iGEM 2019 — Team Alma

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# Team:Alma/Notebook

![](https://static.igem.org/mediawiki/2019/6/60/T--alma--project_logo.png)

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[![](https://static.igem.org/mediawiki/2019/e/ef/T--Alma--Project_logo.png)](https://2019.igem.org/Team%3AAlma)
[HOME](https://2019.igem.org/Team%3AAlma)

TEAM

[About the Team](https://2019.igem.org/Team%3AAlma/Team)
[Collaborations](https://2019.igem.org/Team%3AAlma/Collaborations)

PROJECT

[Description](https://2019.igem.org/Team%3AAlma/Description)
[Design](https://2019.igem.org/Team%3AAlma/Design)
[Model](https://2019.igem.org/Team%3AAlma/Model)
[Experiments](https://2019.igem.org/Team%3AAlma/Experiments)

[Contribution](https://2019.igem.org/Team%3AAlma/Contribution)

[Attributions](https://2019.igem.org/Team%3AAlma/Attributions)

[PARTS](https://2019.igem.org/Team%3AAlma/Parts)

HUMAN PRACTICES

[Human Practices Overview](https://2019.igem.org/Team%3AAlma/Human_Practices)
[Graphic Design](https://2019.igem.org/Team%3AAlma/Graphic_Design)
[Education & Engagement](https://2019.igem.org/Team%3AAlma/Public_Engagement)
[Integrated Human Practices](https://2019.igem.org/Team%3AAlma/Integrated_Human_Practices)

[REFERENCES

[JUDGING FORM ⇗](https://igem.org/2019_Judging_Form?team=Alma)](https://2019.igem.org/Team%3AAlma/References)

# Notebook

Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.

### What should this page have?

* Chronological notes of what your team is doing.
* Brief descriptions of daily important events.
* Pictures of your progress.
* Mention who participated in what task.

### Inspiration

You can see what others teams have done to organize their notes:

* [2018 Munich](https://2018.igem.org/Team%3AMunich/Notebook)
* [2014 ATOMS-Turkiye](https://2014.igem.org/Team%3AATOMS-Turkiye/Notebook)
* [2014 Tec Monterrey](https://2014.igem.org/Team%3ATec-Monterrey/ITESM14_project.html#tab_notebook)
* [2014 Kyoto](https://2014.igem.org/Team%3AKyoto/Notebook/Magnetosome_Formation#title)
* [2014 Cornell](https://2014.igem.org/Team%3ACornell/notebook)


[![](https://2019.igem.org/wiki/images/8/8b/HQ_page_logo.jpg)](https://2019.igem.org)

# Team:Alma/Experiments

![](https://static.igem.org/mediawiki/2019/6/60/T--alma--project_logo.png)

![](https://static.igem.org/mediawiki/2019/e/ee/2019_team_menu_icon.svg)

[![](https://static.igem.org/mediawiki/2019/e/ef/T--Alma--Project_logo.png)](https://2019.igem.org/Team%3AAlma)
[HOME](https://2019.igem.org/Team%3AAlma)

TEAM

[About the Team](https://2019.igem.org/Team%3AAlma/Team)
[Collaborations](https://2019.igem.org/Team%3AAlma/Collaborations)

PROJECT

[Description](https://2019.igem.org/Team%3AAlma/Description)
[Design](https://2019.igem.org/Team%3AAlma/Design)
[Model](https://2019.igem.org/Team%3AAlma/Model)
[Experiments](https://2019.igem.org/Team%3AAlma/Experiments)

[Contribution](https://2019.igem.org/Team%3AAlma/Contribution)

[Attributions](https://2019.igem.org/Team%3AAlma/Attributions)

[PARTS](https://2019.igem.org/Team%3AAlma/Parts)

HUMAN PRACTICES

[Human Practices Overview](https://2019.igem.org/Team%3AAlma/Human_Practices)
[Graphic Design](https://2019.igem.org/Team%3AAlma/Graphic_Design)
[Education & Engagement](https://2019.igem.org/Team%3AAlma/Public_Engagement)
[Integrated Human Practices](https://2019.igem.org/Team%3AAlma/Integrated_Human_Practices)

[REFERENCES

[JUDGING FORM ⇗](https://igem.org/2019_Judging_Form?team=Alma)](https://2019.igem.org/Team%3AAlma/References)

# Experiments and Protocols

This page contains information regarding some of the protocols we most commonly used, as well as the raw notes we took as we conducted the experiments. In addition, the results from some of our experiments can be found either on the [contribution page](https://2019.igem.org/Team%3AAlma/Contribution) or the relevant registry pages for the [parts we made.](https://2019.igem.org/Team%3AAlma/Parts)

* [Amplification of Linearized Plasmid Backbone](https://benchling.com/s/prt-UOe1to0uoTplTa6MoMfA)
* [CCMB80 Transformation](https://benchling.com/s/prt-nuJujpWLsw6aqWVgh1O7)
* [Extraction of DNA from an Agarose Gel](https://benchling.com/s/prt-Zwi59k9BBRU0Qx6VEqC4)
* [IMAC purification of His-tagged proteins](https://benchling.com/s/prt-ASMk0ZbxV51tZyevMjEl)
* [Preparation of Long Term Bacterial Stocks](https://benchling.com/s/prt-mYCHqvb8xO6trfFbYd54)
* [Preparing LB plates with Chloramphenicol](https://benchling.com/s/prt-ug9vjMTmosjpIkCfbBc6)
* [Spin Column Regeneration](https://benchling.com/s/prt-P8K0t34Txo5iQRLMOyK9)
* [TSS Bacterial Transformation](https://benchling.com/s/prt-Mfa778dCHegMwAErIxZn)

