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Thread: how can we find mutations

  1. #1 how can we find mutations 
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    I know how they work, but how can we find a mutation?
    And whats the evidence that they even exist.
    (i just want to know the evidence, because im interested. i'm not refuting genetics)


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  3. #2  
    Forum Ph.D. Heinsbergrelatz's Avatar
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    DNA microarray- this multiplex technology can be used to genetically probe down genes. thereby carrying out genetic tests et cetera


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    Forum Cosmic Wizard spuriousmonkey's Avatar
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    Microarrays aren't commonly used to find mutations.
    "Kill them all and let God sort them out."

    - Arnaud Amalric

    http://spuriousforums.com/index.php
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  5. #4  
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    what is commonly used then?
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    Mutations exhibit themselves phenotypically as new characteristics which are inherited. For example ; the human haemophilia mutation will suddenly appear in a family line. It will appear among individuals in the direct line of descent till, a few generations later, it is weeded out by natural selection.

    The appearance and inheritance of the haemophilia mutation is shown on a chart in the following reference, as it was among the European royal families.
    http://www.sciencecases.org/hemo/hemo.asp

    As a beginning student of biology at university, I saw mutations among the fruit flies we bred. Abnormal traits such as white eye, stunted wing, etc., would appear out of nowhere in a line of descent of fruit flies.

    This was well before genome analysis capability. We knew these were mutations by their sudden appearance in one individual and their inheritance down a line of descent.
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  7. #6  
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    then how do we know/did we find out it's in the dna, the mutation?
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  8. #7  
    Forum Ph.D. Heinsbergrelatz's Avatar
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    Microarrays aren't commonly used to find mutations.
    but they still use it right? i heard one of our professors tell our class an information about Microarrays, and he said one of them was for probing down genes..
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  9. #8  
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    'then how do we know/did we find out it's in the dna, the mutation?'

    You can sequence the DNA. There are a number of ways of doing this, for example the Sanger/dideoxy- method. If you sequence the DNA before and after the mutation, you can see, for example, what base change has occurred in the DNA. You can then decipher the resulting new amino acid sequence encoded by the mRNA transcript from that gene (assuming the mutation occurs in a protein-encoding part of the genome). This may give you hints as to the molecular basis for any macroscopic phenotypic changes you observe.

    All the best,

    Tridimity :wink:
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    isn't measuring the actual base very time-consuming, and for that reason not used very often?
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  11. #10  
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    Dear Questioner,

    'isn't measuring the actual base very time-consuming, and for that reason not used very often?'

    It probably can be time-consuming, and also potentially quite expensive. As others have highlighted, there are other ways of detecting mutations besdies sequencing. I guess it would really depend on the situation; on the reason for detecting the mutation. For example, if you had generated mutants for future use in an experimental system, the results of which you wanted to publish in a scientific journal, then you may well use sequencing in order to be able to confirm for sure that the mutants you have generated are correct.

    Best wishes,

    Tridimity 8)
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  12. #11  
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    Quote Originally Posted by questioner1
    isn't measuring the actual base very time-consuming, and for that reason not used very often?
    DNA sequencing is fast, cheap and routine. At my University we have a core facility which can give you around a kilobase of sequencing data back in a couple of hours for just 8 ($12 US). However, you do need to know a little about the sequence in the first place to be able to design an appropriate primer for the sequencing enzyme to use.
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    Why is the human genome project so expensive then?

    And does it work with one cell at a time? Or do you need multiple cells?
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  14. #13  
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    Simply because it's so large. The human genome is around 3,200,000,000 base pairs in size. If I were to break it up into 3.2 million fragments that were 1 kb long it would cost me 3.2 million x 8 = 25.6 million to sequence the lot!

    In reality you can expect to pay 10-50k for a whole human genome sequence, and technological progress is continually pushing this figure lower.

    You can do it from a single human cell if necessary, since most cells contain the entire 3,200,000,000 base pair genome.
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  15. #14  
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    If you want to test the genome of a certain bacterial colony, would you use one bacterium or more? wouldn't using more give a distoreted image, because the genome varies between individuals?
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  16. #15  
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    The human genome project cost allot because it was the first one we did, over time the cost and time of doing one has decreased rapidly and current estimates are suggesting by 2030 we could do a whole genome in less than a day, for less than $500
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  17. #16  
    Forum Freshman electricant's Avatar
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    Quote Originally Posted by questioner1
    If you want to test the genome of a certain bacterial colony, would you use one bacterium or more? wouldn't using more give a distoreted image, because the genome varies between individuals?
    This is a smart question, and its a tricky one to address. When you see a petri dish with the little bacterial colonies on it, each one is the result of a single original bacterium which has been allowed to divide through dozens of generations until you have a visible colony which consists of billions of bacteria with essentially identical genomes. In ideal situations bacteria can double every 30 mins, so one cell can become 2^48 cells in just one day (thats over 280 trillion cells!).

    Its easy to isolate individual bacteria in this way by either diluting the bacterial culture enough or using a simple technique called streak plating. Then you can start a fresh culture which is descended entirely from one original bacterium. However, you need to consider the background mutation rate in bacteria. A quick internet search suggests that a new mutation arises once every 1200 cells for a bacterium like E. coli. When you are growing billions of cells overnight in a colony you are going to get a large amount of spontaneous mutations arising, so it is impossible to isolate an entirely genetically identical bacterial population.

    There are solutions like trying to PCR the DNA from a single cell to try to get enough to sequence but this itself is going to introduce errors (and probably at a faster rate than in the bacteria themselves). Your sequencing method is also not 100% reliable so you will get errors there as well.

    The best that we can really do is keep sequencing from the same sample, then average out the data until we eliminate most of the errors.
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