iGEM 2022 — Team suny-oneonta

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{% block title %}Notebook{% endblock %}
{% block lead %}This section contains the details of our wet lab work, including our lab notebooks, standard protocols, and safety practices.{% endblock %}
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#### Wet Lab Documentation

As we worked on project CyanoSpectre, Team SUNY\_Oneonta documented our progress and procedures. Our team also participated in this year’s InterLab Study. The results of this work can be found on our [Contribution](https://2022.igem.wiki/suny-oneonta/contribution) page. Our protocols and transcripts of our documentation are linked below.

![Reviewing the protocol.](https://static.igem.wiki/teams/4268/wiki/t-suny-oneonta-notebook01-jacob-julia-jaz-protocol.jpg)

    CyanoSpectre
Protocols

  Lab Notebook
Daily Log

  InterLab Study
Notebook

#### Safety

It was a priority for our team to conduct our work in a safe and responsible manner. To properly equip our team members for the project, each member completed [CITI Responsible Conduct of Research](https://about.citiprogram.org/series/responsible-conduct-of-research-rcr/) training. Additionally, throughout each interaction with stakeholders the team asked for guidance on how to safely work with cyanobacteria and cyanophage. We sought advice on how to handle these organisms and how to mitigate any potential risk that may come from them, such as ensuring that reproductive/infection capabilities have been removed from our phage shell. Before beginning any work on our project, we submitted a check-in form to the iGEM safety committee about our project and have received their approval.

![Jaz in the hood.](https://static.igem.wiki/teams/4268/wiki/t-suny-oneonta-notebook05-jaz-in-hood.jpg)

Our team followed the [SUNY Oneonta Chemical Hygiene Plan](https://suny.oneonta.edu/office-facilities-safety-and-physical-plant/health-safety/environmental-health-safety), which includes waste management protocols. All chemicals and potentially toxic materials were disposed of as toxic waste. Any cultures of E. coli or other biohazard organisms were neutralized prior to disposal as biohazard waste. The team has access to labs that have open benches and a biosafety cabinet that are regularly cleaned before and after use with 70% ethanol, to prevent contamination or spread of any materials used. Additional advice received from stakeholders identified the sensitivity of cyanobacterial growth to outside elements. When the team approaches this portion of the project, sanitation of instruments and spaces will continue to be carried out in accordance with their advice.

The cyanophage we intended to use had not been used by previous iGEM teams. We therefore consulted with the Safety Committee prior to beginning any of the design work on our phagemid to check for any potential hazards that we might be unaware of. We were informed that the Safety Committee did not see any excessive hazards and received their approval for our planned project. The complete record of our work in this area is explained on our [Human Practices](https://2022.igem.wiki/suny-oneonta/human-practices) page.

![Liam and Julia in the lab.](https://static.igem.wiki/teams/4268/wiki/t-suny-oneonta-notebook06-liam-julia-in-lab.jpg)
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| Collection | Name | Strength compared to consensus |
| --- | --- | --- |
| T7 promoters | BBa\_R0085 | 1 |
|  | BBa\_R0180 | 0.72 |
|  | BBa\_R0181 | 0.5 |
|  | BBa\_R0182 | 0.3 |
|  | BBa\_R0183 | 0.09 |
| RBS | BBa\_B0034 | Reference |
|  | BBa\_B0032 | Medium |
|  | BBa\_B0030 | Strong |
|  | BBa\_B0033 | Weak |

*Source: All parts were designed by the group Antiquity on iGEM’s Part Repository.*

More information about our Phagemid Design can be found on our [Design](https://2022.igem.wiki/suny-oneonta/design) page.

#### Museum Exhibit

Our team designed an interactive museum exhibit on bacteriophage for a local science museum. We went through several design cycles for each exhibit component, consulting with experts in exhibit development, science museum operation, and 3D printing. A few of these are described below. We are also collecting feedback from users of a prototype of our exhibit and intend to incorporate their comments into our final round of refinement before deploying our exhibit at the AJ Read Science Discovery Center.

* Doug Reilly, the current Outreach Coordinator at SUNY Oneonta’s Science Discovery Center, provided insight into museum elements and how they can be used to target specific audiences. For instance, due to current day technology, young children are not building their fine motor skills and thus exhibits that have tactile parts are great for children. Thus, when constructing our Build-A-Phage portion of the exhibit, we wanted the assembly process to get the children to utilize those fine motor skills a variety of connection types.
* David Kenny provided additional insight our multiple iterations of the phage model. For example, to increase durability and ease of use, the t-socket that was initially designed for the attachment of the tail to the phage head piece was replaced with a ball-and-joint socket (see Figure below).
* Our first iteration of the phage head included a series of magnets to allow the top half of the capsid head to attach to the bottom. Our first test print revealed that the sizing of the holes made for the magnets needed to be altered.

More information about our museum exhibit development process can be found on our [Education](https://2022.igem.wiki/suny-oneonta/education) page.

![Refinement Process](https://static.igem.wiki/teams/4268/wiki/t-suny-oeonta-engineering01-tail-design-cycle.png)
*The Design -> Prototype -> Test -> Refine cycle for the tail piece of the phage model.*
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{% block title %}Experiments{% endblock %}
{% block lead %}Describe the research, experiments, and protocols you used in your iGEM project.{% endblock %}
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## What should this page contain?

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Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.

If you made Parts this year, please remember to put all information, characterization, and measurement data on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).

## Inspirations

---

* [2019 Nantes](https://2019.igem.org/Team%3ANantes/Experiments)
* [2019 TU Eindhoven](https://2019.igem.org/Team%3ATU_Eindhoven/Experiments)
* [2019 Mingdao](https://2019.igem.org/Team%3AMingdao/Demonstrate)
* [2020 Amsterdam](https://2020.igem.org/Team%3AAmsterdam/Experiments)
* [2020 NCTU Formosa](https://2020.igem.org/Team%3ANCTU_Formosa/Experiments)
* [2020 USAFA](https://2020.igem.org/Team%3AUSAFA/Experiments)

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{% extends "layout.html" %}
{% block title %}Results{% endblock %}
{% block lead %}You can describe the results of your project and your future plans here.{% endblock %}
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## 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

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* 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](http://parts.igem.org/Main_Page).** 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

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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.

## Inspirations

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* [2019 Newcastle](https://2019.igem.org/Team%3ANewcastle/Results)
* [2019 Munich](https://2019.igem.org/Team%3AMunich/Results)
* [2019 Tec Chihuahua](https://2019.igem.org/Team%3ATec-Chihuahua/Results)
* [2020 Aalto Helsinki](https://2020.igem.org/Team%3AAalto-Helsinki/Results)
* [2020 GreatBay SCIE](https://2020.igem.org/Team%3AGreatBay_SCIE/Results)
* [2020 Queens Canada](https://2020.igem.org/Team%3AQueens_Canada/Results)

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