iGEM 2021 — Team Gaston_Day_School

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# Team:Gaston Day School/Notebook

[Judging form](https://igem.org/2021_Judging_Form?id=4063)

[Home](https://2021.igem.org/Team%3AGaston_Day_School)

Awards

[Special Prizes: Inclusivity](https://2021.igem.org/Team%3AGaston_Day_School/Inclusivity)

[Safety](https://2021.igem.org/Team%3AGaston_Day_School/Safety)

Parts

[Contributions](https://2021.igem.org/Team%3AGaston_Day_School/Contribution)

[Parts](https://2021.igem.org/Team%3AGaston_Day_School/Parts)

Human Pratices

[Integrated with Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Human_Practices)

Project

[Description](https://2021.igem.org/Team%3AGaston_Day_School/Description)

[Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Engineering)

[Experiments](https://2021.igem.org/Team%3AGaston_Day_School/Experiments)

[Implementation](https://2021.igem.org/Team%3AGaston_Day_School/Implementation)

[Notebook](https://2021.igem.org/Team%3AGaston_Day_School/Notebook)

[Results](https://2021.igem.org/Team%3AGaston_Day_School/Results)

Team

[Team](https://2021.igem.org/Team%3AGaston_Day_School/Team)

[Attributions](https://2021.igem.org/Team%3AGaston_Day_School/Attributions)

[Collaboration](https://2021.igem.org/Team%3AGaston_Day_School/Collaborations)

![](https://static.igem.org/mediawiki/2015/9/9e/Gds_banner.png)

# Notebook

First Full Lab Meeting Notes - June 11 2021

[June 11, 2021](https://2021.igem.org/File%3AT--Gaston_Day_School--LabMtng1-June12-2021.pdf)

Complete Lab Notebook

[June 2021 - October 2021](https://2021.igem.org/File%3AT--Gaston_Day_School--Revised_Lab_Notebook.pdf)

Complete Lab Images

[June 2021 - October 2021](https://static.igem.org/mediawiki/2021/e/ea/T--Gaston_Day_School--Lab_Images_Revised.pdf)

### Routine Tasks

Every Tuesday and Thursday Mornings our team meets in the lab at Gaston Day and hosts a Zoom meeting for those in China to be able to participate.

These meetings include wet lab tasks and projects, research, designing and testing adaptive lab equipment, and various project management procedures.

Additionally, we hold weekly Zoom meetings at 9 P.M. EST in the United States, 9 A.M. in China compiling research notes and annotations as well as delegating tasks for the upcoming week.

### Who did What?

Summer Lab Work (June-August): Brooke Dillingham, Eric Lan, Kate Klinger, Neha Patel, and Ahmad Alyasjeen.

General Lab Work: Brooke Dillingham, Eric Lan, Kate Klinger, Neha Patel, Ahmad Alyasjeen, Yahoo Wu, Nadia Luo, Jordan Baker, Winston Baker, and Blake Ma.

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# Team:Gaston Day School/Engineering

[Judging form](https://igem.org/2021_Judging_Form?id=4063)

[Home](https://2021.igem.org/Team%3AGaston_Day_School)

Awards

[Special Prizes: Inclusivity](https://2021.igem.org/Team%3AGaston_Day_School/Inclusivity)

[Safety](https://2021.igem.org/Team%3AGaston_Day_School/Safety)

Parts

[Contributions](https://2021.igem.org/Team%3AGaston_Day_School/Contribution)

[Parts](https://2021.igem.org/Team%3AGaston_Day_School/Parts)

Human Pratices

[Integrated with Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Human_Practices)

Project

[Description](https://2021.igem.org/Team%3AGaston_Day_School/Description)

[Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Engineering)

[Experiments](https://2021.igem.org/Team%3AGaston_Day_School/Experiments)

[Implementation](https://2021.igem.org/Team%3AGaston_Day_School/Implementation)

[Notebook](https://2021.igem.org/Team%3AGaston_Day_School/Notebook)

[Results](https://2021.igem.org/Team%3AGaston_Day_School/Results)

Team

[Team](https://2021.igem.org/Team%3AGaston_Day_School/Team)

[Attributions](https://2021.igem.org/Team%3AGaston_Day_School/Attributions)

[Collaboration](https://2021.igem.org/Team%3AGaston_Day_School/Collaborations)

![](https://static.igem.org/mediawiki/2015/9/9e/Gds_banner.png)

# Engineering Success: 3D Design for Students with Disabilities and Visual Impairments

We know from teachers and students with visual and motor difficulties that using a graduated cylinder is a significant difficulty in lab sciences. Our engineering design was made to help people
with visual or physical disabilities have better access to lab sciences. We designed our measuring tool so people with visual disabilities who would have a hard time seeing numbers on a regular graduated cylinder could use it. We did this by making it a predetermined size where you just fill up the whole thing. There is also a high contrast color between the number and the measuring tool itself so people can better see the number. We also put a braille label on the tool. We made a wide pyramidal base so people with motor control disabilities would have a smaller chance of spilling the liquid in the cylinder.

