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Revision as of 13:12, 15 September 2015
Short introduction
“The sea is everything. […] The sea is the vast reservoir of Nature. The globe began with sea, so to
speak”, Nemo said while the “Nautilus” was cruising with a school of hammerhead sharks deep
beneath the waves.
And the captain was right. Deep in the ocean billions of years ago the miracle of nature took place as
a pool of small molecules evolved to self-replicating lifeforms. The flagship role in this development
was probably taken by the most versatile class of molecules in the history of life: RNA.
Seemingly random nucleotides happened to be in the right order to form the first biocatalysts that
made life on the blue planet possible. Today we know those miracles of nature as ribozymes. Inspired
by this, humanity took evolution into their own hands to create aptamers – nucleic acids capable of
encaging molecules. This allows for the detection of virtually anything. Still this process has been
tedious and time consuming much like fishing with a rod in an ocean. We want to revolutionize this
former evolutionary process and want to make it swift like a shark tracking down its prey.
Yet to really bring out the strengths of these simple yet powerful molecules just comprised of A, U, C
and G we want to combine aptamers and ribozymes to create a toolset for the synthetic biologist to
create allosteric ribozymes able to sense a variety of molecules. Therefore, we hope to introduce the
true origins of life and the capabilities of functional RNA to iGEM.
Join us as we sail forth into new
waters of synthetic biology.
Further content
Supporting iGEM Team Paris Bettencourt
iGEM Paris Bettencourt has set up a visual databse that should help various iGEM teams collaborate and find common ground. In that database all teams can enter techniques, keywords, organism and many more thev are knowdledgeable in or have been working on. As common dots are connected automatically, it's easy so see, whom to ask for a collaboration.
Though we came a little late to the party, we really loved the idea and hoped, that the database has helped various teams!
"Rhizi is an open-sourced web of knowledge where nodes are sources of information (e.g. scientific articles, questions, blog posts) and edges are the links between them. The goal of Rhizi is to create information rich links between knowledge, open questions and ideas, through encouraging users to vote, comment, and create new relationships."
Collecting impressions from the community
It’s done. We’ve finally decided upon a logo. It’s beautiful, it’s blue, it’s fishy *wink*. The next step was to choose a color scheme and a general style for the wiki. As we feared that our own ideas might be too similar we thought of asking a broader public how they would design a website based on our logo. In order to do so, we headed to the ’Neckarwiese’. During summer, a big part of Heidelbergs population decideds to go there and enjoy the sun, have a BBQ or just relax – so we caught them off guard.
We have had prepared a little presentatio with which we introduced them to iGEM and Synthetic Biology. Afterwards we explained them what we planned on doing, showed them our logo and asked, how they would design a website, based on what they’ve just heard. The general consens was to go for a blue theme, maybe add a little algae green and generally stick to maritime iconography. Unexpectedly we actually met someone who knew his stuff: Natalie, a student of the history of arts from Berlin. She gave us useful advice on how play with the different colors, what to avoid and even added a little touch of history to it. Lucky catch!
With fresh ideas we headed back to the lab and continued our experiments, being envious of all the people that could continue to sleep in the sun.
Panel Discussion
Synthetic biology - engineering life with its most fundamental units by using DNA BioBricks and other modularly combinable parts, has a potential beyond scope and can improve the quality of life for everyone and mankind as a whole. The ultimate goal of researchers in synthetic biology is not only the understanding of life itself and how it functions, but applying the acquired knowledge to make a change within their community.
To investigate the current state of the research and its acceptance in society, we talked to scientists and asked them how their work has influenced their community. Nonetheless, it is of absolute necessity to include the entire society. We decided to do this by organizing a panel discussion evening dedicated to the topic 'Synthetic biology - Bricks for a healthy life?', i.e. synthetic biology in medicine.
As research in general and especially synthetic biology relies on a community, on interaction between researchers and the exchange of ideas and expertise, we asked experts and researchers from different fields to join us for this evening and we distributed flyers and placards to invite the broad society. However, we wanted to go a step further: The panel discussion was not limited to the audience in Heidelberg, it was simultaneously translated from German to English and broadcasted it via a live stream.
Despite the great enhancements synthetic biology can achieve, engineering with building blocks that are so close to the basic principles of life itself comes with a range of ethical questions and security precautions to consider. We see it as our immanent responsibility as iGEM team to address these questions and to take concerns very seriously. Hence, we invited Prof. Dr. Axel Bauer, who has been member of the German ethics council for several years and Dr. Joachim Boldt who works as assessor for the German ethics commitee for ethical implications of synthetic biology. Both of them are highly involved in the field of medical ethics also due to being professor for this subject. In order to review the safety concerns, we were very glad to have Dr. Harald König, who works at the Institute for Technology Assessment and System Analysis, as our guest.
