Phage , the virus that cures

Discussion in 'Highly Technical' started by William Gaatjes, Oct 10, 2009.

  1. William Gaatjes

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    I recently saw this documentary about bacteriophages.

    Phage- The virus that cures

    Bacteriophages

    Horizontal gene transfers

    You ask perhaps why i posted this message, well i ask for opinions.

    Long ago i bought a scientific american magazine (i think it was). There was some information about the possibility of horizontal gene transfers.

    My Opinion is that through vertical gene transfers (aka offspring through sexual reproduction) and evolution a complex lifeform can loose genes. But with horizontal gene transfers a complex lifeform can gain genetic code. And not just a few basepairs but an entire sequence.

    EDIT START : I think that it is entirely possible that this gene swapping can also occur between bacteria and viruses and cells of complex lifeforms. Most of the time our error detection/ error correction together with self destruction methods (cell apoptosis) and our immune system combat any change in dna code but radiation( or even cosmic radiation) and toxic materials can cause mailfunction to these error detection/correction systems and our immune system.

    Cell apoptosis


    EDIT END


    Would this statement hold ?

    [​IMG]
     
    #1 William Gaatjes, Oct 10, 2009
    Last edited: Apr 7, 2012
  2. Gibsons

    Gibsons Lifer

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    Which statement?

    The immune system can detect changes in the DNA indirectly, but it's far from foolproof. Also, if the change occurs in germline DNA, the immune system of the developing person will see these changes as "self" and not react to them. There are lots and lots of viral sequences in human DNA.
     
  3. William Gaatjes

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    I agree. But to make things clear the error detection /correction inside the cell itself is responsible for reparing the dna. And if it fails the cell will execute apoptosis. This will then be seen by the immunesystem and the by macrophage engulfed cell is taken to the lymphatic system to begin it's journey in i think our bowls to be secreted.


    This statement : :)

     
  4. Gibsons

    Gibsons Lifer

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    Oh okay. I think both statements are correct.

    Syncytin is a pretty well documented case for gaining a sequence.
     
  5. William Gaatjes

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    Yay for me :)

    I read the link you wrote. I had to look up the explanation of all the words in that article.
    Correct me if i am wrong please :

    In our dna their is a gene coding for a protein that is used to build the envelope (or skin) of the virus. And that the same gene is used in to form the envelope of cells that provide nutrients and protect the blastocyst ? These cells are called trophoblasts ?Later these cells form the placenta ?

    If true, Wow. Might be common but very interesting indeed. Is this a human only feature of have all animals using a placenta exhibit this ?


    EDIT :

    HERV-W , It seems this virus is present in many cancer tissues ?

    Herv-W
     
  6. eggrolls

    eggrolls Senior member

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    Our genome encodes for the proteins embedded in the membrane and the enzymes for phospholipid synthesis.

    Viruses with envelopes get their lipid envelopes from either the cellular cytoplasmic membrane or some membrane-bound organelle such as the endoplasmic reticulum or Golgi. They basically "steal" our cell membranes and embed virally-encoded proteins in them.

    Some viruses don't have lipid envelopes, so their outermost layer is the capsid protein, which is virally encoded.
     
  7. William Gaatjes

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    So it is a chicken or the egg question. I wonder if we can ever find out what the oldest virus is. I know there is some research being done on bones and maybe tissues from extincted animals.

    Although i think that with this virus it perhaps borrowed the cell membrane but gave us some genetic code in return ?

    Something else :
    It is proposed that part of life on earth originated from space and another part came from the earth it self.

    I have some links here with theories and findings about life and how tough it can be.

    Bacteria leaving earth

    Bacteria living in the stratosphere


    UV resisitant bacteria found, working together to shield themselves from UV radation.


    Bacteria might be in more control then we think, Some researches suggest it is bacteria that help form clouds as well. And a hibernating bacteria was found to be claimed to be 250 million years old reanimated when given nutrients.

    spacefaring bacteria

    ice clouds

    Bacteria controlling the airflow in a labexperiment

    I wonder if all these bacteria have phages as well...


    And one more scary parasite to finish the behaviour control part.

    Toxoplasma gondii


    EDIT: Bad links
     
    #7 William Gaatjes, Oct 12, 2009
    Last edited: Nov 11, 2011
  8. Gibsons

    Gibsons Lifer

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    eggrolls covered most of the viral assembly stuff - enveloped viruses (usually but not always) use a bit of host membrane as their envelope.