Other experimental procedures were straightforward but varied each time, and are described in experimental notes. Some others include protocols were we followed supplier instructions, such as casting and running 12% SDS PAGE gels. Some of the more notable protocols we followed were as follows:

* **High Fidelity PCR**: When amplifying DNA for use in assembly, we carried out PCR as described on the contribution page. This was essentially as follows (reaction volumes sometimes scaled up x2): 0.5uL template DNA was mixed with 1.25uL of forward primer (@10uM), 1.25uL of reverse primer (@10uM), 9.5uL of dH20, and 12.5uL of the Q5 DNA Polymerase Mix (New England Biolabs).
* **Colony PCR**: To quickly check a number of clones, we would perform colony PCR. We would create a mix that would be multiple times the following volumes: (10uL dH20, 1.25uL primer VF2 (@10uM), 1.25uL primer VR (@10uM), and 12.5uL of 2X Taq Mix (Sigma). Then, from this mix, 25uL would be dispensed into a PCR tube for every clone to be tested. A sterile toothpick would be used to pick cells from a colony, which were then restreaked onto a fresh LB + Cm plate as well as used to 'inoculate' the PCR tube with the above mix. This was sometimes carried out with different primer sets.
* **Agarose Gel Electrophoresis**: Except when purifying DNA bands from agarose gels, we typically used the LAB Buffer - Lithium Acetate and Boric Acid. The recipe can be found here: <https://openwetware.org/wiki/LAB_Media>
* **SDS PAGE Analysis**: Recipes from [Bio-Rad](http://www.bio-rad.com/webroot/web/pdf/lsr/literature/Bulletin_6201.pdf).

  *Resolving Gel:*
  6.0 mL 30% Acrylamide/bis;
  3.75 mL 1.5 M Tris-HCl pH 8.8;
  150 uL 10% SDS;
  5.03 mL diH2O;
  7.5 uL TEMED;
  75 uL 10% APS.

  *Stacking Gel:*
  1.98 mL 30% Acrylamide/bis;
  3.78 mL 0.5 M Tris-HCl pH 6.8;
  150 uL 10% SDS;
  9 mL diH2O;
  15 uL TEMED;
  75 uL 10% APS;

[![](https://2019.igem.org/wiki/images/8/8b/HQ_page_logo.jpg)](https://2019.igem.org)

# Team:Alma/Results

![](https://static.igem.org/mediawiki/2019/6/60/T--alma--project_logo.png)

![](https://static.igem.org/mediawiki/2019/e/ee/2019_team_menu_icon.svg)

[![](https://static.igem.org/mediawiki/2019/e/ef/T--Alma--Project_logo.png)](https://2019.igem.org/Team%3AAlma)
[HOME](https://2019.igem.org/Team%3AAlma)

TEAM

[About the Team](https://2019.igem.org/Team%3AAlma/Team)
[Collaborations](https://2019.igem.org/Team%3AAlma/Collaborations)

PROJECT

[Description](https://2019.igem.org/Team%3AAlma/Description)
[Design](https://2019.igem.org/Team%3AAlma/Design)
[Model](https://2019.igem.org/Team%3AAlma/Model)
[Experiments](https://2019.igem.org/Team%3AAlma/Experiments)

[Contribution](https://2019.igem.org/Team%3AAlma/Contribution)

[Attributions](https://2019.igem.org/Team%3AAlma/Attributions)

[PARTS](https://2019.igem.org/Team%3AAlma/Parts)

HUMAN PRACTICES

[Human Practices Overview](https://2019.igem.org/Team%3AAlma/Human_Practices)
[Graphic Design](https://2019.igem.org/Team%3AAlma/Graphic_Design)
[Education & Engagement](https://2019.igem.org/Team%3AAlma/Public_Engagement)
[Integrated Human Practices](https://2019.igem.org/Team%3AAlma/Integrated_Human_Practices)

[REFERENCES

[JUDGING FORM ⇗](https://igem.org/2019_Judging_Form?team=Alma)](https://2019.igem.org/Team%3AAlma/References)

# Results

Here you can describe the results of your project and your future plans.

### What should this page contain?

* Clearly and objectively describe the results of your work.
* Future plans for the project.
* Considerations for replicating the experiments.

### Describe what your results mean

* Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for.
* Show data, but remember **all measurement and characterization data must also be on the part's Main Page on the Registry.** Otherwise these data will not be in consideration for any medals or part awards!
* Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project.

### Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

* A list of linked bullet points of the successful results during your project
* A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

### Inspiration

See how other teams presented their results.

* [2014 TU Darmstadt](https://2014.igem.org/Team%3ATU_Darmstadt/Results/Pathway)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Results)
* [2014 Paris Bettencourt](https://2014.igem.org/Team%3AParis_Bettencourt/Results)