Politics and law play a very big role when discussing the application of synthetic biology in real life. Researchers need to obey the juridical boundaries and on the contrary the legislature has to react to novel developments and find a compromise between many different opinions, some being more conservative, others more progressive. To reflect this interweaving, we additionally invited local politicians, such as Prof. Dr. Nicole Marmé who is member of the city council of Heidelberg. Dr. Stephan Brandt, chairman of the department for Biotechnological Innovation, Nanotechnology and Genetic Engineering, investigates how laws need to be adapted to the most recent findings in synthetic biology and genetics and we are very glad he joined us for this evening. Finally, the topic that stands in the center of this evening is, after all, research in synthetic biology. For that reason, we asked Dr. Dirk Grimm, who works on the CRISPR-Cas system and who knows the cutting edge developments to be the scientific representative in the panel.
After a lot of planning, organization and set up of all the required technical equipment (thanks again to Dr. Jens Wagner from the Physics Department), the discussion evening could start with a brief introduction to the topic given by Jasmin and Max from our team. As we wanted the main part of the evening to be an open discussion, we deliberately made the introduction very compact. For the remaining 1.5 hours of the evening, Tim navigated our guests, as well as the audience through the discussion.
The involvement of the audience was amazing, proving that this topic is indeed highly interesting to a large part of the society. Most eminently, we were very happy that additional to the approximately 100 guests that joined us physically in our institute, we had almost 400 viewers online, among them also other iGEM teams, such as iGEM Team Cambrige (link). Besides watching, our followers on twitter were also very engaged in asking questions that were then addressed by Tim and the invited experts.
The topics discussed ranged from green to red biotechnology and were contemplated in a highly interdisciplinary way (with the focus on medical applications nonetheless). Besides, and in correspondence to the initialization of the “Community lab” track in iGEM, we addressed biohacking and the implications of it on society, the scientific community and the communication between the two entities. Question were asked about ethical problems and implications of in vivo and in vitro technologies, but also about dreams and wishes of the scientists regarding future developments in this field. The question iGEM team Cambridge nicely summarizes the last part of the discussion: “How can synthetic biologists better communicate their research to the public?” This includes the role of politicians and law makers, as well as the responsibility of everyone who is involved in research to put a focus on the outreach and the interaction, not only with the scientific community, but also with the broader public.
So far, many iGEM teams have organized discussion evenings and invited people from the broad society to join an interdisciplinary evening. This approach is great and helps a lot to improve the communication between scientists and the public. Nonetheless, there are still barriers to overcome:
- The interested population of one city is not representing the entire society. Hence, we decided to provide the opportunity to join us online via live stream. This should not be limited to watching the discussion passively, that is why everyone could ask questions via twitter by #askigemheidelberg. These questions were then shown in the discussion, so that our invited guests could reply or reflect on them.
- The lingua franca in research is English, however not everybody is capable of speaking English fluently. Therefore, we deliberately chose German as the language the discussion was held in. This way, everyone who was interested had the possibility to follow. In order to keep the event international and also understandable for those who watched online, we translated the event simultaneously to English.
week number 38
▼2015-09-14 Test bitte löschen
10 x <i>in vitro</i> transcription buffer
50 mM Tris ph 7.5, 100 mM NaCl, 20 mM MgCl<sub>2</sub>, 0,01 % SDS
week number 37
▼2015-09-10 DNAzyme Activity: DNAzyme with ATP aptamer and calculated Kanamycin aptamer
Samples:
- 10-23 DNAzyme: xxfs032xx
- 7-18 DNAzyme: xxfs033xx
- 10-23 DNAzyme with ATP aptamer with linker: xxfs019xx
