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Biotech Science

DNA Detectives Count Thousands of Fish Using a Glass of Water 61

Posted by samzenpus
from the where's-walleye dept.
vinces99 writes "A mere glass full of water from Monterey Bay Aquarium's 1.2 million-gallon Open Sea tank is all scientists really needed to identify the Pacific Bluefin tuna, dolphinfish and most of the other 13,000 fish swimming there. Researchers also discerned 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. '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."
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DNA Detectives Count Thousands of Fish Using a Glass of Water

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  • by Anonymous Coward

    Fish do piss in the water.

  • by Anonymous Coward

    Fish use glasses of water?

  • Also, for the squeamish, fish, whales, penguins, sharks, jellyfish and manta rays don't use condoms. Not sure about crocodiles or wombats.

    • by Anonymous Coward

      I can confirm that I didn't use a condom with my wombat.

  • yeah (Score:5, Funny)

    by hamburger lady (218108) on Wednesday January 15, 2014 @09:00PM (#45971629)

    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

    "the machine says that by far the pacific is full of a fish called...poly vinyl chloride. hm, that's a funny name."

    • by c0lo (1497653)

      "the machine says that by far the pacific is full of a fish called...poly vinyl chloride. hm, that's a funny name."

      I guess it's more likely to identify the "Poly Yeti Lenne" species - rationale: PVC will sink to the bottom [wikipedia.org] (30-45% denser than the water).

  • You can scan a hotel room and the biologicals will light up like a 70's blacklight poster.

    Why would you do that to yourself, for Odin's sake, if you planned to ever sleep in a hotel bed again?

  • What about... (Score:5, Interesting)

    by c0lo (1497653) on Wednesday January 15, 2014 @09:10PM (#45971711)

    all scientists really needed to identify the Pacific Bluefin tuna, dolphinfish and most of the other 13,000 fish swimming there

    What about species no-one knows about?

    • What about species no-one knows about?

      As with other "soup" DNA techniques those species that they do not have DNA information for (I'm using this term loosely) would simply be separated by their genetic differentiation between each other. This is one of the primary problems with identifying species with "Soup" because organisms can be the same distance apart genetically but some may be different species morphologically and others may be the same.

      In a simplified example say you have organisms A, B and C. A and B are closest genetically, A and

      • by c0lo (1497653)

        In a simplified example say you have organisms A, B and C. A and B are closest genetically, A and C are furthest away while B and C are the same distance away from each other. One would look at this and assume A, B and C are separate species. However you then observe in the wild that B and C are able to breed, perhaps B and C are one species while A is separate? This is one of many examples of how genetic information can mislead species information

        Fine and dandy.
        Now, let's take another case: you know species A, you know nothing about B and C. Thus you can tell "A was here" but... can you tell there are other (exactly) two that "were here" as well? Maybe they were only one, maybe more than two. How can you tell?

        • Fine and dandy.
          Now, let's take another case: you know species A, you know nothing about B and C. Thus you can tell "A was here" but... can you tell there are other (exactly) two that "were here" as well? Maybe they were only one, maybe more than two. How can you tell?

          Welp, that's exactly the problem, that isn't to say there aren't other methods though. For example you could see how much genetic differentiation there is between known species in the area and make assumptions based on that. You could also use other types of DNA, mitochondrial DNA for example which may tell a different story.

          Fact is, taxonomists are always fighting about which species is which, sometimes with fruition. DNA, while it is very useful in determining one species from another has added to the

    • by wbr1 (2538558)
      Since not every thing is fully sequenced, I would wager a guess that they search the 'soup' for specific sequences that are known thought to be unique to a species. The rest would just be noise to the data they are seeking. However, if say bluefin tuna had a lesser or unknown related species that also had the same thought to be unique sequence, it could make their estimates high. However if it was an unknown species the fact that it is unknown means that there are probably very few and the difference wo
    • Stick it in some fish embryos and see what grows.

      (Ok maybe it's not possible NOW but give technology a couple decades.)

    • by riverat1 (1048260)

      Well, in the Monterey Bay Aquarium there probably aren't any species that no-one knows about. But there certainly would also be DNA from the various microorganisms in the water as well. That brings to mind that the water in the tank comes from the ocean anyway and I doubt the filtering is good enough to remove all traces of "wild" DNA before it goes in the tank. So maybe they would find DNA from and unknown species.

