iGEM 2020 — Team RUM-UPRM

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:RUM-UPRM/Notebook

RUM-UPRM Wiki Source Code

[RUM-UPRM](https://2020.igem.org/Team%3ARUM-UPRM)

Menu

* [Team](https://2020.igem.org/Team%3ARUM-UPRM/Members)
  + [Team Members](https://2020.igem.org/Team%3ARUM-UPRM/Members)
  + [Attributions](https://2020.igem.org/Team%3ARUM-UPRM/Attributions)
* [Collaborations](https://2020.igem.org/Team%3ARUM-UPRM/Collaborations)
* [Project](https://2020.igem.org/Team%3ARUM-UPRM/Description)
  + [Description](https://2020.igem.org/Team%3ARUM-UPRM/Description)
  + [Design](https://2020.igem.org/Team%3ARUM-UPRM/Design)
  + [Modelling](https://2020.igem.org/Team%3ARUM-UPRM/Model)
  + [Engineering Success](https://2020.igem.org/Team%3ARUM-UPRM/Engineering)
  + [Proposed Implementation](https://2020.igem.org/Team%3ARUM-UPRM/Implementation)
  + [Notebook](https://2020.igem.org/Team%3ARUM-UPRM/Notebook)
  + [Contributions](https://2020.igem.org/Team%3ARUM-UPRM/Contribution)
  + [Future Projections](https://2020.igem.org/Team%3ARUM-UPRM/Future_Projections)
  + [Parts](https://2020.igem.org/Team%3ARUM-UPRM/Parts)
* [Safety](https://2020.igem.org/Team%3ARUM-UPRM/Safety)
* [Human practices](https://2020.igem.org/Team%3ARUM-UPRM/Human_Practices)
  + [Overview](https://2020.igem.org/Team%3ARUM-UPRM/Human_Practices_Overview)
  + [Integrated Human Practices](https://2020.igem.org/Team%3ARUM-UPRM/Human_Practices)
  + [Education and Engagement](https://2020.igem.org/Team%3ARUM-UPRM/Education)
  + [SynBio101: Summer Camp](https://2020.igem.org/Team%3ARUM-UPRM/SynBio101)
  + [Inclusion](https://2020.igem.org/Team%3ARUM-UPRM/Inclusion)
* [Awards](https://2020.igem.org/Team%3ARUM-UPRM/Judging/Pages_for_Awards)

# Notebook

* [Overview](#section1)
* [Ligation and Digestion](#section2)
* [DNA Extraction](#section3)
* [DNA Precipitation](#section4)
* [DNA Gel Extraction](#section5)
* [Bacterial Transformation](#section6)
* [Preparation of Competent Cells](#section7)
* [Gibson Assembly](#section8)

# Overview

Laboratory Technique Workshops were given to all team members in order to be prepared to perform in the wet lab. The following protocols were discussed and practiced. Unfortunately, plans changed with COVID 19. We are looking forward to the moment we can go back to our lab and apply all this knowledge.

![](https://static.igem.org/mediawiki/parts/1/15/T--RUM-UPRM--labwork.png)

##### Ligation and Digestion

##### DNA Extraction

##### DNA Precipitation

##### DNA Gel Extraction

##### Bacterial Transformation

##### Preparation of Competent Cells

##### Gibson Assembly

## **Our Sponsors**

![Amgen](https://static.igem.org/mediawiki/2020/5/56/T--RUM-UPRM--amgen_logo.png "Amgen")

![Snapgene](https://static.igem.org/mediawiki/2020/4/4d/T--RUM-UPRM--Snapgene_logo.png "Snapgene")

![UPRM](https://static.igem.org/mediawiki/2020/d/db/T--RUM-UPRM--LogoUPRM.png "UPRM")

![Goya](https://static.igem.org/mediawiki/2020/c/c7/T--RUM-UPRM--Goya_logo%2Cpng.png "Goya")

![Genscript](https://static.igem.org/mediawiki/2020/3/38/T--RUM-UPRM--Genscript_logo%2Cpng.png "Gensscript")
![PRABIA](https://static.igem.org/mediawiki/2020/0/02/T--RUM-UPRM--PRABIA_logo.png "PRABIA")
![MolecularCloud](https://static.igem.org/mediawiki/2020/d/df/T--RUM-UPRM--MolecularCloud_logo.png "MolecularCloud")

![MatLab](https://static.igem.org/mediawiki/2020/archive/7/7a/20201021024142%21T--RUM-UPRM--Matlab_logo%2Cpng.png "MatLab")
![IDT](https://static.igem.org/mediawiki/2020/2/29/T--RUM-UPRM--idt_logo.png
 "IDT")
![ReviveRestore](https://static.igem.org/mediawiki/2020/0/0f/T--RUM-UPRM--revive_restore_logo.png
 "ReviveRestore")
![Twist](https://static.igem.org/mediawiki/2020/9/97/T--RUM-UPRM--twist1_logo.png
 "Twist")

## **Follows Us!**

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:RUM-UPRM/Engineering

RUM-UPRM Wiki Source Code

[RUM-UPRM](https://2020.igem.org/Team%3ARUM-UPRM)

