Difference between revisions of "Micro to Macro Water Pollution"

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(Action Plans)
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== Action Plans ==
 
== Action Plans ==
 
+
* Hammerdirt collects baseline and routine water samples for testing
* Hammerdirt collects some water samples for testing
+
* Rachel orders a coliform bacteria testing medium (done)
+
 
* Research what other relevant datasets are out there and document it
 
* Research what other relevant datasets are out there and document it
 +
<br><br>
 
=== Documentation and Collaboration Tools ===
 
=== Documentation and Collaboration Tools ===
 +
----
 +
Agree on documentation and collaboration tools
 +
* Internal communication - hackuarium slack
 +
* Calendar? - we have a biodesign google calendar
 
* Protocols - [http://openwetware.org/]?
 
* Protocols - [http://openwetware.org/]?
 
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events?  
 
* Electronic Lab Notebook - [http://openwetware.org/]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events?  
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=== Coliform Bacteria Counting ===
 
=== Coliform Bacteria Counting ===
 +
----
 
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.
 
Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.
  
  
 
==== Easy Gel ====
 
==== Easy Gel ====
 +
 +
* Rachel orders a coliform bacteria testing medium (done)
 
<br><br>
 
<br><br>
 
==== DIY protocol ====
 
==== DIY protocol ====
 +
 
==== Automatic Colony Counter and Plate Counting ====
 
==== Automatic Colony Counter and Plate Counting ====
 
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]
 
This is not a DIY gel, but [https://en.wikipedia.org/wiki/Endo_agar ENDO agar] was used for the workshops Lifepatch conducted in Indonesia: [http://biodesign.cc/2013/10/27/quantification-of-escherichia-coli-contamination-in-water/ Quantification of e. coli contamination in water]
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=== Community Bioreporter Kit for Switzerland ===
 
=== Community Bioreporter Kit for Switzerland ===
 +
----
 
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.
 
* Our current [http://wiki.biodesign.cc/wiki/Arsenic_Prototype_4.0 prototype] needs to be field-ready - the final design parameters need to be discussed.
 
* The protocol for the bioreporter assay needs to be simplified.
 
* The protocol for the bioreporter assay needs to be simplified.
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<br><br>
 
<br><br>
 
=== Water Multi-meter ===
 
=== Water Multi-meter ===
 +
----
 
* (Art)ScienceBLR
 
* (Art)ScienceBLR
 
* Student Project 2016
 
* Student Project 2016
 
<br><br>
 
<br><br>
 +
 
== Relevant Links ==
 
== Relevant Links ==
 
Discard Studies publishes interesting articles on Water Pollution
 
Discard Studies publishes interesting articles on Water Pollution

Revision as of 17:37, 7 April 2016

Background Information

Hammerdirt came to the BIO-DESIGN for the REAL WORLD's Winter School with data on the macropollutants washing up on the local beaches in and around Montreux (CH). The data format conforms to international norms, and over two years, some patterns can be observed in the level of litter on the shores. The collaboration will be an exchange and complement to what is already on-going at Hammerdirt.
The presentation can be found here:

Aims

To answer: Does the presence of macropollutants on the shores of Lac Leman correlate with micropollutants (biological, chemical, particulate, etc.) in the lake water?

Brainstorm Results

brainstorm board

At Open Hackuarium #88, we came up with some initial ideas.

  • Data Analysis
  • Image analysis and machine learning to readily tabulate the macro-pollutants collected on the beach
  • synching the above data with a phone application in the internationally accepted format
  • Add lake existing data (lake current, meterology, etc.)
  • Water collection and Analysis
  • Standardizing Collection Methods
  • Water chemistry testing - turbidity, pO2, pH, conductivity, temperature
  • DIY free NH2
  • Microparticle counting - DIY
  • Heavy metal analysis DIY equipment of BIODESIGN to be more robust - or
  • Make a fluorescent plate reader for higher throughput (CAUTION: still need P1 to use bioreporters here)
  • antibiotic resistant bacteria (CAUTION: we cannot amplify/concentrate possible pathogens)
  • Fish diseases - ask Maison de la Rivière?
  • Awareness Raising - Recycling
  • Recycle plastics using the extruder and use it to 3D print objects
  • Biodegradation with mycelium


Collaboration Defined

1st stage:

  • coliform bacteria counting
  • easygel
  • DIY version
  • community bioreporter kit field version for Switzerland
  • robust hardware
  • easy to manipulate wetware (remove possibility of error in the protocol - including standard curve generation, etc.)
  • a water multimeter
  • pH, conductivity, dissolved O2, temperature




Action Plans

  • Hammerdirt collects baseline and routine water samples for testing
  • Research what other relevant datasets are out there and document it



Documentation and Collaboration Tools


Agree on documentation and collaboration tools

  • Internal communication - hackuarium slack
  • Calendar? - we have a biodesign google calendar
  • Protocols - [1]?
  • Electronic Lab Notebook - [2]? - a template system where people can write down what they do would be nice, should it be the same as the Data entry format where you comment on unusual procedures or events?
  • Data entry and sharing - Hammerdirt github, compliance with the international standards
  • Hardware design - biodesign github



Coliform Bacteria Counting


Coliform bacteria is an indirect indication of fecal contamination of the waters. There are several methods to distinguish coliform bacteria vs other microorganisms that may grow on an agar plate.


Easy Gel

  • Rachel orders a coliform bacteria testing medium (done)



DIY protocol

Automatic Colony Counter and Plate Counting

This is not a DIY gel, but ENDO agar was used for the workshops Lifepatch conducted in Indonesia: Quantification of e. coli contamination in water

From Lifepatch, we have set this up DIY automatic colony counter.

Other Methods

Biodesign has tried:

  • Hack-a-Taq
  • This early post has a pdf at the end summarizing techniques, including portable sensor, paper strip, etc.



Scaling

Basic calculation for cost for one time analysis:

number of plates = number of sites x number of dilutions x number of replicates + positive control + negative control



Use glass petri-dishes for recycling - we can as Lifepatch how they set it up.

Community Bioreporter Kit for Switzerland


  • Our current prototype needs to be field-ready - the final design parameters need to be discussed.
  • The protocol for the bioreporter assay needs to be simplified.

Otherwise, the system for working with the bioreporters has been approved with the Swiss authorities.



Water Multi-meter


  • (Art)ScienceBLR
  • Student Project 2016



Relevant Links

Discard Studies publishes interesting articles on Water Pollution

Electronic Lab Notebooks