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Posts posted by Bluenoise

  1. Okay seems no one has actionally answered the original question of what factors are involved.


    Here is a simplified version of alternative splicing. Basically there is a site (adenine residue) in every intron where a loop forms making the intron into a structure called a lariat. This lariat is then released and degraded bringing the adjacent introns together. Now if you were to coverup one of these sites the other end of the loop would have nowhere to connect to so instead it connects to the site on the next adjacent intron. Now since there is an exon between these two introns this exon would end up being part of the loop on the lariat. So when the lariat is released and the the adjacent exons bind you loose one exon in the lariat.


    So possible factors could be anything that signals a protein or RNA to cover up this site.


    Now if the cell covers up different sites and cuts them in different orders you can get a huge varient of products.


    Now the process is far more complicated than this. (as is everything to do with Eukaryotes) But that's the gist of one mechanism.


    There are also two other mechanism I can think of that give alternative gene products. I wont go into detail in these since well I don't know them too well.

    Both of these aren't know to occur is animals.


    Trans-splicing occurs in some organisms and involves two different genes splicing togething to give multiple products at the same time.


    Transcript editing is another process that occurs primarily in some mitochondria and chloroplasts where a Guide RNA is used as a template to introduce U residues into mRNA.



    Now all of this is pretty standard knowledge that can be found in almost any good latest edition molecular biology textbook. So I'm unsure why the new scientist article is title "one gene one protein dogma no longer true" All this has been know for about half decade now.

    Maybe I'll dig up the article later. The abstract isn't very specific


    It really is truely amazing how you can have a few genes coding for factors that recursively allow them to code for far more.

  2. Read Jared Diamond's [u']Guns, Germs and Steel[/u]


    Just to repeat it since it was such a good answer.


    Basically it comes down to natural resources. (species available for domestication with good potential)

    And the benefits of Eurasian having a east-west axis.


    If you want an explaination of why exactley these help.


    Read Jared Diamond's [u']Guns, Germs and Steel[/u]
  3. Well It's now well know that genes can be spliced with different combinations of exons to different mRNA's. Actually most of the diversity between us and other mammals results not so much from having different genes but from having different splicing arrangements on the genes we share.

    I'm not sure how they see intron influence as being a stronger case for more then one protein then alternative splicing arrangements. Maybe the mean that it's thought that introns play a large role in regulating how exons are combined? Or the somehow lead to different post translational modifications?

    It's be really nice if you could supply a link or reference at least for that article. :)


    What factors, well you could devide the factors into two types environmental meaning anything coming from outside of the cell and the cells own internal programming. During development when your cells differentiate from stem cells they are giving specific tasks and programs. These cause them to splice mRNA differently, as well as other things.


    I'm pretty sure patterns of methylation are the main factor.. but I'm really tired now and I'll get my sleep and post when I can think/remmeber properly.

  4. Hmmmm heating water to make steam and cause pistons to move....


    .... Sounds a hell of a lot like a steam engine to me.

    Would have been a good idea if you came up with this a few hundred years ago :D


    And how do you propose to heat the water to expand it? Remember heating water takes energy. Gas expands because it's combustion releases energy.

  5. Think about it this way. With no function and thus no natural selection there is no positive force maintaining the presence of this organ. When there is a random mutation between generations that effects this organ there is no force selecting against mutations that might degrade the organ. Since there are far more mutations to genes that could occur that would destroy this organ than maintain it, it's coding eventually looses those regions as they get randomized to oblivion or to surving other usefull functions, and the organ goes.

    Not to mention that without a funtion maintaining the organ it is a pointless load on the metabolism and would probably have natural selection acting against it. i.e. evolving a more efficient organism by removal of unnecessary load.


    At least that's my take on it...

  6. Yeah heat works well, and air, and moisture. I remember a recent documentry about this landfill project that moistense and exposes the garbage to more gas circulation. They achieve far greature decomposition rates. (Plus all the increased activity from the gas/water also raises the temperature and has an even greater effect.)

