AGiR! for genomic integrity

Genomic integrity is a new 'big picture' concept to aid public health efforts and basically includes all the molecular genetic details of cells! So many things we commonly choose to do can impact genomic integrity, also potentially affecting future generations!

At the Hackuarium, AGiR! hopes to really get some citizen science action going - developing DIYbio methods to readily assay *your very own* cells for DNA damage, using classic (circa 1980s) techniques. If these can still be sold in 'kits,' maybe it will also be simple to make them available to all for open source efforts?
Here is the basic plan: using inner cheek cells for micronuclei and comet assays!
Watch this space for more info and visit
the AGiR! site

Introduction

Context

This is a part of a new Hackuarium project on genomic integrity.
This wiki page is under construction, and will help keep track of development of simple protocols for two methods for simple quantitation of DNA damage in human cells.

People

Contact and lead:

• Rachel Aronoff

Participants:

• maybe you?!

Main Goal

Genomic integrity is a topic that can be explored in several ways. Comet and micro-nuclei assay on cheek cells reveals itself to be a nice and easy "workshopable" way of showing people how to assess DNA damage. In other words, this experiment can be used as a gate to demonstrate and raise awareness to everyone on the damages of several substances to your own genetic information.
In the scope of Hackuarium activities, mammalian cell cultures is yet still a no go, but freshly isolated cheek cells from individuals can be used to do tests on DNA damaging compounds or activities.
In order to test compounds that might cause DNA damage, a test of bacteria reversion (i.e. Ames test) or on bulk DNA may also be nice to establish at the Hackuarium.
If people test substances on their cheek cells, and clearly significant effects are observed, we may be able to publish such effects.

Objectives

• Setup lab equipment for the cheek cell Comet and micronuclei assay

• Microscope
• Mercury Lamp Setup
• Agarose, glass slides, and gel running apparatus for embedding cells, treatments and nucleoid migration (for the comet assay)
• Hydrogen peroxide for positive control cells (oxidative damage)
• Design a transilluminator for cell illumination (UV/Fluo as usual for comets, or other alternative tests with histochemical stains) and imaging

• Study the feasability of an assay on either bacteria and bulk DNA

Background & Inspiration

Here is the link to the Prezi Rachel presented (13apr16) at an Open hackuarium night! Prezi on DIYbio for Genomic integrity!

Some theory

More on comet cells and micronuclei to come soon! But in the meantime, here are the references to the cheek cell papers mentioned in the presentation (and in the prezi):
Szeto et al (2005) Mutation Research 578:371-381
(In this paper, green tea is also shown to be protective.)
dos Santos Rocha et al (2014) Genetics and Molecular Biology, 37(4)702-707
(This paper looks at micronuclei in cheek cells (and also analyses apoptosis) from mouthwash and alcohol users.)

Inspiration / References / Similar projects

Inspiration: good pages to come

• [http://]
• [Link 2]

Setup description

General principle:

Materials & budget

• What, size | quantity | where to get it | price / unit

(If it’s an experiment) Parameters

To get baselines first

then To vary | Values

p1 |

p2 |

Constants (Key elements of set-up)

c1 |

c2

To measure/ observe

m1

m2

Protocol (Plan)

Phase 1

do what | frequency | duration

Lab Notebook & News (Real)

Protocols and measurements to be linked from here: [link to other doc]

Run / prototype #2

What's new compared to #1: