Download or read book Applications of DNA Capture in Ancient DNA Research written by Alexander Immel and published by . This book was released on 2020* with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: 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's reconstructed mitochondrial genome I then apply phylogenetic analyses that allow to resolve the giant deer'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.
Download or read book Ancient DNA written by Erika Hagelberg and published by . This book was released on 2014 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Ancient DNA written by Beth Alison Shapiro and published by . This book was released on 2012-01-01 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ancient DNA presents an overview of the many of the protocols commonly used to study ancient DNA. These include laboratory instructions, extraction protocols, laboratory techniques, and suggestions for appropriate analytical approaches to make sense of the sequences obtained.
Download or read book Ancient DNA Typing written by Susanne Hummel and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the definitive source of information on techniques for the identification and sequencing of old DNA (pieces) and their use in biological and medical research and application. Application of aDNA techniques are useful tools for investigations reaching from evolutionary studies to law enforcement approaches. What brings them together is the interest in specific methods of handling aDNA, i.e. elaborated PCR and sequencing techniques and the interpretation of the results. This books serves as an ideal guideline for it demonstrates how problem-solving strategies can be applied in various areas.
Download or read book Applied Uses of Ancient DNA written by Nic Rawlence and published by Frontiers Media SA. This book was released on 2021-06-17 with total page 183 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Investigation and Application of Methods for Ancient DNA Research written by Stephen Malone Richards and published by . This book was released on 2015 with total page 610 pages. Available in PDF, EPUB and Kindle. Book excerpt: The introduction of high throughput sequencing (HTS) in 2005 caused a revolution in the field of ancient DNA (aDNA). Using the large sequencing capacity of HTS, researchers have overcome the abundant environmental contamination present in most aDNA extractions to reconstruct the genomes of long extinct organisms, such as an archaic horse that perished >500,000 years ago. The proliferation of genomes engendered by HTS has also led to the development of potential ancillary technologies for aDNA research such as genotyping microarrays. In this thesis, HTS and genotyping techniques were developed or refined to improve the application of aDNA to larger biological questions in evolution. This thesis successfully: a) describes an in-house hybridization capture system that uses RNA probes generated from long-range PCR amplicons, b) demonstrates that recombinase polymerase amplification is a less biased alternative to PCR in hybridization capture of aDNA, c) develops an analytical approach that improves phylogenies generated with data from the Illumina BovineSNP50 BeadChip (a commercially available genotyping microarray). In contrast, an attempt to determine the identity of modified nucleotides in aDNA with Pacific Bioscience's Single Molecule Real-Time (SMRT) sequencing prove to be unsuccessful and genotyping of ancient bison aDNA with the BovineSNP50 BeadChip generated inconsistent results. Furthermore, a hybridization capture probe design was tested and found to be unsuitable for aDNA enrichment. For the larger biological aspect of this thesis, several of the methods developed were used to study bison, because these animals are ideal models of megafauna evolution. Using the in-house hybridization capture system, whole mitochondrial genomes were enriched from aDNA and used to help identify a new extinct species of bison. Furthermore, the new analytical approach for BovineSNP50 BeadChip data was used to demonstrate a significant genetic split between American woods and plains bison, which supports separating these animals at least at the subspecies level. This genetic split suggests that woods and plains bison should be conserved as separate species, which has considerable economic and political implications.
Download or read book Ancient DNA written by Bernd Herrmann and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ancient DNA refers to DNA which can be recovered and analyzed from clinical, museum, archaeological and paleontological specimens. Ancient DNA ranges in age from less than 100 years to tens of millions of years. The study of ancient DNA is a young field, but it has been revolutionized by the application of polymerase chain reaction technology, and interest is growing very rapidly. Fields as diverse as evolution, anthropology, medicine, agriculture, and even law enforcement have quickly found applications in the recovery of ancient DNA. This book contains contributions from many of the "first generation" researchers who pioneered the development and application of ancient DNA methods. Their chapters present the protocols and precautions which have resulted in the remarkable results obtained in recent years. The range of subjects reflects the wide diversity of applications that are emerging in research on ancient DNA, including the study of DNA to analyze kinship, recovery of DNA from organisms trapped in amber, ancient DNA from human remains preserved in a variety of locations and conditions, DNA recovered from herbarium and museum specimens, and DNA isolated from ancient plant seeds or compression fossils. Ancient DNA will serve as a valuable source of information, ideas, and protocols for anyone interested in this extraordinary field.
Download or read book Biological Anthropology of the Human Skeleton written by M. Anne Katzenberg and published by John Wiley & Sons. This book was released on 2018-10-30 with total page 688 pages. Available in PDF, EPUB and Kindle. Book excerpt: An Indispensable Resource on Advanced Methods of Analysis of Human Skeletal and Dental Remains in Archaeological and Forensic Contexts Now in its third edition, Biological Anthropology of the Human Skeleton has become a key reference for bioarchaeologists, human osteologists, and paleopathologists throughout the world. It builds upon basic skills to provide the foundation for advanced scientific analyses of human skeletal remains in cultural, archaeological, and theoretical contexts. This new edition features updated coverage of topics including histomorphometry, dental morphology, stable isotope methods, and ancient DNA, as well as a number of new chapters on paleopathology. It also covers bioarchaeological ethics, taphonomy and the nature of archaeological assemblages, biomechanical analyses of archaeological human skeletons, and more. Fully updated and revised with new material written by leading researchers in the field Includes many case studies to demonstrate application of methods of analysis Offers valuable information on contexts, methods, applications, promises, and pitfalls Covering the latest advanced methods and techniques for analyzing skeletal and dental remains from archaeological discoveries, Biological Anthropology of the Human Skeleton is a trusted text for advanced undergraduates, graduate students, and professionals in human osteology, bioarchaeology, and paleopathology.
