Difference between revisions of "Team:Heidelberg/SandboxMarita/Collaborations"

Mutagenesis Plasmid Inter-Lab Study

In our directed evolution approaches PREDCEL and PACE, we select for beneficial mutations in a protein of interest encoded on a M13 phage genome. In order to generate a pool of protein mutants to select from in the first place, the efficient introduction of mutations during phage genome replication is essential. Mutagenesis-inducing plasmids (MPs) that enhance the mutation rate in E. coli by inhibiting DNA repair mechanisms have been described badran2015development. When transformed into E. coli hosts, these plasmids should cause mutation rates several orders of magnitude higher than usually expected under laboratory conditions. The exact mutation rate induced by different mutagenesis plasmids could, however, vary between laboratories, as E. coli growth conditions and hence expression strength of the mutagenic proteins (e.g. error-prone polymerase subunits) could differ. However, robust induction of high mutation rates are critical for the success of PREDCEL and PACE and hence of major importance for other teams to reproduce our directed evolution methods. Therefore, we performed a small inter-lab study to evaluate the performance of different mutagenesis inducing plasmids and find the construct setup most robust and hence suitable for future iGEM teams to use for in vivo directed evolution. To enable an inter-lab comparison, we developed a standardized mutagenesis plasmid test kit and assay and distributed it to iGEM team BOKU Vienna, ETH Zurich, Freiburg and Stuttgart. We are very grateful for their kind support and excited to share the results from this small inter lab study with all iGEM teams

Mutagenesis Assay Kit
We shipped 3 mutagenesis plasmids (#1-3). All mutagenesis inducing plasmids contain an arabinose inducible promoter P_BAD. Upstream of P_BAD the araC protein is encoded in the opposite direction and regulates the activity of the P_BAD promoter. The expression cassette downstream P_BAD comprises multiple, different mutagenesis supporting elements, e.g. error-prone polymerase subunits. According to literature badran2015development the mutagenesis plasmids #1-3 were expected to cause increasingly high mutation rates.

Mutagenesis Assay – Spontaneous Resistance Acquisition
Due to exceptionally high mutagenesis levels of E. coli cells transformed with one of the mutagenesis plasmids, these cells can more quickly adopt to environmental changes. Hence, one way to measure the mutagenesis levels is simply to quantify the level of spontaneous antibiotic resistance acquisition. Therefore, E. coli were transformed with mutagenesis plasmids or remain untransformed (as control) followed by incubation in presence or absence of different antibiotics on agar plates. After 18-21 hours of incubation at 37 °C, colonies are counted. A higher number of colonies (i.e. clones with spontaneous resistance acquired) thereby indicates a higher mutation rate in the corresponding E. coli population due to the presence of the mutagenesis plasmid.

Results from the Study
To decide which mutagenesis plasmid to recommend to future iGEM teams for in vivo directed evolution approaches such as PREDCEL, it was essential to determine the mutagenesis plasmid setup most robustly functioning across different laboratories. The results of iGEM team BOKU Vienna, ETH Zürich, Freiburg and Stuttgart indicate that MP #1 induces mutations most reliably . Hence, we recommend to use mutagenesis plasmid #1 for PREDCEL experiments, which is also noted in our corresponding RFC. The results are shown and described on our MP InterLab page
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Cloning for iGEM Freiburg

Collab Text siehe shared Drive

PCR First Aid Service

As we had several PCR problems ourselves in the beginning of our project, we asked our advisors for help and created a PCR troubleshooting protocol, which you can find on our protocol section. Because we considered it to be helpful for other teams as well, we decided to offer help for all other iGEM teams: our First Aid Service for PCR Problems. Happily we could help some teams overcoming their PCR problem.

Help for iGEM Hamburg with PCR problems
!!Text von Alina!!

iGEM goes green

LINK zu iGEM goes green /Collaborations/igemgoesgreen
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Translation Center

Bringing science closer to the public is a major goal in iGEM. As communicating scientific content can be challenging because complex issues need to be unraveled to easy understandable terms, one step could be translating scientific texts into many languages. Following this idea, the iGEM Team KU Leuven started a translation center and asked all teams to participate. Each team uploaded its project description and translated other project descriptions into their mother tongue. This is a first step towards simplification and easier communication with the general public because one barrier, namely the language barrier, can be overcome with the translation center. We translated several project descriptions into German and could thereby hopefully contribute to a better communication between scientists and a broad public.
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Postcards

