Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin

Edwards, Nicholas P.; Barden, Holly E.; Dongen, Bart E. van; Manning, Phillip L.; Larson, Peter L.; Bergmann, Uwe; Sellers, William I.; Wogelius, R. A.

doi:10.1098/rspb.2011.0135

Cited by 54 publications

(59 citation statements)

References 33 publications

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“…It is likely that these, and possibly other reactive residues, progressed down degradative pathways that resulted in additional modifications yielding mass defects and/or possible backbone cleavage. Consistent with this finding, infrared mapping of proteins from 50-my-old soft tissues suggested that diagenesis might affect thiol stability, thereby favoring -SH group modifications hindering MS-detection (66).…”

Section: Table I Proteins Identified In Ice Age Bison Skull (Identifisupporting

confidence: 68%

Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen

Hill

Wither

Nemkov

et al. 2015

Molecular & Cellular Proteomics

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Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ϳ120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in wellpreserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. During the last decade, paleontology and taphonomy (the study of decaying organisms over time and the fossilization processes) have begun to overlap with the field of proteomics to shed new light on preserved organic matter in fossilized bones (1-4). These bones represent a time capsule of ancient biomolecules, owing to their natural resistance to post mortem decay arising from a unique combination of mechanical, structural, and chemical properties (4 -7).Although bones can be cursorily described as a composite of collagen (protein) and hydroxyapatite (mineral), fossilized bones undergo three distinct diagenesis pathways: (i) chemical deterioration of the organic phase; (ii) chemical deterioration of the mineral phase; and (iii) (micro)biological attack of the composite (6). In addition, the rate of these degradation pathways are affected by temperature, as higher burial temperatures have been shown to accelerate these processes (6,8). Though relatively unusual, the first of these three pathways results in a slower deterioration process, which is more generally mitigated under (6) specific environmental constraints, such as geochemical stability (stable temperature and acidity) that promote bone mineral preservation. Importantly, slower deterioration results in more pre...

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Section: Table I Proteins Identified In Ice Age Bison Skull (Identifisupporting

confidence: 68%

Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen

Hill

Wither

Nemkov

et al. 2015

Molecular & Cellular Proteomics

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“…A combination of mass spectrometry and lowdestructive synchrotron techniques, including rapid scan XRF and mXAS imaging and FTIR spectroscopy was used in a recent multitechnique study of fossilised reptile skin, producing spectacular results. [89] We suggest using bulk XAS for quick prescreening and spectroscopic measurements in the whole nail sample to select the samples with the highest arsenic signals. Pre-screened nail samples with high arsenic content can later be re-used in other, more time-consuming measurements, including mXAS imaging, combined with near-infrared Fourier transform Raman spectroscopy and micro-diffraction.…”

Section: Resultsmentioning

confidence: 99%

Synchrotron X-ray absorption spectroscopy analysis of arsenic chemical speciation in human nail clippings

et al. 2014

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Environmental context. Chronic ingestion of arsenic leads to its accumulation in keratinous tissues, which can represent a risk factor for developing cancer. We use synchrotron X-ray absorption spectroscopy to investigate chemical bonding of arsenic in the keratins from nail clippings of volunteers from areas in Atlantic Canada with low-to-moderate arsenic contamination of drinking water. The study helps our understanding of arsenic metabolism and its role in cancer development.Abstract. Drinking water aquifers in many areas of the world have naturally elevated levels of inorganic arsenic exceeding the World Health Organization limit. Arsenic concentrations in human nail clippings are commonly used as a biomarker of exposure to this toxic element. However, the chemical form of arsenic accumulated in nail tissues is not well determined. We employed synchrotron microprobe and bulk X-ray absorption spectroscopy techniques to analyse the concentration and chemical speciation of arsenic in the finger-and toenail clippings of volunteers living in the vicinity of Sackville, New Brunswick, Canada. This area is known to have low-to-moderately elevated levels of arsenic in ground water. Arsenic species in clippings were represented by three main groups, distinguished by the As-K near-edge X-ray absorption fine structure spectra: (1) As III type, which can be fitted as a mixture of As bound to thiols, and also to oxygen or methyl groups, with a small contribution from As V species, (2) As V type, best represented by fitting arsenate in aqueous solution and (3) The As III þ As V mixture type. The high proportion (%) of sulfur-bound arsenic species most likely corresponds to binding between arsenic (in its trivalent and, to a lesser extent, pentavalent forms) and cysteine residues in the sulfur-rich fraction of keratin and keratin-associated proteins. Further work is needed to explore whether these chemical species could be used as toxicity biomarkers of human exposure to elevated levels of As in drinking water.

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“…However, more recently leading workers in the field (Manning et al 2009;Edwards et al 2011) have developed methods involving the use of the latest technology and analytical techniques that includes small angle X-ray scattering, Synchrotron Rapid Scanning X-ray Fluorescence (SRS-XRF Fourier transform infrared spectroscopy (FTIR), gas chromatography mass spectrometry (Py-GCMS), and amino acid analyses, which, importantly is either nondestructive to the fossil material or uses minute samples for analysis. Using such methods, Manning et al (2009) showed that the amino acid composition of the mineralized skin envelope of Edmontosaurus MRF-03 clearly differed from the surrounding matrix.…”

Section: Organic Analysis Of the Dinosaur Integumentmentioning

confidence: 99%

“…It seems that it also ensured that some breakdown products of organic molecules at the point of burial, whether endogenous to MRF-03 or of microbial origin, were preserved. Edwards et al (2011) used nondestructive Fourier Transform Infrared (FTIR) spectroscopy in their work on the mapping of ancient fossil organic material without damage to the fossil specimens. Their results in a study of an Eocene specimen (50 MYR old) of fossilized reptile skin demonstrated that not only was it possible but the material was not a simple impression, mineralized replacement, or an amorphous organic carbon film, but that it contained a partial remnant of the living organism's original chemistry, in this case derived from the animal's proteinaceous skin.…”

Section: Organic Analysis Of the Dinosaur Integumentmentioning

confidence: 99%

Dinosaur Integument

Lingham‐Soliar¹

2014

The Vertebrate Integument Volume 1

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Infrared mapping resolves soft tissue preservation in 50 million year-old reptile skin

Cited by 54 publications

References 33 publications

Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen

Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen

Synchrotron X-ray absorption spectroscopy analysis of arsenic chemical speciation in human nail clippings

Dinosaur Integument

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