With our design we used the fact that one square centimeter equals one milliliter and we created a prototype of a graduated cylinder shaped like a prism. The interior is a square centimeter in area to complete the requirements and five centimeters deep. The walls are 2 millimeters thick and the base is 3 millimeters thick. We wanted to design a separate base to hold it up and in place, so we designed a separate base to hold it up and in place and put a hole in the middle with dimensions one millimeter wider and longer than the walls and deep enough to hold half of the prism. It is quite stable and will not fall if hit. We designed a “5” placed on one side near the top and the braille word for “five” on an adjacent side of the prism at the same height. We came up with two possibilities one was single sized cylinders the other would have graduations that are raised and of contrasting color.

![](https://static.igem.org/mediawiki/2021/2/29/T--Gaston_Day_School--Infographic_revised_revised.jpeg)
![](https://static.igem.org/mediawiki/2021/4/4b/T--Gaston_Day_School--GDS_Engineering_Design-Test_Infographic.png)

After each round of testing, we took the results and modified the design of the device based on the feedback and printed a new version. After testing a final model and directly comparing measuring out 5 mL of water using the 5 mL cuboid to using a standard plastic 10 mL graduated cylinder, the students' response was: “This is SO MUCH easier!”

### Future Modifications Planned

1. Change the non-skid surface on the bottom of the base to a one that is not latex (request from the OT since several of her clients have latex allergies).

2. Print and test a 10 mL cuboid and alter the base so that it will support a taller device without tipping, possibly by adding legs to the current square design.

3. Design larger volume cuboids by increasing the side length of the cuboid rather than increasing height.

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# Team:Gaston Day School/Experiments

[Judging form](https://igem.org/2021_Judging_Form?id=4063)

[Home](https://2021.igem.org/Team%3AGaston_Day_School)

Awards

[Special Prizes: Inclusivity](https://2021.igem.org/Team%3AGaston_Day_School/Inclusivity)

[Safety](https://2021.igem.org/Team%3AGaston_Day_School/Safety)

Parts

[Contributions](https://2021.igem.org/Team%3AGaston_Day_School/Contribution)

[Parts](https://2021.igem.org/Team%3AGaston_Day_School/Parts)

Human Pratices

[Integrated with Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Human_Practices)

Project

[Description](https://2021.igem.org/Team%3AGaston_Day_School/Description)

[Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Engineering)

[Experiments](https://2021.igem.org/Team%3AGaston_Day_School/Experiments)

[Implementation](https://2021.igem.org/Team%3AGaston_Day_School/Implementation)

[Notebook](https://2021.igem.org/Team%3AGaston_Day_School/Notebook)

[Results](https://2021.igem.org/Team%3AGaston_Day_School/Results)

Team

[Team](https://2021.igem.org/Team%3AGaston_Day_School/Team)

[Attributions](https://2021.igem.org/Team%3AGaston_Day_School/Attributions)

[Collaboration](https://2021.igem.org/Team%3AGaston_Day_School/Collaborations)

![](https://static.igem.org/mediawiki/2015/9/9e/Gds_banner.png)

# Experiments and Procedures

Below are the most frequent procedures for the experiments we performed this year.

[Single-temperature Double Digest](https://static.igem.org/mediawiki/2021/1/1f/T--Gaston_Day_School--Growing_Phages_Single-temperature_Double_Digest.pdf)

[Litigation Protocol with T4 Ligase (M0202)](https://static.igem.org/mediawiki/2021/7/73/T--Gaston_Day_School--Litigation_Protocol_with_T4.pdf)

[Plasmid Preparation Procedure](https://static.igem.org/mediawiki/2021/0/0b/T--Gaston_Day_School--Plasmid_Preparation_Procedure_Control_for_Phages.pdf)

[Plasmid Preparation Procedure (By Hand)](https://static.igem.org/mediawiki/2021/b/bd/T--Gaston_Day_School--Plasmid_Preparation_Procedure_By_Hand.pdf)

[Gibson Assembly Protocol (E5510)](https://static.igem.org/mediawiki/2021/f/fa/T--Gaston_Day_School--Different_Resistance_sort.pdf)

[Modified Competent Cells Procedure](https://static.igem.org/mediawiki/2021/6/66/T--Gaston_Day_School--Modified_Compotent_cells_procedure.pdf)

[Sequential Double Digest](https://static.igem.org/mediawiki/2021/5/5d/T--Gaston_Day_School--Sequential_Double_Digest.pdf)

[Transformation Procedure](https://static.igem.org/mediawiki/2021/c/ca/T--Gaston_Day_School--Transformation_Procedure.pdf)

[SeaPhages Procedures for Isolating Environmental Phages](https://seaphagesphagediscoveryguide.helpdocsonline.com/home)

![](https://static.igem.org/mediawiki/2021/5/58/T--Gaston_Day_School--2Phages3strains.jpg)
![](https://static.igem.org/mediawiki/2021/f/fb/T--Gaston_Day_School--GDS_Lab_Phages.png)

Testing the specificity of phages - T4 phage (plates in the right column of each image) grows on standard K-12 and substrain W but not on substrain C. PhiX phage (plates in the left column of each image) does not grow on K-12 or W but does grow somewhat on substrain C.

