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Fosdick  Suspended Member (Idle past 5526 days) Posts: 1793 From: Upper Slobovia Joined: |
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Author | Topic: What about those jumping genes? | |||||||||||||||||||||||||||
Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Neither cite says anything about recovering RNA from dried saliva and using it for genetic fingerprinting.
I wasn't suggesting there was no RNA in Saliva. What I was saying was that the recovery of genetic material for DNA fingerprinting from an item such as an envelope was not based on RNA, as you had claimed. I see you have just now posted something about the recovery of DNA form stamps, good show. TTFN, WK
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Fosdick  Suspended Member (Idle past 5526 days) Posts: 1793 From: Upper Slobovia Joined: |
molbiogirl, you wrote:
So there you have it, HM.
Yes, and...?
I found the DNA evidence for you. However. I'd still like to see some proof of DNA in tsetse fly spit. ("Why not? It's in human spit." is not good enough.
Why not? What principle in molecular biology prohibits tsetse-fly DNA from appearing in tsetse-fly spit?
I'd also like to see some idea how this DNA (if it exists) would manage transposition steps 1-5.
I'll be right back to you on that as soon as I get a PhD in molecular biology. But, hey, stranger things have happened. ”HM
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molbiogirl Member (Idle past 2668 days) Posts: 1909 From: MO Joined: |
"Why not?" is a remarkably unsatisfying answer for a scientist. And a cop out, too.
I don't have my Biochemistry PhD (yet), but I can assure you. Tsetse fly DNA, were it injected into the bloodstream via the bite, WOULD NOT transpose. ABE
Why not? What principle in molecular biology prohibits tsetse-fly DNA from appearing in tsetse-fly spit? The real question is, what principle in molbio would allow tsetse fly DNA in fly spit? The literature is silent on DNA and fly spit. Proteins, yes. Parasites, yes. DNA, no. Edited by molbiogirl, : No reason given. Edited by molbiogirl, : typo
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Fosdick  Suspended Member (Idle past 5526 days) Posts: 1793 From: Upper Slobovia Joined: |
Tsetse fly DNA, were it injected into the bloodstream via the bite, WOULD NOT transpose.
Why not? All they have to do is get involved with meiosis and gametes. Blood-borne tsetse-fly genes might not be much different from the "imported sequences and mobile genetic parasites" that Frederic Bushman speaks of down at The Salk Institute. And he seems to be an expert on transposons. ”HM
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molbiogirl Member (Idle past 2668 days) Posts: 1909 From: MO Joined: |
There is an enormous difference between a chunk of genomic DNA and a transposon.
Did you even bother to read the transposon link?
wiki writes: Transposons work by copying themselves and pasting copies back into the genome in multiple places. A chunk of DNA, injected via a tsetse bite into the bloodstream of a human host, would not be able to: 1. Copy itself 2. Cut open the host DNA 3. Paste itself into the host's DNA
(Transposons) usually move by cut and paste, rather than copy and paste, using the transposase enzyme. Different types of transposase work in different ways. Transposase makes a staggered cut at the target site producing sticky ends, cuts out the transposon and ligates it into the target site. A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase closes the sugar-phosphate backbone. An ordinary piece of tsetse genomic DNA (naked, outside of its cell) would not have the ability to copy itself. Copying DNA requires many support proteins arranged as a complicated piece of cellular machinery. An ordinary piece of tsetse genomic DNA would not have the ability to cut (using transposase) or to paste (using ligase). Transposons have genes for both transposase and ligase. Then there's the problem of getting into the host cell and then into the nucleus to perform the cut and paste maneuver. Injected tsetse genomic DNA would be in the form of a cell (much as in human spit the DNA is contained in buccal cells). The genomic DNA would only get out of that cell if the cell burst. Then that DNA would just be floating free in the bloodstream. How is it that you propose a naked piece of tsetse DNA get into the host cell? Much less a gamete? Cells don't let just anything wander in, you know. Ordinary DNA does not have the ability to cross the cell membrane. In the lab, we get transposons into host cells using phage or plasmids.
