AGiR! for genomic integrity - Revision history

Rachel at 15:41, 29 March 2025

2025-03-29T15:41:05Z

Rachel: /* Objectives */

2024-09-18T15:18:19Z

Objectives

Rachel at 15:16, 18 September 2024

2024-09-18T15:16:30Z

Rachel: /* Recommendation + next steps */

2024-05-13T06:26:16Z

Recommendation + next steps

Rachel at 19:01, 31 January 2024

2024-01-31T19:01:22Z

Rachel: /* Recommendation + next steps */

2022-03-23T11:14:09Z

Recommendation + next steps

Rachel: /* People */

2022-03-23T11:13:45Z

People

Rachel at 11:09, 23 March 2022

2022-03-23T11:09:30Z

Rachel at 11:09, 23 March 2022

2022-03-23T11:09:07Z

Rachel at 15:43, 14 October 2021

2021-10-14T15:43:28Z

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 It was first proposed in 2009, as part of the old EFV Prize (to help End Fashion Victimisation)...
-(AGiR! as a Swiss Association began over 11 years ago, with the first general assembly meeting held on 16sept2013)<br>
+(AGiR! as a Swiss Association began in 16sept2013, with the first general assembly meeting held in the UNIL Biophore building. )
 At Hackuarium, AGiR! hopes to get participative research actions really going - developing DIT research methods to readily assay *your very own* cells for DNA damage, using classic (circa 1980s) techniques.  If these can already be sold in 'kits,' maybe it will also be simple to make them available to all for open source efforts?<br>

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 * Demonstrate methods and 'share the love' with other biohacker groups (La Paillasse etc.)
-* Study the feasibility of further methods that could contribute to this project - i.e. open-source imaging and microscopy techniques, like the [https://openflexure.org/ OpenFlexure] system, which we are trying for imaging comets by epifluorescence. As of 2019 we had gotten to the point of seeing fluor nuclei, but not comet tails, but then the pandemic caused us to put this to the side, to focus on Corona Detective R&D.  Now, in 2022, we hope to get back to all this 'cheek cell chip' work!
+* Study the feasibility of further methods that could contribute to this project - i.e. open-source imaging and microscopy techniques, like the [https://openflexure.org/ OpenFlexure] system, which we are trying for imaging comets by epifluorescence. As of 2019 we had gotten to the point of seeing fluor nuclei, but not comet tails, but then the pandemic caused us to put this to the side, to focus on Corona Detective R&D.  In 2022, we hoped to get back to all this 'cheek cell chip' work, and it is still of great interest!  '''You''' could help!
 '''Cheek cells are continually renewing epithelial cells and are about 50 micrometers in diameter.''' [[File:Cells3.jpg|200px|thumb|right|Three cheek cells imaged on the scope at the Hackuarium. ]]
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 dos Santos Rocha et al (2014) Genetics and Molecular Biology, 37(4)702-707<br>
 (This paper looks at micronuclei in cheek cells (and also analyses apoptosis) from mouthwash and alcohol users.)<br>
-Also <br>
+Also here is a [https://www.sciencedirect.com/science/article/pii/S1383574218300620?via%3Dihub new review about micronuclei]!
 ''To note: the two assays proposed would be analysing only limited aspects of 'genomic integrity' at the DNA level - large scale chromosomal disruption in the micronuclei assay and double-stranded breaks with the comet assay!  <br>There are many more methods that could look at other aspects (particular nucleotide lesions, reactive oxygen species and inflammation, gene expression, microRNAs, etc.) of genomic integrity!''

@@ Line 3: / Line 3: @@
 So many things we commonly choose to do can impact genomic integrity, also potentially affecting future generations. <br>
-'''To Note: the concept of 'dynamic genomic integrity' celebrated its 14th anniversary already.'''  <br>
+'''To Note: the concept of 'dynamic genomic integrity' celebrated its 15th anniversary already.'''  <br>
 It was first proposed in 2009, as part of the old EFV Prize (to help End Fashion Victimisation)...
-(AGiR! as a Swiss Association began over 10 years ago, with the first general assembly meeting held on 16sept2013)<br>
+(AGiR! as a Swiss Association began over 11 years ago, with the first general assembly meeting held on 16sept2013)<br>
 At Hackuarium, AGiR! hopes to get participative research actions really going - developing DIT research methods to readily assay *your very own* cells for DNA damage, using classic (circa 1980s) techniques.  If these can already be sold in 'kits,' maybe it will also be simple to make them available to all for open source efforts?<br>

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 Here is the [https://www.eventbrite.com/e/workshop-open-sourcing-dna-damage-detection-for-citizen-science-tickets-43050819159 link to the 2018 atelier] (21April2018) in Renens. <br>
-Check out the [http://wiki.hackuarium.ch/w/Moss_Menageries_with_AGiR! Moss Menagerie] project also,<br>
+Check out the [http://wiki.hackuarium.ch/w/Moss_Menageries_with_AGiR! Moss Menagerie] project also, esp as there is news about how [https://doi.org/10.1016/j.cub.2024.03.019 up-regulating DNA repair] helps [https://elifesciences.org/reviewed-preprints/92621 waterbears resist radiation] challenges - <br>
 and<br>
 spread the word!<br>

