View source for Bioreporters in Pollutant Detection

== What are Bioreporters ==
A bioreporter is a living organism that produces a signal when it detects a target chemical.<br>
In a very general sense, Bioreporters have 3 parts:
# intact living organism
# have a sensing element for the compound of interest
# have a reporting element that gives a signal when the compound of interest is detected
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Given this definition, most of the bioreporters are genetically engineered to satisfy both part 2 and 3, as can be read on the [https://en.wikipedia.org/wiki/Bioreporter wikipedia page for bioreporters]. Part 3, the reporter element, can be [https://en.wikipedia.org/wiki/Bioreporter#Reporter_gene_systems proteins] that results in generation of light signals, such as bioluminescent reaction catalysers, or fluorescent proteins, or color, amongst other signals. Part 2, then is a genetic element, that allows the reporter protein to be produced (translated and transcribed from the reporter genetic element).
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Bioreporters do not have to be genetically modified organisms (GMOs) however. Any obstruction in the metabolic cycle that produces natural signals (bioluminescence in a naturally bioluminescent organism, for example) can be used as a bioreporter. [http://onlinelibrary.wiley.com/doi/10.1002/9780470061565.hbb014/full Ulitzur 2008, DOI: 10.1002/9780470061565.hbb014]
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See more on our [[Bioreporter_FAQ]].
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== Why Bioreporters ==
'''PROS'''
* no need for expensive equipment
* laypersons can obtain quality results with training
* sensors are self-replicating
* complementary to chemical assays, sometimes as sensitive

'''CONS'''
* compound of interest may not be bioavailable (available for the live-organism to take up and give signal, toxic, etc.)
* signal can be difficult to interpret
* cold chain
* legal aspects of GMOs

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==Current List of Reporters with BIODESIGN==
Our project started with arsenic bioreporting using eGFP as the signal to be detected, that was developed by the [https://www.unil.ch/dmf/en/home/menuinst/research-units/van-der-meer/people/jr-van-der-meer.html van der Meer Lab] at UNIL (University of Lausanne, Switzerland).<br>
The bioreporters are versatile - with the eGFP reporting molecule, there are other bioreporters that can be constructed, as we did in the [[Winter School]] in 2016, a collaboration between biodesign.cc and UNIL. There, we also learned about bioreporters for explosives for the detection of landmines.<br><br>
From that workshop, in our toolbox, we now have eGFP reporters for:
* [[Arsenic]]
* [[Zinc Cadmium]] - heavy metals
* [[Mercury]]
* [[Alkanes]] (oil spill)
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==Bioreporters for Whom?==
===GMO regulations===
Genetically Modified Organisms (GMOs) are highly regulated in most countries. This means that to use the bacterial bioreporters, collaborations have to be established to authorised institutions, such as universities, to maintain, expand, and properly dispose of these bacteria. <br>
In Switzerland, we have resolved it in [[http://wiki.biodesign.cc/wiki/GMO_Containment_in_the_Field this manner]].<br>
===Openness===
The intellectual property around the bioreporters.
US utility patents expire 20 years from the date of filing (US or international). <br>
(For more on the explanation of patent terms, one law firm's explanation [http://www.bpmlegal.com/howtoterm.html here], wikipedia explanation [https://en.wikipedia.org/wiki/Term_of_patent_in_the_United_States here]).

This is the invention patented by our collaborator, encompasses the reporters we have:<br>
* [http://www.google.com/patents/US7625744 US7625744 B2] also in DE, and international [http://www.google.com/patents/WO2014141066A3?cl=en WO 2003102223 A1], Date of Filing: '''May 19, 2003''', inventor: J.R. van der Meer, with original asignee: Helmholtz-Zentrum für Umweltforschung GmbH-UFZ
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Abstract:
The invention is concerned with a biologically based test system for the detection of inorganic and organic pollutants in water samples. In particular, the present invention is concerned with the development of a strategy for the control of background expression of biosensors in the biologically based test system. Furthermore, the present invention provides a test kit for determining concentrations of inorganic and organic pollutants in water samples, the test kits are suitable for field tests.
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We have discussed the intellectual property issues, and [https://www.unil.ch/dmf/en/home/menuinst/research-units/van-der-meer/people/jr-van-der-meer.html Dr. van der Meer] (UNIL) is open to work on community projects with the bioreporters. The patent has been licensed by Helmholtz-Zentrum für Umweltforschung GmbH-UFZ, who has improved the arsenic bioluminescent reporter  ([http://www.ufz.de/arsolux/index.php?en=20675 ArsoLux]), gained [http://www.ufz.de/arsolux/index.php?en=20708 German government approval], is in [http://www.ufz.de/arsolux/index.php?en=20707 6 countries]. We have tried contacting the company in 2013.
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There are other patents filed around bioreporters.<br>
Generally, the patent landscape covers the reporters for sensing specific compounds, methods to generate the sensing element, the reporter systems, and ways to integrate bioreporters into devices.<br>
This is a non-exhaustive list of examples<br>

* Phenols, detection - [http://www.google.com/patents/US20020168636 US 20020168636 A1], Date of Filing: '''Mar 8, 2000'''
* Mercury, detection using MerB, MerT- [http://www.google.com/patents/CN102250819A?cl=en CN 102250819 A], Date of Filing: '''May 18, 2010''' - '''ONLY FILED IN CN'''
* simultaneous detection of multiple metals [http://www.google.com/patents/WO2014141066A3?cl=en WO 2014141066 A3], Date of Filing: '''Mar 11, 2014'''
* screen for specific compounds and make DNA pools to clone bioreporters - [http://www.google.com/patents/US20100029509 US20100029509 A1], Date of Filing: '''Nov 7, 2007''': 


Some for the reporter system have come off patent (e.g. [http://www.google.com/patents/US5491084 US 5491084 A]), however navigating the patent landscape is '''a known challenge''' in the field of synthetic biology.<br>
Quoting [http://www.jbioleng.org/content/7/1/13 Kahl and Endy] Journal of Biological Engineering 2013, 7:13:
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Furthermore, there are literally hundreds, if not thousands, of issued patents covering variants of GFP and their uses. 
...The large number of patents covering variants of GFP and their uses presents a considerable challenge to synthetic biology researchers who wish to use fluorescent reporters in creating standards for characterizing biological parts and devices... 
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== References ==
* A great review by van der Meer and Belkin Nature Reviews Microbiology 2010, Where microbiology meets microengineering: design and applications of reporter bacteria. 
* The parts from iGEM teams' registry for [http://parts.igem.org/Collections/Metal heavy metal sensing biobricks] are nicely documented and extensive.
[[Category:Ongoing Projects]]
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