    • This technique will be used to identify them. It's already being used to that end. I went to a seminar talk years ago which was taking samples of sea water and sequencing every bit of DNA they could amplify from them, much like this. There's a problem in microbiology where what you can see under a microscope doesn't match what you can grow on an agar dish (which is necessary to really study something: you can't very well study a single bacterium cell.)

      The take home message was we don't know anything
  • Next step (Score:5, Funny)

    by easyTree (1042254) on Wednesday January 15, 2014 @09:12PM (#45971727)

    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

    Followed swiftly by fish taxation.

  • Now you've ruined my winter vacation, and while I'm sitting on the beach sipping rum I'll know if I go in the ocean I'll be covered in fish goo.

    *sigh* I'll just have to have another rum. Purely to fight infections you understand.

    • by pcwhalen (230935)

      Put lime in it. Wards off scurvy.

      You're welcome. And wear 50.

      • by gstoddart (321705)

        Put lime in it. Wards off scurvy.

        With some bitters, sugar and mint leaves, we call that a mojito. ;-)

        And wear 50.

        LOL, already on it.

        • by ruir (2709173)
          Actually it have been proved by consumer bodies factors above 35 dont work any better and they are just a scam to rip you off.
          • by gstoddart (321705)

            Actually it have been proved by consumer bodies factors above 35 dont work any better and they are just a scam to rip you off.

            Given my pasty white complexion, I'll err on the side of caution.

            Since 50 doesn't cost any more than 35 in my experience, what's the 'scam' part here?

    • by riverat1 (1048260)

      Don't worry about it, the alcohol in your rum is the piss/shit of yeast cells.

  • But can it tell them when they're gonna need a bigger boat?

    http://www.wingclips.com/movie-clips/jaws/a-bigger-boat [wingclips.com]

  • This is really cool, great use of modern tech! I am curious as to which species they could not detect, and why they think that is? Too small of a population? Too small in size? Sampling size possibly not big enough? It seems like they would want to answer these questions as well.
    • I know this is bad form to reply to your own post. Answering some of my own questions, after catching something I missed reading the article the first pass. "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." Sharks and turtles are pretty big ones to miss, I hope they get this worked out, it sounds really promising in coming up with real numbers about the health of our oceans species versus
  • And you can use the same method at the sewage stations to be able to count the number of individuals in a town or city, then separate out the DNA of everyone that's there illegally and track them down.

    Nobody will be safe from our civil masters.

  • So how many salt water fish would they find in the sewers of every city. I think that just because the dna is present doesn't imply or cause the critter to be present. At least not alive.

  • DNA Detectives Count Thousands of Fish Using a Glass of Water
    Researchers also discerned which of the species were most plentiful in the tank.

    Someone doesn't know what counting is (the article had the good grace to put it in scare quotes).

    • by worf_mo (193770) on Thursday January 16, 2014 @08:17AM (#45974775)

      Two decades ago I worked in a small team of “fish counters” to earn something during my time at university. This team was from the local government’s department of environmental protection and headed by a biologist. We’d drive up to a river, pull out our portable generator, drop one pole in the water, and walk in the river with the other pole, stunning the fish between the poles (they don’t die electrocuted, they are just stunned for a little while). We’d fish them out with nets, place them in large buckets and bring them on land, where the biologist counted and classified them before returning them to the river. His reports were then mainly used to assess the damages after an environmental disaster.

      Once we were called to a spot where an oil truck had ended up in a mountain river. While we approached the place we wondered how that could have happened - the road was straight, no obstacles, excellent road conditions. But when we arrived we understood: right before the spot where the truck had left the road was a huge billboard with an underwear ad, featuring a nice young lady in a thong and nothing else. The driver must have craned his neck until the truck touched down in the river.

  • Almost every day I dive past one of the Smithsonian biomass accretion modules in Aqaba Marine Park, Jordan. You can see one of the collection modules here. [google.com]

    If only academic departments/institutions collaborated or communicated a little bit more, maybe the research dollar would go a little further?

    Cheers.

    G

    PADI instructor 636522

There can be no twisted thought without a twisted molecule. -- R. W. Gerard

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