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Author Topic:   What about those jumping genes?
molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 46 of 102 (421227)
09-11-2007 4:08 PM
Reply to: Message 44 by Fosdick
09-11-2007 12:16 PM


TEs and the genome
I just found this:
TEs are a major component of all genomes and represent between 3 to 50% of the content of the genome, depending on the species (Capy et al., 1997). While TE interactions with the host genome remain poorly understood there are several examples of their impact on host functioning, structure and evolution. For example, Tn, bacterial composite elements (elements flanked by Insertion Sequences), provide several examples in which a gene involved in antibiotic resistance can be horizontally transferred, see for instance Berg & Howe (1989) and more recently, Hall (1997) and Recchia & Hall (1997). In Drosophila melanogaster, LINE-like elements such as TART and Het-A are used as a 'cap' at the extremities of the chromosomes to prevent their degradation (Pardue et al., 1997). Also in this species, the hobo element is involved in chromosomal inversions (Lim, 1988; Lyttle & Haymer, 1992; Lim & Simmons, 1994; Ladeveze et al., 1998). Gene regulation under the partial or complete control of retrotransposon LTRs (long-terminal repeats) or solo LTRs left by retrotransposons are another illustration of TE effects on host genome evolution (White et al., 1994; Britten, 1996; McDonald et al., 1997). This is also seen in the human alpha-amylase gene (Ting et al., 1992). Similarly, in the Saccharomyces cerevisiae genome, 331 Ty insertions (85% of which are solo LTRs) have been detected (Kim et al., 1998). These sequences are frequently inserted in tRNA genes or other transcribed genes (Hani & Feldmann, 1998). Therefore, they may have an impact on the expression profile of these genes. Thus, many of the interactions between TEs and their host genomes can be seen as a domestication of the former by the latter, or as a coevolution between the two entities.
Stress and transposable elements: co-evolution or useful parasites? Heredity, August 2000, Volume 85, Number 2, Pages 101-106
Pierre Capy, Giuliano Gasperi, Christian Biémont and Claude Bazin
You'll notice that, with the exception of HGT in bacteria, the origin of the TEs is not known.
Here's one way mariner may have gotten into humans:
Transposable elements of the mariner/Tc1 family are postulated to have spread by horizontal transfer and be relatively independent of host-specific factors. This was tested by introducing the Drosophila mauritiana element mariner into the human parasite Leishmania major, a trypanosomatid protozoan belonging to one of the most ancient eukaryotic lineages. Transposition in Leishmania was efficient, occurring in more than 20 percent of random transfectants, and proceeded by the same mechanism as in Drosophila. Insertional inactivation of a specific gene was obtained, and a modified mariner element was used to select for gene fusions, establishing mariner as a powerful genetic tool for Leishmania and other organisms. These experiments demonstrate the evolutionary range of mariner transposition in vivo and underscore the ability of this ubiquitous DNA to parasitize the eukaryotic genome.
Trans-kingdom Transposition of the Drosophila Element mariner Within the Protozoan Leishmania, Frederico J. Gueiros-Filho, Stephen M. Beverley Science 13 June 1997: Vol. 276. no. 5319, pp. 1716 - 1719
Again. The mariner element's origin in Drosophilia is unexplained. It hopped into a parasite. It's possible that it could then hop into a human and be transferred again, this time into the human genome.
There's no question that TEs are promiscuous. After all, they're nearly half of our genome. But there isn't any direct HGT between Drosophila and human.

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 47 of 102 (421269)
09-11-2007 8:05 PM
Reply to: Message 46 by molbiogirl
09-11-2007 4:08 PM


Re: TEs and the genome
All very interesting about TEs.
Molbiogirl, a question for you: Do you think it is reasonable to suppose that the bite of a tsetse fly, or many, could introduce enough fly genes via its saliva to find their way to a human male's testicle and become directly incorporated into his DNA somehow in a meiotic fluke (perhaps in the first prophase where crossing-over happens)? Just how much do TEs and other genes jump around?
”HM

This message is a reply to:
 Message 46 by molbiogirl, posted 09-11-2007 4:08 PM molbiogirl has replied

