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Sample records for ancient dna studies

  1. Authenticity in ancient DNA studies

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Willerslev, Eske

    2006-01-01

    Ancient DNA studies represent a powerful tool that can be used to obtain genetic insights into the past. However, despite the publication of large numbers of apparently successful ancient DNA studies, a number of problems exist with the field that are often ignored. Therefore, questions exist...... as to how reliable the conclusions of many of the published studies are. In this paper we outline first the problems associated with aDNA studies, and secondly present potential guidelines designed so as to enable non-specialist readers the opportunity to critically assess the quality of aDNA publications....

  2. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  3. Ancient DNA and Forensics Mutual Benefits a Practical Sampling and Laboratory Guide Through a Virtual Ancient DNA Study

    Directory of Open Access Journals (Sweden)

    Jan Cemper-Kiesslich

    2014-09-01

    In this review the authors give a general overview on the field of ancient DNA analysis focussing of the potentials and limits, fields of application, requirements for samples, laboratory setup, reaction design and equipment as well as a brief outlook on current developments, future perspectives and potential cross links with associated scientific disciplines. Key words: Human DNA, Ancient DNA, Forensic DNA typing, Molecular archaeology, Application.

  4. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L. A.; Gilbert, Tom; Hofreiter, Michael

    2013-01-01

    The analysis of ancient DNA is playing an increasingly important role in conservation genetic, phylogenetic and population genetic analyses, as it allows incorporating extinct species into DNA sequence trees and adds time depth to population genetics studies. For many years, these types of DNA...... analyses (whether using modern or ancient DNA) were largely restricted to the analysis of short fragments of the mitochondrial genome. However, due to many technological advances during the past decade, a growing number of studies have explored the power of complete mitochondrial genome sequences...... (mitogenomes). Such studies were initially limited to analyses of extant organisms, but developments in both DNA sequencing technologies and general methodological aspects related to working with degraded DNA have resulted in complete mitogenomes becoming increasingly popular for ancient DNA studies as well...

  5. Ancient DNA from marine mammals

    DEFF Research Database (Denmark)

    Foote, Andrew David; Hofreiter, Michael; Morin, Philip A.

    2012-01-01

    discuss studies recon- structing inter- and intra-specific phylogenies from aDNA sequences and discuss how aDNA sequences could be used to estimate mutation rates. Finally, we highlight some of the problems of aDNA studies on marine mammals, such as obtaining sufficient sample sizes and calibrating...... such as bone, tooth, baleen, skin, fur, whiskers and scrimshaw using ancient DNA (aDNA) approaches provide an oppor- tunity for investigating such changes over evolutionary and ecological timescales. Here, we review the application of aDNA techniques to the study of marine mammals. Most of the studies have...... focused on detecting changes in genetic diversity following periods of exploitation and environmental change. To date, these studies have shown that even small sample sizes can provide useful information on historical genetic diversity. Ancient DNA has also been used in investigations of changes...

  6. Stories in Genetic Code. The contribution of ancient DNA studies to anthropology and their ethical implications

    Directory of Open Access Journals (Sweden)

    Cristian M. Crespo

    2010-12-01

    Full Text Available For several decades, biological anthropology has employed different molecular markers in population research. Since 1990 different techniques in molecular biology have been developed allowing preserved DNA extraction and its typification in different samples from museums and archaeological sites. Ancient DNA studies related to archaeological issues are now included in the field of Archaeogenetics. In this work we present some of ancient DNA applications in archaeology. We also discuss advantages and limitations for this kind of research and its relationship with ethic and legal norms.

  7. The Small and the Dead: A Review of Ancient DNA Studies Analysing Micromammal Species

    Directory of Open Access Journals (Sweden)

    Roseina Woods

    2017-11-01

    Full Text Available The field of ancient DNA (aDNA has recently been in a state of exponential growth, largely driven by the uptake of Next Generation Sequencing (NGS techniques. Much of this work has focused on the mammalian megafauna and ancient humans, with comparatively less studies looking at micromammal fauna, despite the potential of these species in testing evolutionary, environmental and taxonomic theories. Several factors make micromammal fauna ideally suited for aDNA extraction and sequencing. Micromammal subfossil assemblages often include the large number of individuals appropriate for population level analyses, and, furthermore, the assemblages are frequently found in cave sites where the constant temperature and sheltered environment provide favourable conditions for DNA preservation. This review looks at studies that include the use of aDNA in molecular analysis of micromammal fauna, in order to examine the wide array of questions that can be answered in the study of small mammals using new palaeogenetic techniques. This study highlights the bias in current aDNA studies and assesses the future use of aDNA as a tool for the study of micromammal fauna.

  8. Phylogenetic estimation of timescales using ancient DNA

    DEFF Research Database (Denmark)

    Molak, Martyna; Lorenzen, Eline; Shapiro, Beth

    2013-01-01

    analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise......In recent years, ancient DNA has increasingly been used for estimating molecular timescales, particularly in studies of substitution rates and demographic histories. Molecular clocks can be calibrated using temporal information from ancient DNA sequences. This information comes from the ages...... of the ancient samples, which can be estimated by radiocarbon dating the source material or by dating the layers in which the material was deposited. Both methods involve sources of uncertainty. The performance of Bayesian phylogenetic inference depends on the information content of the data set, which includes...

  9. Ancient and modern environmental DNA

    Science.gov (United States)

    Pedersen, Mikkel Winther; Overballe-Petersen, Søren; Ermini, Luca; Sarkissian, Clio Der; Haile, James; Hellstrom, Micaela; Spens, Johan; Thomsen, Philip Francis; Bohmann, Kristine; Cappellini, Enrico; Schnell, Ida Bærholm; Wales, Nathan A.; Carøe, Christian; Campos, Paula F.; Schmidt, Astrid M. Z.; Gilbert, M. Thomas P.; Hansen, Anders J.; Orlando, Ludovic; Willerslev, Eske

    2015-01-01

    DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field. PMID:25487334

  10. Paleo-Environmental Reconstruction Using Ancient DNA

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther

    The aim of this thesis has been to investigate and expand the methodology and applicability for using ancient DNA deposited in lake sediments to detect and determine its genetic sources for paleo-environmental reconstruction. The aim was furthermore to put this tool into an applicable context...... research on ancient and modern environmental DNA (Paper 1), secondly by setting up a comparative study (Paper 2) to investigate how an ancient plant DNA (mini)-barcode can reflect other traditional methods (e.g. pollen and macrofossils) for reconstructing floristic history. In prolongation of the results...... obtained in paper 2 we developed a holistic metagenomic method combined with shotgun sequencing of ancient DNA in lake sediment samples to reconstruct organismal assemblages in addition to the flora e.g. micro-, meso- and megafauna, fungi and microbial communities (Paper 3). Fundamental processes were...

  11. Fossil avian eggshell preserves ancient DNA

    DEFF Research Database (Denmark)

    Oskam, Charlotte L; Haile, James Seymour; McLay, Emma

    2010-01-01

    Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful...

  12. Damage and repair of ancient DNA

    DEFF Research Database (Denmark)

    Mitchell, David; Willerslev, Eske; Hansen, Anders

    2005-01-01

    Under certain conditions small amounts of DNA can survive for long periods of time and can be used as polymerase chain reaction (PCR) substrates for the study of phylogenetic relationships and population genetics of extinct plants and animals, including hominids. Because of extensive DNA...... such as extinct horses, cave bears, the marsupial wolf, the moa, and Neanderthal. In the past few years, this technology has been extended to the study of infectious disease in ancient Egyptian and South American mummies, the dietary habits of ancient animals, and agricultural practices and population dynamics...

  13. Ancient DNA and the tropics: a rodent's tale

    OpenAIRE

    Gutiérrez-García, Tania A.; Vázquez-Domínguez, Ella; Arroyo-Cabrales, Joaquín; Kuch, Melanie; Enk, Jacob; King, Christine; Poinar, Hendrik N.

    2014-01-01

    Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropi...

  14. Application of Ancient DNA Methods to the Study of the Transatlantic Slave Trade

    DEFF Research Database (Denmark)

    Sandoval Velasco, Marcela

    extractions, sequencing library preparations, and whole-genome capture enrichment methods, with the goal of retrieving ancient genome wide data from poorly preserved archaeological remains. Such data contributes to the study of the transatlantic slave trade, in particular helping shed light upon the origins...... of retrieving ancient genome wide data from poorly preserved archaeological remains. Such data contributes to the study of the transatlantic slave trade, in particular helping shed light upon the origins and diversity of enslaved Africans. Ultimately this will help answer long-standing historical questions...

  15. Use DNA to learn from the past: how modern and ancient DNA studies may help reveal the past and predict the future distribution of species

    Science.gov (United States)

    Edwards, M. E.; Alsos, I. G.; Sjögren, P.; Coissac, E.; Gielly, L.; Yoccoz, N.; Føreid, M. K.; Taberlet, P.

    2015-12-01

    Knowledge of how climate change affected species distribution in the past may help us predict the effect of ongoing environmental changes. We explore how the use of modern (AFLP fingerprinting techniques) and ancient DNA (metabarcoding P6 loop of chloroplast DNA) help to reveal past distribution of vascular plant species, dispersal processes, and effect of species traits. Based on studies of modern DNA combined with species distribution models, we show the dispersal routes and barriers to dispersal throughout the circumarctic/circumboreal region, likely dispersal vectors, the cost of dispersal in term of loss of genetic diversity, and how these relates to species traits, dispersal distance, and size of colonized region. We also estimate the expected future distribution and loss of genetic diversity and show how this relates to life form and adaptations to dispersal. To gain more knowledge on time lags in past range change events, we rely on palaeorecords. Current data on past distribution are limited by the taxonomic and time resolution of macrofossil and pollen records. We show how this may be improved by studying ancient DNA of lake sediments. DNA of lake sediments recorded about half of the flora surrounding the lake. Compared to macrofossil, the taxonomic resolution is similar but the detection rate is considerable improved. By taking into account main determinants of founder effect, dispersal vectors, and dispersal lags, we may improve our ability to forecast effects of climate change, whereas more studies on ancient DNA may provide us with knowledge on distribution time lags.

  16. Non-destructive sampling of ancient insect DNA

    OpenAIRE

    Thomsen, Philip Francis; Elias, Scott; Gilbert, Tom; Haile, James; Munch, Kasper; Kuzmina, Svetlana; Froese, Duane G; Sher, Andrei; Holdaway, Richard N; Willerslev, Eske

    2009-01-01

    Udgivelsesdato: 2009-null BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanentl...

  17. Mitochondrial DNA analysis of ancient Peruvian highlanders.

    Science.gov (United States)

    Shinoda, Ken-ichi; Adachi, Noboru; Guillen, Sonia; Shimada, Izumi

    2006-09-01

    Ancient DNA recovered from 57 individuals excavated by Hiram Bingham at the rural communities of Paucarcancha, Patallacta, and Huata near the famed Inca royal estate and ritual site of Machu Picchu was analyzed by polymerase chain reaction, and the results were compared with ancient and modern DNA from various Central Andean areas to test their hypothesized indigenous highland origins. The control and coding regions of the mitochondrial DNA (mtDNA) of 35 individuals in this group were sequenced, and the haplogroups of each individual were determined. The frequency data for the haplogroups of these samples show clear proximity to those of modern Quechua and Aymara populations in the Peruvian and Bolivian highlands, and contrast with those of pre-Hispanic individuals of the north coast of Peru that we defined previously. Our study suggests a strong genetic affinity between sampled late pre-Hispanic individuals and modern Andean highlanders. A previous analysis of the Machu Picchu osteological collection suggests that the residents there were a mixed group of natives from various coastal and highland regions relocated by the Inca state for varied purposes. Overall, our study indicates that the sampled individuals from Paucarcancha and Patallacta were indigenous highlanders who provided supportive roles for nearby Machu Picchu. 2006 Wiley-Liss, Inc.

  18. Non-destructive sampling of ancient insect DNA

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Elias, Scott; Gilbert, Tom

    2009-01-01

    BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological......-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient...

  19. Studying Ancient History.

    Science.gov (United States)

    Barrow, Robin

    1982-01-01

    Defends the value and relevance of the study of ancient history and classics in history curricula. The unique homogeneity of the classical period contributes to its instructional manageability. A year-long, secondary-level course on fifth-century Greece and Rome is described to illustrate effective approaches to teaching ancient history. (AM)

  20. Differential Nuclear and Mitochondrial DNA Preservation in Post-Mortem Teeth with Implications for Forensic and Ancient DNA Studies

    Science.gov (United States)

    Higgins, Denice; Rohrlach, Adam B.; Kaidonis, John; Townsend, Grant; Austin, Jeremy J.

    2015-01-01

    Major advances in genetic analysis of skeletal remains have been made over the last decade, primarily due to improvements in post-DNA-extraction techniques. Despite this, a key challenge for DNA analysis of skeletal remains is the limited yield of DNA recovered from these poorly preserved samples. Enhanced DNA recovery by improved sampling and extraction techniques would allow further advancements. However, little is known about the post-mortem kinetics of DNA degradation and whether the rate of degradation varies between nuclear and mitochondrial DNA or across different skeletal tissues. This knowledge, along with information regarding ante-mortem DNA distribution within skeletal elements, would inform sampling protocols facilitating development of improved extraction processes. Here we present a combined genetic and histological examination of DNA content and rates of DNA degradation in the different tooth tissues of 150 human molars over short-medium post-mortem intervals. DNA was extracted from coronal dentine, root dentine, cementum and pulp of 114 teeth via a silica column method and the remaining 36 teeth were examined histologically. Real time quantification assays based on two nuclear DNA fragments (67 bp and 156 bp) and one mitochondrial DNA fragment (77 bp) showed nuclear and mitochondrial DNA degraded exponentially, but at different rates, depending on post-mortem interval and soil temperature. In contrast to previous studies, we identified differential survival of nuclear and mtDNA in different tooth tissues. Futhermore histological examination showed pulp and dentine were rapidly affected by loss of structural integrity, and pulp was completely destroyed in a relatively short time period. Conversely, cementum showed little structural change over the same time period. Finally, we confirm that targeted sampling of cementum from teeth buried for up to 16 months can provide a reliable source of nuclear DNA for STR-based genotyping using standard

  1. Non-destructive sampling of ancient insect DNA.

    Directory of Open Access Journals (Sweden)

    Philip Francis Thomsen

    Full Text Available BACKGROUND: A major challenge for ancient DNA (aDNA studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago -- an alternative approach that also does not involve destruction of valuable material. METHODOLOGY/PRINCIPAL FINDINGS: The success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA fragments of 77-204 base pairs (-bp in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.

  2. Non-destructive sampling of ancient insect DNA.

    Science.gov (United States)

    Thomsen, Philip Francis; Elias, Scott; Gilbert, M Thomas P; Haile, James; Munch, Kasper; Kuzmina, Svetlana; Froese, Duane G; Sher, Andrei; Holdaway, Richard N; Willerslev, Eske

    2009-01-01

    A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological damage. We test the applicability of this protocol on historic museum beetle specimens dating back to AD 1820 and on ancient beetle chitin remains from permafrost (permanently frozen soil) dating back more than 47,000 years. Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago -- an alternative approach that also does not involve destruction of valuable material. The success of the methodological approaches are tested by PCR and sequencing of COI and 16S mitochondrial DNA (mtDNA) fragments of 77-204 base pairs (-bp) in size using species-specific and general insect primers. The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient biodiversity.

  3. Ancient DNA and the tropics: a rodent's tale.

    Science.gov (United States)

    Gutiérrez-García, Tania A; Vázquez-Domínguez, Ella; Arroyo-Cabrales, Joaquín; Kuch, Melanie; Enk, Jacob; King, Christine; Poinar, Hendrik N

    2014-06-01

    Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as Ototylomys phyllotis, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome b gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern O. phyllotis, in order to assess the ancestry of the Loltún samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern O. phyllotis, supporting it as a distinct Pleistocene form of the Ototylomys genus. Hence, this rodent's tale suggests that the sister group to modern O. phyllotis arose during the Miocene-Pliocene, diversified during the Pleistocene and went extinct in the Holocene. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  4. Using Ancient DNA to Understand Evolutionary and Ecological Processes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Cooper, Alan

    2014-01-01

    Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of ...

  5. Ancient DNA analysis of dental calculus.

    Science.gov (United States)

    Weyrich, Laura S; Dobney, Keith; Cooper, Alan

    2015-02-01

    Dental calculus (calcified tartar or plaque) is today widespread on modern human teeth around the world. A combination of soft starchy foods, changing acidity of the oral environment, genetic pre-disposition, and the absence of dental hygiene all lead to the build-up of microorganisms and food debris on the tooth crown, which eventually calcifies through a complex process of mineralisation. Millions of oral microbes are trapped and preserved within this mineralised matrix, including pathogens associated with the oral cavity and airways, masticated food debris, and other types of extraneous particles that enter the mouth. As a result, archaeologists and anthropologists are increasingly using ancient human dental calculus to explore broad aspects of past human diet and health. Most recently, high-throughput DNA sequencing of ancient dental calculus has provided valuable insights into the evolution of the oral microbiome and shed new light on the impacts of some of the major biocultural transitions on human health throughout history and prehistory. Here, we provide a brief historical overview of archaeological dental calculus research, and discuss the current approaches to ancient DNA sampling and sequencing. Novel applications of ancient DNA from dental calculus are discussed, highlighting the considerable scope of this new research field for evolutionary biology and modern medicine. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Ancient and modern environmental DNA

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther; Overballe-Petersen, Søren; Ermini, Luca

    2015-01-01

    woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene...

  7. High-resolution analysis of cytosine methylation in ancient DNA.

    Directory of Open Access Journals (Sweden)

    Bastien Llamas

    Full Text Available Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.

  8. Preservation of ancient DNA in thermally damaged archaeological bone

    Science.gov (United States)

    Ottoni, Claudio; Koon, Hannah E. C.; Collins, Matthew J.; Penkman, Kirsty E. H.; Rickards, Olga; Craig, Oliver E.

    2009-02-01

    Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.

  9. Preservation of ancient DNA in thermally damaged archaeological bone.

    Science.gov (United States)

    Ottoni, Claudio; Koon, Hannah E C; Collins, Matthew J; Penkman, Kirsty E H; Rickards, Olga; Craig, Oliver E

    2009-02-01

    Evolutionary biologists are increasingly relying on ancient DNA from archaeological animal bones to study processes such as domestication and population dispersals. As many animal bones found on archaeological sites are likely to have been cooked, the potential for DNA preservation must be carefully considered to maximise the chance of amplification success. Here, we assess the preservation of mitochondrial DNA in a medieval cattle bone assemblage from Coppergate, York, UK. These bones have variable degrees of thermal alterations to bone collagen fibrils, indicative of cooking. Our results show that DNA preservation is not reliant on the presence of intact collagen fibrils. In fact, a greater number of template molecules could be extracted from bones with damaged collagen. We conclude that moderate heating of bone may enhance the retention of DNA fragments. Our results also indicate that ancient DNA preservation is highly variable, even within a relatively recent assemblage from contexts conducive to organic preservation, and that diagenetic parameters based on protein diagenesis are not always useful for predicting ancient DNA survival.

  10. Statistical guidelines for detecting past population shifts using ancient DNA

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon Y. W.; Gilbert, Tom

    2012-01-01

    post-bottleneck recoveries. In contrast, nuclear SNPs can detect bottlenecks followed by rapid recovery, although bottlenecks involving reduction of less than half the population are generally detected with low power unless extensive genetic information from ancient individuals is available. Our...... results provide useful guidelines for scaling sampling schemes and for optimizing our ability to infer past population dynamics. In addition, our results suggest that many ancient DNA studies may face power issues in detecting moderate demographic collapses and/or highly dynamic demographic shifts when...

  11. Correction to 'Ancient DNA and the tropics: a rodent's tale'.

    Science.gov (United States)

    Gutiérrez-García, Tania A; Vázquez-Domínguez, Ella; Arroyo-Cabrales, Joaquín; Kuch, Melanie; Enk, Jacob; King, Christine; Poinar, Hendrik N

    2015-03-01

    The present erratum is in regards to our article entitled ‘Ancient DNA and the tropics: a rodent's tale’. We were made aware of problems with some of the ancient sequences submitted to GenBank and conducted a systematic review of all the files used in our study. We discovered that, unfortunately, an incorrect file was sent to GenBank and was also used in some of our downstream analyses. We immediately contacted GenBank, explained the situation and corrected the file. We have redone some analyses with the correct file and describe these changes below.

  12. Ancient bacteria show evidence of DNA repair

    DEFF Research Database (Denmark)

    Johnson, Sarah Stewart; Hebsgaard, Martin B; Christensen, Torben R

    2007-01-01

    Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over......-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence...... that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability....

  13. Sex identification of ancient DNA samples using a microfluidic device.

    Science.gov (United States)

    Shaw, Kirsty J; Brown, Keri A; Brown, Terence A; Haswell, Stephen J

    2015-01-01

    Ancient DNA is the name given to the degraded, fragmented, and chemically damaged biomolecules that can be recovered from archaeological remains of plants, animals, and humans. Where ancient human DNA has survived at archaeological sites, it can give valuable information and is especially useful for its potential to identify kinship, population affinities, pathogens, and biological sex. Here, we describe the operation of a microfluidic device for the sex identification of ancient DNA samples using an efficient sample handling process. DNA is extracted from powdered bone samples and abasic sites labeled with biotin. Streptavidin-coated superparamagnetic particles are used to isolate the labeled DNA prior to amplification of the Amelogenin sex marker.

  14. Ancient DNA analysis of northeast Pacific humpback whale (Megaptera novaeangliae)

    OpenAIRE

    Arndt, Ursula Maria

    2011-01-01

    The main goal of this ancient DNA-based study was to analyze archaeological whale skeletal remains from the west coast of Vancouver Island, British Columbia to investigate population genetic diversities of humpback whales pre-dating industrial whaling. This study also examined whale hunting practices of early indigenous people by revealing potential species selections. Nuu-chah-nulth people are believed to have hunted whales for millennia and numerous whale bones have been recovered from arch...

  15. Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA

    DEFF Research Database (Denmark)

    Boessenkool, Sanne; Epp, Laura S.; Haile, James Seymour

    2012-01-01

    , or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA, we first optimized the design and concentration of blocking primer in the PCR......Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results because of competition....... Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe...

  16. Quantification and presence of human ancient DNA in burial place ...

    African Journals Online (AJOL)

    For reliable and sensitive DNA quantitation, the application of real time PCR is described. A published real-time PCR assay, which allows for the combined analysis of nuclear or ancient DNA and mitochondrial DNA, was modified. This approach can be used for recovering DNA from the surface of fossil bone remains in ...

  17. Retroviral DNA Sequences as a Means for Determining Ancient Diets.

    Directory of Open Access Journals (Sweden)

    Jessica I Rivera-Perez

    Full Text Available For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host's diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures.

  18. High-Throughput DNA sequencing of ancient wood.

    Science.gov (United States)

    Wagner, Stefanie; Lagane, Frédéric; Seguin-Orlando, Andaine; Schubert, Mikkel; Leroy, Thibault; Guichoux, Erwan; Chancerel, Emilie; Bech-Hebelstrup, Inger; Bernard, Vincent; Billard, Cyrille; Billaud, Yves; Bolliger, Matthias; Croutsch, Christophe; Čufar, Katarina; Eynaud, Frédérique; Heussner, Karl Uwe; Köninger, Joachim; Langenegger, Fabien; Leroy, Frédéric; Lima, Christine; Martinelli, Nicoletta; Momber, Garry; Billamboz, André; Nelle, Oliver; Palomo, Antoni; Piqué, Raquel; Ramstein, Marianne; Schweichel, Roswitha; Stäuble, Harald; Tegel, Willy; Terradas, Xavier; Verdin, Florence; Plomion, Christophe; Kremer, Antoine; Orlando, Ludovic

    2018-03-01

    Reconstructing the colonization and demographic dynamics that gave rise to extant forests is essential to forecasts of forest responses to environmental changes. Classical approaches to map how population of trees changed through space and time largely rely on pollen distribution patterns, with only a limited number of studies exploiting DNA molecules preserved in wooden tree archaeological and subfossil remains. Here, we advance such analyses by applying high-throughput (HTS) DNA sequencing to wood archaeological and subfossil material for the first time, using a comprehensive sample of 167 European white oak waterlogged remains spanning a large temporal (from 550 to 9,800 years) and geographical range across Europe. The successful characterization of the endogenous DNA and exogenous microbial DNA of 140 (~83%) samples helped the identification of environmental conditions favouring long-term DNA preservation in wood remains, and started to unveil the first trends in the DNA decay process in wood material. Additionally, the maternally inherited chloroplast haplotypes of 21 samples from three periods of forest human-induced use (Neolithic, Bronze Age and Middle Ages) were found to be consistent with those of modern populations growing in the same geographic areas. Our work paves the way for further studies aiming at using ancient DNA preserved in wood to reconstruct the micro-evolutionary response of trees to climate change and human forest management. © 2018 John Wiley & Sons Ltd.

  19. New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

    DEFF Research Database (Denmark)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela

    2015-01-01

    An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases >20-fold in some samples. To investigate the behavior of this method, we generated ssDNA...... and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained...

  20. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects.

    Science.gov (United States)

    Yoshida, Kentaro; Sasaki, Eriko; Kamoun, Sophien

    2015-01-01

    The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.

  1. ANALYSIS OF ANCIENT DNA FROM FOSSIL CORALLINES (CORALLINALES, RHODOPHYTA)(1).

    Science.gov (United States)

    Hughey, Jeffery R; Braga, Juan C; Aguirre, Julio; Woelkerling, William J; Webster, Jody M

    2008-04-01

    The field of molecular paleontology has recently made significant contributions to anthropology and biology. Hundreds of ancient DNA studies have been published, but none has targeted fossil coralline algae. Using regions of the SSU gene, we analyzed rDNA from fossil coralline algae of varying ages and states of preservation from Spain, Papua New Guinea (PNG), and the Great Barrier Reef (GBR). Specimens from PNG, GBR, and some localities from Spain did not contain endogenous ancient DNA. Reproducible sequence data were obtained from specimens ∼550 years old from near Cadiz, Spain, and from rocky-shore deposits in Carboneras, Almeria Province of Spain (∼78,000 years before present [YBP]). Based on BLAST searches and a phylogenetic analysis of sequences, an undescribed coralline alga belonging to the Melobesioideae was discovered in the Carboneras material as well as the following coralline genera: Jania, Lithophyllum, Lithothamnion, Mesophyllum, and Phymatolithon. DNA from fleshy brown and red macroalgae was also discovered in the specimens from Carboneras. The coralline algae identified using molecular techniques were in agreement with those based on morphological methods. The identified taxa are common in the present-day southeastern Spain littoral zone. Amino acid racemization, concentration ratios, and specific concentrations failed to show a correlation between biomolecular preservation and PCR amplification success. Results suggest that molecular investigations on fossil algae, although limited by technical difficulties, are feasible. Validity of our results was established using authentication criteria and a self-critical approach to compliance. © 2008 Phycological Society of America.

  2. Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample

    Directory of Open Access Journals (Sweden)

    Chang Seok Oh

    2010-03-01

    Full Text Available In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA report from a medieval Asian country and thus will expand the scope of Ascaris aDNA research.

  3. Ancient bacteria in permafrost soils fact or artefact? Considerations in recovering microbial DNA from geological ancient settings

    Science.gov (United States)

    Willerslev, E.

    2003-04-01

    Several recent reports claim that prokaryotic genetic sequences or viable cultures can survive for millions of years in geological settings. If substantiated, these findings could fundamentally alter views about bacterial physiology, ecology and evolution. However, both the culturing of microbes and the amplification of ancient DNA molecules from fossil remains are beset with difficulties. First, theoretical and empirical studies have shown that small DNA fragments (100 200 bp) do not survive in the geosphere for more than 104 years in temperate environments and 105 years in colder ones due to hydrolytic and oxidative damage. Therefore, the revivals of dormant bacteria with no active DNA repair from remains hundreds of thousands to millions of years old is, from a theoretical point, expected to be difficult, if not impossible. Second, the no specificity of the media used to culture micro organisms, as well as the great sensitivity of PCR, makes the risk of contamination with contemporary ubiquitous microbial cells and exogenous DNA molecules extremely high. Contamination poses risks at all stages of sample processing (e.g.) within the samples themselves, in the chemical reagents, on laboratory disposables or through the air. The high risk of contamination strongly suggests the need for standardized procedures within the field such as independent replication of results. This criterion of authenticity has not yet been full field in any of the studies claiming million year old microbial cultures or DNA. In order to tests the long-term survival of ancient bacteria DNA a study on permafrost was conducted using ancient DNA precautions, controls and criteria. Permafrost must be considered among the most promising environments for long term DNA survival due to its constant low temperatures (-10C to 12C Siberian or 20C Antarctica) and high cell numbers (107). We found that bacteria DNA could reproducibly be obtained from samples dated up to 300-400,000 years B.P. but not

  4. Ancient DNA, climatic change, and loss of genetic diversity in an endemic Patagonian mammal

    Science.gov (United States)

    Chan, Y.; Lacey, E.; Ramakrishnan, U.; Pearson, O.; Hadly, E.

    2004-12-01

    Understanding the response of animal populations to climatic change is essential for the future maintenance of biodiversity. One question that remains difficult to answer, and is particularly important to conservation, is how animals respond over time scales relevant to evolutionary change. Ancient DNA provides a unique opportunity to track animal response to Holocene climate change and to study species replacement patterns and genetic diversity over time. We used ancient DNA to compare response to climatic change in two species, C. sociabilis and C. haigi, over the last 8,000 years. Our study site, Cueva Traful, is a late-Holocene raptor roost in Parque Nacional Nahuel Huapi, Argentina. A lack of genetic diversity in modern C. sociabilis populations is indicative of past bottleneck events and a previous ancient DNA study found that it had remained genetically identical for at least 1000 years in the face of climatic change and human disturbance. Since Cueva Traful goes back further in time, our first goal was to examine genetic diversity in order to place a longer term historical perspective on the modern bottleneck. The second goal was to compare changes in genetic diversity in C. sociabilis to C. haigi a closely related species that may respond differently to climatic change. The use of ancient DNA presents unique challenges due to low copy number, environmental damage to template, and high contamination risk. Despite these challenges, ancient DNA provides a unique perspective on evolutionary history.

  5. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments

    DEFF Research Database (Denmark)

    Hansen, Anders Johannes; Mitchell, D.L.; Wiuf, C.

    2006-01-01

    Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10 to 400 thousand years in age. Despite optimal preservation conditions, we found the sedimentary DNA to be severely modified by interstrand crosslinks, single and double stranded breaks......, and freely exposed sugar, phosphate, and hydroxyl groups. Intriguingly, interstrand crosslinks were found to accumulate about hundred times faster than single stranded breaks, suggesting that crosslinking rather than depurination is the primary limiting factor for ancient DNA amplification under frozen...... conditions. The results question the reliability of the commonly used models relying on depurination kinetics for predicting the long-term survival of DNA under permafrost conditions and suggest that new strategies for repair of ancient DNA must be considered if the yield of amplifiable DNA from permafrost...

  6. Human evolution in Siberia: from frozen bodies to ancient DNA

    Directory of Open Access Journals (Sweden)

    Bouakaze Caroline

    2010-01-01

    Full Text Available Abstract Background The Yakuts contrast strikingly with other populations from Siberia due to their cattle- and horse-breeding economy as well as their Turkic language. On the basis of ethnological and linguistic criteria as well as population genetic studies, it has been assumed that they originated from South Siberian populations. However, many questions regarding the origins of this intriguing population still need to be clarified (e.g. the precise origin of paternal lineages and the admixture rate with indigenous populations. This study attempts to better understand the origins of the Yakuts by performing genetic analyses on 58 mummified frozen bodies dated from the 15th to the 19th century, excavated from Yakutia (Eastern Siberia. Results High quality data were obtained for the autosomal STRs, Y-chromosomal STRs and SNPs and mtDNA due to exceptional sample preservation. A comparison with the same markers on seven museum specimens excavated 3 to 15 years ago showed significant differences in DNA quantity and quality. Direct access to ancient genetic data from these molecular markers combined with the archaeological evidence, demographical studies and comparisons with 166 contemporary individuals from the same location as the frozen bodies helped us to clarify the microevolution of this intriguing population. Conclusion We were able to trace the origins of the male lineages to a small group of horse-riders from the Cis-Baïkal area. Furthermore, mtDNA data showed that intermarriages between the first settlers with Evenks women led to the establishment of genetic characteristics during the 15th century that are still observed today.

  7. Ancient DNA perspectives on American colonization and population history.

    Science.gov (United States)

    Raff, Jennifer A; Bolnick, Deborah A; Tackney, Justin; O'Rourke, Dennis H

    2011-12-01

    Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history. 2011 Wiley Periodicals, Inc.

  8. DNA in ancient bone - where is it located and how should we extract it?

    DEFF Research Database (Denmark)

    Campos, Paula; Craig, Oliver E.; Turner-Walker, Gordon

    2012-01-01

    . The question arises as to whether this may be due to post-collection preservation or just an artefact of the extraction methods used in these different studies? In an attempt to resolve these questions, we examine the efficacy of DNA extraction methods, and the quality and quantity of DNA recovered from both......Despite the widespread use of bones in ancient DNA (aDNA) studies, relatively little concrete information exists in regard to how the DNA in mineralised collagen degrades, or where it survives in the material's architecture. While, at the macrostructural level, physical exclusion of microbes...... and other external contaminants may be an important feature, and, at the ultrastructural level, the adsorption of DNA to hydroxyapatite and/or binding of DNA to Type I collagen may stabilise the DNA, the relative contribution of each, and what other factors may be relevant, are unclear...

  9. Comparison of Suitability of the Most Common Ancient DNA Quantification Methods.

    Science.gov (United States)

    Brzobohatá, Kristýna; Drozdová, Eva; Smutný, Jiří; Zeman, Tomáš; Beňuš, Radoslav

    2017-04-01

    Ancient DNA (aDNA) extracted from historical bones is damaged and fragmented into short segments, present in low quantity, and usually copurified with microbial DNA. A wide range of DNA quantification methods are available. The aim of this study was to compare the five most common DNA quantification methods for aDNA. Quantification methods were tested on DNA extracted from skeletal material originating from an early medieval burial site. The tested methods included ultraviolet (UV) absorbance, real-time quantitative polymerase chain reaction (qPCR) based on SYBR ® green detection, real-time qPCR based on a forensic kit, quantification via fluorescent dyes bonded to DNA, and fragmentary analysis. Differences between groups were tested using a paired t-test. Methods that measure total DNA present in the sample (NanoDrop ™ UV spectrophotometer and Qubit ® fluorometer) showed the highest concentrations. Methods based on real-time qPCR underestimated the quantity of aDNA. The most accurate method of aDNA quantification was fragmentary analysis, which also allows DNA quantification of the desired length and is not affected by PCR inhibitors. Methods based on the quantification of the total amount of DNA in samples are unsuitable for ancient samples as they overestimate the amount of DNA presumably due to the presence of microbial DNA. Real-time qPCR methods give undervalued results due to DNA damage and the presence of PCR inhibitors. DNA quantification methods based on fragment analysis show not only the quantity of DNA but also fragment length.

  10. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure tha...

  11. Highly informative ancient DNA 'snippets' for New Zealand moa.

    Directory of Open Access Journals (Sweden)

    Jonathan McCallum

    Full Text Available BACKGROUND: Analysis of ancient DNA has provided invaluable information on past ecologies, ancient populations, and extinct species. We used a short snippet of highly variable mitochondrial control region sequence from New Zealand's moa to characterise a large number of bones previously intractable to DNA analysis as well as bone fragments from swamps to gain information about the haplotype diversity and phylogeography that existed in five moa species. METHODOLOGY/PRINCIPAL FINDINGS: By targeting such 'snippets', we show that moa populations differed substantially in geographic structure that is likely to be related to population mobility and history. We show that populations of Pachyornis geranoides, Dinornis novaezealandiae, and Dinornis robustus were highly structured and some appear to have occupied the same geographic location for hundreds of thousands of years. In contrast, populations of the moa Anomalopteryx didiformis and Euryapteryx curtus were widespread, with specific populations of the latter occupying both the North and South Islands of New Zealand. We further show that for a specific area, in this case a North Island swamp, complete haplotype diversity and even sex can be recovered from collections of small, often discarded, bone fragments. CONCLUSIONS/SIGNIFICANCE: Short highly variable mitochondrial 'snippets' allow successful typing of environmentally damaged and fragmented skeletal material, and can provide useful information about ancient population diversity and structure without the need to sample valuable, whole bones often held by museums.

  12. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    Science.gov (United States)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic; Olsen, Jesper; Andersen, Kenneth; Holm, Jakob; Funder, Svend; Willerslev, Eske; Kjær, Kurt H.

    2013-09-01

    We use 2nd generation sequencing technology on sedimentary ancient DNA (sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty-eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (Scrophulariaceae and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650 cal yr BP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less detailed than pollen and macrofossil analyses can be a complementary tool for establishing the composition of both terrestrial and aquatic local plant communities and a method for identifying additional taxa.

  13. Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data.

    Science.gov (United States)

    Weiß, Clemens L; Dannemann, Michael; Prüfer, Kay; Burbano, Hernán A

    2015-11-03

    Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.

  14. Combining bleach and mild predigestion improves ancient DNA recovery from bones

    DEFF Research Database (Denmark)

    Boessenkool, Sanne; Hanghøj, Kristian Ebbesen; Nistelberger, Heidi M.

    2017-01-01

    aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750-1350 cal. years before present. Using high......-throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other...... library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre-extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains...

  15. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

    DEFF Research Database (Denmark)

    Avila Arcos, Maria del Carmen; Cappellini, Enrico; Romero-Navarro, J. Alberto

    2011-01-01

    The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples...

  16. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects

    Directory of Open Access Journals (Sweden)

    Kentaro eYoshida

    2015-09-01

    Full Text Available The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.

  17. A guide to ancient protein studies

    DEFF Research Database (Denmark)

    Hendy, Jessica; Welker, Frido; Demarchi, Beatrice

    2018-01-01

    the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies...

  18. Ancient DNA investigations: A review on their significance in ...

    African Journals Online (AJOL)

    throughput DNA sequencing allow DNA fragments of short lengths to be completely sequenced (Krause et al 2010, Briggs et al 2010). aDNA authentication : Genetic analysis of archeological remains is very challenging because of the contamination by current DNA. Several studies have focused on the identification of the.

  19. Conservation archaeogenomics: ancient DNA and biodiversity in the Anthropocene.

    Science.gov (United States)

    Hofman, Courtney A; Rick, Torben C; Fleischer, Robert C; Maldonado, Jesús E

    2015-09-01

    There is growing consensus that we have entered the Anthropocene, a geologic epoch characterized by human domination of the ecosystems of the Earth. With the future uncertain, we are faced with understanding how global biodiversity will respond to anthropogenic perturbations. The archaeological record provides perspective on human-environment relations through time and across space. Ancient DNA (aDNA) analyses of plant and animal remains from archaeological sites are particularly useful for understanding past human-environment interactions, which can help guide conservation decisions during the environmental changes of the Anthropocene. Here, we define the emerging field of conservation archaeogenomics, which integrates archaeological and genomic data to generate baselines or benchmarks for scientists, managers, and policy-makers by evaluating climatic and human impacts on past, present, and future biodiversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Investigating population continuity with ancient DNA under a spatially explicit simulation framework.

    Science.gov (United States)

    Silva, Nuno Miguel; Rio, Jeremy; Currat, Mathias

    2017-12-15

    of serial samples (ancient-ancient or ancient-modern) and to investigate more complex evolutionary scenarios. Although we based our study on mitochondrial DNA sequences, diploid molecular markers of different types (DNA, SNP, STR) can also be simulated with our approach. It thus constitutes a promising tool for the analysis of the numerous aDNA datasets being produced, including genome wide data, in humans but also in many other species.

  1. 'Progress' renders detrimental an ancient mitochondrial DNA genetic variant.

    Science.gov (United States)

    Pacheu-Grau, David; Gómez-Durán, Aurora; López-Gallardo, Ester; Pinós, Tomàs; Andreu, Antoni L; López-Pérez, Manuel J; Montoya, Julio; Ruiz-Pesini, Eduardo

    2011-11-01

    A human mitochondrial DNA (mtDNA) transition, m.1555A>G, in the 12S rRNA gene causes non-syndromic hearing loss. However, this pathological mutation is the wild-type allele in orangutan mtDNA. Here we rule out different genetic factors as the reason for its fixation in orangutans and show that aminoglycosides negatively affect the oxidative phosphorylation function by decreasing the synthesis of mtDNA-encoded proteins and the amount and activity of respiratory complex IV. These drugs also diminish the growth rate of orangutan cells. The m.1555G nucleotide is also the wild-type allele in other mammal species and they might be at risk of suffering a mitochondrial disorder if treated with aminoglycosides. Therefore, pharmacogenomic approaches should be used to confirm this possibility. These observations are important for human health. Due to the fact that old age and high frequency are criteria widely used in mitochondrial medicine to rule out a genetic change as being a pathological mutation, our results prevent against simplistic genetic approaches that do not consider the potential effect of environmental conditions. Hence, these results suggest that some ancient and highly frequent human population polymorphisms, such as those defining mtDNA haplogroups, in mitochondrial rRNA genes can be deleterious in association with new environmental conditions. Therefore, as the discovery of ribosomal antibiotics has allowed to fight infectious diseases and this breakthrough can be considered an important scientific advance or 'progress', our results suggest that 'progress' can also have a negative counterpart and render detrimental many of these mtDNA genotypes.

  2. Assessing the fidelity of ancient DNA sequences amplified from nuclear genes

    DEFF Research Database (Denmark)

    Binladen, Jonas; Wiuf, Carsten Henrik; Gilbert, M. Thomas P.

    2006-01-01

    in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from...

  3. Evidence of ancient DNA reveals the first European lineage in Iron Age Central China.

    Science.gov (United States)

    Xie, C Z; Li, C X; Cui, Y Q; Zhang, Q C; Fu, Y Q; Zhu, H; Zhou, H

    2007-07-07

    Various studies on ancient DNA have attempted to reconstruct population movement in Asia, with much interest focused on determining the arrival of European lineages in ancient East Asia. Here, we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China, and Taiyuan may be the easternmost location of the discovered remains of European lineage in ancient China.

  4. Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys.

    Science.gov (United States)

    Han, Lu; Zhu, Songbiao; Ning, Chao; Cai, Dawei; Wang, Kai; Chen, Quanjia; Hu, Songmei; Yang, Junkai; Shao, Jing; Zhu, Hong; Zhou, Hui

    2014-11-30

    The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced. Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age. This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.

  5. Time to Spread Your Wings: A Review of the Avian Ancient DNA Field

    Directory of Open Access Journals (Sweden)

    Alicia Grealy

    2017-07-01

    Full Text Available Ancient DNA (aDNA has the ability to inform the evolutionary history of both extant and extinct taxa; however, the use of aDNA in the study of avian evolution is lacking in comparison to other vertebrates, despite birds being one of the most species-rich vertebrate classes. Here, we review the field of “avian ancient DNA” by summarising the past three decades of literature on this topic. Most studies over this time have used avian aDNA to reconstruct phylogenetic relationships and clarify taxonomy based on the sequencing of a few mitochondrial loci, but recent studies are moving toward using a comparative genomics approach to address developmental and functional questions. Applying aDNA analysis with more practical outcomes in mind (such as managing conservation is another increasingly popular trend among studies that utilise avian aDNA, but the majority of these have yet to influence management policy. We find that while there have been advances in extracting aDNA from a variety of avian substrates including eggshell, feathers, and coprolites, there is a bias in the temporal focus; the majority of the ca. 150 studies reviewed here obtained aDNA from late Holocene (100–1000 yBP material, with few studies investigating Pleistocene-aged material. In addition, we identify and discuss several other issues within the field that require future attention. With more than one quarter of Holocene bird extinctions occurring in the last several hundred years, it is more important than ever to understand the mechanisms driving the evolution and extinction of bird species through the use of aDNA.

  6. Natural transformation of bacteria by fragmented, damaged and ancient DNA

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren

    . The degrading DNA is fragmented and damaged, often to less than one hundred base pairs. Such DNA is only recognized as microbial nutrients and is not considered as direct contributors to bacterial evolutionary processes. The main study shows natural transformation by very short DNA (≥20bp). Further we also show...... it by damaged short DNA with abasic sites, crosslinks, and miscoding lesions, which are the most common damages in environmental DNA. This is emphasized by successful natural transformation by 43,000-year-old DNA. We find that the process is a simple variant of natural transformation. On top, we illustrate...... with fullgenome comparisons that the process has general relevance in extant bacteria. Our findings reveal that the large environmental reservoir of short and damaged DNA retains capacity for natural transformation, even after thousands of years. This describes for the first time a process by which cells can...

  7. Revising the recent evolutionary history of equids using ancient DNA.

    Science.gov (United States)

    Orlando, Ludovic; Metcalf, Jessica L; Alberdi, Maria T; Telles-Antunes, Miguel; Bonjean, Dominique; Otte, Marcel; Martin, Fabiana; Eisenmann, Véra; Mashkour, Marjan; Morello, Flavia; Prado, Jose L; Salas-Gismondi, Rodolfo; Shockey, Bruce J; Wrinn, Patrick J; Vasil'ev, Sergei K; Ovodov, Nikolai D; Cherry, Michael I; Hopwood, Blair; Male, Dean; Austin, Jeremy J; Hänni, Catherine; Cooper, Alan

    2009-12-22

    The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.

  8. Pathogenic microbial ancient DNA: a problem or an opportunity?

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2006-01-01

    -controlled and rigorous studies that address technical issues and reliability criteria. This is unfortunate, as the rapid evolutionary rate of many pathogens offers a unique means to establish the authenticity of ancient pathogen sequences-since they should clearly be ancestral to modern genetic diversity (e.g. Reid et...... cloning. Yet these studies have used mobile insertion elements (e.g. IS 6110 in tuberculosis) or conserved loci (e.g. 16S) to detect the presence of pathogens, and very similar or identical sequences have been reported from environmental bacteria (Gilbert et al. 2004). For example, Rollo & Marota (1999...

  9. Ancient DNA investigations: A review on their significance in ...

    African Journals Online (AJOL)

    However, its degradation and post-mortem chemical alteration make difficult its quantification and amplification. Moreover the study of aDNA is challenging due to the contamination by exogenous current DNA. Recently, the progress of molecular techniques and the use of sophisticated approaches greatly improved the ratio ...

  10. Bacterial fumarase and L-malic acid are evolutionary ancient components of the DNA damage response

    Science.gov (United States)

    Singer, Esti; Silas, Yardena BH; Ben-Yehuda, Sigal

    2017-01-01

    Fumarase is distributed between two compartments of the eukaryotic cell. The enzyme catalyses the reversible conversion of fumaric to L-malic acid in mitochondria as part of the tricarboxylic acid (TCA) cycle, and in the cytosol/nucleus as part of the DNA damage response (DDR). Here, we show that fumarase of the model prokaryote Bacillus subtilis (Fum-bc) is induced upon DNA damage, co-localized with the bacterial DNA and is required for the DDR. Fum-bc can substitute for both eukaryotic functions in yeast. Furthermore, we found that the fumarase-dependent intracellular signaling of the B. subtilis DDR is achieved via production of L-malic acid, which affects the translation of RecN, the first protein recruited to DNA damage sites. This study provides a different evolutionary scenario in which the dual function of the ancient prokaryotic fumarase, led to its subsequent distribution into different cellular compartments in eukaryotes. PMID:29140245

  11. Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears.

    Science.gov (United States)

    Fortes, Gloria G; Grandal-d'Anglade, Aurora; Kolbe, Ben; Fernandes, Daniel; Meleg, Ioana N; García-Vázquez, Ana; Pinto-Llona, Ana C; Constantin, Silviu; de Torres, Trino J; Ortiz, Jose E; Frischauf, Christine; Rabeder, Gernot; Hofreiter, Michael; Barlow, Axel

    2016-10-01

    Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago. © 2016 John Wiley & Sons Ltd.

  12. Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

    Science.gov (United States)

    Almathen, Faisal; Charruau, Pauline; Mohandesan, Elmira; Mwacharo, Joram M.; Orozco-terWengel, Pablo; Pitt, Daniel; Abdussamad, Abdussamad M.; Uerpmann, Margarethe; Uerpmann, Hans-Peter; De Cupere, Bea; Magee, Peter; Alnaqeeb, Majed A.; Salim, Bashir; Raziq, Abdul; Dessie, Tadelle; Abdelhadi, Omer M.; Banabazi, Mohammad H.; Al-Eknah, Marzook; Walzer, Chris; Faye, Bernard; Hofreiter, Michael; Peters, Joris; Hanotte, Olivier

    2016-01-01

    Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments. PMID:27162355

  13. SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites.

    Science.gov (United States)

    Iñiguez, Alena Mayo; Reinhard, Karl; Carvalho Gonçalves, Marcelo Luiz; Ferreira, Luiz Fernando; Araújo, Adauto; Paulo Vicente, Ana Carolina

    2006-11-01

    Enterobius vermicularis, pinworm, is one of the most common helminths worldwide, infecting nearly a billion people at all socio-economic levels. In prehistoric populations the paleoparasitological findings show a pinworm homogeneous distribution among hunter-gatherers in North America, intensified with the advent of agriculture. This same increase also occurred in the transition from nomad hunter-gatherers to sedentary farmers in South America, although E. vermicularis infection encompasses only the ancient Andean peoples, with no record among the pre-Colombian populations in the South American lowlands. However, the outline of pinworm paleoepidemiology has been supported by microscopic finding of eggs recovered from coprolites. Since molecular techniques are precise and sensitive in detecting pathogen ancient DNA (aDNA), and also could provide insights into the parasite evolutionary history, in this work we have performed a molecular paleoparasitological study of E. vermicularis. aDNA was recovered and pinworm 5S rRNA spacer sequences were determined from pre-Columbian coprolites (4110 BC-AD 900) from four different North and South American archaeological sites. The sequence analysis confirmed E. vermicularis identity and revealed a similarity among ancient and modern sequences. Moreover, polymorphisms were identified at the relative positions 160, 173 and 180, in independent coprolite samples from Tulán, San Pedro de Atacama, Chile (1080-950 BC). We also verified the presence of peculiarities (Splicing leader (SL1) RNA sequence, spliced donor site, the Sm antigen biding site, and RNA secondary structure) which characterise the SL1 RNA gene. The analysis shows that the SL1 RNA gene of contemporary pinworms was present in pre-Columbian E. vermicularis by 6110 years ago. We were successful in detecting E. vermicularis aDNA even in coprolites without direct microscopic evidence of the eggs, improving the diagnosis of helminth infections in the past and further

  14. King penguin population on Macquarie Island recovers ancient DNA diversity after heavy exploitation in historic times.

