Preservation of feather fibers from the Late Cretaceous dinosaur Shuvuuia deserti raises concern about immunohistochemical analyses on fossils

Saitta, Evan T.; Fletcher, Ian; Martin, Peter; Pittman, Michael; Kaye, Thomas G.; True, Lawrence D.; Norell, Mark A.; Abbott, Geoffrey D.; Summons, Roger E.; Penkman, Kirsty; Vinther, Jakob

doi:10.1016/j.orggeochem.2018.09.008

Cited by 30 publications

(47 citation statements)

References 73 publications

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“…Despite the many well‐established ways to control for cross reactivity, the issue remains a topic of active debate in the paleomolecular community. For example, a recent study claimed to refute previous immunological data derived from Shuvuuia fibers, a study that was repeated by different investigators, using different antibodies to feather β‐keratin (or corneous β‐protein, CβP), yet which yielded similar results. However, the multiple differences in sample treatment and analytical methodology between the original study and the follow up study make this claim a tenuous one.…”

Section: Protein Studies On Mesozoic Fossilsmentioning

confidence: 95%

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

et al. 2019

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Mary Higby Schweitzer would like to dedicate this review to Rune Martinson, a brave warrior in the fight against cancer who left us far too soon.Molecular studies have contributed greatly to our understanding of evolutionary processes that act upon virtually every aspect of living organisms. However, these studies are limited with regard to extinct organisms, particularly those from the Mesozoic because fossils pose unique challenges to molecular workflows, and because prevailing wisdom suggests no endogenous molecular components can persist into deep time. Here, the power and potential of a molecular approach to Mesozoic fossils is discussed. Molecular methods that have been applied to Mesozoic fossils-including iconic, non-avian dinosaurs-and the challenges inherent in such analyses, are compared and evaluated. Taphonomic processes resulting in the transition of living organisms from the biosphere into the fossil record are reviewed, and the possible effects of taphonomic alteration on downstream analyses that can be problematic for very old material (e.g., molecular modifications, limitations of on comparative databases) are addressed. Molecular studies applied to ancient remains are placed in historical context, and past and current studies are evaluated with respect to producing phylogenetically and/or evolutionarily significant data. Finally, some criteria for assessing the presence of endogenous biomolecules in very ancient fossil remains are suggested as a starting framework for such studies.

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Section: Protein Studies On Mesozoic Fossilsmentioning

confidence: 95%

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

et al. 2019

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“…Nevertheless, the values obtained from both estimations are roughly similar. Therefore, the paleotemperature inscribed in A. vesicularis from the Wido Volcanics would be roughly 340 ± 30 • C. This temperature is sufficient to burn avian feathers into a complete black ash (Saitta et al, 2018, Supplementary Figures S142, S143).…”

Section: Raman Spectroscopymentioning

confidence: 99%

“…Unfortunately, many of the reports were merely based on the morphology of putative biological structure, thereby another line of evidence should be applied to guarantee the biogenicity of those structures (e.g., Schidlowski, 2001;Gupta et al, 2007;Stein et al, 2019; see also discussion of Schopf et al, 2005). On the other hand, Schweitzer et al (2005) showed the presence of organic materials in the radial section of a titanosaur eggshell using an immunohistochemical approach, which is a superb tool to see a distribution of in situ organic materials and can identify the type of organic material using antigen-antibody reaction (but see also Saitta et al, 2018). Nevertheless, this approach requires rather complicated preparation steps and laboratory resources (see electronic appendix of Schweitzer et al, 2005) that are not easily available to most paleontologists.…”

Section: Introductionmentioning

confidence: 99%

Raman Spectroscopy Detects Amorphous Carbon in an Enigmatic Egg From the Upper Cretaceous Wido Volcanics of South Korea

et al. 2020

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Raman spectroscopy has been widely used in micropaleontology and organic geochemistry to identify carbonaceous materials and evaluate their thermal maturity in fossils or metasedimentary rocks. Meanwhile, fossil egg researches have mostly focused on biomineralized calcite, but preserved carbonaceous (or possibly organic) materials inside the eggshells have been usually neglected until recently. Here we report an enigmatic egg from the Wido Volcanics (Upper Cretaceous) of South Korea that was analyzed using diverse methods including polarized light microscope, scanning electron microscope, electron probe microanalyzer, electron backscatter diffraction, and Raman spectroscopy. The eggshell not only shows the crystallography of archosaurian eggshells but also contains peculiar dark bands, which were previously known as the trait of fossil and modern Crocodyliformes eggshells. Raman spectroscopic analysis showed that the dark bands are mainly due to amorphous carbon, as evidenced by the clear graphite (G) and disordered (D) bands. The deconvolution of amorphous carbon peaks and resultant parameters made it possible to infer the paleotemperature inscribed in the eggshell. The result suggests that preserved amorphous carbon in the fossil eggshells can be identified using Raman spectroscopy and Raman parameters may make it possible to compare the thermal maturity of spatiotemporally diverse fossil eggshells. The biogenicity of the dark band is not clear because Raman spectroscopic analysis is not sufficient to confirm biogenicity. However, overall distribution of the dark band may imply the biogenic origin. It is apparent that the material of this study is not a dinosaur egg but might belong to a crocodyliform or choristoderan egg, and even other non-dinosaur archosaur can be a candidate as well.

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“…The reports of collagen peptides from Mesozoic dinosaur fossils are often viewed as particularly exciting in paleontology as they, if genuine, could dramatically enhance our understanding of the evolutionary biology of extinct organisms through deep time [5]. Despite the increasing number of reports about the preservation of endogenous biocomponents in dinosaur fossils over the last decade, their existence remains controversial due to concerns about exogenous contamination from microbial biofilms [12] and other sources associated with analytical procedures [13][14][15], and to the difficulty in reasonably explaining the mechanisms for their exceptional preservation [5].…”

Section: Discussionmentioning

confidence: 99%

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

Liang

Lau

Saitta

et al. 2020

Environmental Microbiome

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Background: Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone. Results: Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenomeassembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate.

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Preservation of feather fibers from the Late Cretaceous dinosaur Shuvuuia deserti raises concern about immunohistochemical analyses on fossils

Cited by 30 publications

References 73 publications

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils

Raman Spectroscopy Detects Amorphous Carbon in an Enigmatic Egg From the Upper Cretaceous Wido Volcanics of South Korea

Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America

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