Fluoridation of a lizard bone embedded in Dominican amber suggests open-system behavior

Barthel, H. Jonas; Fougerouse, Denis; Geisler, Thorsten; Rust, Jes

doi:10.1371/journal.pone.0228843

Cited by 14 publications

(44 citation statements)

References 48 publications

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“…One difficulty in searching for ancient proteins comes from environmental and laboratory contamination (Buckley et al 2008(Buckley et al , 2017Bern et al 2009). There is mixed evidence that amber might act to trap some ancient amino acids, but the amino acid profiles and racemization patterns are not what would be expected from a closed system of ancient amino acids (McCoy et al 2019;Barthel et al 2020). Examining proteins deposited within biomineralised calcium carbonate (intra-crystalline) helps to mitigate this issue.…”

mentioning

confidence: 99%

Non-Avian Dinosaur Eggshell Calcite Contains Ancient, Endogenous Amino Acids

Saitta

Vinther

Crisp³

et al. 2020

Preprint

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Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded.However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, thermally matured, sub-fossil, and ~3.8 Ma avian eggshell, as well as ~30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, along with similar concentrations of free versus total hydrolysable amino acids, likely suggests complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, suggestive of kerogen formation deriving from eggshell lipids. Raman spectroscopy yields bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules.Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation even if such reactions might be slowed in exceptional circumstances.The evidence for complete hydrolysis and degradation of most amino acids in the eggshell raises concern about the validity of reported polypeptide sequences from open-system nonavian dinosaur bone and other Mesozoic fossils.3

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confidence: 99%

Non-Avian Dinosaur Eggshell Calcite Contains Ancient, Endogenous Amino Acids

Saitta

Vinther

Crisp³

et al. 2020

Preprint

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“…When Alleon et al (21) subtracted the summed 64 cm -1 and 128 cm -1 frequency components from the original spectra (21, figs. 1b, d) virtually no signal remained, not even the significant D-and G-bands (-C=C-and -C-Nfunctional groups in unmetamorphosed carbonaceous residues) associated with unordered organic matter (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(25)(26)(27)(28)(29)(30)(31)(32). Alleon et al (21) did not discuss this unlikely result.…”

Section: Summed Frequency Components Closely Resemble Their Original mentioning

confidence: 98%

“…Raman spectroscopy is an established method for characterizing the total chemical composition of potentially heterogenous materials (1,2). Applications of non-destructive, in situ Raman microspectroscopy have resulted in rapid progress in understanding biomolecule fossilization and the detection of biosignatures based on comparative statistical analyses of fossil organic matter (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). The in situ approach facilitates rapid non-destructive analysis of surfacecleaned bio-and geomaterials without requiring timeconsuming extractions of the organic matter.…”

Section: Introductionmentioning

confidence: 99%

“…Ordination methods are most commonly used for comparative spectral analyses in the search for patterns in the total organic composition of complex biological samples (16)(17)(18)(19)(20). A number of advantages, including time-efficient nondestructive analysis, wide availability and low operating cost of equipment, and utility of the results, make Raman and complementary types of light spectroscopy ideal for initial molecular assessments of paleontological and geological materials (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15).…”

Section: Introductionmentioning

confidence: 99%

“…A diversity of studies conducted by different laboratories (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) have recovered very similar patterns in the molecular makeup of fossil organic matter in independently acquired in situ Raman spectra. However, a recent Perspective by Alleon et al (21) claimed that the results of a selected subset of these studies (3,4,6,11,12,15) are invalid, based on the assertion that published spectra, despite resembling previous independent Raman analyses (7-10, 13, 14), are the result of instrumental artefacts reflecting sinusoidal edge filter ripples.…”

Section: Introductionmentioning

confidence: 99%

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Validation of biosignatures confirms the informative nature of fossil organic Raman spectra

Wiemann

Deg

2021

Preprint

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Raman spectroscopy has facilitated rapid progress in the understanding of patterns and processes associated with biomolecule fossilization and revealed the preservation of biological and geological signatures in fossil organic matter. Nonetheless six large-scale statistical studies of Raman spectra of carbonaceous fossils, selected from a number of independent assessments producing similar trends, have been disputed. Alleon et al. applied a wavelet transform analysis in an unconventional way to identify frequency components contributing to two baselined spectra selected from these studies and claimed similarities with a downloaded edge filter transmission spectrum. On the basis of indirect comparisons and qualitative observations they argued that all spectral features detected, including significant mineral peaks, can be equated to edge filter ripples and are therefore artefactual. Alleon et al. extrapolated this conclusion to dispute not only the validity of n>200 spectra in the studies in question, but also the utility of Raman spectroscopy, a well established method, for analysing organic materials in general. Here we test the claims by Alleon et al. using direct spectral comparisons and statistical analyses. We present multiple independent lines of evidence that demonstrate the original, biologically and geologically informative nature of the Raman spectra in question. We demonstrate that the methodological approach introduced by Alleon et al. is unsuitable for assessing the quality of spectra and identifying noise within them. Statistical analyses of large Raman spectral data sets provide a powerful tool in the search for compositional patterns in biomaterials and yield invaluable insights into the history of life.

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Raman spectroscopy is a powerful tool in molecular paleobiology: An analytical response to Alleon et al. (https://doi.org/10.1002/bies.202000295)

Wiemann

Briggs

2022

BioEssays

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A recent article argued that signals from conventional Raman spectroscopy of organic materials are overwhelmed by edge filter and fluorescence artefacts. The article targeted a subset of Raman spectroscopic investigations of fossil and modern organisms and has implications for the utility of conventional Raman spectroscopy in comparative tissue analytics. The inferences were based on circular reasoning centered around the unconventional analysis of spectra from just two samples, one modern, and one fossil. We validated the disputed signals with in situ Fourier‐Transform Infrared (FT‐IR) Spectroscopy and through replication with different lasers, filters, and operators in independent laboratories. Our Raman system employs a holographic notch filter which is not affected by edge filter or other artefacts. Multiple lines of evidence confirm that conventional Raman spectra of fossils contain biologically and geologically meaningful information. Statistical analyses of large Raman and FT‐IR spectral data sets reveal patterns in fossil composition and yield valuable insights into the history of life.

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Fluoridation of a lizard bone embedded in Dominican amber suggests open-system behavior

Cited by 14 publications

References 48 publications

Non-Avian Dinosaur Eggshell Calcite Contains Ancient, Endogenous Amino Acids

Non-Avian Dinosaur Eggshell Calcite Contains Ancient, Endogenous Amino Acids

Validation of biosignatures confirms the informative nature of fossil organic Raman spectra

Raman spectroscopy is a powerful tool in molecular paleobiology: An analytical response to Alleon et al. (https://doi.org/10.1002/bies.202000295)

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