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#1
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Genetic fingerprints
The Feb issue of 'Orchids' has a nice article that's way over my head on the
genetic fingerprint for Phrag. kovachii. Finally I can see the results of a so-called fingerprint and I can see how the A,T,G and C's all match up - so I can see how they'd be valuable in forensics. Now. How does one recognise and isolate one individual from another? Is "CSI/Orchids" our next TV program? K Barrett (Yes, I'm amazed you have to explain this to me. I *love* reading forensic murder mysteries, yet I know that the forensic DNA PCR tests that are used in a court of law only check 9 or so places in order to determine within a certain probability that the DNA in question comes from a certain individual or not. However the article makes note that 'they' will be using the genome of P. kovachii to forensically identify individuals - presumably tracking them from known source materials - and tracking the use of this 'known source DNA' in hybrids. Surely making P. kovachii one of the best (worst) known and tracked individuals on the planet! I tell you, its a Shakespearian tale! - A tale told by an idiot, full of wind and fury, signifying nothing...) |
#2
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The basic idea is to use an enzyme (restriction enzyme) to cut the
organism's DNA strands at particular base sequence (ATGC...) regions. The resulting pieces are placed on a gel and an electrical field is applied to the gel causing the pieces to move across the gel at pacing that varies with fragment size. After awhile, the various fragments form separate bands that can be compared to other sample. The possibility of having two digestion results that match that are not in truth identical is low. Refinements of this technique, and other evidence, bring the mismatch rate even lower. Jim ============================================ James Aldridge - Fort Worth, Texas, USA www.JamesAldridge.com - |
#3
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In this instance they tested 4 separate plants of Phrag kovachii and the
resultant DNA sequences were all the same. Wouldn't there have been some sort of difference in their DNA if they were individuals? I'm thinking they tested 4 plants that were pieces of one original plant. Some Phrags will make separate plantlets along one long rhizome, like besseae for example. I'm wondering if all kovachiis aren't really from one plant, that they are a clone - like what happens with sea anemones. (Sorry, that's what I have my degree in, so that's what I fall back on) K Barrett "James Aldridge" wrote in message ... The basic idea is to use an enzyme (restriction enzyme) to cut the organism's DNA strands at particular base sequence (ATGC...) regions. The resulting pieces are placed on a gel and an electrical field is applied to the gel causing the pieces to move across the gel at pacing that varies with fragment size. After awhile, the various fragments form separate bands that can be compared to other sample. The possibility of having two digestion results that match that are not in truth identical is low. Refinements of this technique, and other evidence, bring the mismatch rate even lower. Jim ============================================ James Aldridge - Fort Worth, Texas, USA www.JamesAldridge.com - |
#4
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K Barrett wrote:
In this instance they tested 4 separate plants of Phrag kovachii and the resultant DNA sequences were all the same. Wouldn't there have been some sort of difference in their DNA if they were individuals?................. If you can believe that more than 98% of human DNA is identical to chimpanzee DNA, it makes it easier to believe that they would find zero difference between four different (but probably closely related) kovachii plants. Keep in mind that I'm not talking about the DNA actually having zero difference. I'm assuming that Jim is right about how the analysis was done. Breaking up the DNA strands at certain points still allows for some undetected differences in between the breaks. When pictures of different kovachii plants started to hit the print and the internet, there seemed to be some obvious differences between plants. If someone could map the entire genome of these different plants, then some little variations would be seen. Steve |
#5
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Though I feel it would be more appropriate to comment in two weeks when
I receive my copy here at the end of the postal world, Ohio, if we must jump the gun, I take my cue from your note to OGD quoting the article I won't see for fourteen more days: On page 135, second paragraph they write "The individual and combined analyses demonstrate the distinctiveness of the molecular sequence data of Phrag. kovachii. All four plants of Phrag. kovachii were identical for each sequence analysed." I think the key phrase is: "for each sequence analyzed". Indicating to me that only certain parts of its DNA were analyzed. I'm not entirely sure, but think items ALL of whose DNA has been sequenced are pretty rare. |
#6
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tennis maynard wrote:
