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Thread: Barcodes for tracking species

  1. #1 Barcodes for tracking species 
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    I just read today in Science Daily -article - Genetic Markers for Tracking Species: Barcodes. It stated that there are sections of our DNA that are different for each species. They want to use 4 colors as "barcodes" that correspond to one of the letters of the genetic code. My question is, "How can 4 colors or letters cover the entire biodiversity on this planet?


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    Brassica oleracea Strange's Avatar
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    Genes are encoded using four bases (guanine, adenine, thymine and cytosine). These are "read" in groups of three to define the sequence of amino acids in a protein defined by the gene. So, presumably, the 4 color barcode represents the sequence of these four bases.


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    Quote Originally Posted by Strange View Post
    Genes are encoded using four bases (guanine, adenine, thymine and cytosine). These are "read" in groups of three to define the sequence of amino acids in a protein defined by the gene. So, presumably, the 4 color barcode represents the sequence of these four bases.
    So the arrangement of this 4 color barcode can identify each and every species?
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    As far as I can tell, it is not an actual barcode, that you run through a scanner like in the supermarket checkout line. I don't think there are actually colors used, either. That's just an analogy.

    Capillary electrophoresis of multigene barc... [Methods Mol Biol. 2012] - PubMed - NCBI

    Recently, the term "DNA barcoding" has been coined to describe the use of a short gene sequence from a standardized region of the genome as a molecular tool for species identification.
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    Brassica oleracea Strange's Avatar
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    Quote Originally Posted by Barbi View Post
    So the arrangement of this 4 color barcode can identify each and every species?
    Presumably, if you take a long enough sequence from the right part of the genome.

    Remember that if you do this for the entire genome, you can identify every individual organism. And, in fact, you don't have to look at the entire genome. DNA identification in criminal investigation, for example, looks at a small number of locations that tend to differ between individuals such that a given profile is very unlikely to be shared by two people.
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    Quote Originally Posted by Strange View Post
    Quote Originally Posted by Barbi View Post
    So the arrangement of this 4 color barcode can identify each and every species?
    Presumably, if you take a long enough sequence from the right part of the genome.

    Remember that if you do this for the entire genome, you can identify every individual organism. And, in fact, you don't have to look at the entire genome. DNA identification in criminal investigation, for example, looks at a small number of locations that tend to differ between individuals such that a given profile is very unlikely to be shared by two people.
    Actually on forensic science they look at non coding heritage markers, in heavily mutating DNA segments, at the edges of the bends forming the chromosomes. Well, say a chromosome is an H, then the left and the right side is covered with TATATATA sequences to provide flexibility. In the intronic sequences anyway. These TATATA, have several small mutations of A->C so C-G and on another account the G->T can break it back to T-A. This is where forensic scientists look at. The number of corresponding sequences of certain parts of the human genome. They have chosen a primer that is aselective, and mostly shows multiple bands in replication. They take PCR clonation time into the equation. So at average there are 10-30 pieces of DNA that get enough coverage to form a Clone to implicate the Forward and reverse primer at the same time, with only using less then 1000 basepairs in between. They will see a random pattern, which is compared to some known standards DNA, the culprit, the victim and some other controls.

    I'm just saying that this part of forensic science is totally random use of a non specific primer in a Junk DNA region (can incorporate valid DNA, this will mostly show the same among everyone)
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    In a blind study where a scientists does not know the species of the genome, they can now identify what it is from looking at certain sequences of the DNA?
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    Brassica oleracea Strange's Avatar
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    Quote Originally Posted by Barbi View Post
    In a blind study where a scientists does not know the species of the genome, they can now identify what it is from looking at certain sequences of the DNA?
    Yes. You sound surprised. This is used in food testing, for example, to make sure the "chicken" in that seedy restaurant really is chicken and not ...
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    Quote Originally Posted by Strange View Post
    Quote Originally Posted by Barbi View Post
    In a blind study where a scientists does not know the species of the genome, they can now identify what it is from looking at certain sequences of the DNA?
    Yes. You sound surprised. This is used in food testing, for example, to make sure the "chicken" in that seedy restaurant really is chicken and not ...
    Yes, I am surprised because I asked this very question on other well known science forums a year ago and they said it couldn't be done in a blind study.
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    Yes, it could be done to test chicken, but i was thinking more like, does this product contain peanuts, or other allergens.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    The article is found at : Genetic markers for tracking species: Barcodes

    T
    here relevent bit is :

    " "In the DNA of living beings, we have identified sections as "DNA barcodes" that, while being almost identical within a certain species, differ among the various species," explained Prof. Dr. Dietmar Quandt from the Nees Institute for Biodiversity of Plants at the University of Bonn. "Based on these markers, we can then identify species unambiguously and relatively fast." The result of this analysis resembles a barcode at the supermarket; only that it does not come in black and white, but in four colors, with each one corresponding to one of the four letters of the genetic code."
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    Brassica oleracea Strange's Avatar
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    Quote Originally Posted by Barbi View Post
    Yes, I am surprised because I asked this very question on other well known science forums a year ago and they said it couldn't be done in a blind study.
    Bear in mind that you can't just take a sample and ask "which of the 100 million [or whatever] species on earth is this?". You can only test the sample against known species that have had their genome analysed. That is what this "barcode" project is about; building up such a library of species data.

