterial cell stress. The system will consist of multiple stress promoters that are combined with chromoproteins. This results in a bacterial strain that produces a specific colour when the
bacteria
experience a specific kind of stress. This way our system visualises which type of stress is experienced by the bacteria. With our system, we hope to
expand the current screening methods for antibiotics. Nowadays, potential new antibiotics are screened for by assessing the lethality of a compound for bacteria. However, compounds that cause
stress to the
bacteria, but do not kill them are overlooked. Our theory is that a cocktail of these stress inducing compounds can be deadly. By using such cocktails, we will expand the pool of potential
antibiotics.
Simultaneously this obstructs the development of antibiotic resistance, as becoming resistant to one specific antibiotic is easier than to a cocktail of stress-inducing compounds.
Design update
The last couple of weeks we have launched two new pages on our Wiki. The Events page where you can stay up to date on all the events we have visited and read a small review. Besides
the
Events page we have also launched our Sponors page. If you are interested to see who makes our project possible, then this page is a must see. Want to see more of our Wiki? Click on the button
below.
The past couple of weeks we have been filming for our first crowdfunding promotion. Working with the Media Department of Leiden University, we are sure the result will be amazing. In August
our crowdfunding will be launched, so stay tuned for more updates!
Working in the lab
In order to start our lab work as efficiently as possible we have made sure that the lab and all the equipment are ready for us to get to work the coming weeks. The materials and disposables
are on their way, the DNA-primers have been ordered and some
early enthusiasts have prepared the first batches of competent cells. From the 9th of July until the end of August it will only be lab work, more lab work and even more labwork. Wish us luck!
Human Practices
Working in the field of Synthetic Biology comes with enormous responsibility. We feel the importance of thinking about the impact of our project on society. This is why we have planned to
discuss
our project with experts in the field of antibiotics. Besides the opinion of experts, we also find it important to make people aware of the problem that we are facing, which is antibiotic
resistance.
We try to attend as much events as possible and inform visitors in a fun way about synthetic biology and how we can use it in our battle against bacteria. Come visit us at one of our upcoming
events
and share your opinion on synthetic biology!
In the spotlight
The past month we have attended several events. Here we have been introducing the broader public to our project and to Synthetic Biology in general. To make the subject more comprehensible we
have offered them the opportunity to draw with bacteria. This
resulted in some very beautiful pictures. On the left you can see some of the results from our visit to UTwente. Interested? Come visit us at one of our upcoming events.
Agenda
Science Day; Hannover Messe Challenge - 23 April 2018 RIVM: Safe By Design - 14 May 2018 Industry Day - 17 May 2018 Science Meets Business Café - 17 May 2018 Netherlands Biotechnology Conference - 29 May 2018 Museum Night - 2 June 2018
COMING UP
Werfpop - 8 July 2018
Giant Jamboree Boston - 24 to 28 October 2018
Dear reader, thank you for subscribing to our monthly newsletter. Via this platform we will keep you up to date on our project: Fifty Shades of Stress!
Our first month in the lab
July was the first month working full time in the lab on our project: Fifty Shades of Stress. The first succesful transformations were performed and the the first results using
the GFP-strains were obtained. Our PCR experts Daphne and Mees succeeded in isolating the DNA from all the promoters we intend to use during our project. Daphne is also the current record
holder within our team for using the most
pipette tips. Together with Germaine, they finished the first transformations. Our own “Classy” Jazzy explored the dangerous world of Streptomyces together with Marijke. Despite a few really smelly
infections,
Jazzy finished the first overlay to test our bacteria. Lotte has become an expert in pouring agar plates in the first few weeks, while Maaike performed the first attempt to synthesize a
megaplasmid,
unfortunately without success. Our programming manager Chiel, has set his computer aside for two weeks to focus on the Interlab studies, a necessity to win a gold medal in the competition this
year.
