The Ketchum Report (Continued)

[Guest]

Southernyahoo - didn't Melba provide you with the specific data in reference to your particular sample? Or was it agreed early on that she would not provide the submitters with that kind of detail about their samples?

She did offer me the raw data at one point, but at that time, I didn't feel I would need it as it was to be part of the paper. She still owns the data as part of the agreement, but I still think she would give it to me.

Thank you SY. If I were you, I might want to ask for the data she offered to send prior. I would comply with what you previously agreed to - but I don't think it would hurt for you to get the data from your own submitted sample.

[Guest thermalman]

And then what Melissa? Just so SY could be pressured into releasing it?

[southernyahoo]

I think this is why Ketchum was puzzled by the single stands. Is it possible a primer can write itself into a genome where there is no counterpart for the sequence it attempts to find? Or would the primer completely fail and leave a gap in the sequence? How would a primer sequence a single stranded virus when it has to find a counterpart to perform it's function in the first place? Maybe I'm off in my understanding of how primers work but have watched a video on PCR.

I believe the single strand theory came about from the fact that a number of her PCR reactions failed to provide a product. This is a common problem when doing any pcr. There are a number of variables that are involved - degree of homology of the primer to the template, temperature of annealing (hybridizing the primer to the template), salt conditions, as well as GC content of the template and repetitive sequences. IMO, failure of a pcr does not lead me to think of alternative types of DNA, just that the conditions were not correct. This then lead MK to do the electron microscopy work. Reading their protocol, they did not RNAse treat their samples, which could account for some of the single stranded material. Also, if the sample DNA was degraded, or at any time "denatured" by the sample being heated then rapidly cooled, this could lead to some random single stranded DNA when the sequences improperly reannealed. If the DNA sample was degraded or denatured, this could also potentially lead to the pcr failures. BUT I do not believe the DNA described as in the electron microscopy study is in any way a native type of DNA. IMO, it is an artifact.

I have never heard of a primer writing itself into a genomic sequence (if I am understanding your question correctly). If you were doing standard sequencing (like dideoxy sequencing) failure would provide no sequence, or if it annealed incorrectly (due to too low a hybridization temp), this could generate spurious sequence that is not relevant to the region of interest. For sequencing a single stranded DNA virus, you would need to synthesize the complementary strand first, which could then be used as a template for pcr. The same primer could be used to synthesize the complementary strand as well as one of the two primers of the pcr reaction. Hope this answers your questions.

Do you think if the samples were from known animals, that an outside lab like SeqRight should have trouble sequencing nuclear DNA when the gels showed good target DNA?

[Guest njjohn]

TM - no, I don't think SY would or should be pressured. If he were to get the data, he can do with it what he chooses. He could approach someone he trusted and have it looked at. The mtDNA isn't as time consuming to view as the nuDNA, and because it's already sequenced, he can get a second opinion. At the very least, he'd always have a copy for future reference.

If it does turn out to be what Dr. Ketchum claims it is, it's a piece of history. Why wouldn't you want a copy?

[Guest thermalman]

REALLY, njjohn REALLY? History on this board has proven otherwise.

[Guest]

Thermalman read this sentence I typed again -

I would comply with what you previously agreed to

I never even asked him to post it publicly or anything else. This is HIS sample - these are HIS results. If that were my sample with all these questions floating around - I would want that data for my own information.

Please don't put words in my mouth. Thanks

[Guest thermalman]

Never put any words in your mouth Melissa. Just a general surmise on my part, as that what seems to be the trend and precedent on the board towards those who have info and refuse to release it to the members. Just reread the past 15 pages of posts. No wonder witnesses are hesitant to come forth on the forum.

Edited March 27, 2013 by thermalman

[Guest maelsquatch]

The single-strand DNA is a major problem for me. As I have posted before, NO known organism besides some viruses have single-strand DNA, certainly no known primates, extant or extinct. So, we are to accept that an unknown hominin with a DNA structure not seen anywhere else in the known world hybridized with a human female with a different DNA structure and created a viable, fertile offspring? Humans cannot even produce an offspring with our closest known relative and they have the same DNA structure. I could accept that a hybridization event occurred between two closely related species, but not two that are so different that the very structure of the DNA is different.

For the scientific community to accept that the single-strand DNA components of the genome are anything more than the result of problems in the lab would require a totally new understanding of how nuclear chemistry works.