    As for syncytin in particular, it seems to be necessary for cell fusion at some developmental stages. This makes some sense, as enveloped viruses usually (maybe always) encode a gene that induces membrane fusion (fusion of the viral envelope with host cell or endosomal membrane).

    Difficult for me to sort out just what animals have syncytin and which ones don't. There's more than one, and it's derived from a pretty large family of endogenous retroviruses, so there are homologs, orthologs etc. to worry about. I'd guess all placentals do, but just a guess. Too lazy to blast it right now. :p

    The big picture of what's going on with all the endogenous retroviruses is largely unknown. Roughly 8% of the human genome is apparently derived from viral sequences (can't find the ref, it's in my notes). A lot of these seem to be inactive/degraded/degenerate... But some are not. Some of these do get transcribed in cancer, but I don't think anyone's figured out cause and effect. That doesn't mean that actual infectious virus is produced in those cancers, but it is possible.

    For something interesting and scary, read about the Phoenix virus.
     
  9. William Gaatjes

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    Amazing...

    That virus is scary indeed. But what worries me is there are no enforced guidelines.
    I am sure that the people who work with extinct viruses or lethal ones like polio or the 1918 flu virus do not need enforced guidelines , they know how dangerous the material is they work with. What do you think about this ? Are the precautions taken really that strict ?

    My personal opinion is that almost all cancers must be virus related. I think that toxic materials that cause cancer, are not the primary cause, but a catalyst to jump start the process.

    What was mentioned in the article was interesting :



    Here are some more links about viruses and cancer. Might come in handy, however i would not be surprised you already know about them...

    Cervical cancer

    JC virus

    Virus inside brain tumors.


    EDIT : typing errors and link :

    cache, main memory and mass storage

    active, gene-rich and inactive, gene-poor stretches

    Now does that not sound like cache, main memory and mass storage ? :)

     
  10. Gibsons

    Gibsons Lifer

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    Pretty much a certainty that all cancers are not virus related.

    Of course some are, and there are probably a few that are that we don't know about. But the data for some cancers is way too clean, imo, for their to still be a hidden virus lurking around playing a role.

    Also there are restrictions and regulations on handling infectious material in every country that I'm aware of.
     
  11. William Gaatjes

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    I agree on that :)
    Some cancers are virus related some are not.

    I have been thinking more about toxic materials...
    I do not know all the details when and how specific genes are expressed,
    Can it be that certain toxic materials (causing cancer) cause parts of one gene and parts of the next gene to be expressed ? That codons are no longer seen as end or start codons but as part of a an expression ? Perhaps toxic materials cause havoc on a higher level. Perhaps these toxins influence proteins that certain genes are expressed to much , causing an chemical unbalance ?
     
  12. Gibsons

    Gibsons Lifer

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    The vast majority of carcinogens are mutagens. They cause changes in the DNA sequence of a cell. Some genes cause or regulate cellular growth, and changes in those genes (the right kind of changes) can lead to cancer. There are a few other things that can contribute, but that's the basic idea.

    For a start, look here and here.
     
  13. William Gaatjes

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    Some information about talking bacteria by Bonnie Bassler :

    talking bacteria
     
  14. Chriscross3234

    Chriscross3234 Senior member

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    It's kind of a coincidence that I came across this thread. Tomorrow I meet with my research professor/mentor to discuss the details of my undergraduate research project that involves phage display technology. I guess I'll update when I know exactly what I'm going to do.
     
  15. jagec

    jagec Lifer

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    It is foolish to put your faith in "regulations". As most smart people know, rules created by the ignorant leave huge gaps for the better-informed, and rules created by the well-informed require self-enforcement since the details are simply not understood by anyone else. The fact of the matter is that if a well-trained scientist working in a lab wanted to sneak out some dangerous material, it would simply be a matter of pipetting it into a tube and putting it in their pocket, and then walking right out of the lab. One tube with a clear liquid in it looks much the same as another.
    Now, as far as brewing industrial batches of the stuff is concerned, that would be a little bit harder. But still achievable for someone determined.

    It's only scary if you don't think about the fact that it would be easier and more effective to just buy a bunch of fertilizer and diesel fuel if you wanted to become a mass-murderer. Modern society has placed a great deal of potential power into each and every one of our hands. People rightly fear power, but it's not going away.
     
