Water quality monitoring and
Participatory research at
Hackuarium
MCBP 2022 ‘Wrap’
Special #Open Hackuarium
12october22
hammerdirt with their beach litter surveys really started it all…
Scientific Method - controls and replicates
Venoges river
as our positive control
tap water (negative)
3 -> 6 replicates
Microbiology Classic (Water Watch)
1st year with ‘colorimetric’ petri dishes ‘EasyGel’
2nd year - UV+ confirmation plates & card trial
-> pandemic year did ‘classic’ plates
seqs also to confirm species IDs
for 2022 went for the latest cards…
-blue for bioindicator, red for coliform
THE ‘JAZZ’ EFFECT?
Microbiology Classic (Water Watch)
1st year with ‘colorimetric’ petri dishes ‘EasyGel’
2nd year - UV+ confirmation plates & card trial
-> pandemic year did ‘classic’ plates
seqs also to confirm species IDs
for 2022 went for the latest cards…
-blue for bioindicator, red for coliform
A silver lining from the pandemic - summer 2020
While our open data showing the ‘Jazz effect’ was openly available for years, and even discussed in media, it was because of the first pandemic summer that we got results that enabled us to go for the open publication.
The local free paper 20Minutes put out an article pushing local politicians to take some action, but they are seemingly still not on board, even though they were repeatedly invited… (any here? =) There was also a video and their latest article was out on 21 sept.
Bootstrapping by Masoud and Carlos
helped convince us to push for the publication - even had open review!
All the data is archived in Zenodo, too.
For 2022, we not only went forward to do more, even with collaboration with people from the Jazz, but also went out on the platform LéXPLORE to compare the lake proper to the lake shore…
Images from the first visit and sampling
48h
cards
from
LéXPLORE
One dark blue spot per card is already at the Swiss limit
for
recreational
waters!
(ave 400cfus of
bioind/100ml)
They cleaned off lots, just before the public visiting day!!
Subsequent samplings were clean!!
(except 5m deep in the post-season sampling, see slide 14… another thing to learn about!)
launch day images (13june22)
the view from
LéXPLORE
12.9.22
analysis
Did sampling more frequently during the jazz, too!
bioindicators
and
coliforms
(all sites together)
analysis
bioindicators only
(all sites together)
analysis
bioindicators only
and rainfall
(all sites together)
analysis
site by site
with error bars
2022 campaign, summary
0.5m & 5m depths (from LéXPLORE plateform)
2022 campaign, summary
0.5m & 5m depths (from LéXPLORE plateform)
!! !! & Clarens swimming beach
official results still not obtained!
no rain from 6 July to 18 July…
Jazz from 1 July to 16 July
?s
How to get the powers that be to join in?
Maybe our water quality work provides a good example…
More ahead, together !!
Open Sourcing DNA Damage Detection using Open Science Hardware
with AGiR!
at Hackuarium
Micronucleus & Comet Assays
both methods used for
risk analyses since
around 1970…
Shows
big pieces of
broken off
chromosomes
Shows
overall levels
of double- stranded breaks
Need Epifluorescence microscopy to see Comet tails!
Tried pre-pandemic - got fluor nuclei, but not comet tails
Lorem ipsum dolor sit amet.
30june22
Delta stage
OpenFlexure
v7 alpha2
RaspberryPI
12.3Mpixel
x2
Trying Better Resolution RPi cameras and Objective Lens
Obtained!
Funding by GOSH!
(also for the
workshop by
Mitch Altman)
Cheek Cell Chip -plan
Will compare the Delta format and the latest version of the OpenFlexure, with better optical and imaging elements than in our first build, to see if comet tails will also be visible.
Then, for the best system in this context, will make a third build with a modified stage holder for millifluidics to do: first, imaging of cells for micronuclei, and then, treatments and e- for comets, and then image it all again.
That will provide good measurements of the level of DNA damage in each cell of the sample.
The idea is that ‘biohackers’ everywhere will determine their baseline level of damage and see what influences it.
-participatory research to help reduce risks!
What happens if you
eat blueberries every day?
go running?
do …xyz…
Cheek Cell Chip
Will compare the Delta format and the latest version of the OpenFlexure, with better optical and imaging elements than in our first build, to see if comet tails will also be visible.
Then, for the best system in this context, will make a third build with a modified stage holder for millifluidics to do: first, imaging of cells for micronuclei, and then, treatments and e- for comets, and then image it all again.
That will provide good measurements of the level of DNA damage in each cell of the sample.
The idea is that ‘biohackers’ everywhere will determine their baseline level of damage and see what influences it.
-participatory research to help reduce risks!
What happens if you
eat blueberries every day?
go running?
do …xyz…
panorama possibilities
take images of whole cell sample to score micronuclei, then do comet protocol and repeat the imaging
-for quantitative measures of your cells’ level of DNA damage
Stitching advice: Collect images in a predictable pattern e.g. right → left → up → left → right → up and so on. This will help you remember where you are and will help the stitching software. Another tool
to add example …
doing outlines in photoshop take time, but more samples make a better algorithm
automatic
recognition
of micronuclei
with Tatiana
-another project
pushed to the
side because of
the pandemic…
could be
reactivated?
training on a
limited set
actually gave
very good
predictive
power
probabilities
AGiR! Flyer Campaign
To raise awareness about avoiding products and activities that can damage DNA and thus affect health!
17 languages (ukrainian being proofed now!)
?s
Who would like to join in?
To do an OpenFlexure build for EpiFluor and the cheek cell chip development?
To join in for an actual research trial? (still would need to organise review and oversight!)