    Science.gov (United States)

    Heupink, Tim H; van den Hoff, John; Lambert, David M

    2012-08-23

    Historically, king penguin populations on Macquarie Island have suffered greatly from human exploitation. Two large colonies on the island were drastically reduced to a single small colony as a result of harvesting for the blubber oil industry. However, recent conservation efforts have resulted in the king penguin population expanding in numbers and range to recolonize previous as well as new sites. Ancient DNA methods were used to estimate past genetic diversity and combined with studies of modern populations, we are now able to compare past levels of variation with extant populations on northern Macquarie Island. The ancient and modern populations are closely related and show a similar level of genetic diversity. These results suggest that the king penguin population has recovered past genetic diversity in just 80 years owing to conservation efforts, despite having seen the brink of extinction.

  15. DNA FROM ANCIENT STONE TOOLS AND BONES EXCAVATED AT BUGAS-HOLDING, WYOMING

    Science.gov (United States)

    Traces of DNA may preserve on ancient stone tools. We examined 24 chipped stone artifacts recovered from the Bugas-Holding site in northwestern Wyoming for the presence of DNA residues, and we compared DNA preservation in bones and stone tools from the same stratigraphic context...

  16. The characterization of Helicobacter pylori DNA associated with ancient human remains recovered from a Canadian glacier.

    Directory of Open Access Journals (Sweden)

    Treena Swanston

    2011-02-01

    Full Text Available Helicobacter pylori is a gram-negative bacterium that colonizes the stomach of nearly half of the world's population. Genotypic characterization of H. pylori strains involves the analysis of virulence-associated genes, such as vacA, which has multiple alleles. Previous phylogenetic analyses have revealed a connection between modern H. pylori strains and the movement of ancient human populations. In this study, H. pylori DNA was amplified from the stomach tissue of the Kwäday Dän Ts'ìnchi individual. This ancient individual was recovered from the Samuel Glacier in Tatshenshini-Alsek Park, British Columbia, Canada on the traditional territory of the Champagne and Aishihik First Nations and radiocarbon dated to a timeframe of approximately AD 1670 to 1850. This is the first ancient H. pylori strain to be characterized with vacA sequence data. The Tatshenshini H. pylori strain has a potential hybrid vacA m2a/m1d middle (m region allele and a vacA s2 signal (s region allele. A vacA s2 allele is more commonly identified with Western strains, and this suggests that European strains were present in northwestern Canada during the ancient individual's time. Phylogenetic analysis indicated that the vacA m1d region of the ancient strain clusters with previously published novel Native American strains that are closely related to Asian strains. This indicates a past connection between the Kwäday Dän Ts'ìnchi individual and the ancestors who arrived in the New World thousands of years ago.

  17. Ancient DNA in historical parchments - identifying a procedure for extraction and amplification of genetic material.

    Science.gov (United States)

    Lech, T

    2016-05-06

    Historical parchments in the form of documents, manuscripts, books, or letters, make up a large portion of cultural heritage collections. Their priceless historical value is associated with not only their content, but also the information hidden in the DNA deposited on them. Analyses of ancient DNA (aDNA) retrieved from parchments can be used in various investigations, including, but not limited to, studying their authentication, tracing the development of the culture, diplomacy, and technology, as well as obtaining information on the usage and domestication of animals. This article proposes and verifies a procedure for aDNA recovery from historical parchments and its appropriate preparation for further analyses. This study involved experimental selection of an aDNA extraction method with the highest efficiency and quality of extracted genetic material, from among the multi-stage phenol-chloroform extraction methods, and the modern, column-based techniques that use selective DNA-binding membranes. Moreover, current techniques to amplify entire genetic material were questioned, and the possibility of using mitochondrial DNA for species identification was analyzed. The usefulness of the proposed procedure was successfully confirmed in identification tests of historical parchments dating back to the 13-16th century AD.

  18. Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures.

    Science.gov (United States)

    Storey, Alice A; Athens, J Stephen; Bryant, David; Carson, Mike; Emery, Kitty; deFrance, Susan; Higham, Charles; Huynen, Leon; Intoh, Michiko; Jones, Sharyn; Kirch, Patrick V; Ladefoged, Thegn; McCoy, Patrick; Morales-Muñiz, Arturo; Quiroz, Daniel; Reitz, Elizabeth; Robins, Judith; Walter, Richard; Matisoo-Smith, Elizabeth

    2012-01-01

    Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing.

  19. Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures

    Science.gov (United States)

    Storey, Alice A.; Athens, J. Stephen; Bryant, David; Carson, Mike; Emery, Kitty; deFrance, Susan; Higham, Charles; Huynen, Leon; Intoh, Michiko; Jones, Sharyn; Kirch, Patrick V.; Ladefoged, Thegn; McCoy, Patrick; Morales-Muñiz, Arturo; Quiroz, Daniel; Reitz, Elizabeth; Robins, Judith; Walter, Richard; Matisoo-Smith, Elizabeth

    2012-01-01

    Data from morphology, linguistics, history, and archaeology have all been used to trace the dispersal of chickens from Asian domestication centers to their current global distribution. Each provides a unique perspective which can aid in the reconstruction of prehistory. This study expands on previous investigations by adding a temporal component from ancient DNA and, in some cases, direct dating of bones of individual chickens from a variety of sites in Europe, the Pacific, and the Americas. The results from the ancient DNA analyses of forty-eight archaeologically derived chicken bones provide support for archaeological hypotheses about the prehistoric human transport of chickens. Haplogroup E mtDNA signatures have been amplified from directly dated samples originating in Europe at 1000 B.P. and in the Pacific at 3000 B.P. indicating multiple prehistoric dispersals from a single Asian centre. These two dispersal pathways converged in the Americas where chickens were introduced both by Polynesians and later by Europeans. The results of this study also highlight the inappropriate application of the small stretch of D-loop, traditionally amplified for use in phylogenetic studies, to understanding discrete episodes of chicken translocation in the past. The results of this study lead to the proposal of four hypotheses which will require further scrutiny and rigorous future testing. PMID:22848352

  20. Pros and cons of methylation-based enrichment methods for ancient DNA

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio

    2015-01-01

    enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved......The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules...

  1. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

    Science.gov (United States)

    Pääbo, S

    1989-03-01

    Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links. This renders molecular cloning difficult. However, the polymerase chain reaction can be used to amplify and study short mitochondrial DNA sequences that are of anthropological and evolutionary significance. This opens up the prospect of performing diachronical studies of molecular evolutionary genetics.

  2. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

    DEFF Research Database (Denmark)

    Gamba, Cristina; Hanghøj, Kristian Ebbesen; Gaunitz, Charleen

    2016-01-01

    The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs...... of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning...... a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules...

  3. Moessbauer studies on ancient Jizhon plain Temmoku porcelains

    International Nuclear Information System (INIS)

    Yu Zhengfang; Zheng Yufang; Lin Yongqiang

    1994-01-01

    Three kinds of ancient Jizhou plain Temmoku wares and their several ware-making raw materials were studied by means of X-ray diffraction (XRD) and Moessbauer spectroscopy. The firing technique of ancient Jizhou Temmoku porcelains is discussed. (orig.)

  4. A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA

    DEFF Research Database (Denmark)

    Kuch, Melanie; Gröcke, Darren R; Knyf, Martin C

    2007-01-01

    We have used a systematic protocol for extracting, quantitating, sexing and validating ancient human mitochondrial and nuclear DNA of one male and one female Beothuk, a Native American population from Newfoundland, which became extinct approximately 180 years ago. They carried mtDNA haplotypes, w...

  5. DNA analysis of ancient dogs of the Americas: identifying possible founding haplotypes and reconstructing population histories.

    Science.gov (United States)

    Witt, Kelsey E; Judd, Kathleen; Kitchen, Andrew; Grier, Colin; Kohler, Timothy A; Ortman, Scott G; Kemp, Brian M; Malhi, Ripan S

    2015-02-01

    As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) of mitochondrial DNA (mtDNA) to indicate that prior to European contact the dogs of Native Americans originated in Eurasia. In this study, we summarize past DNA studies of both humans and dogs to discuss their population histories in the Americas. We then sequenced a portion of the mtDNA HVR of 42 pre-Columbian dogs from three sites located in Illinois, coastal British Columbia, and Colorado, and identify four novel dog mtDNA haplotypes. Next, we analyzed a dataset comprised of all available ancient dog sequences from the Americas to infer the pre-Columbian population history of dogs in the Americas. Interestingly, we found low levels of genetic diversity for some populations consistent with the possibility of deliberate breeding practices. Furthermore, we identified multiple putative founding haplotypes in addition to dog haplotypes that closely resemble those of wolves, suggesting admixture with North American wolves or perhaps a second domestication of canids in the Americas. Notably, initial effective population size estimates suggest at least 1000 female dogs likely existed in the Americas at the time of the first known canid burial, and that population size increased gradually over time before stabilizing roughly 1200 years before present. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA

    DEFF Research Database (Denmark)

    Malmström, Helena; Svensson, Emma M; Gilbert, M Thomas P

    2007-01-01

    so, we also produce data that describes the efficiency of bleach incubation of bone powder and its relative detrimental effects on contaminant and authentic ancient DNA. We note that bleach treatment is significantly more detrimental to contaminant than to authentic aDNA in the bleached bone powder...

  7. Improving the performance of true single molecule sequencing for ancient DNA

    Science.gov (United States)

    2012-01-01

    Background Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. Results We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted. Conclusions We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted. PMID:22574620

  8. Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times.

    Science.gov (United States)

    Calvignac, Sebastien; Hughes, Sandrine; Tougard, Christelle; Michaux, Jacques; Thevenot, Michel; Philippe, Michel; Hamdine, Watik; Hänni, Catherine

    2008-04-01

    The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.

  9. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha.

    Directory of Open Access Journals (Sweden)

    Bobbi M Johnson

    Full Text Available The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha. Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins

  10. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha.

    Science.gov (United States)

    Johnson, Bobbi M; Kemp, Brian M; Thorgaard, Gary H

    2018-01-01

    The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed "the four H's": habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have divergent

  11. Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha

    Science.gov (United States)

    Kemp, Brian M.; Thorgaard, Gary H.

    2018-01-01

    The Columbia River and its tributaries provide essential spawning and rearing habitat for many salmonid species, including Chinook salmon (Oncorhynchus tshawytscha). Chinook salmon were historically abundant throughout the basin and Native Americans in the region relied heavily on these fish for thousands of years. Following the arrival of Europeans in the 1800s, salmon in the basin experienced broad declines linked to overfishing, water diversion projects, habitat destruction, connectivity reduction, introgression with hatchery-origin fish, and hydropower development. Despite historical abundance, many native salmonids are now at risk of extinction. Research and management related to Chinook salmon is usually explored under what are termed “the four H’s”: habitat, harvest, hatcheries, and hydropower; here we explore a fifth H, history. Patterns of prehistoric and contemporary mitochondrial DNA variation from Chinook salmon were analyzed to characterize and compare population genetic diversity prior to recent alterations and, thus, elucidate a deeper history for this species. A total of 346 ancient and 366 contemporary samples were processed during this study. Species was determined for 130 of the ancient samples and control region haplotypes of 84 of these were sequenced. Diversity estimates from these 84 ancient Chinook salmon were compared to 379 contemporary samples. Our analysis provides the first direct measure of reduced genetic diversity for Chinook salmon from the ancient to the contemporary period, as measured both in direct loss of mitochondrial haplotypes and reductions in haplotype and nucleotide diversity. However, these losses do not appear equal across the basin, with higher losses of diversity in the mid-Columbia than in the Snake subbasin. The results are unexpected, as the two groups were predicted to share a common history as parts of the larger Columbia River Basin, and instead indicate that Chinook salmon in these subbasins may have

  12. Ancient DNA Reveals Late Pleistocene Existence of Ostriches in Indian Sub-Continent.

    Directory of Open Access Journals (Sweden)

    Sonal Jain

    Full Text Available Ancient DNA (aDNA analysis of extinct ratite species is of considerable interest as it provides important insights into their origin, evolution, paleogeographical distribution and vicariant speciation in congruence with continental drift theory. In this study, DNA hotspots were detected in fossilized eggshell fragments of ratites (dated ≥25000 years B.P. by radiocarbon dating using confocal laser scanning microscopy (CLSM. DNA was isolated from five eggshell fragments and a 43 base pair (bp sequence of a 16S rRNA mitochondrial-conserved region was successfully amplified and sequenced from one of the samples. Phylogenetic analysis of the DNA sequence revealed a 92% identity of the fossil eggshells to Struthio camelus and their position basal to other palaeognaths, consistent with the vicariant speciation model. Our study provides the first molecular evidence for the presence of ostriches in India, complementing the continental drift theory of biogeographical movement of ostriches in India, and opening up a new window into the evolutionary history of ratites.

  13. Ancient DNA from nomads in 2500-year-old archeological sites of Pengyang, China.

    Science.gov (United States)

    Zhao, Yong-Bin; Li, Hong-Jie; Cai, Da-Wei; Li, Chun-Xiang; Zhang, Quan-Chao; Zhu, Hong; Zhou, Hui

    2010-04-01

    Six human remains (dating approximately 2500 years ago) were excavated from Pengyang, China, an area occupied by both ancient nomadic and farming people. The funerary objects found with these remains suggested they were nomads. To further confirm their ancestry, we analyzed both the maternal lineages and paternal lineages of the ancient DNA. From the mitochondrial DNA, six haplotypes were identified as three haplogroups: C, D4 and M10. The haplotype-sharing populations and phylogenetic analyses revealed that these individuals were closely associated with the ancient Xiongnu and modern northern Asians. Single-nucleotide polymorphism analysis of Y chromosomes from four male samples that were typed as haplogroup Q indicated that these people had originated in Siberia. These results show that these ancient people from Pengyang present a close genetic affinity to nomadic people, indicating that northern nomads had reached the Central Plain area of China nearly 2500 years ago.

  14. Establishing the validity of domestication genes using DNA from ancient chickens

    Science.gov (United States)

    Girdland Flink, Linus; Allen, Richard; Barnett, Ross; Malmström, Helena; Peters, Joris; Eriksson, Jonas; Andersson, Leif; Dobney, Keith

    2014-01-01

    Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone. PMID:24753608

  15. Establishing the validity of domestication genes using DNA from ancient chickens.

    Science.gov (United States)

    Girdland Flink, Linus; Allen, Richard; Barnett, Ross; Malmström, Helena; Peters, Joris; Eriksson, Jonas; Andersson, Leif; Dobney, Keith; Larson, Greger

    2014-04-29

    Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼ 280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone.

  16. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    DEFF Research Database (Denmark)

    Pedersen, M.W.; Ginolhac, Aurélien; Orlando, Ludovic Antoine Alexandre

    2013-01-01

    -eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (. Scrophulariaceae...

  17. Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers.

    Science.gov (United States)

    Gamba, C; Fernández, E; Tirado, M; Deguilloux, M F; Pemonge, M H; Utrilla, P; Edo, M; Molist, M; Rasteiro, R; Chikhi, L; Arroyo-Pardo, E

    2012-01-01

    The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations-N* and X1-are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (F(ST) ∼0.13, Ppopulation structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East. © 2011 Blackwell Publishing Ltd.

  18. Natural transformation of bacteria by fragmented, damaged and ancient DNA

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren

    Organisms release DNA both when they live and die. Eventually the DNA disintegrates entirely or it is re-metabolized. There is a constant deposition and decomposition that maintains an environmental pool with large quantities of extracellular DNA, some of which can be thousands of years old. The ...... in chemistry. In addition to qualitative DNA sequencing, statistical analysis of the numerous sequencing reads yields quantitative measurements of DNA modifying reactions....

  19. Toward a new history and geography of human genes informed by ancient DNA.

    Science.gov (United States)

    Pickrell, Joseph K; Reich, David

    2014-09-01

    Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture, and population replacement subsequent to the initial out-of-Africa expansion have altered the genetic structure of most of the world's human populations. In light of this we argue that it is time to critically reevaluate current models of the peopling of the globe, as well as the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Is the ancient permafrost bacteria able to keep DNA stable?

    Indian Academy of Sciences (India)

    repair for cell structures (Brouchkov and Williams 2002) or preserve those otherwise prone to collapse because of the duration of their existence. If so, their mutation rates must be extremely low. This explains genome homology between ancient permafrost bacteria and modern strains. A number of publications as well as ...

  1. The importance of studying inherited hematological disorders in ancient Anatolian populations

    Directory of Open Access Journals (Sweden)

    Yeşim Doğan Alakoç

    2011-12-01

    Full Text Available Before analysis of DNA from ancient remains was possible, anthropologists studied evolution and migration patterns using data obtained from population genetic studies on modern populations combined with data obtained from morphological evaluations of ancient remains. Currently, DNA analysis of ancient populations is making a valuable contribution to these efforts. Researchers that perform ancient DNA analysis prefer to study polymorphisms on the Y chromosome or mitochondrial DNA because the results are easier to statistically evaluate. To evaluate polymorphisms on diploid genomes, which are more informative, only mutations that have been extensively examined in modern populations should be chosen. The most extensively evaluated mutations are those related to prevalent inherited disorders. As such, beta-thalassemia, sickle cell anemia, FVL mutation of globin and the factor V genes are good candidates for DNA studies in ancient populations. These mutations are common in Anatolia, host to many civilizations since the Paleolithic period. This history makes Anatolia a good place for conducting research that could enhance our understanding of human evolution and migration patterns.

  2. Enterobius vermicularis: ancient DNA from north and south American human coprolites

    Directory of Open Access Journals (Sweden)

    Iñiguez Alena M

    2003-01-01

    Full Text Available A molecular paleoparasitological diagnostic approach was developed for Enterobius vermicularis. Ancient DNA was extracted from 27 coprolites from archaeological sites in Chile and USA. Enzymatic amplification of human mtDNA sequences confirmed the human origin. We designed primers specific to the E. vermicularis 5S ribosomal RNA spacer region and they allowed reproducible polymerase chain reaction identification of ancient material. We suggested that the paleoparasitological microscopic identification could accompany molecular diagnosis, which also opens the possibility of sequence analysis to understand parasite-host evolution.

  3. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability

    DEFF Research Database (Denmark)

    Jørgensen, Tina; Haile, James Seymour; Möller, Per

    2012-01-01

    approach. SedaDNA and macrofossils share greater overlap in plant identifications than with pollen, suggesting that sedaDNA is local in origin. These two proxies also permit identification to lower taxonomic levels than pollen, enabling investigation into temporal changes in species composition...... and the determination of indicator species to describe environmental changes. Combining data from all three proxies reveals an area continually dominated by a mosaic vegetation of tundra-steppe, pioneer and wet-indicator plants. Such vegetational stability is unexpected, given the severe climate changes taking place...

  4. Ancient microbes from halite fluid inclusions: optimized surface sterilization and DNA extraction.

    Directory of Open Access Journals (Sweden)

    Krithivasan Sankaranarayanan

    Full Text Available Fluid inclusions in evaporite minerals (halite, gypsum, etc. potentially preserve genetic records of microbial diversity and changing environmental conditions of Earth's hydrosphere for nearly one billion years. Here we describe a robust protocol for surface sterilization and retrieval of DNA from fluid inclusions in halite that, unlike previously published methods, guarantees removal of potentially contaminating surface-bound DNA. The protocol involves microscopic visualization of cell structures, deliberate surface contamination followed by surface sterilization with acid and bleach washes, and DNA extraction using Amicon centrifugal filters. Methods were verified on halite crystals of four different ages from Saline Valley, California (modern, 36 ka, 64 ka, and 150 ka, with retrieval of algal and archaeal DNA, and characterization of the algal community using ITS1 sequences. The protocol we developed opens up new avenues for study of ancient microbial ecosystems in fluid inclusions, understanding microbial evolution across geological time, and investigating the antiquity of life on earth and other parts of the solar system.

  5. Is amino acid racemization a useful tool for screening for ancient DNA in bone?

    Science.gov (United States)

    Collins, Matthew J; Penkman, Kirsty E H; Rohland, Nadin; Shapiro, Beth; Dobberstein, Reimer C; Ritz-Timme, Stefanie; Hofreiter, Michael

    2009-08-22

    Many rare and valuable ancient specimens now carry the scars of ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02-0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for ancient DNA from bone.

  6. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing.

    Science.gov (United States)

    Gamba, Cristina; Hanghøj, Kristian; Gaunitz, Charleen; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Bradley, Daniel G; Orlando, Ludovic

    2016-03-01

    The DNA molecules that can be extracted from archaeological and palaeontological remains are often degraded and massively contaminated with environmental microbial material. This reduces the efficacy of shotgun approaches for sequencing ancient genomes, despite the decreasing sequencing costs of high-throughput sequencing (HTS). Improving the recovery of endogenous molecules from the DNA extraction and purification steps could, thus, help advance the characterization of ancient genomes. Here, we apply the three most commonly used DNA extraction methods to five ancient bone samples spanning a ~30 thousand year temporal range and originating from a diversity of environments, from South America to Alaska. We show that methods based on the purification of DNA fragments using silica columns are more advantageous than in solution methods and increase not only the total amount of DNA molecules retrieved but also the relative importance of endogenous DNA fragments and their molecular diversity. Therefore, these methods provide a cost-effective solution for downstream applications, including DNA sequencing on HTS platforms. © 2015 John Wiley & Sons Ltd.

  7. Ancient pathogen DNA in human teeth and petrous bones

    DEFF Research Database (Denmark)

    Margaryan, Ashot; Hansen, Henrik B.; Rasmussen, Simon

    2018-01-01

    pestis. Based on shotgun sequencing data, four of these five plague victims showed clearly detectable levels of Y.pestis DNA in the teeth, whereas all the petrous bones failed to produce Y.pestis DNA above baseline levels. A broader comparative metagenomic analysis of teeth and petrous bones from 10...

  8. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

    OpenAIRE

    Pääbo, S

    1989-01-01

    Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links....

  9. Mortar alteration: experimental study and ancient analogues

    International Nuclear Information System (INIS)

    Rassineux, Francois

    1987-01-01

    As the durability of cemented matrices is a matter of great importance in numerous domains, notably for the long term reliability of surface storages of radioactive wastes, the objective of this research thesis is to define mechanisms of evolution of cemented matrices when in contact with diluted aqueous solutions. The author notably studied the influence of the lixiviation mode on the evolution of two mortars having different compositions (pH, CO 2 pressure, system containment, and cement mineralogical nature appear to be the main governing parameters), the alteration (dissolution is the prevailing process in the interaction between cemented matrices and a diluted solution such as rain water), and ancient binders (archaeological binders containing mineral phases such as hydrated calcium silicates or hydro-grossulars). The obtained results lead to the definition of alteration mechanisms in modern cements, and highlight factors governing the durability of these materials when submitted to meteoric alteration [fr

  10. Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae).

    Science.gov (United States)

    Garrigos, Yareli Esquer; Hugueny, Bernard; Koerner, Kellie; Ibañez, Carla; Bonillo, Celine; Pruvost, Patrice; Causse, Romain; Cruaud, Corinne; Gaubert, Philippe

    2013-01-01

    Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of O. pentlandii), so

  11. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past.

    Science.gov (United States)

    Der Sarkissian, Clio; Pichereau, Vianney; Dupont, Catherine; Ilsøe, Peter C; Perrigault, Mickael; Butler, Paul; Chauvaud, Laurent; Eiríksson, Jón; Scourse, James; Paillard, Christine; Orlando, Ludovic

    2017-09-01

    Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high-throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome-scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management. © 2017 John Wiley & Sons Ltd.

  12. Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach

    Directory of Open Access Journals (Sweden)

    Iñiguez Alena M

    2003-01-01

    Full Text Available The aim of this work was to determine approaches that would improve the quality of ancient DNA (aDNA present in coprolites to enhance the possibility of success in retrieving specific sequence targets. We worked with coprolites from South American archaeological sites in Brazil and Chile dating up to 7,000 years ago. Using established protocols for aDNA extraction we obtained samples showing high degradation as usually happens with this kind of material. The reconstructive polymerization pretreatment was essential to overcome the DNA degradation and the serial dilutions helped with to prevent polymerase chain reaction (PCR inhibitors. Moreover, the random amplified polymorphic DNA-PCR has been shown to be a reliable technique for further experiments to recover specific aDNA sequences.

  13. Comparing ancient DNA preservation in petrous bone and tooth cementum

    DEFF Research Database (Denmark)

    Hansen, Henrik B.; Damgaard, Peter de Barros; Margaryan, Ashot

    2017-01-01

    preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average...

  14. Is the ancient permafrost bacteria able to keep DNA stable?

    Indian Academy of Sciences (India)

    Navya

    According to the preliminary DNA analysis, bacterial cells collected from the relict permafrost appeared to be Bacillus sp. strains, which are close to modern bacteria at a molecular level. Therefore, a number of question raises. For example, are isolated bacteria as old as the permafrost itself or could contamination with more ...

  15. Characterising the potential of sheep wool for ancient DNA analyses

    DEFF Research Database (Denmark)

    Brandt, Luise Ørsted; Tranekjer, Lena D.; Mannering, Ulla

    2011-01-01

    can be PCR-amplified from wool derived from a variety of breeds, regardless of the body location or natural pigmentation. Furthermore, although DNA can be PCR-amplified from wool dyed with one of four common plant dyes (tansy, woad, madder, weld), the use of mordants such as alum or iron leads...

  16. Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Pichereau, Vianney; Dupont, Catherine

    2017-01-01

    -) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA...... environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA...

  17. Ancient mitochondrial DNA analyses of ascaris eggs discovered in coprolites from joseon tomb.

    Science.gov (United States)

    Oh, Chang Seok; Seo, Min; Hong, Jong Ha; Chai, Jong-Yil; Oh, Seung Whan; Park, Jun Bum; Shin, Dong Hoon

    2015-04-01

    Analysis of ancient DNA (aDNA) extracted from Ascaris is very important for understanding the phylogenetic lineage of the parasite species. When aDNAs obtained from a Joseon tomb (SN2-19-1) coprolite in which Ascaris eggs were identified were amplified with primers for cytochrome b (cyt b) and 18S small subunit ribosomal RNA (18S rRNA) gene, the outcome exhibited Ascaris specific amplicon bands. By cloning, sequencing, and analysis of the amplified DNA, we obtained information valuable for comprehending genetic lineage of Ascaris prevalent among pre-modern Joseon peoples.

  18. Ancient mtDNA genetic variants modulate mtDNA transcription and replication.

    Directory of Open Access Journals (Sweden)

    Sarit Suissa

    2009-05-01

    Full Text Available Although the functional consequences of mitochondrial DNA (mtDNA genetic backgrounds (haplotypes, haplogroups have been demonstrated by both disease association studies and cell culture experiments, it is not clear which of the mutations within the haplogroup carry functional implications and which are "evolutionary silent hitchhikers". We set forth to study the functionality of haplogroup-defining mutations within the mtDNA transcription/replication regulatory region by in vitro transcription, hypothesizing that haplogroup-defining mutations occurring within regulatory motifs of mtDNA could affect these processes. We thus screened >2500 complete human mtDNAs representing all major populations worldwide for natural variation in experimentally established protein binding sites and regulatory regions comprising a total of 241 bp in each mtDNA. Our screen revealed 77/241 sites showing point mutations that could be divided into non-fixed (57/77, 74% and haplogroup/sub-haplogroup-defining changes (i.e., population fixed changes, 20/77, 26%. The variant defining Caucasian haplogroup J (C295T increased the binding of TFAM (Electro Mobility Shift Assay and the capacity of in vitro L-strand transcription, especially of a shorter transcript that maps immediately upstream of conserved sequence block 1 (CSB1, a region associated with RNA priming of mtDNA replication. Consistent with this finding, cybrids (i.e., cells sharing the same nuclear genetic background but differing in their mtDNA backgrounds harboring haplogroup J mtDNA had a >2 fold increase in mtDNA copy number, as compared to cybrids containing haplogroup H, with no apparent differences in steady state levels of mtDNA-encoded transcripts. Hence, a haplogroup J regulatory region mutation affects mtDNA replication or stability, which may partially account for the phenotypic impact of this haplogroup. Our analysis thus demonstrates, for the first time, the functional impact of particular mtDNA

  19. Attitudes to Ancient Greek in Three Schools: A Case Study

    Science.gov (United States)

    Foster, Frances

    2018-01-01

    This study comes in response to recent changes in UK policy, whereby Ancient Greek and Latin have been included alongside modern languages as part of the curriculum at Key Stage 2. It aims to understand how Ancient Greek is surviving and thriving in three different types of schools. After a short overview of the history of Greek teaching in the…

  20. Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds.

    Science.gov (United States)

    Niemi, Marianna; Bläuer, Auli; Iso-Touru, Terhi; Nyström, Veronica; Harjula, Janne; Taavitsainen, Jussi-Pekka; Storå, Jan; Lidén, Kerstin; Kantanen, Juha

    2013-01-22

    Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval periods by sequencing a partial mitochondrial DNA D-loop and the 5'-promoter region of the SRY gene. We compared the maternal (mitochondrial DNA haplotypes) and paternal (SNP oY1) genetic diversity of ancient sheep in Finland with modern domestic sheep populations in Europe and Asia to study temporal changes in genetic variation and affinities between ancient and modern populations. A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY1, which is frequent in modern north-European sheep breeds. Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past

  1. The genetic impact of Aztec imperialism: ancient mitochondrial DNA evidence from Xaltocan, Mexico.

    Science.gov (United States)

    Mata-Míguez, Jaime; Overholtzer, Lisa; Rodríguez-Alegría, Enrique; Kemp, Brian M; Bolnick, Deborah A

    2012-12-01

    In AD 1428, the city-states of Tenochtitlan, Texcoco, and Tlacopan formed the Triple Alliance, laying the foundations of the Aztec empire. Although it is well documented that the Aztecs annexed numerous polities in the Basin of Mexico over the following years, the demographic consequences of this expansion remain unclear. At the city-state capital of Xaltocan, 16th century documents suggest that the site's conquest and subsequent incorporation into the Aztec empire led to a replacement of the original Otomí population, whereas archaeological evidence suggests that some of the original population may have remained at the town under Aztec rule. To help address questions about Xaltocan's demographic history during this period, we analyzed ancient DNA from 25 individuals recovered from three houses rebuilt over time and occupied between AD 1240 and 1521. These individuals were divided into two temporal groups that predate and postdate the site's conquest. We determined the mitochondrial DNA haplogroup of each individual and identified haplotypes based on 372 base pair sequences of first hypervariable region. Our results indicate that the residents of these houses before and after the Aztec conquest have distinct haplotypes that are not closely related, and the mitochondrial compositions of the temporal groups are statistically different. Altogether, these results suggest that the matrilines present in the households were replaced following the Aztec conquest. This study therefore indicates that the Aztec expansion may have been associated with significant demographic and genetic changes within Xaltocan. Copyright © 2012 Wiley Periodicals, Inc.

  2. Ancient DNA analyses of museum specimens from selected Presbytis (primate: Colobinae) based on partial Cyt b sequences

    Science.gov (United States)

    Aifat, N. R.; Yaakop, S.; Md-Zain, B. M.

    2016-11-01

    The IUCN Red List of Threatened Species has categorized Malaysian primates from being data deficient to critically endanger. Thus, ancient DNA analyses hold great potential to understand phylogeny, phylogeography and population history of extinct and extant species. Museum samples are one of the alternatives to provide important sources of biological materials for a large proportion of ancient DNA studies. In this study, a total of six museum skin samples from species Presbytis hosei (4 samples) and Presbytis frontata (2 samples), aged between 43 and 124 years old were extracted to obtain the DNA. Extraction was done by using QIAGEN QIAamp DNA Investigator Kit and the ability of this kit to extract museum skin samples was tested by amplification of partial Cyt b sequence using species-specific designed primer. Two primer pairs were designed specifically for P. hosei and P. frontata, respectively. These primer pairs proved to be efficient in amplifying 200bp of the targeted species in the optimized PCR conditions. The performance of the sequences were tested to determine genetic distance of genus Presbytis in Malaysia. From the analyses, P. hosei is closely related to P. chrysomelas and P. frontata with the value of 0.095 and 0.106, respectively. Cyt b gave a clear data in determining relationships among Bornean species. Thus, with the optimized condition, museum specimens can be used for molecular systematic studies of the Malaysian primates.

  3. Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans

    Science.gov (United States)

    Slatkin, Montgomery

    2016-01-01

    When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters—including drift times and admixture rates—for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called ‘Demographic Inference with Contamination and Error’ (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. PMID:27049965

  4. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics

    DEFF Research Database (Denmark)

    Campos, Paula; Willerslev, Eske; Sher, Andrei

    2010-01-01

    , as it was the geographic origin of all samples studied and held a large diverse population until local extinction at approximately 45,000 radiocarbon years before present ((14)C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 (14)C YBP, recontracted at ca. 18,000 (14)C YBP, and finally recovered...... to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population...

  5. Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management.

    Directory of Open Access Journals (Sweden)

    Antonia T Rodrigues

    Full Text Available Rockfish (Sebastes spp. are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.

  6. Ancient DNA analysis of Indigenous rockfish use on the Pacific Coast: Implications for marine conservation areas and fisheries management.

    Science.gov (United States)

    Rodrigues, Antonia T; McKechnie, Iain; Yang, Dongya Y

    2018-01-01

    Rockfish (Sebastes spp.) are a common marine fish in nearshore and continental shelf environments in the North Pacific Ocean. They are frequently identified in coastal archaeological sites in western North America; however, the morphological similarity of rockfish species limits conventional zooarchaeological identifications to the genus level. This study applies ancient DNA analysis to 96 archaeological rockfish specimens from four sites on separate islands in an archipelago on western Vancouver Island, British Columbia, Canada. Two of the archaeological sites are located within a marine protected area specifically designed to facilitate the recovery of inshore rockfish populations; two sites are located outside this boundary and remain subject to considerable fishing pressure. Using mitochondrial 16S and control region DNA sequences, we identify at least twelve different rockfish species utilized during the past 2,500 years. Identification of rockfish at closely spaced and contemporaneously occupied sites confirms that a variety of Sebastes species were consistently exploited at each site, with more exposed areas having a higher number of species present. Identification results indicate that four of the twelve species did not occur within the conservation area boundary and, instead, were found in sites where commercial and recreational fishing continues to be permitted. This study demonstrates that ancient DNA identifications of archaeological assemblages can complement and expand perspective on modern day fisheries conservation and management in this National Park Reserve and First Nations ancestral territory.

  7. Ancient DNA and morphometric analysis reveal extinction and replacement of New Zealand's unique black swans.

    Science.gov (United States)

    Rawlence, Nicolas J; Kardamaki, Afroditi; Easton, Luke J; Tennyson, Alan J D; Scofield, R Paul; Waters, Jonathan M

    2017-07-26

    Prehistoric human impacts on megafaunal populations have dramatically reshaped ecosystems worldwide. However, the effects of human exploitation on smaller species, such as anatids (ducks, geese, and swans) are less clear. In this study we apply ancient DNA and osteological approaches to reassess the history of Australasia's iconic black swans ( Cygnus atratus ) including the palaeo-behaviour of prehistoric populations. Our study shows that at the time of human colonization, New Zealand housed a genetically, morphologically, and potentially ecologically distinct swan lineage ( C. sumnerensis , Poūwa), divergent from modern (Australian) C. atratus Morphological analyses indicate C. sumnerensis exhibited classic signs of the 'island rule' effect, being larger, and likely flight-reduced compared to C. atratus Our research reveals sudden extinction and replacement events within this anatid species complex, coinciding with recent human colonization of New Zealand. This research highlights the role of anthropogenic processes in rapidly reshaping island ecosystems and raises new questions for avian conservation, ecosystem re-wilding, and de-extinction. © 2017 The Author(s).

  8. Ancient mitogenomics

    DEFF Research Database (Denmark)

    Ho, Simon Y. W.; Gilbert, Tom

    2010-01-01

    The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtai...

  9. Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.

    Science.gov (United States)

    Juras, Anna; Chyleński, Maciej; Krenz-Niedbała, Marta; Malmström, Helena; Ehler, Edvard; Pospieszny, Łukasz; Łukasik, Sylwia; Bednarczyk, Józef; Piontek, Janusz; Jakobsson, Mattias; Dabert, Miroslawa

    2017-01-01

    We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS 14 C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq™ Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct

  10. PIXE study on ancient pottery from Chinese Shanghai area

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, H.S. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China)]. E-mail: hscheng@fudan.edu.cn; Zhang, Z.Q. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China); Song, J. [Shanghai Museum, Shanghai 200003 (China); Gao, M.H. [Department of Cultural Relics and Museology, Fudan University, Shanghai 200433 (China); Zhu, D. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China); Lin, J.W. [Institute of Modern Physics, Fudan University, 220 Handan Road, Shanghai 200433 (China); Feng, S.L. [Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Science, P.O. Box 918, Beijing 100039 (China)

    2006-08-15

    Shanghai is the largest city in China, and it also has a very long history. Archaeologists have found that six thousand yeas ago, there were ancient people living at Songze, Qingpu County, Shanghai. This paper reports the study of ancient potteries unearthed from the Guangfulin site located at Songjiang, Shanghai. The potteries unearthed from Guangfulin site belonged to two different culture types: the Liangzhu culture type (local culture) and a new culture, which might be derived from elsewhere. PIXE has been used to measure the chemical compositions of samples and factor analysis was used. Experimental results show that the compositions of the pottery from the two phases are different from each other. It means that the raw materials used to make the ancient pottery originate from different places. This results support the idea suggested by archaeologists that a group of ancient people migrated to the Shanghai area from some other place 4000 years ago.

  11. PIXE study on ancient pottery from Chinese Shanghai area

    International Nuclear Information System (INIS)

    Cheng, H.S.; Zhang, Z.Q.; Song, J.; Gao, M.H.; Zhu, D.; Lin, J.W.; Feng, S.L.

    2006-01-01

    Shanghai is the largest city in China, and it also has a very long history. Archaeologists have found that six thousand yeas ago, there were ancient people living at Songze, Qingpu County, Shanghai. This paper reports the study of ancient potteries unearthed from the Guangfulin site located at Songjiang, Shanghai. The potteries unearthed from Guangfulin site belonged to two different culture types: the Liangzhu culture type (local culture) and a new culture, which might be derived from elsewhere. PIXE has been used to measure the chemical compositions of samples and factor analysis was used. Experimental results show that the compositions of the pottery from the two phases are different from each other. It means that the raw materials used to make the ancient pottery originate from different places. This results support the idea suggested by archaeologists that a group of ancient people migrated to the Shanghai area from some other place 4000 years ago

  12. A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis.

    Science.gov (United States)

    Sirak, Kendra A; Fernandes, Daniel M; Cheronet, Olivia; Novak, Mario; Gamarra, Beatriz; Balassa, Tímea; Bernert, Zsolt; Cséki, Andrea; Dani, János; Gallina, József Zsolt; Kocsis-Buruzs, Gábor; Kővári, Ivett; László, Orsolya; Pap, Ildikó; Patay, Róbert; Petkes, Zsolt; Szenthe, Gergely; Szeniczey, Tamás; Hajdu, Tamás; Pinhasi, Ron

    2017-06-01

    Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses. We assessed this method by comparing the aDNA results from one petrous bone processed using our novel method to its pair, which was processed using established protocols for sampling disarticulated petrous bones. We show a decrease in endogenous DNA and molecular copy numbers when the drilling method is used; however, we also show that this method produces more endogenous DNA and higher copy numbers than any postcranial bone. Our results demonstrate that this minimally-invasive method reduces the loss of genetic data associated with the use of other skeletal elements and enables the combined craniometric and genetic study of individuals with archeological, cultural, and evolutionary value.

  13. Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

    Science.gov (United States)

    Pacioni, Carlo; Hunt, Helen; Allentoft, Morten E; Vaughan, Timothy G; Wayne, Adrian F; Baynes, Alexander; Haouchar, Dalal; Dortch, Joe; Bunce, Michael

    2015-12-01

    The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000-4000 years in association with a dramatic population decline. In addition, we obtained near-complete 11-loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of 'new' microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current-day conservation strategies. © 2015 John Wiley & Sons Ltd.

  14. Ancient DNA reveals genetic connections between early Di-Qiang and Han Chinese.

    Science.gov (United States)

    Li, Jiawei; Zeng, Wen; Zhang, Ye; Ko, Albert Min-Shan; Li, Chunxiang; Zhu, Hong; Fu, Qiaomei; Zhou, Hui

    2017-12-04

    Ancient Di-Qiang people once resided in the Ganqing region of China, adjacent to the Central Plain area from where Han Chinese originated. While gene flow between the Di-Qiang and Han Chinese has been proposed, there is no evidence to support this view. Here we analyzed the human remains from an early Di-Qiang site (Mogou site dated ~4000 years old) and compared them to other ancient DNA across China, including an early Han-related site (Hengbei site dated ~3000 years old) to establish the underlying genetic relationship between the Di-Qiang and ancestors of Han Chinese. We found Mogou mtDNA haplogroups were highly diverse, comprising 14 haplogroups: A, B, C, D (D*, D4, D5), F, G, M7, M8, M10, M13, M25, N*, N9a, and Z. In contrast, Mogou males were all Y-DNA haplogroup O3a2/P201; specifically one male was further assigned to O3a2c1a/M117 using targeted unique regions on the non-recombining region of the Y-chromosome. We compared Mogou to 7 other ancient and 38 modern Chinese groups, in a total of 1793 individuals, and found that Mogou shared close genetic distances with Taojiazhai (a more recent Di-Qiang population), Hengbei, and Northern Han. We modeled their interactions using Approximate Bayesian Computation, and support was given to a potential admixture of ~13-18% between the Mogou and Northern Han around 3300-3800 years ago. Mogou harbors the earliest genetically identifiable Di-Qiang, ancestral to the Taojiazhai, and up to ~33% paternal and ~70% of its maternal haplogroups could be found in present-day Northern Han Chinese.

  15. Bona fide colour: DNA prediction of human eye and hair colour from ancient and contemporary skeletal remains

    NARCIS (Netherlands)

    J. Draus-Barini (Jolanta); S. Walsh (Susan); E. Pośpiech (Ewelina); T. Kupiec (Tomasz); H. Głab (Henryk); W. Branicki (Wojciech); M.H. Kayser (Manfred)

    2013-01-01

    textabstractBackground: DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing

  16. Ancient DNA reveals lack of continuity between neolithic hunter-gatherers and contemporary Scandinavians

    DEFF Research Database (Denmark)

    Malmström, Helena; Gilbert, M Thomas P; Thomas, Mark G

    2009-01-01

    The driving force behind the transition from a foraging to a farming lifestyle in prehistoric Europe (Neolithization) has been debated for more than a century [1-3]. Of particular interest is whether population replacement or cultural exchange was responsible [3-5]. Scandinavia holds a unique place...... of the two cultures in Scandinavia has been cited as an argument against population replacement between the Mesolithic and the present [7, 8]. Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern...

  17. Mitochondrial DNA variation, but not nuclear DNA, sharply divides morphologically identical chameleons along an ancient geographic barrier.

    Directory of Open Access Journals (Sweden)

    Dan Bar Yaacov

    Full Text Available The Levant is an important migration bridge, harboring border-zones between Afrotropical and palearctic species. Accordingly, Chameleo chameleon, a common species throughout the Mediterranean basin, is morphologically divided in the southern Levant (Israel into two subspecies, Chamaeleo chamaeleon recticrista (CCR and C. c. musae (CCM. CCR mostly inhabits the Mediterranean climate (northern Israel, while CCM inhabits the sands of the north-western Negev Desert (southern Israel. AFLP analysis of 94 geographically well dispersed specimens indicated moderate genetic differentiation (PhiPT = 0.097, consistent with the classical division into the two subspecies, CCR and CCM. In contrast, sequence analysis of a 637 bp coding mitochondrial DNA (mtDNA fragment revealed two distinct phylogenetic clusters which were not consistent with the morphological division: one mtDNA cluster consisted of CCR specimens collected in regions northern of the Jezreel Valley and another mtDNA cluster harboring specimens pertaining to both the CCR and CCM subspecies but collected southern of the Jezreel Valley. AMOVA indicated clear mtDNA differentiation between specimens collected northern and southern to the Jezreel Valley (PhiPT = 0.79, which was further supported by a very low coalescent-based estimate of effective migration rates. Whole chameleon mtDNA sequencing (∼17,400 bp generated from 11 well dispersed geographic locations revealed 325 mutations sharply differentiating the two mtDNA clusters, suggesting a long allopatric history further supported by BEAST. This separation correlated temporally with the existence of an at least 1 million year old marine barrier at the Jezreel Valley exactly where the mtDNA clusters meet. We discuss possible involvement of gender-dependent life history differences in maintaining such mtDNA genetic differentiation and suggest that it reflects (ancient local adaptation to mitochondrial-related traits.

  18. Mitochondrial DNA Variation, but Not Nuclear DNA, Sharply Divides Morphologically Identical Chameleons along an Ancient Geographic Barrier

    Science.gov (United States)

    Zilka, Yael; Ovadia, Ofer; Bouskila, Amos; Mishmar, Dan

    2012-01-01

    The Levant is an important migration bridge, harboring border-zones between Afrotropical and palearctic species. Accordingly, Chameleo chameleon, a common species throughout the Mediterranean basin, is morphologically divided in the southern Levant (Israel) into two subspecies, Chamaeleo chamaeleon recticrista (CCR) and C. c. musae (CCM). CCR mostly inhabits the Mediterranean climate (northern Israel), while CCM inhabits the sands of the north-western Negev Desert (southern Israel). AFLP analysis of 94 geographically well dispersed specimens indicated moderate genetic differentiation (PhiPT = 0.097), consistent with the classical division into the two subspecies, CCR and CCM. In contrast, sequence analysis of a 637 bp coding mitochondrial DNA (mtDNA) fragment revealed two distinct phylogenetic clusters which were not consistent with the morphological division: one mtDNA cluster consisted of CCR specimens collected in regions northern of the Jezreel Valley and another mtDNA cluster harboring specimens pertaining to both the CCR and CCM subspecies but collected southern of the Jezreel Valley. AMOVA indicated clear mtDNA differentiation between specimens collected northern and southern to the Jezreel Valley (PhiPT = 0.79), which was further supported by a very low coalescent-based estimate of effective migration rates. Whole chameleon mtDNA sequencing (∼17,400 bp) generated from 11 well dispersed geographic locations revealed 325 mutations sharply differentiating the two mtDNA clusters, suggesting a long allopatric history further supported by BEAST. This separation correlated temporally with the existence of an at least 1 million year old marine barrier at the Jezreel Valley exactly where the mtDNA clusters meet. We discuss possible involvement of gender-dependent life history differences in maintaining such mtDNA genetic differentiation and suggest that it reflects (ancient) local adaptation to mitochondrial-related traits. PMID:22457709

  19. Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics

    Directory of Open Access Journals (Sweden)

    Lumibao Candice Y

    2011-01-01

    Full Text Available Abstract Background Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes. Results We successfully sequenced DNA from 64 samples (out of 126 comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments Conclusions An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.

  20. Surveying the repair of ancient DNA from bones via high-throughput sequencing.

    Science.gov (United States)

    Mouttham, Nathalie; Klunk, Jennifer; Kuch, Melanie; Fourney, Ron; Poinar, Hendrik

    2015-07-01

    DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive.

  1. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

    Science.gov (United States)

    Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

    2014-04-01

    Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

  2. Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska.

    Science.gov (United States)

    West, Catherine; Hofman, Courtney A; Ebbert, Steve; Martin, John; Shirazi, Sabrina; Dunning, Samantha; Maldonado, Jesus E

    2017-10-01

    The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

  3. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp. and a recently extinct lineage of spotted kiwi.

    Directory of Open Access Journals (Sweden)

    Lara D Shepherd

    Full Text Available The little spotted kiwi (Apteryx owenii is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis, with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species survived on the South Island mainland until more recently than previously thought.

  4. Using ancient DNA and coalescent-based methods to infer extinction.

    Science.gov (United States)

    Chang, Dan; Shapiro, Beth

    2016-02-01

    DNA sequences extracted from preserved remains can add considerable resolution to inference of past population dynamics. For example, coalescent-based methods have been used to correlate declines in some arctic megafauna populations with habitat fragmentation during the last ice age. These methods, however, often fail to detect population declines preceding extinction, most likely owing to a combination of sparse sampling, uninformative genetic markers, and models that cannot account for the increasingly structured nature of populations as habitats decline. As ancient DNA research expands to include full-genome analyses, these data will provide greater resolution of the genomic consequences of environmental change and the genetic signatures of extinction. © 2016 The Author(s).

  5. Application of PIXE to study ancient Iranian silver coins

    International Nuclear Information System (INIS)

    Oliaiy, P.; Shokouhi, F.; Lamehi-Rachti, M.; Rahighi, J.; Andami, P.; Dilmaghani, J.; Etezadi, M.

    1999-01-01

    Ancient Iranian silver coins minted in various parts of the ancient Iran from Transoxiana to Mesopotamia over a time span of 460 years (247BC-208AD) during Parthians dynasty were analysed by PIXE with a 2.2 MeV proton beam. Forty seven silver coins owned by Tamashagah-e-Pool (museum of money) in Tehran were examined in this study. The possible correlation between the composition of coins and the minting time or the minting location of coins has been the prime objective of the present study. Elemental analysis of ancient coins could also reveal the direct relation with the political and economical situation and also with the metallurgy of the minting time. Results on the contents of principal component elements (Fe, Ni, Cu, As, Br, Ag, Sn, Sb, Ba, Au and Pb) are presented and discussed. (author)

  6. Application of PIXE to study ancient Iranian silver coins

    Energy Technology Data Exchange (ETDEWEB)

    Oliaiy, P.; Shokouhi, F.; Lamehi-Rachti, M.; Rahighi, J. [Van de Graaff Laboratory, AEOI, Tehran (Iran); Andami, P.; Dilmaghani, J.; Etezadi, M. [Tamashagah-e-Pool, General Office of Museums, MDFIR, Tehran (Iran)

    1999-07-01

    Ancient Iranian silver coins minted in various parts of the ancient Iran from Transoxiana to Mesopotamia over a time span of 460 years (247BC-208AD) during Parthians dynasty were analysed by PIXE with a 2.2 MeV proton beam. Forty seven silver coins owned by Tamashagah-e-Pool (museum of money) in Tehran were examined in this study. The possible correlation between the composition of coins and the minting time or the minting location of coins has been the prime objective of the present study. Elemental analysis of ancient coins could also reveal the direct relation with the political and economical situation and also with the metallurgy of the minting time. Results on the contents of principal component elements (Fe, Ni, Cu, As, Br, Ag, Sn, Sb, Ba, Au and Pb) are presented and discussed. (author)

  7. Ancient Dwarka: Study based on recent underwater archaeological investigations

    Digital Repository Service at National Institute of Oceanography (India)

    Gaur, A.S.; Sundaresh; Tripati, S.

