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| Xna, Xna, Read all about it |
In this series we are perusing the Nature Journal Paper about "aeDNA" (ancient environmental DNA).
We are doing so in the sense that modern human DNA segments used by cells to make "mRNA" (see short video below) are found in that ancient environment's DNA according to the results of the process explained in this Dredd Blog series.
This discovery brings up some interesting "questions".
The first such "question" emerges from current dogma-generated opinions.
It has been uttered over and over down thru modern times: "modern human DNA can not survive that long".
It has been declared in vain many times because some new discoveries are not always accepted ("contaminated!") at first, but later "ok, I guess so" takes place:
"It’s no secret that modern humans and Neanderthals interbred: most of the world’s population today has around 1 or 2 percent of Neanderthal DNA" ... "New technique pinpoints human DNA inherited from ‘ghost’ ancestors" ... "Neanderthals and Denisovans interbred with modern human ancestors, leaving behind telltale DNA in our genomes. Now we have evidence of modern human interbreeding with two much older but unknown ancestors."
(Neanderthal genes ..., New Technique). The "justification" for rejecting new age of DNA discoveries is, in this case and many others, "the samples were contaminated".
Contamination is a well known possibility, but it is so well known that competent researchers will take special care when handling ancient environmental DNA containing material.
II. RE: contamination
The authors of the aforesaid Nature paper, realizing that it is important to handle such material with the utmost care, pointed out:
"Sediment samples were obtained from the Kap København Formation in North Greenland (82° 24′ 00′′ N 22° 12′ 00′′ W) in the summers of 2006, 2012 and 2016 (see Supplementary Table 3.1.1). Sampled material consisted of organic-rich permafrost and dry permafrost. Prior to sampling, profiles were cleaned to expose fresh material. Samples were hereafter collected vertically from the slope of the hills either using a 10 cm diameter diamond headed drill bit or cutting out ~40 × 40 × 40 cm blocks. Sediments were kept frozen in the field and during transportation to the lab facility in Copenhagen. Disposable gloves and scalpels were used and changed between each sample to avoid cross-contamination. In a controlled laboratory environment, the cores and blocks were further sub-sampled for material taking only the inner part of sediment cores, leaving 1.5–2 cm between the inner core and the surface that provided a subsample of approximately 6–10 g. Subsequently, all samples were stored at temperatures below −22 °C."
(ibid, Nature Journal Paper, p. 292, emphasis added). As was pointed out in a previous post of this series, contamination can be avoided:
"Handle scientific research with care:
"The labs and protocols are designed to safeguard these precious samples from contamination. A strict working procedure guides researchers through the labs. This system, combined with positive air pressure, full personal protective equipment and a meticulous cleaning regime, provides the environment essential for preventing cross-contamination, whether from modern human DNA or between different eDNA samples."
(Human DNA Found In 2-3 Mya eDNA? - 6). Which leaves us with another possibility which is: did I extract the nucleotides properly from the FASTQ files?
III. RE: Did Dredd Blog Extract Fastq Data Properly?
Note first that the Project ENA PRJEB55522 download files are .gz files.
Some of those .gz files are ~30 gigabytes in size which will expand to ~70 gigabytes when decompressed, but those are the extremes (most files are megabytes in size, not gigabytes).
Anyway, the process I use is detailed in APNDX ONE.
IV. The Search
The search is made more difficult because of the use of fastq files rather than using fasta or gbff (GenBank) format.
Some recent results are shown in APNDX TWO.
These are from my SQL database that was populated from the NUCCORE FASTA database which has no "*" or "|" characters in it as my SQL database does.
And the way NUCCORE FASTA format is constructed with broken lines, the segments shown in APNDX TWO will not have the same sequence unless it is broken up into several lines like the NUCCORE fasta database.
To find the location in NUCCORE remove the "*" and "|" characters from the APNDX TWO segments, then begin looking for the sequence beginning with the "ATG" start codon.
You can then see if the NUCCORE segment is broken over several lines, and follow the nucleotides to the stop codon.
NOTE that the appendix is not designed to match the NUCCORE, rather it is to show how the aeDNA is found in many of the fastq files, but not in others.
The thought exercise, then, is to notice that saturation would tend to be in all samples, not scattered thin in some, but massively in others.
In future appendices I will select slices of the NUCCORE fasta data which show where the sequences in today's appendices are located with the whole.
One interesting thing easy to notice is that the "found" indicator in APNDIX TWO gives the NUCCORE record number (e.g. "found NW_025791777.1" ...
"found NW_016107297.1") which when you type it in HERE tells you the chromsome number, a lot more about that human DNA area, and gives a link to the FASTA format.
The previous post in this series is here.
