Bioreporters in Pollutant Detection

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What are Bioreporters

Arsenic-reporter-horizontal.gif

A bioreporter is a living organism that produces a signal when it detects a target chemical.
In a very general sense, Bioreporters have 3 parts:

  1. intact living organism
  2. have a sensing element for the compound of interest
  3. have a reporting element that gives a signal when the compound of interest is detected


Given this definition, most of the bioreporters are genetically engineered to satisfy both part 2 and 3, as can be read on the wikipedia page for bioreporters. Part 3, the reporter element, can be 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).
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. Ulitzur 2008, DOI: 10.1002/9780470061565.hbb014

See more on our Bioreporter_FAQ, and the review by van der Meer in the reference section.

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


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 van der Meer Lab at UNIL (University of Lausanne, Switzerland).
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.

From that workshop, in our toolbox, we now have eGFP reporters for:



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.
In Switzerland, we have resolved it in this manner: GMO Containment in the Field.

Openness

The intellectual property around the bioreporters. US utility patents expire 20 years from the date of filing (US or international).
(For more on the explanation of patent terms, one law firm's explanation here, wikipedia explanation here).

This is the invention patented by our collaborator, encompasses the reporters we have:

  • US7625744 B2 also in DE, and international WO 2003102223 A1, Date of Filing: May 19, 2003, inventor: J.R. van der Meer, with original asignee: Helmholtz-Zentrum für Umweltforschung GmbH-UFZ
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.

We have discussed the intellectual property issues, and Dr. van der Meer (UNIL) is open to work on community projects with the bioreporters. Our current reporters are cloned into the plasmid pBBR1MCS-2 backbone (GenBank U23751.1). The patent has been licensed by Helmholtz-Zentrum für Umweltforschung GmbH-UFZ, who has improved the arsenic bioluminescent reporter (ArsoLux), gained German government approval, is in 6 countries. We have tried contacting the company in 2013.

There are other patents filed around bioreporters.
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.
This is a non-exhaustive list of examples

  • Phenols, detection - US 20020168636 A1, Date of Filing: Mar 8, 2000
  • Mercury, detection using MerB, MerT- CN 102250819 A, Date of Filing: May 18, 2010 - ONLY FILED IN CN
  • simultaneous detection of multiple metals WO 2014141066 A3, Date of Filing: Mar 11, 2014
  • screen for specific compounds and make DNA pools to clone bioreporters - US20100029509 A1, Date of Filing: Nov 7, 2007:


Some for the reporter system have come off patent (e.g. US 5491084 A), however navigating the patent landscape is a known challenge in the field of synthetic biology.
Quoting Kahl and Endy Journal of Biological Engineering 2013, 7:13 (Endy is the co-creator of the iGEM competition):

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... 

There may be legal work-arounds depending on the patent to make a license-free transgenic organism to be used in biotechnological applications. On the other hand, many plasmids may be based on biotechnologies protected by intellectual property (see list of third party technologies, by Addgene, a non-profit plasmid repository, for example).

There are open source movements in biology and biotechnology.
For example, the OpenPlant initiative plans to implement foundational technologies for plant synthetic biology. The domain of agro-engineering has a large market, with little space to operate.

Current IP practices and restrictive licensing threaten to restrict innovation as the scale of DNA systems increases. We believe that the field needs to explore new “two-tier” intellectual property models that will protect investment in applications, while promote sharing of DNA components and freedom-to-operate for small companies in commercial applications of Synthetic Biology. We will create new forums and opportunities for open innovation in plant synthetic biology.

For more house-keeping reagents, Gene and Cell Technologies already sells MTA, patent, or other forms of intellectual property restriction-free (off-patent) DNA ladder plasmid, Taq polymerase expression plasmid, and mammalian resistance plasmid.



References

  • A great review by van der Meer and Belkin Nature Reviews Microbiology 2010, Where microbiology meets microengineering: design and applications of reporter bacteria. (not open access, publisher's site link)
  • The parts from iGEM teams' registry for heavy metal sensing biobricks are nicely documented and extensive.
  • Open Source Biology Evolves [www.wired.com/2005/01/open-source-biology-evolves/ Wired article] 2005
  • P2P Foundation entry on Open Source Biotechnology
  • P2P Foundation entry on Open Biology