Genomic Integrity 2018

Summer 2018 Genomic Integrity Project.

Issue

Assessing genomic integrity (showing the amount of damage one's genome has endured) would be of a great help for public health. Unfortunately, the tests allowing to check the genomic integrity can be complex or expensive.

Objectives

Therefore, the objectives of this internship would be:

To make a ready to use device, the best being automatic, for people (even non-scientist) to use easily;
To use "kitchen-sink-ingredients" to promote easy to do and safe citizen science;
Finally, to develop an Automatic Cell Counter Algorithm able to count cells and control different parameters (their sizes, the length of their comet tails and recognition of micronuclei).

Asides Objectives

To use a Foldscope<ref>Official website of the Foldcope.Retrieved 2 August 2018.</ref> <ref>Wiki of the hackuarium.Retrieved 28 August 2018.</ref> or a microscope to make photos with a RaspBerry Pi, using an automatic stage;
DIY Fluorescence Microscope

Procedure

Precisely, we will use two methods Micronuclei Assay 2018 and Comet Cell Assay 2018, find a way to make the procedures as simple as possible using a chip and make an algorithm to handle the results.

For both, we tried to replace all the toxic or hard to find components by "kitchen-sink-ingredients", in order to make this technique widely usable by anyone, even without the appropriate equipment.

The first target was SYBR Safe.<ref>ThermoFischer's documentations for SYBR Safe. Retrieved 27 August 2018.</ref> Even though SYBR Safe is far less toxic than Ethidium Bromide, SYBR Gold or other fluorescent dyes, it has not zero toxicity. By its mode of action (intercalation), it can be carcinogenic and the obligation to use a specific light (here a powerful blue light) is an obstacle for easy procedures and it can cause harm to the eyes of the user.

Therefore, we wanted to use Methylene Blue.<ref>Wikipedia page for Methylene Blue. Retrieved 27 August 2018.</ref> As it is positively charged, it will bind to the outside structure of the DNA, without intercalating within it and without triggering much mutation. Plus, Methylene Blue is easy to find (it is on the WHO's list of essential medicines). Whereas for the Micronuclei Assay the methylene blue worked well, for the Comet Assay methylene blue did not give satisfactory results.

Photos of comet

Protocol

For the detailed protocol, see Step by step protocol for comet assay

Ready to use chip

Detailed article: Chip for genomic integrity 2018

References