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Anywhere, anytime DNA diagnostics for conservation

The detailed, real-time information provided by DNA diagnostics could be game changing for a range of conservation activities in New Zealand. Yet, traditional approaches to DNA testing are laboratory-based and, therefore, they have not become front tools for conservation.

This situation is about to change with new technologies making robust, cost effective, field-deployable DNA testing a reality. We are now able to create highly sensitive and specific DNA tests that can be performed in minutes by almost anyone, almost anywhere, at almost any time. Think conservation workers at a remote site or citizen scientists in a back garden, not scientists in a laboratory. These new technologies mean that we now have the opportunity to harness DNA diagnostics for applications in conservation; for example, enabling immediate decision-making or contributing to wider monitoring.

We currently have projects underway that implement these new technologies and we are now looking to bring the power of DNA diagnostics to the wider conservation community.

What conservation problem are you trying to solve?

There are various ways that conservation projects could utilise anywhere, anytime DNA testing. One involves tracking diseases that threaten New Zealand’s unique biota. For example, iconic plant species including mānuka and pōhutukawa are currently threatened by myrtle rust. Typically, our response to disease is reactive; we wait for visual signs of disease before taking action. To improve outcomes we need to be proactive. We need the ability to detect disease and initiate a response before physical symptoms appear. The quicker we intervene the more likely positive outcomes are.

Recent high-profile incursions highlight the scale of the problem we face. It is clear that we cannot continue to protect New Zealand’s unique biota from disease – whether already here or yet to arrive – without changing the status quo.

How are you going to solve this conservation problem?

We will make it possible to perform rapid, cost-effective genetic testing for disease-causing organisms anywhere, anytime without the need for high-end laboratory equipment or highly trained operators. Devices that enable on-the-spot DNA testing are available and our work has already developed tests for several diseases threatening some of New Zealand most iconic native species (e.g., kauri dieback, myrtle rust and a fungal pathogen of tuatara).

We already have proof of principal for our approach. The Department of Conservation is using one of our genetic tests to monitor a tuatara fungal pathogen. To date some 800 tests have been conducted and this information is informing disease management. But this is just one of many possible uses for new diagnostic technologies. We now need to grow public awareness as well as the number of situations for which an anywhere, anytime diagnostics is available.

What makes your idea new and unique?

Our project is novel because at its core is the idea that DNA testing should not be limited to a laboratory. Instead, these tools should be available to anyone, anywhere, anytime.

We have achieved this goal,

  • using an innovative workflow that reduces the time and cost of developing DNA tests (e.g., the tuatara pathogen test was funded by a $7000 investment and one for myrtle rust has taken 10 weeks to develop).
  • by taking advantage of new technologies to implement cheap, robust and field-deployable DNA tests (e.g., the tuatara pathogen test currently costs ~$3 per sample [compared to $80-200 for laboratory tests] and can be made cheaper with further work).

We have already had some contact with groups who are interesting in using our approach to develop tests for several applications. Yet, our aim is to empower day-to-day decision-making so we need to grow public awareness of what is possible with such testing and identify opportunities for implementation.

Who will use your idea, and how will they benefit?

The long-term goal is to make a range of diagnostic tests available from which individual conservation projects – whether run by a local school, a community group or national organization – can choose. While these diagnostics could be implemented into an existing project, they might also enable new conservation opportunities. For example, using rapid DNA diagnostics, it may be possible to extend the concept of a bioblitz to capture a detailed regional- or national-level snapshot of an organism’s distribution on a given day.

What tasks or activities do you need investment for? How would you spend a $25,000 grant?

The funding would go towards,

  • purchasing additional test devices that would allow us to run further trials.
  • production of prototype test kits for trialling.
  • validation of the testing procedures to ensure that they are as straightforward as possible.
  • engaging with a wider group of potential users to increase awareness and identify opportunities for test implementation.

Are you a New Zealand citizen or resident?

YES

I have read and agree to the Crowdicity Terms of Use, the Conservation Innovation Awards 2017 Supplemental Terms and Conditions, and the Crowdicity Privacy Policy

YES

List five other ideas posted in the challenge that excite you. Why?

1. A data collective allowing communities to collaborate and share knowledge, leading to better community engagement and more Tui

2. X-Specs

Why? “Big Data” shapes many aspects of modern life; a wide range of organisations now gather and analyse very large, complex data sets because they recognise the potential for transformative insights. The benefits of utilising big data to inform conservation decision-making and actions cannot be overstated. This pair of ideas addresses complementary parts of process, collecting big data and analysing it. 

 

3. Ur-bins

4.Compost and catch, spreading the predator free movement.

Why? Composting has positive environmental impacts, yet it also provides a potential food source for key targets of the Predator Free 2050 goals. These two entries use the same approach, cleverly turning what is a limitation into an advantage by using the compost to “bait the trap.” Also potentially reduces the use of poisons in urban areas.

 

5. He Toitu He Kauri: Science and Learning Hub

Why? Our team are currently involved in projects investigating where the causal agent of kauri dieback, Phytophthora agathidicida, came from and when it arrived. As part of this work we have become interested in how to improve detection of P. agathidicida in the field; this is important for ongoing monitoring, informed decision-making and evaluation of control measures.

How could you improve your idea?

It has been really encouraging to read the comments, it is great to see others suggesting potential applications for real-time field DNA diagnostics in a variety of conservation or broader environmental contexts. Some we are already looking at. For example, members of our group are helping build capacity around water quality monitoring with partners in Samoa. Globally there is a lot of interest in these approaches, especially in the health sector, so the R & D around the tests and their implementation is moving quickly. 