- 7-18 DNAzyme with ATP aptamer with linker: xxfs027xx
- 10-23 DNAzyme with ATP aptamer A: xxfs017xx, B: xxfs018xx
- 7-18 DNAzyme with ATP aptamer A: xxfs025, B: xxfs026xx
- 10-23 DNAzyme with calculated Kan aptamer: xxfs034xx
- 7-18 DNAzyme with calculated Kan aptamer candidate I: xxfs035xx
- 7-18 DNAzyme with calculated Kan aptamer candidate II: xxfs036xx
- 7-18 DNAzyme with calculated Kan aptamer candidate III: xxfs037xx
Stock solutions and conditions:
cStock |
cFinal |
|
Tris HCl ph 7.5 |
1 M |
50 mM |
DNAzyme (A) |
10 µM |
500 nM |
DNAzyme B |
10 µM |
500 nM |
Substrate |
1 µM |
200 nM |
NaCl |
1 M |
100 mM |
MgCl2 |
1 M |
20 mM |
SDS |
20 % |
0,01 % |
Adenosine in H2O:DMSO 1:2 |
33 mM |
5 mM |
H2O |
|
ad 25 µL |
Pipetting scheme:
# |
|
|
Tris HCl ph 7.5 |
DNAzyme A |
DNAzyme B |
Substrate |
NaCl |
MgCl2 |
SDS |
Adenosine |
H2O |
Final |
1 |
FS032 |
10-23D |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
3,75 |
9,50 |
25,00 |
2 |
FS033 |
7-18D |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
3,75 |
9,50 |
25,00 |
3 |
FS019 |
10-23DmLink |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
3,75 |
9,50 |
25,00 |
4 |
FS027 |
7-18DmLink |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
3,75 |
9,50 |
25,00 |
5 |
FS017+18 |
10-23D_A+B |
1,25 |
1,25 |
6,25 |
5,00 |
2,50 |
0,50 |
1,25 |
3,75 |
3,25 |
25,00 |
6 |
FS025+26 |
7-18D_A+B |
1,25 |
1,25 |
6,25 |
5,00 |
2,50 |
0,50 |
1,25 |
3,75 |
3,25 |
25,00 |
7 |
FS032 |
10-23D |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
0,00 |
13,25 |
25,00 |
8 |
FS033 |
7-18D |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
0,00 |
13,25 |
25,00 |
9 |
FS019 |
10-23DmLink |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
0,00 |
13,25 |
25,00 |
10 |
FS027 |
7-18DmLink |
1,25 |
1,25 |
0,00 |
5,00 |
2,50 |
0,50 |
1,25 |
0,00 |
13,25 |
25,00 |
11 |
FS017+18 |
10-23D_A+B |
1,25 |
1,25 |
6,25 |
5,00 |
2,50 |
0,50 |
1,25 |
0,00 |
7,00 |
25,00 |
12 |
FS025+26 |
7-18D_A+B |
1,25 |
1,25 |
6,25 |
5,00 |
2,50 |
0,50 |
1,25 |
0,00 |
7,00 |
25,00 |
13 |
FS032 |
-10-23D |
1,25 |
1,25 |
0 |
0 |
2,5 |
0,5 |
1,25 |
0 |
18,25 |
25,00 |
14 |
FS033 |
-7-18D |
1,25 |
1,25 |
0 |
0 |
2,5 |
0,5 |
1,25 |
0 |
18,25 |
25,00 |
15 |
FS019 |
-10-23DmLink |
1,25 |
1,25 |
0 |
0 |
2,5 |
0,5 |
1,25 |
0 |
18,25 |
25,00 |
16 |
FS027 |
-7-18DmLink |
1,25 |
1,25 |
0 |
0 |
2,5 |
0,5 |
1,25 |
0 |
18,25 |
25,00 |
17 |
FS017+18 |
-10-23D_A+B |
1,25 |
1,25 |
6,25 |
0 |
2,5 |
0,5 |
1,25 |
0 |
12 |
25,00 |
18 |
FS025+26 |
-7-18D_A+B |
1,25 |
1,25 |
6,25 |
0 |
2,5 |
0,5 |
1,25 |
0 |
12 |
25,00 |
19 |
Adenosine |
Substrate only |
1,25 |
0 |
0 |
5 |
2,5 |
0,5 |
1,25 |
3,75 |
10,75 |
25,00 |
# |
Tris HCl ph 7.5 |
DNAzyme A |
DNAzyme B |
Substrate |
NaCl |
MgCl2 |
SDS |
Kan |
H2O |
Final |
||
20 |
FS032 |
10-23D |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
1,25 |
12 |
25 |
21 |
FS033 |
7-18D |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
1,25 |
12 |
25 |
22 |
FS034 |
Kan |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
1,25 |
12 |
25 |
23 |
FS035 |
Kan I |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
1,25 |
12 |
25 |
24 |
FS036 |
Kan II |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
1,25 |
12 |
25 |
25 |
FS037 |
Kan III |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
1,25 |
12 |
25 |
26 |
FS032 |
10-23D |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
0 |
13,25 |
25 |
27 |
FS033 |
7-18D |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
0 |
13,25 |
25 |
28 |
FS034 |
Kan |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
0 |
13,25 |
25 |
29 |
FS035 |
Kan I |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
0 |
13,25 |
25 |
30 |
FS036 |
Kan II |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
0 |
13,25 |
25 |
31 |
FS037 |
Kan III |
1,25 |
1,25 |
0 |
5 |
2,5 |
0,5 |
1,25 |
0 |
13,25 |
25 |
32 |
Kan |
Substrate only |
1,25 |
0 |
0 |
5 |
2,5 |
0,5 |
1,25 |
1,25 |
13,25 |
25,00 |
33 |
Substrate only |
1,25 |
0 |
0 |
5 |
2,5 |
0,5 |
1,25 |
0 |
14,5 |
25,00 |
Results and Outlook:
Positive controls worked, Adenosine dependency could be detected for one candidate.
▼2015-09-10 Click reaction of Label-, Label AU RNA [1, 2, 3]
For 51.5µL |
Cstock |
Cfinal |
V[µL] |
Phosphate Buffer - pH 7, 0.1M |
100mM |
50mM |
25 |
Alexa 488 azide |
10µM |
400nM |
2 |
RNA |
1µM |
200nM |
10 |
CuSO4 |
20mM |
1mM |
2.5 |
THPTA |
50mM |
5mM |
5 |
NaAsc |
100mM |
1mM |
0.5 |
H2O |
|
|
6.5 |
- Alexa 488 azide was solved in DMSO
- Incubation at 37 °C for 12-14 hours (overnight)