    -1 Migration & Diffusion, Vol. 6, Issue Number 21, 2005 ANCIENT DWARKA: STUDY BASED ON RECENT UNDERWATER ARCHAEOLOGICAL INVESTIGATIONS by A.S. Gaur, Sundaresh and Sila Tripati Summary Dwarka, one of the best-studied underwater sites in India, has...). Dwarka has been the attraction for historians since the beginning of the 20th century. The ancient town Dwarka has been described as 56 Migration & Diffusion, Vol 6, Issue Number 21, 2005 Fig.l: Dwarka is headquarter of the Okhamandal taluka in Jamnagar...

  8. Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities

    Science.gov (United States)

    Haak, Wolfgang; Balanovsky, Oleg; Sanchez, Juan J.; Koshel, Sergey; Zaporozhchenko, Valery; Adler, Christina J.; Der Sarkissian, Clio S. I.; Brandt, Guido; Schwarz, Carolin; Nicklisch, Nicole; Dresely, Veit; Fritsch, Barbara; Balanovska, Elena; Villems, Richard; Meller, Harald; Alt, Kurt W.; Cooper, Alan

    2010-01-01

    In Europe, the Neolithic transition (8,000–4,000 b.c.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 b.c.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated b.c.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated b.c.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major

  9. Application of neutron activation analysis in study of ancient ceramics

    International Nuclear Information System (INIS)

    Li Guoxia; Zhao Weijuan; Gao Zhengyao; Xie Jianzhong; Huang Zhongxiang; Jia Xiuqin; Han Song

    2000-01-01

    Trace-elements in ancient ceramics and imitative ancient ceramics were determined by neutron activation analysis (NAA). The NAA data are then analyzed by fuzzy cluster method and the trend cluster diagram is obtained. The raw material sources of ancient ceramics and imitative ancient ceramics are determined. The path for improving quality of imitative ancient ceramics is found

  10. Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

    Science.gov (United States)

    Ahmed, Engy; Parducci, Laura; Unneberg, Per; Ågren, Rasmus; Schenk, Frederik; Rattray, Jayne E.; Han, Lu; Muschitiello, Francesco; Pedersen, Mikkel W.; Smittenberg, Rienk H.; Yamoah, Kweku Afrifa; Slotte, Tanja; Wohlfarth, Barbara

    2018-02-01

    The Lateglacial/early Holocene sediments from the ancient lake at Hässeldala Port, southern Sweden provide an important archive for the environmental and climatic shifts at the end of the last ice age and the transition into the present Interglacial. The existing multi-proxy data set highlights the complex interplay of physical and ecological changes in response to climatic shifts and lake status changes. Yet, it remains unclear how microorganisms, such as Archaea, which do not leave microscopic features in the sedimentary record, were affected by these climatic shifts. Here we present the metagenomic data set of Hässeldala Port with a special focus on the abundance and biodiversity of Archaea. This allows reconstructing for the first time the temporal succession of major Archaea groups between 13.9 and 10.8 ka BP by using ancient environmental DNA metagenomics and fossil archaeal cell membrane lipids. We then evaluate to which extent these findings reflect physical changes of the lake system, due to changes in lake-water summer temperature and seasonal lake-ice cover. We show that variations in archaeal composition and diversity were related to a variety of factors (e.g., changes in lake water temperature, duration of lake ice cover, rapid sediment infilling), which influenced bottom water conditions and the sediment-water interface. Methanogenic Archaea dominated during the Allerød and Younger Dryas pollen zones, when the ancient lake was likely stratified and anoxic for large parts of the year. The increase in archaeal diversity at the Younger Dryas/Holocene transition is explained by sediment infilling and formation of a mire/peatbog.

  11. Cheek Tooth Morphology and Ancient Mitochondrial DNA of Late Pleistocene Horses from the Western Interior of North America: Implications for the Taxonomy of North American Late Pleistocene Equus

    OpenAIRE

    Barron-Ortiz, Christina; Rodrigues, Antonia; Theodor, Jessica; Kooyman, Brian; Yang, Dongya; Speller, Camilla Filomena

    2017-01-01

    Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Inter...

  12. Aberration corrected STEM to study an ancient hair dyeing formula

    Science.gov (United States)

    Patriarche, G.; Van Elslande, E.; Castaing, J.; Walter, P.

    2014-05-01

    Lead-based chemistry was initiated in ancient Egypt for cosmetic preparation more than 4000 years ago. Here, we study a hair-dyeing recipe using lead salts described in text since Greco-Roman times. We report direct evidence about the shape and distribution of PbS nanocrystals that form within the hair during blackening.

  13. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequen...

  14. Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

    Science.gov (United States)

    Kimura, Birgitta; Marshall, Fiona B.; Chen, Shanyuan; Rosenbom, Sónia; Moehlman, Patricia D.; Tuross, Noreen; Sabin, Richard C.; Peters, Joris; Barich, Barbara; Yohannes, Hagos; Kebede, Fanuel; Teclai, Redae; Beja-Pereira, Albano; Mulligan, Connie J.

    2011-01-01

    Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass. PMID:20667880

  15. Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany.

    Science.gov (United States)

    Star, Bastiaan; Boessenkool, Sanne; Gondek, Agata T; Nikulina, Elena A; Hufthammer, Anne Karin; Pampoulie, Christophe; Knutsen, Halvor; André, Carl; Nistelberger, Heidi M; Dierking, Jan; Petereit, Christoph; Heinrich, Dirk; Jakobsen, Kjetill S; Stenseth, Nils Chr; Jentoft, Sissel; Barrett, James H

    2017-08-22

    Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fish-bone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod ( Gadus morhua ) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.

  16. Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations.

    Directory of Open Access Journals (Sweden)

    Nadezhda V Vorobieva

    Full Text Available BACKGROUND: The extant roe deer (Capreolus Gray, 1821 includes two species: the European roe deer (C. capreolus and the Siberian roe deer (C. pygargus that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia, where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan, Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples. CONCLUSION/SIGNIFICANCE: Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian

  17. Genotyping of Capreolus pygargus Fossil DNA from Denisova Cave Reveals Phylogenetic Relationships between Ancient and Modern Populations

    Science.gov (United States)

    Vorobieva, Nadezhda V.; Sherbakov, Dmitry Y.; Druzhkova, Anna S.; Stanyon, Roscoe; Tsybankov, Alexander A.; Vasil'ev, Sergey K.; Shunkov, Mikhail V.; Trifonov, Vladimir A.; Graphodatsky, Alexander S.

    2011-01-01

    Background The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences. The Siberian roe deer occupies a vast area of Asia and is considerably less studied than the European roe deer. Modern systematics of the Siberian roe deer remain controversial with 4 morphological subspecies. Roe deer fossilized bones are quite abundant in Denisova cave (Altai Mountains, South Siberia), where dozens of both extant and extinct mammalian species from modern Holocene to Middle Pleistocene have been retrieved. Methodology/Principal Findings We analyzed a 629 bp fragment of the mitochondrial control region from ancient bones of 10 Holocene and four Pleistocene Siberian roe deer from Denisova cave as well as 37 modern specimen belonging to populations from Altai, Tian Shan (Kyrgyzstan), Yakutia, Novosibirsk region and the Russian Far East. Genealogical reconstructions indicated that most Holocene haplotypes were probably ancestral for modern roe deer populations of Western Siberia and Tian Shan. One of the Pleistocene haplotypes was possibly ancestral for modern Yakutian populations, and two extinct Pleistocene haplotypes were close to modern roe deer from Tian Shan and Yakutia. Most modern geographical populations (except for West Siberian Plains) are heterogeneous and there is some tentative evidence for structure. However, we did not find any distinct phylogenetic signal characterizing particular subspecies in either modern or ancient samples. Conclusion/Significance Analysis of mitochondrial DNA from both ancient and modern samples of Siberian roe deer shed new light on understanding the evolutionary history of roe deer. Our data indicate that during the last 50,000 years multiple replacements of populations of the Siberian roe deer took place in the Altai Mountains correlating with climatic changes. The Siberian roe deer

  18. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Binladen, Jonas; Miller, Webb

    2007-01-01

    strand of origin of observed damage events. With the advent of emulsion-based clonal amplification (emPCR) and the sequencing-by-synthesis technology this has changed. In this paper we demonstrate how data produced on the Roche GS20 genome sequencer can determine miscoding lesion strands of origin....... Furthermore, considerable disagreement and speculation exists on which specific damage events underlie observed miscoding lesions. The root of the problem is that it has previously been difficult to assemble sufficient data to test the hypotheses, and near-impossible to accurately determine the specific......, and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved...

  19. Radiocarbon-dating and ancient DNA reveal rapid replacement of extinct prehistoric penguins

    Science.gov (United States)

    Rawlence, Nicolas J.; Perry, George L. W.; Smith, Ian W. G.; Scofield, R. Paul; Tennyson, Alan J. D.; Matisoo-Smith, Elizabeth A.; Boessenkool, Sanne; Austin, Jeremy J.; Waters, Jonathan M.

    2015-03-01

    Prehistoric faunal extinctions dramatically reshaped biological assemblages around the world. However, the timing of such biotic shifts is often obscured by the fragmentary nature and limited temporal resolution of fossil records. We use radiocarbon-dating and ancient-DNA analysis of prehistoric (ca A.D. 1450-1834) Megadyptes penguin specimens to assess the time-frame of biological turnover in coastal New Zealand following human settlement. These data suggest that the final extirpation of the endemic Megadyptes waitaha, and subsequent replacement by the previously sub-Antarctic-limited Megadyptes antipodes, likely occurred within a narrow temporal window (e.g. a century or less). This transition represents one of the most rapid prehistoric faunal turnover events documented, and is likely linked to human demographic and cultural transitions during the 15th Century. Our results suggest that anthropogenic forces can trigger rapid biogeographic shifts.

  20. Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum.

    Science.gov (United States)

    Kehlmaier, Christian; Barlow, Axel; Hastings, Alexander K; Vamberger, Melita; Paijmans, Johanna L A; Steadman, David W; Albury, Nancy A; Franz, Richard; Hofreiter, Michael; Fritz, Uwe

    2017-01-11

    Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1 000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galápagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galápagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact. © 2017 The Author(s).

  1. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing.

    Science.gov (United States)

    Teasdale, M D; van Doorn, N L; Fiddyment, S; Webb, C C; O'Connor, T; Hofreiter, M; Collins, M J; Bradley, D G

    2015-01-19

    Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

  2. Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins.

    Science.gov (United States)

    Grosser, Stefanie; Rawlence, Nicolas J; Anderson, Christian N K; Smith, Ian W G; Scofield, R Paul; Waters, Jonathan M

    2016-02-10

    The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional 'cryptic' invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts. © 2016 The Author(s).

  3. DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Fredensborg, Brian Lund; Nejsum, Peter

    paleoparasitological techniques such as morphological examination and molecular identification. Hard-shelled parasite eggs can be recovered from the environment even after extended periods of time and they have shown to be excellent reservoirs of ancient DNA (aDNA). aDNA analysis has enabled identifying which species...... parasite eggs from environmental samples collected at a Viking-age settlement (1018-1030 A.D.) are DNA typed to the species level. The human whipworm (Trichuris trichiura) and the human roundworm (Ascaris lumbricoides) are identified indicating that these parasites were endemic in Denmark in the Viking...

  4. Ancient DNA analysis of the oldest canid species from the Siberian Arctic and genetic contribution to the domestic dog.

    Directory of Open Access Journals (Sweden)

    Esther J Lee

    Full Text Available Modern Arctic Siberia provides a wealth of resources for archaeological, geological, and paleontological research to investigate the population dynamics of faunal communities from the Pleistocene, particularly as the faunal material coming from permafrost has proven suitable for genetic studies. In order to examine the history of the Canid species in the Siberian Arctic, we carried out genetic analysis of fourteen canid remains from various sites, including the well-documented Upper Paleolithic Yana RHS and Early Holocene Zhokhov Island sites. Estimated age of samples range from as recent as 1,700 years before present (YBP to at least 360,000 YBP for the remains of the extinct wolf, Canis cf. variabilis. In order to examine the genetic affinities of ancient Siberian canids species to the domestic dog and modern wolves, we obtained mitochondrial DNA control region sequences and compared them to published ancient and modern canid sequences. The older canid specimens illustrate affinities with pre-domestic dog/wolf lineages while others appear in the major phylogenetic clades of domestic dogs. Our results suggest a European origin of domestic dog may not be conclusive and illustrates an emerging complexity of genetic contribution of regional wolf breeds to the modern Canis gene pool.

  5. Investigation of ancient DNA from Western Siberia and the Sargat culture.

    Science.gov (United States)

    Bennett, Casey C; Kaestle, Frederika A

    2010-04-01

    Mitochondrial DNA from 14 archaeological samples at the Ural State University in Yekaterinburg, Russia, was extracted to test the feasibility of ancient DNA work on their collection. These samples come from a number of sites that fall into two groupings. Seven samples are from three sites, dating to the 8th-12th century AD, that belong to a northern group of what are thought to be Ugrians, who lived along the Ural Mountains in northwestern Siberia. The remaining seven samples are from two sites that belong to a southern group representing the Sargat culture, dating between roughly the 5th century BC and the 5th century AD, from southwestern Siberia near the Ural Mountains and the present-day Kazakhstan border. The samples are derived from several burial types, including kurgan burials. They also represent a number of different skeletal elements and a range of observed preservation. The northern sites repeatedly failed to amplify after multiple extraction and amplification attempts, but the samples from the southern sites were successfully extracted and amplified. The sequences obtained from the southern sites support the hypothesis that the Sargat culture was a potential zone of intermixture between native Ugrian and/or Siberian populations and steppe peoples from the south, possibly early Iranian or Indo-Iranian, which has been previously suggested by archaeological analysis.

  6. Ancient DNA from 8400 Year-Old Çatalhöyük Wheat: Implications for the Origin of Neolithic Agriculture.

    Directory of Open Access Journals (Sweden)

    Hatice Bilgic

    Full Text Available Human history was transformed with the advent of agriculture in the Fertile Crescent with wheat as one of the founding crops. Although the Fertile Crescent is renowned as the center of wheat domestication, archaeological studies have shown the crucial involvement of Çatalhöyük in this process. This site first gained attention during the 1961-65 excavations due to the recovery of primitive hexaploid wheat. However, despite the seeds being well preserved, a detailed archaeobotanical description of the samples is missing. In this article, we report on the DNA isolation, amplification and sequencing of ancient DNA of charred wheat grains from Çatalhöyük and other Turkish archaeological sites and the comparison of these wheat grains with contemporary wheat species including T. monococcum, T. dicoccum, T. dicoccoides, T. durum and T. aestivum at HMW glutenin protein loci. These ancient samples represent the oldest wheat sample sequenced to date and the first ancient wheat sample from the Middle East. Remarkably, the sequence analysis of the short DNA fragments preserved in seeds that are approximately 8400 years old showed that the Çatalhöyük wheat stock contained hexaploid wheat, which is similar to contemporary hexaploid wheat species including both naked (T. aestivum and hulled (T. spelta wheat. This suggests an early transitory state of hexaploid wheat agriculture from the Fertile Crescent towards Europe spanning present-day Turkey.

  7. Archaeogeophysical Studies in Ancient Tios, Zonguldak-Caycuma-Filyos, Turkey

    Science.gov (United States)

    Ahmet Yuksel, Fethi; Hoskan, Nihan; Sumer Atasoy, Yusuf

    2010-05-01

    Ancient Tios is located in the Filyos township of the Caycuma District of Zonguldak on the western Black Sea region, Turkey. The ancient city was probably founded by Milesians in the 7th cent. B.C. The region was inhabited through the centuries by Persians, Romans, Genoese and all the way to the Ottoman times. About the archaeological history of the city , we have relatively limited knowledge both in ancient records and in contemporary archaeological research. In the Roman period coastal defensive walls, acquaduct, theatre, defensive tower and the port with its breakwater are the only visible remains of the city. The acropolis of the ancient city is located immediately to the east of the present Filyos township on a hill. The original architectural form of the defensive wall located in the acropolis will be revealed after research to its foundation completed. A partially destroyed stone building is another remaining ruin in the acropolis .The Roman period theatre of Tios is located in the north of the road leading into Filyos. Built on a sloping land, local stones were used in its construction. Mostly ruined its original stones have been used later in other buildings. Only a few of the arches of the aquaduct, located to the north of the theatre, are still standing. There are the remains of another structure which could have been a defensive tower located in 200 meters to the west of the theatre. GPR measurements display the exact location of any sub-surface structures. To the west of the acropolis and within the ancient port, there are the under water remains of a breakwater. The local sandstones, quarries were studied archaeogeologically as they provided the main building materials. Since there has been no archaeological research done on the site until the 2006 season, archaeogeopysical data are reveal additional information about ancient Tios. Surface survey and georadar, magnetic and geoelectric studies have been done and after that, excavations were started

  8. Tamil merchant in ancient Mesopotamia.

    Directory of Open Access Journals (Sweden)

    Malliya Gounder Palanichamy

    Full Text Available Recent analyses of ancient Mesopotamian mitochondrial genomes have suggested a genetic link between the Indian subcontinent and Mesopotamian civilization. There is no consensus on the origin of the ancient Mesopotamians. They may be descendants of migrants, who founded regional Mesopotamian groups like that of Terqa or they may be merchants who were involved in trans Mesopotamia trade. To identify the Indian source population showing linkage to the ancient Mesopotamians, we screened a total of 15,751 mitochondrial DNAs (11,432 from the literature and 4,319 from this study representing all major populations of India. Our results although suggest that south India (Tamil Nadu and northeast India served as the source of the ancient Mesopotamian mtDNA gene pool, mtDNA of these ancient Mesopotamians probably contributed by Tamil merchants who were involved in the Indo-Roman trade.

  9. Tamil Merchant in Ancient Mesopotamia

    Science.gov (United States)

    Palanichamy, Malliya gounder; Mitra, Bikash; Debnath, Monojit; Agrawal, Suraksha; Chaudhuri, Tapas Kumar; Zhang, Ya-Ping

    2014-01-01

    Recent analyses of ancient Mesopotamian mitochondrial genomes have suggested a genetic link between the Indian subcontinent and Mesopotamian civilization. There is no consensus on the origin of the ancient Mesopotamians. They may be descendants of migrants, who founded regional Mesopotamian groups like that of Terqa or they may be merchants who were involved in trans Mesopotamia trade. To identify the Indian source population showing linkage to the ancient Mesopotamians, we screened a total of 15,751 mitochondrial DNAs (11,432 from the literature and 4,319 from this study) representing all major populations of India. Our results although suggest that south India (Tamil Nadu) and northeast India served as the source of the ancient Mesopotamian mtDNA gene pool, mtDNA of these ancient Mesopotamians probably contributed by Tamil merchants who were involved in the Indo-Roman trade. PMID:25299580

  10. Tamil merchant in ancient Mesopotamia.

    Science.gov (United States)

    Palanichamy, Malliya Gounder; Mitra, Bikash; Debnath, Monojit; Agrawal, Suraksha; Chaudhuri, Tapas Kumar; Zhang, Ya-Ping

    2014-01-01

    Recent analyses of ancient Mesopotamian mitochondrial genomes have suggested a genetic link between the Indian subcontinent and Mesopotamian civilization. There is no consensus on the origin of the ancient Mesopotamians. They may be descendants of migrants, who founded regional Mesopotamian groups like that of Terqa or they may be merchants who were involved in trans Mesopotamia trade. To identify the Indian source population showing linkage to the ancient Mesopotamians, we screened a total of 15,751 mitochondrial DNAs (11,432 from the literature and 4,319 from this study) representing all major populations of India. Our results although suggest that south India (Tamil Nadu) and northeast India served as the source of the ancient Mesopotamian mtDNA gene pool, mtDNA of these ancient Mesopotamians probably contributed by Tamil merchants who were involved in the Indo-Roman trade.

  11. Earthquake Archaeology: a case study from Ancient Cnidus

    Science.gov (United States)

    Stewart, I. S.; Altunel, E.; Piccardi, L.

    2003-04-01

    Ancient earthquakes can leave their mark in the mythical practices and literary accounts of ancient peoples, the stratigraphy of their site histories, and the structural integrity of their constructions. The ancient Greek/Roman city of Cnidus in southwestern Turkey records all three. A spectacular exposed fault plane cliff bordering the northern edge of the city appears to have been an important revered site, bearing votive niches carved into the near-vertical slip plane and associated with a Sanctuary of Demeter that implies a connection to the underworld. Stratigraphic evidence for earthquake faulting can be found in the form of a destruction horizon of contorted soil, relics and human remains exposed in the original excavations of the Sanctuary of Demeter by Sir Charles Newton (1857-58) and in a destruction horizon of burnt soil and bone uncovered by the ongoing excavation of a colonnaded street. Structural damage to constructions is widespread across the site, with warped and offset walls in the Sanctuary of Demeter, collapsed buildings in several places, and a parallel arrangement of fallen columns in the colonnaded street. The most remarkable structural evidence for fault activity, however, is the rupture of the ancient city's famous Round Temple of Aphrodite, whose podium reveals a history of damage and which is unambiguously displaced across a bedrock fault. While these phenomena are equivocal when viewed in isolation, collectively they imply at least two damaging earthquakes at the site, one (possibly both) of which ruptured along the fault on which the city is found. The Cnidus case study highlights how reliable identification of archaeoseismic damage relies on compiling an assemblage of indicators rather than the discovery of a diagnostic "smoking gun".

  12. Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

    Science.gov (United States)

    Fernández, Eva; Pérez-Pérez, Alejandro; Gamba, Cristina; Prats, Eva; Cuesta, Pedro; Anfruns, Josep; Molist, Miquel; Arroyo-Pardo, Eduardo; Turbón, Daniel

    2014-01-01

    The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700–6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and

  13. Towards the onset of fruit tree growing north of the Alps: ancient DNA from waterlogged apple (Malus sp.) seed fragments.

    Science.gov (United States)

    Schlumbaum, Angela; van Glabeke, Sabine; Roldan-Ruiz, Isabel

    2012-01-20

    Wild apples (Malus sp.) have been a major food source in the northern Alpine region since prehistory and their use is well understood. The onset of deliberate fruit tree growing in the area is, however, less clear. It is generally assumed that horticulture was practised in Roman times, but it might be even earlier. In the archaeological record seed testa and pericarp remains are particularly frequent at sites with waterlogged preservation such as lakeshore settlements or wells, pits and ditches, but the distinction between wild and domestic plants is not morphologically possible. With waterlogged remains being one main source of information about past fruit cultivation, we have tested the feasibility of analysing ancient DNA from waterlogged preserved bulk samples of testa fragments. We studied apple seeds from three Neolithic and three Roman sites with waterlogged preservation in the Alpine foreland. Chloroplast markers failed in all samples, but nuclear ITS1 (internal transcribed spacer region 1) of the ribosomal DNA was successfully typed in two Roman samples from the site Oedenburg/Biesheim-Kunheim (Haut-Rhin, F). The retrieved ITS1 sequences are identical to each other and are shared with wild Malus sylvestris and Malus sieversii, and with domestic apple cultivars, supporting the potential of using waterlogged remains for identifying the genetic status of apple diachronically. Copyright © 2011 Elsevier GmbH. All rights reserved.

  14. Use of pollen and ancient DNA as conservation baselines for offshore islands in New Zealand.

    Science.gov (United States)

    Wilmshurst, Janet M; Moar, Neville T; Wood, Jamie R; Bellingham, Peter J; Findlater, Amy M; Robinson, James J; Stone, Clive

    2014-02-01

    Islands play a key role globally in the conservation of endemic species. Many island reserves have been highly modified since human colonization, and their restoration and management usually occur without knowledge of their prehuman state. However, conservation paleoecology is increasingly being recognized as a tool that can help to inform both restoration and conservation of island reserves by providing prehuman vegetation baselines. Many of New Zealand's mammal-free offshore islands are foci for biological diversity conservation and, like many islands in the Polynesian region, were deforested following initial human settlement. Therefore, their current restoration, replanting, and management are guided either by historic vegetation descriptions or the occurrence of species on forested islands. We analyzed pollen and ancient DNA in soil cores from an offshore island in northern New Zealand. The result was a 2000-year record of vegetation change that began >1200 years before human settlement and spanned 550 years of human occupation and 180 years of forest succession since human occupation ceased. Between prehuman and contemporary forests there was nearly a complete species turnover including the extirpation of a dominant conifer and a palm tree. The podocarp-dominated forests were replaced by a native but novel angiosperm-dominated forest. There is no modern analog of the prehuman forests on any northern New Zealand island, and those islands that are forested are dominated by angiosperms which are assumed to be climax forests. The pollen and DNA evidence for conifer- and palm-rich forests in the prehuman era challenge this climax forest assumption. Prehuman vegetation records can thus help to inform future restoration of degraded offshore islands by informing the likely rate and direction of successional change; helping to determine whether natural rates of succession are preferable to more costly replanting programs; and providing past species lists if

  15. DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in viking-age settlement

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Nejsum, Peter; Fredensborg, Brian Lund

    2015-01-01

    selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura, using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology......Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully....... The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced...

  16. Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

    Science.gov (United States)

    Carpenter, Meredith L.; Buenrostro, Jason D.; Valdiosera, Cristina; Schroeder, Hannes; Allentoft, Morten E.; Sikora, Martin; Rasmussen, Morten; Gravel, Simon; Guillén, Sonia; Nekhrizov, Georgi; Leshtakov, Krasimir; Dimitrova, Diana; Theodossiev, Nikola; Pettener, Davide; Luiselli, Donata; Sandoval, Karla; Moreno-Estrada, Andrés; Li, Yingrui; Wang, Jun; Gilbert, M. Thomas P.; Willerslev, Eske; Greenleaf, William J.; Bustamante, Carlos D.

    2013-01-01

    Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062–147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217–73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples. PMID:24568772

  17. Ancient DNA Reveals That the Genetic Structure of the Northern Han Chinese Was Shaped Prior to 3,000 Years Ago

    Science.gov (United States)

    Zhang, Quan-Chao; Li, Hong-Jie; Cui, Ying-Qiu; Xu, Zhi; Jin, Li; Zhou, Hui; Zhu, Hong

    2015-01-01

    The Han Chinese are the largest ethnic group in the world, and their origins, development, and expansion are complex. Many genetic studies have shown that Han Chinese can be divided into two distinct groups: northern Han Chinese and southern Han Chinese. The genetic history of the southern Han Chinese has been well studied. However, the genetic history of the northern Han Chinese is still obscure. In order to gain insight into the genetic history of the northern Han Chinese, 89 human remains were sampled from the Hengbei site which is located in the Central Plain and dates back to a key transitional period during the rise of the Han Chinese (approximately 3,000 years ago). We used 64 authentic mtDNA data obtained in this study, 27 Y chromosome SNP data profiles from previously studied Hengbei samples, and genetic datasets of the current Chinese populations and two ancient northern Chinese populations to analyze the relationship between the ancient people of Hengbei and present-day northern Han Chinese. We used a wide range of population genetic analyses, including principal component analyses, shared mtDNA haplotype analyses, and geographic mapping of maternal genetic distances. The results show that the ancient people of Hengbei bore a strong genetic resemblance to present-day northern Han Chinese and were genetically distinct from other present-day Chinese populations and two ancient populations. These findings suggest that the genetic structure of northern Han Chinese was already shaped 3,000 years ago in the Central Plain area. PMID:25938511

  18. The effect of ancient DNA damage on inferences of demographic histories

    DEFF Research Database (Denmark)

    Axelsson, Erik; Willerslev, Eske; Gilbert, Marcus Thomas Pius

    2008-01-01

    of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after......, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal...

  19. Kinship and Y-chromosome analysis of 7th century human remains: novel DNA extraction and typing procedure for ancient material.

    Science.gov (United States)

    Vanek, Daniel; Saskova, Lenka; Koch, Hubert

    2009-06-01

    To develop novel DNA extraction and typing procedure for DNA identification of the 7th century human remains, determine the familiar relationship between the individuals, estimate the Y-chromosome haplogroup, and compare the Y-chromosome haplotype with the contemporary populations. DNA from preserved femur samples was extracted using the modified silica-based extraction technique. Polymerase chain reaction amplification was performed using human identification kits MiniFiler, Identifiler, and Y-filer and also laboratory-developed and validated Y-chromosome short tandem repeat (STR) pentaplexes with short amplicons. For 244A, 244B, 244C samples, full autosomal DNA profiles (15 STR markers and Amelogenin) and for 244D, 244E, 244F samples, MiniFiler profiles were produced. Y-chromosome haplotypes consisting of up to 24 STR markers were determined and used to predict the Y-chromosome haplogroups and compare the resulting haplotypes with the current population. Samples 244A, 244B, 244C, and 244D belong to Y-chromosome haplogroup R1b and the samples 244E and 244F to haplogroup G2a. Comparison of ancient haplotypes with the current population yielded numerous close matches with genetic distance below 2. Application of forensic genetics in archaeology enables retrieving new types of information and helps in data interpretation. The number of successfully typed autosomal and Y-STR loci from ancient specimens in this study is one of the largest published so far for aged samples.

  20. Cheek tooth morphology and ancient mitochondrial DNA of late Pleistocene horses from the western interior of North America: Implications for the taxonomy of North American Late Pleistocene Equus.

    Directory of Open Access Journals (Sweden)

    Christina I Barrón-Ortiz

    Full Text Available Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus and a non-caballine (E. conversidens species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study.

  1. Cheek tooth morphology and ancient mitochondrial DNA of late Pleistocene horses from the western interior of North America: Implications for the taxonomy of North American Late Pleistocene Equus.

    Science.gov (United States)

    Barrón-Ortiz, Christina I; Rodrigues, Antonia T; Theodor, Jessica M; Kooyman, Brian P; Yang, Dongya Y; Speller, Camilla F

    2017-01-01

    Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to the end-Pleistocene extinction. Based on the morphological and molecular data analyzed, a caballine (Equus ferus) and a non-caballine (E. conversidens) species were identified from different localities across most of the Western Interior. A second non-caballine species (E. cedralensis) was recognized from southern localities based exclusively on the morphological analyses of the cheek teeth. Notably the separation into caballine and non-caballine species was observed in the Bayesian phylogenetic analysis of ancient mtDNA as well as in the geometric morphometric analyses of the upper and lower premolars. Teeth morphologically identified as E. conversidens that yielded ancient mtDNA fall within the New World stilt-legged clade recognized in previous studies and this is the name we apply to this group. Geographic variation in morphology in the caballine species is indicated by statistically different occlusal enamel patterns in the specimens from Bluefish Caves, Yukon Territory, relative to the specimens from the other geographic regions. Whether this represents ecomorphological variation and/or a certain degree of geographic and genetic isolation of these Arctic populations requires further study.

  2. Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe.

    Science.gov (United States)

    Horn, Susanne; Prost, Stefan; Stiller, Mathias; Makowiecki, Daniel; Kuznetsova, Tatiana; Benecke, Norbert; Pucher, Erich; Hufthammer, Anne K; Schouwenburg, Charles; Shapiro, Beth; Hofreiter, Michael

    2014-04-01

    After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000 years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.

  3. Romanian ancient gold objects studies using nuclear methods

    International Nuclear Information System (INIS)

    Constantinescu, B.; Cojocaru, V.; Bugoi, R.; Herrmann, F.; Grambole, D.

    2002-01-01

    The study of trace-elements in archaeological metallic objects can provide important clues about the metal provenance and the involved manufacturing procedures, leading to important conclusions regarding the commercial, cultural and religious exchanges between the antique populations. Ancient metallic materials are usually inhomogeneous on a scale of 20 microns or less: they contain remains of imperfect smelting, segregated phases in alloys, inclusions. Due to their exceptional chemical stability, gold artifacts remain essentially unchanged during weathering and aging processes. Several fragments of ancient gold objects coming from an Eneolithic treasury and from Pietroasa 'Closca cu Puii de Aur' (The Golden Brood Hen with Its Chickens) hoard, unearthed on Romanian territory and two Romanian native gold nuggets samples were analysed using micro-PIXE technique. The purpose of the study was to clarify the metal provenance, establishing if the hypothesis of local gold holds. To reach this goal, trace elements (Cu, Te, Sn, Pb, Hg, As, Zr, Sb) and PGE (Platinum Group Elements) concentrations were determined. The presence of inclusions (micrometric size areas of composition different from the surroundings) was also checked. We found some Si, Ca, Fe ones on two Eneolithic samples, and Ta and Cr on a sample from Pietroasa hoard. The measurements led to conclusions regarding the alluvial origin of the gold for the Eneolithical samples and gave some indications for the possible gold ore sources of Pietroasa treasury, confirming the heterogeneity of this treasury (the two analysed pieces belonged to different stylistic and compositional groups). (authors)

  4. Pre-Columbian Population Dynamics and Cultural Development in South Coast Perú as Revealed by Analysis of Ancient DNA

    OpenAIRE

    Fehren-Schmitz, Lars

    2012-01-01

    In this paper I report on a study whose principal aim is to understand the development and decline of the southern Peruvian Nasca culture in the upper Río Grande de Nasca drainage, and its cultural and biological affinities to the preceding Paracas culture. Ancient DNA analyses were conducted on over 300 pre-Columbian individuals from various cemeteries in southern Perú, from periods ranging from the Formative Period to the Middle Horizon. Our results show that the Nasca populations are close...

  5. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe.

    Science.gov (United States)

    Krüttli, Annina; Bouwman, Abigail; Akgül, Gülfirde; Della Casa, Philippe; Rühli, Frank; Warinner, Christina

    2014-01-01

    Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary

  6. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910 in medieval central europe.

    Directory of Open Access Journals (Sweden)

    Annina Krüttli

    Full Text Available Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72% exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic

  7. Ancient Egypt.

    Science.gov (United States)

    Evers, Virginia

    This four-week fourth grade social studies unit dealing with religious dimensions in ancient Egyptian culture was developed by the Public Education Religion Studies Center at Wright State University. It seeks to help students understand ancient Egypt by looking at the people, the culture, and the people's world view. The unit begins with outlines…

  8. Moessbauer studies on ancient Chinese pottery of Yangshao Culture Period

    International Nuclear Information System (INIS)

    Yu Zhengfang; Zheng Qi; Zheng Yufang; Zhongshan Univ., Guangzhou

    1988-01-01

    Eleven pieces of ancient Chinese pottery (4770 B.C. - 2960 B.C.) of Yangshao Culture Period collected from the Xi'an area have been studied by means of Moessbauer spectroscopy. The samples were refired up to 1100 0 C in steps of 100 0 C for 2 h in air. The highest temperature up to which the Moessbauer pattern remains basically unchanged can be identified with the original firing temperature. The result indicates that the firing temperatures for most of the sherds were between 900-1000 0 C. The function of the grit contained in the pottery has been discussed. The crimson and reddish painted materials on the surface of sherds have been studied, respectively. The first appearance of pottery can probably be traced back to an even earlier period. (orig.)

  9. Perspectives for DNA studies on polar ice cores

    DEFF Research Database (Denmark)

    Hansen, Anders J.; Willerslev, E.

    2002-01-01

    Recently amplifiable ancient DNA was obtained from a Greenland ice core. The DNA revealed a diversity of fungi, plants, algae and protists and has thereby expanded the range of detectable organic material in fossil glacier ice. The results suggest that ancient DNA can be obtained from other ice c...

  10. Mitochondrial DNA diversity of modern, ancient and wild sheep(Ovis gmelinii anatolica) from Turkey: new insights on the evolutionary history of sheep.

    Science.gov (United States)

    Demirci, Sevgin; Koban Baştanlar, Evren; Dağtaş, Nihan Dilşad; Pişkin, Evangelia; Engin, Atilla; Ozer, Füsun; Yüncü, Eren; Doğan, Sükrü Anıl; Togan, Inci

    2013-01-01

    In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum Höyük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E. To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations. Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).

  11. Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight into Social Organization at the Fujia Site.

    Science.gov (United States)

    Dong, Yu; Li, Chunxiang; Luan, Fengshi; Li, Zhenguang; Li, Hongjie; Cui, Yinqiu; Zhou, Hui; Malhi, Ripan S

    2015-01-01

    To gain insight into the social organization of a population associated with the Dawenkou period, we performed ancient DNA analysis of 18 individuals from human remains from the Fujia site in Shandong Province, China. Directly radiocarbon dated to 4800-4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage was de-emphasized compared with the bonds of descent at Fujia.

  12. Ancient DNA from Giant Panda (Ailuropoda melanoleuca of South-Western China Reveals Genetic Diversity Loss during the Holocene

    Directory of Open Access Journals (Sweden)

    Gui-Lian Sheng

    2018-04-01

    Full Text Available The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae. Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

  13. Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene.

    Science.gov (United States)

    Sheng, Gui-Lian; Barlow, Axel; Cooper, Alan; Hou, Xin-Dong; Ji, Xue-Ping; Jablonski, Nina G; Zhong, Bo-Jian; Liu, Hong; Flynn, Lawrence J; Yuan, Jun-Xia; Wang, Li-Rui; Basler, Nikolas; Westbury, Michael V; Hofreiter, Michael; Lai, Xu-Long

    2018-04-06

    The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cyt b and 12s rRNA, partial 16s rRNA and ND1 , and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

  14. The examination of ancient DNA: guidelines on precautions, controls, and sample processing

    Directory of Open Access Journals (Sweden)

    Scholz, M.

    2000-06-01

    Full Text Available The young discipline of palaeogenetics has developed into a successful and expectant field of archaeobiological research within the last decade. Palaeogenetic investigation (e.g. PCR, DNA sequencing of ancient specimens is, however, susceptible to falsification by the presence of contamination from more recent times. Contamination which can lead to amplification of non-authentic sequences is known to stem from several sources: (i human biomolecules derived from the persons performing the genetic experiments, perhaps also from the archeologists and other persons who have previously handled the specimens or (ii edaphic DNA sequences derived primarily from bacterial or fungal growth upon the specimen. A third source of contamination can arise from (iii substances used for conservation of specimens. Here we give advice on the correct processing of prehistoric bone samples when further molecular biological examination is required. Along with the demonstration of necessary precautions and working conditions, we further explain how an unequivocal DNA contamination monitoring is performed.

    La paleogenética se ha convertido en los últimos años en una disciplina coronada de éxito que ofrece grandes expectativas para el desarrollo de la investigación arqueobiológica. No obstante, la investigación paleogenética (p. ej: PCR, secuenciación del ADN de especímenes antiguos es susceptible de ser falsificada por la presencia de una contaminación más reciente. Actualmente sabemos que la contaminación que provoca la amplificación de secuencias ''no auténticas" procede de las siguientes fuentes: (i las biomoléculas humanas provienen de la persona que realiza el experimento genético o incluso también del arqueólogo u otras personas que previamente hayan tenido contacto con el espécimen; (ii de secuencias de ADN edáficas derivadas básicamente del crecimiento bacterial o fúngico en el seno del espécimen. La tercera fuente de contaminaci

  15. Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice.

    Directory of Open Access Journals (Sweden)

    Alice Beau

    Full Text Available In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in "non-conventional" positions (deposited in the pits without any particular treatment. If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace. At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i the occidental origin of the Michelsberg groups and (ii the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.

  16. Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice.

    Science.gov (United States)

    Beau, Alice; Rivollat, Maïté; Réveillas, Hélène; Pemonge, Marie-Hélène; Mendisco, Fanny; Thomas, Yohann; Lefranc, Philippe; Deguilloux, Marie-France

    2017-01-01

    In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in "non-conventional" positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.

  17. Recent advances in ancient DNA research and their implications for archaeobotany

    DEFF Research Database (Denmark)

    Brown, Terence A.; Cappellini, Enrico; Kistler, Logan

    2015-01-01

    with archaeobotanical explants, not just with charred grain but with most if not all species likely to be encountered in an archaeobotanical setting. Distinctions between different subspecies groups such as cereal landraces will also be possible in the near future. Phenotypic characterization, in which aDNA sequencing...... is used to infer the biological characteristics of an archaeological specimen, will become possible, improving our understanding of traits such as flowering behaviour of cereals, and when combined with studies of preserved RNA and protein will enable complex phenotypes such as environmental tolerance...

  18. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses

    DEFF Research Database (Denmark)

    Lira, Jaime; Linderholm, Anna; Olaria, Carmen

    2010-01-01

    Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern....... Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other...... ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local...

  19. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost

    DEFF Research Database (Denmark)

    Bellemain, Eva; Davey, Marie L.; Kauserud, Håvard

    2013-01-01

    and endophytes) typical of graminoid- and forb-rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous...... knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community....

  20. First ancient DNA sequences from the Late Pleistocene red deer (Cervus elaphus) in the Crimea, Ukraine

    Science.gov (United States)

    Stanković, Ana; Nadachowski, Adam; Doan, Karolina; Stefaniak, Krzysztof; Baca, Mateusz; Socha, Paweł; Wegleński, Piotr; Ridush, Bogdan

    2010-05-01

    The Late Pleistocene has been a period of significant population and species turnover and extinctions among the large mammal fauna. Massive climatic and environmental changes during Pleistocene significantly influenced the distribution and also genetic diversity of plants and animals. The model of glacial refugia and habitat contraction to southern peninsulas in Europe as areas for the survival of temperate animal species during unfavourable Pleistocene glaciations is at present widely accepted. However, both molecular data and the fossil record indicate the presence of northern and perhaps north-eastern refugia in Europe. In recent years, much new palaeontological data have been obtained in the Crimean Peninsula, Ukraine, following extensive investigations. The red deer (Cervus elaphus) samples for aDNA studies were collected in Emine-Bair-Khosar Cave, situated on the north edge of Lower Plateau of the Chatyrdag Massif (Crimean Mountains). The cave is a vertical shaft, which functioned as a huge mega-trap over a long period of time (probably most of the Pleistocene). The bone assemblages provided about 5000 bones belonging to more than 40 species. The C. elaphus bones were collected from three different stratigraphical levels, radiocarbon dated by accelerator mass spectrometry (AMS) method. The bone fragments of four specimens of red deer were used for the DNA isolation and analysis. The mtDNA (Cytochome b) was successfully isolated from three bone fragments and the cytochrome b sequences were amplified by multiplex PCR. The sequences obtained so far allowed for the reconstruction of only preliminary phylogenetic trees. A fragment of metatarsus from level dated to ca. 48,500±2,000 years BP, yielded a sequence of 513 bp, allowing to locate the specimen on the phylogenetic tree within modern C. elaphus specimens from southern and middle Europe. The second bone fragment, a fragment of mandible, collected from level dated approximately to ca. 33,500±400 years BP

  1. Ancient DNA reveals substantial genetic diversity in the California Condor (Gymnogyps californianus) prior to a population bottleneck

    Science.gov (United States)

    D'Elia, Jesse; Haig, Susan M.; Mullins, Thomas D.; Miller, Mark P.

    2016-01-01

    Critically endangered species that have undergone severe population bottlenecks often have little remaining genetic variation, making it difficult to reconstruct population histories to apply in reintroduction and recovery strategies. By using ancient DNA techniques, it is possible to combine genetic evidence from the historical population with contemporary samples to provide a more complete picture of a species' genetic variation across its historical range and through time. Applying this approach, we examined changes in the mitochondrial DNA (mtDNA) control region (526 base pairs) of the endangered California Condor (Gymnogyps californianus). Results showed a >80% reduction in unique haplotypes over the past 2 centuries. We found no spatial sorting of haplotypes in the historical population; the periphery of the range contained haplotypes that were common throughout the historical range. Direct examination of mtDNA from California Condor museum specimens provided a new window into historical population connectivity and genetic diversity showing: (1) a substantial loss of haplotypes, which is consistent with the hypothesis that condors were relatively abundant in the nineteenth century, but declined rapidly as a result of human-caused mortality; and (2) no evidence of historical population segregation, meaning that the available genetic data offer no cause to avoid releasing condors in unoccupied portions of their historical range.

  2. Pre-Columbian population dynamics in coastal southern Peru: A diachronic investigation of mtDNA patterns in the Palpa region by ancient DNA analysis.

    Science.gov (United States)

    Fehren-Schmitz, Lars; Reindel, Markus; Cagigao, Elsa Tomasto; Hummel, Susanne; Herrmann, Bernd

    2010-02-01

    Alternative models have been proposed to explain the formation and decline of the south Peruvian Nasca culture, ranging from migration or invasion to autochthonous development and ecological crisis. To reveal to what extent population dynamic processes accounted for cultural development in the Nasca mainland, or were influenced by them, we analyzed ancient mitochondrial DNA of 218 individuals, originating from chronologically successive archaeological sites in the Palpa region, the Paracas Peninsula, and the Andean highlands in southern Peru. The sampling strategy allowed a diachronic analysis in a time frame from approximately 800 BC to 800 AD. Mitochondrial coding region polymorphisms were successfully analyzed and replicated for 130 individuals and control region sequences (np 16021-16408) for 104 individuals to determine Native American mitochondrial DNA haplogroups and haplotypes. The results were compared with ancient and contemporary Peruvian populations to reveal genetic relations of the archaeological samples. Frequency data and statistics show clear proximity of the Nasca populations to the populations of the preceding Paracas culture from Palpa and the Peninsula, and suggest, along with archaeological data, that the Nasca culture developed autochthonously in the Rio Grande drainage. Furthermore, the influence of changes in socioeconomic complexity in the Palpa area on the genetic diversity of the local population could be observed. In all, a strong genetic affinity between pre-Columbian coastal populations from southern Peru could be determined, together with a significant differentiation from ancient highland and all present-day Peruvian reference populations, best shown in the differential distribution of mitochondrial haplogroups. 2009 Wiley-Liss, Inc.

  3. Moessbauer study of ancient iron smelting slag in Japan

    International Nuclear Information System (INIS)

    Nakanishi, A.

    2008-01-01

    For an investigation of the ancient iron manufacturing technique, a reproducing experiment was carried out by archaeologists, where ancient type of iron smelting furnace was built and iron sand with high titanium contents was used as the raw material. During the operation of furnace, a large amount of slag flowed away from the furnace. In order to investigate the possibility for the estimation about the operative condition of furnace and the raw material, 57 Fe Moessbauer spectroscopy was applied for characterizing these slags and it was found that these slags mainly consisted of ferropseudobrookite (FeTi 2 O 5 ).

  4. A study on provenance relation between Jiaotanxia ancient Guan porcelain and Qingliangsi ancient Ru porcelain by NAA

    International Nuclear Information System (INIS)

    Li Rongwu; Feng Songlin; Huang Zhongxiang; Jia Xiuqin

    2004-01-01

    11 samples of ancient Chinese Ru porcelain from Qingliangsi kiln, 23 samples of ancient Chinese Guan porcelain from Jiaotanxia kiln and 4 samples of modern archaized Guan porcelain were obtained to determine the contents of elements in each of them by neutron activation analysis (NAA). The NAA data were further analyzed using fuzzy cluster analysis to obtain the fuzzy cluster trend diagrams for the bodies' samples and the glazes samples respectively. The analysis shows that the raw material origins of the Jiaotanxia ancient Chinese Guan porcelain bodies samples are very concentrated; those of the Qingliangsi ancient Chinese Ru porcelain bodies samples are a little dispersed; those of ancient Chinese Guan porcelain glazes samples are relatively concentrated; those of ancient Chinese Ru porcelain glazes samples are dispersed; and the origins of the raw material of ancient Chinese Guan porcelain glazes samples are obviously different from those of ancient Chinese Ru porcelain glazes samples. The bodies samples and glazes samples of Jiaotanxia ancient Chinese Guan porcelain and those of Qingliangsi ancient Chinese Ru porcelain have some difference but can be compared with each other. (authors)

  5. Ancient DNA Analysis Suggests Negligible Impact of the Wari Empire Expansion in Peru's Central Coast during the Middle Horizon.

    Directory of Open Access Journals (Sweden)

    Guido Valverde

    Full Text Available The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD, Wari (Middle Horizon, 800-1000 AD and Ychsma (Late Intermediate Period, 1000-1450 AD. We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.

  6. The last Viking King: a royal maternity case solved by ancient DNA analysis

    DEFF Research Database (Denmark)

    Dissing, Jørgen; Binladen, Jonas; Hansen, Anders

    2006-01-01

    doubts among historians whether the woman entombed was indeed Estrid. To shed light on this problem, we have extracted and analysed mitochondrial DNA (mtDNA) from pulp of teeth from each of the two royals. Four overlapping DNA-fragments covering about 400bp of hypervariable region 1 (HVR-1) of the D...... Estridsen to haplogroup H; Estrid's sequence differed from that of Sven at two positions in HVR-1, 16093T-->C and 16304T-->C, indicating that she belongs to subgroup H5a. Given the maternal inheritance of mtDNA, offspring will have the same mtDNA sequence as their mother with the exception of rare cases...

  7. Scanning Auger microscopy studies of an ancient bronze

    International Nuclear Information System (INIS)

    Paparazzo, E.; Lea, A.S.; Baer, D.R.; Northover, J.P.