Like the true team manager she is, Charlotte was able to set us up with some Bacillus plasmids from iGEM Groningen. While the plasmids were transported from Groningen to Leiden, Laurens was busy
trying
to let E. coli produce colours and Carli and Tim set the record for the longest measurement, using the FACS-machine for over four hours. Each activity was carefully supervised by our
Science
manager, Marjolein, who lies awake at night to think about all the problems we could not fix ourselves. By: Germaine Aalderink & Carli Koster
European iGEM MeetUp
From July 20 to 22 five of our team members went to the iGEM European meet-up in Munich to meet 35 other European iGEM teams. The Munich team organized a
lot of interesting and educational lectures
and workshops. We also discussed our project with the other teams and learned about their projects during the poster presentations. Beside all the educational activities, of course we also
did
some sightseeing in the beautiful city center of Munich. By: Maaike de Jong
Fundraising Update
Since the last newsletter we are proud to announce that we have two new sponsors:
United Consumers and the Leiden Institute of Chemistry! We are very grateful for their support in our journey to
Boston.
August is a big month for fundraising, as we are launching our crowdfunding campaign on August 13th. You will be able to find it on
www.steunleiden.nl, be sure to check it out! Also, stay tuned for a special newsletter all about our campaign and how you can contribute to the fight against antibiotic resistance. By: Tim de Jong
Werfpop
On the 8th of July we organised “Drawing with bacteria” at Werfpop, a free music and art festival in Leiden. We were invited by Science meets Business to
organise a workshop involving some crazy
science. We decided to do some bacterial painting with coloured bacteria. Werfpop visitors used cotton sticks to scrape some bacteria from the petri dishes we brought and drew on a small plate.
Although
nothing was visible while painting, the drawings magically appeared after three days as the bacteria had grown. We were really impressed by all the amazing works of art people made! The workshop was
a
great success with both young and old participating. Besides the drawing we also explained our project to anyone who was interested. It was great to hear all the different opinions everyone had on
genetic
modification and antibiotic resistance. We had many great discussions with the Werfpop visitors and look forward to all the events to come! By: Mees Fox
Chiel and Daphne explaining how to draw with bacteria to Werfpop visitors.
Maaike and Mees promoting our stand to Werfpop visitors.
In the spotlight
At Werfpop we organized a contest for the most beautiful drawing made using the bacteria:
Micrococcus luteus and Micrococcus roseus. The winner was: Felicity Thomaidou, congratulations! She drew a beautiful butterfly! Also an honourable mention to Ilse
and
Jasper for their runner up positions. By: Carli Koster
August Meme Month
Agenda
Science Day; Hannover Messe Challenge - 23 April 2018 RIVM: Safe By Design - 14 May 2018 Industry Day - 17 May 2018 Science Meets Business Café - 17 May 2018 Netherlands Biotechnology Conference - 29 May 2018 Museum Night - 2 June 2018
Werfpop - 8 July 2018
European iGEM Meet-up - 20 to 22 July 2018
COMING UP Dutch iGEM meetup: BBQ (organised by iGEM Leiden) - 17 August 2018 ELCID - 13 to 17 August 2018
Giant Jamboree Boston - 24 to 28 October 2018
Dear reader, welcome to the crowdfunding special of our newsletter series. In this edition we will tell you all about our crowdfunding campaign and how you can help in
the fight against
antibiotic resistance: Say YES to stress! Read all about how you can donate in this newsletter special!
Say Yes to Stress
Bacteria that make us ill are very clever. Through natural evolution, they constantly develop new strategies to arm themselves against our antibiotics. These resistant bacteria put all of
mankind at risk. In order to ensure humanity’s future
health, we must develop new strategies to deal with bacterial infections.
To combat these resistant bacteria we need new antibiotics, but scientists have been unable to discover new marketable ones. To tackle this problem, we came up with an innovative
approach:
bacteria that can show us what kind of stress they are experiencing by changing colour. Stressful substances are not deadly to bacteria by themselves, however, the right combination
can result
in a lethal cocktail. Our ‘stress bacteria’ will enable us to identify substances that can enhance the effect of existing medicines or create entirely new ones. This means we can outsmart the
resistant bacteria.