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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 48 of 102 (421283)
09-11-2007 8:46 PM
Reply to: Message 47 by Fosdick
09-11-2007 8:05 PM


Tsetse Genes
I don't know about your saliva, but mine doesn't have any genes in it.
And neither does a tsetse fly's.
wiki writes:
Produced in salivary glands, saliva is 98% water, but it contains many important substances, including electrolytes, mucus, antibacterial compounds and various enzymes.
So the answer to your question is ABSOLUTELY NOT.
Rather than lecture you on transposition, I suggest you read this.
Edited by molbiogirl, : spelling

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 49 of 102 (421370)
09-12-2007 10:48 AM
Reply to: Message 48 by molbiogirl
09-11-2007 8:46 PM


Re: Tsetse Genes
molbiogirl wrote:
I don't know about your saliva, but mine doesn't have any genes in it.
I seriously doubt that. How do you suppose it's possible to do a DNA analysis on a licked and sealed envelop?
And neither does a tsetse fly's.
Not true! A tsetse fly's saliva has a lot of genes in it, usually including those of trypanosomes and other parasites.
”HM

This message is a reply to:
 Message 48 by molbiogirl, posted 09-11-2007 8:46 PM molbiogirl has replied

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 50 of 102 (421372)
09-12-2007 11:22 AM
Reply to: Message 49 by Fosdick
09-12-2007 10:48 AM


Re: Tsetse Genes
I thought something along those lines as well, that saliva might carry some cells, such as cheek cells in humans. Not that this then necessarily leads to a pathway for genetic transfer.
TTFN,
WK

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 51 of 102 (421376)
09-12-2007 11:31 AM
Reply to: Message 50 by Wounded King
09-12-2007 11:22 AM


Re: Tsetse Genes
WK wrote:
I thought something along those lines as well, that saliva might carry some cells, such as cheek cells in humans. Not that this then necessarily leads to a pathway for genetic transfer.
You're right. For that to occur in a heritable way the transfer would have to extend all the way into meiosis (for many eukaryotes, at least).
”HM

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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 52 of 102 (421387)
09-12-2007 12:59 PM
Reply to: Message 49 by Fosdick
09-12-2007 10:48 AM


Re: Tsetse Genes
I seriously doubt that. How do you suppose it's possible to do a DNA analysis on a licked and sealed envelop?
Thru the tidbits of RNA that are present in saliva. Not DNA.
FYI. When genetic testing outfits say they test "saliva", they mean buccal swabs.
Not true! A tsetse fly's saliva has a lot of genes in it, usually including those of trypanosomes and other parasites.
Those aren't tsetse genes.

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Replies to this message:
 Message 54 by Fosdick, posted 09-12-2007 3:44 PM molbiogirl has replied
 Message 57 by Wounded King, posted 09-12-2007 5:58 PM molbiogirl has replied

  
molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 53 of 102 (421388)
09-12-2007 1:08 PM
Reply to: Message 51 by Fosdick
09-12-2007 11:31 AM


Steps of HGT
Here's what needs to happen with those putative tsetse genes (which you have yet to show would be present in the saliva):
nature reviews microbiology writes:
For any gene to be horizontally transferred from one genome to another, at least four (sometimes five) distinct steps need to occur. First, a nucleic-acid molecule in the donor organism is prepared for transfer. This might entail the active packaging of nucleic acids into phage particles, plasmid replication from an origin that leads to conjugal transfer, or integron assembly. Second, the transfer step, which might or might not require physical contact between the donor and recipient organism, takes place. Third, the nucleic acid enters the recipient organisms through specific or non-specific means. Fourth, the nucleic-acid molecule is established in the recipient either as a self-replicating element or through recombination with, or transposition into, the recipient's chromosome. This existence can be transitory, as is the case with many plasmids of which maintenance by the recipient genome depends on selective pressure. Last, in step 5, stable inheritance in the recipient genome might ensue.
In other words, not too bloody likely.
Edited by molbiogirl, : No reason given.