    2001-01-01

    Scanning Auger microscopy (SAM) has been used to study the surface and interface microchemistry of a sheet bronze belt from the Urartian kingdom in NE Syria of the early first millennium B.C. We find that the patina contains no copper species at all (decuprification), whereas carbonaceous species, Ca-silicates and N-bearing species are detected, the last being tentatively identified as organic (primarily amine-like) residues deriving from the soil. A textured grain, which we qualify as a second phase of bronze originated by an imperfect alloying of the two major metals (i.e., consisting of Cu-rich and Sn-rich domains) is observed on the metallic side lying beneath the patina. SAM imaging with a submicron spatial resolution highlights the presence of SnO 2 oxide inside what appears to be the hollow veins of the grain, whereas a Cu 2 O-like oxide is confined exclusively to the flat regions of the grain. We explain these results by noting that the hollow veins, offering a higher exposure to external fluids, are likely to have promoted preferential formation of the more stable tin oxide over copper oxide. In another region of the metal side we studied the chemistry of grain boundaries and their surrounding areas. We find that S species lie exclusively inside the grain boundaries, whereas Sn and Zn species accumulate just outside the boundary channels, and this lateral chemical inhomogeneity is highlighted with a ∼200 nm spatial resolution. Lateral segregation of Cu and Sn domains is imaged in another region with a spatial resolution of ∼15 nm. This result marks the best spatial resolution any analytical method has yet achieved in highlighting chemical heterogeneities of ancient bronzes. Although archaeomaterials lie outside the mainstream applications of Auger techniques, this study provides convincing evidence that SAM can greatly advance our understanding of these materials, as it provides clues relating to corrosion and patination phenomena, as well as

  8. The History of Tree and Shrub Taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data

    Directory of Open Access Journals (Sweden)

    Heike H. Zimmermann

    2017-10-01

    Full Text Available Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA metabarcoding, we reveal vegetation changes on Bol’shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.

  9. Subspecific Status of the Korean Tiger Inferred by Ancient DNA Analysis

    Directory of Open Access Journals (Sweden)

    Mu-Yeong Lee

    2012-01-01

    Full Text Available The tiger population that once inhabited the Korean peninsula was initially considered a unique subspecies (Panthera tigris coreensis, distinct from the Amur tiger of the Russian Far East (P. t. altaica. However, in the following decades, the population of P. t. coreensis was classified as P. t. altaica and hence forth the two populations have been considered the same subspecies. From an ecological point of view, the classification of the Korean tiger population as P. t. altaica is a plausible conclusion. Historically, there were no major dispersal barriers between the Korean peninsula and the habitat of Amur tigers in Far Eastern Russia and northeastern China that might prevent gene flow, especially for a large carnivore with long-distance dispersal abilities. However, there has yet to be a genetic study to confirm the subspecific status of the Korean tiger. Bone samples from four tigers originally caught in the Korean peninsula were collected from two museums in Japan and the United States. Eight mitochondrial gene fragments were sequenced and compared to previously published tiger subspecies’ mtDNA sequences to assess the phylogenetic relationship of the Korean tiger. Three individuals shared an identical haplotype with the Amur tigers. One specimen grouped with Malayan tigers, perhaps due to misidentification or mislabeling of the sample. Our results support the conclusion that the Korean tiger should be classified as P. t. altaica, which has important implications for the conservation and reintroduction of Korean tigers.

  10. Whole genome amplification and microsatellite genotyping of herbarium DNA revealed the identity of an ancient grapevine cultivar

    Science.gov (United States)

    Malenica, Nenad; Šimon, Silvio; Besendorfer, Višnja; Maletić, Edi; Karoglan Kontić, Jasminka; Pejić, Ivan

    2011-09-01

    Reconstruction of the grapevine cultivation history has advanced tremendously during the last decade. Identification of grapevine cultivars by using microsatellite DNA markers has mostly become a routine. The parentage of several renowned grapevine cultivars, like Cabernet Sauvignon and Chardonnay, has been elucidated. However, the assembly of a complete grapevine genealogy is not yet possible because missing links might no longer be in cultivation or are even extinct. This problem could be overcome by analyzing ancient DNA from grapevine herbarium specimens and other historical remnants of once cultivated varieties. Here, we present the first successful genotyping of a grapevine herbarium specimen and the identification of the corresponding grapevine cultivar. Using a set of nine grapevine microsatellite markers, in combination with a whole genome amplification procedure, we found the 90-year-old Tribidrag herbarium specimen to display the same microsatellite profile as the popular American cultivar Zinfandel. This work, together with information from several historical documents, provides a new clue of Zinfandel cultivation in Croatia as early as the beginning of fifteenth century, under the native name Tribidrag. Moreover, it emphasizes substantial information potential of existing grapevine and other herbarium collections worldwide.

  11. Studies on protozoa in ancient remains - A Review

    Directory of Open Access Journals (Sweden)

    Liesbeth Frías

    2013-02-01

    Full Text Available Paleoparasitological research has made important contributions to the understanding of parasite evolution and ecology. Although parasitic protozoa exhibit a worldwide distribution, recovering these organisms from an archaeological context is still exceptional and relies on the availability and distribution of evidence, the ecology of infectious diseases and adequate detection techniques. Here, we present a review of the findings related to protozoa in ancient remains, with an emphasis on their geographical distribution in the past and the methodologies used for their retrieval. The development of more sensitive detection methods has increased the number of identified parasitic species, promising interesting insights from research in the future.

  12. Assessment of the extirpated Maritimes walrus using morphological and ancient DNA analysis.

    Directory of Open Access Journals (Sweden)

    Brenna A McLeod

    Full Text Available Species biogeography is a result of complex events and factors associated with climate change, ecological interactions, anthropogenic impacts, physical geography, and evolution. To understand the contemporary biogeography of a species, it is necessary to understand its history. Specimens from areas of localized extinction are important, as extirpation of species from these areas may represent the loss of unique adaptations and a distinctive evolutionary trajectory. The walrus (Odobenus rosmarus has a discontinuous circumpolar distribution in the arctic and subarctic that once included the southeastern Canadian Maritimes region. However, exploitation of the Maritimes population during the 16th-18th centuries led to extirpation, and the species has not inhabited areas south of 55°N for ∼250 years. We examined genetic and morphological characteristics of specimens from the Maritimes, Atlantic (O. r. rosmarus and Pacific (O. r. divergens populations to test the hypothesis that the first group was distinctive. Analysis of Atlantic and Maritimes specimens indicated that most skull and mandibular measurements were significantly different between the Maritimes and Atlantic groups and discriminant analysis of principal components confirmed them as distinctive groups, with complete isolation of skull features. The Maritimes walrus appear to have been larger animals, with larger and more robust tusks, skulls and mandibles. The mtDNA control region haplotypes identified in Maritimes specimens were unique to the region and a greater average number of nucleotide differences were found between the regions (Atlantic and Maritimes than within either group. Levels of diversity (h and π were lower in the Maritimes, consistent with other studies of species at range margins. Our data suggest that the Maritimes walrus was a morphologically and genetically distinctive group that was on a different evolutionary path from other walrus found in the north Atlantic.

  13. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia.

    Science.gov (United States)

    Drancourt, M; Aboudharam, G; Signoli, M; Dutour, O; Raoult, D

    1998-10-13

    Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on which to base such research. We hypothesized that it would be a lasting refuge for Yersinia pestis, the plague agent. DNA extracts were made from the dental pulp of 12 unerupted teeth extracted from skeletons excavated from 16th and 18th century French graves of persons thought to have died of plague ("plague teeth") and from 7 ancient negative control teeth. PCRs incorporating ancient DNA extracts and primers specific for the human beta-globin gene demonstrated the absence of inhibitors in these preparations. The incorporation of primers specific for Y. pestis rpoB (the RNA polymerase beta-subunit-encoding gene) and the recognized virulence-associated pla (the plasminogen activator-encoding gene) repeatedly yielded products that had a nucleotide sequence indistinguishable from that of modern day isolates of the bacterium. The specific pla sequence was obtained from 6 of 12 plague skeleton teeth but 0 of 7 negative controls (P plague was achieved for historically identified victims, and we have confirmed the presence of the disease at the end of 16th century in France. Dental pulp is an attractive target in the quest to determine the etiology of septicemic illnesses detected in ancient corpses. Molecular techniques could be applied to this material to resolve historical outbreaks.

  14. Pomology observations, morphometric analysis, ultrastructural study and allelic profiles of "olivastra Seggianese" endocarps from ancient olive trees (Olea europaea L.).

    Science.gov (United States)

    Milanesi, Claudio; Sorbi, Andrea; Paolucci, Elisa; Antonucci, Francesca; Menesatti, Paolo; Costa, Corrado; Pallottino, Federico; Vignani, Rita; Cimato, Antonio; Ciacci, Andrea; Cresti, Mauro

    2011-01-01

    Preliminary studies of historical sources and remote sensing were used to identify ancient olive trees near archaeological sites and heritage buildings in the Orcia Valley (Siena, Italy). Distinctive characters were assessed by traditional pomological observation. Trees with similar characters were selected on the basis of the features of endocarps, the only structure that survives aerobic deterioration and conserves useful botanical information for centuries. Non-invasive morphometric analysis of endocarp size and shape established morphological variations in individuals of different populations. Plastid organization in the endocarp and location of DNA in the endocarp tegument were detected by morphological and ultrastructural observations using light and electron microscopy. Cytoplasmic markers with high polymorphism were used to test similarity of endocarp and leaf DNA within individuals and to confirm low variability and minimal divergence between individuals. The ancient trees studied showed the same allelic profiles and therefore belonged to a distinct cultivar. The traditional pomological descriptions of the trees, leaves and fruits, morphometric analysis of size, and shape elliptic Fourier analysis of endocarp outline, ultrastructural observations and allelic profiles of endocarp tegument delineated the general species-specific qualities of the cultivar "olivastra Seggianese" of the Orcia Valley. Copyright © 2010 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  15. Ancient genes of Saccharomyces cerevisiae.

    Science.gov (United States)

    Veiga-Crespo, P; Poza, M; Prieto-Alcedo, M; Villa, T G

    2004-07-01

    Amber is a plant resin mainly produced by coniferous trees that, after entrapping a variety of living beings, was subjected to a process of fossilization until it turned into yellowish, translucent stones. It is also one of the best sources of ancient DNA on which to perform studies on evolution. Here a method for the sterilization of amber that allows reliable ancient DNA extraction with no actual DNA contamination is described. Working with insects taken from amber, it was possible to amplify the ATP9, PGU1 and rRNA18S ancient genes of Saccharomyces cerevisiae corresponding to samples from the Miocene and Oligocene. After comparison of the current genes with their ancient (up to 35-40 million years) counterparts it was concluded that essential genes such as rRNA18S are highly conserved and that even normal 'house-keeping' genes, such as PGU1, are strikingly conserved along the millions of years that S. cerevisiae has evolved.

  16. Pre-Whaling Genetic Diversity and Population Ecology in Eastern Pacific Gray Whales: Insights from Ancient DNA and Stable Isotopes

    Science.gov (United States)

    Alter, S. Elizabeth; Newsome, Seth D.; Palumbi, Stephen R.

    2012-01-01

    Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ∼5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size. PMID:22590499

  17. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.

    Science.gov (United States)

    Alter, S Elizabeth; Newsome, Seth D; Palumbi, Stephen R

    2012-01-01

    Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.

  18. Pre-whaling genetic diversity and population ecology in eastern Pacific gray whales: insights from ancient DNA and stable isotopes.

    Directory of Open Access Journals (Sweden)

    S Elizabeth Alter

    Full Text Available Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ~5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size.

  19. Historias en código genético: Los aportes de los estudios de ADN antiguo en antropología y sus implicancias éticas Historias em código genético: As contribuições dos estudos de ADN antigo em antropologia e suas implicâncias éticas Stories in Genetic Code: The contribution of ancient DNA studies to anthropology and their ethical implications

    Directory of Open Access Journals (Sweden)

    Cristian M. Crespo

    2010-12-01

    Full Text Available Desde hace varias décadas, la antropología biológica comenzó a utilizar marcadores moleculares en estudios poblacionales. A partir de la década de 1990 se desarrollaron diferentes técnicas en biología molecular que permitieron extraer y tipificar ADN conservado en diferentes restos provenientes de museos y sitios arqueológicos. Los estudios de ADN antiguo relacionados con problemáticas arqueológicas conforman hoy un campo de estudio denominado Arqueogenética. Se presentan en este trabajo algunas de las aplicaciones del ADN antiguo. Se discuten las ventajas y limitaciones de estos estudios y su relación con temas éticos y legales.Faz já varias décadas que à antropologia biológica tem começado a usar marcadores moleculares em estudos de população. Ao começo da década de 1990, se desenvolveram técnicas diferentes em biologia molecular que permitiram obter e tipificar o ADN conservado em restos diferentes vindos de museus e sítios arqueológicos. Os estudos de ADN antigo relacionados a problemáticas arqueológicas são hoje um campo de estudo chamado de Arqueogenética. Se apresentam neste trabalho algumas das aplicações do ADN antigo. Também se discutem as vantagens e limitações desses estudos e a sua relação com assuntos éticos e legais.For several decades, biological anthropology has employed different molecular markers in population research. Since 1990 different techniques in molecular biology have been developed allowing preserved DNA extraction and its typification in different samples from museums and archaeological sites. Ancient DNA studies related to archaeological issues are now included in the field of Archaeogenetics. In this work we present some of ancient DNA applications in archaeology. We also discuss advantages and limitations for this kind of research and its relationship with ethic and legal norms.

  20. Molecular dating of caprines using ancient DNA sequences of Myotragus balearicus, an extinct endemic Balearic mammal

    Directory of Open Access Journals (Sweden)

    Alcover Josep Antoni

    2005-12-01

    Full Text Available Abstract Background Myotragus balearicus was an endemic bovid from the Balearic Islands (Western Mediterranean that became extinct around 6,000-4,000 years ago. The Myotragus evolutionary lineage became isolated in the islands most probably at the end of the Messinian crisis, when the desiccation of the Mediterranean ended, in a geological date established at 5.35 Mya. Thus, the sequences of Myotragus could be very valuable for calibrating the mammalian mitochondrial DNA clock and, in particular, the tree of the Caprinae subfamily, to which Myotragus belongs. Results We have retrieved the complete mitochondrial cytochrome b gene (1,143 base pairs, plus fragments of the mitochondrial 12S gene and the nuclear 28S rDNA multi-copy gene from a well preserved Myotragus subfossil bone. The best resolved phylogenetic trees, obtained with the cytochrome b gene, placed Myotragus in a position basal to the Ovis group. Using the calibration provided by the isolation of Balearic Islands, we calculated that the initial radiation of caprines can be dated at 6.2 ± 0.4 Mya. In addition, alpine and southern chamois, considered until recently the same species, split around 1.6 ± 0.3 Mya, indicating that the two chamois species have been separated much longer than previously thought. Conclusion Since there are almost no extant endemic mammals in Mediterranean islands, the sequence of the extinct Balearic endemic Myotragus has been crucial for allowing us to use the Messinian crisis calibration point for dating the caprines phylogenetic tree.

  1. Study of provenance character on ancient porcelain of Yue Kiln at Silongkou with NAA

    International Nuclear Information System (INIS)

    Jihao Zhu; Songlin Feng; Dongyu Fan; Xiangqian Feng; Qing Xu; Yueming Shen; Zhenxi Zhuo; Wenjiang Zhang

    2007-01-01

    Chemical composition is an important information of studying the provenance character of ancient pottery and porcelain. The ancient celadon samples produced in Later Tang (850-907 A.D.) to Former Southern Song (1127-1279 A.D.) have been analyzed with NAA. Its provenance characteristic was compared with that of Hongzhou Kiln of Jiangxi Province and Yaozhou Kiln of Shanxi Province in this paper. The experimental data were studied with statistic methods. The results indicated that the chemical compositions of ancient porcelain body samples made in three kilns were different. The difference is able to be identified. The porcelain body materials of both Silongkou Yue Kiln and Hongzhou Kiln were similar. The samples of Yaozhou kiln in north of China existed obvious difference. (author)

  2. A study on the migration policy in ancient China.

    Science.gov (United States)

    Wang, Y

    1995-01-01

    During the Chinese dynasties of Sui and Tang, neighboring minority groups were forced to migrate to less settled areas of China. During the Song dynasty (960-1279) the Han government lost control of neighboring ethnic groups. Ethnically dominated states on their own expanded to the hinterlands, formed the national governments of Yuan and Qing, and established the local power of Liao and Jin in Han-dominated areas. During the Han dynasty the movement of minorities fulfilled the purpose of helping cultivate undeveloped land. The Han governments of feudal China held compulsory migration policies and policies encouraging minorities to move to less inhabited places. Han governments prior to the Tang and Song dynasties held policies favorable to minority settlements. During the Tang dynasty land was given to minority settlers. During the Song dynasty the Han government held a policy which prohibited taxation and harassment of new minority settlers. Minorities gained improved living conditions and the government achieved pacification. Resettlement of minorities either from forced or voluntary migration facilitated communication with the Han and promoted the exchange of culture, but also intensified ethnic conflict. The reason for the ethnic conflict was a question of control. Ethnic governments encouraged in-migration and adopted policies of compulsory and voluntary migration. Ethnic minorities in the north and west practiced mainly compulsory migration. Ethnic conflict in the Qin and Han dynasties occurred between the Han and the Huns. During the Eastern Jin and Northern dynasties minority governments captured Han and other ethnic groups. The rule of minority government was strengthened by voluntary migration. The frequent power shifts in ancient China contributed to the blending of Chinese nationalities.

  3. Cytotoxic, DNA binding, DNA cleavage and antibacterial studies of ...

    Indian Academy of Sciences (India)

    fluoroquinolone complexes. Mohan N ... DNA-binding properties of Ru complexes have been studied by means of absorption spectrophotometry and viscosity measurements as well as their HS DNA cleavage properties by means of agarose gel ...

  4. Removal of natural organic dyes from wool-implications for ancient textile provenance studies

    DEFF Research Database (Denmark)

    Frei, Karin Margarita; Vanden Berghe, Ina; Frei, Robert

    2010-01-01

    Ancient wool textiles recovered from archaeological sites are in many cases originally dyed with natural organic dyestuffs from vegetable sources. These include among others woad (Isatis tinctoria L.), weld (Reseda luteola L.), and madder (Rubia tinctorum L.). These dyestuffs could be a threat...... to the use of the strontium isotopic system as a tracer for provenance studies of ancient wool, because they could potentially contaminate the signature of the textile's raw material. We present a novel method which allows for efficient removal of organic dyestuffs in wool prior to strontium isotopic...

  5. The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses

    Directory of Open Access Journals (Sweden)

    Boland Wilhelm

    2008-04-01

    Full Text Available Abstract Background Ectocarpus siliculosus virus-1 (EsV-1 is a lysogenic dsDNA virus belonging to the super family of nucleocytoplasmic large DNA viruses (NCLDV that infect Ectocarpus siliculosus, a marine filamentous brown alga. Previous studies indicated that the viral genome is integrated into the host DNA. In order to find the integration sites of the viral genome, a genomic library from EsV-1-infected algae was screened using labelled EsV-1 DNA. Several fragments were isolated and some of them were sequenced and analyzed in detail. Results Analysis revealed that the algal genome is split by a copy of viral sequences that have a high identity to EsV-1 DNA sequences. These fragments are interspersed with DNA repeats, pseudogenes and genes coding for products involved in DNA replication, integration and transposition. Some of these gene products are not encoded by EsV-1 but are present in the genome of other members of the NCLDV family. Further analysis suggests that the Ectocarpus algal genome contains traces of the integration of a large dsDNA viral genome; this genome could be the ancestor of the extant NCLDV genomes. Furthermore, several lines of evidence indicate that the EsV-1 genome might have originated in these viral DNA pieces, implying the existence of a complex integration and recombination system. A protein similar to a new class of tyrosine recombinases might be a key enzyme of this system. Conclusion Our results support the hypothesis that some dsDNA viruses are monophyletic and evolved principally through genome reduction. Moreover, we hypothesize that phaeoviruses have probably developed an original replication system.

  6. The activities of The Institute for the Studies on Ancient Mediterranean in North Africa

    Directory of Open Access Journals (Sweden)

    Alessandro Naso

    2016-12-01

    Full Text Available The Institute for the Studies on Ancient Mediterranean of the National Research Council of Italy (ISMA-CNR carries out from several years archaeological excavations and other researches in North Africa in Egypt, Algeria, Tunisia and Morocco, which are briefly illustrated.

  7. High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens

    DEFF Research Database (Denmark)

    Murray, Dáithí C.; Pearson, Stuart G.; Fullagar, Richard

    2012-01-01

    The study of arid palaeoenvironments is often frustrated by the poor or non-existent preservation of plant and animal material, yet these environments are of considerable environmental importance. The analysis of pollen and macrofossils isolated from herbivore middens has been an invaluable sourc...

  8. Ancient DNA extracted from Danish aurochs (Bos primigenius)

    DEFF Research Database (Denmark)

    Nielsen, Peter Gravlund; Aaris-Sørensen, Kim; Hofreiter, Michael

    2012-01-01

    in an archeological or geological context. We find that aurochs from southern Scandinavia display a star-shaped population genetic structure, that is indicative of a local and relatively recent diversification from a few ancestral haplotypes that may have originated in the ancestral Western European population before...... cattle in our aurochs suggests that introgression between these species must have been limited, if it occurred at all. We found that the successful recovery of genetic material for PCR amplification correlates with sample age and local geographic conditions. However, contrary to other studies, we found...

  9. Genetic characteristics and migration history of a bronze culture population in the West Liao-River valley revealed by ancient DNA.

    Science.gov (United States)

    Li, Hongjie; Zhao, Xin; Zhao, Yongbin; Li, Chunxiang; Si, Dayong; Zhou, Hui; Cui, Yinqiu

    2011-12-01

    In order to study the genetic characteristics of the Lower Xiajiadian culture (LXC) population, a main bronze culture branch in northern China dated 4500-3500 years ago, two uniparentally inherited markers, mitochondrial DNA and Y-chromosome single-nucleotide polymorphisms (Y-SNPs), were analyzed on 14 human remains excavated from the Dadianzi site. The 14 sequences, which contained 13 haplotypes, were assigned to 9 haplogroups, and Y-SNP typing of 5 male individuals assigned them to haplogroups N (M231) and O3 (M122). The results indicate that the LXC population mainly included people carrying haplogroups from northern Asia who had lived in this region since the Neolithic period, as well as genetic evidence of immigration from the Central Plain. Later in the Bronze Age, part of the population migrated to the south away from a cooler climate, which ultimately influenced the gene pool in the Central Plain. Thus, climate change is an important factor, which drove the population migration during the Bronze Age in northern China. Based on these results, the local genetic continuity did not seem to be affected by outward migration, although more data are needed especially from other ancient populations to determine the influence of return migration on genetic continuity.

  10. Range shifts or extinction? Ancient DNA and distribution modelling reveal past and future responses to climate warming in cold-adapted birds.

    Science.gov (United States)

    Lagerholm, Vendela K; Sandoval-Castellanos, Edson; Vaniscotte, Amélie; Potapova, Olga R; Tomek, Teresa; Bochenski, Zbigniew M; Shepherd, Paul; Barton, Nick; Van Dyck, Marie-Claire; Miller, Rebecca; Höglund, Jacob; Yoccoz, Nigel G; Dalén, Love; Stewart, John R

    2017-04-01

    Global warming is predicted to cause substantial habitat rearrangements, with the most severe effects expected to occur in high-latitude biomes. However, one major uncertainty is whether species will be able to shift their ranges to keep pace with climate-driven environmental changes. Many recent studies on mammals have shown that past range contractions have been associated with local extinctions rather than survival by habitat tracking. Here, we have used an interdisciplinary approach that combines ancient DNA techniques, coalescent simulations and species distribution modelling, to investigate how two common cold-adapted bird species, willow and rock ptarmigan (Lagopus lagopus and Lagopus muta), respond to long-term climate warming. Contrary to previous findings in mammals, we demonstrate a genetic continuity in Europe over the last 20 millennia. Results from back-casted species distribution models suggest that this continuity may have been facilitated by uninterrupted habitat availability and potentially also the greater dispersal ability of birds. However, our predictions show that in the near future, some isolated regions will have little suitable habitat left, implying a future decrease in local populations at a scale unprecedented since the last glacial maximum. © 2016 John Wiley & Sons Ltd.

  11. Ancient DNA reveals temporal population structure within the South-Central Andes area.

    Science.gov (United States)

    Russo, M Gabriela; Mendisco, Fanny; Avena, Sergio A; Crespo, Cristian M; Arencibia, Valeria; Dejean, Cristina B; Seldes, Verónica

    2018-04-01

    The main aim of this work was to contribute to the knowledge of pre-Hispanic genetic variation and population structure among the South-central Andes Area by studying individuals from Quebrada de Humahuaca, North-western (NW) Argentina. We analyzed 15 autosomal STRs in 19 individuals from several archaeological sites in Quebrada de Humahuaca, belonging to the Regional Developments Period (900-1430 AD). Compiling autosomal, mitochondrial, and Y-chromosome data, we evaluated population structure and differentiation among eight South-central Andean groups from the current territories of NW Argentina and Peru. Autosomal data revealed a structuring of the analyzed populations into two clusters which seemed to represent different temporalities in the Andean pre-Hispanic history: pre-Inca and Inca. All pre-Inca samples fell into the same cluster despite being from the two different territories of NW Argentina and Peru. Also, they were systematically differentiated from the Peruvian Inca group. These results were mostly confirmed by mitochondrial and Y-chromosome analyses. We mainly found a clearly different haplotype composition between clusters. Population structure in South America has been mostly studied on current native groups, mainly showing a west-to-east differentiation between the Andean and lowland regions. Here we demonstrated that genetic population differentiation preceded the European contact and might have been more complex than thought, being found within the South-central Andes Area. Moreover, divergence among temporally different populations might be reflecting socio-political changes occurred in the evermore complex pre-Hispanic Andean societies. © 2018 Wiley Periodicals, Inc.

  12. Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology.

    Science.gov (United States)

    Scheel, Dirk-Martin; Slater, Graham J; Kolokotronis, Sergios-Orestis; Potter, Charles W; Rotstein, David S; Tsangaras, Kyriakos; Greenwood, Alex D; Helgen, Kristofer M

    2014-01-01

    Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M. tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and "New World monk seals" (Hawaiian and Caribbean) is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus) represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.

  13. The globalization of naval provisioning: ancient DNA and stable isotope analyses of stored cod from the wreck of the Mary Rose, AD 1545.

    Science.gov (United States)

    Hutchinson, William F; Culling, Mark; Orton, David C; Hänfling, Bernd; Lawson Handley, Lori; Hamilton-Dyer, Sheila; O'Connell, Tamsin C; Richards, Michael P; Barrett, James H

    2015-09-01

    A comparison of ancient DNA (single-nucleotide polymorphisms) and carbon and nitrogen stable isotope evidence suggests that stored cod provisions recovered from the wreck of the Tudor warship Mary Rose, which sank in the Solent, southern England, in 1545, had been caught in northern and transatlantic waters such as the northern North Sea and the fishing grounds of Iceland and Newfoundland. This discovery, underpinned by control data from archaeological samples of cod bones from potential source regions, illuminates the role of naval provisioning in the early development of extensive sea fisheries, with their long-term economic and ecological impacts.

  14. Molecular studies of organic residues preserved in ancient vessels

    NARCIS (Netherlands)

    Oudemans, Tatiana Frederica Margreta

    2006-01-01

    This study is aimed at the molecular characterisation of solid organic (food) residues preserved in an assemblage of vessels recovered from an indigenous settlement dating back to the Iron Age and Roman period at Uitgeest – Groot Dorregeest (The Netherlands). Analytical thermal-fragmentation

  15. Study on provenance of ancient pottery excavated from Huating Ruins, Xinyi County by INAA

    International Nuclear Information System (INIS)

    Xu Anwu; Wang Changsui; Chi Jinqi; Satoshi Koshimizu; Kazai Manabu; Kushihara Koichi

    1997-01-01

    The ancient pottery excavated from Huating Ruins, Xinyi Country, Jiangsu Province, was measured and studied by INAA. The data were manipulated by multivariate statistic analysis, such as cluster and factor analysis. It has been shown that the specimens can be divided into two groups, which are related to Liangzhu Culture area and Dawenkou Culture area respectively. The result seems to support the viewpoint that the pottery specimens of Liangzhu Culture from Huating Ruins belong to war trophies

  16. Ancient DNA analysis might suggest external origin of individuals from chamber graves placed in medieval cemetery in Pień, Central Poland.

    Science.gov (United States)

    Płoszaj, Tomasz; Jędrychowska-Dańska, Krystyna; Zamerska, Alicja; Drozd-Lipińska, Alicja; Poliński, Dariusz; Janowski, Andrzej; Witas, Henryk

    2017-12-01

    The participation of immigrants during early days in Poland of Piast's dynasty is a debated issue among archaeologists and anthropologists alike. Such hypotheses were formulated on the basis of, amongst others, the discovery of early medieval chamber graves characterized by construction features typical of the Scandinavian culture area. Archaeological and anthropological studies to date have not provided an unequivocal answer as to whether the individuals interred in those graves were autochthons who adopted a different burial rite, or perhaps immigrants from foreign lands. To characterize the gene pool of this population we analyzed the C/T allele of the nuclear gene LCT-13910 as well as fragments of the mitochondrial genome from individuals buried in very richly furnished chamber graves at the medieval cemetery in Pień. The obtained results for the nuclear allele and mtDNA do not corroborate the Scandinavian origin of the analyzed population. Moreover, we did not find haplogroup I, which is the one typical of populations that historically inhabited the north of Europe; and the frequency of the LCT-13910 T allele was similar to that of past and present Polish populations. On the other hand, we identified the atypical haplogroup C5c1, which suggests Asian origin of the studied individuals and confirms our previous reports concerning ancient human migrations from Asia to the territory of present-day Poland. While our findings do not conclusively disprove a Scandinavian lineage of the studied population, they certainly shed some new light on the origin of the individuals buried in chamber graves, which may be very different from the one initially proposed by archaeologists.

  17. A neutron diffraction study of ancient Greek ceramics

    Science.gov (United States)

    Siouris, I. M.; Walter, J.

    2006-11-01

    Non-destructive neutron diffraction studies were performed on three 2nd-century BC archaeological pottery fragments from the excavation site of Neos Scopos, Serres, in North Greece. In all the 273 K diagrams quartz and feldspars phase fractions are dominant. Diopside and iron oxide phases were also identifiable. The diopside content is found to decrease with increasing quartz-feldspar compositions. Iron oxides containing minerals were found to be present and the phase compositions reflect upon the coloring of the samples. However, the different content compositions of the phases may suggest different regions of the original clay materials as well as different preparation techniques. The firing temperatures were determined to be in the range of 900-1000 °C.

  18. A neutron diffraction study of ancient Greek ceramics

    International Nuclear Information System (INIS)

    Siouris, I.M.; Walter, J.

    2006-01-01

    Non-destructive neutron diffraction studies were performed on three 2nd-century BC archaeological pottery fragments from the excavation site of Neos Scopos, Serres, in North Greece. In all the 273 K diagrams quartz and feldspars phase fractions are dominant. Diopside and iron oxide phases were also identifiable. The diopside content is found to decrease with increasing quartz-feldspar compositions. Iron oxides containing minerals were found to be present and the phase compositions reflect upon the coloring of the samples. However, the different content compositions of the phases may suggest different regions of the original clay materials as well as different preparation techniques. The firing temperatures were determined to be in the range of 900-1000 deg. C

  19. Moessbauer studies on ancient pottery from a neolithic site in Tung Wan, Hong Kong

    International Nuclear Information System (INIS)

    Zheng Yufang; Tang Chung

    1994-01-01

    Twelve ceramic sherds unearthed from different archaeological layers at a neolithic site in Tung Wan, Hong Kong, were studied by means of X-ray diffraction (XRD) and Moessbauer spectroscopy. The results show that the firing techniques used for ancient pottery wares at different layers were very different. For the oldest sherds (4000-3000 B.C.) from layer No. 4, the original firing temperature was low and craftmanship was inferior. For the sherds (1650-250 B.C.) from layer No. 2, the original firing temperature was above 1000 C. In addition, the results indicate that the ancient pottery wares from the ruins might not have been manufactured in the Tung Wan region. (orig.)

  20. A microclimate study on hypogea environments of ancient roman building.

    Science.gov (United States)

    Scatigno, C; Gaudenzi, S; Sammartino, M P; Visco, G

    2016-10-01

    Roman hypogea, vernacular settlements or crypts, are underground places characterised by specific and unique challenges (RHRome-Italy), with the aim of characterising the indoor environment as the structure suffers of several conservation problems (biocolonisation, efflorescences, evaporating and condensing cycle for wall-building materials). The campaign involving multipoint continuous measurement was carefully planned to better describe this micro-clime. In addition to underground environmental data available in literature, we have also performed, as a checkpoint control, a thermo-hygrometric monitoring campaign in the "Terme di Mitra" Hypogeum, a few meters from the "Casa di Diana". The recorded data was analysed by multivariate statistical and chemometric analyses. The results brought to light the presence of different microclimates (three areas) within a single Mithraeum: a room (pre-Mithraeum) and an area (Mithraeum: 2-4m) present a thermo-hygrometric environmental behaviour in accordance with a semi-confined environment, another area (Mithraeum: 1-2m) behaves accordingly with underground environments (although it cannot be described as such), and the last area (Mithraeum: 0-1m) where was recording RH values close to saturation (96-99%), associated with non-ventilated areas where the rising damp is "held" and not dispersed, describing an own micro-clime, comparable to a "small greenhouse". This study has allowed to identify some critical areas in view of planning future conservation solutions, without exporting the artefacts kept inside. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Analytical study of ancient pottery from the archaeological site of Aiani, northern Greece

    International Nuclear Information System (INIS)

    Iordanidis, A.; Garcia-Guinea, J.; Karamitrou-Mentessidi, G.

    2009-01-01

    The present study is a multi-analytical approach on the characterization of several potsherd samples, dated from prehistoric to hellenistic times, from Aiani, ancient Upper Macedonia, northern Greece. In particular, X-ray Diffraction (XRD), X-ray Fluorescence (XRF) and Environmental Scanning Electron Microscopy, coupled with Energy Dispersive X-ray system (ESEM-EDX) were used for the determination of the morphological, chemical and mineralogical characteristics of the potsherds. The preliminary results indicated a rather local provenance of the analyzed ancient pottery samples and a finer texture and thus better ceramic manufacture as getting to hellenistic era. The use of a silicious or calcerous raw material is probably related to the specific utilization of each ceramic vessel in ancient times. The presence of gehlenite or pyroxene minerals in the ceramic matrix indicated higher firing temperatures, while lower temperatures were deduced when finding phylosilicate minerals. The preliminary results of this study do not necessarily imply that all the pottery of this area, belonging to the same chronological type, have similar physicochemical characteristics

  2. Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA

    Science.gov (United States)

    Hristova, Lidia T.; Edwards, Susan R.; Wedding, Jeffrey R.; Snow, Meradeth; Kruger, Brittany R.; Moser, Duane P.

    2018-01-01

    Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource. PMID:29522562

  3. Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

    Directory of Open Access Journals (Sweden)

    Eveson J Paige

    2006-08-01

    Full Text Available Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide. This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will

  4. Medicine in Ancient Assur

    DEFF Research Database (Denmark)

    Arbøll, Troels Pank

    This dissertation is a microhistorical study of a single individual named Kiṣir-Aššur who practiced medicine in the ancient city of Assur (modern northern Iraq) in the 7th century BCE. The study provides the first detailed analysis of one healer’s education and practice in ancient Mesopotamia...

  5. The provenance study of Chinese ancient architectonical colored glaze by INAA

    International Nuclear Information System (INIS)

    Cheng Lin; Feng Songlin; Li Rongwu; Lue Zhirong; Li Guoxia

    2008-01-01

    The colored glazes are very popular and famous in Chinese ancient architectures. In order to exactly locate the provenance of ancient architectonical colored glazes, 196 pieces of ancient colored glaze bodies and porcelain bodies fired in Xiyue Temple and Lidipo kiln are analyzed by INAA. The results of factor analysis and some archaeological questions are reported and discussed in this paper

  6. RNA Study Using DNA Nanotechnology.

    Science.gov (United States)

    Tadakuma, Hisashi; Masubuchi, Takeya; Ueda, Takuya

    2016-01-01

    Transcription is one of the fundamental steps of gene expression, where RNA polymerases (RNAPs) bind to their template genes and make RNAs. In addition to RNAP and the template gene, many molecules such as transcription factors are involved. The interaction and the effect of these factors depend on the geometry. Molecular layout of these factors, RNAP and gene is thus important. DNA nanotechnology is a promising technology that allows controlling of the molecular layout in the range of nanometer to micrometer scale with nanometer resolution; thus, it is expected to expand the RNA study beyond the current limit. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Ancient Chinese Precedents in China

    National Research Council Canada - National Science Library

    Geddis, Robert

    1999-01-01

    ... classics from ancient china. The assumption is that since China's political and military leaders state openly that their strategy is based on traditional Chinese strategic concepts, a study of ancient classics on strategy...

  8. A study of essential elements in ancient Thai fighting swords by chemical and nuclear techniques

    International Nuclear Information System (INIS)

    Janposri, K.

    1980-01-01

    Four ancient Thai fighting swords from the Bangkok National Museum and iron ore from Kao Tab Kwai, Lopburi were studied by neutron activation analysis, metallography and chemical analysis. The results of these scientific studies show that all of these four swords are made of plain carbon steel, containing trace elements which have no effect on the physical and mechanical properties of the steel. The trace elements which were found in the iron ore are quite similar to those found in one of these swords. This means that the iron in one of the swords may have come from ore found at Kao Tab Kwai, Lopburi

  9. Development and trends in synchrotron studies of ancient and historical materials

    International Nuclear Information System (INIS)

    Bertrand, Loïc; Cotte, Marine; Stampanoni, Marco; Thoury, Mathieu; Marone, Federica; Schöder, Sebastian

    2012-01-01

    Synchrotron photon-based methods are increasingly being used for the physico-chemical study of ancient and historical materials (archaeology, palaeontology, conservation sciences, palaeo-environments). In particular, parameters such as the high photon flux, the small source size and the low divergence attained at the synchrotron make it a very efficient source for a range of advanced spectroscopy and imaging techniques, adapted to the heterogeneity and great complexity of the materials under study. The continuous tunability of the source — its very extended energy distribution over wide energy domains (meV to keV) with a high intensity — is an essential parameter for techniques based on a very fine tuning of the probing energy to reach high chemical sensitivity such as XANES, EXAFS, STXM, UV/VIS spectrometry, etc. The small source size attained (a few micrometres) at least in the vertical plane leads to spatial coherence of the photon beams, giving rise in turn to a series of imaging methods already crucial to the field. This review of the existing literature shows that microfocused hard X-ray spectroscopy (absorption, fluorescence, diffraction), full-field X-ray tomography and infrared spectroscopy are the leading synchrotron techniques in the field, and presents illustrative examples of the study of ancient and historical materials for the various methods. Fast developing analytical modalities in scanning spectroscopy (STXM, macro-XRF scanning) and novel analytical strategies regarding optics, detectors and other instrumental developments are expected to provide major contributions in the years to come. Other energy domains are increasingly being used or considered such as far-infrared and ultraviolet/visible for spectroscopy and imaging. We discuss the main instrumental developments and perspectives, and their impact for the science being made on ancient materials using synchrotron techniques.

  10. Development and trends in synchrotron studies of ancient and historical materials

    Energy Technology Data Exchange (ETDEWEB)

    Bertrand, Loic, E-mail: loic.bertrand@synchrotron-soleil.fr [IPANEMA, USR 3461 CNRS/MCC, Synchrotron SOLEIL, Gif-sur-Yvette (France); Cotte, Marine [European Synchrotron Radiation Facility, Polygone Scientifique Louis Néel, Grenoble (France) and Centre de Recherche et de Restauration des Musées de France, UMR 171 CNRS, Palais du Louvre, Paris (France); Stampanoni, Marco [Swiss Light Source, Paul Scherrer Institut, Villegen (Switzerland) and Institute for Biomedical Engineering, University and Eidgenössische Technische Hochschule Zurich, Zurich (Switzerland); Thoury, Mathieu [IPANEMA, USR 3461 CNRS/MCC, Synchrotron SOLEIL, BP48 Saint-Aubin, F-91192 Gif-sur-Yvette (France); Marone, Federica [Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen (Switzerland); Schöder, Sebastian [IPANEMA, USR 3461 CNRS/MCC, Synchrotron SOLEIL, Gif-sur-Yvette (France)

    2012-10-01

    Synchrotron photon-based methods are increasingly being used for the physico-chemical study of ancient and historical materials (archaeology, palaeontology, conservation sciences, palaeo-environments). In particular, parameters such as the high photon flux, the small source size and the low divergence attained at the synchrotron make it a very efficient source for a range of advanced spectroscopy and imaging techniques, adapted to the heterogeneity and great complexity of the materials under study. The continuous tunability of the source — its very extended energy distribution over wide energy domains (meV to keV) with a high intensity — is an essential parameter for techniques based on a very fine tuning of the probing energy to reach high chemical sensitivity such as XANES, EXAFS, STXM, UV/VIS spectrometry, etc. The small source size attained (a few micrometres) at least in the vertical plane leads to spatial coherence of the photon beams, giving rise in turn to a series of imaging methods already crucial to the field. This review of the existing literature shows that microfocused hard X-ray spectroscopy (absorption, fluorescence, diffraction), full-field X-ray tomography and infrared spectroscopy are the leading synchrotron techniques in the field, and presents illustrative examples of the study of ancient and historical materials for the various methods. Fast developing analytical modalities in scanning spectroscopy (STXM, macro-XRF scanning) and novel analytical strategies regarding optics, detectors and other instrumental developments are expected to provide major contributions in the years to come. Other energy domains are increasingly being used or considered such as far-infrared and ultraviolet/visible for spectroscopy and imaging. We discuss the main instrumental developments and perspectives, and their impact for the science being made on ancient materials using synchrotron techniques.

  11. Scanning RBS-PIXE study of ancient artifacts from South America using a microbeam

    Science.gov (United States)

    Ruvalcaba-Sil, J. L.; Demortier, G.

    1997-07-01

    Pre-Hispanic goldsmiths developed original techniques to manufacture and to gild ornaments and artifacts. Gold metallurgy in ancient America was mainly a surface technology. Surface studies of artifacts from various regions of pre-Hispanic South America were carried out using a 2 MeV proton microbeam (10 μm diameter). Several regions of the artifacts were scanned: RBS and PIXE were used simultaneously to determine the elemental composition and to characterize the homogeneity in depth and at the surface. Complementary information is provided from previous analyses using a macrobeam. Outstanding aspects about the metallurgical processes involved in the gilding of the artifacts have been established.

  12. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Tomsho, Lynn P; Rendulic, Snjezana

    2007-01-01

    Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously...

  13. Archaeological Studies of the Ancient Turkestan Site: results of 2011-2012 excavations

    Directory of Open Access Journals (Sweden)

    Smagulov Yerbulat A.

    2013-03-01

    Full Text Available The results of the 2011-12 excavations on the Eski-Turkestan site conducted by the Turkestani archaeological expedition (Institute of archaeology named after A. Margulan are presented. The site contains the remains of the ancient town of Yasy (modern town of Turkestan, South Kazakhstan oblast. The aim of the excavations was to study the earliest layers of the settlement, the primary stages of the city formation, and to identify construction elements of the ancient citadel in particular. It has been established that the most ancient nucleus of the city was located under Kultobe hill on the eastern edge of the settlement. The oldest architectural object of the citadel is a cruciform construction with powerful rammed clay defensive walls having narrow loopholes, preserved to a height of over 3 m. The three rooms were connected by arched doorways. In the second construction horizon, a building with long narrow rooms around a small open courtyard had been added to this "castle". During this period, around the perimeter of the citadel powerful rammed clay and mud-brick defensive walls had been erected, with the space between them and the extended castle being just partially built up. These two periods can be dated to the 1st–3rd centuries AD. This stage comes to an end with defeat and a fire. In the fire layer, numerous ceramic vessels in disassembling have been found. Individual unique finds have been made, and alabaster idols are of special interest. The restoration of the fortification wall and a new stage of the citadel development refer to the 9th-11th centuries. At the base of the new wall, pots with sacrificial food have been discovered, one of them bearing a runic inscription.

  14. Evidence of a high-Andean, mid-Holocene plant community: An ancient DNA analysis of glacially preserved remains.

    Science.gov (United States)

    Gould, Billie A; León, Blanca; Buffen, Aron M; Thompson, Lonnie G

    2010-09-01

    Around the world, tropical glaciers and ice caps are retreating at unprecedented rates because of climate change. In at least one location, along the margin of the Quelccaya Ice Cap in southeastern Peru, ancient plant remains have been continually uncovered since 2002. We used genetic analysis to identify plants that existed at these sites during the mid-Holocene. • We examined remains between 4576 and 5222 yr old, using PCR amplification, cloning, and sequencing of a fragment of the chloroplast trnL intron. We then matched these sequences to sequences in GenBank. • We found evidence of at least five taxa characteristic of wetlands, which occur primarily at lower elevations in the region today. • A diverse community most likely existed at these locations the last time they were ice-free and thus has the potential to reestablish with time. This is the first genetic analysis of vegetation uncovered by receding glacial ice, and it may become one of many as ancient plant materials are newly uncovered in a changing climate.

  15. Living with the world heritage. An ethnographic study of the ancient city of Nessebar, Bulgaria

    Directory of Open Access Journals (Sweden)

    Luleva Ana

    2015-01-01

    Full Text Available Since the mid-1950s the Ancient city of Nessebar has had the status of national cultural heritage; in 1983 it was inscribed in the World heritage list of UNESCO. The article makes an attempt to study the regimes of using of and living in the city - world cultural heritage in two different political and economic contexts. The pressure of the tourism industry on the value, which was visible even in the years of the late state socialism, became irresistible after 1989 in the context of the liberalised market economy, the interests of the private investors and the accepted as part of the "normal" market order corrupt practices of the institutions that are responsible for the safeguarding and management of the cultural heritage. The ethnographic study argues that intertwined in a Gordian knot around the central question for the residents of the ancient city of Nessebar, viz. the occupation of the city, which has been declared a world heritage site, are issues like trust and distrust in the institutions, the experience of abiding by formal and informal rules for operation with private property, the notions of social justice, local identity, the use of the cultural heritage as symbolic capital by different social actors and its transformation into economic one, with the conflicting interconnection between tourist industry and cultural heritage.

  16. Chinese herbal dose in ancient and modern times: a comparative study.

    Science.gov (United States)

    He, Shimin

    2013-04-01

    Appropriate dose guarantees Chinese herb's safety and effectiveness. There are adult dose criteria for Chinese herbs in decoction in the Pharmacopoeia of the People's Republic of China (2010 Edition) at present. But Chinese herbs have been frequently used in much higher doses than the dose criteria. This study has been conducted to test the dependability of the dose criteria. Twenty Chinese herbs were selected as representatives and their adult doses in decoction in Bei Ji Qian Jin Yao Fang, a famous ancient literature, have been reviewed and compared with those in the Pharmacopoeia of the People's Republic of China (2010 Edition). The adult dose criteria for all these 20 Chinese herbs in the Pharmacopoeia of the People's Republic of China (2010 Edition) haven't covered those in Bei Ji Qian Jin Yao Fang. Furthermore, maximal adult doses in the dose criteria are much lower than those in Bei Ji Qian Jin Yao Fang. The dose criteria in the Pharmacopoeia of the People's Republic of China (2010 Edition) are not comprehensive enough. Studying ancient literatures is an effective method to gain precious Chinese herbs' dose data and helps for new dose criteria's establishment in the future.

  17. Experimental designs for evaluation of genetic variability and selection of ancient grapevine varieties: a simulation study.

    Science.gov (United States)

    Gonçalves, E; St Aubyn, A; Martins, A

    2010-06-01

    Classical methodologies for grapevine selection used in the vine-growing world are generally based on comparisons among a small number of clones. This does not take advantage of the entire genetic variability within ancient varieties, and therefore limits selection challenges. Using the general principles of plant breeding and of quantitative genetics, we propose new breeding strategies, focussed on conservation and quantification of genetic variability by performing a cycle of mass genotypic selection prior to clonal selection. To exploit a sufficiently large amount of genetic variability, initial selection trials must be generally very large. The use of experimental designs adequate for those field trials has been intensively recommended for numerous species. However, their use in initial trials of grapevines has not been studied. With the aim of identifying the most suitable experimental designs for quantification of genetic variability and selection of ancient varieties, a study was carried out to assess through simulation the comparative efficiency of various experimental designs (randomized complete block design, alpha design and row-column (RC) design). The results indicated a greater efficiency for alpha and RC designs, enabling more precise estimates of genotypic variance, greater precision in the prediction of genetic gain and consequently greater efficiency in genotypic mass selection.

  18. Lipid biomarkers for bacterial ecosystems: studies of cultured organisms, hydrothermal environments and ancient sediments

    Science.gov (United States)

    Summons, R. E.; Jahnke, L. L.; Simoneit, B. R.

    1996-01-01

    This paper forms part of our long-term goal of using molecular structure and carbon isotopic signals preserved as hydrocarbons in ancient sediments to improve understanding of the early evolution of Earth's surface environment. We are particularly concerned with biomarkers which are informative about aerobiosis. Here, we combine bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems to construct models for the nature, behaviour and preservation potential of primitive microbial communities. We use a combined molecular and isotopic approach to characterize lipids produced by cultured bacteria and test a variety of culture conditions which affect their biosynthesis. This information is then compared with lipid mixtures isolated from contemporary hot springs and evaluated for the kinds of chemical change that would accompany burial and incorporation into the sedimentary record. In this study we have shown that growth temperature does not appear to alter isotopic fractionation within the lipid classes produced by a methanotropic bacterium. We also found that cultured cyanobacteria biosynthesize diagnostic methylalkanes and dimethylalkanes with the latter only made when growing under low pCO2. In an examination of a microbial mat sample from Octopus Spring, Yellowstone National Park (USA), we could readily identify chemical structures with 13C contents which were diagnostic for the phototrophic organisms such as cyanobacteria and Chloroflexus. We could not, however, find molecular evidence for operation of a methane cycle in the particular mat samples we studied.

  19. Role of radiation physics in the study and authentication of ancient gold work

    International Nuclear Information System (INIS)

    Guerra, M.F.