A common way of delivering transposons is to use a "suicide plasmid" that cannot replicate in the recipient cells. If naked DNA could get into a cell, we could skip the phage/plasmid. We could just incubate the cells with the transposons. Now do you get it?
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Fosdick  Suspended Member (Idle past 5526 days) Posts: 1793 From: Upper Slobovia Joined: |
molbiogirl wrote:
Did you even bother to read the transposon link?
Who's "wiki"? Wikipedia is not an authoritative source for this discussion. Did you even bother to read what Frederic Bushman said, quoted in Message 44?
Now do you get it?
No. You haven't explained yet how: "Our own DNA is a complex composite of imported sequences and mobile genetic parasites" (F. Bushman). You can't tell me how those mobile genetic parasites got into our DNA complex. You're saying it can't happen. But it did. Do you know more about this than Bushman does? ”HM
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Come on Hoot, you've gone from ...
Blood-borne tsetse-fly genes might not be much different from the "imported sequences and mobile genetic parasites" that Frederic Bushman speaks of down at The Salk Institute. And he seems to be an expert on transposons. to
No. You haven't explained yet how: "Our own DNA is a complex composite of imported sequences and mobile genetic parasites" (F. Bushman). You can't tell me how those mobile genetic parasites got into our DNA complex. You're saying it can't happen. But it did. Do you know more about this than Bushman does? Suddenly the tenuous connection you were drawing, with no evidence to support it, is supposed to be expert opinion from Bushman? The incorporation of viral sequences or sequences from organelles both involve genetic sequence already on the inside of the cell membrane and either present or capable of propagating to cells throughout the body. There is no need for some magical route for DNA from a tsetse cell in saliva to be incorporated into the genomic DNA of a gamete in order to explain Bushman's statement, just the known factors such as retroviral insertion and transposase activity. There may be some unknown mechanism of DNA incorporation out there but you have given us no reason to suppose they exist as the current known routes are sufficient to account for the elements you have brought up. Perhaps a more suitable avenue to explore for your approach would be the mechanisms leading to the incorporation of mitochondrial genetic elements into the nuclear genome (Schmidt and Blanchard, 1996).
Roth and Wilson (1988) suggest that free chromosomal ends are generated from errors in DNA metabolism and at these sites segments of foreign DNA can integrate regardless of their terminal sequences. During this process, end-joining of multiple DNA fragments can occur. But you still have along way to got to make any sort of case that such a mechanism is required or indeed that there is anything to be explained. TTFN, WK
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molbiogirl Member (Idle past 2668 days) Posts: 1909 From: MO Joined: |
Who's "wiki"? Wikipedia is not an authoritative source for this discussion. Did you even bother to read what Frederic Bushman said, quoted in Message 44? Everything I've quoted from wiki is absolutely true. I read the original paper on transposons that Barbara McClintock published in 1950. McCLINTOCK, B. (Jun 1950). The origin and behavior of mutable loci in maize. Proc Natl Acad Sci U S A. 36 (6): 344-55. I've performed genomic transformations in lab. We've known how transposons work for 60 years, HM. To wit: Molecular Reconstruction of Sleeping Beauty, a Tc1-like Transposon from Fish, and Its Transposition in Human Cells, CellVolume 91, Issue 4, 14 November 1997, Pages 501-510 These transposable elements transpose through a cut-and-paste mechanism; the element-encoded transposase catalyzes the excision of the transposon from its original location and promotes its reintegration elsewhere in the genome. Autonomous members of a transposon family can express an active transposase, the trans-acting factor for transposition, and thus are capable of transposing on their own. Nonautonomous elements have mutated transposase genes but may retain cis-acting DNA sequences necessary for transposition. These sequences, usually embedded in the terminal inverted repeats (IRs) of the elements, are required for mobilization in the presence of a complementary transposase. I'm assuming you recognize the authority of Cell. "Non autonomous" means "can't move without the help of transposase".
Unfortunately, not a single autonomous element has been isolated from vertebrates; they seem to be defective for having mutations as a result of a process called “vertical inactivation” This was published in 2005. Not a single autonomous (read: can move by itself) element has been isolated in vertebrates. Now. Why don't you go back to your book and find a quote that explains how transposons move. I am certain it's in there. I would do it for you, but the book isn't available online.
