iGEM 2022 — Team portland

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{% block lead %}Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.{% endblock %}
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## What should this page contain?

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

## Inspirations

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* [2018 Munich](http://2018.igem.org/Team%3AMunich/Notebook)
* [2019 Georgia State](https://2019.igem.org/Team%3AGeorgia_State/Notebook)
* [2019 Newcastle](https://2019.igem.org/Team%3ANewcastle/Notebook)
* [2020 IISER Pune India](https://2020.igem.org/Team%3AIISER-Pune-India/Notebook)
* [2020 Lund](https://2020.igem.org/Team%3ALund/Notebook)
* [2020 NOVA LxPortugal](https://2020.igem.org/Team%3ANOVA_LxPortugal/Notebook)
* [2020 RDFZ China](https://2020.igem.org/Team%3ARDFZ-China/NoteBook)

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Engineering
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![engineering](https://static.igem.wiki/teams/4457/wiki/logo/engineering.png)
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#### Silver Medal Criterion #2

Collaborate with one (or more) 2022 iGEM team(s) in a meaningful way.

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Please see the [2022 Medals Page](https://competition.igem.org/judging/medals) for more information.

## Which teams can we work with?

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You can work with any other iGEM 2022 team in the competition. You can also work with non-iGEM research groups, but they do not count towards the iGEM team collaboration silver medal criterion.

## Some suggestions

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* Improve the function of another team's BioBrick Part or Device
* Characterize another team's part
* Debug a construct
* Model or simulate another team's system
* Test another team's software
* Help build and test another team's hardware project

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Experiments
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![experiment1](https://static.igem.wiki/teams/4457/wiki/logo/experiment1.png)
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# **General Experimental Protocols**

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![notebooks](https://static.igem.wiki/teams/4457/wiki/logo/notebooks.png)
**#### Preparing Overnight Cultures

[Download PDF](https://tinyurl.com/3jksebfn)

#### Miniprep Protocol (Qiagen)

[Download PDF](https://tinyurl.com/yua6r4kb)

#### Making New LB Media

[Download PDF](https://tinyurl.com/2p8f7mwz)

#### LB+Agar Media and Agar Plates

[Download PDF](https://tinyurl.com/4hu6pzwd)

#### Cell Fixation

[Download PDF](https://tinyurl.com/y9kfcfhz)

#### qPCR

[Download PDF](https://tinyurl.com/4ayekwrp)

#### Making a Replication of Plates

[Download PDF](https://tinyurl.com/2s464uc7)

#### Making an Agarose Gel

[Download PDF](https://tinyurl.com/yjmr6h27)

#### Making TAE Buffer

[Download PDF](https://tinyurl.com/3x7vb4m9)

#### Restriction Enzyme Digest

[Download PDF](https://tinyurl.com/ybxbzxdf)

#### E. Coli Electroporation

[Download PDF](https://tinyurl.com/39u4hzpa)

#### Gel Extraction

[Download PDF](https://tinyurl.com/5n6zsp9d)

#### Heat Shock Transformation

[Download PDF](https://tinyurl.com/5n8u6dk2)

#### Creating Electrocompetent Cells

[Download PDF](https://tinyurl.com/hcf942ye)

#### Making Oligo Stock

[Download PDF](https://tinyurl.com/3smdu5ee)

#### Diluting Oligo Stock 1:10

[Download PDF](https://tinyurl.com/4b3a264y)

#### Overnight Cells in Glycerol

[Download PDF](https://tinyurl.com/43x2kdtf)

#### Gibson Assembly

[Download PDF](https://tinyurl.com/rnmd4kxe)**
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Results
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![results](https://static.igem.wiki/teams/4457/wiki/logo/results1.png)
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![graph4](https://static.igem.wiki/teams/4457/wiki/logo/graph4.png)
![graph5](https://static.igem.wiki/teams/4457/wiki/logo/graph5.png)

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# **Summary of Results from Plate Readings (OD)**

Above are results from using a plate reader to measure the OD levels of a 96 well plate. Both experiments (1) and (2) followed the same protocol and antibiotic combinations. Experiment (1) shows the expected results from the new plasmids built in Aim 2. Experiment (2) shows the expected results from Aim 1.

Experiment 2: The samples which were of most relevancy and discussion in the whole picture of our project were the 1229C, 1230C, and 1229F samples. These contained the 1229 or 1230 plasmids. The 1229 plasmid is "special" because when the switch comes in contact with a specific gRNA trigger, the plasmid will "turn off" gRNA activity. The characteristic that we are targeting with 1230 was the “always on".

The 872 plasmid was also transformed into the same electrocompetent cell, with 1229 or 1230. The 872 plasmid includes the ability to cut using Cas12a.

Each of the samples further included a random and correct trigger RNA oligo which in theory should have shut off or activated cell growth – spike in OD measurements. The expected results were as follows.

There was expected growth in the electrocompetent cells that previously had 1229 and were co-transformed with 872 and the control (random) RNA. Similarly, there was not that much growth in the 1230 cells co-transformed with 872 and the control RNA. Importantly, there wasn't growth in the electrocompetent cells that previously had 1229 and were co-transformed with 872 and the experimental RNA. This slight growth is expected behavior from LB after a long duration of time. These results are exciting as they demonstrate the possibility of detecting exogenous RNA with our engineered E. coli.

The rest of our results are shown in the pages for **Aim 1, Aim 2** and **Aim 3.**

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