Difference between revisions of "Team:Heidelberg/Collaborations"

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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 <i>E. coli</i> by inhibiting DNA repair mechanisms have been described <x-ref>badran2015development</x-ref>. When transformed into <i>E. coli</i> hosts, these plasmids should cause mutation rates several orders of magnitude higher than usually expected under laboratory conditions.  
 
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 <i>E. coli</i> by inhibiting DNA repair mechanisms have been described <x-ref>badran2015development</x-ref>. When transformed into <i>E. coli</i> hosts, these plasmids should cause mutation rates several orders of magnitude higher than usually expected under laboratory conditions.  
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The exact mutation rate induced by different mutagenesis plasmids could, however, vary between laboratories, as <i>E. coli</i> 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 <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab"> mutagenesis plasmid test kit and assay
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The exact mutation rate induced by different mutagenesis plasmids could, however, vary between laboratories, as <i>E. coli</i> 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 <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab_HD"> mutagenesis plasmid test kit and assay
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</a> 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 <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab">results</a> from this small inter lab study with all iGEM teams  
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</a> 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 <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab_HD">results</a> from this small inter lab study with all iGEM teams  
 
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<b>Results from the Study</b>
 
<b>Results from the Study</b>
 
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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 <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab">results</a> of iGEM team BOKU Vienna, ETH Zürich, Freiburg and Stuttgart indicate that MP #1 induces mutations most reliably .
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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 <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab_HD">results</a> of iGEM team BOKU Vienna, ETH Zürich, Freiburg and Stuttgart indicate that MP #1 induces mutations most reliably .
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Hence, we recommend to use mutagenesis plasmid #1 for PREDCEL experiments, which is also noted in our corresponding <a href="RFC https://2017.igem.org/Team:Heidelberg/RFC">RFC</a>. The results are shown and described on our <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab"> MP InterLab page</a>
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Hence, we recommend to use mutagenesis plasmid #1 for PREDCEL experiments, which is also noted in our corresponding <a href="RFC https://2017.igem.org/Team:Heidelberg/RFC">RFC</a>. The results are shown and described on our <a href="https://2017.igem.org/Team:Heidelberg/Collaborations/InterLab_HD"> MP InterLab page</a>
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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 <a href:"https://2017.igem.org/Team:Heidelberg/Collaborations/Translation">many languages</a>. Following this idea, the iGEM Team KU Leuven started a translation center and asked all teams to participate. Each team uploaded its <a href:"https://2017.igem.org/Team:Heidelberg/Collaborations/Translation">project description</a> 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.
 
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 <a href:"https://2017.igem.org/Team:Heidelberg/Collaborations/Translation">many languages</a>. Following this idea, the iGEM Team KU Leuven started a translation center and asked all teams to participate. Each team uploaded its <a href:"https://2017.igem.org/Team:Heidelberg/Collaborations/Translation">project description</a> 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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Revision as of 11:58, 30 October 2017

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 PBAD. Upstream of PBAD the araC protein is encoded in the opposite direction and regulates the activity of the PBAD promoter. The expression cassette downstream PBAD 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
https://static.igem.org/mediawiki/2017/1/1d/T--Heidelberg--HP_Collab_ETH.png
https://static.igem.org/mediawiki/2017/5/53/T--Heidelberg--HP_Collab_Freiburg.png
https://static.igem.org/mediawiki/2017/3/3e/T--Heidelberg--HP_Collab_Stuttgart.png
https://static.igem.org/mediawiki/2017/5/5e/T--Heidelberg--HP_Collab_Vienna.png

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
https://static.igem.org/mediawiki/2017/9/93/T--TU_Dresden--gogreen_logo_withoutbackground.png

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.
https://static.igem.org/mediawiki/2017/7/79/Collaboration_Medal.png

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

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

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