    2014-01-01

    Ancient gold items are important expressions of different aspects of past civilisations. By using non-destructive techniques of analysis and exam it is possible to obtain data kept within the objects morphology and within the materials employed, providing information, among others, on the manufacturing technologies, on the functions attributed to the objects, and on the sources of raw material exploited. This paper aims to give an overview of the questions raised by cultural heritage objects made with gold, and the role of science-based techniques applied to their study and authentication. Two examples serve to illustrate this: one concerns 19th century restorations of Etruscan objects and the other the provenance of Merovingian gold. - Highlights: ► An overview of the application of radiation techniques for the analysis of ancient gold work is given. ► We focused on non-destructive SEM-EDS, IBA techniques, X-radiography, and optical microscopy. ► Exam is illustrated by the authentication of Etruscan gold jewellery kept in museum collections. ► Fingerprinting gold is illustrated by the elemental analysis of Merovingian items from tombs in Gaul

  20. µ-XRF Studies on the Colour Brilliance in Ancient Wool Carpets

    Directory of Open Access Journals (Sweden)

    Markus Meyer

    2017-01-01

    Full Text Available Many handmade ancient and recent oriental wool carpets show outstanding brilliance and persistence of colour that is not achieved by common industrial dyeing procedures. Anthropologists have suggested the influence of wool fermentation prior to dyeing as key technique to achieve the high dyeing quality. By means of μ-XRF elemental mapping of mordant metals we corroborate this view and show a deep and homogenous penetration of colourants into fermented wool fibres. Furthermore we are able to apply this technique and prove that the fermentation process for ancient specimens cannot be investigated by standard methods due to the lack of intact cuticle layers. This finding suggests a broad range of further investigations that will contribute to a deeper understanding of the development of traditional dyeing techniques. Spectroscopic studies add information on the oxidation states of the metal ions within the respective mordant-dye-complexes and suggest a partial charge transfer as basis for a significant colour change when Fe mordants are used.

  1. Originating relation studies on ancient porcelains of chines Ru and Jun by NAA

    International Nuclear Information System (INIS)

    Zhao Weijuan; Xie Jianzhong; Gao Zhengyao; Li Guoxia; Li Rongwu; Zhang Bin

    2002-01-01

    50 samples of glazes and bodies of the ancient Chinese Ru porcelain, Jun porcelain and imitative ancient ceramics were analyzed by neutron activation analysis (NAA). The contents of 36 elements in each sample were measured. The NAA data were statistically treated by fuzzy cluster method and the trend cluster diagram was obtained. Their classes and raw material sources were determined. The results show that although these samples spanned hundreds of years, came from different kilns and had different glazes colors, the bodies of the ancient Chinese Ru porcelain and Jun porcelain belong to the same kind, the glazes of the ancient Chinese Ru porcelain is similar to the glazes of the ancient Chinese Jun porcelain. The originating places of the body raw material were concentrated, and that of the glaze raw materials were scattered, the source of the glaze raw material covered that the body raw material. The ancient Chinese Ru porcelain and Jun porcelain have basically the same raw material sources and the sources of raw material are stable in long time. It is found that most modern Jun porcelain samples are similar to the ancient Chinese Jun porcelain. Two modern Ru porcelain samples are similar to the ancient Chinese Ru porcelain, but another one drifts apart from the ancient Chinese Ru porcelain. Jingdezhen porcelain has no relation to Ru porcelain and Jun porcelain

  2. DNA repair enzyme APE1 from evolutionarily ancient Hydra reveals redox activity exclusively found in mammalian APE1.

    Science.gov (United States)

    Pekhale, Komal; Haval, Gauri; Perween, Nusrat; Antoniali, Giulia; Tell, Gianluca; Ghaskadbi, Surendra; Ghaskadbi, Saroj

    2017-11-01

    Only mammalian apurinic/apyrimidinic endonuclease1 (APE1) has been reported to possess both DNA repair and redox activities. C terminal of the protein is required for base excision repair, while the redox activity resides in the N terminal due to cysteine residues at specific positions. APE1s from other organisms studied so far lack the redox activity in spite of having the N terminal domain. We find that APE1 from the Cnidarian Hydra exhibits both endonuclease and redox activities similar to mammalian APE1. We further show the presence of the three indispensable cysteines in Hydra APE1 for redox activity by site directed mutagenesis. Importance of redox domain but not the repair domain of APE1 in regeneration has been demonstrated by using domain-specific inhibitors. Our findings clearly demonstrate that the redox function of APE1 evolved very early in metazoan evolution and is not a recent acquisition in mammalian APE1 as believed so far. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Study of provenance properties on ancient porcelain of Yue Kiln at Si-long-kou with NAA

    International Nuclear Information System (INIS)

    Feng Songlin; Fan Dongyu; Feng Xiangqian; Cheng Lin; Lei Yong; Xu Qing; Quan Huishan; Shen Yueming; Zhou Zhexi; Zhang Wenjiang

    2005-01-01

    Chinese ancient porcelain history has lasted about three thousands years from Shang Dynasty (1100∼1600 BC). A large amount of ancient porcelain sherds with accuracy provenance and ages were excavated from a lot of kiln sites in China. Archaeologists and ceramic experts have recognized and researched it with excavated stratum, utensil shape, body quality, glaze color and painting pattern. However, the appearance characteristic of some ancient porcelain manufactured in different kilns is similar. Therefore, it is still difficult to identify the provenance and ages of the samples excavated from some sites using traditional methods. Up, to now, many problems of Chinese ancient porcelain are confused for archaeologist and collecting experts. The elemental composition of ancient porcelain shows certain information of provenance and age. Especially, the sorts and contents of the elements in porcelain didn't change, so it is very useful to determine the provenance of ancient porcelain with elemental composition characteristics. Provenance characteristic is the important scientific information to identify ancient porcelain wares excavated from sites and graves. The porcelain samples of Si-Long-Kou Yue kiln in Zhejiang Province of china have been analyzed with NAA in this paper. The provenance characteristic was compared with it of Hong-Zhou kiln of Jiang-Xi Province and Yao-Zhou kiln of Shan-Xi Province. The experimental data were studied with statistic methods. The results show that the chemical compositions of porcelain body samples for three kilns were different. The difference was been able identified. The porcelain body materials of both Si-Long-Kou Yue kiln and Hong-Zhou kiln of Jiang-Xi were similar. The samples of Yao-Zhou kiln in north of China existed obvious difference.

  4. Ancient mtDNA Analysis of Early 16th Century Caribbean Cattle Provides Insight into Founding Populations of New World Creole Cattle Breeds

    Science.gov (United States)

    Speller, Camilla F.; Burley, David V.; Woodward, Robyn P.; Yang, Dongya Y.

    2013-01-01

    The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15th to early 16th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle. PMID:23894505

  5. Study on distinguishing of Chinese ancient porcelains by neutron activation and fuzzy cluster analysis

    International Nuclear Information System (INIS)

    Wang An

    1992-01-01

    By means of the method of neutron activation, the contents of trace elements in some samples of Chinese ancient porcelains from different places of production were determined. The data were analysed by fuzzy cluster analysis. On the basis of the above mentioned works, a method with regard to the distinguishing and determining of Chinese ancient porcelain was suggested

  6. Tracking down human contamination in ancient human teeth

    DEFF Research Database (Denmark)

    Sampietro, María Lourdes; Gilbert, M Thomas P; Lao, Oscar

    2006-01-01

    DNA contamination arising from the manipulation of ancient calcified tissue samples is a poorly understood, yet fundamental, problem that affects the reliability of ancient DNA (aDNA) studies. We have typed the mitochondrial DNA hypervariable region I of the only 6 people involved in the excavation...... identified as contaminants, with those derived from the people involved in the retrieval and washing of the remains present in higher frequencies than those of the anthropologist and genetic researchers. This finding confirms, for the first time, previous hypotheses that teeth samples are most susceptible...... to contamination at their initial excavation. More worrying, the cloned contaminant sequences exhibit substitutions that can be attributed to DNA damage after the contamination event, and we demonstrate that the level of such damage increases with time: contaminants that are >10 years old have approximately 5...

  7. Study of the circumstance influence on the elemental distribution in ancient animal bone using μ-XRF

    International Nuclear Information System (INIS)

    Yan Lingtong; Feng Songlin; Li Li; Xu Wei; Feng Xiangqian; Xie Guoxi

    2010-01-01

    Elemental analysis of archaeological bone plays an important role in the study of the dietary habits of ancient animals. The elemental characteristic of diagenetic skeletons depends on the surrounding circumstance. The study of environmental influence on the elemental concentration of ancient bone is significant. In this paper, the diagenetic influence on archaeological skeletons is analyzed by microbeam X-ray fluorescence (μ-XRF). The results show that the enamel is an excellent barrier to the diagenesis and the element Sr in bone isn't susceptible to contamination from the buried environment. (authors)

  8. Statistical Methods for Population Genetic Inference Based on Low-Depth Sequencing Data from Modern and Ancient DNA

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand

    Due to the recent advances in DNA sequencing technology genomic data are being generated at an unprecedented rate and we are gaining access to entire genomes at population level. The technology does, however, not give direct access to the genetic variation and the many levels of preprocessing tha...

  9. Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies

    NARCIS (Netherlands)

    van der Kuyl, A. C.; Kuiken, C. L.; Dekker, J. T.; Perizonius, W. R.; Goudsmit, J.

    1995-01-01

    Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S

  10. Single molecule Studies of DNA Mismatch Repair

    Science.gov (United States)

    Erie, Dorothy A.; Weninger, Keith R.

    2015-01-01

    DNA mismatch repair involves is a widely conserved set of proteins that is essential to limit genetic drift in all organisms. The same system of proteins plays key roles in many cancer related cellular transactions in humans. Although the basic process has been reconstituted in vitro using purified components, many fundamental aspects of DNA mismatch repair remain hidden due in part to the complexity and transient nature of the interactions between the mismatch repair proteins and DNA substrates. Single molecule methods offer the capability to uncover these transient but complex interactions and allow novel insights into mechanisms that underlie DNA mismatch repair. In this review, we discuss applications of single molecule methodology including electron microscopy, atomic force microscopy, particle tracking, FRET, and optical trapping to studies of DNA mismatch repair. These studies have led to formulation of mechanistic models of how proteins identify single base mismatches in the vast background of matched DNA and signal for their repair. PMID:24746644

  11. DNA binding studies of tartrazine food additive.

    Science.gov (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary

    2011-07-01

    The interaction of native calf thymus DNA with tartrazine in 10 mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75 × 10(4) M(-1).

  12. Natural analogue study on backfill materials from ancient Chinese constructions for LILW disposal. Appendix 5: China (b)

    International Nuclear Information System (INIS)

    Cunli, G.; Zhiwen, F.; Xiuzhen, L.; Yawen, H.; Anxi, C.; Jinsheng, Z.

    2001-01-01

    Full text: The objective of this work was to contribute to the demonstration of the long term safety of low-and-intermediate level radioactive waste (LILW) disposal using information from a natural analogue study on ancient Chinese constructions. The work firstly compared LILW near surface disposal facilities with Chinese ancient tombs in respects of siting, engineering structures, design and construction procedures and indicates that they are both based upon multi-barrier principle. After extensive literature and field survey, three materials were collected from two Chinese ancient tombs and one ancient architectures for further laboratory study. The three materials were studied in laboratories from the point of view of radioactive waste disposal in near surface facilities to obtain information concerning their basic physical and chemical properties, engineering properties and radionuclide adsorption abilities. The results show that the two materials from the ancient tombs have low permeability and strong adsorption for 60 Co and 134 Cs. The saturated permeabilities of the two ancient materials are in the order of 10 -1 0 m/s and the distribution coefficients for the two radionuclides are all in the order of 10 1 m 3 /kg. The conclusion was that the then current LILW disposal option in near-surface would be effective for a long term period of time, and clay materials, as backfill materials for LILW near-surface disposal facilities would very effective in preventing water intrusion and retarding radionuclide release even over a long term of period. Overall the LILW disposal option was considered to be safe in long term. (author)

  13. Study of provenance properties on ancient celadon of different kilns with NAA

    International Nuclear Information System (INIS)

    Feng Songlin; Fan Dongyu; Feng Xiangqian; Xu Qing; Cheng Lin; Lei Yong; Shen Yueming; Zhang Wenjiang; Zhua Zhenxi

    2005-01-01

    Provenance characteristic is an important scientific parameter to identify ancient porcelain wares unearthed from sites and graves. The porcelain samples of Si-Long-Kou Yue kiln of Zhejiang Province, Hong-Zhou kiln of Jiangxi Province and Yao-Zhou kiln of Shanxi Province have been analyzed with neutron activation analysis (NAA). The experimental data were studied with statistic methods. The results show that the chemical compositions of porcelain body samples for three kilns were different. The difference was able to be identified. The body materials of both Si-Long-Kou Yue kiln and Hong-Zhou kiln of Jiangxi were similar. The samples of Yao-Zhou kiln in north of China existed obvious difference. (authors)

  14. A phase-transition model for the rise and collapse of ancient civilizations: A pre-ceramic Andean case study

    Science.gov (United States)

    Flores, J. C.

    2015-12-01

    For ancient civilizations, the shift from disorder to organized urban settlements is viewed as a phase-transition simile. The number of monumental constructions, assumed to be a signature of civilization processes, corresponds to the order parameter, and effective connectivity becomes related to the control parameter. Based on parameter estimations from archaeological and paleo-climatological data, this study analyzes the rise and fall of the ancient Caral civilization on the South Pacific coast during a period of small ENSO fluctuations (approximately 4500 BP). Other examples considered include civilizations on Easter Island and the Maya Lowlands. This work considers a typical nonlinear third order evolution equation and numerical simulations.

  15. Reflections on Tutoring Ancient Greek Philosophy: A Case Study of Teaching First-Year Undergraduates in the UK

    Science.gov (United States)

    Vázquez, Daniel

    2014-01-01

    This is a case study of my reflections on teaching a first-year undergraduate tutorial on Ancient Greek Philosophy in the UK. This study draws upon the notion of reflective practice as an essential feature of teaching, in this case applied to Higher Education. My aim is to show how a critical engagement with my teaching practices and the overall…

  16. Deep Sequencing of RNA from Ancient Maize Kernels

    Science.gov (United States)

    Rasmussen, Morten; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Alquezar-Planas, David E.; Penfield, Steven; Brown, Terence A.; Vielle-Calzada, Jean-Philippe; Montiel, Rafael; Jørgensen, Tina; Odegaard, Nancy; Jacobs, Michael; Arriaza, Bernardo; Higham, Thomas F. G.; Ramsey, Christopher Bronk; Willerslev, Eske; Gilbert, M. Thomas P.

    2013-01-01

    The characterization of biomolecules from ancient samples can shed otherwise unobtainable insights into the past. Despite the fundamental role of transcriptomal change in evolution, the potential of ancient RNA remains unexploited – perhaps due to dogma associated with the fragility of RNA. We hypothesize that seeds offer a plausible refuge for long-term RNA survival, due to the fundamental role of RNA during seed germination. Using RNA-Seq on cDNA synthesized from nucleic acid extracts, we validate this hypothesis through demonstration of partial transcriptomal recovery from two sources of ancient maize kernels. The results suggest that ancient seed transcriptomics may offer a powerful new tool with which to study plant domestication. PMID:23326310

  17. Use of Drosophila to study DNA repair

    International Nuclear Information System (INIS)

    Boyd, J.B.; Harris, P.V.; Sakaguchi, K.

    1988-01-01

    This paper discusses Drosophila, the premier metazoan organism for analyzing many fundamental features of eukaryotic gene regulation. The authors present adaptations of several approaches for studying DNA repair to an analysis of repair-defective mutants in Drosophila. A current understanding of Drosophila DNA repair is described

  18. DNA Interaction Studies of Selected Polyamine Conjugates

    Directory of Open Access Journals (Sweden)

    Marta Szumilak

    2016-09-01

    Full Text Available The interaction of polyamine conjugates with DNA double helix has been studied. Binding properties were examined by ethidium bromide (EtBr displacement and DNA unwinding/topoisomerase I/II (Topo I/II activity assays, as well as dsDNA thermal stability studies and circular dichroism spectroscopy. Genotoxicity of the compounds was estimated by a comet assay. It has been shown that only compound 2a can interact with dsDNA via an intercalative binding mode as it displaced EtBr from the dsDNA-dye complex, with Kapp = 4.26 × 106 M−1; caused an increase in melting temperature; changed the circular dichroism spectrum of dsDNA; converted relaxed plasmid DNA into a supercoiled molecule in the presence of Topo I and reduced the amount of short oligonucleotide fragments in the comet tail. Furthermore, preliminary theoretical study has shown that interaction of the discussed compounds with dsDNA depends on molecule linker length and charge distribution over terminal aromatic chromophores.

  19. Provenance study of ancient Chinese Yaozhou porcelain by neutron activation analysis

    International Nuclear Information System (INIS)

    Li, R.W.; Zhao, W.J.; Li, G.X.; Xie, J.Z.; Guo, M.; Gao, Z.Y.; Feng, S.L.; Fan, D.Y.; Zhang, Y.; Cai, Z.F.; Zhuo, Z.X.

    2004-01-01

    The glaze samples of ancient Chinese Yaozhou porcelain were analyzed by neutron activation analysis (NAA). The contents of 29 elements for each sample were measured. the scattergram of the coloring elements shows some informations of soueces of raw materials. (authors)

  20. Study on the provenance of ancient porcelain excavated in Maojiawan ruin by WDXRF analysis

    International Nuclear Information System (INIS)

    Xie Guoxi

    2007-01-01

    In order to determine the provenance of two different kinds of ancient celadons which were excavated in Maojiawan ruin located in Beijing of China and named FLQ (imitated celadon) and WLNQ which is celadon outside and blue-white inside, ten components of each sample's body and glaze were measured by the wave length dispersive X-ray fluorescence (WDXRF) analysis. Multivariates statistical analysis was used to analyze and compare the experiment data with those of LQY (ancient celadon) made in Zhejiang and ancient Jingdezhen porcelain (JDZ) made in Jingdezhen. The results show that the two different kinds of ancient celadons have the same provenance as JDZ, that is, they were produced in Jingdezhen. (authors)

  1. Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis.

    Science.gov (United States)

    Barnett, Ross; Yamaguchi, Nobuyuki; Shapiro, Beth; Ho, Simon Y W; Barnes, Ian; Sabin, Richard; Werdelin, Lars; Cuisin, Jacques; Larson, Greger

    2014-04-02

    Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.

  2. 2500 years from dendrochronology back to ancient French human biotopes. Trees studied: low altitude oaks

    OpenAIRE

    Lambert, Georges-Noël; Durost, Sébastien; Cuaz, Jacques

    2005-01-01

    We propose an experimental method, using curvilinear regressions, called corridor method, for dating and building a global useful signal based on oak ring widths in northern and eastern France. The resulting signal seems to be more useful than others to progress in the domains of ancient climate and ancient environments: dendrodating, dendroclimatology, dendroecology and, of course, human history (Lambert, 2002, Houbrechts and Lambert, 2004, Durost, 2005). However, we were lead to adapt or re...

  3. Preliminary Study of Ancient Town Protection and Rural Tourism Development of Caoshi Town in Hengdong County, Hunan Province

    OpenAIRE

    Liu, Tian-zhao; Yang, Zai-tian; Liu Pei-lin

    2012-01-01

    The typical style and features of mountains and waters in Caoshi Ancient Town, have hitherto been well preserved. Caoshi Ancient Town boasts superior base of the natural eco-environment and deep-rooted background of regional culture, where mountains, waters, shoals, towns and other landscape elements are merged harmoniously, the transportation and geographical conditions have been fundamentally changed. Ancient towns, old temples, ancient forests, ancient wells and ancient piers are unique in...

  4. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: An approach to the diagnosis of ancient septicemia

    OpenAIRE

    Drancourt, Michel; Aboudharam, Gérard; Signoli, Michel; Dutour, Olivier; Raoult, Didier

    1998-01-01

    Ancient septicemic plague epidemics were reported to have killed millions of people for 2 millenniums. However, confident diagnosis of ancient septicemia solely on the basis of historical clinical observations is not possible. The lack of suitable infected material has prevented direct demonstration of ancient septicemia; thus, the history of most infections such as plague remains hypothetical. The durability of dental pulp, together with its natural sterility, makes it a suitable material on...

  5. DNA hydration studied by neutron fiber diffraction

    International Nuclear Information System (INIS)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J.

    1994-01-01

    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix

  6. [Herbological study of the botanical origin of Chinese crude drugs "Du-hua" and "Qiang-hua" in ancient China].

    Science.gov (United States)

    Mikage, Masayuki; Ochimori, Akane

    2007-01-01

    The Chinese crude drug Qiang-hua was listed as an alias of Du-hua in Shen-nong-ben-cao-jing, an herbal journal written during the Han Dynasty, China. Du-hua and Qiang-hua are recognized as different herbs in China these days; the main botanical origin of Du-hua is Angelica spp. and that of Qiang-hua is Notopterygium spp., of the family Umbelliferae. To make clear the botanical origins of Du-hua and Qiang-hua in ancient China, the authors made a herbological study. The findings were as follows: the name of Qiang-hua was given to the genuine Du-hua, which is produced in Qiang Province, an ancient province located in northwest China; the botanical origin of Qiang-hua is presumed to be Notopterygium incisum Ting ex H.T. Chang and N. forbesii Boissieu based on both the morphology and habitat written in ancient herbal journals. Both species are prescribed as having the plant origin of Qiang-hua in the present Chinese Pharmacopoeia. Therefore, we concluded that Du-hua and Qiang-hua were essentially the same drug, and were originally derived from the Notopterygium species in ancient China.

  7. Quantum Mechanical Studies of DNA and LNA

    DEFF Research Database (Denmark)

    Koch, Troels; Shim, Irene; Lindow, Morten

    2014-01-01

    Quantum mechanical (QM) methodology has been employed to study the structure activity relations of DNA and locked nucleic acid (LNA). The QM calculations provide the basis for construction of molecular structure and electrostatic surface potentials from molecular orbitals. The topologies...

  8. Archaeomagnetic study of ancient slag mounds in Cyprus: continuous paleointensity curves in high resolution

    Science.gov (United States)

    Shaar, R.; Tauxe, L.; Ben-Yosef, E.; Levy, T. E.; Kassianidou, V.; Lorentzen, B. E.

    2012-12-01

    One of the main challenges in paleointensity research is obtaining continuous high-resolution records that describe the behavior of the geomagnetic field on short time scales. One difficulty in obtaining such records is the problem of precise dating of suitable samples. Another fundamental difficulty is the assessment of the uncertainty involved in the interpretation of paleointensity experiments. Here we present an archaeomagnetic study of ancient slag mounds, which is designed to minimize these difficulties. We study two archaeological slag mounds in the Troodos foothills of Cyprus; one from the massive Roman mines at Skouriotissa, and another pre Roman near Mitsero Kokkinoyia. The mounds consist of industrial layers of copper slag intermixed with charcoal, which were deposited during times of intense copper smelting activity. The slag mound at Skouriotissa represents one of the largest copper production sites in the ancient world, including a 25 m high section and more than 40 archaeological layers. The mound at Mitsero is ca. 10 m high and contains about 32 layers. Hundreds of slag samples and associated charcoals from both mounds were collected, from which more than 600 slag specimens from more than 150 individual samples were analyzed for paleointensity. In addition,19 charcoals were radiocarbon dated. To minimize the uncertainty in the radiocarbon dating we applied a Bayesian model for each mound, which takes into account the relative stratigraphy of the layers. To reduce the uncertainty involved in the subjective interpretation of the paleointensity experiments (conventionally done by manually selecting temperature bounds in the Arai plot of each specimen) we designed new optimization software. The optimization software uses the assumption that paleointensity estimates from samples that were collected from the same level, should be similar. The optimization algorithm finds the selecting criteria that yields minimum scatter within each level, assigns

  9. Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China.

    Science.gov (United States)

    Li, Chunxiang; Ning, Chao; Hagelberg, Erika; Li, Hongjie; Zhao, Yongbin; Li, Wenying; Abuduresule, Idelisi; Zhu, Hong; Zhou, Hui

    2015-07-08

    The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers. Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5. Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

  10. Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process.

    Science.gov (United States)

    Malmström, Helena; Linderholm, Anna; Skoglund, Pontus; Storå, Jan; Sjödin, Per; Gilbert, M Thomas P; Holmlund, Gunilla; Willerslev, Eske; Jakobsson, Mattias; Lidén, Kerstin; Götherström, Anders

    2015-01-19

    The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  11. Experimental study of oxidative DNA damage

    DEFF Research Database (Denmark)

    Loft, S; Deng, Xiaohong; Tuo, J

    1998-01-01

    of the use of 2-nitropropane as a model for oxidative DNA damage relate particularly to formation of 8-aminoguanine derivatives that may interfere with HPLC-EC assays and have unknown consequences. Other model compounds for induction of oxidative DNA damage, such as ferric nitriloacetate, iron dextran...... studies provide powerful tools to investigate agents inducing and preventing oxidative damage to DNA and its role in carcinogenesis. So far, most animal experiments have concerned 8-oxodG and determination of additional damaged bases should be employed. An ideal animal model for prevention of oxidative......Animal experiments allow the study of oxidative DNA damage in target organs and the elucidation of dose-response relationships of carcinogenic and other harmful chemicals and conditions as well as the study of interactions of several factors. So far the effects of more than 50 different chemical...

  12. A comparative study between OSL and TL techniques for the dating of ancient chinese bricks

    International Nuclear Information System (INIS)

    Leung, P.L.; Li, M.; Tang Qiang; Zhang Chunxiang

    2004-01-01

    The single-aliquot regenerative-dose (SAR) protocol to the optically stimulated luminescence (OSL) was applied to measure the paleodose of ancient Chinese bricks with an age range from 180 to 1600 years. In the protocol, sensitivity changes can be corrected by using OSL response to a fixed test dose during measurement. For comparative study between OSL and TL, thermoluminescence (TL) measurement procedures were also applied to determine the paleodose of the bricks. Both results of OSL and TL are in good agreement with, and the paleodose ratios (De OSL /De TL ) are between 0.96 and 1.21, with a mean value of 1.08 ± 0.07. The annual dose of the bricks, estimated by the paleodoses and the known ages, ranges from 5.07 to 6.85 mGy/a, comparable with the measured annual dose values. Therefore, it is concluded that the SAR protocol is a rapid and effective OSL technique to authenticate Chinese bricks. (authors)

  13. A radiologic study of an ancient Egyptian mummy with a prosthetic toe.

    Science.gov (United States)

    Brier, Bob; Vinh, Phuong; Schuster, Michael; Mayforth, Howard; Johnson Chapin, Emily

    2015-06-01

    A radiologic examination (both CT and traditional X-ray) of two mummies curated at the Albany Institute of History and Art revealed the identity of the mummified remains as well as details of the person's life style parameters (markers of occupational stress). These mummies, brought to the Institute over 100 years ago, were unstudied until 1989. This preliminary study led to the misappropriation of the remains, and subsequent switching of the remains within their coffins. Recent and more detailed analyses lead to the correct identification of sex, a re-association of the remains to their interment coffins, as well as a detailed analysis of occupational markers. A prosthetic toe was identified in one of the mummies which lead to the functional exploration of prosthetics in the past including their use as part of funerary processing in ancient Egypt. Finally, details of the embalming process place the wrapped mummy within the time frame identified on the coffin of the mummy identified as Ankhefenmut as well as confirming his social status. © 2015 Wiley Periodicals, Inc.

  14. Luminescence dating of flash flood deposits: a new approach for the chronological study of ancient irrigation perimeters in southern Yemen

    International Nuclear Information System (INIS)

    Balescu, S.; Lamothe, M.; Coque-Delhuille, B.

    1998-01-01

    This study is an attempt to assess the age of ancient irrigation silts from Southern Yemen using the optically stimulated luminescence (OSL) of the constituent K-feldspar grains. This OSL dating method is tested on the al-Haraja irrigation sequence (Wadi Bayhan) which overlies an archaeological occupation level previously dated at 2 203±123 years BP by 14 C. The OSL age estimates range between 2 097±177 years at the bottom of the sequence and 1 555±150 years at the top. This study demonstrates the potential of the luminescence dating method to provide chronological information on the deposition of ancient silts following irrigation in arid environment where 14 C datable material is rare. (authors)

  15. An ancient harbour at Dwarka: Study based on the recent underwater explorations

    Digital Repository Service at National Institute of Oceanography (India)

    Gaur, A; Sundaresh; Tripati, S.

    at the eastern side of Dwarka, served as a safe harbour till the 19th century AD. Offshore explorations have brought to light a large number of stone structures, which appear to be the remains of an ancient jetty. This hypothesis is supported also...

  16. A model system for DNA repair studies

    International Nuclear Information System (INIS)

    Lange, C.S.; Perlmutter, E.

    1984-01-01

    The search for the ''lethal lesion:'' which would yield a molecular explanation of biological survival curves led to attempts to correlate unrepaired DNA lesions with loss of reproductive integrity. Such studies have shown the crucial importance of DNA repair systems. The unrepaired DSB has been sought for such correlation, but in such study the DNA was too large, polydisperse, and/or structurally complex to permit precise measurement of break induction and repair. Therefore, an analog of higher order systems but with a genome of readily measurable size, is needed. Bacteriophage T4 is such an analog. Both its biological (PFU) and molecular (DNA) survival curves are exponentials. Its aerobic /sub PFU/D/sub 37///sub DNA/D/sub 37/ ratio, (410 +- 4.5Gy/540 +- 25 Gy) indicates that 76 +- 4% of lethality at low multiplicity infection (moi 1) the survival is greater than can be explained if the assumption of no parental DSB repair were valid. Both T4 and its host have DSB repair systems which can be studied by the infectious center method. Results of such studies are discussed

  17. HGIS AND ARCHIVE RESEARCHES: A TOOL FOR THE STUDY OF THE ANCIENT MILL CHANNEL OF CESENA (ITALY

    Directory of Open Access Journals (Sweden)

    G. Bitelli

    2016-06-01

    Full Text Available The present study aims to demonstrate the usefulness of GIS to support archive searches and historical studies (e.g. related to industrial archaeology, in the case of an ancient channel for mill powering near Cesena (Emilia-Romagna, Italy, whose history is weaved together with the history of the Compagnia dei Molini di Cesena mill company, the most ancient limited company in Italy. Several historical maps (about 40 sheets in total inherent the studied area and 80 archive documents (drawings, photos, specifications, administrative acts, newspaper articles, over a period of more than 600 years, were collected. Once digitized, historical maps were analysed, georeferenced and mosaicked where necessary. Subsequently, in all the maps the channel with its four mills and the Savio river were vectorized. All the additional archive documents were digitized, catalogued and stored. Using the QGIS open source platform, a Historical GIS was created, encompassing the current cartographic base and all historical maps, with their vectorized elements; each archive document was linked to the proper historical map, so that the document can be immediately retrieved and visualized. In such a HGIS, the maps form the base for a spatial and temporal navigation, facilitated by a specific interface; the external documents linked to them complete the description of the represented elements. This simple and interactive tool offers a new approach to archive searches, as it allows reconstruction in space and time of the evolution of the ancient channel and the history of this important mill company.

  18. Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematics

    NARCIS (Netherlands)

    Pirie, M.D.; Vargas, M.P.B.; Botermans, M.; Bakker, F.T.; Chatrou, L.W.

    2007-01-01

    The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses

  19. SAR interferometry monitoring along the ancient Rome City Walls -the PROTHEGO project case study

    Science.gov (United States)

    Carta, Cristina; Cimino, Maria gabriella; Leoni, Gabriele; Marcelli, Marina; Margottini, Claudio; Spizzichino, Daniele

    2017-04-01

    Led by the Italian Institute for Environmental Protection and Research, in collaboration with NERC British Geological Survey, Geological and Mining Institute of Spain, University of Milano-Bicocca and Cyprus University of Technology, the PROTHEGO project, co-funded in the framework of JPI on Cultural Heritage EU program (2015-2018), brings an innovative contribution towards the analysis of geo-hazards in areas of cultural heritage in Europe. The project apply InSAR techniques to monitor monuments and sites that are potentially unstable due to natural geo-hazard. After the remote sensing investigation, detailed geological interpretation, hazard analysis, local-scale monitoring, advanced modeling and field surveying for some case studies is implemented. The selected case studies are: the Alhambra in Granada (ES); the Choirokoitia village (CY); the Derwent Valley Mills (UK); the Pompei archaeological site and Historical centre of Rome (IT). In this work, in particular, we will focus on ground deformation measurements (obtained by satellite SAR Interferometry) and on their interpretation with respect to the ancient Rome City Walls. The research activities carried out jointly with the Superintendence's technicians, foresee the implementation of a dedicated web GIS platform as a final repository for data storage and spatial data elaboration. The entire circuit of the ancient city walls (both Mura Aureliane and Mura Gianicolensi), was digitalized and georeferenced. All the elements (towers, gates and wall segments) were drawn and collected in order to produce a map of elements at risk. A detailed historical analysis (during the last twenty years) of the ground and structural deformations were performed. A specific data sheet of ruptures was created and fulfilled in order to produce a geographic inventory of past damage. This data sheet contains the following attributes: triggering data; typology of damage; dimension, triggering mechanism; presence of restoration works

  20. DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement

    DEFF Research Database (Denmark)

    Søe, Martin Jensen; Fredensborg, Brian Lund; Nejsum, Peter

    Human worm infections have, to a large extent, been eradicated in countries with high sanitary standards by preventing the fecal-oral transmission of infective eggs. It is possible to study parasite infections among past populations by retrieving and analyzing parasite eggs using paleoparasitolog......-age. Further, eggs of the Liver Fluke (Fasciola hepatica), whose primary hosts are cows and sheep, are identified indicating that grazing animals were kept in close proximity of the settlement....

  1. Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America.

    Science.gov (United States)

    Mitchell, Kieren J; Bray, Sarah C; Bover, Pere; Soibelzon, Leopoldo; Schubert, Blaine W; Prevosti, Francisco; Prieto, Alfredo; Martin, Fabiana; Austin, Jeremy J; Cooper, Alan

    2016-04-01

    The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos ornatus), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears (Tremarctos), South American short-faced bears (Arctotherium) and North American short-faced bears (Arctodus) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears (Arctodus and Arctotherium), potentially as an adaptation to dominate competition for megafaunal carcasses. © 2016 The Author(s).

  2. Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology

    Directory of Open Access Journals (Sweden)

    Dirk-Martin Scheel

    2014-05-01

    Full Text Available Extinctions and declines of large marine vertebrates have major ecological impacts and are of critical concern in marine environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported in 1952, was one of the few marine mammal species to become extinct in historical times. Despite its importance for understanding the evolutionary biogeography of southern phocids, the relationships of M.tropicalis to the two living species of critically endangered monk seals have not been resolved. In this study we present the first molecular data for M. tropicalis, derived from museum skins. Phylogenetic analysis of cytochrome b sequences indicates that M. tropicalis was more closely related to the Hawaiian rather than the Mediterranean monk seal. Divergence time estimation implicates the formation of the Panamanian Isthmus in the speciation of Caribbean and Hawaiian monk seals. Molecular, morphological and temporal divergence between the Mediterranean and “New World monk seals” (Hawaiian and Caribbean is profound, equivalent to or greater than between sister genera of phocids. As a result, we classify the Caribbean and Hawaiian monk seals together in a newly erected genus, Neomonachus. The two genera of extant monk seals (Monachus and Neomonachus represent old evolutionary lineages each represented by a single critically endangered species, both warranting continuing and concerted conservation attention and investment if they are to avoid the fate of their Caribbean relative.

  3. Ancient Egypt

    Science.gov (United States)

    Swamy, Ashwin Balegar

    This thesis involves development of an interactive GIS (Geographic Information System) based application, which gives information about the ancient history of Egypt. The astonishing architecture, the strange burial rituals and their civilization were some of the intriguing questions that motivated me towards developing this application. The application is a historical timeline starting from 3100 BC, leading up to 664 BC, focusing on the evolution of the Egyptian dynasties. The tool holds information regarding some of the famous monuments which were constructed during that era and also about the civilizations that co-existed. It also provides details about the religions followed by their kings. It also includes the languages spoken during those periods. The tool is developed using JAVA, a programing language and MOJO (Map Objects Java Objects) a product of ESRI (Environmental Science Research Institute) to create map objects, to provide geographic information. JAVA Swing is used for designing the user interface. HTML (Hyper Text Markup Language) pages are created to provide the user with more information related to the historic period. CSS (Cascade Style Sheets) and JAVA Scripts are used with HTML5 to achieve creative display of content. The tool is kept simple and easy for the user to interact with. The tool also includes pictures and videos for the user to get a feel of the historic period. The application is built to motivate people to know more about one of the prominent and ancient civilization of the Mediterranean world.

  4. A case study and mechanism investigation of typical mortars used on ancient architecture in China

    International Nuclear Information System (INIS)

    Zeng Yuyao; Zhang Bingjian; Liang Xiaolin

    2008-01-01

    Mortars sampled from Dutifulness Monument, where typical ancient China mortar formulas and manufacturing processes were used, were analyzed by starch-iodine test, FTIR, DSC-TG, SEM and XRD methods. Several modeling samples were then made according to historical records of Chinese ancient mortar formulas and analyzed with the same techniques. The modeling formulas also were used to consolidate loose specimens. The results show that sticky rice plays a crucial role in the microstructure and the consolidation properties of lime mortars. A possible mechanism was suggested that biomineralization may occur during the carbonation of calcium hydroxide, where the sticky rice functions as a template and controls the growth of calcium carbonate crystal. The organic-inorganic materials formed based on this mechanism will be more favorable for consolidating the loose samples both in strength improvement and durability

  5. A case study and mechanism investigation of typical mortars used on ancient architecture in China

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Yuyao [Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang (China); Zhang Bingjian [Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang (China)], E-mail: zbj@mail.hz.zj.cn; Liang Xiaolin [Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang (China)

    2008-07-10

    Mortars sampled from Dutifulness Monument, where typical ancient China mortar formulas and manufacturing processes were used, were analyzed by starch-iodine test, FTIR, DSC-TG, SEM and XRD methods. Several modeling samples were then made according to historical records of Chinese ancient mortar formulas and analyzed with the same techniques. The modeling formulas also were used to consolidate loose specimens. The results show that sticky rice plays a crucial role in the microstructure and the consolidation properties of lime mortars. A possible mechanism was suggested that biomineralization may occur during the carbonation of calcium hydroxide, where the sticky rice functions as a template and controls the growth of calcium carbonate crystal. The organic-inorganic materials formed based on this mechanism will be more favorable for consolidating the loose samples both in strength improvement and durability.

  6. Study on Anti-seismic Strengthening of the Ancient Stone Archway

    Directory of Open Access Journals (Sweden)

    Zhang Ding

    2016-01-01

    Full Text Available Chinese ancient stone archways are in flat structure. And joints of their members are of half tenons and mortises. Under the influence of the earthquake, the resisting ability of archway’s uneven sides is relatively poor and the relevant members have little reliable joints. This paper is to analyze seismic strengthening feasibility of Tiantai mountain stone archway which is damaged from the earthquake and to research on the aspects of the loading mode, structure layout and soundness. On the premise of guaranteeing the authenticity and beauty, we use earthquake damaging mechanism of stone archways and the modern anti-seismic structure designing theory and modern building materials. We also follow the way of the modern construction technology and ancient construction and strengthen the anti-seismic way of the resisting ability of Tiantai mountain stone archway’s uneven sides and joints of tenons and mortises. The best anti-seismic strengthening schemes are put forward as well.

  7. An experimental study on the sound and frequency of the Chinese ancient variable bell

    International Nuclear Information System (INIS)

    Chen Dongsheng; Hu Haining; Xing Lirong; Liu Yongsheng

    2009-01-01

    This paper describes an interesting sound phenomenon from a modern copy of the Chinese ancient variable bell which can emit distinctly different sounds at different temperatures. By means of audition-spectrum analyser software-and PC, the sound signals of the variable bell are collected and the fundamental spectra are shown on the PC. The configuration is simple and cheap, suitable for demonstration and laboratory exercises

  8. An experimental study on the sound and frequency of the Chinese ancient variable bell

    Energy Technology Data Exchange (ETDEWEB)

    Chen Dongsheng; Hu Haining; Xing Lirong; Liu Yongsheng [Department of Maths and Physics, Shanghai University of Electric Power, 200090 Shanghai (China)], E-mail: cds781@hotmail.com

    2009-05-15

    This paper describes an interesting sound phenomenon from a modern copy of the Chinese ancient variable bell which can emit distinctly different sounds at different temperatures. By means of audition-spectrum analyser software-and PC, the sound signals of the variable bell are collected and the fundamental spectra are shown on the PC. The configuration is simple and cheap, suitable for demonstration and laboratory exercises.

  9. Studies of ancient concrete as analogs of cementitious sealing materials for a repository in tuff

    Energy Technology Data Exchange (ETDEWEB)

    Roy, D.M.; Langton, C.A.

    1989-03-01

    The durability of ancient cementitious materials has been investigated to provide data applicable to determining the resistance to weathering of concrete materials for sealing a repository for storage of high-level radioactive waste. Because tuff and volcanic ash are used in the concretes in the vicinity of Rome, the results are especially applicable to a waste repository in tuff. Ancient mortars, plasters, and concretes collected from Rome, Ostia, and Cosa dating to the third century BC show remarkable durability. The aggregates used in the mortars, plasters, and concretes included basic volcanic and pyroclastic rocks (including tuff), terra-cotta, carbonates, sands, and volcanic ash. The matrices of ancient cementitious materials have been characterized and classified into four categories: (1) hydraulic hydrated lime and hydrated lime cements, (2) hydraulic aluminous and ferruginous hydrated lime cements ({plus_minus} siliceous components), (3) pozzolana/hydrated lime cements, and (4) gypsum cements. Most of the materials investigated are in category (3). The materials were characterized to elucidate aspects of the technology that produced them and their response to the environmental exposure throughout their centuries of existence. Their remarkable properties are the result of a combination of chemical, mineralogical, and microstructural factors. Their durability was found to be affected by the matrix mineralogy, particle size, and porosity; aggregate type, grading and proportioning; and the methodology of placement. 30 refs.

  10. Ancient Bedforms

    Science.gov (United States)

    2004-01-01

    18 August 2004 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows groupings of large ripple-like windblown bedforms on the floor of a large crater (larger than the image shown here) in Sinus Sabaeus, south of Schiaparelli Basin. These ripple-like features are much larger than typical wind ripples on Earth, but smaller than typical sand dunes on either planet. Like most of the other ripple-like bedforms in Sinus Sabaeus, they are probably ancient and no longer mobile. Dark streaks on the substrate between the bedforms were formed by passing dust devils. This image is located near 13.0oS, 343.7oW. The image covers an area about 3 km (1.9 mi) across and sunlight illuminates the scene from the upper left.

  11. Genetic diversity among ancient Nordic populations

    DEFF Research Database (Denmark)

    Melchior, Linea Cecilie; Lynnerup, Niels; Siegismund, Hans Redlef

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however...... samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300-3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least...... the ancient Danes (average 13%) than among extant Danes and Scandinavians ( approximately 2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type "diluted" by later immigration events. Interestingly, the two Neolithic...

  12. Mitochondrial DNA study in domestic chicken.

    Science.gov (United States)

    Lan, Dan; Hu, Yaodong; Zhu, Qing; Liu, Yiping

    2017-01-01

    Mitochondrial DNA has the characteristic of quick evolution, matrilineal inheritance, and simple molecular structure, and it serves as the most used marker for molecular study. As an important role of genomics, studying it can help understand the origins, history, and adaptation of domestication. Because of its wide spread popularity, chicken is one of the important domestic animals, which provides humans with a stable source of protein, including both meat and eggs. This article reviews recent studies of chicken mitochondrial DNA. Mitochondrial D-loop and mitochondrial genomics pinpoint the geographic origins of the domestic chicken which was multiple origins; moreover, the mitochondria gene mutation has an association with high-altitude adaptation and the mitochondria-associated diseases' study in poultry is not performed.

  13. Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe.

    Directory of Open Access Journals (Sweden)

    Montserrat Hervella

    Full Text Available BACKGROUND/PRINCIPAL FINDINGS: The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe. METHODOLOGY/SIGNIFICANCE: Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria. In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples and replication of the results (43% of the samples by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe. CONCLUSION: The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different

  14. Resurrection imageries: A study of the motives for extravagant burial rituals in ancient Egypt

    Directory of Open Access Journals (Sweden)

    Jock M. Agai

    2015-03-01

    Full Text Available Unlike in the New Testament whereby faith in Christ can resurrect the dead, the ancient Egyptians believed that the bereaved created the resurrection of their deceased through burial rituals and by encouraging the living to serve their kings. They thought that faith alone in god or the gods was not enough to resurrect the dead, thus they seemingly superimposed resurrection alongside burials. Using the various forms of Egyptian burial rituals and evaluated from the perspective of the Christian concept of resurrection, this researcher attempts to search for the motives behind specific Egyptian burial rituals. The researcher proposes that the activities of the bereaved or of the living over the dead were paramount in resurrecting the dead in ancient Egypt. The purpose of this research is, firstly, to explain how the Egyptian burial rituals influenced their thoughts on resurrection and, secondly, to show that the Egyptian god(s might have depended on the living to raise the dead.Intradisciplinary and/or interdisciplinary implications: The ancient Egyptians lived their lives mainly to satisfy the interests of the dead, hence their extensive burial rituals. Whilst they believed in the power of the gods to raise the dead, there seemed to be another motive behind their burial practices which suggested that the living may have had more power to raise the dead. The power was realised in the activities of the living in the form of burials, tomb designs, mummification, food offering, and in remembering the dead. This research explains that these burial activities were relevant in resurrecting the dead without which the gods alone were not able to do that.

  15. DNA oligonucleotide conformations: high resolution NMR studies

    International Nuclear Information System (INIS)

    Mellema, J.-R.

    1984-01-01

    The present work describes a DNA double-helix model, which is well comparable with the models derived from fibre-diffraction studies. The model has a mononucleotide repeat with torsion angles in accordance with average geometries as derived from 1 H NMR studies. Special attention was paid to reduce the number of short H-H nonbonding contacts, which are abundantly present in the 'classical' fibre-diffraction models. Chapter 3 describes the first complete assignment of a 1 H NMR spectrum of a DNA tetramer, d(TAAT). Preliminary conformational data derived from the spectral parameters recorded at 27 0 C are given. A more detailed analysis employing temperature-dependence studies is given in Chapter 4. (Auth.)

  16. Cytotoxic, DNA binding, DNA cleavage and antibacterial studies of ...

    Indian Academy of Sciences (India)

    All the complexes show excellent efficiency of cleaving DNA than respective fluoroquinolones. Brine shrimp lethality bioassay has been performed to check the cytotoxic activity. The IC50 values of the complexes are in the range of 6.27 to 16.05 μg mL. −1 . Keywords. Ruthenium; fluoroquinolone; LC50; partial intercalation; ...

  17. Ancient shorelines of Gujarat, India, during the Indus civilization (Late Mid-Holocene): A study based on archaeological evidences

    Digital Repository Service at National Institute of Oceanography (India)

    Gaur, A.S.; Vora, K.H.

    to be the ancient ports or centres busy in exploiting the marine resources and clearly suggest migration of shoreline. Several studies have reported changes in sea-levels and shoreline migration with special reference to the Gujarat and Maharashtra coasts 9... at Dholavira. There are evidences of navigation in the Rann of Kachchh during the historical period. The author of Periplus of Erythraean Sea writes ‘Beyond the river Sinthus there is another gulf, not navigable, running in towards the north; it is called...

  18. Study of skin degradation in ancient Egyptian mummies: complementarity of Fourier transform infrared spectroscopy and histological analysis

    Directory of Open Access Journals (Sweden)

    Mariachiara Stani

    2014-01-01

    Full Text Available Some dynastic and pre-dynastic Egyptian mummies from the Giovanni Marro Museum of Anthropology and Ethnography, University of Turin, Italy have been studied by means of the combined approach of both Fourier transform infrared spectroscopy and histological analysis, with the aim of investigating the preservation state of the skin of ancient archaeological remains, as a consequence of the differences between the two kinds of mummification processes, i.e. natural and by means of embalming substances. The results suggest that the balms used in the dynastic mummies embalming process really could have played an important role in the prevention of corpse deterioration.

  19. Ancient DNA Analysis of Mid-Holocene Individuals from the Northwest Coast of North America Reveals Different Evolutionary Paths for Mitogenomes

    Science.gov (United States)

    Cui, Yinqiu; Lindo, John; Hughes, Cris E.; Johnson, Jesse W.; Hernandez, Alvaro G.; Kemp, Brian M.; Ma, Jian; Cunningham, Ryan; Petzelt, Barbara; Mitchell, Joycellyn; Archer, David; Cybulski, Jerome S.; Malhi, Ripan S.

    2013-01-01

    To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast. PMID:23843972

  20. Characterization of cement-based ancient building materials in support of repository seal materials studies

    International Nuclear Information System (INIS)

    Roy, D.M.; Langton, C.A.

    1983-12-01

    Ancient mortars and plasters collected from Greek and Cypriot structures dating to about 5500 BC have been investigated because of their remarkable durability. The characteristics and performance of these and other ancient cementitious materials have been considered in the light of providing information on longevity of concrete materials for sealing nuclear waste geological repositories. The matrices of these composite materials have been characterized and classified into four categories: (1) gypsum cements; (2) hydraulic hydrated lime and hydrated-lime cements; (3) hydraulic aluminous and ferruginous hydrated-lime cements (+- siliceous components); and (4) pozzolana/hydrated-lime cements. Most of the materials investigated, including linings of ore-washing basins and cisterns used to hold water, are in categories (2) and (3). The aggregates used included carbonates, sandstones, shales, schists, volcanic and pyroclastic rocks, and ore minerals, many of which represent host rock types of stratigraphic components of a salt repository. Numerous methods were used to characterize the materials chemically, mineralogically, and microstructurally and to elucidate aspects of both the technology that produced them and their response to the environmental exposure throughout their centuries of existence. Their remarkable properties are the result of a combination of chemical (mineralogical) and microstructural factors. Durability was found to be affected by matrix mineralogy, particle size and porosity, and aggregate type, grading, and proportioning, as well as method of placement and exposure conditions. Similar factors govern the potential for durability of modern portland cement-containing materials, which are candidates for repository sealing. 29 references, 29 figures, 6 tables

  1. Charge transfer through DNA/DNA duplexes and DNA/RNA hybrids: complex theoretical and experimental studies.

    Science.gov (United States)

    Kratochvílová, Irena; Vala, Martin; Weiter, Martin; Špérová, Miroslava; Schneider, Bohdan; Páv, Ondřej; Šebera, Jakub; Rosenberg, Ivan; Sychrovský, Vladimír

    2013-01-01

    Oligonucleotides conduct electric charge via various mechanisms and their characterization and understanding is a very important and complicated task. In this work, experimental (temperature dependent steady state fluorescence spectroscopy, time-resolved fluorescence spectroscopy) and theoretical (Density Functional Theory) approaches were combined to study charge transfer processes in short DNA/DNA and RNA/DNA duplexes with virtually equivalent sequences. The experimental results were consistent with the theoretical model - the delocalized nature of HOMO orbitals and holes, base stacking, electronic coupling and conformational flexibility formed the conditions for more effective short distance charge transfer processes in RNA/DNA hybrids. RNA/DNA and DNA/DNA charge transfer properties were strongly connected with temperature affected structural changes of molecular systems - charge transfer could be used as a probe of even tiny changes of molecular structures and settings. © 2013. Published by Elsevier B.V. All rights reserved.