Menu

* [Team](https://2020.igem.org/Team%3ARUM-UPRM/Members)
  + [Team Members](https://2020.igem.org/Team%3ARUM-UPRM/Members)
  + [Attributions](https://2020.igem.org/Team%3ARUM-UPRM/Attributions)
* [Collaborations](https://2020.igem.org/Team%3ARUM-UPRM/Collaborations)
* [Project](https://2020.igem.org/Team%3ARUM-UPRM/Description)
  + [Description](https://2020.igem.org/Team%3ARUM-UPRM/Description)
  + [Design](https://2020.igem.org/Team%3ARUM-UPRM/Design)
  + [Modelling](https://2020.igem.org/Team%3ARUM-UPRM/Model)
  + [Engineering Success](https://2020.igem.org/Team%3ARUM-UPRM/Engineering)
  + [Proposed Implementation](https://2020.igem.org/Team%3ARUM-UPRM/Implementation)
  + [Notebook](https://2020.igem.org/Team%3ARUM-UPRM/Notebook)
  + [Contributions](https://2020.igem.org/Team%3ARUM-UPRM/Contribution)
  + [Future Projections](https://2020.igem.org/Team%3ARUM-UPRM/Future_Projections)
  + [Parts](https://2020.igem.org/Team%3ARUM-UPRM/Parts)
* [Safety](https://2020.igem.org/Team%3ARUM-UPRM/Safety)
* [Human practices](https://2020.igem.org/Team%3ARUM-UPRM/Human_Practices)
  + [Overview](https://2020.igem.org/Team%3ARUM-UPRM/Human_Practices_Overview)
  + [Integrated Human Practices](https://2020.igem.org/Team%3ARUM-UPRM/Human_Practices)
  + [Education and Engagement](https://2020.igem.org/Team%3ARUM-UPRM/Education)
  + [SynBio101: Summer Camp](https://2020.igem.org/Team%3ARUM-UPRM/SynBio101)
  + [Inclusion](https://2020.igem.org/Team%3ARUM-UPRM/Inclusion)
* [Awards](https://2020.igem.org/Team%3ARUM-UPRM/Judging/Pages_for_Awards)

# Engineering Success

* [Phase I](#section1)
* [Phase II](#section2)

# Phase I

![](https://static.igem.org/mediawiki/2020/5/59/T--RUM-UPRM--PHASE1.png)

##### I. Research

Before starting the design of our project, we turned to our communities to see what challenges they were facing and how we could use Synthetic Biology to help. We came across the contamination in the Island of Vieques and the health and biodiversity consequences faced.

##### II.Identify a Problem

We researched further into this situation and after consulting with experts in the field, we identified Mercury and RDX as two of the most present contaminants that we could bioremediate using Synthetic Biology.

##### III. Finding the Solution

We found past IGEM projects that focused on the bioremediation of Mercury and used these ideas to create our own. We also found genes that can biodegrade RDX that we could implement as well.

##### IV. Design

Working on our solution, we decided to construct genetic circuits that would help us achieve the bioremediation of Mercury and the biodegradation of RDX. During this process, we consulted different individuals about their perspectives of the situation including our Advisors & Primary Investigators, citizens, engineers, professors and students.

##### V. Phase II Preparation

Due to Covid-19, there are many things we were not able to do. We did not have access to the lab, nevertheless we prepared a [plan to return to the lab](https://2020.igem.org/Team%3ARUM-UPRM/Covid_Precaution), [a proposal to gain access to Vieques](https://2020.igem.org/Team%3ARUM-UPRM/Human_Practices) to gain access to Vieques, [a hardware competition](https://2020.igem.org/https%3A//2020.igem.org/Team%3ARUM-UPRM/Design_Competition) and an experimental design for the next cycle. We will also take into consideration the judges’ feedback after this year’s competition for the improvement of our project

# Phase II

![](https://static.igem.org/mediawiki/2020/a/af/T--RUM-UPRM--PHASEII.png)

##### I. Building Prototype in Lab

When we finally gain access to the lab, we will build our prototype. This will require a lot of hard work and dedication. This will consist of constant lab work.

##### II.Building Hardware

We will also finish the design of the hardware of our project taking into account the results from the Hardware Competition.

##### III. Test prototype and hardware with samples from Vieques

After the hardware and prototype are built, we will use the samples obtained from Vieques to test the efficiency and viability of our project.

##### IV. Optimization of prototype

Using the data obtained from our tests, we will make the changes needed to optimize the efficiency of our bioremediation system.

##### V. Implementation

After final tests and changes, we will implement our system in Vieques.

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:RUM-UPRM/Experiments

# Experiments

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).

### What should this page contain?

* Protocols
* Experiments

### Inspiration

* [2014 Colombia](https://2014.igem.org/Team%3AColombia/Protocols)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Protocols)
* [2014 Caltech](https://2014.igem.org/Team%3ACaltech/Project/Experiments)

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:RUM-UPRM/Results

# Results

You can describe the results of your project and your future plans here.

### 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](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

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)