![](https://static.igem.org/mediawiki/2021/4/4b/T--Gaston_Day_School--ecoliresults.png)

Testing Environmental Samples for the presence of phage - Two samples (in the upper 2 sections of the plate) show cleared rings around the inoculation site which indicates that bacteriophages are likely present in the sample. The bottom section shows no cleared area, indicating a lack of bacteriophages in that sample.

![](https://static.igem.org/mediawiki/2021/3/3a/T--Gaston_Day_School--RFPmonarch.png)
![](https://static.igem.org/mediawiki/2021/d/d9/T--Gaston_Day_School--RFPplasmidprep.jpg)

Can bacteriophages transfer plasmid DNA? The bacteria in these tubes show the presence of Red Fluorescent Protein after being infected with T4 bacteriophages grown on bacteria carrying an RFP plasmid. This shows that bacteriophages can transfer plasmid DNA just as they can transfer genomic DNA.

![](https://static.igem.org/mediawiki/2021/9/91/T--Gaston_Day_School--Itisaplasmid.png)

Is the plasmid transferred as a plasmid or is it incorporated into the genome? Lanes 2 and 3 on the gel show the DNA isolated from transduced bacteria using a plasmid prep kit from New England Biolabs. The band in lane 4 is the plasmid isolated from the originating bacteria. This strongly supports the direct transfer of the plasmid and that the RFP and antibiotic resistance genes have not been incorporated into the genome of the bacteria.

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# Team:Gaston Day School/Results

[Judging form](https://igem.org/2021_Judging_Form?id=4063)

[Home](https://2021.igem.org/Team%3AGaston_Day_School)

Awards

[Special Prizes: Inclusivity](https://2021.igem.org/Team%3AGaston_Day_School/Inclusivity)

[Safety](https://2021.igem.org/Team%3AGaston_Day_School/Safety)

Parts

[Contributions](https://2021.igem.org/Team%3AGaston_Day_School/Contribution)

[Parts](https://2021.igem.org/Team%3AGaston_Day_School/Parts)

Human Pratices

[Integrated with Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Human_Practices)

Project

[Description](https://2021.igem.org/Team%3AGaston_Day_School/Description)

[Engineering](https://2021.igem.org/Team%3AGaston_Day_School/Engineering)

[Experiments](https://2021.igem.org/Team%3AGaston_Day_School/Experiments)

[Implementation](https://2021.igem.org/Team%3AGaston_Day_School/Implementation)

[Notebook](https://2021.igem.org/Team%3AGaston_Day_School/Notebook)

[Results](https://2021.igem.org/Team%3AGaston_Day_School/Results)

Team

[Team](https://2021.igem.org/Team%3AGaston_Day_School/Team)

[Attributions](https://2021.igem.org/Team%3AGaston_Day_School/Attributions)

[Collaboration](https://2021.igem.org/Team%3AGaston_Day_School/Collaborations)

![](https://static.igem.org/mediawiki/2015/9/9e/Gds_banner.png)

# Results

Results: Lab Images

[June 2021 - October 2021](https://static.igem.org/mediawiki/2021/e/ea/T--Gaston_Day_School--Lab_Images_Revised.pdf)

Facing the possible risks of the transfer of plasmid DNA by different bacteriophages, in order to test our idea that there were bacteriophages in the environment, we were able to collect over 20 environmental samples from the areas near our school and test them on 5 different bacteria and 5 subtypes of E.coli K-12. Even though we did not discover any existence of the bacteriophages which belong to non-E.coli species, we found indications of phages that target E.coli B (from Carolina Biological), which was the most permissive one of the strains for growing and maintaining T4 bacteriophages.

The next step, we worked mainly on the T4 pages. RFP was used as a marker in the experiment and after the plasmid preparation in which we extracted and purified the E.coli, the plasmid could still be discovered, which proved that bacteriophage could make plasmid DNA transformation possible.

Through the project, it is significant for us to better understand the bacteriophage-assisted lateral transfer. First, the risk of spreading both antibiotic resistance and the specific gene released out of a certain space such as a biology lab would increase since we have known that phages are capable of transferring plasmid DNA. Also, we noticed that the remaining DNA of the bacteria as a plasmid further increases the danger through multiple mechanisms for the transfer. What is worth mentioning is that the at least environment uncontaminated like areas near our school provided lower risks of the lateral transfer due to the relatively very few existence of E.coli phages, while possible animal waste raises the likelihood for the E.coli to be detected.

Besides our wet lab experiments, our engineering sub-project to design more convenient and suitable equipment offered new options for students with low or even no vision as well as motor control problems to work in the lab to learn science using 3D printing. Along with results of the test with young students in school and other iGEM teams this year, we received very useful feedback and we were able to make improvements and made three prototypes step by step on time to fit their needs.