% pubman genre = thesis
@phdthesis{item_3488479,
title = {{Applications of DNA capture in ancient DNA research}},
author = {Immel, Alexander},
language = {eng},
doi = {10.22032/dbt.41330},
school = {Friedrich-Schiller-Universit{\"a}t Jena, Fakult{\"a}t f{\"u}r Biowissenschaften},
address = {Jena},
year = {2020},
abstract = {{Ancient DNA has become an indispensable resource of fundamental research. Especially the combination of DNA capture methods and Next Generation Sequencing (NGS) has allowed to exploit the full potential of ancient DNA. In this dissertation I present three studies which involve capture of ancient DNA to answer different scientific questions. In my first study I bioinformatically reconstruct the mitochondrial genome of the extinct giant deer Megaloceros giganteus after applying mitochondrial DNA capture and sequencing. Using the giant deer{\&}{\#}39;s reconstructed mitochondrial genome I then apply phylogenetic analyses that allow to resolve the giant deer{\&}{\#}39;s placement within the cervid family tree and reaffirm the fallow deer being its closest extant relative. Mitochondrial DNA capture also provides the basis for the next study, in which I investigate the effects of X-rays on ancient DNA. Different radiation settings are explored including those commonly used in computed tomography (CT) of anthropological and palaeontological specimens. The results allow to define 200 Gray (Gy) as the maximum absorbed X-ray dose which can still be regarded harmless to ancient DNA molecules. No X-radiation induced effects can be observed below this threshold. In my third study I develop and apply capture of 488 human immunity genes in order to compare the immunogenetic makeup of Late Medieval plague (Yersinia pestis) victims and their modern day successors from Ellwangen, Southern Germany. Applying bioinformatic tools allows me to investigate kinship within both populations, determine genetic continuity between past and present, and reconstruct the Human Leukocyte Antigen (HLA) allelic profiles of both populations. While the majority of HLA alleles do not differ in their frequencies, HLA-B51:01 and HLA-DRB113 show significant frequency differences between both populations, potentially indicative of selective pressure through Yersinia pestis.}},
contents = {1 ancient DNA research - History and Methods 1.1 A Short History of aDNA Research 1.2 aDNA Retrieval from Old Bone 1.3 DNA Libraries 1.4 Next Generation Sequencing 2 Applications of aDNA Capture 2.1 Current Methods for Target DNA Enrichment 2.2 Study 1: Capture of Giant Deer Mitochondrial DNA 2.2.1 Archaeological Material 2.2.2 Extraction of Giant Deer DNA and Library Preparation 2.2.3 Bait Preparation and Capture 2.2.4 Sequence Processing and Assembly 2.2.5 Multiple Sequence Alignment 2.2.6 Phylogenetic Analyses Publication: Mitochondrial Genomes of Giant Deers Suggest their Late Survival in Central Europe 2.3 Study 2: Effect of X-rays on ancient DNA 2.3.1 Background and Previous Work 2.3.2 Investigating X-ray effects on aDNA after Mitochondrial DNA Capture Publication: Effect of X-ray {\textquotesingle}irradfotion on anC{\textquotesingle}ient DNA {\textquotesingle}in s{\textquotesingle}Ub-fossil bones - G{\textquotesingle}Uidel{\textquotesingle}ines for safe X-ray imaging 2.4 Study 3: Immunity Capture 2.4.1 Background: Plague, HLA and other Immunity Genes 2.4.2 Initial Array Design for Immunity Capture 2.4.3 Improved Array Design 2.4.4 In-Solution Capture 2.4.5 Evaluation of the In-Solution Capture Efficiency 2.4.6 Application of the Immunity Capture to 16th Cent. Plague Victims 2.4.7 HLA Typing and Allele Frequency Comparisons 2.4.8 CCR5-6 32 Mutation in Plague Victims and Contemporary Ell- wangen 3 Discussion 3.1 Giant Deer and Megafauna 3.2 X-rays and aDNA 3.3 In-Solution Immunity Capture 3.4 Stability of the CCR5-6 32 Mutation 3.5 Frequency Shifts in particular HLA alleles 4 Conclusion Appendix and Supplementary Material},
}