Portable DNA device can detect tree pests in under two hours
New method tests for harmful species like the Asian gypsy moth and sudden
oak death pathogen

Date:
July 20, 2020
Source:
University of British Columbia
Summary:
A new rapid DNA detection method can identify forest pests and
pathogens like Asian gypsy moths and white pine blister rust
in less than two hours, without using complicated processes or
chemicals -- a substantial time savings compared to the several
days it currently takes to send samples to a lab for testing.



FULL STORY ========================================================================== Asian gypsy moths feed on a wide range of important plants and
trees. White pine blister rust can kill young trees in only a couple
of years. But it's not always easy to detect the presence of these
destructive species just by looking at spots and bumps on a tree, or on
the exterior of a cargo ship.


==========================================================================
Now a new rapid DNA detection method developed at the University of
British Columbia can identify these pests and pathogens in less than two
hours, without using complicated processes or chemicals -- a substantial
time savings compared to the several days it currently takes to send
samples to a lab for testing.

"Sometimes, a spot is just a spot," explains forestry professor Richard Hamelin, who designed the system with collaborators from UBC, Natural
Resources Canada and the Canadian Food Inspection Agency. "Other times,
it's a deadly fungus or an exotic bug that has hitched a ride on a
shipping container and has the potential to decimate local parks, forests
and farms. So you want to know as soon as possible what you're looking at,
so that you can collect more samples to assess the extent of the invasion
or begin to formulate a plan of action." Hamelin's research focuses
on using genomics to design better detection and monitoring methods for invasive pests and pathogens that threaten forests. For almost 25 years,
he's been looking for a fast, accurate, inexpensive DNA test that can be performed even in places, like forests, without fast Internet or steady
power supply.

He may have found it. The method, demonstrated in a preview last year for forestry policymakers in Ottawa, is straightforward. Tiny samples like
parts of leaves or branches, or insect parts like wings and antennae,
are dropped into a tube and popped into a small, battery-powered device
(the Franklin thermo cycler, made by Philadelphia-based Biomeme). The
device checks to see if these DNA fragments match the genomic material
of the target species and generates a signal that can be visualized on
a paired smartphone.

"With this system, we can tell with nearly 100 per cent accuracy if it is
a match or not, if we're looking at a threatening invasive species or one that's benign," said Hamelin. "We can analyze up to nine samples from the
same or different species at a time, and it's all lightweight enough --
the thermocycler weighs only 1.3 kilos -- to fit into your backpack with
room to spare." The method relies on PCR testing, the method that is
currently also the gold standard for COVID-19. PCR testing effectively
analyzes even tiny amounts of DNA by amplifying (through applying heating
and cooling cycles) a portion of the genetic material to a level where
it can be detected.

Hamelin's research was supported by Genome Canada, Genome BC and Genome
Quebec and published in PLOS One. The UBC team, including lead author
Arnaud Capron, tested this approach on species such as the Asian gypsy
moth, white pine blister rust and sudden oak death pathogen, which are
listed among the most destructive invasive pests worldwide.

"Our forestry, agriculture and horticulture are vital industries
contributing billions of dollars to Canada's economy so it's essential
that we protect them from their enemies," added Hamelin. "With early
detection and steady surveillance, we can ensure that potential problems
are nipped, so to speak, in the bud."

========================================================================== Story Source: Materials provided by University_of_British_Columbia. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Arnaud Capron, Don Stewart, Kelly Hrywkiw, Kiah Allen, Nicolas Feau,
Guillaume Bilodeau, Philippe Tanguay, Michel Cusson, Richard
C. Hamelin.

In Situ Processing and Efficient Environmental Detection (iSPEED)
of tree pests and pathogens using point-of-use real-time PCR. PLOS
ONE, 2020; 15 (4): e0226863 DOI: 10.1371/journal.pone.0226863 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/07/200720093234.htm

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