Download or read book Applications of Second Generation Sequencing to Ancient DNA Studies written by Morten Rasmussen and published by . This book was released on 2010 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.
Download or read book Ancient DNA written by Beth Shapiro and published by Humana Press. This book was released on 2019-05-15 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: This fully updated second edition explores protocols that address the most challenging aspects of experimental work in ancient DNA, such as preparing ancient samples for DNA extraction, the DNA extraction itself, and transforming extracted ancient DNA molecules for sequencing library preparation. The volume also examines the analysis of high-throughput sequencing data recovered from ancient specimens, which, because of the degraded nature of ancient DNA and common co-extraction of contaminant DNA, has challenges that are unique compared to data recovered from modern specimens.Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Ancient DNA: Methods and Protocols, Second Edition aims to serve both experts and beginners by presenting protocols in a manner that makes them easily accessible for everyday use in the lab.
Download or read book Tumuli Graves written by Valeriu Sîrbu and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book How to Clone a Mammoth written by Beth Shapiro and published by Princeton University Press. This book was released on 2020-09-08 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: An insider's view on bringing extinct species back to life Could extinct species, like mammoths and passenger pigeons, be brought back to life? In How to Clone a Mammoth, Beth Shapiro, an evolutionary biologist and pioneer in ancient DNA research, addresses this intriguing question by walking readers through the astonishing and controversial process of de-extinction. From deciding which species should be restored to anticipating how revived populations might be overseen in the wild, Shapiro vividly explores the extraordinary cutting-edge science that is being used to resurrect the past. Considering de-extinction's practical benefits and ethical challenges, Shapiro argues that the overarching goal should be the revitalization and stabilization of contemporary ecosystems. Looking at the very real and compelling science behind an idea once seen as science fiction, How to Clone a Mammoth demonstrates how de-extinction will redefine conservation's future.
Download or read book Paleogenomics written by Charlotte Lindqvist and published by Springer. This book was released on 2019-01-07 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.
Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.
Download or read book Africa the Cradle of Human Diversity written by and published by BRILL. This book was released on 2021-11-22 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores important chapters of past and recent African history from a multidisciplinary perspective. It covers an extensive time range from the evolution of early humans to the complex cultural and genetic diversity of modern-day populations in Africa. Through a comprehensive list of chapters, the book focuses on different time-periods, geographic regions and cultural and biological aspects of human diversity across the continent. Each chapter summarises current knowledge with perspectives from a varied set of international researchers from diverse areas of expertise. The book provides a valuable resource for scholars interested in evolutionary history and human diversity in Africa. Contributors are Shaun Aron, Ananyo Choudhury, Bernard Clist, Cesar Fortes-Lima, Rosa Fregel, Jackson S. Kimambo, Faye Lander , Marlize Lombard, Fidelis T. Masao, Ezekia Mtetwa, Gilbert Pwiti, Michèle Ramsay, Thembi Russell, Carina Schlebusch, Dhriti Sengupta, Plan Shenjere-Nyabezi, Mário Vicente.
Download or read book Human Genetics and Genomics written by Bruce R. Korf and published by John Wiley & Sons. This book was released on 2012-11-19 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This fourth edition of the best-selling textbook, Human Genetics and Genomics, clearly explains the key principles needed by medical and health sciences students, from the basis of molecular genetics, to clinical applications used in the treatment of both rare and common conditions. A newly expanded Part 1, Basic Principles of Human Genetics, focuses on introducing the reader to key concepts such as Mendelian principles, DNA replication and gene expression. Part 2, Genetics and Genomics in Medical Practice, uses case scenarios to help you engage with current genetic practice. Now featuring full-color diagrams, Human Genetics and Genomics has been rigorously updated to reflect today’s genetics teaching, and includes updated discussion of genetic risk assessment, “single gene” disorders and therapeutics. Key learning features include: Clinical snapshots to help relate science to practice 'Hot topics' boxes that focus on the latest developments in testing, assessment and treatment 'Ethical issues' boxes to prompt further thought and discussion on the implications of genetic developments 'Sources of information' boxes to assist with the practicalities of clinical research and information provision Self-assessment review questions in each chapter Accompanied by the Wiley E-Text digital edition (included in the price of the book), Human Genetics and Genomics is also fully supported by a suite of online resources at www.korfgenetics.com, including: Factsheets on 100 genetic disorders, ideal for study and exam preparation Interactive Multiple Choice Questions (MCQs) with feedback on all answers Links to online resources for further study Figures from the book available as PowerPoint slides, ideal for teaching purposes The perfect companion to the genetics component of both problem-based learning and integrated medical courses, Human Genetics and Genomics presents the ideal balance between the bio-molecular basis of genetics and clinical cases, and provides an invaluable overview for anyone wishing to engage with this fast-moving discipline.