We have progressed towards infield DNA testing for several threats to New Zealand’s biodiversity. The feedback reinforces to us that our current projects represent only a small proportion of the possible applications for these approaches. But now we have these initial projects well advanced we can look to engage more broadly. At its core our idea is simple but with each new application we will need to refine and improve the implementation in order to ensure the best possible outcomes. For example, we would look to incorporate new advances such as embedding tests within a paper strip rather than using a handheld device.

edited on Oct 14, 2017 by Richard Winkworth

Daniel Cutmore Oct 5, 2017

Great idea, hope it goes far. Being able to do DNA testing outside of a lab will no doubt be a massive help for conservationists.

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Richard Winkworth Oct 14, 2017

Thanks Daniel!

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Nigel Binks Oct 5, 2017

Is your field application on possible with pathogens or could the COI mitochondrial gene be sequenced from invertebrates and vertebrates in the field? If so I'm dead keen to discuss this further.

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Richard Winkworth Oct 6, 2017

Hi Nigel,

Pathogens have been our initial focus just because there is a clear need and advantage over laboratory-based testing. However, it is possible to target any organism with the approach and we are starting to look at these. For example. we are exploring the possibility of fish monitoring.

Happy to talk further

Cheers

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Brent Beaven Oct 6, 2017

I like this idea and can see the advantages for disease detection and monitoring. As I have a focus on PF2050, do you see potential for this to be used for monitoring vertebrate pests at low densities?
Brent

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Richard Winkworth Oct 7, 2017

Hi Brent,

Thanks for the comment. There is definitely potential to use this type of DNA testing for applications where a species of interest (whether pest or native) is at low density or difficult to survey by other means.

In the case of monitoring vertebrate pests I think the issues are likely to revolve around how to use DNA testing effectively rather than getting the test or tests up and running. For example, what density, site, frequency etc. of testing is required if we want to be confident of detecting the remaining individuals. Determining how to sample effectively is unlikely to be a major hurdle but a solution would need to be worked though.

Cheers

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Brent Beaven Oct 12, 2017

Thanks for the reply Richard. I will keep that in the back of my mind for now. Good luck. Brent

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View all replies (2)

Fiona Edwards Oct 8, 2017

Kia ora, low cost, onsite DNA testing for pathogens will also be a game-changer for monitoring water quality. Potentially, this tool could be used both for education/information and enforcement/prosecution.
Good luck with your project

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Richard Winkworth Oct 14, 2017

Hi Fiona,

Completely agree, there is lots of scope for these approaches to be applied to other areas of environmental concern.

Water quality is an area thats receiving quite a bit of attention in terms of rapid diagnostics. For example, some of the work in our group is helping build capacity for water quality monitoring with DNA diagnostics in Samoa. Any approach that speeds up our ability to evaluate water quality is a potential game-changer from both conservation and health perspectives

Thanks for the comment

Richard

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Jay Gonsalkorale Oct 9, 2017

Great idea. I hear that the concept is extended to humans and research is done in the UK so that the best medication for a human can be identified based on the DNA profile.

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Richard Winkworth Oct 14, 2017

Hi Jay,

Thanks for the comment. The potential gains from DNA-based approaches mean that there is interest from various fields; areas such as human health are driving much of the R & D mainly because the level of investment is high.

We hope that by making these approaches more accessible we can help address conservation issues in New Zealand.

Thanks again

Reply

JWTauranga Oct 10, 2017

An exciting, pragmatic delvelopment that will ensure ease of access to testing in the field, as well as, options and flexibility not currently enjoyed.

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Richard Winkworth Oct 14, 2017

Thanks JW!

Our team is excited by the potential for this testing to make a real difference in our decision-making

Thanks Richard

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Jennifer Mcguire Oct 10, 2017

Really excited to see how this project progresses. Good luck!

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Richard Winkworth Oct 14, 2017

Thanks Jennifer!

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Kevin Bain Oct 10, 2017

Good morning Richard, I don't know anything about DNA testing except DNA lab testing does sound expensive and slow. Your words indicate you offer a solution to this, good work.

A couple of costs also elimited or reduced would be the transport costs of samples and the cost of a sample kit designed for transport to a lab would be far greater than a kit designed for a portable testing station?? Im guessing but I suspect both of these costs would be greater than the est $3 for your test??
kevin

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Richard Winkworth Oct 14, 2017

Hi Kevin,

Yes, the science is at a point where cheap, rapid DNA testing is a possibility for many applications.

You are right. It depends a little on the type of sampling involved but the cost of getting a useable sample back to a laboratory could well be over the current ~$3 cost of our approach. As important is the time saved. Potentially an infield test could be completed in less time than it takes to get that sample to the post office.

Cheers

Richard

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Joanne Jackson Oct 12, 2017

Hello Richard. WAI NZ is developing a real-time E. coli water borne pathogen tester. Does your idea have the potential to be embedded into an automated device?

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Richard Winkworth Oct 14, 2017

Hi Joanne,

The short answer is yes. There are a range of devices already available for running these tests (e.g. handhelds, lab-on-chip etc.) with a lot of ongoing research in this space.

One approach I really think could greatly expand the reach of this technology is the use of a paper-based system. The sample is dotted onto a paper strip and at the end of the process a coloured dot appears if the target organism is present. I could see this being useful for water quality testing by individuals or community groups; no chance of dropping a battery-powered device in the water!

Good luck with your project!!!

Cheers

Richard

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Michele Frank Oct 14, 2017

The idea has been progressed to the next milestone

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