  2. Analysis of ancient silver coins

    International Nuclear Information System (INIS)

    Flament, Christophe; Marchetti, Patrick

    2004-01-01

    Writing from the numismatist point of view, the authors open this paper by reviewing critically the use of scientific methods for the studies of ancient coins. They also report about an application of the PIXE method at low incident proton energy to one of the most celebrated and known coinage in the ancient history: the Athenian silver coins of the fifth century BC. The results of those analyses indicate that the metallic composition of several coins usually taken as ancient imitations of Athenian coins does not differ from that of the genuine ones. Those analyses confirm what the authors have inferred from numismatic sources: These coins are probably genuinely Athenian

  3. Bacteria in ancient sediments

    International Nuclear Information System (INIS)

    Izzo, G.

    1986-01-01

    In order to ascertain the role of biological activity in ancient sediments, two microbiological studies were carried out. The first was on pleistocenic clay sediments on land, the second on deep oceanic sediments. In the present paper by direct counting the samples is demonstrated the presence of bacteria in a range of 10 5 to 10 7 . Further studies must be carried out to ascertain the activities by in situ incubation methods

  4. Inferring Past Environments from Ancient Epigenomes.

    Science.gov (United States)

    Gokhman, David; Malul, Anat; Carmel, Liran

    2017-10-01

    Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Monitoring Biodiversity using Environmental DNA

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis

    of mammalian DNA in leech guts is shown to persist for at least 4 months post feeding. Subsequently, it is shown that DNA from wild leeches, collected in tropical rainforest in Vietnam, contains DNA from wild mammals living in the area, representing poorly known, cryptic and threatened species. Finally......, a study tests the applicability of non-destructive DNA extraction from old and ancient insect remains. DNA is successfully retrieved, amplified and equenced from dried museum beetle specimens up to 188 years old, ermafrost-preserved macrofossils up to 26.000 years old and directly from 1800-3000 years old...

  6. XRF and micro-PIXE studies of inhomogeneity of ancient bronze and silver alloys

    Science.gov (United States)

    Vasilescu, A.; Constantinescu, B.; Stan, D.; Talmatchi, G.; Ceccato, D.

    2017-09-01

    New results regarding alloy composition and microstructure for a series of ancient bronze and silver items by X-ray Fluorescence and micro-Particle Induced X-ray Emission spectrometry were obtained in the framework of an extensive numismatic project (Scythian-type arrowheads, arrowhead-shaped monetary signs and wheel coins produced by Histria, 7th-4th century of BCE, and Dacian Radulesti-Hunedoara-type silver tetradrachms, 2nd-1st century of BCE). In Histria, warfare arrowheads were used for trade with Barbarian neighbors at first, then mechanically modified, next melted and cast as dedicated monetary signs, being, in the end, replaced by wheel coins. Three different types of alloys have been identified, and Cu-Mn and Cu-Pb segregation shown. In a blank for Radulesti-Hunedoara-type coins, Ag-(Cu+Pb) segregation has been demonstrated, suggesting an imperfectly alloyed silver-leaded bronze.

  7. Response to Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"

    DEFF Research Database (Denmark)

    Gilbert, Marcus Thomas Pius; Miller, Webb; Schuster, Stephan C.

    2008-01-01

    Debruyne et al. challenge the findings of our study and imply that we argue that hair shafts are an overall superior source of ancient DNA than bone. However, the authors are misreading and misinterpreting the conclusions of our study; we claim nothing further than that hair shaft represents an e...

  8. Response to Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"

    DEFF Research Database (Denmark)

    Gilbert, Marcus Thomas Pius; Miller, Webb; Schuster, Stephan C.

    2008-01-01

    Debruyne et al. challenge the findings of our study and imply that we argue that hair shafts are an overall superior source of ancient DNA than bone. However, the authors are misreading and misinterpreting the conclusions of our study; we claim nothing further than that hair shaft represents...

  9. Genetics of the Steller's Sea Cow (Hydrodamalis gigas): A Study of Ancient Bone Material

    Science.gov (United States)

    Crerar, Lorelei D.

    Georg Wilhelm Steller was born 100 years before Darwin in 1709 and he was part of a vast exploration fifty years before Lewis and Clark explored America. Steller was important to the study of marine mammals because he was the only naturalist to see and describe the great northern sea cow ( Hydrodamalis gigas). Knowledge of an extinct population can be used to aid the conservation of a current population. Extraction of DNA from this extinct animal was performed in order to determine the population structure of the Steller's sea cow. A test was also developed that can definitively state whether or not a random bone sample came from H. gigas. This test could be used by the Fish and Wildlife Service (FWS) and the National Oceanic and Atmospheric Administration (NOAA) to examine material distributed in the North Pacific to determine whether samples are legally traded extinct Steller's sea cow or illegally traded extant marine mammal species protected under the Marine Mammal Protection Act (MMPA).

  10. Complexities of Nitrogen Isotope Biogeochemistry in Plant-Soil Systems: Implications for the Study of Ancient Agricultural and Animal Management Practices

    Directory of Open Access Journals (Sweden)

    Paul eSzpak

    2014-06-01

    Full Text Available Nitrogen isotopic studies have potential to shed light on the structure of ancient ecosystems, agropastoral regimes, and human-environment interactions. Until relatively recently, however, little attention was paid to the complexities of nitrogen transformations in ancient plant-soil systems and their potential impact on plant and animal tissue nitrogen isotopic compositions. This paper discusses the importance of understanding nitrogen dynamics in ancient contexts, and highlights several key areas of archaeology where a more detailed understanding of these processes may enable us to answer some fundamental questions. This paper explores two larger themes that are prominent in archaeological studies using stable nitrogen isotope analysis: (1 agricultural practices (use of animal fertilizers, burning of vegetation or shifting cultivation, and tillage and (2 animal domestication and husbandry (grazing intensity/stocking rate and the foddering of domestic animals with cultigens. The paucity of plant material in ancient deposits necessitates that these issues are addressed primarily through the isotopic analysis of skeletal material rather than the plants themselves, but the interpretation of these data hinges on a thorough understanding of the underlying biogeochemical processes in plant-soil systems. Building on studies conducted in modern ecosystems and under controlled conditions, these processes are reviewed, and their relevance discussed for ancient contexts.

  11. Linen in Ancient Egypt

    Directory of Open Access Journals (Sweden)

    dr.Rehab Mahmoud Ahmed Elsharnouby

    2014-01-01

    Full Text Available Egypt was famous through the Ancient Near East for both weaving linen cloth and the produced quantities. Cloth was sent as expensive gifts from one king to another and given to a laborer as wages in return for his work. Cloth was regarded as an essential element in everyday life as it could be used for everything: clothing, bedding, trappings for animals, or sails of a ship. It was in fact one of the most widely used item throughout Ancient Egypt. Although other textile fibers were used in Pharaonic Egypt, namely, sheep's wool, goat hair and a form of coir, the majority of textiles were made from the plant Linum usitatissimum, flax. Cloth made from this fiber is defined as linen. The research starts with a brief definition of the flax, and then reviews the scenes representing the sowing and the harvesting of its seeds. It also focuses on the way of removing the seeds heads, the preparing of the flax for spinning: retting, beating and scutching. After that, it deals with transforming flax into orderly lengths, and rolling it into balls or coils. The researcher as well studies the Ancient Egyptian spinning techniques: grasped spindle, support spindle and drop spinning; the different types of weaving: tabby weaves, basket weaves, tapestry weaves and warps-patterned weave and the types of looms that were in use in Egypt, namely, the horizontal and vertical looms.

  12. Study on the elemental features of ancient Chinese white porcelain at Jingdezhen by INAA

    International Nuclear Information System (INIS)

    Xie Guoxi; Feng Songlin; Feng Xiangqian; Li Yongqiang; Han Hongye; Wang Yanqing; Zhu Jihao; Yan Lingtong; Li Li

    2009-01-01

    Shards of ancient Chinese white porcelain, which were excavated at Maojiawan in the city of Beijing, were analyzed by instrumental neutron activation analysis (INAA). These shards were fired in the period between the Yuan (AD 1271-1368) and Ming (AD 1368-1644) dynasties at Jingdezhen in southern China. According to the analytical results, different raw materials were used for making porcelain body in this period. Fe and Na are the characteristic elements which can be used for identifying the specific date of these porcelains. Furthermore, shards of Hongwu era (AD 1368-1398), Yongle-Xuande era (AD 1403-1435) and Chenghua-Zhengde era (AD 1465-1561) of the Ming dynasty can be clearly distinguished by their elemental body composition. The temporal chemical variation in the porcelain body of these eras is observed. The elemental body composition of Zhengde-Tianshun era (AD 1436-1464) is mainly similar to that of the Hongwu and Yongle-Xuande eras. The temporal chemical feature of Zhengtong-Tianshun era was not found.

  13. A standardless approach of INAA for grouping study of ancient potteries

    International Nuclear Information System (INIS)

    Dasari, K.B.; GITAM University, Visakhapatnam; Acharya, R.; Lakshmana Das, N.; Reddy, A.V.R.

    2012-01-01

    The k 0 based internal monostandard neutron activation analysis was used to analyze 41 ancient pottery samples from three major locations of Andhra Pradesh state, India, belonging to two different age groups namely Megalithic and Buddhist periods. Samples were irradiated with neutron flux obtained from CIRUS reactor and radioactive assay was carried out using a 40% relative efficiency HPGe detector coupled to 8 k MCA. Concentration ratios of 21 elements were calculated with respect to internal monostandard Sc. Absolute concentrations for six (three each from both Megalithic and Buddhist periods) representative samples along with a modern pottery were obtained for comparison. Elemental concentration ratios with respect to Sc were used for grouping of these archaeological samples. Preliminary grouping of these artifacts was done using La/Ce values, and the grouping was confirmed by statistical cluster analysis using eleven selected trace elements. The IAEA RM SL-3 sample was analysed for validation of the method, where in both concentration ratios and absolute concentrations were calculated. (author)

  14. PIXE study on ancient glass samples of the Han dynasty unearthed from Hepu county, Guangxi

    International Nuclear Information System (INIS)

    Zhao Hongxia; Gan Fuxi; Cheng Huansheng

    2007-01-01

    Combining the modified external-beam proton induced X-ray emission (PIXE), inductively coupled plasma atomic emission spectrometry (ICP-AES) and other techniques, the chemical compositions, structures and other properties of some ancient glass samples of the Han Dynasty, which were unearthed from Hepu county, Guangxi, were determined. These glass samples can be classified to several glass systems, such as K 2 O-SiO 2 , PbO-BaO-SiO 2 , PbO-SiO 2 , Na 2 O-K 2 O-PbO-SiO 2 and (Na 2 O)K 2 O-CaO-SiO 2 . But most of the samples belong to K 2 O-SiO 2 system glass. Due to the surface corrosion, the flux K 2 O in the surface of the K 2 O-SiO 2 glass was lost, but with the relative enrichment of the SiO 2 . Based on the characteristics of chemical composition and appearance of these samples, it is thought that, during the Han Dynasty, the making technique of the K 2 O-SiO 2 glass in China was influenced by the technique related to the PbO-BaO-SiO 2 glass from abroad. (authors)

  15. Study on the elemental features of ancient Chinese white porcelain at Jingdezhen by INAA

    Energy Technology Data Exchange (ETDEWEB)

    Xie Guoxi [Institute of High Energy Physics, Chinese Academy of Sciences, 19 Yu Quan Lu, Beijing 100049 (China); Graduated University of Chinese Academy of Sciences, Beijing 100049 (China); Feng Songlin [Institute of High Energy Physics, Chinese Academy of Sciences, 19 Yu Quan Lu, Beijing 100049 (China)], E-mail: fengsl@ihep.ac.cn; Feng Xiangqian [Institute of High Energy Physics, Chinese Academy of Sciences, 19 Yu Quan Lu, Beijing 100049 (China); Li Yongqiang; Han Hongye [Beijing Institute of Cultural Relics, Beijing 100009 (China); Wang Yanqing; Zhu Jihao; Yan Lingtong; Li Li [Institute of High Energy Physics, Chinese Academy of Sciences, 19 Yu Quan Lu, Beijing 100049 (China)

    2009-03-15

    Shards of ancient Chinese white porcelain, which were excavated at Maojiawan in the city of Beijing, were analyzed by instrumental neutron activation analysis (INAA). These shards were fired in the period between the Yuan (AD 1271-1368) and Ming (AD 1368-1644) dynasties at Jingdezhen in southern China. According to the analytical results, different raw materials were used for making porcelain body in this period. Fe and Na are the characteristic elements which can be used for identifying the specific date of these porcelains. Furthermore, shards of Hongwu era (AD 1368-1398), Yongle-Xuande era (AD 1403-1435) and Chenghua-Zhengde era (AD 1465-1561) of the Ming dynasty can be clearly distinguished by their elemental body composition. The temporal chemical variation in the porcelain body of these eras is observed. The elemental body composition of Zhengde-Tianshun era (AD 1436-1464) is mainly similar to that of the Hongwu and Yongle-Xuande eras. The temporal chemical feature of Zhengtong-Tianshun era was not found.

  16. Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics

    NARCIS (Netherlands)

    Paijmans, Johanna L.A.; Barnett, Ross; Gilbert, M. Thomas P.; Zepeda-Mendoza, M. Lisandra; Reumer, Jelle W.F.; de Vos, John; Zazula, Grant; Nagel, Doris; Baryshnikov, Gennady F.; Leonard, Jennifer A.; Rohland, Nadin; Westbury, Michael V.; Barlow, Axel; Hofreiter, Michael

    2017-01-01

    Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of

  17. Multiple maternal origins of native modern and ancient horse populations in China.

    Science.gov (United States)

    Lei, C Z; Su, R; Bower, M A; Edwards, C J; Wang, X B; Weining, S; Liu, L; Xie, W M; Li, F; Liu, R Y; Zhang, Y S; Zhang, C M; Chen, H

    2009-12-01

    To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.

  18. Ancient DNA unravels the truth behind the controversial GUS Greenlandic Norse fur samples: the bison was a horse, and the muskox and beats were goats

    DEFF Research Database (Denmark)

    Sinding, Mikkel-Holger; Arneborg, Jette; Nyegaard, Georg

    2015-01-01

    The Norse Greenlandic archaeological site known as ‘the Farm Beneath the Sand’ (GUS) has sourced many well-preserved and unique archaeological artefacts. Some of the most controversial finds are tufts of hair, which previous morphological-based examination concluded derive from bison, black bear......, brown bear and muskox, all species whose natural presence in South Greenland is unlikely. If true, the consequences are potentially significant, as they could imply Viking trading with, or hunting within, North America. To validate these previous findings, we genetically profiled the samples, through...... mitochondrial 16S DNA analysis. The results revealed that the putative bison was, in fact horse, while the bears and muskox were goat. The results demonstrate the importance of using genetic analyses to validate results derived from morphological analyses on hair, in particular where such studies lead...

  19. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

    DEFF Research Database (Denmark)

    Campos, Paula; Kristensen, Tommy; Orlando, Ludovic Antoine Alexandre

    2010-01-01

    of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two...... Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation...

  20. The Study of Prehistoric Artefacts in National Context: Belgian Archaeologists and the Problem of Ancient Stone Implements

    Directory of Open Access Journals (Sweden)

    Matthew R. Goodrum

    2013-09-01

    Full Text Available During the early nineteenth century European archaeologists were formulating new ideas about the significance of ancient stone artefacts. Some, such as Christian Thomsen in Copenhagen, believed that in Scandinavia, a Stone Age had preceded the Bronze and Iron Ages. In France some excavations had retrieved stone artefacts from deep levels of peat and cave deposits that suggested that these objects were of very great antiquity. While the collection and study of stone artefacts occurred across much of Europe, there were regional variations in their interpretation. Assisted by local institutions and motivated by patriotism, Belgian archaeologists who participated in this research, had much in common with their colleagues elsewhere in Europe, but the nature of local archaeological sites and the ideas of local researchers had an impact on the development and contributions of Belgian prehistoric archaeology.

  1. Lead (Pb) Isotope Baselines for Studies of Ancient Human Migration and Trade in the Maya Region.

    Science.gov (United States)

    Sharpe, Ashley E; Kamenov, George D; Gilli, Adrian; Hodell, David A; Emery, Kitty F; Brenner, Mark; Krigbaum, John

    2016-01-01

    We examined the potential use of lead (Pb) isotopes to source archaeological materials from the Maya region of Mesoamerica. The main objectives were to determine if: 1) geologic terrains throughout the Maya area exhibit distinct lead isotope ratios (206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb), and 2) a combination of lead and strontium ratios can enhance sourcing procedures in the Mesoamerica region. We analyzed 60 rock samples for lead isotope ratios and a representative subset of samples for lead, uranium, and thorium concentrations across the Maya region, including the Northern Lowlands of the Mexican Yucatan Peninsula, the Southern Lowlands of Guatemala and Belize, the Volcanic Highlands, the Belizean Maya Mountains, and the Metamorphic Province/Motagua Valley. Although there is some overlap within certain sub-regions, particularly the geologically diverse Metamorphic Province, lead isotopes can be used to distinguish between the Northern Lowlands, the Southern Lowlands, and the Volcanic Highlands. The distinct lead isotope ratios in the sub-regions are related to the geology of the Maya area, exhibiting a general trend in the lowlands of geologically younger rocks in the north to older rocks in the south, and Cenozoic volcanic rocks in the southern highlands. Combined with other sourcing techniques such as strontium (87Sr/86Sr) and oxygen (δ18O), a regional baseline for lead isotope ratios can contribute to the development of lead isoscapes in the Maya area, and may help to distinguish among geographic sub-regions at a finer scale than has been previously possible. These isotope baselines will provide archaeologists with an additional tool to track the origin and movement of ancient humans and artifacts across this important region.

  2. Lead (Pb Isotope Baselines for Studies of Ancient Human Migration and Trade in the Maya Region.

    Directory of Open Access Journals (Sweden)

    Ashley E Sharpe

    Full Text Available We examined the potential use of lead (Pb isotopes to source archaeological materials from the Maya region of Mesoamerica. The main objectives were to determine if: 1 geologic terrains throughout the Maya area exhibit distinct lead isotope ratios (206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb, and 2 a combination of lead and strontium ratios can enhance sourcing procedures in the Mesoamerica region. We analyzed 60 rock samples for lead isotope ratios and a representative subset of samples for lead, uranium, and thorium concentrations across the Maya region, including the Northern Lowlands of the Mexican Yucatan Peninsula, the Southern Lowlands of Guatemala and Belize, the Volcanic Highlands, the Belizean Maya Mountains, and the Metamorphic Province/Motagua Valley. Although there is some overlap within certain sub-regions, particularly the geologically diverse Metamorphic Province, lead isotopes can be used to distinguish between the Northern Lowlands, the Southern Lowlands, and the Volcanic Highlands. The distinct lead isotope ratios in the sub-regions are related to the geology of the Maya area, exhibiting a general trend in the lowlands of geologically younger rocks in the north to older rocks in the south, and Cenozoic volcanic rocks in the southern highlands. Combined with other sourcing techniques such as strontium (87Sr/86Sr and oxygen (δ18O, a regional baseline for lead isotope ratios can contribute to the development of lead isoscapes in the Maya area, and may help to distinguish among geographic sub-regions at a finer scale than has been previously possible. These isotope baselines will provide archaeologists with an additional tool to track the origin and movement of ancient humans and artifacts across this important region.

  3. Lead (Pb) Isotope Baselines for Studies of Ancient Human Migration and Trade in the Maya Region

    Science.gov (United States)

    Kamenov, George D.; Gilli, Adrian; Hodell, David A.; Emery, Kitty F.; Brenner, Mark; Krigbaum, John

    2016-01-01

    We examined the potential use of lead (Pb) isotopes to source archaeological materials from the Maya region of Mesoamerica. The main objectives were to determine if: 1) geologic terrains throughout the Maya area exhibit distinct lead isotope ratios (206Pb/204Pb, 207Pb/204Pb, and 208Pb/204Pb), and 2) a combination of lead and strontium ratios can enhance sourcing procedures in the Mesoamerica region. We analyzed 60 rock samples for lead isotope ratios and a representative subset of samples for lead, uranium, and thorium concentrations across the Maya region, including the Northern Lowlands of the Mexican Yucatan Peninsula, the Southern Lowlands of Guatemala and Belize, the Volcanic Highlands, the Belizean Maya Mountains, and the Metamorphic Province/Motagua Valley. Although there is some overlap within certain sub-regions, particularly the geologically diverse Metamorphic Province, lead isotopes can be used to distinguish between the Northern Lowlands, the Southern Lowlands, and the Volcanic Highlands. The distinct lead isotope ratios in the sub-regions are related to the geology of the Maya area, exhibiting a general trend in the lowlands of geologically younger rocks in the north to older rocks in the south, and Cenozoic volcanic rocks in the southern highlands. Combined with other sourcing techniques such as strontium (87Sr/86Sr) and oxygen (δ18O), a regional baseline for lead isotope ratios can contribute to the development of lead isoscapes in the Maya area, and may help to distinguish among geographic sub-regions at a finer scale than has been previously possible. These isotope baselines will provide archaeologists with an additional tool to track the origin and movement of ancient humans and artifacts across this important region. PMID:27806065

  4. A multi-analytical approach to gold in Ancient Egypt: Studies on provenance and corrosion

    Energy Technology Data Exchange (ETDEWEB)

    Tissot, I., E-mail: isabeltissot@gmail.com [LIBPhys – UNL, Faculty of Science and Technology, 2829-516 Caparica (Portugal); Department of Physics, Faculty of Sciences, University of Lisbon, Campo Grande, 1649-004 Lisbon (Portugal); Troalen, L.G. [National Museums Scotland, Collections Services Department, 242 West Granton Road, Edinburgh EH5 1JA (United Kingdom); Manso, M. [LIBPhys – UNL, Faculty of Science and Technology, 2829-516 Caparica (Portugal); Faculdade de Belas-Artes da Universidade de Lisboa, Largo da Academia Nacional de Belas-Artes, 1249-058 Lisbon (Portugal); Ponting, M. [Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ (United Kingdom); Radtke, M.; Reinholz, U. [BAM Federal Institute for Materials Research and Testing, Richard-Willstaetter-Strasse 11, 12489 Berlin (Germany); Barreiros, M.A. [LNEG, I.P., Estrada do Paço do Lumiar, 22, 1649-038 Lisbon (Portugal); Shaw, I. [Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ (United Kingdom); Carvalho, M.L. [LIBPhys – UNL, Faculty of Science and Technology, 2829-516 Caparica (Portugal); Guerra, M.F. [ArchAm, UMR 8096 CNRS - Université Paris Sorbonne, MAE, 21 allée de l' Université, 92023 Nanterre (France)

    2015-06-01

    Recent results from a three-year multi-disciplinary project on Ancient Egyptian gold jewellery revealed that items of jewellery from the Middle Kingdom to the New Kingdom were manufactured using a variety of alluvial gold alloys. These alloys cover a wide range of colours and the majority contain Platinum Group Elements inclusions. However, in all the gold foils analysed, these inclusions were found to be absent. In this work a selection of gilded wood and leather items and gold foil fragments, all from the excavations by John Garstang at Abydos (primarily from Middle Kingdom graves), were examined using Scanning Electron Microscopy-Energy Disperse Spectroscopy (SEM-EDS), X-Ray Fluorescence (μXRF), Particle Induced X-Ray Emission (µPIXE) and Double Dispersive X-Ray Fluorescence (D{sup 2}XRF). The work allowed us to characterise the composition of the base-alloys and also to reveal the presence of Pt at trace levels, confirming the use of alluvial gold deposits. Corrosion products were also investigated in the foils where surface tarnish was visually observed. Results showed that the differences in the colour of corrosion observed for the foils are related not only to the thickness of the corrosion layer but also to a multi-layer structure containing the various corrosion products. - Highlights: • Multi-analytical protocol based on techniques with different MDLs and spatial resolution • Application of D{sup 2}XRF developed at synchrotron BESSY II for determination of Pt in Au with a MDL of 1 ppm • Egyptian gold alloys have nanoporous corrosion layers where distinct corrosion phases could be identified. • Egyptian gold foils are made with different gold base alloys, but all containing alluvial gold.

  5. Apps for Ancient Civilizations

    Science.gov (United States)

    Thompson, Stephanie

    2011-01-01

    This project incorporates technology and a historical emphasis on science drawn from ancient civilizations to promote a greater understanding of conceptual science. In the Apps for Ancient Civilizations project, students investigate an ancient culture to discover how people might have used science and math smartphone apps to make their lives…

  6. Non-destructive study of ancient documents and books by means of ion beams; Estudio no destructivo de documentos y libros antiguos mediante haces de iones

    Energy Technology Data Exchange (ETDEWEB)

    Ruvalcaba S, J.L.; Monroy, M. [IFUNAM, A.P. 20-364, 01000 Mexico D.F. (Mexico)

    2004-07-01

    In this work, a non destructive methodology for the analysis of ancient manuscripts and books using an external beam system and the techniques Particle Induced X-ray Emission Spectroscopy (PIXE) and Rutherford Backscattering Spectrometry (RBS) is presented. This application shows the analytical features of the particle accelerator based techniques for the characterization of this kind of historical materials. This methodology was used for the analysis of inks of an European book from XVII century. This is the first study in Mexico of an ancient book using simultaneously PIXE and RBS non-vacuum techniques. (Author) 21 refs., 9 figs.

  7. Suicide in ancient Greece.

    Science.gov (United States)

    Laios, K; Tsoukalas, G; Kontaxaki, M-I; Karamanou, M; Androutsos, G

    2014-01-01

    The theme of suicide appears several times in ancient Greek literature. However, each such reference acquires special significance depending on the field from which it originates. Most of the information found in mythology, but the suicide in a mythological tale, although in terms of motivation and mental situation of heroes may be in imitation of similar incidents of real life, in fact is linked with the principles of the ancient Greek religion. In ancient drama and mainly in tragedies suicide conduces to the tragic hypostasis of the heroes and to the evolution of the plot and also is a tool in order to be presented the ideas of poets for the relations of the gods, the relation among gods and men and the relation among the men. In ancient Greek philosophy there were the deniers of suicide, who were more concerned about the impact of suicide on society and also these who accepted it, recognizing the right of the individual to put an end to his life, in order to avoid personal misfortunes. Real suicides will be found mostly from historical sources, but most of them concern leading figures of the ancient world. Closer to the problem of suicide in the everyday life of antiquity are ancient Greek medicines, who studied the phenomenon more general without references to specific incidents. Doctors did not approve in principal the suicide and dealt with it as insane behavior in the development of the mental diseases, of melancholia and mania. They considered that the discrepancy of humors in the organ of logic in the human body will cause malfunction, which will lead to the absurdity and consequently to suicide, either due to excessive concentration of black bile in melancholia or due to yellow bile in mania. They believed that greater risk to commit suicide had women, young people and the elderly. As therapy they used the drugs of their time with the intention to induce calm and repression in the ill person, therefore they mainly used mandragora. In general, we would say

  8. The application of Flow Cytometry to the study of ancient agriculture: Evidence for Mesolithic farming in Northern Britain 7200 Cal yr BP.

    Science.gov (United States)

    Jones, Richard; Tennant, Richard; Hatton, Jackie; Lee, Rob; Love, John

    2017-04-01

    The onset of agriculture in the UK, (the Mesolithic-Neolithic transition 6000 - 5500 Cal yr BP), has commonly been viewed as the end point of a cultural and technological wave that began in Eastern Europe on the Hungarian Plain 7500 Cal yr BP. This view is not without its critics, due in part to the uncertainty regarding the timing and rate of expansion and the difficulty in identifying the point at which agriculture first arrived in a particular location. Evidence for potential 'episodes' of Mesolithic agricultural activity in the UK has been identified in the UK pollen record, but this data is very tentative. Cereal pollen is typically present in very low concentrations (requiring very large, time consuming counts) and differentiating early cereal pollen from local grasses is very problematic, particularly in areas where the local grasses were domesticated. We present a multi-proxy record from Mere Tarn (54°8'12.09" N 3°7'24.28"W), 2km from the Morecambe Bay coast in South Cumbria, UK; a region with a long history of human occupation extending back into the Palaeolithic. A lacustrine core spanning the Mesolithic and Neolithic has been analysed using a combination of 'traditional' pollen analysis, Flow Cytometry and ancient DNA (aDNA). Flow Cytometry is employed to increase the concentration of cereal type grains in a sample, whilst also providing a more 'targeted' sample for aDNA analysis. The results so far provide clear evidence for an early phase of 'Mesolithic' agriculture in the catchment, spanning only two centuries ( 7300 to 7100 Cal yr BP). This phase is characterised by the occurrence of large cereal type grains (> 38µm), evidence for woodland clearance and the expansion of key anthropogenic indicators such as P. lanceolata. It occurred over 1600 years before the main transition into permanent and intensive agriculture in the catchment, at a time of significant changes in regional climate and sea-level. The results from Mere Tarn provide the earliest

  9. Studies of interaction between two alkaloids and double helix DNA

    International Nuclear Information System (INIS)

    Sun, Yantao; Peng, Tingting; Zhao, Lei; Jiang, Dayu; Cui, Yuncheng

    2014-01-01

    This article presents the study on the interaction of two alkaloids (matrine and evodiamine) and hs-DNA by absorption, fluorescence, circular dichroism (CD), DNA melting and viscosity experiments. The spectroscopic studies suggested that two alkaloids can bind to DNA through an intercalative mode. The viscosity measurement and thermal denaturation also indicated that two alkaloids can intercalate to DNA. The binding constants (K A ) and the number of binding sites (n) were determined. At the same time, some significant thermodynamic parameters of the binding of the alkaloids to DNA were obtained. Competitive binding studies revealed that alkaloids had an effect on ethidium bromide (EB) bound DNA. In addition, it was also proved that the fluorescence quenching was influenced by ionic strength. - Highlights: • Interaction between two alkaloids and DNA is studied by spectral methods. • The binding constant and the binding sites between two alkaloids and DNA are obtained. • There are a classical intercalative mode between alkaloids and DNA. • The binding of matrine with DNA is weaker than that of evodiamine. • It is important for us to understand the alkaloids–DNA interactions at a molecular level

  10. Pharmacogenomic study using bio- and nanobioelectrochemistry: Drug-DNA interaction.

    Science.gov (United States)

    Hasanzadeh, Mohammad; Shadjou, Nasrin

    2016-04-01

    Small molecules that bind genomic DNA have proven that they can be effective anticancer, antibiotic and antiviral therapeutic agents that affect the well-being of millions of people worldwide. Drug-DNA interaction affects DNA replication and division; causes strand breaks, and mutations. Therefore, the investigation of drug-DNA interaction is needed to understand the mechanism of drug action as well as in designing DNA-targeted drugs. On the other hand, the interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. For this purpose, electrochemical methods/biosensors can be used toward detection of drug-DNA interactions. The present paper reviews the drug-DNA interactions, their types and applications of electrochemical techniques used to study interactions between DNA and drugs or small ligand molecules that are potentially of pharmaceutical interest. The results are used to determine drug binding sites and sequence preference, as well as conformational changes due to drug-DNA interactions. Also, the intention of this review is to give an overview of the present state of the drug-DNA interaction cognition. The applications of electrochemical techniques for investigation of drug-DNA interaction were reviewed and we have discussed the type of qualitative or quantitative information that can be obtained from the use of each technique. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Obscuring the ancient artifacts

    International Nuclear Information System (INIS)

    Tugrul, B.

    1987-01-01

    Radiography is a non-destructive method which is preferable for ancient artifacts. X-rays, gama rays, beta rays and neutrons can be used for radiography. Differences of them and application materials can be different. In this study, the radiographic techniques are determined with application parameters according to materials of the artifacts, and some interesting examples are given. Therefore, investigation of the artifacts can be realized for definition of physical properties, manufacturing techniques and quality controls of them easily by the application of the radiography. (author)

  12. Cytotoxic, DNA binding, DNA cleavage and antibacterial studies of ...

    Indian Academy of Sciences (India)

    ofloxacin and sparfloxacin with diverse metal ions.9–17. In continuation of our previous work,18 this paper ... minimum inhibitory concentration (MIC) study has been performed by means of laminar air flow cabinet ..... the volume has been adjusted with artificial seawater to. 2.5 mL per vial. After 24 h. the number of survivors.

  13. Raman spectroscopic study of plasma-treated salmon DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Geon Joon; Kim, Yong Hee; Choi, Eun Ha [Plasma Bioscience Research Center, Kwangwoon University, Seoul 139-701 (Korea, Republic of); Kwon, Young-Wan [Department of Chemistry, Korea University, Seoul 136-701 (Korea, Republic of)

    2013-01-14

    In this research, we studied the effect of plasma treatment on the optical/structural properties of the deoxyribonucleic acid (DNA) extracted from salmon sperm. DNA-cetyltrimethylammonium (CTMA) films were obtained by complexation of DNA with CTMA. Circular dichroism (CD) and Raman spectra indicated that DNA retained its double helical structure in the solid film. The Raman spectra exhibited several vibration modes corresponding to the nuclear bases and the deoxyribose-phosphate backbones of the DNA, as well as the alkylchains of CTMA. Dielectric-barrier-discharge (DBD) plasma treatment induced structural modification and damage to the DNA, as observed by changes in the ultraviolet-visible absorption, CD, and Raman spectra. The optical emission spectra of the DBD plasma confirmed that DNA modification was induced by plasma ions such as reactive oxygen species and reactive nitrogen species.

  14. Insights into Modern Human Prehistory Using Ancient Genomes.

    Science.gov (United States)

    Yang, Melinda A; Fu, Qiaomei

    2018-03-01

    The genetic relationship of past modern humans to today's populations and each other was largely unknown until recently, when advances in ancient DNA sequencing allowed for unprecedented analysis of the genomes of these early people. These ancient genomes reveal new insights into human prehistory not always observed studying present-day populations, including greater details on the genetic diversity, population structure, and gene flow that characterized past human populations, particularly in early Eurasia, as well as increased insight on the relationship between archaic and modern humans. Here, we review genetic studies on ∼45000- to 7500-year-old individuals associated with mainly preagricultural cultures found in Eurasia, the Americas, and Africa. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. DNA-binding, DNA cleavage and cytotoxicity studies of two anthraquinone derivatives.

    Science.gov (United States)

    Gholivand, M B; Kashanian, S; Peyman, H

    2012-02-15

    The interaction of native calf thymus DNA (CT-DNA) with two anthraquinones including quinizarin (1,4-dihydroxy anthraquinone) and danthron (1,8-dihydroxy anthraquinone) in a mixture of 0.04M Brittone-Robinson buffer and 50% of ethanol were studied at physiological pH by spectrofluorometric and cyclic voltammetry techniques. The former technique was used to calculate the binding constants of anthraquinones-DNA complexes at different temperatures. Thermodynamic study indicated that the reactions of both anthraquinone-DNA systems are predominantly entropically driven. Furthermore, the binding mechanisms on the reaction of the two anthraquinones with DNA and the effect of ionic strength on the fluorescence property of the system have also been investigated. The results of the experiments indicated that the binding modes of quinizarin and danthron with DNA were evaluated to be groove binding. Moreover, the cytotoxic activity of both compounds against human chronic myelogenous leukemia K562 cell line and DNA cleavage were investigated. The results indicated that these compounds slightly cleavage pUC18 plasmid DNA and showed minor antitumor activity against K562 (human chronic myeloid leukemia) cell line. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. Environmental DNA calibration study interim technical review report December 2014

    Science.gov (United States)

    Baerwaldt, Kelly; Bartron, Meredith L.; Schilling, Kurt; Lee, Debbie; Russo, Edmond; Estes, Trudy; Fischer, Richard; Fleming, Beth; Guilfoyle, Michael P.; Killgore, Jack; Lance, Richard; Perkins, Edward; Schultz, Martin; Smith, David; Amberg, Jon J.; Chapman, Duane C.; Gaikowski, Mark P.; Klymus, Katy E.; Richter, Cathy

    2015-01-01

    The Environmental DNA Calibration Study (ECALS) is a multi-year study to improve the understanding and interpretation of the detection of Asian carp DNA in environmental samples (eDNA) used in early detection monitoring. eDNA surveillance programs seek to detect the presence of genetic material (DNA in cells sloughed off in slime, feces, urine, etc.) extracted from water samples; the detection of genetic material is linked to the possible presence of Asian carp. The study involves collaboration between the U.S. Army Corps of Engineers, the U.S. Geological Survey, and the U.S. Fish and Wildlife Service. ECALS addresses three major Action Items from the Asian Carp Regional Coordinating Committee (ACRCC) Asian Carp Control Strategy Framework, of which results to date are presented below. Initial ECALS efforts focused on eDNA vectors whereas marker development and calibration experiments received greater attention in 2013.

  17. Ancient celtic horns

    Science.gov (United States)

    Campbell, Murray

    2002-11-01

    There is considerable evidence from iconographic and documentary sources that musical lip-reed instruments were important in the early celtic communities of Scotland and Ireland. In recent years several studies have been undertaken with the aim of gaining a better understanding of the musical nature of these ancient horns, and of their place in the life and culture of the time. A valuable source of tangible evidence is to be found in the archaeological remains deposited across Scotland and the whole of Ireland. A project is now under way, under the auspices of the Kilmartin House Trust and the general direction of John Purser, which has brought together an international team of musicians, craftsmen, archaeologists, musicologists and physicists with the aim of analyzing ancient musical artifacts, reconstructing some of the original instruments, and analyzing the sounds they produce. This paper describes acoustical studies carried out on a number of recent reconstructions of wooden and bronze instruments, and discusses the role of acoustics in this type of investigation. [Work supported by Sciart and EPSRC.

  18. Comparison of two Neolithic mtDNA haplotypes from a Czech excavation site with the results of mitochondrial DNA studies on European Neolithic and Mesolithic individuals

    Czech Academy of Sciences Publication Activity Database

    Votrubová, J.; Emmerová, B.; Brzobohatá, Hana; Šumberová, Radka; Vaněk, D.

    2017-01-01

    Roč. 6, December (2017), „e125”-„e128” ISSN 1875-1768 R&D Projects: GA ČR GB14-36938G Institutional support: RVO:67985912 Keywords : ancient DNA * mtDNA * sequencing * haplotype * haplogroup Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology http://www.fsigeneticssup.com/article/S1875-1768(17)30162-2/pdf

  19. The early colonial atlantic world: New insights on the African Diaspora from isotopic and ancient DNA analyses of a multiethnic 15th-17th century burial population from the Canary Islands, Spain.

    Science.gov (United States)

    Santana, Jonathan; Fregel, Rosa; Lightfoot, Emma; Morales, Jacob; Alamón, Martha; Guillén, José; Moreno, Marco; Rodríguez, Amelia

    2016-02-01

    The Canary Islands are considered one of the first places where Atlantic slave plantations with labourers of African origin were established, during the 15th century AD. In Gran Canaria (Canary Islands, Spain), a unique cemetery dated to the 15th and 17th centuries was discovered adjacent to an ancient sugar plantation with funerary practices that could be related to enslaved people. In this article, we investigate the origin and possible birthplace of each individual buried in this cemetery, as well as the identity and social status of these people. The sample consists of 14 individuals radiocarbon dated to the 15th and 17th centuries AD. We have employed several methods, including the analysis of ancient human DNA, stable isotopes, and skeletal markers of physical activity. 1) the funerary practices indicate a set of rituals not previously recorded in the Canary Islands; 2) genetic data show that some people buried in the cemetery could have North-African and sub-Saharan African lineages; 3) isotopic results suggest that some individuals were born outside Gran Canaria; and 4) markers of physical activity show a pattern of labour involving high levels of effort. This set of evidence, along with information from historical sources, suggests that Finca Clavijo was a cemetery for a multiethnic marginalized population that had being likely enslaved. Results also indicate that this population kept practicing non-Christian rituals well into the 17th century. We propose that this was possible because the location of the Canaries, far from mainland Spain and the control of the Spanish Crown, allowed the emergence of a new society with multicultural origins that was more tolerant to foreign rituals and syncretism. © 2015 Wiley Periodicals, Inc.

  20. Optimal and Sustainable Plant Refurbishment in Historical Buildings: A Study of an Ancient Monastery Converted into a Showroom in Florence

    Directory of Open Access Journals (Sweden)

    Carla Balocco

    2013-04-01

    Full Text Available The aim of this research is to study the possibility and sustainability of retrofit and refurbishment design solutions on historical buildings converted to different uses and often clashing with their original purpose and architectural features. The building studied is an ancient monastery located in the historical center of Florence (Italy. Today the original cloister is covered over by a single glazed pitched roof and used as a fashion showroom. Our proposed solution concerns a reversible and sustainable plant design integrated with an active transparent building casing. The existing glazed pitched roof was reconsidered and re-designed as part of the existing heating, ventilation and air conditioning (HVAC plant system, based on the functioning of an active thermal buffer to control the high heat flow rates and external thermal loads due to solar radiation. Hourly whole building energy analysis was carried out to check the effectiveness and energy sustainability of our proposed solution. Results obtained showed, from the historical-architectural, energy and environmental points of view, its sustainability due to the building-plant system integration and interaction with its location, the external climatic conditions and defined expected uses, in particular with reference to indoor thermal comfort.

  1. Single molecule study of a processivity clamp sliding on DNA

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, T A; Kwon, Y; Johnson, A; Hollars, C; O?Donnell, M; Camarero, J A; Barsky, D

    2007-07-05

    Using solution based single molecule spectroscopy, we study the motion of the polIII {beta}-subunit DNA sliding clamp ('{beta}-clamp') on DNA. Present in all cellular (and some viral) forms of life, DNA sliding clamps attach to polymerases and allow rapid, processive replication of DNA. In the absence of other proteins, the DNA sliding clamps are thought to 'freely slide' along the DNA; however, the abundance of positively charged residues along the inner surface may create favorable electrostatic contact with the highly negatively charged DNA. We have performed single-molecule measurements on a fluorescently labeled {beta}-clamp loaded onto freely diffusing plasmids annealed with fluorescently labeled primers of up to 90 bases. We find that the diffusion constant for 1D diffusion of the {beta}-clamp on DNA satisfies D {le} 10{sup -14} cm{sup 2}/s, much slower than the frictionless limit of D = 10{sup -10} cm{sup 2}/s. We find that the {beta} clamp remains at the 3-foot end in the presence of E. coli single-stranded binding protein (SSB), which would allow for a sliding clamp to wait for binding of the DNA polymerase. Replacement of SSB with Human RP-A eliminates this interaction; free movement of sliding clamp and poor binding of clamp loader to the junction allows sliding clamp to accumulate on DNA. This result implies that the clamp not only acts as a tether, but also a placeholder.

  2. On Ancient Babylonian Algebra and Geometry

    Indian Academy of Sciences (India)

    Introduction. In an earlier article [1] we had discussed some aspects of ancient Babylonian mathematics as deciphered froIn various clay tablets excavated from modern Iraq, viz. the Pythagoras theorem and also the sexagesimal num- ber system prevalent during the ancient Mesopotamian civilization. In this article, we study ...

  3. Amplification success rate of DNA from museum skin collections: a case study of stoats from 18 museums

    Czech Academy of Sciences Publication Activity Database

    Martínková, Natália; Searle, J. B.

    2006-01-01

    Roč. 6, č. 4 (2006), s. 1014-1017 ISSN 1471-8278 Institutional research plan: CEZ:AV0Z60930519 Keywords : ancient DNA * mitochondrial DNA, * Mustela erminea * museum collections * polymerase chain reaction Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.220, year: 2006

  4. Single Molecule Study of DNA Organization and Recombination

    Science.gov (United States)

    Xiao, Botao

    We have studied five projects related to DNA organization and recombination using mainly single molecule force-spectroscopy and statistical tools. First, HU is one of the most abundant DNA-organizing proteins in bacterial chromosomes and participates in gene regulation. We report experiments that study the dependence of DNA condensation by HU on force, salt and HU concentration. A first important result is that at physiological salt levels, HU only bends DNA, resolving a previous paradox of why a chromosome-compacting protein should have a DNA-stiffening function. A second major result is quantitative demonstration of strong dependencies of HU-DNA dissociation on both salt concentration and force. Second, we have used a thermodynamic Maxwell relation to count proteins driven off large DNAs by tension, an effect important to understanding DNA organization. Our results compare well with estimates of numbers of proteins HU and Fis in previous studies. We have also shown that a semi-flexible polymer model describes our HU experimental data well. The force-dependent binding suggests mechano-chemical mechanisms for gene regulation. Third, the elusive role of protein H1 in chromatin has been clarified with purified H1 and Xenopus extracts. We find that H1 compacts DNA by both bending and looping. Addition of H1 enhances chromatin formation and maintains the plasticity of the chromatin. Fourth, the topology and mechanics of DNA twisting are critical to DNA organization and recombination. We have systematically measured DNA extension as a function of linking number density from 0.08 to -2 with holding forces from 0.2 to 2.4 pN. Unlike previous proposals, the DNA extension decreases with negative linking number. Finally, DNA recombination is a dynamic process starting from enzyme-DNA binding. We report that the Int-DBD domain of lambda integrase binds to DNA without compaction at low Int-DBD concentration. High concentration of Int-DBD loops DNA below a threshold force

  5. Study and characterization of an ancient European flint white maize rich in anthocyanins: Millo Corvo from Galicia.

    Science.gov (United States)

    Lago, Chiara; Landoni, Michela; Cassani, Elena; Cantaluppi, Enrico; Doria, Enrico; Nielsen, Erik; Giorgi, Annamaria; Pilu, Roberto

    2015-01-01

    In the second half of the last century, the American dent hybrids began to be widely grown, leading to the disappearance or marginalization of the less productive traditional varieties. Nowadays the characterization of traditional landraces can help breeders to discover precious alleles that could be useful for modern genetic improvement and allow a correct conservation of these open pollinated varieties (opvs). In this work we characterized the ancient coloured cultivar "Millo Corvo" typical of the Spanish region of Galicia. We showed that this cultivar accumulates high amounts of anthocyanins (83.4 mg/100g flour), and by TLC (Thin Layer Chromatography) and HPLC (High Pressure Liquid Chromatography) analysis, we demonstrated that they mainly consisted of cyanidin. Mapping and sequencing data demonstrate that anthocyanin pigmentation is due to the presence of the red color1 gene(r1), a transcription factor driving the accumulation of this pigment in the aleurone layer. Further chemical analysis showed that the kernels are lacking in carotenoids, as confirmed by genetic study. Finally a DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging ability test showed that Millo Corvo, even though lacking carotenoids, has a high antioxidant ability, and could be considered as a functional food due to the presence of anthocyanins.

  6. A positron annihilation study of hydrated DNA

    DEFF Research Database (Denmark)

    Warman, J. M.; Eldrup, Morten Mostgaard

    1986-01-01

    Positron annihilation measurements are reported for hydrated DNA as a function of water content and as a function of temperature (20 to -180.degree. C) for samples containing 10 and 50% wt of water. The ortho-positronium mean lifetime and its intensity show distinct variations with the degree of ...

  7. A positron annihilation study of hydrated DNA

    DEFF Research Database (Denmark)

    Warman, J. M.; Eldrup, Morten Mostgaard

    1986-01-01

    Positron annihilation measurements are reported for hydrated DNA as a function of water content and as a function of temperature (20 to -180.degree. C) for samples containing 10 and 50% wt of water. The ortho-positronium mean lifetime and its intensity show distinct variations with the degree...

  8. Hole transfer in DNA studied by pulse radiolysis

    International Nuclear Information System (INIS)

    Majima, T.; Kawai, K.; Takada, T.

    2003-01-01

    Attention has been paid to charge transfer in DNA with respect to oxidation damage of DNA and nano bio-devices such as DNA molecular wire. We report hole transfer in DNA during pulse radiolysis of molecule-conjugated DNA (M-DNA). Direct measurement of the charge transfer in DNA has never been reported due to the low extinction coefficient of nucleobase radical ions and to difficult definition of nucleobases. We have used M-DNA in which M radical cation has enough extinction coefficient and distinct absorption. Radical cation was generated in M-DNA during pulse radiolysis in water, and hole transfer through DNA was monitored by time-resolved transient absorption spectra of the radical cations. Hole was generated in Py-DNA by pulse radiolysis in water. Hole transfer to Py through DNA was monitored by transient absorption of Py'+ at 465 nm. The hole hopping rate (k) from G-region to Py was determined to be 104 s-1 which decreased with intervening A-T base-pairs between Py and G-region. We suppose that G(-H+)-radical and C(+H+) basepair can alive in DNA more than 100 us and that this long lifetime is responsible to the long-distance hole transfer. The dependence of k against the distance between the G-region and Py led to the slope of 0.3 Angstroms-1 which is due to multi-step k with the smaller distance dependence. On the other hand, beta = 0.6 Angstroms-1 was found for the single-step k in DNA. On the basis of pulse radiolytic studied on various molecule-conjugated DNA, we found that hole transfer between two chromophores (A and B)-conjugated DNA increased with decreasing the distance between A and B and was accelerated slightly with increasing the number of Gs of the bridge between A and B, and that k was modulated by the bridged base sequences. We also found that weak distance dependent hole transfer in DNA by adenine hopping mechanism

  9. Synthesis, characterization, crystal structure and DNA-binding study ...

    Indian Academy of Sciences (India)

    BOLIN

    SYNOPSIS. Synthesis and characterization of four mononuclear eight coordinated cadmium(II) complexes with newly explored carboxamide derivatives and study of interaction with calf-thymus DNA are reported. The results suggest that neutral complexes 2a and 2b bind to DNA in an intercalative mode. On the other hand, ...