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 54 of 102 (421411)
09-12-2007 3:44 PM
Reply to: Message 52 by molbiogirl
09-12-2007 12:59 PM


Re: Tsetse Genes
HM wrote:
How do you suppose it's possible to do a DNA analysis on a licked and sealed envelop?
molbiogirl responded:
Thru the tidbits of RNA that are present in saliva. Not DNA.
The National Institutes of Health would disagree. Check out this article on Saliva: Your Spitting Image:
quote:
When you lick that envelope, you may be sending a more detailed message than you realize. Your saliva leaves a DNA fingerprint that not only says who you are, but also whether you have a genetic predisposition for certain diseases.
A tsetse fly's saliva has a lot of genes in it, usually including those of trypanosomes and other parasites.
Those aren't tsetse genes.
Are you sure? If human genes are found in human saliva why can't tsetse-fly genes be found in tsetse-fly saliva?
”HM

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Replies to this message:
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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 55 of 102 (421415)
09-12-2007 4:45 PM
Reply to: Message 54 by Fosdick
09-12-2007 3:44 PM


Re: Tsetse Genes
The National Institutes of Health would disagree. Check out this article on Saliva: Your Spitting Image
Here is a quote from another article re: the National Institute of Dental Research study:
Saliva testing can be effective because it contains many of the same proteins that blood and urine do, the researchers said. New research shows these molecules can reveal the presence of diseases like cancer, and can be used to predict the number of cavities in a person's teeth.
Proteins. Not DNA.
Tony Raymond says there has been much misinformation about the invasiveness of sampling techniques.
"There is some concern that the taking of a buccal swab involved the aggressive and vigorous insertion of a large brush into the mouth of a suspect," he said. "Nothing could be further from the truth. The buccal swab itself is smaller and softer than a toothbrush."
They used a buccal swab. Of course they collected DNA. They scraped the cheek.
Are you sure? If human genes are found in human saliva why can't tsetse-fly genes be found in tsetse-fly saliva?
Google tsetse and saliva. Look on scholar.google. Look in pubmed. And let me know what literature you find on what is in tsetse fly saliva (other than parasites, I mean.)

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 Message 54 by Fosdick, posted 09-12-2007 3:44 PM Fosdick has replied

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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 56 of 102 (421424)
09-12-2007 5:39 PM
Reply to: Message 54 by Fosdick
09-12-2007 3:44 PM


Tsetse Spit
Here's a quote from this month's Insect Biochemistry and Molecular Biology:
However, molecular information on the individual tsetse salivary proteins and their biological activity remains scanty. Previous studies on Glossina morsitans saliva have reported the presence of a 11.3 kDa inhibitor of thrombin serine protease and esterase activities (Parker and Mant, 1979) and a >30 kDa protein fraction that inhibited the ADP-induced thrombocyte aggregation (Mant and Parker, 1981). In addition, a potent 32 AA blood meal-induced tsetse thrombin inhibitor (TTI), was characterised in salivary gland extracts. Purified TTI has been shown to abolish thrombin-induced platelet aggregation ([Cappello et al., 1996] and [Cappello et al., 1998]). Salivary extracts have also been demonstrated to exert an adenosine deaminase activity that might depend on translation of tsetse salivary growth factors 1 and 2 (TSGF-1 and TSGF-2).
Insect Biochemistry and Molecular Biology
Volume 37, Issue 10, October 2007, Pages 1075-1085
Scanty.
And that just proteins. Nothing in the literature at all about genetic material.
But let's ignore that.
Let's pretend tsetse fly spit is teeming with tsetse DNA.
How does this DNA perform HGT steps 1-5 (above)?
Oh. One more thing.
HM writes:
A tsetse fly's saliva has a lot of genes in it, usually including those of trypanosomes and other parasites.
molbiogirl writes:
Those aren't tsetse genes.
HM writes:
Are you sure? If human genes are found in human saliva why can't tsetse-fly genes be found in tsetse-fly saliva?
Yes, I am sure that trypanosomes (and other parasites) are not tsetse.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 57 of 102 (421429)
09-12-2007 5:58 PM
Reply to: Message 52 by molbiogirl
09-12-2007 12:59 PM