[Guest]

@rr "TM, I do believe you have misquoted me - I don't recall saying that (please note the post # and I will double check)."

I couldn't have possibly misquoted you, as I cut and pasted your direct comments to my post.

That is technically correct, but misleading. You were quoting Ridgerunner, who was quoting Maelsquatch. See Maelsquatch @ 2016; Ridgerunner at 2028.

@ lc "Now, assuming your interpretation is correct, how would Dr. Ketchum, DVM determine which base pairs came from which parent?"

@rr "And if you are looking at one's DNA, you can not say the male progenitor nuclear DNA is novel (which I am interpreting as coming from the paternal lineage), as the resulting genome is a mixture of both parents. The only case where you could say this is with the Y chromosome, but all nuDNA data is from CH11. Unless you have the paternal DNA to compare it to, you can not make this statement."

Cannot both, the maternal and paternal nDNA, be seperated and determined from which parent it came from through DNA Profiling?

No.

Edited March 27, 2013 by leisureclass

[Guest]

Do you think if the samples were from known animals, that an outside lab like SeqRight should have trouble sequencing nuclear DNA when the gels showed good target DNA?

They should know their business. But MK does report in the paper several times that things either failed to amplify or gave different sized product. And if the labs were told the samples were human (directly or implied), they may have had some problems with primer choices. I have never worked with this lab and don't know the scope of project that MK had employed them to do.

The samples in fig 10 do not look excessively degraded (sample 140 looks to have a good amount of lower molecular weight material (RNA?)). Denatured DNA would also run as a high mw band (or may even be stuck in the well of the gel). I don't know of the quality of the other samples but given that they were not fresh samples (and some may have been stored for years in less that perfect conditions), degradation would not surprise me.

[Guest thermalman]

Well, how do you like that. It seems I did quote ms in rr's post. My apologies to rr. But my question should now be directed to ms instead.

[Guest maelsquatch]

Well, how do you like that. It seems I did quote ms in rr's post. My apologies to rr. But my question should now be directed to ms instead.

OK, here is the quote from Thomsquatch:

The findings were remarkably consistent: mtDNA (mitochondrial DNA), which is indicative of the female component of the genome, came back as human! The nDNA (nuclear DNA from the male progenitor) was found to be ‘novel’, which is geneticist code for “doesn’t match anything previously extracted.â€

Emphasis mine.

If Mr. Powell wanted to indicate that he was discussing only the male contribution to the nuDNA, he should have worded it more clearly. When he describes nDNA as "nuclear DNA from the male progenitor", it makes it appear that he is saying ALL nuDNA is from the male progenitor. And stating that just after saying mtDNA is indicative of the female component of the genome emphasizes that implication.

Perhaps he did mean to only discuss the male contribution to the nuDNA. That's not how I read it, however. Actually, I read it at first as the female part of the genome came from mtDNA and the male part from the nuDNA. And that makes NO SENSE.

The nuclear DNA as interpreted by Dr. Ketchum is novel in and of itself. The only reason she is claiming that the novel parts of the nuDNA are from the male progenitor is because the mtDNA came back 100% human. That's the only reason to talk about the mtDNA in relation to the nuDNA. Otherwise, they don't have anything to do with one another. If the mtDNA had come back part human and part unknown or totally unknown, then she couldn't conclude which progenitor was male and which was female.

[Guest thermalman]

Thank you ms. In other words, any "novel/new" nDNA, from the paternal contributor, can be stated as such, a new species, as long as the mtDNA is 100% human? Or, how would a "novel/new nDNA otherwise be declared by geneticists?

Edited March 27, 2013 by thermalman

[southernyahoo]

Y chromosome DNA is nuclear and from the male progenitor only, and TP could have spoken in reference to it, but if the mtDNA had come back part human and part unknown , then that would have been a red flag to anyone because it doesn't recombine. Unknown or sufficiently diverged from other great apes but closest to those would be perfect, yet doesn't happen.

[Guest]

Y chromosome DNA is nuclear and from the male progenitor only, and TP could have spoken in reference to it, but if the mtDNA had come back part human and part unknown , then that would have been a red flag to anyone because it doesn't recombine. Unknown or sufficiently diverged from other great apes but closest to those would be perfect, yet doesn't happen.

Did Ketchum's findings mention the Y-chromosome at all? I don't recall seeing it her paper.