Participating in the Postcard campaign of Duesseldorf-Cologne was a real success. Thanks to the inspiring and eye-catching designs of all postcards we started talks about synthetic biology, GMOs and other issues addressed by over 36 postcards we received.
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No Science without Tolerance

Respect is an essential iGEM value and tolerance an important aspect of it. We were thus very happy to support the tolerance campaign by iGEM Team Technion (Israel). All our creativity was used to draw this lab-associated tolerance lettering and we can hopefully contribute to draw more attention to the fundamental value of tolerance in the scientific community and in public.
PICS
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Surveys – Supporting Responsible and Efficient Technology Development within iGEM

Bostons Microfluidic Survey
The Boston University Hardware team worked with microfluidic chips and wanted to establish an archive with different designs and protocols. Their goal is to fit the archival structure to any needs of its users. To support this project, we filled in their survey and could thereby hopefully contribute to a well applied, sustainable design of their archive.

Beijing Institute of Technology: Survey according health care and liver cancer
iGEM Team BIT worked on a liver cancer related project and wanted to integrate the opinion of us iGEMers into the design of their project. We answered their survey and are looking forward to seeing their great ideas realized.

Biological Material Transport Survey from State University of Amazonas
Shipment of biological material often faces problems when cooling is required and long distances need to be conquered. This is particularly true for less developed countries and regions with no direct access to an (freight) airport. The Amazonas Brazil team wanted to collect information from all over the world to get a deeper insight into import and export regulation processes of countries around the world. We hope that we supported your collection of information by thoroughly answering your questionnaire.

Air pollution survey from iGEM Pasteur Paris
Environmental pollution and climate change are two of the major challenges we desperately need to solve towards our agreed goal of a sustainable human civilization on our planet. The iGEM Team Pasteur Paris focused on environmental issues and highlighted the problem of air pollution, which is particularly strong problem in quickly industrialized countries with low standards of waste air cleaning in fossil fuel power stations, industrial facilities and transportation vehicles. To receive an impression about the air pollution situation in different regions all over the world they created a comprehensive survey. We hope that we could convey an impression about the situation in Heidelberg, which fortunately is a rather small, bicycle-friendly city closely surrounded by five beautiful nature reserves. iGEM Team Heidelberg is also taking part in the iGEM goes green initiative by team TU Dresden.

Survey about methane production from UNebraska-Lincoln
The iGEM Team UNebraska-Lincoln aims at inhibiting the methane production in cattle and wanted to integrate the general public opinion into the design of their project. All members of iGEM team Heidelberg filled in their survey and we are looking forward to helping you gather information and maybe even contribute to decreasing the alarming speed of climate change.

Survey about cholera from iGEM Toulouse
In order to tackle the cholera disease, the iGEM Team Toulouse asked everyone to answering their questionnaire to receive an impression about the informational situation according to cholera disease. Hopefully we could contribute a little bit to succeeding with your project on eradicating Vibrio cholerae.

Genetic modification to produce medicines - Cardiff iGEM
To investigate the public´s view on genetic modification for pharmaceutical production the Cardiff iGEM Team created a survey. They aim at treating the Grave´s Disease, an autoimmune disease affecting the thyroid, with the help of genetically modified organisms. We filled in their questionnaire and hope that they succeed with realizing their innovative therapeutic approach.

GMO perception survey from Ionis Paris
To gain more information about GMO perception by the public the iGEM Team Ionis Paris conducted a survey we took part in. They aim at creating an interactive map to make the comprehensive information from their interesting questionnaire easily accessible. This map contains regimentations and opinions about GMOs and could provide novel insights into region-specific, public perception on the creation and use of GMOs.

CRISPR along the iGEM: survey from Amazonas Brazil
No doubt that CRISPR is a breakthrough technology that should be easily accessible by any (responsible) researcher around the globe. To establish a simple and standardized methodology for applying CRISPR the iGEM Team Amazonas Brazil created a survey to communicate with other iGEM teams and exchange information about problems when working with the CRISPR technology. We participated in this survey and are eager to see your solutions for an easier handling of this method come into play in iGEM.

Diagnosis device survey from iGEM Team Munich
The iGEM Team Munich collected opinions about diagnostic devices in a survey that was distributed to people with different professional backgrounds. In certain countries access to regular medical care is limited, either due to regional fluctuation in the density of hospitals, pharmacies and doctors or due to country-specific healthcare laws. This issue affects millions of people world-wide, both in developing as well as modern countries. iGEM Team Munich aims at developing diagnostic devices, that could be used at home and provide people with diagnosis and hence medical care that would otherwise have no access to.