HM writes: "Our own DNA is a complex composite of imported sequences and mobile genetic parasites" I've already agreed that our genome is 45% TEs. So what? That doesn't mean naked genomic DNA can move by itself. Here's a picture of the mechanism needed to copy DNA:
That mechanism exists only within a living cell. A naked piece of DNA from a burst cell would not have the capability to copy itself in order to insert itself into the host cell. The transposons that are in human DNA come from viruses and other parasites that are capable of inserting themselves into our cells. The parasites sometimes carry transposons. Here's a description of a virus:
wiki writes: At the most basic level, viruses consist of genetic material contained within a protective protein coat called a capsid. They infect a wide variety of organisms: both eukaryotes (animals, plants, protists, and fungi) and prokaryotes (bacteria and archaea). A virus that infects bacteria is known as a bacteriophage, often shortened to phage. Here's a description of how a virus enters a cell: UW Bacteriology | Error page
In eukaryotes, there are three general methods for entry into the cell. Some viruses are capable of uncoating merely by contact at the cellular membrane. In some cases binding of receptor triggers a process whereby a pore forms in the membrane between the inside of the capsid and the cytoplasm, causing the nucleic acid to enter the cell (Figure 5-4). In some enveloped viruses, the viral membrane fuses with the cell membrane, dumping the viral capsid into the cytoplasm. The capsid then uncoats releasing the nucleic acid. In the second general mechanism, viruses enter by utilizing uptake pathways normally used by the host for the transport of extracellular particles into the cell. This engulfment can be non-specific (phagocytosis) or, more typically, mediated by a receptor (endocytosis). In endocytosis, binding of a receptor by the virus particle causes it to migrate to a clathrin-coated pit, which is an area coated with protein (clathrin) that serves as a gathering point for transport of molecules into the cell. This triggers an invagination by the pit and the formation of a clathrin-coated vesicle. The vesicle uncoats by losing its clathrin and an endosome is formed. Proton-pumping proteins in the endosome membrane then cause a drop in pH. Finally, the endosome fuses with a lysosome and enzymes that degrade sugars, nucleic acids, proteins and lipids attack the contents of the vesicle. At all of these steps, viruses take advantage of the cells actions, using them as signals to initiate escape from the endocytotic pathway and invade the cytoplasm. These signals cause the virus to inject its nucleic acid into the cytoplasm in a fashion somewhat similar to that used by most bacterial viruses. The third method of entry to a eukaryotic cell involves the intact virus being endocytosed, but instead of just the nucleic acid entering the cytoplasm, the entire virus does. The virus then triggers lysis of the endosome membrane and enters the cytoplasm intact. Viral uncoating then occurs at the nuclear membrane. In all cases, the eukaryotic virus must carefully regulate entry. If not, the nucleic acid may be delivered into the wrong compartment in the cell or be released into the environment, destroying infectivity. Must carefully REGULATE entry. Ordinary genomic DNA is not capable of regulating entry into a cell. HM. Look in the index of Bushman's book. Find "transposition" or "method of transposition" and you will see that I am right.
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Fosdick  Suspended Member (Idle past 5526 days) Posts: 1793 From: Upper Slobovia Joined: |
WK wrote:
Roth and Wilson (1988) suggest that free chromosomal ends are generated from errors in DNA metabolism and at these sites segments of foreign DNA can integrate regardless of their terminal sequences. During this process, end-joining of multiple DNA fragments can occur. But you still have along way to got to make any sort of case that such a mechanism is required or indeed that there is anything to be explained. ”HM
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molbiogirl Member (Idle past 2668 days) Posts: 1909 From: MO Joined: |
Then genes can hop onto those cabooses of terminal sequences. How does the genomic material get into the cell?
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Fosdick  Suspended Member (Idle past 5526 days) Posts: 1793 From: Upper Slobovia Joined: |
molbiogirl wrote:
Must carefully REGULATE entry.
