PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

DNA detectives able to 'count' thousands of fish using as little as a glass of water

2014-01-16
(Press-News.org) Contact information: Sandra Hines
shines@uw.edu
206-543-2580
University of Washington
DNA detectives able to 'count' thousands of fish using as little as a glass of water

A mere glass full of water from Monterey Bay Aquarium's 1.2 million-gallon Open Sea tank, among the 10 largest aquariums in the world, is all scientists really needed to identify the Pacific Bluefin tuna, dolphinfish and most of the other 13,000 fish swimming there.

Researchers also for the first time used DNA from water samples to discern which of the species were most plentiful in the tank.

Being able to determine the relative abundance of fish species in a body of water is the next step in possibly using modern DNA identification techniques to census fish in the open ocean, according to Ryan Kelly, University of Washington assistant professor of marine and environmental affairs, and lead author of a paper in the Jan. 15 issue of PLOS ONE.

Currently most scientists net, see or in other ways count fish to determine what species are present and in what proportions in marine environments.

"It might be unpleasant to think about when going for a swim in the ocean, but the water is a soup of cells shed by what lives there," Kelly said. Fish shed cells from their skin, damaged tissues and as body wastes.

"Every one of those cells has DNA and if you have the right tools you can tell what species the cell came from. Now we're working to find the relative abundance of each species present," he said.

It was barely two years ago that an influential paper was published by scientists who determined the presence of an endangered species they were seeking in a river using this "environmental DNA" or "eDNA." Since then the technique has been used to look for other specific species in both freshwater and one marine setting.

"Clearly this is an effective tool in the wild when you know what you're looking for," Kelly said.

He and his co-authors, Jesse Port, Kevan Yamahara and Larry Crowder with Stanford University's Center for Ocean Solutions, took the work another step further with funding from the David and Lucile Packard Foundation. The researchers wanted to see how well they could detect DNA using a single set of "primers," molecular probes designed by another group just the year before this study, that zero in on portions of DNA that indicate an animal has a backbone and is a vertebrate. The sea tank at Monterey Bay Aquarium was suggested because the inhabitants are known and could be compared to what the new technique revealed was present, giving the authors a way to judge the technique's accuracy. The researchers analyzed about two pint glasses worth of water in the course of their project and Ryan said the DNA data of what's in the tank likely could have been revealed by an even smaller sample.

The approach proved effective by both identifying the eight bony fishes in the tank and determining that tuna and sardines made up the greatest amount of biomass in the tank, which tank managers could document. The technique turned out to be so finely tuned that it also picked up DNA from long-dead menhaden from the Atlantic Ocean, fish that had been processed, transported and added to the tank as food. It was a surprise when an Atlantic species turned up, until the researchers realized where the DNA was coming from, and then they made calculations to take that into account.

The primers were unable to detect DNA from two groups of vertebrates in the tank: the turtles and the fish with cartilage in place of bones, such as rays and sharks. Kelly said that these kinds of biases in detection are inevitable, highlighting the need to focus on the design of additional general primers.

Being able to determine what's living in a body of water in the ocean using environmental DNA could be less expensive and time consuming than traditional census methods. The process could help scientists charged with monitoring and managing aquatic habitats, could reveal the arrival of invasive species before they become a major problem, or provide ways to look at food webs and other basic ecosystem functions, Kelly said.

The mixing of ocean waters by tides, currents or other forces is one hurdle to using this technique in the open ocean. But the group's preliminary work in Monterey Bay revealed DNA differences between areas of near-shore sea grass areas and kelp beds farther out but still within sight of each other. Additional field testing is planned in San Francisco Bay.

While fish research using environmental DNA only started in recent years, the revolution using DNA to detect what's present in particular habitats started in the early 2000s. Since then the cost of gene sequencing has plummeted, with what was $5,300 in 2001 costing about 6 cents today, Kelly said. Microbiologists developed and used techniques to survey bacteria, viruses and other microorganisms in everything from the human gut to the ocean for a decade before any research group published results using it for fish and other aquatic organisms that could actually be seen.



INFORMATION:



For more information:

Ryan, 206-616-0185, rpkelly@uw.edu

Suggested websites:

Ryan Kelly http://depts.washington.edu/smea/users/rpkelly

PLOS ONE http://www.plosone.org/

Monterey Bay Aquarium http://www.montereybayaquarium.org/

Jesse Port http://www.centerforoceansolutions.org/people/early-career-fellows/jesse-port

Kevan Yamahara http://www.centerforoceansolutions.org/people/early-career-fellows/kevan-yamahara

Larry Crowder http://www.centerforoceansolutions.org/people/staff/larry-crowder



ELSE PRESS RELEASES FROM THIS DATE:

Oldest trees are growing faster, storing more carbon as they age

2014-01-16
Oldest trees are growing faster, storing more carbon as they age CORVALLIS, Ore. – In a finding that overturns the conventional view that large old trees are unproductive, scientists have determined that for most species, the biggest trees increase their ...

