Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally well-preserved dinosaur cartilage (!!!)

1) is simple differences in disciplines and expertise, there are very different realities when it comes to extinct vs extant DNA and a true understanding of molecular approaches (we have had discussions surrounding assessing nuclear receptors). There is a hesitation to use unaccepted approaches, and a hesitation to do genetic material at a base-pair resolution because of Jurassic Park! ——I had “a feeling” that this paper represented a work published from “a universe different from our own.” What THEY think and conclude and wish to do … is simply FAR AWAY from our approaches to the same data.

2) they used approaches that were “accepted” in the field. The reality is the approach to their science is alien compared to anything molecular biology or medically related. Really a cultural difference and I think a reality that any sequences they recover will likely be very high abundance and likely conserved to extant species. The group previously suffered much grief related to their MS analysis of preserved protein fragments in T-Rex. ——I didn’t know this.

3) reality – the only thing she will get is garbage as far a sequence; I discussed with her the specificity of her “DNA-stains”, and she wasn’t open to some of my suggestions/critiques, and never came through with some of her T-Rex “cells” for me to work with – I think she is seeing remnant biomolecules, but not sure how far this can go beyond high abundance repetitive sequences of either protein or nucleic acid. ——I’m sure the DNA will be “garbage sequence”, but even 2 or more nuclleotides hooked together … would confirm “direct evidence that DNA was detected,” as compared to these silly PI and DAPI stains showing indirect evidence.

Any how – Mary is an interesting scientist and is at the forefront in this research area – this is the leading edge! ——Again, thank you MUCH for the clarification. 😊 Dan

On Tue, Mar 3, 2020 at 8:39 PM Nebert, Daniel (nebertdw) wrote:

This fascinating topic falls within the scope of these GEITP pages that continuously search for cutting-edge articles on evolution. A dinosaur nesting-ground — yielding dozens of disarticulated nestlings that have been assigned to the herbivorous duck-billed dinosaur Hypacrosaurus stebingeri was discovered during the 1980s in the Upper Cretaceous Period (from 100.5 until 66 million years ago) in northern Montana. Several limb and skull fragments of these nestlings were examined microscopically to answer growth-related questions and to describe different types of cartilage. A calcified cartilage fragment found within a supraoccipital region (top of the posterior skull) in ground-section was especially remarkable.

Within the chondro-osseous junction (i.e. that part of the growth plate where bone replaces cartilage) closest to the left exoccipital, the tissues exhibited excellent microscopic preservation, such that cartilage could be distinguished from bone — by revealing a translucent (semi-transparent), amorphous (without a clearly defined shape or form) extracellular matrix (ECM) and round, hypertrophic (enlarged) chondrocyte lacunae (air-filled spaces in cartilage). At higher magnification, cellular structures still sharing a single lacuna (i.e. air pocket with a cell doublet) were seen — consistent with cartilage cells (chondrocytes) at the end of mitosis (cell division resulting in two daughter cells). Although many lacunae appeared empty, other lacunae contained a material distinct from

the matrix — including a darker material, consistent in shape and location with a nucleus. This microscopic picture is comparable to features of extant calcified cartilage, observed in ground sections of juvenile emu (defleshed) skulls, where some lacunae are

empty, and others retain cells and intracellular contents, including nuclei.

Authors [see attached article] found histochemical and immunological evidence that supports in situ preservation of ECM components found in extant cartilage — including glycosaminoglycans and collagen type II. Moreover, the isolated Hypacrosaurus chondrocytes reacted positively with two DNA-intercalating stains — suggesting that DNA, or at least the chemical markers of DNA [e.g. chemically altered base-pairs that can still react to PI (propidium iodide) and DAPI (4′,6-diamino-2-phenylindole-dihydrochloride)] may be stable for millions of years. Specific DNA staining was only observed inside the isolated cells, suggesting that endogenous nuclear material had survived the process of fossilization. These findings support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material (era between the Paleozoic and Cenozoic eras, comprising the Triassic, Jurassic, and Cretaceous periods), and suggest that remnants of once-living chondrocytes, including their DNA, may be preserved for millions of years.

Shades of Michael Crichton’s Jurassic Park…?? However, what these GEITP pages cannot understand is: Why, in this day-and-age, this group — (of paleontology, anatomy, biology and geology researchers) — did not team up with some DNA-sequencing lab (before publishing the attached article), to detect any nucleotide sequence. [Or perhaps they tried, and it was unsuccessful?] Authors do mention (at the end of the ‘Discussion’ section) that “Although extensive research and sequencing is required to further understand DNA preservation of Mesozoic material, along with its chemical and molecular alterations, our data suggest the preserved nuclear material in Hypacrosaurus was in a condensed state at the time of the death of the animal, which may have contributed to its stability. We propose that DNA condensation may be a favorable process to its fossilization. Additionally, as

was suggested for protein fossilization, crosslinking may be another mechanism involved in the preservation of DNA in deep time.”

Natl Sci Rev doi: 10.1093/nsr/nwz206; ePub 12 Jan 2020

COMMENT:
I thought I was being “a bit harsh” — in criticizing this “dinosaur DNA” paper (which YOU had suggested for GEITP) — but I received a message from someone in the same department with the senior author. And it’s exactly as I thought: this paleontologists are not in the same universe as molecular geneticists and biologists. 😊

Best, Dan

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Subject: Re: Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally well-preserved dinosaur cartilage (!!!)

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