With your support we want to tackle the global issue of antibiotic resistance, take home the grand prize in Boston and put Leiden University on the map as a world-class university. Our
project
is part of ongoing research within the university and will be continued when we achieve promising results, even if we do not win in Boston. Our project requires funding to buy lab
materials,
chemicals, and a lot of DNA. You can decide to what extent you want to support us in the battle against antibiotic resistance. Pick the colour of stress you want to expose resistant
bacteria
to and together we will defeat them. In short, say yes to stress!
Opening of the crowdfunding - 13 August
ELCID symposium - 17 August
Biology Alumni Evening - 31 August
Opening Academic Year - 4 September
Night of Discoveries - 15 September
Family day Science Faculty - 6 October End of the crowdfunding - 6 October
Dear reader, thank you for subscribing to our monthly newsletter. Via this platform we will keep you up to date on our project: Fifty Shades of Stress!
Our progress in the lab!
August already marked our last month of full time lab work in our ‘own’ lab, so we made the most of it.
Maaike and Lotte were able to amplify the SoxS stress-signal - which responds to DNA damage - by fusing multiple SoxS-GFP combinations together. Consequently, Tim and Carli, our validation team,
confirmed that all these strains worked, and at a much higher
efficiency than our previous singular SoxS-GFP strains. Additionally, Laurens made progress on enhancing the GFP signal using a different system called: T7, while helping others in the lab as our
interim-Science manager.
On the other side of the lab, Jazzy and Marijke were able to freeze dry bacteria and revive them successfully, thereby enabling safer transport and storage of our bacteria.
This brings us closer to our goal of creating a safe and easy to use application for testing bacterial stress. Meanwhile, Daphne finished her project (to produce 32 stress detecting strains) by
isolating
7 new stress promoters and coupling them to GFP. These
new constructs will be tested for their stress detecting capacity in the upcoming month.
This week, we are getting used to our new lab and office environments and setting up the systems for sequencing all our newly made parts. We have also made an extensive planning for our final two
months
until the wiki freeze, coming up on the 17th of october.
With this planning we intend to acquire a golden medal in Boston, and win the grand prize! By: Marijke Grundeken & Laurens ter Haar
Result of a disk diffusion experiment with a constitutive (always on) blue chromoprotein on the right. On the left the negative control, so a
strain that contains no chromoprotein, and in the middle
a lesser succesful strain is visible. Our next task is getting a blue colour only when stressed.
Disk diffusion for dummies:
Disk diffusion is a method that can be used to easily determine whether a compound is lethal to bacteria. To do this, small discs containing
a potential antibiotic are placed on growing bacteria.
The compound in the disc will then slowly spread out. If the compound is lethal to these bacteria, a “halo” will form around the disc where bacteria can not grow.
Dutch iGEM Meet-Up: BBQ and PubQuiz
On the 17th of August iGEM Leiden hosted a meet-up and BBQ for all Dutch iGEM teams. We were happy to see representatives from all 6 teams
attend our
meeting. During the barbecue itself, our chef Chiel made sure all food was seasoned deliciously and cooked to perfection. We also prepared a pub quiz about the Dutch iGEM projects, to allow
everyone to familiarize themselves with eachothers projects. The winners
of the pubquiz were iGEM Delft and iGEM Eindhoven, they took home the grand prize (some delicious candy!).
By: Charlotte de Ceuninck van Capelle
Chef Chiel handing out some delicious food to Dutch iGEMers!
