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Enamel Amino Acid Racemisation Dating and Its Application to Building Proboscidean Geochronologies

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Enamel Amino Acid Racemisation Dating and Its Application to Building Proboscidean Geochronologies Enamel Amino Acid Racemisation Dating and its Application to Building Proboscidean Geochronologies Marc R Dickinson PhD University of York Chemistry July 2018 Abstract Analysis of the predictable breakdown of proteins and amino acids in ancient biominerals enables age estimation over the Quaternary, but to date, its application to mammalian remains has been challenging. It has been postulated that enamel is a suitable biomineral for the long-term survival of endogenous amino acids and thus, it can be used for age estimation. Directly dating mammalian remains is integral to understanding mammalian evolution and for understanding palaeoecology and palaeoclimatology. Analysis of multiple amino acids for geochronological studies is typically achieved using a RP-HPLC method. However, the low concentrations of amino acids coupled with high concentrations of inorganic species makes accurate determination of amino concentrations challenging. The initial focus of this thesis covers the development of a novel method for the separation of amino acids from inorganic species. This was initially attempted via a HILIC SPE, but was later superseded by a biphasic separation method, which was shown to greatly improve the RP-HPLC analysis of amino acids in enamel. Bleaching experiments have shown that the amino acids isolated from enamel through prolonged exposure to a strong oxidant, exhibit effectively closed system behaviour, signifying a potentially stable environment over geological time-scales. Elevated temperature experiments investigating the processes of intra-crystalline protein degradation do not appear to match the fossil patterns, reinforcing the need for a comprehensive understanding of the underlying mechanisms of protein degradation. The methods developed in this thesis have been used to build an enamel amino acid racemisation geochronology based on Proboscidean teeth from UK sites with independent evidence of age. This model has shown good adherence to the UK stratigraphical framework, signifying enamel is a suitable biomineral for AAR age estimation. Finally, enamel AAR has been used in a pilot study to begin to build a chronology for elephants from the isle of Sicily. This framework has been constructed to aid in understanding the process behind island dwarfing of insular elephant species on Sicily. ii Table of Contents Abstract ………………………………………………………………………………………………………………………… ii Table of contents …………………………………………………………………………………………………………… iii List of tables …………………………………………………………………………………………………………………. viii List of figures ………………………………………………………………………………………………………………… ix Acknowledgements ……………………………………………………………………………………………………… xvi Declaration …………………………………………………………………………………………………………………. xvii Chapter 1: An introduction to amino acid geochronology ............................................. 1 1.1. Understanding the Quaternary ......................................................................................... 2 1.1.1. Drivers of long term climate change over the Quaternary ...................................................... 3 1.1.2. Marine oxygen isotope stages (MIS) ........................................................................................ 4 1.1.3. Quaternary Geochronology ................................................................................................... 10 1.2. Amino acid racemisation ................................................................................................ 17 1.2.1. The general structure of amino acids .................................................................................... 17 1.3. Survival of peptides and amino acids in the fossil record............................................... 18 1.4. Hydrolysis ........................................................................................................................ 19 1.5. Racemisation ................................................................................................................... 20 1.5.1. Deamidation and the succinimide intermediate ................................................................... 23 1.5.2. Diketopiperazine and N-terminal racemisation ..................................................................... 25 1.5.3. Free vs bound racemisation and the impact of hydrolysis .................................................... 26 1.5.4. Physical factors affecting amino acid racemisation ............................................................... 27 1.5.5. Chemical factors affecting amino acid racemisation ............................................................. 28 1.5.6. How extrinsic chemical factors are addressed in AAR dating ................................................ 30 1.6. Closed system ................................................................................................................. 30 1.7. Calcium carbonate-based biomineral ............................................................................. 32 1.7.1. Molluscs ................................................................................................................................. 32 1.7.2. Avian eggshell ........................................................................................................................ 32 iii 1.8. Calcium phosphate-based biominerals ........................................................................... 33 1.8.1. Bone ....................................................................................................................................... 33 1.8.2. Dentine .................................................................................................................................. 34 1.8.3. Enamel ................................................................................................................................... 34 1.9. Mineral composition of enamel ...................................................................................... 34 1.10. Organic composition of enamel .................................................................................... 35 1.11. In vivo racemisation in teeth ......................................................................................... 37 1.12. Geochronological application of enamel AAR .............................................................. 38 1.13. Thesis aims .................................................................................................................... 39 Chapter 2: Isolation of amino acids from phosphate species by HILIC–SPE ................. 40 2.1. Introduction .................................................................................................................... 40 2.1.1. Problems of peak suppression ............................................................................................... 40 2.1.2. Hydrophilic interaction liquid chromatography (HILIC) ......................................................... 42 2.2. Materials and standard procedures ................................................................................ 48 2.3. Chemicals and reagents .................................................................................................. 48 2.4. 1:1 reference samples ..................................................................................................... 48 2.5. Powdering and bleaching (fossil samples only) .............................................................. 48 2.6. Hydrolysis of peptide-bound amino acids (fossil samples only) ..................................... 48 2.7. Demineralisation/dissolution of samples for use with neutral pH eluents .................... 48 2.8. HILIC SPE general protocol .............................................................................................. 49 2.9. RP-HPLC analysis ............................................................................................................. 50 2.10. LhArg peak response ..................................................................................................... 51 2.11. Analysis of D/L values ................................................................................................... 51 2.12. Fixed composition acetonitrile / H2O mobile phase at low pH ..................................... 51 2.12.1. Choice of acetonitrile as mobile phase solvent ................................................................... 51 2.12.2. Fixed composition acetonitrile / H2O mobile phase at low pH: Background ....................... 52 2.12.3. Fixed composition acetonitrile / H2O mobile phase at low pH: Experimental .................... 52 2.12.4. Fixed composition acetonitrile / H2O mobile phase at low pH: Results and discussion ...... 53 iv 2.13. Fixed composition acetonitrile / H2O mobile phase at neutral pH ............................... 56 2.13.1. Fixed composition acetonitrile / H2O mobile phase at neutral pH: Experimental ............... 57 2.13.2. Fixed composition acetonitrile / H2O mobile phase at neutral pH: Results and discussion 57 2.14. Variable composition acetonitrile / H2O mobile phase at neutral pH .......................... 59 2.14.1. Elution of amino acids .......................................................................................................... 59 2.14.2. Variable composition acetonitrile / H2O mobile phase at neutral pH: Experimental .......... 59 2.14.3. Variable composition acetonitrile / H2O mobile phase at neutral pH: Results & discussion ........................................................................................................................................................
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