BioInformatics, Genomics, "10-factors", SNES & LNES?

dant

dant

The Living Force
In a strange set of events, I happened to be working with
a M$ "rep" in IT in trying to fix my M$ server (of which M$ broke),
and I noticed the rep's Internet Messenger comment in regards to
"DNA FORMS THE BASIS OF LIFE...", and I asked: "Do you know of
the 10-factors in DNA called "junk" DNA?" and she responded: "I
have a degree in BioInformatiics (Genomics) and working towards
my PHD, and yes, what you are referring to is known as LNES and
SNES in DNA terminology."

I tried googling for "Bioinformatics genome LNES SNES" and found
sparse information on this subject trying to learn a bit more of what
she is taking about... I guess it is over my head.

Is there any truth to what she said, is this mentioned anywhere on
the SOTT site or by Laura/C's on this subject in case I might have
missed it?

Curious....

FWIW,
Dan
 
perhaps she meant LINEs and SINEs, that is "long/short interspersed nuclear elements"? they are mentioned here on Wikipedia:

_http://en.wikipedia.org/wiki/Retrotransposon

LINEs

Long interspersed repetitive elements or Long interspersed nuclear elements[8] are a group of genetic elements that are found in large numbers in eukaryotic genomes. They are transcribed (or are the evolutionary remains of what was once transcribed) to an RNA using an RNA polymerase II promoter that resides inside the LINE. LINEs code for the enzyme reverse transcriptase, and many LINEs also code for an endonuclease (e.g. RNase H). The reverse transcriptase has a higher specificity for the LINE RNA than other RNA, and makes a DNA copy of the RNA that can be integrated into the genome at a new site.[9]

The 5' UTR contains the promoter sequence, while the 3' UTR contains a polyadenylation signal (AATAAA) and a poly-A tail.[10] Because LINEs move by copying themselves (instead of moving, like transposons do), they enlarge the genome. The human genome, for example, contains about 20,000-40,000 LINEs, which is roughly 21% of the genome.[11]
[edit]

SINEs

Short interspersed repetitive elements or Short interspersed nuclear elements[8] are short DNA sequences (<500 bases[12]) that represent reverse-transcribed RNA molecules originally transcribed by RNA polymerase III into tRNA, rRNA, and other small nuclear RNAs. SINEs do not encode a functional reverse transcriptase protein and rely on other mobile elements for transposition. The most common SINEs in primates are called Alu sequences. Alu elements are 280 base pairs long, do not contain any coding sequences, and can be recognized by the restriction enzyme AluI (hence the name). With about 1,500,000 copies, SINEs make up about 13% of the human genome.[11] While historically viewed as "junk DNA", recent research suggests that in some rare cases both LINEs and SINEs were incorporated into novel genes, so as to evolve new functionality.[13]. The distribution of these elements has been implicated in some genetic diseases and cancers.
Click to expand...
 
But I noticed that only SNES shows up sporadically in various
places... so I am still not sure what it is. What you said sounds
plausible though....

Thanks for responding!
Dan
 
Lostinself is right, though, I think she misunderstood your questions. First of all, there is no 10-factors concerning current genetics. When you said junk DNA she must have made the association, because LINES and SINES are part of that system.

I think the problem, the confusion occurs because to my knowledge Laura or C's didn't adress exactly if junk DNA is 10-factor DNA or not, I may be wrong though. Are those 10 factors currently in our genome, or are they available as blueprints for actual bases to come? There were instances in transcripts where C's mentioned a group member obtained another strand. If they are junk DNA and they are currently in our organism, what does obtaining or receiving means in this sense?

Or are they different from the junk DNA, and junk DNA is a passage, a gateway to enable us to receive those 10 strands? After all, C's said there were 135 chromosomes before the Fall, yet chromosome length is another issue, maybe we used to have short chromosomes and after the Fall, those sequences get together in 46 chromosomes.

Another interesting question might be, are those strands physical, or are they etheral?

These are the questions I thought in the past, I have no answer to them, I just think it is a really complicated issue with different possible explanations. Or maybe I am the one who misunderstood the material, and all of those questions are answered. If this is the case, I would be happy if someone points out the links.


Just my two cents, fwiw.
 
Biomast:

My thoughts exactly! I am just a perplexed to understand it as well!!
All good questions!

I also understood that one could become a superconductor when the
DNA[?] is restored... that is in the transcripts somewhere.... and the
talk of detoxing to achieve this aim?

Thanks!!
Dan
 
Biomiast said:
I think the problem, the confusion occurs because to my knowledge Laura or C's didn't adress exactly if junk DNA is 10-factor DNA or not, I may be wrong though. Are those 10 factors currently in our genome, or are they available as blueprints for actual bases to come? There were instances in transcripts where C's mentioned a group member obtained another strand. If they are junk DNA and they are currently in our organism, what does obtaining or receiving means in this sense?

Or are they different from the junk DNA, and junk DNA is a passage, a gateway to enable us to receive those 10 strands? After all, C's said there were 135 chromosomes before the Fall, yet chromosome length is another issue, maybe we used to have short chromosomes and after the Fall, those sequences get together in 46 chromosomes.

Another interesting question might be, are those strands physical, or are they etheral?
Click to expand...

There is this bit from session 12/10/94:

Q: (T) How many strands of DNA do we have?
A: Terry, 4; Freddy, 4; Jan, 3; Laura, 3.

Q: (L) Well, gee... does this have anything to do with sex?
A: No.

Q: (L) Are you telling us that Freddy and Terry are smarter than Jan and me?
A: You are growing your 4th, 5th and 6th right now.

Q: (T) If our 3rd density were to examine our DNA right now would they see this?
A: They would call it Junk DNA.

Q: (T) Would it be noticeable as DNA that was not there before?
A: Maybe.
Click to expand...