  7. AH I see I see. Why would I suck it out with a pipette? Sure it'd look better? The idea is to evaporate it and get it more concentrated. Because I put to much water in which diluted it to much.


    I think I'm just going to weigh a new sample. An hour in the oven isn't much really, it would have been nice to have it free though.

  8. As an added note I think that the biggest problem with RNAi use currently is directing it to the site of interest. It's in a long double stranded form originally I think. Injecting RNA into someones blood streem will not have any effect since it will not be take up by cells. Some sort of vector is necessary. I remember reading a paper earlier about linking it to a protein to facilitated transport across the cell membrane that got some results. A virus should work fine as well.

  9. RNAi doesn't block a ribosome from translating mRNA per se.

    It binds to the mRNA strand which causes machienery within the cell to mark it for being cut into smaller fragments. These smaller fragments produced actually act simular to the RNAi and have a kind of cascade chain reaction mechanism that silences the translation of the gene. Well that's at least how I remember it.


    Nature has a good section on it acutally if you have time. With a really cool video.


    here's the link for the animation.



    And here's the link for the main page of thier focus.


  10. THis is just a quick question. I have a solution of ~0.01M primary standard Potassium iodate (KIO3)made up that happened to accidently get filled past the mark on a volumetric flask. So my question is if I leave it out for a couple of nights in a dark place to evaporate down to the mark will I loose a noticible amount of KIO3

  11. If the reason we don't have restriction enzymes is because methylation is reserved for higher purposes, then it'd make sense that RENs are able to enter the nuclues. If they couldn't methylation wouldn't matter either way. So either evolution didn't create REN's that are not able to acess Eukaryotic DNA, or having REN'S not active towards the Host's Chromosome lowers their usefullness to the point where they wouldn't be maintained in an Eukaryotic population. If they can't cut out of the nucleus, some viral DNA might still slip by and infect it at which point it'd be safe from restriction enzymes. Maybe the metabolic load of maintaining enough REN to be usefull might also be too high, we have other imune defenses already.

    Yeah lots of questions.

  12. I think the main question you should ask is why do Eukaryotes not have restriction enzymes in the first place? They seem like a very valuable defense so there might be a good reason behind their absense. I'll ask molecular biology proff of mine and see what she has to say.


    Here's something you should think of. HIV is a retero virus, so it doesn't contain DNA. If the reverse transcription happens in a manner where the DNA might get into the nucleus before the REN can get to it then you might need a REN that has to be able to access the neucleus to remove it. Which would also require methylase activity to protect the host. hmm

  13. Just a running thought here.


    Well microbes that produce REN's have thier REN sites methylated to protect themselves right? So wouldn't producing functional REN's in eukaryotes lacking these protection cut-up thier own DNA? Assuming the REN is capable of moving accross the nuclear membrane.


    There should be no reason why the ORF cannot be properly transcribed and translated. I guess It boils down to

    1) if the protein produced will be functional (my guess yes).

    2) What interaction said REN if functional will have with a eukaryotic cell.

    I think this second question is where the problem lies that either the cell will actively degrade the REN or that the REN will degrade your hosts DNA. So you'd either get no RENS, or a cell that dies once properly modified.

  14. if: cos(ln(x+1)) = 0


    use: 0 = cos(pi/2 + n*pi)


    cos(ln(x+1)) = cos(pi/2 + n*pi)

    ln(x+1) = pi/2 + n*pi

    x+1 = e^(pi/2 + n*pi)


    therefor: x = e^(pi/2 + n*pi) - 1


    I believe that's it. But correct me if I'm wrong. I'm just a poor biochemist who tried to escape math a long time ago

  15. Hi I'm bluenoise as the title says. You can call me Casper.

    I'm currently majoring in Biochemistry in Canada, though I'd like to think that my interests touch upon every area of science (probably not though).

    Currently I've been lurking on these forums just reading the occasional thread as I've been pretty swamped latley. But I'd love to post more and discuss once I get some freedom. :cool:

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