  10. Ancient Astronomy in Armenia

    Science.gov (United States)

    Parsamian, Elma S.

    2007-08-01

    The most important discovery, which enriched our knowledge of ancient astronomy in Armenia, was the complex of platforms for astronomical observations on the Small Hill of Metzamor, which may be called an ancient “observatory”. Investigations on that Hill show that the ancient inhabitants of the Armenian Highlands have left us not only pictures of celestial bodies, but a very ancient complex of platforms for observing the sky. Among the ancient monuments in Armenia there is a megalithic monument, probably, being connected with astronomy. 250km South-East of Yerevan there is a structure Zorats Kar (Karahunge) dating back to II millennium B.C. Vertical megaliths many of which are more than two meters high form stone rings resembling ancient stone monuments - henges in Great Britain and Brittany. Medieval observations of comets and novas by data in ancient Armenian manuscripts are found. In the collection of ancient Armenian manuscripts (Matenadaran) in Yerevan there are many manuscripts with information about observations of astronomical events as: solar and lunar eclipses, comets and novas, bolides and meteorites etc. in medieval Armenia.

  11. Mechanisms in ancient Chinese books with illustrations

    CERN Document Server

    Hsiao, Kuo-Hung

    2014-01-01

    This book presents a unique approach for studying mechanisms and machines with drawings that were depicted unclearly in ancient Chinese books. The historical, cultural and technical backgrounds of the mechanisms are explained, and various mechanisms described and illustrated in ancient books are introduced. By utilizing the idea for the conceptual design of modern mechanisms, all feasible designs of ancient mechanisms with uncertain members and joints that meet the technical standards of the subjects’ time periods are synthesized systematically. Ancient Chinese crossbows (the original crossbow and repeating crossbows), textile mechanisms (silk-reeling mechanism, spinning mechanisms, and looms), and many other artisan's tool mechanisms are used as illustrated examples.  Such an approach provides a logical method for the reconstruction designs of ancient mechanisms with uncertain structures. It also provides an innovative direction for researchers to further identify the original structures of mechanisms...

  12. Lipopolythiourea/DNA interaction: A biophysical study

    Czech Academy of Sciences Publication Activity Database

    Kral, Teresa; Leblond, J.; Hof, Martin; Scherman, D.; Hersovici, J.; Mignet, N.

    2010-01-01

    Roč. 148, 1-3 (2010), s. 68-73 ISSN 0301-4622 R&D Projects: GA AV ČR IAA400400621; GA MŠk(CZ) LC06063 Institutional research plan: CEZ:AV0Z40400503 Keywords : lipopolythiourea * FCS * plasmid DNA compaction * 31P NMR Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.108, year: 2010

  13. Astronomical References in Chaucer: What Can Modern Students Learn from Studying Ancient Texts?

    Directory of Open Access Journals (Sweden)

    Victor Kennedy

    2005-06-01

    Full Text Available One of the problems in the field of English literature studies is that, with compartmentalization and specialization, it becomes introspective to the point where it devolves into the study of metafiction and metacriticism. At its heart, however, literature has to be about something: Thackeray claimed its subject is human nature, but human nature is based in the interface between human and nature. This paper explores some of the problems in the interface between human knowledge, institutions, and nature, and will offer an example of cross-disciplinary, historical study to illustrate a well-known but, to most modern readers, impenetrable medieval text, Chaucer’s Treatise on the Astrolabe. It ends with three recommendations: look to history, cross boundaries between academic fields, and use practical, as well as theoretical, teaching methods.

  14. An experimental study of velocities under pressure for ancient oceanic rocks

    Digital Repository Service at National Institute of Oceanography (India)

    Sarma, K.V.L.N.S.

    Seismic velocities of Indus suture rock types from Dras-Sanko-Kargil, Kashmir Himalaya, as a function of pressure up to 10 kbar were studied. The high-pressure measurements on the rocks reflect the depthwise increase in velocity, and in general...

  15. Estimation of otitis media in ancient populations: A study of past and present Greenlandic Inuit

    DEFF Research Database (Denmark)

    Homøe, P; Lynnerup, N; Skovgaard, Lene Theil

    1996-01-01

    Examination of disease patterns in the past has often been difficult due to lack of morphological evidence. This study presents a new unbiased method for estimation of occurrence of infectious middle ear disease (IMED) in childhood. The method is based on the relation between IMED in childhood an...

  16. Was Pythagoras Chinese? An Examination of Right Triangle Theory in Ancient China. The Pennsylvania State University Studies No. 40.

    Science.gov (United States)

    Swetz, Frank J.; Kao, T. I.

    This book is primarily a scholarly monograph on ancient Chinese theory and application concerning the right triangle, based on evidence contained in classical mathematics texts and scrolls. It is also the first complete English translation of the ninth chapter of the Chiu chang suan chu, the richest source of problems from antiquity dealing with…

  17. A Moessbauer study of an ancient pottery figure (Western-Han Dynasty)

    International Nuclear Information System (INIS)

    Zhou Yan; Dai Kaimei; Liu Rongchuan; Hsia Yuanfu; Jiang Zanchu

    1992-01-01

    The grey pottery figure manufactured in the Western-Han Dynasty (175-118 B.C.) and the clay gathered from the same site of Beidongshan in Xuzhou have been studied by X-ray Diffration (XRD), X-ray Fluorescence (XRF), and Moessbauer spectroscopy. They were simultaneously fired under the same conditions in different atmospheres at various temperature up to 1100degC. This study deals with the original firing atmosphere, original firing temperature and its provenance. The information mentioned above can be inferred from the method of the refiring pottery and the firing clay. The results of the original firing temperature deduced from both of them are in goodself agreement. It is found that the values of the Moessbauer parameters for the unrefired pottery figure are approximately the same as those for the clay fired at 950degC for five hours in a reduced atmosphere. The XRF analysis confirmed the locality of this pottery figure. (orig.)

  18. Studies of Ancient Russian Cultural Objects Using the Neutron Tomography Method

    Directory of Open Access Journals (Sweden)

    Sergey Kichanov

    2018-01-01

    Full Text Available Neutron radiography and tomography is a non-destructive method that provides detailed information about the internal structure of cultural heritage objects. The differences in the neutron attenuation coefficients of constituent elements of the studied objects, as well as the application of modern mathematical algorithms to carry out three-dimensional imaging data analysis, allow one to obtain unique information about the spatial distribution of different phases, the presence of internal defects, or the degree of structural degradation inside valuable cultural objects. The results of the neutron studies of several archaeological objects related to different epochs of the Russian history are reported in order to demonstrate the opportunities provided by the neutron tomography method. The obtained 3D structural volume data, as well as the results of the corresponding data analysis, are presented.

  19. An ancient satellite DNA has maintained repetitive units of the original structure in most species of the living fossil plant genus Zamia.

    Science.gov (United States)

    Cafasso, Donata; Chinali, Gianni

    2014-03-01

    ZpS1 satellite DNA is specific to the genus Zamia and presents repetitive units organized as long arrays and also as very short arrays dispersed in the genome. We have characterized the structure of the ZpS1 repeats in 12 species representative of the whole geographic distribution of the genus. In most species, the clone most common sequences (cMCS) were so similar that a general most common sequence (GMCS) of the ZpS1 repetitive unit in the genus could be obtained. The few partial variations from the GMCS found in cMCS of some species correspond to variable positions present in most other species, as indicated by the clone consensus sequences (cCS). Two species have an additional species-specific variety of ZpS1 satellite. The dispersed repeats were found to contain more mutations than repeats from long arrays. Our results indicate that all or most species of Zamia inherited the ZpS1 satellite from a common ancestor in Miocene and have maintained repetitive units of the original structure till present. The features of ZpS1 satellite in the genus Zamia are poorly compatible with the model of concerted evolution, but they are perfectly consistent with a new model of satellite evolution based on experimental evidences indicating that a specific amplification-substitution repair mechanism maintains the homogeneity and stability of the repeats structure in each satellite DNA originally present in a species as long as the species exists.

  20. DNA-lipid systems: A physical chemistry study

    Directory of Open Access Journals (Sweden)

    R. Dias

    2002-05-01

    Full Text Available It is well known that the interaction of polyelectrolytes with oppositely charged surfactants leads to an associative phase separation; however, the phase behavior of DNA and oppositely charged surfactants is more strongly associative than observed in other systems. A precipitate is formed with very low amounts of surfactant and DNA. DNA compaction is a general phenomenon in the presence of multivalent ions and positively charged surfaces; because of the high charge density there are strong attractive ion correlation effects. Techniques like phase diagram determinations, fluorescence microscopy, and ellipsometry were used to study these systems. The interaction between DNA and catanionic mixtures (i.e., mixtures of cationic and anionic surfactants was also investigated. We observed that DNA compacts and adsorbs onto the surface of positively charged vesicles, and that the addition of an anionic surfactant can release DNA back into solution from a compact globular complex between DNA and the cationic surfactant. Finally, DNA interactions with polycations, chitosans with different chain lengths, were studied by fluorescence microscopy, in vivo transfection assays and cryogenic transmission electron microscopy. The general conclusion is that a chitosan effective in promoting compaction is also efficient in transfection.

  1. [Civilization of Song Dynasty and studies on the rearrangement of ancient literatures of TCM].

    Science.gov (United States)

    Cai, Y M; Li, Y

    1999-10-01

    The features and causes of flourishing of Song civilization were dealt with from the viewpoints of style of learning, art and literature etc., were explored based on contemporaneous political and economical factors. The achievements in the study and systematization are explained through the collection, collation, and research on TCM books. The relationship between the highly cultural prosperity and systematization of Song TCM books is also analyzed on the characteristics of Song civilization. Based on these backgrounds, the features of systemtization of Song TCM books and its influence on the development of medicine in the Song dynasty are also discussed.

  2. A Mössbauer study of an ancient pottery figure (Western-Han dynasty)

    Science.gov (United States)

    Zhou, Yan; Dai, Kaimei; Liu, Rongchuan; Hsia, Yuanfu; Jiang, Zanchu

    1992-04-01

    The grey pottery figure manufactured in the Western-Han Dynasty (175-118 B.C.) and the clay gathered from the same site of Beidongshan in Xuzhou have been studied by X-ray Diffraction(XRD). X-ray Fluorescence (XRF), and Mössbauer spectroscopy. They were simultaneously fired under the same conditions in different atmospheres at various temperature up to 1100°C. This study deals with the original firing atmosphere, original firing temperature and its provenance. The information mentioned above can be inferred from the method of the refiring pottery and the firing clay. The results of the original firing temperature deduced from both of them are in goodself agreement. It is found that the values of the Mössbauer parameters for the unrefired pottery figure are approximately the same as those for the clay fired at 950°C for five hours in a reduced atmosphere. The XRF analysis confirmed the locality of this pottery figure.

  3. Ancient Chinese Sundials

    Science.gov (United States)

    Deng, Kehui

    Timekeeping was essential in the agricultural society of ancient China. The use of sundials for timekeeping was associated with the use of the gnomon, which had its origin in remote antiquity. This chapter studies three sundials (guiyi 晷仪) from the Qin and Han dynasties, the shorter shadow plane sundial (duanying ping yi 短影平仪) invented by Yuan Chong in the Sui Dynasty, and the sundial chart (guiyingtu 晷影图) invented by Zeng Minxing in the Southern Song dynasty. This chapter also introduces Guo Shoujing's hemispherical sundial (yang yi 仰仪). A circular stone sundial discovered at the Small Wild Goose Pagoda in Xi'an is also mentioned. It is dated from the Sui and Tang dynasties. A brief survey of sundials from the Qing dynasty shows various types of sundials.

  4. Characterization of Ancient Tripitaka

    Directory of Open Access Journals (Sweden)

    Y. X. Gong

    2015-08-01

    Full Text Available Tripitaka is the world’s most comprehensive version of Buddhist sutra. There are limited numbers of Tripitaka currently preserved, most of them present various patterns of degradation. As little is known about the materials and crafts used in Tripitaka, it appeared necessary to identify them, and to further define adapted conservation treatment. In this work, a study concerning the paper source and dyestuff of the Tripitaka from approximate 16th century was carried out using fiber analysis and thin-layer chromatography (TLC. The results proved that the papers were mainly made from hemp or bark of mulberry tree, and indigo was used for colorizing the paper. At the end, we provide with suggestions for protecting and restoring the ancient Tripitaka.

  5. Study of ancient Islamic gilded pieces combining PIXE-RBS on external microprobe with sem images

    International Nuclear Information System (INIS)

    Ynsa, M.D.; Gutierrez, P.C.; Enguita, O.; Chamon, J.; Pardo, A.I.; Arroyo, M.; Barrio, J.; Gomez-Morilla, I.; Ferretti, M.; Climent-Font, A.

    2008-01-01

    Numerous metallic objects with very aesthetic and technological qualities have been recovered by archaeological excavations. Adequate processes of restoration and conservation treatments require the accurate determination of the elemental composition and distribution within the objects, as well as the identification of the nature and distribution of the corrosion products. Ideally the identification method should cause no alteration in the sample. In this work, different archaeological pieces with a gilded look have been characterized using simultaneously PIXE and RBS at the CMAM external microprobe in order to study the gilding metalworking done in the Iberian Peninsula during the Middle Ages. The gold layer thickness and its elemental concentrations of Ag, Au and Hg were determined by both techniques and compared with the scanning electron microscopy images obtained for some fragments of pieces. (orig.)

  6. The Traveling Optical Scanner – Case Study on 3D Shape Models of Ancient Brazilian Skulls

    DEFF Research Database (Denmark)

    Trinderup, Camilla Himmelstrup; Dahl, Vedrana Andersen; Gregersen, Kristian Murphy

    2016-01-01

    , inoffensive and inexpensive 3D scanning modality based on structured light, suitable for capturing the morphology and the appearance of specimens. Benefits of having 3D models are manifold. The 3D models are easy to share among researchers and can be made available to the general public. Advanced...... morphological modelling is possible with accurate description of the specimens provided by the models. Furthermore, performing studies on models reduces the risk of damage to the original specimen. In our work we employ a high resolution structured light scanner for digitalizing a collection of 8500 year old...... human skulls from Brazil. To evaluate the precision of our setup we compare the structured light scan to micro-CT and achieve submillimetre difference. We analyse morphological features of the Brazilian skulls using manual landmarks, but a research goal is to automate this, fully utilize the dense 3D...

  7. An integrated study for mapping the moisture distribution in an ancient damaged wall painting.

    Science.gov (United States)

    Capitani, Donatella; Proietti, Noemi; Gobbino, Marco; Soroldoni, Luigi; Casellato, Umberto; Valentini, Massimo; Rosina, Elisabetta

    2009-12-01

    An integrated study of microclimate monitoring, IR thermography (IRT), gravimetric tests and portable unilateral nuclear magnetic resonance (NMR) was applied in the framework of planning emergency intervention on a very deteriorated wall painting in San Rocco church, Cornaredo (Milan, Italy). The IRT investigation supported by gravimetric tests showed that the worst damage, due to water infiltration, was localized on the wall painting of the northern wall. Unilateral NMR, a new non-destructive technique which measures the hydrogen signal of the moisture and that was applied directly to the wall, allowed a detailed map of the distribution of the moisture in the plaster underlying the wall panting to be obtained. With a proper calibration of the integral of the recorded signal with suitable specimens, each area of the map corresponded to an accurate amount of moisture. IRT, gravimetric tests and unilateral NMR applied to investigate the northern wall painting showed the presence of two wet areas separated by a dry area. The moisture found in the lower area was ascribed to the occurrence of rising damp at the bottom of the wall due to the slope of the garden soil towards the northern exterior. The moisture found in the upper area was ascribed to condensation phenomena associated with the presence of a considerable amount of soluble, hygroscopic salts. In the framework of this integrated study, IRT investigation and gravimetric methods validated portable unilateral NMR as a new analytical tool for measuring in situ and without any sampling of the distribution and amount of moisture in wall paintings.

  8. Dating a composite ancient wooden artefact and its modifications. A case study

    International Nuclear Information System (INIS)

    Poldi, G.; Quartana, L.; Galli, A.

    2008-01-01

    The recent restoration of the large wooden doors of the medieval St. Ambrogio Basilica in Milan gave the opportunity for a, broad project of scientific examination, including dating with radiocarbon and dendrochronology. The two doors represented a puzzle for art historians, because of the non-documented modifications occurred during their history. In fact; they are composed of various wooden elements, some of them surely modified with the 1750 jubilee restoration, assembled into three layers. The large number of these elements suggested not to restrict the samples only to the main carved scenes, but to extend them to frames and back-boards, in order to obtain a consistent set. of data, and a more reliable chronology. Analytical campaign oriented to dating, coordinated by Quartana Restauri and LAM (University of Bergamo), took into account the different characteristics of woods, needing 24 samples carefully extracted from hidden areas to be radiocarbon dated by ANIS (Accelerator Mass Spectrometry) at CEDAD (Centre for Dating and Diagnostics, University of Salento, Lecce, Italy) laboratories, and two of them dated at LABEC (Laboratory of nuclear techniques for cultural heritage, University of Florence and INFN, Italy) for comparison. The results obtained for the vertical woods of the back, belonging to Renaissance period, suggested further studies employing dendrochronological analyses based on high-resolution photographs, carried out by CUDaM (University of Milano-Bicocca). ED-XRF (Energy Dispersive X-ray Fluorescence) analyses were also carried on, by LAM, with portable instruments. in order to study the composition of the residues of polychromy, where present.

  9. Study of materials and technology of ancient floor mosaics' substrate

    Directory of Open Access Journals (Sweden)

    Vincenzo Starinieri

    2008-01-01

    Full Text Available A floor mosaic's substrate is composed of a variety of preparatory layers of mortar built on natural levelled ground or on top of a previous pavement. Mosaics' substrates differ one from the other in number, thickness and nature of the mortar layers. In this sense, it has been considered relevant to state how these differences are related with historical period, geographical position, function of the pavements within the building, technology of the substrates. A number of floor mosaics' substrates of Hellenistic and Roman period from archaeological sites in Greece and Italy are under study. The stratigraphy of substrates is recorded in situ, and samples from each mortar layer are analysed in the laboratory by means of different techniques. Results obtained so far indicate that characteristics of the Roman substrates mortar layers are clearly dependant on their position in the substrate stratigraphy, whereas in the case of the Hellenistic substrates, characteristics of the mortar layers are less varying with the stratigraphic position. Furthermore results show that floor mosaics' substrates are different according to the function of the pavement in the building.

  10. SEM morphological studies of carbonates and the search for ancient life on Mars

    Science.gov (United States)

    D'Elia, M.; Blanco, A.; Galiano, A.; Orofino, V.; Fonti, S.; Mancarella, F.; Guido, A.; Russo, F.; Mastandrea, A.

    2017-04-01

    Next space missions will investigate the possibility of extinct or extant life on Mars. Studying the infrared spectral modifications, induced by thermal processing on different carbonate samples (recent shells and fossils of different ages), we developed a method able to discriminate biogenic carbonates from their abiogenic counterparts. The method has been successfully applied to microbialites, i.e. bio-induced carbonates deposits, and particularly to stromatolites, the laminated fabric of microbialites, some of which can be ascribed to among the oldest traces of biological activity known on Earth. These results are of valuable importance since such carbonates are linked to primitive living organisms that can be considered as good analogues for putative Martian life forms. Considering that the microstructures of biogenic carbonate are different from those of abiogenic origin, we investigated the micromorphology of shells, skeletal grains and microbialites at different scale with a scanning electron microscope. The results show that this line of research may provide an alternative and complementary approach to other techniques developed in the past by our group to distinguish biotic from abiotic carbonates. In this paper, we present some results that can be of valuable interest since they demonstrate the utility for a database of images concerning the structures and textures of relevant carbonate minerals. Such data may be useful for the analysis of Martian samples, coming from sample return missions or investigated by future in situ explorations, aimed to characterize the near-subsurface of Mars in search for past or present life.

  11. Geomicrobiological study of modern microbialites from Mexico: towards a better understanding of the ancient fossil record

    Directory of Open Access Journals (Sweden)

    Benzerara K.

    2014-02-01

    Full Text Available Microbialites are sedimentary formations that are found throughout the geological record and are usually considered as one of the oldest traces of life on Earth. Although they have been known for more than a century and hold as an emblematic object in Earth Sciences, we yet do not understand in details how they form and how microbial processes impact their chemistry, structure and macroscopic morphology. Here, we show recent advances achieved owing to funding provided by the EPOV program on the formation of modern microbialites in the crater Lake Alchichica (Mexico. We first show that very diverse microbial communities populate these microbialites, including diverse microbial groups able to induce carbonate precipitation. We demonstrate that this microbial diversity can be preserved for several years in laboratory aquaria offering a nice opportunity for future studies to assess the relationships between biodiversity and microbialite formation. We then detail the textural modifications affecting cyanobacterial cells during the first steps of fossilization as captured in Alchichica microbialites. Finally, we report the discovery of a new deepbranching cyanobacterium species, Candidatus Gloeomargarita lithophora, able to form intracellular Ca-, Mg-, Sr- and Ba-rich carbonates and discuss the implications for the interpretation of the fossil record.

  12. Scanning tunneling spectroscopy study of DNA conductivity

    Czech Academy of Sciences Publication Activity Database

    Kratochvílová, Irena; Král, Karel; Bunček, M.; Nešpůrek, Stanislav; Todorciuc, Tatiana; Weiter, M.; Navrátil, J.; Schneider, Bohdan; Pavluch, J.

    2008-01-01

    Roč. 6, č. 3 (2008), s. 422-426 ISSN 1895-1082 R&D Projects: GA AV ČR KAN401770651; GA MŠk OC 137; GA AV ČR KAN400720701; GA AV ČR KAN200100801 Institutional research plan: CEZ:AV0Z10100520; CEZ:AV0Z40500505; CEZ:AV0Z40550506 Keywords : molecular electronics * DNA * scanning tunneling microscopy * conductivity * charge carrier transport Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.448, year: 2008

  13. Saccharomyces cerevisiae-based system for studying clustered DNA damages

    Energy Technology Data Exchange (ETDEWEB)

    Moscariello, M.M.; Sutherland, B.

    2010-08-01

    DNA-damaging agents can induce clustered lesions or multiply damaged sites (MDSs) on the same or opposing DNA strands. In the latter, attempts to repair MDS can generate closely opposed single-strand break intermediates that may convert non-lethal or mutagenic base damage into double-strand breaks (DSBs). We constructed a diploid S. cerevisiae yeast strain with a chromosomal context targeted by integrative DNA fragments carrying different damages to determine whether closely opposed base damages are converted to DSBs following the outcomes of the homologous recombination repair pathway. As a model of MDS, we studied clustered uracil DNA damages with a known location and a defined distance separating the lesions. The system we describe might well be extended to assessing the repair of MDSs with different compositions, and to most of the complex DNA lesions induced by physical and chemical agents.

  14. Antimicrobial activity, cytotoxicity and DNA binding studies of carbon dots

    Science.gov (United States)

    Jhonsi, Mariadoss Asha; Ananth, Devanesan Arul; Nambirajan, Gayathri; Sivasudha, Thilagar; Yamini, Rekha; Bera, Soumen; Kathiravan, Arunkumar

    2018-05-01

    In recent years, quantum dots (QDs) are one of the most promising nanomaterials in life sciences community due to their unexploited potential in biomedical applications; particularly in bio-labeling and sensing. In the advanced nanomaterials, carbon dots (CDs) have shown promise in next generation bioimaging and drug delivery studies. Therefore the knowledge of the exact nature of interaction with biomolecules is of great interest to designing better biosensors. In this study, the interaction between CDs derived from tamarind and calf thymus DNA (ct-DNA) has been studied by vital spectroscopic techniques, which revealed that the CDs could interact with DNA via intercalation. The apparent association constant has been deduced from the absorption spectral changes of ct-DNA-CDs using the Benesi-Hildebrand equation. From the DNA induced emission quenching experiments the apparent DNA binding constant of the CDs (Kapp) have also been evaluated. Furthermore, we have analyzed the antibacterial and antifungal activity of CDs using disc diffusion assay method which exhibited excellent activity against E. coli and C. albicans with inhibition zone in the range of 7-12 mm. The biocompatible nature of CDs was confirmed by an in vitro cytotoxicity test on L6 normal rat myoblast cells by using MTT assay. The cell viability is not affected till the high dosage of CDs (200 μg/mL) for >48 h. As a consequence of the work, future development of CDs for microbial control and DNA sensing among the various biomolecules is possible in view of emerging biofields.

  15. Historical analysis of rainfall-triggered rockfalls: the case study of the disaster of the ancient hydrothermal Sclafani Spa (Madonie Mts, northern-central Sicily, Italy) in 1851

    Science.gov (United States)

    Contino, Antonio; Bova, Patrizia; Esposito, Giuseppe; Giuffré, Ignazio; Monteleone, Salvatore

    2017-12-01

    In 1851, the region of Sicily experienced many rainstorm-induced landslides. On 13 March 1851, a rainstorm brought about a severe rockfall disaster near the small town of Sclafani (Madonie Mountains, northern-central Sicily, Italy). Rocks detached from the carbonate crest of Mt Sclafani (813 m above sea level) and fell downslope, causing the collapse of the ancient hydrothermal spa (about 430 m above sea level) and burying it. Fortunately, there were no injuries or victims. Given its geological, geomorphological and tectonic features, the calcareous-dolomitic and carbonate-siliciclastic relief of Mt Sclafani is extremely prone to landsliding. This study combines the findings of detailed geological and geomorphological field surveys and of a critical review of documentary data. A thorough analysis of documentary sources and historical maps made it possible to identify the location (previously unknown) of the ancient spa. The rockfall dynamics was reconstructed by comparing field reconnaissance data and documentary sources. The 1851 event reconstruction is an example of the application of an integrated methodological approach, which can yield a propaedeutic, yet meaningful picture of a natural disaster, paving the way for further research (e.g. slope failure susceptibility, future land-use planning, protection of thermal springs and mitigation of the impact of similar disasters in this area). Indeed, the intensification of extreme weather events, caused by global warming induced by climate change, has increased the risk of recurrence of a catastrophic event, like that of the ancient Sclafani spa, which is always a potential threat.

  16. Business Managers in Ancient Rome: A Social and Economic Study of Institores, 200 B.C. - A.D. 250

    OpenAIRE

    Aubert, Jean-Jacques

    2008-01-01

    Business Managers in Ancient Rome deals with the law of indirect agency in the classical period and explores the technical aspects and historical development of a set of praetorian remedies (actionesadiecticixqualitatis}, their role in the economy and their incidence on the society. The first part (Chapters 1-2) examines the picture of business managers (institores) yielded by literary and juridical sources. The second part (Chapters 3-5) focuses on the role of such managers in various sector...

  17. Development of a defined-sequence DNA system for use in DNA misrepair studies

    International Nuclear Information System (INIS)

    Sutton, S.; Tobias, C.A.

    1984-01-01

    The authors have developed a system that allows them to study cellular DNA repair processes at the molecular level. In particular, the authors are using this system to examine the consequences of a misrepair of radiation-induced DNA damage, as a function of dose. The cells being used are specially engineered haploid yeast cells. Maintained in the cells, at one copy per cell, is a cen plasmid, a plasmid that behaves like a functional chromosome. This plasmid carries a small defined sequence of DNA from the E. coli lac z gene. It is this lac z region (called the alpha region) that serves as the target for radiation damage. Two copies of the complimentary portion of the lac z gene are integrated into the yeast genome. Irradiated cells are screened for possible mutation in the alpha region by testing the cells' ability to hydrolyze xgal, a lactose substrate. The DNA of interest is then extracted from the cells, sequenced, and the sequence is compared to that of the control. Unlike the usual defined-sequence DNA systems, theirs is an in vivo system. A disadvantage is the relatively high background mutation rate. Results achieved with this system, as well as future applications, are discussed

  18. Study of the activity of DNA polymerases β and λ using 5-formyluridine containing DNA substrates

    Directory of Open Access Journals (Sweden)

    Lavrik O. I.

    2012-06-01

    Full Text Available Aim. To investigate the TLS-activity of human DNA polymerases β and λ (pols β and λ using 5-formyluridine (5-foU containing DNA duplexes which are imitating the intermediates during replication of the leading DNA strand, and to study the influence of replication factors hRPA and hPCNA on this activity. Methods. The EMSA and the methods of enzyme’s kinetics were used. Results. The capability of pols β and λ to catalyze DNA synthesis across 5-foU was investigated and the kinetic characteristics of this process in the presence and in the absence of protein factors hRPA and hPCNA were evaluated. Conclusions. It was shown that: (i both proteins are able to catalyze TLS on used DNA substrates regardless of the reaction conditions, however, pol λ was more accurate enzyme; (ii hRPA can stimulate the efficacy of the nonmutagenic TLS catalyzed by pol at the nucleotide incorporation directly opposite of 5-foU, at the same time it doesn’t influence the incorporation efficacy if the damage displaced into the duplex; (iii hPCNA doesn’t influence the efficacy of TLS catalyzed by both enzymes.

  19. Studies on sildenafil citrate (Viagra) interaction with DNA using electrochemical DNA biosensor.

    Science.gov (United States)

    Rauf, Sakandar; Nawaz, Haq; Akhtar, Kalsoom; Ghauri, Muhammad A; Khalid, Ahmad M

    2007-05-15

    The interaction of sildenafil citrate (Viagra) with DNA was studied by using an electrochemical DNA biosensor. The binding mechanism of sildenafil citrate was elucidated by using constant current potentiometry and differential pulse voltammetry at DNA-modified glassy carbon electrode. The decrease in the guanine oxidation peak area or peak current was used as an indicator for the interaction in 0.2M acetate buffer (pH 5). The binding constant (K) values obtained were 2.01+/-0.05 x 10(5) and 1.97+/-0.01 x 10(5)M(-1) with constant current potentiometry and differential pulse voltammetry, respectively. A linear dependence of the guanine peak area or peak current was observed within the range of 1-40 microM sildenafil citrate with slope=-2.74 x 10(-4)s/microM, r=0.989 and slope=-2.78 x 10(-3)microA/microM, r=0.995 by using constant current potentiometry and differential pulse voltammetry, respectively. Additionally, binding constant values for sildenafil citrate-DNA interaction were determined for the pH range of 4-8 and in biological fluids (serum and urine) at pH 5. The influence of sodium and calcium ions was also studied to elucidate the mechanism of sildenafil citrate-DNA interaction under different solution conditions. The present study may prove to be helpful in extending our understanding of the anticancer activity of sildenafil citrate from cellular to DNA level.

  20. Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa.

    Science.gov (United States)

    Shehata, H R; Lyons, E M; Jordan, K S; Raizada, M N

    2016-03-01

    The aim of this study was to determine if endophytes from wild and ancient Zea plants (corn family) have anti-fungal activities, specifically against the most important fungal pathogen (Sclerotinia homoeocarpa) of creeping bentgrass, a relative of Zea, used here as a model grass. A library of 190 bacterial endophytes from wild, ancient and modern Zea plants were tested for their ability to suppress S. homoeocarpa in vitro, followed by in planta testing of candidates using greenhouse trials. Three endophytes could suppress S. homoeocarpa, originating from wild maize and an ancient Mexican landrace, consistent with our hypothesis. 16S phylogenetic analysis and BOX-PCR DNA fingerprinting suggest that the anti-fungal endophytes are distinct strains of Burkholderia gladioli. One strain (3A12) was confirmed to colonize creeping bentgrass using green fluorescent protein (GFP) tagging. Evans blue vitality staining demonstrated that the bacterial endophytes exhibited fungicidal activities against the pathogen. The endophytes inhibited a wide spectrum of plant-associated fungi including diverse crop pathogens. The results support the hypothesis that wild and ancient Zea genotypes host bacterial endophytes that can control fungal pathogen(s). These results suggest that wild and ancient crops may be an unexplored reservoir of anti-fungal bacterial endophytes. © 2016 The Society for Applied Microbiology.

  1. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

    Science.gov (United States)

    Ziesemer, Kirsten A; Mann, Allison E; Sankaranarayanan, Krithivasan; Schroeder, Hannes; Ozga, Andrew T; Brandt, Bernd W; Zaura, Egija; Waters-Rist, Andrea; Hoogland, Menno; Salazar-García, Domingo C; Aldenderfer, Mark; Speller, Camilla; Hendy, Jessica; Weston, Darlene A; MacDonald, Sandy J; Thomas, Gavin H; Collins, Matthew J; Lewis, Cecil M; Hofman, Corinne; Warinner, Christina

    2015-11-13

    To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

  2. Reviewing population studies for forensic purposes: Dog mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Sophie Verscheure

    2013-12-01

    Full Text Available The identification of dog hair through mtDNA analysis has become increasingly important in the last 15 years, as it can provide associative evidence connecting victims and suspects. The evidential value of an mtDNA match between dog hair and its potential donor is determined by the random match probability of the haplotype. This probability is based on the haplotype’s population frequency estimate. Consequently, implementing a population study representative of the population relevant to the forensic case is vital to the correct evaluation of the evidence. This paper reviews numerous published dog mtDNA studies and shows that many of these studies vary widely in sampling strategies and data quality. Therefore, several features influencing the representativeness of a population sample are discussed. Moreover, recommendations are provided on how to set up a dog mtDNA population study and how to decide whether or not to include published data. This review emphasizes the need for improved dog mtDNA population data for forensic purposes, including targeting the entire mitochondrial genome. In particular, the creation of a publicly available database of qualitative dog mtDNA population studies would improve the genetic analysis of dog traces in forensic casework.

  3. Study on DNA damages induced by UV radiation

    International Nuclear Information System (INIS)

    Doan Hong Van; Dinh Ba Tuan; Tran Tuan Anh; Nguyen Thuy Ngan; Ta Bich Thuan; Vo Thi Thuong Lan; Tran Minh Quynh; Nguyen Thi Thom

    2015-01-01

    DNA damages in Escherichia coli (E. coli) exposed to UV radiation have been investigated. After 30 min of exposure to UV radiation of 5 mJ/cm 2 , the growth of E. coli in LB broth medium was about only 10% in compared with non-irradiated one. This results suggested that the UV radiation caused the damages for E. coli genome resulted in reduction in its growth and survival, and those lesions can be somewhat recovered. For both solutions of plasmid DNAs and E. coli cells containing plasmid DNA, this dose also caused the breakage on single and double strands of DNA, shifted the morphology of DNA plasmid from supercoiled to circular and linear forms. The formation of pyrimidine dimers upon UV radiation significantly reduced when the DNA was irradiated in the presence of Ganoderma lucidum extract. Thus, studies on UV-induced DNA damage at molecular level are very essential to determine the UV radiation doses corresponding to the DNA damages, especially for creation and selection of useful radiation-induced mutants, as well as elucidation the protective effects of the specific compounds against UV light. (author)

  4. NMR studies of artificial double-crossover DNA tiles.

    Science.gov (United States)

    Veerapandian, Murugan; Kim, Byeonghoon; Amin, Rashid; Lee, Junwye; Yun, Kyusik; Park, Sung Ha

    2012-03-01

    This report documents the design and characterization of DNA molecular nanoarchitectures consisting of artificial double crossover DNA tiles with different geometry and chemistry. The Structural characterization of the unit tiles, including normal, biotinylated and hairpin loop structures, are morphologically studied by atomic force microscopy. The specific proton resonance of the individual tiles and their intra/inter nucleotide relationships are verified by proton nuclear magnetic resonance spectroscopy and 2-dimensional correlation spectral studies, respectively. Significant up-field and down-field shifts in the resonance signals of the individual residues at various temperatures are discussed. The results suggest that with artificially designed DNA tiles it is feasible to obtain structural information of the relative base sequences. These tiles were later fabricated into 2D DNA lattice structures for specific applications such as protein arrangement by biotinylated bulged loops or pattern generation using a hairpin structure.

  5. Preliminary results of detailed geochemical study of mercury at the ancient ore roasting site Pšenk (Idrija area, Slovenia

    Directory of Open Access Journals (Sweden)

    Tamara Teršič

    2009-06-01

    Full Text Available PŠenk is one out of 21 localities of ancient roasting sites in the woods surrounding Idrija and one of the largest localities of roasting vessels fragments. The most abundant pottery remains are found in the central western part of the area, which is about 60 m long and up to 50 m wide and is supposed to be the location of the roasting process it self. Detailed soil sampling was performed on 210 x 180 m big area. 156 soil (0–15 cm and 15–30 cm and humus samples were collected from 73 sampling points. 3 soil profiles were sampled to determine vertical distribution ofHg in soil. The prevailing soil types are Cambisols with the typical A-B-C layers sequence. In general soils are richin organic matter to the depth of 30–40 cm; deeper the clayey loam prevails. The determined Hg contents in soiland humus samples of the investigated area are in the range 1.6–8,600 mg/kg with the median of 62.5 mg/kg. At thearea of supposed roasting site the Hg contents range between 20 and 8,600 mg/kg with the median of 580 mg/kg.Spatial distribution of mercury in humus and soils of the investigated area show the highest Hg concentrations atthe supposed roasting site area where the largest quantity of pottery fragments were found and to the east of thisarea, at the narrow tract between the footpath on the north and the bed of La~na voda brook on the south. Extremely high Hg contents were found in profile P4 where it riches 37,020 mg/kg at the depth of 20–30 cm; in general Hg concentrations in all three studied profiles show a gradual decrease with depth. The soils of the investigated area are enriched with mercury to a high degree. Further investigations on Hg speciation are needed to determine the mobility and bioavailability of Hg in soil.

  6. Utility of DNA viruses for studying human host history: case study of JC virus.

    Science.gov (United States)

    Kitchen, Andrew; Miyamoto, Michael M; Mulligan, Connie J

    2008-02-01

    Microbial pathogens, and viruses in particular, can serve as important complements to traditional genetic markers when investigating the population histories of their human host. The range of mutation rates for DNA viruses suggests that DNA viruses can be useful markers of both recent and ancient events in their host histories. Here, we assess the utility of a well known DNA virus, JC virus (JCV), for investigating human history and demography. Using complete coding viral genomes, we confirm the phylogeographic structure of JCV in populations worldwide and provide coalescent estimates of its evolutionary rate under two alternative models of its history. Using these rate estimates, we compare Bayesian skyline plots of population size changes for JCV to those of its human host as estimated with coding mitochondrial genomes of the latter. These comparisons, when combined with other evidence including a log Bayes Factor model test, show that JCV is evolving rapidly and is therefore tracking the recent history of its human host. These results support the hypothesis that post-World War II societal changes are most likely responsible for the recent demographic patterns observed among different regional JCV populations. In sum, fast evolving DNA viruses, such as JCV, can complement RNA viruses to provide novel insights about the recent history and demography of their human host.

  7. Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).

    Science.gov (United States)

    Brouchkov, Anatoli; Kabilov, Marsel; Filippova, Svetlana; Baturina, Olga; Rogov, Victor; Galchenko, Valery; Mulyukin, Andrey; Fursova, Oksana; Pogorelko, Gennady

    2017-12-15

    Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Studies of DNA supercoiling in vivo and in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Cook, D.N.

    1990-10-01

    This thesis describes a number of diverse experiments whose common theme is to elaborate some aspect of DNA supercoiling. The torsion elastic constant of DNA is measure as a function of superhelix density using the technique of picosecond Time Resolved Fluorescence Polarization Anisotropy (FPA) of intercalated ethidium bromide. The results agree with theories which predict that the anisotropy decay should vary with the square root of the relative viscosity. This experiment furthermore demonstrates a sensitivity of FPA to a change in torsion elastic constant of less than 10%. A number of covalently closed DNA samples, ranging in superhelix density from = [minus]0.123 to [plus]0.042, are then examined. A novel method for measuring changes in local supercoiling on a large PNA molecule which is sensitive to changes in supercoiling of regions of chromosomal DNA as short as 1 kilobase in length is presented. Study of chromosomal supercoiling regulating anaerobic gene expression in the facultative photosynthetic bacterium, Rhodobacter capsulatus showed that no stable change in chromosomal supercoiling upon a shift from aerobic respiratory growth to anaerobic photosynthetic conditions. Studies to detect transient changes in DNA supercoiling indicate that DNA downstream from heavily transcribed genes for the photosynthetic reaction center are relaxed or perhaps overwound upon the induction of photosynthetic metabolism. These results are interpreted in terms of the twin domain model of transcriptional supercoiling.

  9. Studies of DNA supercoiling in vivo and in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Cook, David Nelson [Univ. of California, Berkeley, CA (United States)

    1990-10-01

    This thesis describes a number of diverse experiments whose common theme is to elaborate some aspect of DNA supercoiling. The torsion elastic constant of DNA is measure as a function of superhelix density using the technique of picosecond Time Resolved Fluorescence Polarization Anisotropy (FPA) of intercalated ethidium bromide. The results agree with theories which predict that the anisotropy decay should vary with the square root of the relative viscosity. This experiment furthermore demonstrates a sensitivity of FPA to a change in torsion elastic constant of less than 10%. A number of covalently closed DNA samples, ranging in superhelix density from = -0.123 to +0.042, are then examined. A novel method for measuring changes in local supercoiling on a large PNA molecule which is sensitive to changes in supercoiling of regions of chromosomal DNA as short as 1 kilobase in length is presented. Study of chromosomal supercoiling regulating anaerobic gene expression in the facultative photosynthetic bacterium, Rhodobacter capsulatus showed that no stable change in chromosomal supercoiling upon a shift from aerobic respiratory growth to anaerobic photosynthetic conditions. Studies to detect transient changes in DNA supercoiling indicate that DNA downstream from heavily transcribed genes for the photosynthetic reaction center are relaxed or perhaps overwound upon the induction of photosynthetic metabolism. These results are interpreted in terms of the twin domain model of transcriptional supercoiling.

  10. Dreams in ancient Greek Medicine.

    Science.gov (United States)

    Laios, K; Moschos, M M; Koukaki, E; Vasilopoulos, E; Karamanou, M; Kontaxaki, M-I; Androutsos, G

    2016-01-01

    Dreams preoccupied the Greek and Roman world in antiquity, therefore they had a prominent role in social, philosophical, religious, historical and political life of those times. They were considered as omens and prophetic signs of future events in private and public life, and that was particularly accentuated when elements of actions which took place in the plot of dreams were associated directly or indirectly with real events. This is why it was important to use them in divination, and helped the growth of superstition and folklore believes. Medicine as a science and an anthropocentric art, could not ignore the importance of dreams, having in mind their popularity in antiquity. In ancient Greek medicine dreams can be divided into two basic categories. In the first one -which is related to religious medicine-dreams experienced by religionists are classified, when resorted to great religious sanctuaries such as those of Asclepius (Asclepieia) and Amphiaraos (Amfiaraeia). These dreams were the essential element for healing in this form of religious medicine, because after pilgrims underwent purifications they went to sleep in a special dwelling of the sanctuaries called "enkoimeterion" (Greek: the place to sleep) so that the healing god would come to their dreams either to cure them or to suggest treatment. In ancient Greek literature there are many reports of these experiences, but if there may be phenomena of self-suggestion, or they could be characterized as propaganda messages from the priesthood of each sanctuary for advertising purposes. The other category concerns the references about dreams found in ancient Greek medical literature, where one can find the attempts of ancient Greek physicians to interpret these dreams in a rational way as sings either of a corporal disease or of psychological distress. This second category will be the object of our study. Despite the different ways followed by each ancient Greek physician in order to explain dreams, their

  11. The Development and Characteristics of Ancient Harbours-Applying the PADM Chart to the Case Studies of Ostia and Portus.

    Directory of Open Access Journals (Sweden)

    Ferreol Salomon

    Full Text Available Over the last 20 years, the geoarchaeology of ancient harbours has been a very active area of research around the Mediterranean basin, generating much palaeoenvironmental data from many sites, including estimations of sedimentation rates, the height of the ancient sea-level at different dates and palaeo-geographical reconstructions. Combining this information has proved a major challenge. This article proposes a new chart called the Palaeoenvironmental Age-Depth Model (PADM chart, that allows the researchers to combine all relevant indicators in order to estimate harbour potential of a given ancient port, and to generate comparable data between harbours in terms of degree of closure and water depth available against a synchronised chronology. This new approach, developed in the context of the ERC-funded RoMP Portuslimen project, takes into account estimations of water depths relating to differing Roman ship draughts at different periods. It is tested against the palaeoenvironmental evidence published over 10 years from two Roman harbours located at the mouth of the river Tiber: Ostia and Portus. This reveals that: (1 there has been an underestimate of the real sedimentation rates due to the margins of error of the radiocarbon dates; (2 there was effective control of the water column by dredging; (3 there were different periods of control of the sedimentation. We suggest that the navigability of the Ostia harbour by ships with shallower draughts was maintained until sometime between the 2nd c. BC and 1st c. AD, while at Portus it was retained until the 6th-7th c. AD.

  12. The Development and Characteristics of Ancient Harbours-Applying the PADM Chart to the Case Studies of Ostia and Portus.

    Science.gov (United States)

    Salomon, Ferreol; Keay, Simon; Carayon, Nicolas; Goiran, Jean-Philippe

    2016-01-01

    Over the last 20 years, the geoarchaeology of ancient harbours has been a very active area of research around the Mediterranean basin, generating much palaeoenvironmental data from many sites, including estimations of sedimentation rates, the height of the ancient sea-level at different dates and palaeo-geographical reconstructions. Combining this information has proved a major challenge. This article proposes a new chart called the Palaeoenvironmental Age-Depth Model (PADM chart), that allows the researchers to combine all relevant indicators in order to estimate harbour potential of a given ancient port, and to generate comparable data between harbours in terms of degree of closure and water depth available against a synchronised chronology. This new approach, developed in the context of the ERC-funded RoMP Portuslimen project, takes into account estimations of water depths relating to differing Roman ship draughts at different periods. It is tested against the palaeoenvironmental evidence published over 10 years from two Roman harbours located at the mouth of the river Tiber: Ostia and Portus. This reveals that: (1) there has been an underestimate of the real sedimentation rates due to the margins of error of the radiocarbon dates; (2) there was effective control of the water column by dredging; (3) there were different periods of control of the sedimentation. We suggest that the navigability of the Ostia harbour by ships with shallower draughts was maintained until sometime between the 2nd c. BC and 1st c. AD, while at Portus it was retained until the 6th-7th c. AD.

  13. The Development and Characteristics of Ancient Harbours—Applying the PADM Chart to the Case Studies of Ostia and Portus

    Science.gov (United States)

    Keay, Simon; Carayon, Nicolas; Goiran, Jean-Philippe

    2016-01-01

    Over the last 20 years, the geoarchaeology of ancient harbours has been a very active area of research around the Mediterranean basin, generating much palaeoenvironmental data from many sites, including estimations of sedimentation rates, the height of the ancient sea-level at different dates and palaeo-geographical reconstructions. Combining this information has proved a major challenge. This article proposes a new chart called the Palaeoenvironmental Age-Depth Model (PADM chart), that allows the researchers to combine all relevant indicators in order to estimate harbour potential of a given ancient port, and to generate comparable data between harbours in terms of degree of closure and water depth available against a synchronised chronology. This new approach, developed in the context of the ERC-funded RoMP Portuslimen project, takes into account estimations of water depths relating to differing Roman ship draughts at different periods. It is tested against the palaeoenvironmental evidence published over 10 years from two Roman harbours located at the mouth of the river Tiber: Ostia and Portus. This reveals that: (1) there has been an underestimate of the real sedimentation rates due to the margins of error of the radiocarbon dates; (2) there was effective control of the water column by dredging; (3) there were different periods of control of the sedimentation. We suggest that the navigability of the Ostia harbour by ships with shallower draughts was maintained until sometime between the 2nd c. BC and 1st c. AD, while at Portus it was retained until the 6th—7th c. AD. PMID:27631985

  14. Time of flight Laue fiber diffraction studies of perdeuterated DNA

    International Nuclear Information System (INIS)

    Forsyth, V.T.; Whalley, M.A.; Mahendrasingam, A.; Fuller, W.

    1994-01-01

    The diffractometer SXD at the Rutherford Appleton Laboratory ISIS pulsed neutron source has been used to record high resolution time-of-flight Laue fiber diffraction data from DNA. These experiments, which are the first of their kind, were undertaken using fibers of DNA in the A conformation and prepared using deuterated DNA in order to minimis incoherent background scattering. These studies complement previous experiments on instrument D19 at the Institute Laue Langevin using monochromatic neutrons. Sample preparation involved drawing large numbers of these deuterated DNA fibers and mounting them in a parallel array. The strategy of data collection is discussed in terms of camera design, sample environment and data collection. The methods used to correct the recorded time-of-flight data and map it into the final reciprocal space fiber diffraction dataset are also discussed. Difference Fourier maps showing the distribution of water around A-DNA calculated on the basis of these data are compared with results obtained using data recorded from hydrogenated A-DNA on D19. Since the methods used for sample preparation, data collection and data processing are fundamentally different for the monochromatic and Laue techniques, the results of these experiments also afford a valuable opportunity to independently test the data reduction and analysis techniques used in the two methods

  15. Single molecule studies of DNA packaging by bacteriophages

    Science.gov (United States)

    Fuller, Derek Nathan

    The DNA packaging dynamics of bacteriophages φ29, gamma, and T4 were studied at the single molecule level using a dual trap optical tweezers. Also, a method for producing long DNA molecules by PCR for optical tweezers studies of protein DNA interactions is presented and thoroughly characterized. This DNA preparation technique provided DNA samples for the φ29 and T4 studies. In the studies of φ29, the role of charge was investigated by varying the ionic conditions of the packaging buffer. Ionic conditions in which the DNA charge was highly screened due to divalent and trivalent cations showed the lowest resistance to packaging of the DNA to high density. This confirmed the importance of counterions in shielding the DNA interstrand repulsion when packaged to high density. While the ionic nature of the packaging buffer had a strong effect on packaging velocities, there was no clear trend between the counterion-screened charge of the DNA and the maximum packaging velocity. The packaging studies of lambda and T4 served as systems for comparative studies with φ29. Each system showed similarities to the φ29 system and unique differences. Both the lambda and T4 packaging motors were capable of generating forces in excess of 50 pN and showed remarkably high processivity, similar to φ29. However, dynamic structural transitions were observed with lambda that are not observed with φ29. The packaging of the lambda genome showed capsid expansion at approximately 30 percent of the genome packaged and capsid rupture at 90 percent of the genome packaged in the absence of capsid stabilizing protein gpD. Unique to the T4 packaging motor, packaging dynamics showed a remarkable amount of variability in velocities. This variability was seen both within individual packaging phages and from one phage to the next. This is possibly due to different conformational states of the packaging machinery. Additionally, lambda and T4 had average packaging velocities under minimal load of 600

  16. Resurrecting ancient animal genomes: the extinct moa and more.

    Science.gov (United States)

    Huynen, Leon; Millar, Craig D; Lambert, David M

    2012-08-01

    Recently two developments have had a major impact on the field of ancient DNA (aDNA). First, new advances in DNA sequencing, in combination with improved capture/enrichment methods, have resulted in the recovery of orders of magnitude more DNA sequence data from ancient animals. Second, there has been an increase in the range of tissue types employed in aDNA. Hair in particular has proven to be very successful as a source of DNA because of its low levels of contamination and high level of ancient endogenous DNA. These developments have resulted in significant advances in our understanding of recently extinct animals: namely their evolutionary relationships, physiology, and even behaviour. Hair has been used to recover the first complete ancient nuclear genome, that of the extinct woolly mammoth, which then facilitated the expression and functional analysis of haemoglobins. Finally, we speculate on the consequences of these developments for the possibility of recreating extinct animals. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Correlation between chemical composition of dental calculus and bone samples in ancient human burials: perspectives in paleonutritional studies

    International Nuclear Information System (INIS)

    Capasso, L.; Di Tota, G.; Bondioli, L.