Crowdfunding
On the 13th of August we launched our crowdfunding campaign: Say YES to stress! In the first 3 weeks we have already raised over
€4.000! However, we still
have a long way to go, so check out our campaign and support us by choosing your colour and saying YES to stress! By: Carli Koster
This month we would like to give a special mention to our major sponsors: Medical
Delta and Sarstedt.Medical Deltasupports cooperation in Life Sciences, Health & Technology in Leiden, Delft and Rotterdam. Within the three Universities of these cities they are
represented by YOUNG Medical
Delta. Sarstedt is a
distributor of disposable
lab material. They were kind enough to provide us with enough disposables for our project and even paid a visit to our lab. By: Carli Koster
EL CID
Every year Leiden welcomes thousands of new first year students during its introduction week in August, the EL CID. This week is filled with fun activities, allowing
the new students
to get to know each other, the city and the university. This year the EL CID hosted their very first EL CID symposium and iGEM Leiden was there! We informed students visiting the symposium about
our project and invited them to draw with coloured bacteria.
Moreover, we tested our newly developed “Escape Room board game”! In this game, the students were faced with a problem: drug resistant bacteria. In order to find the cure, the students had to solve
four minigames in time. We received lots of great feedback,
which will allow us to make the game even more fun and educational. By: Charlotte de Ceuninck van Capelle
EL CID participants working hard on finding a cure for the multi-resistant bacteria of our "Escape Room board
game" during
the Symposium.
Wiki Update
With the interlab study finished Chiel, our Programming Manager, could - in theory - dedicate all his time to programming the wiki.
In practice - of course - this was not the case, as the preparations for the iGEM barbecue, the EL CID and the launch of our crowdfunding campaign took a lot of time as well. Still, we managed to
publish
three new pages: The featured page, the newsletter page
and the crowdfunding page. Furthermore, the team page received an extensive update. It is now possible to learn more about each of our team members by clicking on their picture.
The crowdfunding page took a lot of time, particularly to incorporate some cool features. The page started out as a countdown to the start of our crowdfunding campaign and automatically changed to a
'Click-here-to-donate' page when our campaign launched. On
desktops, a very soothing animation of rising circles complements the DONATE-button. Programming this seamingly simple animation took great effort!
With the start of our crowdfunding campaign, the crowdfunding page (on our wiki) was in need of another update, including the Hall of Fame for our donors. In this Hall of Fame, the rising circles
return
once again, even more glorious this time. All donors are
given their own circle floating across the page. It took more than a week to get this concept to a working web page. Make sure to check this page out (on a desktop) and don’t forget to donate if you
also
want a personal floating circle on this page! By: Chiel van Amstel
During the EL CID Symposium we had multiple teams participating in our self-made Escape Room. The goal of an Escape Room is to solve the puzzles as fast as possible and escape to freedom
before the
timer runs out. This of course enabled us to pick a winner!
The team that was fasted to escape the drug resistant bacteria and thus find a cure was composed of Maxim van Delft and Daan Roossien, well done! By: Carli Koster
Agenda
Opening Academic Year - 4 September 2018 Introduction Day Biomedical Sciences Workshop - 4 September 2018 Night of Discoveries - 15 September 2018
Family day Science Faculty - 6 October 2018 End of the crowdfunding - 6 October 2018
Wiki Freeze - 17 October 2018
Dutch Mini Jamboree - 18 October 2018
Giant Jamboree Boston - 24 to 28 October 2018
Dear reader, welcome to the October issue of the iGEM Leiden newsletter. This newsletter will be the last one before we go to Boston to present our project at the Giant Jamboree (24-28 October). For
updates during the Jamboree please check out our social media! Enjoy the reading.
Our last month in the lab!
September has been a rather exciting month for the team. The initial goals of our research phase
went according to schedule. We had successfully produced
our bacterial strains in the previous months, which meant that this month we could focus more on completing the loose ends of the project and we started the analytical phase. Unfortunately, we also
had
to move out of our ‘own’ lab this month. Now we share
a new lab space with multiple PhD researchers, who are kind enough to share their space with us.
In the lab, we mostly focussed on creating evidence and demonstrations of our product for the Jamboree at the end of October.
Furthermore, our strains that contain handcrafted plasmids
(small pieces of DNA that are separated from chromosomal DNA) were isolated this month and sequenced. DNA sequencing is the process of determining the precise order of the bases of our
plasmids.
This process is done by a company in Amsterdam.
The results are send to us by email during the night and we can verify our plasmids the next morning. It is mandatory to sequence
our DNA before submitting it to iGEM. We have produced
many different strains of bacteria that all need to be tested before the submission deadline. Charlotte and Marjolein were mostly responsible for these verifications.
Tim and Carli were in charge of testing the bacterial strains with different types of stress, to
check the responsiveness and effectiveness. We have found
at least 6 strains that showed interesting results. Lastly, Jazzy made beautiful agar plates which demonstrated the potency of our project (see picture below). The dark line around the clear
circles are
bacteria that produce a “blue/grey” chromoprotein in
response to DNA damage, proving that our project works! By: Marjolein Crooijmans
The picture shows a plate containing our growing "stress bacteria". The three white discs contain antibiotics, which can be seen from the
lack of
growth in the surrounding circle. On the edge of that
circle you can see a dark color. Those are bacteria that are producing a grey/blue chromoprotein in response to stress caused by a low antibiotic concentration!
Disk diffusion for dummies:
Disk diffusion is a method that can be used to easily determine whether a compound is lethal to bacteria. To do this, small discs containing
a
potential antibiotic are placed on growing bacteria.
The compound in the disc will then slowly spread out. If the compound is lethal to these bacteria, a “halo” will form around the disc where bacteria can not grow.
Night of Discoveries
During the week of 10 - 16 september we had the honour of organising a workshop for the Night of
Discoveries (formerly known as the “Nacht van kunst en
kennis”). We provided people with the opportunity to create their own bacterial drawings and play our renewed "Escape Room"-game, while learning something about antibiotic resistance on the way. We
explained our project to everyone who was interested, and
fortunately many people were. It was great to be part of such a big event! We loved the experience and hope that the next iGEM team will also be able to participate.
By: Mees Fox
Maaike and Germaine preparing our stand for the Night of Discoveries
Crowdfunding
Our crowdfunding campaign: "Say YES to Stress!" received a major boost during
the month of September. Thanks to all our amazing donors, we have
reached over 80% of our total goal, which equals an amount of €7.820. The crowdfunding will end on October 6th during the Family Day of the Science Faculty at Leiden University. So, please
help
us reach 100% by choosing your colour and saying YES to stress!
On the fourth of September we had the pleasure to attend the ceremonial opening of the academic year at the Faculty of Science. We
were welcomed by the dean Geert de Snoo, were entertained
by a fascinating lecture on ecotoxicology and enjoyed a musical intermezzo. Afterwards we were of course present at the drinks to promote our project and our crowdfunding campaign! We even quickly
met up
with Ionica Smeets, an endorser of our project and known
from TV and radio. By: Charlotte de Ceuninck van Capelle
Ionica Smeets showing her support for our project: Fifty Shades of
Stress
Wiki Update
Calm before the storm… The deadline for the wiki freeze is approaching fast. Although it seems as if not much has happened with
the wiki, behind the scenes a lot of work has been done.
The past month a template for all our major pages has been programmed, so that the final text can be easily inserted when ready. For navigation purposes these templates also include an
automatically
generated quick-navigation, soft-links and even a few custom
designed icons. As soon as the text is done for a page, it will be - in theory - just a case of copy and paste and all will be done. Let’s hope the iGEM servers will not give in under the pressure
of
over 300 teams uploading files at the same time… By: Chiel van Amstel
On wednesday the 26th of September a delagation of our team visited the old High School of Laurens and Marijke: Da Vinci College. Here they presented our awereness programme including an
interactive presentation on Antibiotic Resistance, drawing with bacteria
and the final version of our Escape Room.
Agenda
Family day Science Faculty - 6 October 2018 End of the crowdfunding - 6 October 2018
Wiki Freeze - 17 October 2018
Dutch Mini Jamboree - 18 October 2018
Giant Jamboree Boston - 24 to 28 October 2018