    The progress in the technology is amazing. It took over 15 years, I think, to map the first human genome. Now a new organism can be done in days or hours.
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    The press release is a little misleading in that it sort of gives the impression that DNA barcoding has just been invented. This group has just used a different genomic region as a marker than that which is normally used for plants. Probably a more reliable marker, or combination of markers, or something. The press release wasn't particularly forthcoming on the details.

    Ideally, you want to sequence some region that evolves quite quickly. Fast enough for differences to exist between species, but not too fast that it becomes useless and ends up identifying everything as unique. In animals studies, parts of a gene for a sub-unit of the cytochrome c oxidase enzyme are typically used. This gene sits on the quickly-mutating mitochondrial DNA.

    DNA sequencing machines typically spit out their results in colourful patterns such as these:








    You can take those four colours and fashion a barcode from it, for fun, like this:


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    Why is the mitochondrial DNA preferred over the nucleur DNA since this has most of the mitochondrial DNA?
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    If you used nuclear-encoded genes it's more than likely you'd not see any difference when comparing closely related species. You'd probably end up with a "barcode" (just a DNA sequence) that was very coarse-grained and not of much use for the intended purpose. On the other hand, if you sequenced the highly variable parts, like the tandem repeats, you'd have a barcode so fine-grained that you'd be able to distinguish individuals from each other - basically a DNA fingerprint. Again, that wouldn't be of much use for species identification. So, your looking for a shortish region that varies a lot between species and not so much within a species.

    Since the interior of the mitochondria isn't a particularly friendly place and the DNA repair process of mitochondria isn't as efficient as that of the nucleus, the mtDNA mutation rate is considerably faster than that of nuclear DNA, perhaps about 10 times faster. This fast mutation rate results in a lot of variability between the mtDNA genomes of different species. The insertion and deletion categories of mutation are also very uncommon in mtDNA, which is a very useful property to have when looking for a sequence to use as a barcode. The use of mitochondrial sequences for species identification goes back to at least 2002, possibly before.

    Plant barcoding studies have often used chloroplast genes,

    It's a sad fact that the ability of biologists to go out into the field and identify species is a fast-disappearing skill. Less training and less funding coupled with the fact there are millions of species means that we might become reliant on such barcoding technologies to identify species.
    Last edited by Zwirko; April 28th, 2012 at 05:55 AM. Reason: major spelling gaff
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    Quote Originally Posted by Zwirko View Post
    If you used nuclear-encoded genes it's more than likely you'd not see any difference when comparing closely related species. You'd probably end up with a "barcode" (just a DNA sequence) that was very coarse-grained and not of much use for the intended purpose. On the other hand, if you sequenced the highly variable parts, like the tandem repeats, you'd have a barcode so fine-grained that you'd be able to distinguish individuals from each other - basically a DNA fingerprint. Again, that wouldn't be of much use for species identification. So, your looking for a shortish region that varies a lot between species and not so much within a species.

    Since the interior of the mitochondria isn't a particularly friendly place and the DNA repair process of mitochondria isn't as efficient as that of the nucleus, the mtDNA mutation rate is considerably faster than that of nuclear DNA, perhaps about 10 times faster. This fast mutation rate results in a lot of variability between the mtDNA genomes of different species. The insertion and deletion categories of mutation are also very uncommon in mtDNA, which is a very useful property to have when looking for a sequence to use as a barcode. The use of mitochondrial sequences for species identification goes back to at least 2002, possibly before.

    Plant barcoding studies have often used chloroplast genes,

    It's a sad fact that the ability of biologists to go out into the field and identify species is a fast-disappearing skill. Less training and less funding coupled with the fact there are millions of species means that we might become reliant on such barcoding technologies to identify species.
    My understanding of mtDNA have structures that convert the energy from food into a form cells can use and involved in converting oxygen into ATP. The mutation rate to me would indicate precursors of one of the many diseases associated with the mitochondria and this I assume would indicate a bell curve within all differents groups of species in the individuals. I don't understand why this would be preferred in identifying species.
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    Quote Originally Posted by Zwirko View Post
    Since the interior of the mitochondria isn't a particularly friendly place and the DNA repair process of mitochondria isn't as efficient as that of the nucleus, the mtDNA mutation rate is considerably faster than that of nuclear DNA, perhaps about 10 times faster.
    To be honest, i didn't know that yet. Interesting. I knew mitochondrial DNA had a problem with his DNA repair system, but to identify species with it. It sounds logical though.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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