    #15 jagec, Nov 5, 2009
    Last edited: Nov 5, 2009
  16. Gibsons

    Gibsons Lifer

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    luv XKCD :)

    yes, regulations and rules are only useful if they are enforced and enforceable. One of the scary scenarios is someone setting up a lab in a warehouse somewhere. They just have to know what they're doing, be a bit clever, and have some money. Assuming they don't make some fairly obvious mistakes, I don't see how anyone could catch them until they've done their damage. That's probably what happened with the anthrax attacks.
     
  17. William Gaatjes

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    Indeed.

    The problem occurs the most when the materials used are so called "of the shelf" materials.
    You need a big database to cross-reference what people buy. And that is privacy related.

    To come back to my former posts :

    I found this virus to be intriguing. : SV40.

    http://en.wikipedia.org/wiki/SV40.

    I quote:


    Melanocytes from fetuses seem to be affected by the sv40 virus and may hold an explanation to some melanocyte related cancers. That the chance occurs when the person affected is still in the womb can explain a lot.

    Since not too long ago i learned that the human genome is not big enough to hold our basic blueprint. That not for every step of the process of development and maintenance and for just learning there is a seperate gene. The way we are "build" is by simultaneously switching different but multiple genes on and off.

    It really seems if many of the virus related cancerous diseases are the result of multiple virus infections or a combination of a virus and carcinogen. That our error detection / error correction works great until that system is compromised as well in a cell. Other cancers may even be a combination of carcinogens

    The p53 gene is in effect not the repair agent but the part that stops the cell division from completetion if an error is detected and must be corrected. If the p53 fails, the error correction can not occur and daughter cells with faulty DNA emerge. P53 stalls the cell division process until the dna damage is corrected.

    EDIT: forgot to mention that the p53 also can activate cell apoptosis.

    Amazing when it comes to smoking : Benzopyrene interference causes dna damage. But something must have altered the DNA sequence of p53 already. Because the p53 only halts the division, nothing else. That is , if i can assume that what i have read is correct. This is not really surprising because we inhale air and air is saturated with many particles from organic to inorganic. The air we breath is also filled with bacteria and viruses.





    This may seem as pretty standard, but for me it is just an interest and i find it amazing to see how life works.


    On a Side note, has anybody else encountered that the password system failed on them ?
    I had to reset the password to be able to log in again.
    And when i wanted to change my password, i never got to that specific page.
    I guess there are a few bugs to be worked out. Although i would expect that some tests where done on a test environment prior before the roll out. Perhaps the problem occurred after a certain maximum number of users was encountered.

    I understood that the dailytech forum and the anandtech forum are powered by the same system. My old password still works on dailytech even after the change to a new password for the anandtech forum. It seems the forum is a work in progress. When editting, i can not preview anymore.
    I do find the old version of the forum a bit more relaxing. There are way to many buttons and double functions.
     
    #17 William Gaatjes, Nov 7, 2009
    Last edited: Nov 7, 2009
  18. William Gaatjes

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    Indeed. Very true. That is why i am convinced that the only way the human race will survive is through knowledge and compassion. The knowledge is needed to know that you can do something wrong no matter what your hands will carry. The compassion is needed to know that you can hurt other living beings. Besides that, knowledge just comes in handy when you are encountering problems.
    And compassion makes you feel good.

    Just making people smarter will not make them better persons. I once have seen a documentary about one of the engineers of the H-bomb. He was at the end of his life but did not stop him hoping to see the H-bomb used. You would think that someone with the intelligence to build such a device would also be very human. I was wrong about that and saddened too. But at the same time it does explain human history, the present and unfortunately the future.
     
    #18 William Gaatjes, Nov 7, 2009
    Last edited: Nov 7, 2009
  19. Gibsons

    Gibsons Lifer

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    p53 does a lot of things. I can't see why benzopyrene can't cause mutations in p53, there's pretty strong evidence it does. http://www.ncbi.nlm.nih.gov/pubmed/...med_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2
     
  20. William Gaatjes

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    Grrrr.
    I am seriously starting too lose my patience with this untested crap called vbulletin style forum. I just had to log in 7 times in a row while i was already logged in just to be able to post this message. Crapware in my opinion based on experience.


