A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time

Marine, Earth, and Atmospheric Sciences, North Carolina State University, , Campus Box 8208, Raleigh, NC 27695, USA, North Carolina Museum of Natural Sciences, , 11 West Jones Street, Raleigh, NC 27601, USA, Museum of Paleontology, University of California, , Berkeley, CA 94720, USA, Department of Material Sciences and Engineering, University of California, , Berkeley, CA 94720, USA, CHORI (Children's Hospital Oakland Research Institute), , 5700 Martin Luther King, Jr. Way, Oakland, CA 94609, USA, Department of Molecular and Structural Biochemistry, North Carolina State University, , Raleigh, NC 27695-7622, USA, Advanced Light Source, Lawrence Berkeley National Laboratory, , Berkeley, CA 94720, USA.
Proceedings of the Royal Society B: Biological Sciences (Impact Factor: 5.05). 01/2014; 281(1775):20132741. DOI: 10.1098/rspb.2013.2741
Source: PubMed


The persistence of original soft tissues in Mesozoic fossil bone is not explained by current chemical degradation models. We identified iron particles (goethite-αFeO(OH)) associated with soft tissues recovered from two Mesozoic dinosaurs, using transmission electron microscopy, electron energy loss spectroscopy, micro-X-ray diffraction and Fe micro-X-ray absorption near-edge structure. Iron chelators increased fossil tissue immunoreactivity to multiple antibodies dramatically, suggesting a role for iron in both preserving and masking proteins in fossil tissues. Haemoglobin (HB) increased tissue stability more than 200-fold, from approximately 3 days to more than two years at room temperature (25°C) in an ostrich blood vessel model developed to test post-mortem 'tissue fixation' by cross-linking or peroxidation. HB-induced solution hypoxia coupled with iron chelation enhances preservation as follows: HB + O2 > HB - O2 > -O2 ≫ +O2. The well-known O2/haeme interactions in the chemistry of life, such as respiration and bioenergetics, are complemented by O2/haeme interactions in the preservation of fossil soft tissues.

    • "Even if the best peptides to use for degradation assessment can be reliably predicted in advance from a closely related species, they may not always be preserved in a given fossil, or may not be recovered in analysis even when they are preserved. [28] Furthermore, it is unknown how changes to the sequence and 3D structure of proteins by diagenetic modifications, such as formation of advanced glycation end products (AGEs) [29] or inclusion of diagenetic iron on the proteins, [30] may further alter deamidation rates, potentially arresting this process while preserving peptides into geologic time and resulting in extreme deviations from 'expected' glutamine deamidation levels. Additional factors may further complicate efforts to establish a reliable relationship between age and deamidation. "
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    ABSTRACT: Rationale Much credence has been given in the paleoproteomic community to glutamine deamidation as a proxy for the age of proteins derived from fossil and subfossil material, and this modification has been invoked as a means for determining the endogeneity of molecules recovered from very old fossil specimens. Methods We re-evaluated the relationship between glutamine deamidation and geologic time by examining previously published data from five recent mass spectrometry studies of archeaological fossils. Deamidation values recovered for fossils were graphed against their reported chronologic age using WebPlotDigitizer. Results The experimental data that has been produced from fossil material to date show that the extent of glutamine deamidation does not correspond to the absolute age of the specimens being examined, but rather show extreme variation between specimens of similar age and taxonomic affinity. Conclusions Because deamidation rates and levels can be greatly affected by numerous chemical and environmental factors, we propose that glutamine deamidation is better suited as an indicator of preservational quality and/or environmental conditions than a mark of the endogeneity or authenticity of ancient proteins.
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    ABSTRACT: Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ~67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.
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    ABSTRACT: We used here a scanning electron microscopy (SEM) approach that detected backscattered electrons (BSE) and X-rays (from ionisation processes) along a large-field (LF) scan, applied on a Cretaceous fossil of a shrimp (area ~280 mm2) from Araripe Sedimentary Basin. High-definition LF images from BSE and X-rays were essentially generated by assembling thousands of magnified images that covered the whole area of the fossil, thus unveiling morphological and compositional aspects at length scales from micrometres to centimetres. Morphological features of the shrimp such as pleopods, pereopods and antenna located at near-surface layers (undetected by photography techniques) were unveiled in detail by LF BSE images and in calcium and phosphorus elemental maps (mineralised as hydroxyapatite). LF elemental maps for zinc and sulphur indicated a rare fossilisation event observed for the first time in fossils from Araripe Sedimentary Basin: the mineralisation of zinc sulphide (ZnS) interfacing to hydroxyapatite in the fossil. Finally, a dimensional analysis of the phosphorous map led to an important finding: the existence of a fractal characteristic (D=1.63) for the hydroxyapatite-matrix interface, a result of physical-geological events occurring with spatial scale invariance on the specimen, over millions of years.
    Full-text · Article · Sep 2015 · Analytical Chemistry