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 So many things we commonly choose to do can impact genomic integrity, also potentially affecting future generations. <br>
-'''To Note: the concept of 'dynamic genomic integrity' celebrated its 12th anniversary already.'''  <br>
+'''To Note: the concept of 'dynamic genomic integrity' celebrated its 14th anniversary already.'''  <br>
 It was first proposed in 2009, as part of the old EFV Prize (to help End Fashion Victimisation)...
-(but AGiR! as a Swiss Association only began around 8 years ago, with the first general assembly meeting held on 16sept2013)<br>
+(AGiR! as a Swiss Association began over 10 years ago, with the first general assembly meeting held on 16sept2013)<br>
 At Hackuarium, AGiR! hopes to get participative research actions really going - developing DIT research methods to readily assay *your very own* cells for DNA damage, using classic (circa 1980s) techniques.  If these can already be sold in 'kits,' maybe it will also be simple to make them available to all for open source efforts?<br>
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 == Introduction ==
 === Context ===
-This is a part of a Hackuarium project by AGiR! on genomic integrity, to find out more and help raise awareness in the public interest. <br>
+This is a part of a Hackuarium project by AGiR! on [[genomic integrity]], to find out more and help raise awareness in the public interest. <br>
 This wiki page is under construction, and will help keep track as we develop open source simple protocols of two classic methods for quantitation of DNA damage in human cells, the micronuclei and comet assays.
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 To do both comet cell and micronuclei assays by the simplest possible methods, with the bare minimal laboratory reagents/infrastructure...
+To potentially get a 'cheek cell chip' working - so that micronuclei scoring then the comet assay will allow one to assess the level of damage for all the cells in the sample for both methods...
 === Setup description ===
 General principle for both assays: looking at treated cells on slides through a microscope, imaging and quantitating the effects (i.e. counting number of cells with micronuclei relative to the total number of cells, or determining the length of the 'comet tail' - the longer the 'tail' the more DNA breaks - on average). <br>
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 :::* Mercury Lamp Setup and filters for fluorescent dye detection.
 :::* Could also try to design a transilluminator suitable for cellular resolution (UV/Fluo as usual for comets) when imaging (to look for open source models)
 * Other reagents and histochemical stains (methylene blue)
-::* Other reagents and histochemical stains (methylene blue)
+* Hydrogen peroxide for positive control cells (oxidative damage)
-::* Hydrogen peroxide for positive control cells (oxidative damage)
+* Antioxidant molecules as possible 'protective' intervention . (i.e. green tea as in Szeto et al...)
-::* Antioxidant molecules as possible 'protective' intervention . (i.e. green tea as in Szeto et al...)
+<nowiki>*</nowiki>Proteinase K is recommended in buccal cell protocols, but DIY alternatives are being considered, like tablets for contact lens cleaning  <br>
 '** To protect the DNA from digestion
 Very likely, working in pairs will be ideal for workshops based on these assays, since 'self-reporting' is generally so biased!
 (AGiR! is actively investigating this issue, too, since it has effects on both sides of the equation, for producers as well as consumers!)
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 More to come!  Who else wants to try?<br>
-update 2017oct14:  more on the difficulties in getting to the 'kitchen sink' level, and Anna's 8 weeks as an intern ('faire un stage' is the local term) will come soon...
+update 2017oct14:  more on the difficulties in getting to the 'kitchen sink' level, and Anna's 8 weeks as an intern ('faire un stage' is the local term) was still not fully discussed...
 <br>
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 == Recommendation + next steps ==
 Check out the levels of DNA damage in your own cheek cells:<br>
-Here is the [https://www.eventbrite.com/e/workshop-open-sourcing-dna-damage-detection-for-citizen-science-tickets-43050819159 link to the upcoming atelier] (21April2018) in Renens. <br>
+Here is the [https://www.eventbrite.com/e/workshop-open-sourcing-dna-damage-detection-for-citizen-science-tickets-43050819159 link to the 2018 atelier] (21April2018) in Renens. <br>
 Check out the [http://wiki.hackuarium.ch/w/Moss_Menageries_with_AGiR! Moss Menagerie] project also,<br>

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 and, [http://interspecifics.cc/comunicacionesespeculativas/media/TL10%20.mp4?fbclid=IwAR21X5tyOei3Aupwb5O3reVfHjnX9RP0sKufG6IMLJzqsC4XvKAOWE4IOTA if this inspires you], what do you think about joining in on a new [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2268691/ project about swarming bacteria] like these?? (potentially!)<br>
 <br>
 == Introduction ==
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 '''Participants:'''
 * Tatiana Eliseeva
 * Anna Dussuet
@@ Line 56: / Line 56: @@
 * Demonstrate methods and 'share the love' with other biohacker groups (La Paillasse etc.)
-* Study the feasibility of further methods that could contribute to this project - i.e. open-source imaging and microscopy techniques, like the [https://openflexure.org/ OpenFlexure] system, which we are trying for imaging comets by epifluorescence now (2019).
+* Study the feasibility of further methods that could contribute to this project - i.e. open-source imaging and microscopy techniques, like the [https://openflexure.org/ OpenFlexure] system, which we are trying for imaging comets by epifluorescence. As of 2019 we had gotten to the point of seeing fluor nuclei, but not comet tails, but then the pandemic caused us to put this to the side, to focus on Corona Detective R&D.  Now, in 2022, we hope to get back to all this 'cheek cell chip' work!
 '''Cheek cells are continually renewing epithelial cells and are about 50 micrometers in diameter.''' [[File:Cells3.jpg|200px|thumb|right|Three cheek cells imaged on the scope at the Hackuarium. ]]

@@ Line 25: / Line 25: @@
 <br>
-<br>
+<br><br>
 == Introduction ==