Analysis of kerogens and model compounds by time-of-flight secondary ion mass spectrometry (TOF-SIMS)

2022

Preprint

Reports of preserved cells and other soft tissues in pre-Pleistocene vertebrates, including dinosaurs, have been met with controversy within the field of vertebrate paleontology. To explain such reports, Schweitzer et al. ( 2014) hypothesized that iron-mediated radical crosslinking preserves ancient soft tissues in a manner somewhat analogous to histological tissue fixation. In 2018, Wiemann et al. proposed a second hypothesis that these soft tissues were preserved as advanced glycation/lipoxidation end products (AGEs/ALEs). The biogeochemistry underlying these hypotheses, however, remains poorly described for fossil vertebrates.This review posits a novel chemical framework describing the persistence of biological "soft" tissues into deep time. The prior iron-mediated radical crosslinking and AGE/ALE mechanisms are re-described in context of established chemistry from a diversity of scientific fields. Significantly, this framework demonstrates the hypotheses presented by Schweitzer et al. (2014) and Wiemann et al. (2018) are, in many cases, subsequent steps of a single, unified reaction mechanism, and not separate hypotheses. Knowledge of the chemical mechanisms underlying vertebrate soft tissue preservation has direct implications for molecular paleontology and archeology, including efforts at molecular sequence recovery within the ancient DNA and paleoproteomic communities. Such implications that are immediately apparent from examining the chemical framework are discussed. I.

Section: Carbonizationmentioning

confidence: 89%

A Chemical Framework for the Preservation of Fossil Vertebrate Cells and Soft Tissues

2022

Preprint

“…Recorded intensities for polyaromatic hydrocarbon and peptiderelated ion fragments (such as those detected in the Jurassic ichthyosaur 31 ) can be compared across extant and ancient histological structures. For example, elevated levels of polyaromatic related ions in one specimen relative to another would be predicted to indicate a higher degree of chemical degradation 68,[74][75][76][77] . This is one potential method for evaluating changes in fossil/sub-fossil molecular histology by geologic timepoint and depositional environment.…”

Section: Methods For Studying Fossil Molecular Histologymentioning

confidence: 99%

Molecular Histology as a Novel Proxy for Ancient DNA and Protein Sequence Preservation

2022

Preprint

Researcher ability to accurately screen fossil and sub-fossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of limited use for specimens of similar depositional environments and/or ages. Cell and tissue molecular histology is thus proposed as a proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Molecular histology as a proxy is hypothesized to elucidate why fossil/sub-fossils of some depositional environments and or geologic ages preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.

“…Recorded intensities for polyaromatic hydrocarbon and peptide-related ion fragments (such as those detected in the Jurassic ichthyosaur 38 ) can be compared across extant and ancient histological structures. For example, elevated levels of polyaromatic related ions in one specimen relative to another would be predicted to indicate a higher degree of chemical degradation 78,[100][101][102][103] . This is one potential method for evaluating changes in fossil/sub-fossil biomolecular histology by geologic timepoint and depositional environment.…”

Section: Methods For Studying Fossil/sub-fossil Biomolecular Histologymentioning

confidence: 99%

Biomolecular Histology as a Novel Proxy for Ancient DNA and Protein Sequence Preservation

2022

Preprint

Researcher ability to accurately screen fossil and sub-fossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of limited use for specimens of similar depositional environments and/or ages. Cell and tissue biomolecular histology is thus proposed as a proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossil/sub-fossils of some depositional environments and or geologic ages preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.