Head injuries triple long-term risk of early death

2014-01-16
Head injuries triple long-term risk of early death Survivors of traumatic brain injuries are 3 times more likely to die prematurely than the general population, often from suicide or fatal injuries, finds an Oxford University-led study Survivors ...

Study highlights growing threat of intense tropical cyclones hitting East Asia

2014-01-16
Study highlights growing threat of intense tropical cyclones hitting East Asia The intensity of tropical cyclones hitting East Asia has significantly increased over the past 30 years, according to a new study published today. The coastlines of China, Korea ...

Mercury and ozone depletion events in the Arctic linked to sea-ice dynamics

2014-01-16
Mercury and ozone depletion events in the Arctic linked to sea-ice dynamics DRI scientists' co-author study examining changing atmospheric chemistry in fragile northern ecosystems RENO - This week a new study published in Nature and co-authored by Drs. Chris ...

Crittercam captures crocodilian foraging behaviors (videos)

2014-01-16
Crittercam captures crocodilian foraging behaviors (videos) Video footage reveals novel insights into alligator's cryptic foraging behaviors Animal-borne camera reveals that alligators may attempt to capture prey most often at night, even though the calculated probability ...

Using progesterone for hot flashes shown safe for women's cardiovascular health

2014-01-16
Using progesterone for hot flashes shown safe for women's cardiovascular health Treatment with progesterone, a naturally occurring hormone that has been shown to alleviate severe hot flashes and night sweats in post-menopausal women, poses little ...

Breakthrough announced in treatment of patient with rare type of leukemia

2014-01-16
Breakthrough announced in treatment of patient with rare type of leukemia University of Leicester researchers deploy 'precision medicine' to successfully target advanced form of leukaemia with skin cancer drug A team of scientists from the University of Leicester ...

A deeper look at interfaces

2014-01-16
A deeper look at interfaces Researchers at Berkeley Lab's Advanced Light Source develop new technique for probing subsurface electronic structure "The interface is the device," Nobel laureate Herbert Kroemer famously observed, referring to the remarkable ...

Trees grow faster and store more carbon as they age

2014-01-16
Trees grow faster and store more carbon as they age Trees put on weight faster and faster as they grow older, according to a new study in the journal Nature. The finding that most trees' growth accelerates as they age suggests that large, old trees may ...

2 diabetes studies in Jan. 2014 Health Affairs

2014-01-16
2 diabetes studies in Jan. 2014 Health Affairs Jan. articles examine the toll of diabetes, both in the US and abroad Poorer Americans: depleted food budgets can mean higher risk of hypoglycemia. For generations, economists have noted that low-income households spend much ...

LAST 30 PRESS RELEASES:

Endangered Kangaroo Island ground dweller found in trees

Guardians of the coast: Philippine scientists unlock the climate power of mangroves in Eastern Visayas

Nano-biochar helps rice roots turn silver ions into less toxic nanoparticles

New ‘liquid metal’ composite material enables recyclable, flexible and reconfigurable electronics

Extinction rates have slowed across many plant and animal groups, study shows

Tiny fossil bone helps unlock history of the bowerbird

AI tool beats humans at detecting parasites in stool samples, Utah study finds

Innovative biochar research to boost circular economy: Join live talk by Prof. Salah Jellali on October 29

Early life sugar restriction linked to lasting heart benefits in adulthood

The Lancet: Study confirms cardiovascular benefits of semaglutide beyond weight loss

‘Weight loss’ drug helps heart regardless of amount of weight lost

First truly global picture of wide inequalities in care for women’s cancers

International Consortium of Women’s Mental Health Experts present scientific evidence to support classification of postpartum psychosis as a distinct disease

PET imaging of inflammation predicts recovery, guides therapy after heart attack

Pennington Biomedical awarded renewal of NIH-funded Center to Advance Metabolic Disease Research and train future scientists

Planetary scientists link Jupiter’s birth to Earth’s formation zone

University of Louisville, UofL Health receive $11.5 million to develop new cancer immunotherapies

Survey: Californians don’t know cannabis driving laws

Gum disease and cavities linked to increased stroke risk

Gum disease associated with changes in the brain

Brian Cleary awarded $2.25 million NIH grant to advance single-cell gene expression research

Gut parasites identified from feces of ancient Mexican people

Remission achievable for 1 in 3 Indian diabetics through intensive app-based lifestyle program

Idiopathic hypersomnia is a rare disease of excessive sleepiness, with patients revealing they never feel rested or awake no matter how much sleep they get, in analysis of online posts

Backyard birders in South Africa may continue to enjoy biodiversity in visiting birds under climate change scenarios, while climate change and declining biodiversity may decrease birding in protected

Ingestible pill developed to diagnose intestinal disorder

‘Chronic lung-transplant rejection has been a black box.’ New study gives answers, drug targets.

Neutrino experiments in US and Japan join forces

Hunting for the chromosomal genes that break the heart

Trial enrollment and survival disparities among patients with advanced epithelial ovarian carcinoma

[Press-News.org] DNA detectives able to 'count' thousands of fish using as little as a glass of water