This seems to indicate that extra strands are physical, not just ethereal, and may be present in a disassembled form but still physically there. If this interpretation is correct, then 'gaining strands' would mean that these strands are reassembled and made functional again.
 
Shijing said:
Q: (T) How many strands of DNA do we have?
A: Terry, 4; Freddy, 4; Jan, 3; Laura, 3.

Q: (L) Well, gee... does this have anything to do with sex?
A: No.

Q: (L) Are you telling us that Freddy and Terry are smarter than Jan and me?
A: You are growing your 4th, 5th and 6th right now.

Q: (T) If our 3rd density were to examine our DNA right now would they see this?
A: They would call it Junk DNA.

Q: (T) Would it be noticeable as DNA that was not there before?
A: Maybe.
Click to expand...

This seems to indicate that extra strands are physical, not just ethereal, and may be present in a disassembled form but still physically there. If this interpretation is correct, then 'gaining strands' would mean that these strands are reassembled and made functional again.
Click to expand...

I tend to agree that they are physical, at least those in question in the transcript, on the other hand, as you know there is variability of physicality at higher levels, I remember thinking for fun that there could be 6 physical and 6 etheral strands, and based on the variability of physicality those numbers may vary in a given situation.

It can be that they are disassembled, it is a possibility, yet this isn't the only meaning I derive from the excerpt. It can be that there is a strand that is newly made, but since current science isn't looking for it, they would dismiss it as junk DNA. It may be my limited English, but I don't think C's say junk DNA is a precursor of additional strands, they merely say if anybody would look into our additional DNA strands, they would call it junk.

Yet, this doesn't mean junk DNA can't be additional strands, it is one of many possibilities. I just don't think that exchange clarifies the issue at hand.

Maybe I am misunderstanding what they are trying to say?

Just my two cents, fwiw.
 
Biomiast said:
It can be that they are disassembled, it is a possibility, yet this isn't the only meaning I derive from the excerpt. It can be that there is a strand that is newly made, but since current science isn't looking for it, they would dismiss it as junk DNA. It may be my limited English, but I don't think C's say junk DNA is a precursor of additional strands, they merely say if anybody would look into our additional DNA strands, they would call it junk.

Yet, this doesn't mean junk DNA can't be additional strands, it is one of many possibilities. I just don't think that exchange clarifies the issue at hand.
Click to expand...

That's true, Biomiast -- your alternate proposal hadn't occurred to me when I read that excerpt, but that's actually also possible.
 
I beleive I may have found the reference to '10' and JUNK? -RNA!

5 September 2005
Junk RNA Begins To Yield Its Secrets
by Kate Melville

http://www.scienceagogo.com/news/20050805002810data_trunc_sys.shtml

A paper in the journal Science details how a team of investigators from The Scripps Research Institute and the Genomics Institute of the Novartis Research Foundation have discovered a way to screen hundreds of non-coding RNA molecules to discover their functions within cells. Unlike mainstream RNA, which is copied from DNA to build proteins, these non-coding RNA molecules are not translated into proteins. Sometimes referred to as "junk", there are many thousands of these non-coding RNA molecules inside human cells. Scientists believe that even if only a small percentage are functional, this would equate to hundreds of molecules that may play important roles in the control of cellular functions.

It's only recently that scientists have become interested in non-coding RNA. One of the reasons for the turnaround is that they have begun to recognize just how abundant non-coding RNA is. In the same issue of Science, two reports describe the work of other scientists showing that there are far more non-coding RNAs than most researchers would have imagined even a few months ago.

The question scientists have been asking is: why would the cell expend so much energy making RNA if that RNA doesn't do anything? They have speculated that perhaps some non-coding RNAs play cellular roles. And while computational approaches and analysis have been used, nobody has come up with a way of experimentally determining whether the non-coding RNAs have a cellular function. So how can researchers rapidly assess what the function of these non-coding RNAs might be? "That's the million-dollar question," says Neurobiology Professor John Hogenesch, from Scripps. "Until now we have not had a generalized way of answering it."

But now they have. And it appears that the team has established the first proof of a cellular function by non-coding RNA. To apply a high-throughput approach to the problem, the teams began by collecting a library of 512 evolutionarily conserved non-coding RNAs. A technique called RNA interference was then used to silence the non-coding RNA within cells. The researchers then screened for changes, such as the increase or decrease of activity related to a certain cellular protein. In theory, if this change occurs as a sole result of altering the level of a non-coding RNA, then that non-coding RNA could well be involved.

Out of the 512 target non-coding RNAs, eight of them appeared to have a cellular function. Six appeared to affect cell proliferation, one influenced the hedgehog (Hh) signal transduction pathway, and the final one was a strong modifier of nuclear factor of activated T-cells (NFAT) signaling. The researchers decided to examine in detail this last non-coding RNA. Suspecting that it might interact with proteins, they used a technique to trap the proteins with which the non-coding RNA was interacting. There were ten, a few of which were of the class known as "importins," involved in the transport of materials from the cytoplasm to the cell nucleus. Among these was the protein "nuclear factor of activated T cells" (NFAT). The scientists found that when they blocked the non-coding RNA, the activity of NFAT increased dramatically. For this reason, they dubbed the non-coding RNA the non-coding repressor of NFAT "NRON."

The researchers are excited about their new experimental strategy which they say could be ramped up to screen thousands, rather than hundreds, of RNA samples. "You could apply this methodology to look for functions of many other non-coding RNAs," said Scripps researcher Aaron Willingham. "We have only just hit the tip of the iceberg," added Professor Peter G. Schultz, also from Scripps. "There's a whole world of this non-coding RNA."

Source: Scripps Research Institute

Edit : Merged two messages (article content and article address).
 
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