OK, molbiogirl, you have pretty much won this argument. But bear in mind that protists take DNA into their cells as part of their ingested food. In those cases "ordinary genomic DNA" is allowed entry into the cell without such "regulation." Wouldn't that leave open the possibility of undigested fugitive genomic DNA running loose and wild inside the plasma membrane of a paramecium? Ordinary genomic DNA is not capable of regulating entry into a cell. HM. Look in the index of Bushman's book. Find "transposition" or "method of transposition" and you will see that I am right. ”HM
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molbiogirl Member (Idle past 2668 days) Posts: 1909 From: MO Joined: |
From the article Wounded cited:
transfer to the nucleus has been suggested to be facilitated by transposable or viral elements because of their proximity to many numtDNA sequences. Just like I said.
The mitochondrial genome indicate that fragments join together from an intracellular pool of RNA and/or DNA before they integrate into the nuclear genome. Intracellular. That means "inside the cell", HM.
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molbiogirl Member (Idle past 2668 days) Posts: 1909 From: MO Joined: |
University of Chicago Press Journals: Cookie absent
On its course through the body, the food-vacuole usually decreases greatly in size, and the acidity of its content increases greatly; the acidity ... increases to a maximum at least as high as pH 1.4 and then decreases approximately to pH 7.8. Let's see your evidence that DNA would survive the digestion process. DNA stability - OpenWetWare
DNA under physiological conditions has been estimated to depurinate at a rate of 3 x 10e11/sec at 37C and pH 7.4 Depurination involves the loss of purine bases forming abasic sites Amines greatly increase the rate of strand breakage at abasic sites In other words, the DNA is wrecked and then torn apart. Other cites: Lindahl T and Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 1972 Sep 12; 11(19) 3610-8. Lindahl T and Andersson A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 1972 Sep 12; 11(19) 3618-23. Frederico LA, Kunkel TA, and Shaw BR. Cytosine deamination in mismatched base pairs. Biochemistry 1993 Jul 6; 32(26) 6523-30. Let's assume however, that thru some miracle, the DNA survives. How do you propose the DNA gets out of the paramecium and into the human cell? You've run into the same problem.
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Except you don't seem to have made a case.
Without some actual reference to determine what sequences that were studied actually were there is nothing but the claims Brass et al. made in their report to the MAFF to allow us to determine how close the sequences actually were. BLASTing the 3 sequences on pubmed does turn up one with a 75% similarity to a human sequence, but whether this is the sequences that Brass's group studied is unclear. So apart from this homology why are we to believe there has been some direct HGT between tsetse and human? And if because simply of this homology what should presuppose us to believe that it is the result of direct HGT? TTFN, WK
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Fosdick  Suspended Member (Idle past 5526 days) Posts: 1793 From: Upper Slobovia Joined: |
WK responded to my statement:
You haven't explained yet how: "Our own DNA is a complex composite of imported sequences and mobile genetic parasites" (F. Bushman).
Suddenly the tenuous connection you were drawing, with no evidence to support it, is supposed to be expert opinion from Bushman? The incorporation of viral sequences or sequences from organelles both involve genetic sequence already on the inside of the cell membrane and either present or capable of propagating to cells throughout the body. There is no need for some magical route for DNA from a tsetse cell in saliva to be incorporated into the genomic DNA of a gamete in order to explain Bushman's statement, just the known factors such as retroviral insertion and transposase activity. Why not? Where, then, did they come from? I'm not looking for magical insertions. They must have physical origins. And where do all those introns come from? I doubt that they came from copying errors and mutations alone; some of them must have come from other organisms. Why not tsetse flies? It seems possible to me that some constantly bitten Africans could have sustained levels of tsetse-fly saliva in their bloodstream, possibly carrying tsetse-fly DNA, which circulates right through the human host's reproductive organs and tissues. The rest of the trip into the human genome was then facilitated by the TE chemistry you and mbg have so ellegantly narrated. Please tell me why your own selected reference does not support my argument:
Roth and Wilson (1988) suggest that free chromosomal ends are generated from errors in DNA metabolism and at these sites segments of foreign DNA can integrate regardless of their terminal sequences. During this process, end-joining of multiple DNA fragments can occur. ”HM
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