Re: Tsetse Genes
Thru the tidbits of RNA that are present in saliva. Not DNA.
Really, that sounds wrong to me. It takes a heck of a lot of work to maintain RNAs in a sufficiently stable state for analysis but you are suggesting that a potentially days old licked envelope will have sufficient recoverable sequence to allow a viable genetic fingerprint to be retrieved?
I'd have thought that DNA contained in leftover cheek or tongue epithelial cells would be a more viable source of genetic information. I've sent plenty of plasmids out on dried filter paper, but I've never sent RNA samples out that way.
TTFN,
WK

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Replies to this message:
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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 58 of 102 (421446)
09-12-2007 6:39 PM
Reply to: Message 57 by Wounded King
09-12-2007 5:58 PM


RNA and Saliva
Really, that sounds wrong to me.
Here's one cite:
The page you’re looking for isn’t available. | National Institutes of Health (NIH)
This so-called "proof-of-principle" study marks the first report in the scientific literature that distinct patterns of "messenger RNA" not only are measurable in saliva but can indicate a developing tumor. Messenger RNA (mRNA) is the molecular intermediate between gene and protein, serving as a chemical record that an individual gene has been expressed.
And another:
RNA profiling of cell-free saliva using microarray technology, Zhou et. al., Journal of Dental Research 2004, vol. 83, no3, pp. 199-203
Saliva, like other bodily fluids, has been used to monitor human health and disease. This study tests the hypothesis that informative human mRNA exists in cell-free saliva. If present, salivary mRNA may provide potential biomarkers to identify populations and patients at high risk for oral and systemic diseases. Unstimulated saliva was collected from ten normal subjects. RNA was isolated from the cell-free saliva supernatant and linearly amplified. High-density oligonucleotide microarrays were used to profile salivary mRNA. The results demonstrated that there are thousands of human mRNAs in cell-free saliva. Quantitative PCR (Q-PCR) analysis confirmed the present of mRNA identified by our microarray study. A reference database was generated based on the mRNA profiles in normal saliva. Our finding proposes a novel clinical approach to salivary diagnostics, Salivary Transcriptome Diagnostics (STD), for potential applications in disease diagnostics as well as normal health surveillance.
Edited by molbiogirl, : another cite

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molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 59 of 102 (421451)
09-12-2007 7:02 PM
Reply to: Message 57 by Wounded King
09-12-2007 5:58 PM


Stamps and Spit
Found the stamp thing:
PCR-based DNA typing of saliva on stamps and envelopes, Biotechniques 1994 Sep;17(3):546-52
In forensic cases involving mail bombs, extortion, kidnapping or threatening letters, biological evidence such as the saliva used to attach the stamp and seal the envelope could be used for genetic analysis. We have developed a highly sensitive semi-nested PCR method for the HLA-DRB1 locus; suitable for the analyses of very limited amounts of DNA. When applied to a set of stamps and envelopes with saliva from control individuals, typing results were consistent with those obtained using hairs drawn from the same individuals. No interference was found due to DNA from the fingerprints of people handling the letters. The system was applied to three forensic cases with threatening letters. The first case resulted in an exclusion of the suspect. In the second case, the suspect could not be excluded (probability of identical genotype by chance > 0.01). These results demonstrate that biological evidence in cases with threatening letters is amenable to genetic typing.
So there you have it, HM.
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.) I'd also like to see some idea how this DNA (if it exists) would manage transposition steps 1-5.

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 60 of 102 (421453)
09-12-2007 7:06 PM
Reply to: Message 55 by molbiogirl
09-12-2007 4:45 PM


Genes in saliva
molbiogirl wrote:
Here is a quote from another article re: the National Institute of Dental Research study:
quote:
Saliva testing can be effective because it contains many of the same proteins that blood and urine do, the researchers said. New research shows these molecules can reveal the presence of diseases like cancer, and can be used to predict the number of cavities in a person's teeth.
Proteins. Not DNA.
But why would the National Institutes of Health say this?
When you lick that envelope, you may be sending a more detailed message than you realize. Your saliva leaves a DNA fingerprint that not only says who you are, but also whether you have a genetic predisposition for certain diseases.
That's a "DNA fingerprint." They're not talking about proteins here.
”HM

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 Message 55 by molbiogirl, posted 09-12-2007 4:45 PM molbiogirl has not replied

  
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