🎉 JOGL is soon launching a new version. All the users of the v1 will be migrated to the new version. In the time being, we do not allow the creation of new users on this platform.
Open Source DNA damage detection banner
Project
4
Members

Status:
Active/Ongoing
Project maturity:
Implementation

Open Source DNA damage detection

About reviewed project
Research to investigate levels of DNA damage visible in our own cheek cells is based on work as long ago as when the first biologist noticed a micronucleus under a microscope back in the 19th century. DIT biohackers got serious in 2016.

We are made of cells, and each cell has a nucleus which contains long molecules of genetic information, the chromosomes, carrying genes expressed first as RNA, which themselves encode proteins (as messengers, mRNA) or help regulate gene expression and make proteins (with at least four different flavors, the micro, long non-coding, ribosomal, or transfer RNAs). For all these molecules of life, structure gives function. 


Damage can disrupt essential structures, to poison life processes.


Our cells are subject to all sorts of damaging agents, from inside and out, sometimes even due to our own choices. Some damage hits the various molecules of life, DNA, RNA, lipids and proteins, with cross-linking between components also detrimental. Some damage can be repaired, but sometimes repair actually makes things worse, as not all repair is perfect. New mutations can even be generated during repair of damage!

Ideally, in the case of genetic elements, restoring the 'sequence' - the order of the GATC base pairs- or its structure (to restore previous base-pairs for active RNAs) as before the damage occurred, is necessary to restore proper function. 


Prevention of damage is the focus of AGiR! Action for Genomic integrity through Research!, a Swiss association, founded over 9 years ago with the aims of promoting research and providing information on the many aspects of genomic integrity.


DNA is just one of these.

Genomic integrity is meant to include not only dynamic aspects of all the molecules of life, but epigenetic tags that can also control gene expression.


If one of your chromosomes breaks, this is a big deal, nonetheless, and can be 'fatal' for that cell, which immune system components will hopefully tidy up without too much inflammation. However, sometimes the damaged cell can survive with a micronucleus formed. Levels of micronuclei can be correlated with exposure to various risks to health and even certain illnesses...


Doing the micronucleus assay not only shows the frequency of such serious damage, but provides a fun workshop event for do-it-together participatory research! Here is one of the early handouts for these workshops (ca. 2018). 


Crucial for this workshop are biosafety issues and notions of frequency. 


First of all, anyone can carry potential pathogens as part of their 'normal flora' - so each participant makes slides with their own cells, and the slides are fixed with both heat and alcohol, so they are sterile and safe. Then, slides can be exchanged for counting by other participants (to help avoid bias). 

Secondly, finding a micronucleus on a slide is no cause for panic. DNA breaks and is repaired, and that is normal. The rule of thumb used counts 1-5 micronuclei per 1000 cells as nothing to worry about. However, if the frequency of micronuclei is increased, say from 20-50 micronuclei per 1000 cells, either exposure to something genotoxic or issues with DNA repair should be considered seriously (and the workshop participant should be advised to go to their doctor, just in case).


There are hopes that further integration of the micronuclei and another method to see overall levels of DNA damage, the comet assay, will be possible with the OpenFlexure microscopy system, to allow even better assessment of the levels of DNA damage in our own inner cheek cells. Work to see whether this open source system, when equipped for epifluorescence detection to allow the comet assay, is in progress as part of the 'cheek cell chip' project at Hackuarium. We had even begun some tests of artificial intelligence to automatically detect micronuclei from our cell images, before the pandemic, to make things easier, and our transdisciplinary team may just find time to follow up on that soon... =)

The idea is to provide a way for biohackers anywhere to follow their levels of DNA damage, for open science.


Rachel Aronoff has run the micronucleus workshop in London, Brussels, Lausanne, Bilbao, Quibdó, and also virtually for colleagues, over the last few years, for instance, in Spain, Colombia, the USA, and other countries. Molecular biologist, founder of AGiR!, and President of the open science public service community laboratory association, Hackuarium (pronounced 'aquarium' in the Swiss/French region where it is located), Rachel loves learning by doing, and hopes you might want to try this out, too!  


Here is one of the protocols for doing this simple micronucleus assay in order to see if a big piece of one of your chromosomes might have broken off not so long ago, the Spanish version, used around the project 'Micronuclei and Mercury' in collaboration with Colombian colleague, Yuber Palacios, from an academic lab in Choco, and also the Bogota group, Màs Arte Màs Acción.


Here is the link to the Hackuarium wiki page with the protocol in English (with link to French)

Have a look at the Prezi for the workshop done 18may19)!

Here is the 'timelapse' made during the workshop - two hours in 30s??

Here is one video compilation from one of our really early sessions, back in Renens at the old Hackuarium. 

Here is the Kapaw coverage (in German) of another of our micronuclei workshops in our current space, in Ecublens. 


This is a project of AGiR! at Hackuarium. 

We are really hoping to do a special micronucleus workshop this winter, with support from JOGL!

You can already try it or even join in for more development, too!


(questions or concerns? contact @Rachel Aronoff)

Additional information
  • Short Name: #OpenSourceDNAdamagedetection
  • Created on: September 19, 2022
  • Last update: September 22, 2022
Keywords
Biotech
Cell and molecular biology
Genetic
3Good Health and Well-being
4Quality Education
6Clean Water and Sanitation
11Sustainable Cities and Communities