Though I feel it would be more appropriate to comment in two weeks when I receive my copy here at the end of the postal world, Ohio, if we must jump the gun, I take my cue from your note to OGD quoting the article I won't see for fourteen more days: On page 135, second paragraph they write "The individual and combined analyses demonstrate the distinctiveness of the molecular sequence data of Phrag. kovachii. All four plants of Phrag. kovachii were identical for each sequence analysed." I think the key phrase is: "for each sequence analyzed". Indicating to me that only certain parts of its DNA were analyzed. I'm not entirely sure, but think items ALL of whose DNA has been sequenced are pretty rare. Why yes, I am a bioinformatician... This is what I do for a living. I haven't seen the article on P. kovachii yet (and knowing how things work, might not for a week). However, it is not at all unusual that they might sequence four markers with identical sequence. Why? They probably have selected genes that they know are well conserved. While it is true that these genes will vary in sequence across long evolutionary distances, they don't vary that much in the short term. In fact, if they were really variable, we could never use those sequences to determine the relationship between kovachii and other phragmipediums. In a very abstract and simplified nutshell, it is the difference between the marker sequences that gives an indication of how far apart (in time) two species are. If you have only a few changes between the species, you hypothesize that they are closely related. More changes indicate that they may be more distantly related. However, you can't have too many changes. Why does P. kovachii look so different (even amongst themselves) if they are identical at these four markers? Simple, these markers are derived from genes that are required for survival (Cytochrome C, ribosomal proteins, etc). The four examined don't reflect even a tiny percentage of all the genes in the organism. Genes that have absolutely required functions can't change that much (or they lose function). Genes for flower size, color, and other things can (and do) vary quite a bit, even in the same population. Quite a bit means (in humans, which have been most studied for obvious reasons) 1 in every 100 bases or so. Does that help? Rob -- Rob's Rules: http://www.msu.edu/~halgren 1) There is always room for one more orchid 2) There is always room for two more orchids 2a) See rule 1 3) When one has insufficient credit to obtain more orchids, obtain more credit LittlefrogFarm - Growing the plants Rob likes. ) |
#7
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You have a degree in sea anemones? Or do you mean marine biology?
Just curious, Murri "K Barrett" wrote in message ... In this instance they tested 4 separate plants of Phrag kovachii and the resultant DNA sequences were all the same. Wouldn't there have been some sort of difference in their DNA if they were individuals? I'm thinking they tested 4 plants that were pieces of one original plant. Some Phrags will make separate plantlets along one long rhizome, like besseae for example. I'm wondering if all kovachiis aren't really from one plant, that they are a clone - like what happens with sea anemones. (Sorry, that's what I have my degree in, so that's what I fall back on) K Barrett "James Aldridge" wrote in message ... The basic idea is to use an enzyme (restriction enzyme) to cut the organism's DNA strands at particular base sequence (ATGC...) regions. The resulting pieces are placed on a gel and an electrical field is applied to the gel causing the pieces to move across the gel at pacing that varies with fragment size. After awhile, the various fragments form separate bands that can be compared to other sample. The possibility of having two digestion results that match that are not in truth identical is low. Refinements of this technique, and other evidence, bring the mismatch rate even lower. Jim ============================================ James Aldridge - Fort Worth, Texas, USA www.JamesAldridge.com - |
#8
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*laughing at imagining Kathy with a degree solely in sea anemones*
*laughing again at how she would decorate the waiting room at her dentistry practice today if she had a degree in sea anemones* -Eric in SF www.orchidphotos.org "Lady Blacksword" wrote in message ... You have a degree in sea anemones? Or do you mean marine biology? Just curious, |
#9
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Eric Hunt wrote:
*laughing at imagining Kathy with a degree solely in sea anemones* *laughing again at how she would decorate the waiting room at her dentistry practice today if she had a degree in sea anemones* Eric, you haven't seen her office, have you? Steve (just kidding, I haven't seen it either) |
#10
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Don't laugh! My land lady painted my office building's hallways with a
truly horrid red and blue sponge-paint technique that simply begs to have little Nemo-like fish poking their heads from beneath it. Makes me (and the architect next door) shudder whenever we venture out to get the mail. He swears his clientele thinks it a reflection of his taste and that business has dropped off since she did it last year. Personally, I think his lease is up for negociation.... The degree was actually called "Aquatic Biology", in that there was some limnology tossed in there, too. Nevertheless it was all so long ago that it seems a dream now. K "Eric Hunt" wrote in message ... *laughing at imagining Kathy with a degree solely in sea anemones* *laughing again at how she would decorate the waiting room at her dentistry practice today if she had a degree in sea anemones* -Eric in SF www.orchidphotos.org "Lady Blacksword" wrote in message ... You have a degree in sea anemones? Or do you mean marine biology? Just curious, |
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