The isolation and amino acid composition of the bone collagen in pleistocene mammals

A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics

The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.

Fossil proteins in vertebrate calcified tissues

Selected fossil vertebrates and the enclosing sediments dating from 1300 years B.C. to approximately 400 million years ago were subjected to amino acid assay. The amino acid analyses revealed little evidence of intact collagen in fossils of Tertiary, Mesozoic or Palaeozoic age. There was, however, evidence of contemporary proteinaceous material which may have been derived from bacteria. In Palaeozoic material the analyses detected a general background of amino acids common to both fossils and sediments. The degree of racemization was routinely determined as a means of measuring modern contamination of geologically older samples. An electron microscope study of Quaternary (Pleistocene) collagen revealed a significant reduction of the 64 nm banding to about 50 nm. The same Pleistocene material gave amino acid compositional profiles typical of collagen. However, when this material was subjected to digestion by the proteolytic enzymes collagenase, pronase and subtilisin, the resulting peptide fingerprints showed small but significant differences from those obtained from modern collagen digests, indicating the possibility of changes having occurred during fossilization affecting susceptible cleavage sites in the molecule.

Microscopical focal destruction (tunnels) in exhumed human bones

This is a survey of microscopical focal destruction in exhumed human bones from several countries and burial times. The single change (destruction) seen in these bones contrasts with the sequence of changes in pathological processes (destruction, cellular infiltration, new bone formation and healing). The absence of cells stresses the importance of size and shape, in three dimensions, and contents of the destructive foci. Focal mineral redeposition (e.g. cuffing) is characteristic of most forms of tunnels, and is usually associated with focal loss of mineral and bone matrix, partial or whole. In one kind of foci/tunnels (Wedl's) redeposition is restricted to packed osteons. The accumulation of the waste products of the invading organism in the surrounding tissue may hinder or stop the growth of the organism and consequential bone destruction. Later the redeposited mineral may be leached out and the bone thus ‘returned to normal’ will allow further growth of the invader and renewed destruction. Desiccation after exhumation soon ‘fixes’ the redeposited mineral. Mineral redeposition is never found in pathological changes.

Examination of transverse and longitudinal sections together with the comparison of the changes in the mid-zone of cortical bone with those in the inner and outer zones is helpful in understanding the progress of the changes. No invasion by organisms of the lamellar tissue from the osteon canals was seen although this must be the rule. The tunnels in bones and teeth are compared, and show that the contents are, with one exception, not related to any anatomical structure. There is only destruction, and no new bone can be laid down in these postmortem changes.

One kind of focus/tunnel does not change into or overlap another. The results of experimental burials in garden soils were indecisive.

Four kinds of such well-defined changes are described, but the examination of specimens from a wider range of provenances will almost certainly reveal others and may call for modifications of the conclusions of this paper. The cause of these changes is yet to be established; it is not physico-chemical, but is probably bacterial or fungal. Although the invasion must proceed from the cortical surfaces via the osteon canals, these canals persist in even the oldest specimens. These foci/tunnels probably occur in buried bones throughout the world where the inhumation environment is favourable. They have been reported from early geological periods, and in this study were found in pterodactyl bones from the Jurassic period about 190 million years ago.

Complete packing of exhumed bone tissue with microscopical destructive foci/tunnels can completely obscure the pattern of pathological changes.

The application of more sophisticated techniques would contribute to the fuller understanding of these changes and their causes.

Preservation of proteins in mummified tissues

Protein material was extracted from the dessicated tissues of several Egyptian mummies and a frozen Eskimo. The distribution and degree of preservation of high molecular weight protein was analyzed by gel filtration, protein assays, amino acid analysis, and polyacrylamide gel electrophoresis. The protein has undergone considerable degradation although some high molecular weight protein (C. 130,000 daltons) remains intact. Amino acid analysis of the extracted protein indicates the basic amino acids have undergone a chemical modification and may represent a point of preferential breakdown in the polypeptide chain. Atomic absorption spectrophotometry of tissue cations suggests a correlation between degree of preservation of mummified tissue and levels of sodium salts (natron) in the tissue.

Experimental investigations in post-mortem protein degradation

Samples of thoracic fluid were obtained at regular intervals from the putrefying bodies of dead dogs. For quantitative estimation of the proteins two-dimensional immunoelectrophoresis was employed and for the amino acids and amines two-dimensional thin-layer chromatography. The results lead to speculation that the initially lagging proteolytic changes are due to catalysis of autoenzymes, whereas bacteriological processes are responsible for a distinct acceleration from the 20th day after death. At this time the amino-acid concentrations showed a marked increase, which is followed by a maximum of bacterial growth, that ultimately leads to a sudden regression of amino acids. Simultaneously amines appear. The drying up of the thoracic cavity after 35 to 45 days marks the change from liquefaction to the terminal decay.

Radiocarbon dating of petroleum-impregnated bone from tar pits at Rancho La Brea, California

A liquid-chromatography method has been developed for the separation of amino acids with the same specific activity in radiocarbon from bones impregnated with isotopically dead petroleum compounds found in the La Brea tar pits. This technique permits the application of radiocarbon dating to such bone assemblages.