    To come back to your post, I am wondering if the benzopyrene has a specific preference
    to lock onto parts of the dna. This is what i retreived from your link :


    and :

    If i read it correctly, it means that the benzopyrene binds to already mutated parts of p53.
    Please correct me if i am wrong. If i am right the question is, what caused the mutation in the p53 gene ? Could it been benzopyrene ? Have there been tests performed that show that benzopyrene also binds preferentially to a working form of p53 ? Is it known that p53 can have naturally occurring mutations that do not interfere with it's function ? And does benzopyrene preferentially binds to the same spots in all these version of p53 ?

    If i am wrong, then benzopyrene caused the mutation to form first and that this mutation made it easier for benzopyrene to bind to that specific part in the p53 gene.
    That if it is the case i find strange but interesting.

    I do find that interesting questions.
    Sincerely awaiting your answer...

    Me.
     
    #20 William Gaatjes, Nov 7, 2009
    Last edited: Nov 7, 2009
  21. Gibsons

    Gibsons Lifer

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    p53 has been studied pretty intensely for a very long time. Lots of people have sequenced lots of p53 genes from many many different cancers and normal tissues. When you compile this data, you see some bases mutated very often in cancer samples (usually leading to specific amino acid changes), some not so much.

    The general theory is that all the bases are, roughly, equally prone to mutation (this is never exactly true). So, when you sequence p53 from cancer cells, your data is selected - you're looking at mutations that lead to cancer (with some noise too, of course). If you see a few bases mutated over and over again, and a lot of other bases only rarely mutated, the conclusion is usually that those bases lead to cancer.

    Another explanation though, is simply that cancer cells have a high mutation rate and there's some bias in these mutations. i.e. the mutations are an effect of cancer, not a cause.

    Other data suggests that the former is correct - the mutations in p53 lead to cancer. When you look at the mutated proteins for instance, the common mutations lead to loss or change of function of the protein. Also, some unfortunate people are born with a mutated p53 and they get cancer early and often.
    http://en.wikipedia.org/wiki/Li-Fraumeni_syndrome

    What the article I linked is talking about is that they can detect a known mutagen/carcinogen binding to some of the specific sequences. I didn't read the whole paper, but they might be suggesting that benzopyrene has a higher than-you-might-expect propensity to cause the cancer associated mutations. i.e. it's not randomly mutating all bases, it's more prone to mutate the important ones than unimportant ones.
     
  22. William Gaatjes

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    I wonder if it is tested what those preferred codons actually do.


    i think both explanations are relevant. The damage in p53 leads to dna damage which is not is no longer corrected. That means that mutation after mutation can arise without a mechanism to correct it. Especially since it is known what p53 has as function.

    I have no doubt about that, knowing what p53 does : Stalling the cell division for dna repaires or setting off apoptosis when the dna damage can not be repaired.

    I still wonder if it can do that. Perhaps it latches on and causes the p53 gene to be interpreted wrong. Or that when the benzopyrene is latched on, that the reading mechanism accidently together with the benzopyrene changes the dna chemicals. I guess that is all in the realm of binding energy and chemistry /physics.

    Not so long ago the name super atom was used for an artificially configuration of atoms that collectively behaved like an atom of another element depending on it's elektron configuration.

    http://en.wikipedia.org/wiki/Superatom
    http://www.sciencedaily.com/releases/2008/07/080701092153.htm

    Perhaps nature uses a manipulation form similair as this one described in the link.



    Grrrr. i have to enter my password multiple times again while i am logged in. It is only in this thread it seems.
     
  23. William Gaatjes

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    Cool indeed.

    Gene therapy is very promising. But in my opinion should be limited in use until it is actually known how life works. These are dangerous grounds to play on if you can not see the whole playing field. We are constantly invested by bacteria and viruses and recombining of dna happens often. Maybe i am over cautious.
     
  24. Gibsons

    Gibsons Lifer

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    In large part, yes. It's not really the codons that are preferred, it's the amino acids they code for. You can take these mutant p53s and compare their properties to wild type p53 and demonstrate biochemical differences. i.e. wild type binds DNA, mutant doesn't.

    As for benzopyrene, after some metabolic processing, it covalently attaches to a base in the double helix. If nothing else, this makes it difficult to impossible for DNA polymerase to copy faithfully. (see pic, notice how the opposing bases don't pair up correctly).
    http://en.wikipedia.org/wiki/File:Benzopyrene_DNA_adduct_1JDG.png

    Finally, I'd bet a reproductive organ that superatoms have nothing whatsoever to do with any of this.