INTRODUCTION TO PALAEOPROTEOMICS AND PALAEOGENOMICS EVA CHOCHOLOVÁ LABORATORY OF BIOLOGICAL AND MOLECULAR ANTHROPOLOGY DEPARTMENT OF EXPERIMENTAL BIOLOGY SYLLABUS 1. Introduction to palaeoproteomics and palaeogenomics. History, main principles and differences, molecular preservation. 2. Methods in palaeogenomics. 3. Palaeogenomics of human populations. 4. Metagenomics. 5. Palaeogenomics of pathogens. 6. Sedimentary ancient DNA. 7. Methods in palaeoproteomics I 8. Methods in palaeoproteomics II 9. Collagens, keratins and other proteins used in taxonomy. 10. Palaeoproteomics of human populations. Sex typing, evolution, skeletal and mummified remains. 11. Metaproteomics. Diet, health and culture studied by proteomic approach. 12. Dental calculus as a complex material in biomolecular archaeology. 13. Opportunities, challenges, and ethics in palaeoproteomic and palaeogenomics research. LESSON PLAN • Quiz • Lecture • Collection of important concepts/terms (1-3) • Online resources for voluntary self-directed learning. ASSESSMENT METHODS • Written examination with possibility to take an oral exam. (A: 100-93 points, B: 92-85 points, C: 84-77, D: 76-69, E: 68-60, F: 60-0) • Students can obtain up to 20 bonus points during the semester for voluntary assignments (presentation, paper analysis, involvement in discussion). Flash talk (5 points/each talk, up to 3 talks) 1) Choose a paper based on given topic 2) Read and analyse paper 3) Choose most important and interesting information 4) Prepare 1 slide with this information 5) Present in 3 minutes Case study (5 points) Last lecture – choose a case study (archaeological situation), prepare and share suggested solution and what analyses you would recommend. PALAEOGENOMICS, PALAEOPROTEOMICS • Importance • Life of ancient populations • Migrations and contact • Evolutionary processes, adaptations • Current organisms and diseases • Extinct organisms • Epidemiology and public health implications • … NOBEL PRIZE – SVANTE PÄÄBO https://www.nobelprize.org/prizes/medicine/2022/summary/ NOBEL PRIZE – SVANTE PÄÄBO https://www.nobelprize.org/prizes/medicine/2022/summary/ NOBEL PRIZE – SVANTE PÄÄBO https://www.nobelprize.org/prizes/medicine/2022/summary/ WHAT TO STUDY WHAT TO STUDY WHAT TO STUDY WHAT TO STUDY WHAT TO STUDY WHAT TO STUDY WHAT TO STUDY BRIEF HISTORY OF PALAEOGENOMICS • Genetics Genomics • Quagga (Higuchi et al., 1984), Egyptian mummies (Pääbo, 1985) Mitochondrial DNA, identification Whole genomes Last died in Amsterdam Zoo, 12 August 1883 https://www.quaggaproject.org/ Lan and Lindqvist, 2018 DOI: 10.1007/13836_2017_7 Fu Qiaomei et al, 2022; DOI: 10.1016/j.cell.2022.06.009 Neandertal Genome Project - 2006 https://www.mpg.de/13894984/neandertal-genome-project BRIEF HISTORY OF PALAEOGENOMICS Dalén et al., 2023; DOI: 10.1126/science.adh7943 BRIEF HISTORY OF PALAEOGENOMICS Mitchell et al., 2021; DOI: 10.1016/j.tree.2020.10.005 BRIEF HISTORY OF PALAEOGENOMICS Brunson and Reich, 2019; DOI: 10.1016/j.tig.2019.02.006 Kistler et al., 2017; DOI: 10.1093/nar/gkx361 BRIEF HISTORY OF PALAEOPROTEOMICS Cappellini et al., 2014 DOI: 10.1126/science.1249274 PROTEINS • Macromolecules, polypeptides • Peptide – less than 30 AA • Shape crucial for function National Human Genome Research Institute CENTRAL DOGMA OF MOLECULAR BIOLOGY Peter Grindrod Introduction of mutations - diversity Alternation of function usually pathological - conservation CONSERVED PROTEINS Genomics Education Programme GCA GCG GCT TGC Ala Ala Ala Trp SAME DNA, DIFFERENT PROTEINS DNA VS PROTEINS AMPLIFICATION MISTAKES AND CONTAMINATION CAN DISTIGUISH CLOSER SPECIES WORSE PRESERVATION THE SAME FOR ALL CELLS NO AMPLIFICATION OFTEN CONSERVED BETTER PRESERVATION SHOWS FUNCTION AND ACTIVE PROCESES – TISSUE DIFFERENCES MOLECULAR PRESERVATION pH DNA - 1 mil Proteins – 3,8 mil DNA - 2 mil MOLECULAR PRESERVATION PRESERVATION OF DNA Dabney et al., 2013; DOI: 10.1101/cshperspect.a012567 Dalén et al., 2023; DOI: 10.1126/science.adh7943 Lindahl, 1993; DOI:10.1038/362709a0 MOLECULAR PRESERVATION - DNA Willerslev and Cooper, 2005; DOI: 10.1098/rspb.2004.2813 PRESERVATION OF DNA Willerslev and Cooper, 2005; DOI: 10.1098/rspb.2004.2813 PRESERVATION OF DNA Willerslev and Cooper, 2005; DOI: 10.1098/rspb.2004.2813 PRESERVATION OF DNA PRESERVATION OF PROTEINS Hydrolysis, deamidation, racemination c&en PRESERVATION OF PROTEINS Hydrolysis, deamidation, racemination c&en asparagine and glutamine aspartic and glutamic acid PRESERVATION OF PROTEINS Hydrolysis, deamidation, racemination c&en L to D form, can break from the chain ! • UDG treatment • Relevance of older method • Extrapolation from ancient genomes is biased by sampling • Preservation influences • Quagga • Genes from Denisovans • Cultural objects • Oldest proteins (3.8 M), oldest aDNA (1 M, 2 M) • Deamination in aDNA, deamidation in proteins