    1997-01-01

    Full text: The authors describe the results of an assay based on the comparison between chemical composition of dental calculus and bone respectively obtained from teeth and bones of ancient skeletons. The chemical analysis has been performed by synchrotron light. The concentrations of the following oligoelements having paleonutritional correlations were analysed: Fe, Cu, Zn, Pb, Sr and Ca. The authors demonstrate that- in a given individual the concentration of such elements in the bone sample were in the range of those obtained for the same elements in the sample of dental calculus. Such correspondence suggests that the chemical analysis of dental calculus may give paleonutritional indications analogous to those deriving from the analysis of bone samples. The authors underline also that the use of dental calculus has a distinct advantage over the use of bone samples, since it may allow a diachronic investigation. In fact, dental calculus typically presents a concentric pattern of growth, and the chemical composition of each layer may vary in accordance with temporal dietary variations. This is not the case for bone. This fact is the theoretical basis for the possible future development of techniques directed to the reconstruction of variations in the dietary habits of ancient individuals, possibly in relation to environmental seasonal changes

  18. Correlation between chemical composition of dental calculus and bone samples in ancient human burials: perspectives in paleonutritional studies

    Energy Technology Data Exchange (ETDEWEB)

    Capasso, L.; Di Tota, G. [National Aechaeological Museum, Chieta, (Italy); Bondioli, L. [Prehistory and Ethnology Museum, Rome (Italy)

    1997-12-31

    Full text: The authors describe the results of an assay based on the comparison between chemical composition of dental calculus and bone respectively obtained from teeth and bones of ancient skeletons. The chemical analysis has been performed by synchrotron light. The concentrations of the following oligoelements having paleonutritional correlations were analysed: Fe, Cu, Zn, Pb, Sr and Ca. The authors demonstrate that- in a given individual the concentration of such elements in the bone sample were in the range of those obtained for the same elements in the sample of dental calculus. Such correspondence suggests that the chemical analysis of dental calculus may give paleonutritional indications analogous to those deriving from the analysis of bone samples. The authors underline also that the use of dental calculus has a distinct advantage over the use of bone samples, since it may allow a diachronic investigation. In fact, dental calculus typically presents a concentric pattern of growth, and the chemical composition of each layer may vary in accordance with temporal dietary variations. This is not the case for bone. This fact is the theoretical basis for the possible future development of techniques directed to the reconstruction of variations in the dietary habits of ancient individuals, possibly in relation to environmental seasonal changes.

  19. Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences.

    Science.gov (United States)

    Mandell, Kathleen E; Vallone, Peter M; Owczarzy, Richard; Riccelli, Peter V; Benight, Albert S

    2006-06-15

    Melting curves and circular dichroism spectra were measured for a number of DNA dumbbell and linear molecules containing dinucleotide repeat sequences of different lengths. To study effects of different sequences on the melting and spectroscopic properties, six DNA dumbbells whose stems contain the central sequences (AA)(10), (AC)(10), (AG)(10), (AT)(10), (GC)(10), and (GG)(10) were prepared. These represent the minimal set of 10 possible dinucleotide repeats. To study effects of dinucleotide repeat length, dumbbells with the central sequences (AG)(n), n = 5 and 20, were prepared. Control molecules, dumbbells with a random central sequence, (RN)(n), n = 5, 10, and 20, were also prepared. The central sequence of each dumbbell was flanked on both sides by the same 12 base pairs and T(4) end-loops. Melting curves were measured by optical absorbance and differential scanning calorimetry in solvents containing 25, 55, 85, and 115 mM Na(+). CD spectra were collected from 20 to 45 degrees C and [Na(+)] from 25 to 115 mM. The spectral database did not reveal any apparent temperature dependence in the pretransition region. Analysis of the melting thermodynamics evaluated as a function of Na(+) provided a means for quantitatively estimating the counterion release with melting for the different sequences. Results show a very definite sequence dependence, indicating the salt-dependent properties of duplex DNA are also sequence dependent. Linear DNA molecules containing the (AG)(n) and (RN)(n), sequences, n = 5, 10, 20, and 30, were also prepared and studied. The linear DNA molecules had the exact sequences of the dumbbell stems. That is, the central repeat sequence in each linear duplex was flanked on both sides by the same 12-bp sequence. Melting and CD studies were also performed on the linear DNA molecules. Comparison of results obtained for the same sequences in dumbbell and linear molecular environments reveals several interesting features of the interplay between

  20. Dentistry in ancient mesopotamia.

    Science.gov (United States)

    Neiburger, E J

    2000-01-01

    Sumer, an empire in ancient Mesopotamia (southern Iraq), is well known as the cradle of our modern civilization and the home of biblical Abraham. An analysis of skeletal remains from cemeteries at the ancient cities of Ur and Kish (circa 2000 B.C.), show a genetically homogeneous, diseased, and short-lived population. These ancient Mesopotamians suffered severe dental attrition (95 percent), periodontal disease (42 percent), and caries (2 percent). Many oral congenital and neoplastic lesions were noted. During this period, the "local dentists" knew only a few modern dental techniques. Skeletal (dental) evidence indicates that the population suffered from chronic malnutrition. Malnutrition was probably caused by famine, which is substantiated in historic cuneiform and biblical writings, geologic strata samples, and analysis of skeletal and forensic dental pathology. These people had modern dentition but relatively poor dental health. The population's lack of malocclusions, caries, and TMJ problems appear to be due to flat plane occlusion.

  1. Science and Library in the Ancient Age

    Directory of Open Access Journals (Sweden)

    Hasan Sacit Keseroğlu

    2016-09-01

    Full Text Available Science assumes its contemporary identity as a result of the stages of magic, religion and reason. The religious stage starts with the invention of writing and this stage leaves its place to reason with Thales in Ancient Greece. Knowledge eludes from religious beliefs. Ways to reach accurate, reliable and realistic knowledge are sought, along with the answer for what knowledge is. Therefore, beginning of the science is taken into consideration together with science and philosophy. The purpose of this study is to approach knowledge and science of the ancient age in Mesopotamia, Egypt and Ancient Greece in general terms and to determine the relationship between the knowledge produced in those places and libraries established. The hypothesis has been determined as “Egypt and Mesopotamia at the starting point of the history of science and science, and libraries in Ancient Greece have developed parallelly to each other.” The scope of the study has been limited to Mesopotamia, Egypt and Ancient Greece; and Ancient Greece has been explained, with descriptive method, in the frame of the topics of Ionia, Athens, Hellenistic Period and Rome. Many archives and libraries have been established in the ancient age. The difference between an archive and a library has been mentioned first, and then, various libraries have been introduced such as Nineveh in Mesopotamia, Alexandria in Ancient Greece and many others in Egypt. It has been clearly distinguished that there had been a very tight relationship between knowledge production and library, especially with the Library of Alexandria.

  2. Study of DNA uptake locations in single E. coli cells

    Science.gov (United States)

    Xu, C. Shan; Meadow Anderson, L.; Yang, Haw

    2006-03-01

    Artificial gene transfer of bacteria, such as E. coli, has become the main stream technique in genetic engineering and molecular cell biology studies. In spite of the great improvements in transformation efficiency, some fundamental questions remained to be answered. For instance, what are the DNA uptake channels and how do they form and function under external stimuli? Furthermore, where are these channels located on the cell membrane? Here we report a study aimed at DNA uptake locations in the two widely used gene transformation techniques: electroporation and heat shock. A direct visualization of the settling location of single DNA molecules inside individual E. coli cells was obtained by fluorescence imaging and spectroscopy. Electroporation and heat shock exhibit two distinct characteristics of DNA uptake locations. A preferential distribution toward cell poles during electroporation is consistent with earlier experiments and previously proposed models. However, the result from heat shock is unanticipated in which the majority of DNA enters the cell near the center. Such observation suggests that uptake channels form preferentially where newly-synthesized membrane is located under cation and low temperature treatment

  3. DNA binding, photo-induced DNA cleavage and cytotoxicity studies of lomefloxacin and its transition metal complexes

    Science.gov (United States)

    Ragheb, Mohamed A.; Eldesouki, Mohamed A.; Mohamed, Mervat S.

    2015-03-01

    This work was focused on a study of the DNA binding and cleavage properties of lomefloxacin (LMF) and its ternary transition metal complexes with glycine. The nature of the binding interactions between compounds and calf thymus DNA (CT-DNA) was studied by electronic absorption spectra, fluorescence spectra and thermal denaturation experiments. The obtained results revealed that LMF and its complexes could interact with CT-DNA via partial/moderate intercalative mode. Furthermore, the DNA cleavage activities of the compounds were investigated by gel electrophoresis. Mechanistic studies of DNA cleavage suggest that singlet oxygen (1O2) is likely to be the cleaving agent via an oxidative pathway, except for Cu(II) complex which proceeds via both oxidative and hydrolytic pathways. Antimicrobial and antitumor activities of the compounds were also studied against some kinds of bacteria, fungi and human cell lines.

  4. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis).

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J; Robertson, Bruce C

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  5. Ancient and contemporary DNA reveal a pre-human decline but no population bottleneck associated with recent human persecution in the kea (Nestor notabilis.

    Directory of Open Access Journals (Sweden)

    Nicolas Dussex

    Full Text Available The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis. Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000-5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410, historical (n = 15 and fossil samples (n = 4 showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 - 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines.

  6. Ancient and Contemporary DNA Reveal a Pre-Human Decline but No Population Bottleneck Associated with Recent Human Persecution in the Kea (Nestor notabilis)

    Science.gov (United States)

    Dussex, Nicolas; Rawlence, Nicolas J.; Robertson, Bruce C.

    2015-01-01

    The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000–5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 – 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines. PMID:25719752

  7. Study of the ancient iron-smelting sites at Pantaki, Tsauni and Samaru-west, Nigeria, using neutron activation analysis

    International Nuclear Information System (INIS)

    Oladipupo, M.D.; OIadipo, M.O.A.; Mallam, S.P.; Akpa, T.C.

    2010-01-01

    Neutron activation analysis was used to obtain concentrations of some elements in samples of potsherds and furnaces obtained from Pantaki, Tsauni and Samaru-west ancient iron-smelting sites. Using WARD method, cluster analysis of the elements was carried out to establish the relationship between the archaeological samples in term of similarity in elemental concentrations. It was found that there is some level of similarity among the potsherd samples from the three sites. Also, most of furnace samples display some similarity. It was established that there was cultural linkage between the iron-smelters at the different sites. The similarity between the samples lead to a conclusion that pot makers and furnace makers could have existed, who obtained clays from common sources, made and sold the products to users in different communities.

  8. Influence of a 10-Day Mimic of Our Ancient Lifestyle on Anthropometrics and Parameters of Metabolism and Inflammation: The “Study of Origin”

    Directory of Open Access Journals (Sweden)

    Leo Pruimboom

    2016-01-01

    Full Text Available Chronic low-grade inflammation and insulin resistance are intimately related entities that are common to most, if not all, chronic diseases of affluence. We hypothesized that a short-term intervention based on “ancient stress factors” may improve anthropometrics and clinical chemical indices. We executed a pilot study of whether a 10-day mimic of a hunter-gatherer lifestyle favorably affects anthropometrics and clinical chemical indices. Fifty-five apparently healthy subjects, in 5 groups, engaged in a 10-day trip through the Pyrenees. They walked 14 km/day on average, carrying an 8-kilo backpack. Raw food was provided and self-prepared and water was obtained from waterholes. They slept outside in sleeping bags and were exposed to temperatures ranging from 12 to 42°C. Anthropometric data and fasting blood samples were collected at baseline and the study end. We found important significant changes in most outcomes favoring better metabolic functioning and improved anthropometrics. Coping with “ancient mild stress factors,” including physical exercise, thirst, hunger, and climate, may influence immune status and improve anthropometrics and metabolic indices in healthy subjects and possibly patients suffering from metabolic and immunological disorders.

  9. Mathematics in Ancient India

    Indian Academy of Sciences (India)

    In this series of articles, we intend to have a glimpse of some of the landmarks in ancient In- dian mathematics with special emphasis on num- ber theory. This issue features a brief overview of some of the high peaks of mathematics in an- cient India. In the next part we shall describe. Aryabhata's general solution in integers ...

  10. Printing Ancient Terracotta Warriors

    Science.gov (United States)

    Gadecki, Victoria L.

    2010-01-01

    Standing in awe in Xian, China, at the Terra Cotta warrior archaeological site, the author thought of sharing this experience and excitement with her sixth-grade students. She decided to let her students carve patterns of the ancient soldiers to understand their place in Chinese history. They would make block prints and print multiple soldiers on…

  11. Trepanation in Ancient China.

    Science.gov (United States)

    Hobert, Leah; Binello, Emanuela

    2017-05-01

    Trepanation, the process of making a burr hole in the skull to access the brain, is an ancient form of a primitive craniotomy. There is widespread evidence of contributions made to this practice by ancient civilizations in Europe, Africa, and South America, where archaeologists have unearthed thousands of trepanned skulls dating back to the Neolithic period. Little is known about trepanation in China, and it is commonly believed that the Chinese used only traditional Chinese medicine and nonsurgical methods for treating brain injuries. However, a thorough analysis of the available archeological and literary evidence reveals that trepanation was widely practiced throughout China thousands of years ago. A significant number of trepanned Chinese skulls have been unearthed showing signs of healing and suggesting that patients survived after surgery. Trepanation was likely performed for therapeutic and spiritual reasons. Medical and historical works from Chinese literature contain descriptions of primitive neurosurgical procedures, including stories of surgeons, such as the legendary Hua Tuo, and surgical techniques used for the treatment of brain pathologies. The lack of translation of Chinese reports into the English language and the lack of publications on this topic in the English language may have contributed to the misconception that ancient China was devoid of trepanation. This article summarizes the available evidence attesting to the performance of successful primitive cranial surgery in ancient China. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Ancient Egypt: History 380.

    Science.gov (United States)

    Turk, Laraine D.

    "Ancient Egypt," an upper-division, non-required history course covering Egypt from pre-dynastic time through the Roman domination is described. General descriptive information is presented first, including the method of grading, expectation of student success rate, long-range course objectives, procedures for revising the course, major…

  13. Ancient Egypt: Personal Perspectives.

    Science.gov (United States)

    Wolinski, Arelene

    This teacher resource book provides information on ancient Egypt via short essays, photographs, maps, charts, and drawings. Egyptian social and religious life, including writing, art, architecture, and even the practice of mummification, is conveniently summarized for the teacher or other practitioner in a series of one to three page articles with…

  14. Mathematics in Ancient India

    Indian Academy of Sciences (India)

    Number Theory for its own sake, as a great 'intellectual challenge, has a long history, particularly here in India. Already in the 7th century, Brahmagupta made impor- tant contributions to what is now known (incorrectly) as. Pell's equation.: Michael Atiyah ([1], p.913). In number theory, the grandest achievements of ancient.

  15. Ancient deforestation revisited.

    Science.gov (United States)

    Hughes, J Donald

    2011-01-01

    The image of the classical Mediterranean environment of the Greeks and Romans had a formative influence on the art, literature, and historical perception of modern Europe and America. How closely does is this image congruent with the ancient environment as it in reality existed? In particular, how forested was the ancient Mediterranean world, was there deforestation, and if so, what were its effects? The consensus of historians, geographers, and other scholars from the mid-nineteenth century through the first three quarters of the twentieth century was that human activities had depleted the forests to a major extent and caused severe erosion. My research confirmed this general picture. Since then, revisionist historians have questioned these conclusions, maintaining instead that little environmental damage was done to forests and soils in ancient Greco-Roman times. In a reconsideration of the question, this paper looks at recent scientific work providing proxy evidence for the condition of forests at various times in ancient history. I look at three scientific methodologies, namely anthracology, palynology, and computer modeling. Each of these avenues of research offers support for the concept of forest change, both in abundance and species composition, and episodes of deforestation and erosion, and confirms my earlier work.

  16. Creative Ventures: Ancient Civilizations.

    Science.gov (United States)

    Stark, Rebecca

    The open-ended activities in this book are designed to extend the imagination and creativity of students and encourage students to examine their feelings and values about historic eras. Civilizations addressed include ancient Egypt, Greece, Rome, Mayan, Stonehenge, and Mesopotamia. The activities focus upon the cognitive and affective pupil…

  17. Mathematics in Ancient India

    Indian Academy of Sciences (India)

    SERIES I ARTICLE. Mathematics in Ancient India. 3. Brahmagupta's Lemma: The Samasabhavana. Amartya Kumar Dutta is an Associate Professor of. Mathematics at the. Indian Statistical. Institute, Kolkata. His research interest is in commutative algebra. Part 1, An overview, Reso- nance, VoL7, No.4, pp.4-19,. 2002. Part 2.

  18. Incest in Ancient Egypt

    Directory of Open Access Journals (Sweden)

    Škorić Marko

    2005-01-01

    Full Text Available There are many controversies that surround the problem of incest in Ancient Egypt. One of them is belief that incest was practiced exclusively by the Royal families, which is incorrect. I will try to show that at this time we don’t have satisfactory explanation of this kind of behavior, but that there are interesting suggestions for further research.

  19. Ancient ports of Kalinga

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    which plied between Kalinga and south east Asian countries. Nanda Raja, is said to have attacked Kalinga with the intention of getting access to the sea for the landlocked Kingdom of Magadha (Bihar). The ancient texa Artha Sastra (3rd-4th century B...

  20. Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera, Italy

    DEFF Research Database (Denmark)

    Gilbert, M. T. P.; Rudbeck, L.; Willerslev, E.

    2005-01-01

    The majority of ancient DNA studies on human specimens have utilised teeth and bone as a source of genetic material. In this study the levels of endogenous contamination (i.e. present within the sample prior to sampling for the DNA analysis) are assessed within human bone and teeth specimens samp...

  1. Urology and the scientific method in ancient Egypt.

    Science.gov (United States)

    Gordetsky, Jennifer; O'Brien, Jeanne

    2009-03-01

    To examine the practice of urology in ancient Egypt using various sources, including the Edwin Smith and Ebers Papyri. The sources of knowledge of ancient Egyptian medicine include medical papyri, paleopathology, art, and hieroglyphic carvings. A brief overview of the medical system in ancient Egypt was completed, in addition to an examination of the training and specialization of the physician in the ancient world. Urologic diseases treated in ancient Egypt and some of the first documented urologic surgeries are presented. Finally, we studied the role of the physician-priest and the intertwined use of religion and magic in ancient Egyptian medicine. The same medical conditions urologists treat in the office today were methodically documented thousands of years ago. Medical papyri show evidence that the ancient Egyptians practiced medicine using a scientific method based on the clinical observation of disease. This has been exemplified by the Edwin Smith Surgical Papyrus, a collection of surgical cases that gives a diagnosis, treatment, and prognosis for each ailment, and the discovery of medical specialization in ancient Egypt, giving us perhaps the world's first urologists. Intertwined with the scientific method was also the rich mysticism and religion of ancient Egypt, which were integral components of the healing process. We present an overview of the practice of urology in ancient Egypt, in terms of both pharmacologic and surgical intervention, as well as with a look into the religion of medicine practiced at that time.

  2. Pilot study of DNA extraction from archival unstained bone marrow ...

    African Journals Online (AJOL)

    coagulant whole blood, bloodstains, hairs, tissue samples and buccal epithelial cells. The purpose of this study was to compare yield and quality of DNA samples obtained with the use of three different methods. The ability of these procedures to ...

  3. SSR marker based DNA fingerprinting and diversity study in rice ...

    African Journals Online (AJOL)

    The genetic diversity and DNA fingerprinting of 15 elite rice genotypes using 30 SSR primers on chromosome numbers 7-12 was investigated. The results revealed that all the primers showed distinct polymorphism among the cultivars studied indicating the robust nature of microsatellites in revealing polymorphism. Cluster ...

  4. MAGNETIC TWEEZERS FOR THE STUDY OF DNA TRACKING MOTORS

    Science.gov (United States)

    Manosas, Maria; Meglio, Adrien; Spiering, Michelle M.; Ding, Fangyuan; Benkovic, Stephen J.; Barre, François-Xavier; Saleh, Omar A.; Allemand, Jean François; Bensimon, David; Croquette, Vincent

    2011-01-01

    Single-molecule manipulation methods have opened a new vista on the study of molecular motors. Here we describe the use of magnetic traps for the investigation of the mechanism of DNA based motors, in particular helicases and translocases. PMID:20627163

  5. Photo-induced antimicrobial and DNA cleavage studies of ...

    Indian Academy of Sciences (India)

    J. Chem. Sci. Vol. 125, No. 5, September 2013, pp. 1015–1027. c Indian Academy of Sciences. Photo-induced antimicrobial and DNA cleavage studies ... †Present address: Department of Chemistry, Bannari Amman Institute of Technology, Sathyamangalam, India. #Present address: ..... C overnight and exam- ined for ...

  6. Radioautographic DNA synthesis study on mice Mus musculus gingival epithelium

    International Nuclear Information System (INIS)

    Silveira Tarelho, Z.V. da; Hetem, S.

    1984-01-01

    The DNA-synthetizing cells frequency in the gingival epithelium basal layer of the first lower molar region in young and adult mice were studied. The 3H-thymidine and radioautography were used. The labeled cells frequency was determined by calculating their proportions. The data were statiscally analysed. (M.A.C.) [pt

  7. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Myungkoo [Iowa State Univ., Ames, IA (United States)

    1995-12-06

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ~25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G2 or G3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N2-dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N2-dG.

  8. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    International Nuclear Information System (INIS)

    Suh, Myungkoo.

    1995-01-01

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7β, 8α-dihydoxy-9α, l0α-epoxy-7,8,9, 10-tetrahydrobenzo[α]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, (-)-trans-, (+)-cis- and (-)-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( ∼ 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant π-π stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G 2 or G 3 (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N 2 -dG in DNA isolated from the skin of mice treated topically with benzo[α]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N 2 -dG

  9. A study on ancient glass of Western Han Dynasty from Tangpai, Hepu, Guangxi by the lead isotopic technique

    International Nuclear Information System (INIS)

    Wang Junxin; Li Ping; Zhang Xun

    1994-01-01

    The ancient glaze of Western Han Dynasty from Tangpai, Hepu, Guangxi has been investigated by XRD, XRF methods. The XRD results showed that the glaze was real glass with the index of refraction in a range of 1.473-1.479, while the XRF analysis indicated that the contents of SiO 2 , K 2 O, CaO, Al 2 O 3 , MgO and Na 2 O in the glass corresponded to 75.8%-79.0%, 10.4-14.5%, 1.3%-2.1%, 1.9%-2.7%, 0.22-0.50% and 0.21%-0.87% respectively, belonging to the Si-K vitreous system. The values of 207 Pb/ 206 Pb and 208 Pb/ 206 Pb in the range of 0.8746-0.8953 and 2.142-2.178 respectively, were close to the distribution of other Chinese early glass, but far from that of the European and Egyptian ones. Therefore, a conclusion can be reached that Si-K glass of Tangpai was made in China and impossible from foreign countries

  10. The theory of «basic myth» as a structural method in the study of ancient pagan and Slavic mythology

    Directory of Open Access Journals (Sweden)

    O. V. Usenko

    2016-05-01

    Full Text Available The method of structural analysis of the Soviet Union was first used philologists, linguists V.V. Ivanov and V.N. Toporov for the study of ancient Russian mythology. It was developed by them in 60-70 years. Then it was tested in the study of Slavic mythology and the ancient Russian paganism. The name of this scientific approach it is the Theory of «basic myth. It has become something of a free zone from Marxist methodology. It was dominated in France. French structural anthropologist Claude Lévi-Strauss created this method. In Russian historiography there was the influence of the old «mythological» school (A.N Afanas’ev etc.. Thus, the authors of this theory draw huge source material – folklore (fairy tales, myths, legends, proverbs, signs, epic, Vedic hymns etc. «Basic myth» proposed by scientists, was the reconstruction that based on mythological reconstructions. The basis of the reconstruction was the story about struggle between snake and Peru. With this opposition correlate all others: light-dark, top-bottom and others. This «basic myth» has been designed by researchers based on a comparison of the Vedic myth of the fight of Indra with Vritroyu, Baltic mythology and stories about Perkunas and Velnyase. Authors identified the snake-demon Vrytra with Valo and then with Veles (Volos. It was antagonist of Thunder (Perun. The authors of this theory considered that «basic myth» was the basis for the mythology of Indo-European population. The «basic myth» was reflected in East tales of struggle heroes of the dragon – the authors conducted a parallel between Ilya Muromets, Ilya the Prophet and between Perun and Veles and Gorynych-Snake. The author of the article presents the situation historiographical discourse emerged against the background of the existence of the theory of «basic myth», presented by followers’ motivations of and its opponents. The main feature of representatives of structural school is the concentration

  11. [Ancient clinical application of massage therapy on navel].

    Science.gov (United States)

    Yang, Xing-Yue; Ma, Yu-Xiao; Tian, Si-Sheng; Gao, Shu-Zhong

    2014-07-01

    To further explore the clinical effect of massage therapy on navel,the related ancient literatures were arranged and analyzed,and several methods in ancient clinical were introduced, including stroking navel, rubbing navel, pushing navel, tapping navel and puffing navel. In addition, the theoretical basis of massage therapy on navel were discussed. The results revealed ancient literatures offered abundant theoretical basis to modern clinical practice, and there were evidences of treating gastroenteric and gynecological diseases with this therapy. Comprehensively, through the study of ancient literatures and modern research, therapy of massage on navel is believed to be promising and will gain popularity in the future.

  12. Childbirth in ancient Egypt.

    Science.gov (United States)

    Chamberlain, Geoffrey

    2004-11-01

    Medicine in ancient Egypt was much more advanced than the rest of the Biblical world, especially in trauma surgery. Care at the time of childbirth was however virtually non-existent. There were no trained obstetricians or midwives but a galaxy of gods were at hand. This article traces what we can piece together about pregnancy of childbirth from the evidence we have in tombs and papyri of Egypt.

  13. Did ossification of the posterior longitudinal ligament of the spine evolve in the modern period? A paleopathologic study of ancient human skeletons in Japan.

    Science.gov (United States)

    Hukuda, S; Inoue, K; Nakai, M; Katayama, K

    2000-11-01

    To investigate the historical origins of ligamentous ossifications of the spine in Japan. We studied skeletons of Jomonese of the period 5000-2300 years BP, of Japanese of the 17th-19th century Edo Period, and of Ainu of the 18th-20th century in Japan with special emphasis on spinal ligament ossifications as in the posterior longitudinal ligament. A comparison to our previous study on ancient Chinese skeletons was done. Cervical ossification of the posterior longitudinal ligament (OPLL) was the only ossification that increased significantly in prevalence in people of the near-modern period in comparison to the Neolithic gathering-hunting people. Socioeconomic changes from a subsistence gathering-hunting economy to the near-modern livelihood depending on rice-eating and a diet high in vegetable protein are speculated to be responsible for the prevalence increase of cervical OPLL.

  14. Prediction of autosomal STR typing success in ancient and Second World War bone samples.

    Science.gov (United States)

    Zupanič Pajnič, Irena; Zupanc, Tomaž; Balažic, Jože; Geršak, Živa Miriam; Stojković, Oliver; Skadrić, Ivan; Črešnar, Matija

    2017-03-01

    Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded. Therefore the new commercial qPCR kits able to assess the degree of degradation are potentially able to predict the success of downstream short tandem repeat (STR) typing. The goal of this study was to verify the quantification step using the PowerQuant kit with regard to its suitability as a screening method for autosomal STR typing success on ancient and Second World War (WWII) skeletal remains. We analysed 60 skeletons excavated from five archaeological sites and four WWII mass graves from Slovenia. The bones were cleaned, surface contamination was removed and the bones ground to a powder. Genomic DNA was obtained from 0.5g of bone powder after total demineralization. The DNA was purified using a Biorobot EZ1 device. Following PowerQuant quantification, DNA samples were subjected to autosomal STR amplification using the NGM kit. Up to 2.51ng DNA/g of powder were extracted. No inhibition was detected in any of bones analysed. 82% of the WWII bones gave full profiles while 73% of the ancient bones gave profiles not suitable for interpretation. Four bone extracts yielded no detectable amplification or zero quantification results and no profiles were obtained from any of them. Full or useful partial profiles were produced only from bone extracts where short autosomal (Auto) and long degradation (Deg) PowerQuant targets were detected. It is

  15. DNA Self-Assembly and Computation Studied with a Coarse-grained Dynamic Bonded Model

    DEFF Research Database (Denmark)

    Svaneborg, Carsten; Fellermann, Harold; Rasmussen, Steen

    2012-01-01

    We utilize a coarse-grained directional dynamic bonding DNA model [C. Svaneborg, Comp. Phys. Comm. (In Press DOI:10.1016/j.cpc.2012.03.005)] to study DNA self-assembly and DNA computation. In our DNA model, a single nucleotide is represented by a single interaction site, and complementary sites can...

  16. The Vindolanda Tablets and the Ancient Economy

    DEFF Research Database (Denmark)

    Evers, Kasper Grønlund

    , a model is outlined which takes into account the different economic behaviours revealed by the tablets and attempts to fit them together into one coherent, economic system, whilst also relating the activities to questions of scale in the ancient economy; moreover, the conclusions drawn in the study......, the aim is to investigate how best to comprehend the economic system attested at Vindolanda and to consider the wider implications for studies of the ancient economy in general. This is accomplished by a three-step approach: first, the nature of the Vindolandan evidence is assessed, and the state...... of research on both studies of the ancient economy and the economy of early Roman Britain is accounted for, so as to highlight the value of the Vindolanda Tablets and lay the ground for the interpretations which follow. Secondly, the economic activities attested by the tablets are analysed in terms of market...

  17. Genetic data suggests that the Jinggouzi people are associated with the Donghu, an ancient nomadic group of North China.

    Science.gov (United States)

    Wang, Haijing; Chen, Lu; Ge, Binwen; Zhang, Ye; Zhu, Hong; Zhou, Hui

    2012-08-01

    Nomadic populations have played a significant role in the history of not only China but also in many nations worldwide. Because they had no written language, an important aspect in the study of these people is the discovery of their tombs. It has been generally accepted that Xiongnu was the first empire created by a nomadic tribe in the 3rd century BC. However, little population genetic information is available concerning the Donghu, another flourishing nomadic tribe at the same period because of the restriction of materials until the Jinggouzi site was excavated. In order to test the genetic characteristics of ancient people in this site and to explore the relationship between Jinggouzis and Donghus, two uniparentally inherited markers were analyzed from 42 human remains in this site, which was located in northern China, dated approximately 2500 years ago. With ancient DNA technology, four mtDNA haplogroups (D, G, C, and M10) and one Y chromosome haplogroup (C) were identified using mitochondrial DNA and Y-chromosome single nucleotide polymorphisms. Those haplogroups are common in North Asia and East Asia. The Jinggouzi people were genetically closest to the Xianbeis in ancient populations and to the Oroqens among extant populations, who were all pastoralists. This might indicate that ancient Jinggouzi people were nomads. Meanwhile, according to the genetic data and the evidences in archaeology, we inferred that Jinggouzi people were associated with Donghu. It is of much value to trace the history of the Donghu tribe and this might show some insight into the ancient nomadic society.

  18. Micro-Raman and FT-IR spectroscopic studies of ceramic shards excavated from ancient Stratonikeia city at Eskihisar village in West-South Turkey

    Science.gov (United States)

    Bahçeli, Semiha; Güleç, Gamze; Erdoğan, Hasan; Söğüt, Bilal

    2016-02-01

    In this study, micro-Raman and Fourier transformed infrared (FT-IR) spectroscopies, X-ray diffraction (XRD) and scanning electron microscope with energy dispersive X-ray (SEM-EDX) were used to characterize the mineralogical structures of pigments of four ceramic fragments in which one of them belongs to Hellenistic period (1st - IVth century BC) and other three ceramic shards belong to Early Rome (IVth century BC- 1st century AD) excavated from Stratonikeia ancient city. In the results of investigations on these four ceramic fragments, the various phases were identified: quartz, kaolinite, albit (or Na-feldspar), calcite, anastase, hematite and magnetite. Furthermore, the obtained findings indicate that firing temperature is about 800-850 °C for all the shards.

  19. Archaeochemical study of the ancient Egyptian glass from the collection of the Ancient Egyptian Museum, Tokyo using a newly developed portable X-ray fluorescence spectrometer equipped with a CMOS camera

    International Nuclear Information System (INIS)

    Kikugawa, Tadashi; Abe, Yoshinari; Nakai, Izumi; Sanada, Takashi

    2009-01-01

    An improved version of the portable X-ray fluorescence spectrometer, OURSTEX FA-IV was manufactured; its weight was reduced to 16 kg. and a CMOS camera was installed for pinpoint analysis of the artifacts. By applying this spectrometer to element analysis of ancient Egyptian glass in the collection of the Ancient Egyptian Museum, Shibuya, Tokyo, copper and cobalt were identified in the blue colorant of the glasses. A combination with a portable X-ray powder diffractometer was also examined, and disclosed lead antimonate Pb 2 Sb 2 O 7 and lead stannate PbSnO 3 as the yellow colorants and calcium antimonite Ca 2 Sb 2 O 7 as the white colorant of the glass. The results provide new examples of historical use of cobalt alum in the Roman period (A.D.2 C.) which was believed to be used only in the New Kingdom (B.C.14-11 C.), and that of lead stannate PbSnO 3 in the A.D.2 C, which was thought to be used after A.D.4 C. Further, XRF imaging utilizing laboratory X-ray microscope or synchrotron radiation X-ray microbeam was also applied to reveal colorants of yellow, blue, white and black colors used in complex archaeological patterns. (author)

  20. NMR studies on DNA binding specificity of the lac repressor

    NARCIS (Netherlands)

    Kopke Salinas, Roberto

    2005-01-01

    The thesis describes NMR structures of two protein-DNA complexes. The first structure shows how the protein, the DNA binding domain of lac repressor, recognizes its natural DNA binding site, by adaptation and read out of the nucleotide sequence. The second one shows how the DNA binding specificity

  1. Suiformes conservation: a study case of strategies for DNA utilization

    Indian Academy of Sciences (India)

    applied to the DNA extracted from faeces using GenomiPhi. V2 DNA Amplification kit (GE Healthcare, Canada) and. REPLI-gR Mini Kit (Qiagen, Hilden, Germany), following manufacturer's instructions. The WGA DNA was further compared with genomic DNA. PCR amplification of a nuclear histone H4 gene fragment and a.

  2. 800,000 year old mammoth DNA, modern elephant DNA or PCR artefact?

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Willerslev, Eske

    2007-01-01

    Poulakakis and colleagues (Poulakakis et al. 2006: Biol. Lett. 2, 451-454), report the recovery of 'authentic' mammoth DNA from an 800,000-year-old fragment of bone excavated on the island of Crete. In light of results from other ancient DNA studies that indicate how DNA survival is unlikely in s...... polymorphisms. Finally, we demonstrate using a simple BLAST search in GenBank that the claimed 'uniquely derived character state' for mammoths is in fact also found within modern elephants. Udgivelsesdato: 2007-Feb-22...

  3. Study on construction of cDNA library of the treated changliver cell and quality analysis

    OpenAIRE

    Juntang, Lin; Pramanik, Jogenananda; Congrui, Wang; Huiyong, Zhang; Huigen, Feng; Baosheng, Yang; Yuchang, Li; Cunshuan, Xu

    2004-01-01

    The study aims to construct cDNA library of Changliver cell by SMART (switching mechanism at 5′ end of RNA transcript) technique and analyze its quality. cDNA of Changliver cell was made with RT-PCR and LD-PCR (long-distance PCR), the cDNA library was constructed with SMART cDNA library construction kit. Through testing, the high quality cDNA library containing whole long cDNA of Changliver cell had been constructed. The titer of the amplified cDNA library was 4.5 × 1010 pfu/ml and the averag...

  4. Microbial dissolution of hematite and associated cellular fossilization by reduced iron phases: a study of ancient microbe-mineral surface interactions.

    Science.gov (United States)

    Kolo, Kamal; Konhauser, Kurt; Krumbein, Wolfgang Elisabeth; Ingelgem, Yves Van; Hubin, Annick; Claeys, Philippe

    2009-10-01

    We report here on magnetite- and wustite-encrusted and geometrically oriented microbial-like structures (MLS) attached to the surfaces of hematite (alpha-Fe(2)O(3)) crystals in a banded iron formation. Field emission scanning electron microscope (FE-SEM) and scanning electron microscope (SEM) imaging showed a 3-D network of MLS arranged in 1 microm x approximately 20 microm coccoidal-like chains (CLC) of various geometrical shapes: dichotomous and budding-like protrusions, parallel, intersecting, triangular, or sinusoidal. Individual spheroidal forms ( approximately 1 mum in diameter), some displaying what appears to be division, were also abundant. In addition to their size, morphology, and preferred orientations, a microbial origin of these chains and single spheroidal forms is inferred by the presence of material that resembles extracellular polymeric substances (EPS) extending from the base of the chains along the mineral surface: the attachment sites show circular dissolution pits of about 100 nm diameter. Other thin structures protruding from the CLC are reminiscent of bacterial "nanowires." We were, however, unable to find any extant cells, organic carbon, or even recover DNA from the MLS, which suggests that they, if microbial, are possibly mineralogically replaced casts or mineral encrustations of cells. It is further speculated that, given the nature of the substrate upon which the forms are attached and their preferential orientations, it seems plausible that the "original cells" may have been Fe(III)-reducing bacteria that exploited structural imperfections in the crystal lattice. Importantly, the preservation of the ancient microbial shapes in mineral casts of magnetite, wustite, or both may be an overlooked means by which cellular features in the rock record are retained.

  5. Mechanistic Studies with DNA Polymerases Reveal Complex Outcomes following Bypass of DNA Damage

    Directory of Open Access Journals (Sweden)

    Robert L. Eoff

    2010-01-01

    Full Text Available DNA is a chemically reactive molecule that is subject to many different covalent modifications from sources that are both endogenous and exogenous in origin. The inherent instability of DNA is a major obstacle to genomic maintenance and contributes in varying degrees to cellular dysfunction and disease in multi-cellular organisms. Investigations into the chemical and biological aspects of DNA damage have identified multi-tiered and overlapping cellular systems that have evolved as a means of stabilizing the genome. One of these pathways supports DNA replication events by in a sense adopting the mantra that one must “make the best of a bad situation” and tolerating covalent modification to DNA through less accurate copying of the damaged region. Part of this so-called DNA damage tolerance pathway involves the recruitment of specialized DNA polymerases to sites of stalled or collapsed replication forks. These enzymes have unique structural and functional attributes that often allow bypass of adducted template DNA and successful completion of genomic replication. What follows is a selective description of the salient structural features and bypass properties of specialized DNA polymerases with an emphasis on Y-family members.

  6. Myth Today: the Traditional Understanding of Myth in Critical Theories of Society and the Usefulness of Vernant's Concept of Ancient Greek Mythology for Contemporary Cultural Studies

    Directory of Open Access Journals (Sweden)

    Jože Vogrinc

    2004-12-01

    Full Text Available There is no shortage of speaking about »myths« in contemporary popular culture, and often ancient Greek myths are evoked. »Myth«, however, is usually taken to mean a widely distributed story or belief which is inexact, false and/or fabricated – typically, to manipulate the multitude. In critical theories of society after Marx there are hints of different, theoretically more productive accounts of modern heritage or modern correspondences with Greek mythology. Marx himself has influenced cultural theorists with his account of the relationship between Greek mythology and Greek art as given in his Grundrisse. In his view, mythology serves as the arsenal and foundation of art because in mythology »nature and social forms are already reworked in an unconsciously artistic way by the popular imagination«. This account, together with a hint that there exist (in newspapers modern correspondences with such a relationship, has led to various theoretical elaborations of contemporary popular culture and ideology (e.g. in A. Gramsci, R. Williams, L. Althusser, P. Macherey etc.. None of them, however, retains »myth« as a concept; the word, when used, refers to ideology. Even R. Barthes, who developed a semiological concept of myth, did not refer to its Greek cultural meaning but used it explicitly as a tool for analysing the ideological manipulation of popular culture. C. Lévi-Strauss in social anthropology in general and J.-P. Vernant in the anthropology of ancient worlds have, on the other hand, developed the structural analysis of myths as essential to a culture without reducing it disparagingly to ideology. In our view, it should be possible to transpose Vernant's treatment of myth as a variable and shifting popular account of topics vital to its consumers to the study of today's popular culture and media.

  7. Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics.

    Science.gov (United States)

    Paijmans, Johanna L A; Barnett, Ross; Gilbert, M Thomas P; Zepeda-Mendoza, M Lisandra; Reumer, Jelle W F; de Vos, John; Zazula, Grant; Nagel, Doris; Baryshnikov, Gennady F; Leonard, Jennifer A; Rohland, Nadin; Westbury, Michael V; Barlow, Axel; Hofreiter, Michael

    2017-11-06

    Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (∼18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6]. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Palaeoparasitology - Human Parasites in Ancient Material.

    Science.gov (United States)

    Araújo, Adauto; Reinhard, Karl; Ferreira, Luiz Fernando

    2015-01-01

    Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Study on the Ancient Star Map Carved on the Stone in DPR Korea: Present Status and Prospect

    Science.gov (United States)

    Miley, George; Kim, Kyong Chol; Jong, Sok; Ji, Kwang Nam

    2015-08-01

    Korean Dolmens are the most distinctive and impressive megalithic monuments in Korean history. It has been known that Korean dolmens are typical funerary monuments of the New Stone Age and Bronze Age.We have searched and analyzed some Korean dolmens in astronomical aspects. Korean dolmen consists of two foundation stones, two dammed stones and one cover stone. Two foundation stones were put up on both sides and two small stones were dammed right and left so as to make a room for grave. Then tens of ton stone was covered on them. For example, one of the cover stones of Korean dolmens is 6.3m in length, 4m in width and 70cm in thickness. And the height of this dolmen is about 1.75m.More than twenty thousand dolmens are scattered around the Korean peninsula. Especially the Taedong River basin including Pyongyang that was a capital of Ancient Korea is the birthplace and centre of dolmens in our country, where about fourteen thousand dolmens are distributed. This region is of the highest density in terms of the distribution of dolmen and has every different kind of dolmens. Korean dolmen was very popular from BC.3000 to BC.2000 and began to disappear in the late BC.2000.It is interesting that we have found dolmens with star map on the cover stone. We found two hundred dolmens with various star atlas-like patterns of cup-marks. We analyzed the star maps on the cover stones of some dolmens and identified the constellations such as Big Dipper, Aquila, Cygnus, Draco and so on.It is thought that ancestor carved stars in the sky at that time on the cover stone of Korean dolmens, archaeological stone tombs. We also consider that Korean Dolmen is one of the oldest stone monuments relative to astronomy.We assume that there are many unidentified dolmens with star map on the cover stone and also many unexcavated dolmens in northern part of Korean peninsula yet, which are expected to arouse the great interest of astronomers and archaeologists.

  10. Pulse radiolysis studies of electron migration in DNA from DNA base-radical anions to nitroacridine intercalators in aqueous solution

    International Nuclear Information System (INIS)

    Anderson, R.F.; Patel, K.B.

    1991-01-01

    The reactions of the aquated electron (e aq - ) with intercalators of high reduction potential (nitracrine and related basic nitroacridines) has been investigated by pulse radiolysis in the presence of DNA in aqueous solution. Under conditions where the majority of the e aq - species react initially with DNA bases (high DNA:drug ratios) a slower subsequent electron transfer to the intercalator was observed. The rate of this intra-complex transfer, expressed as DNA base pairs traversed per second, was in the range (1.2-3.1) x 10 5 base pairs s -1 and increased in order of the one-electron reduction potentials of the DNA-bound intercalators. No transfer was seen to the much less electron affinic des-nitro analogue of the nitroacridines. Only a small proportion of the initial DNA base radicals (≤50%) underwent this intra-complex electron transfer. Even for the most efficient electron trap, nitracrine, the apparent mean electron migration distance was only three base pairs. A slow secondary reduction of nitroacridines [(0.08-5.0) x 10 4 base pairs s -1 ] was also observed with a proportion of the essentially immobile . OH-induced DNA radicals. This secondary reaction may well serve as a measure of the mobility of the DNa-bound intercalators. This study therefore implies a lack of extensive migration of DNA-associated electrons in aqueous solution, although it does not exclude the possibility that more mobile electrons produced by direct ionization of DNA might migrate over large distances. (author)

  11. Electron microscopic and physico-chemical studies of DNA complexes with synthetic oligopeptides: binding specificity and DNA compact structures.

    Science.gov (United States)

    Vengerov, Y Y; Semenov, T E; Surovaya, A N; Sidorova NYu; Streltsov, S A; Khorlin, A A; Zhuze, A L; Gursky, G V

    1988-10-01

    Binding to DNA of two synthetic peptides, Val-Thr-Thr-Val-Val-NH-NH-Dns and Thr-Val-Thr-Lys-Val-Gly-Thr-Lsy-Val-Gly-Thr-Val-Val-NH-NH-Dns (where Dns is a residue of 5-dimethylaminonaphthalene-1-sulfonic acid), has been studied by circular dichroism, electron microscopy and fluorescence methods. It has been found that these two peptides can self-associate in aqueous solution as follows from the fact that concentration-dependent changes are observed in the UV absorbance and fluorescence spectra. The two peptides can bind to DNA both in self-associated and monomeric forms. The pentapeptide in the beta-associated form binds more strongly to poly(dG).poly(dC) than to poly[d(A-C)].poly[d(G-T)] and poly(dA).poly(dT) whereas the tridecapeptide exhibits an opposite order of preferences binding more strongly to poly[d(A-C)].poly[d(G-T)] and poly(dA).poly(dT) than to poly(dG).poly(dC). Binding is a cooperative process which is accompanied by the DNA compaction at peptide/DNA base pair ratios greater than 1. At the initial stage of the compaction process, the coalescence of DNA segments covered by bound peptide molecules leads to the formation of DNA loops stabilized by the interaction between peptide molecules bound to different DNA segments. Further increase in the peptide/DNA ratio leads to the formation of rod-like structures each consisting of two or more double-stranded DNA segments. The final stage of the compaction process involves folding of fibrillar macromolecular complexes into a globular structure containing only one DNA molecule.

  12. Climate and Ancient Societies

    DEFF Research Database (Denmark)

    Climate, and human responses to it, have a strongly interconnected relationship. This when climate change occurs, the result of either natural or human causes, societies should react and adapt to these. But do they? If so, what is the nature of that change, and are the responses positive...... or negative for the long-term survival of social groups? In this volume, scholars from diverse disciplines including archaeology, geology and climate sciences explore scientific and material evidence for climate changes in the past, their causes, their effects on ancient societies and how those societies...

  13. Urology in ancient India

    Directory of Open Access Journals (Sweden)

    Sakti Das

    2007-01-01

    Full Text Available The practice of medical and surgical measures in the management of urological ailments prevailed in ancient India from the Vedic era around 3000 BC. Subsequently in the Samhita period, the two stalwarts - Charaka in medicine and Susruta in surgery elevated the art of medicine in India to unprecedented heights. Their elaboration of the etiopathological hypothesis and the medical and surgical treatments of various urological disorders of unparalleled ingenuity still remain valid to some extent in our contemporary understanding. The new generation of accomplished Indian urologists should humbly venerate the legacy of the illustrious pioneers in urology of our motherland.

  14. [Sexuality in Ancient Egypt].

    Science.gov (United States)

    Androutsos, G; Marketos, S

    1994-10-01

    The present article explores the sexuality in ancient Egypt. In particular in this article are presented the ways of concubinage (marriage, concubinage, adultery), the incest, loves of the pharaohs and of the common people, the freedom of choice in garments, the status of the hetairas and of the whores, the sexual perversions (male and female homosexuality, necrophilia, sodomism, bestiality, rape, masturbation, exhibitionism), the operations of the genitals (circumcision, excision, castration) and finally the level of knowledge in gynaecology, fertility, contraception and obstetrics that even today demands our admiration.

  15. Mathematics in ancient Greece

    CERN Document Server

    Dantzig, Tobias

    2006-01-01

    More than a history of mathematics, this lively book traces mathematical ideas and processes to their sources, stressing the methods used by the masters of the ancient world. Author Tobias Dantzig portrays the human story behind mathematics, showing how flashes of insight in the minds of certain gifted individuals helped mathematics take enormous forward strides. Dantzig demonstrates how the Greeks organized their precursors' melange of geometric maxims into an elegantly abstract deductive system. He also explains the ways in which some of the famous mathematical brainteasers of antiquity led

  16. The TL dating of ancient porcelain

    International Nuclear Information System (INIS)

    Leung, P.L.; Stokes, M.J.; Wang Weida; Xia Junding; Zhou Zhixin

    1997-01-01

    The age determination of ancient porcelain using the pre-dose technique in TL dating was reported. The variation of beta dose with depth below the surface of the porcelain slice, the thermal activation characteristic (TAC) for 110 degree C peak, the measurement of paleodose and the estimation of annual dose were studied. The results show that this technique is suitable for authenticity testing of ancient porcelain, but both accuracy and precision for porcelain dating are worse than those for pottery, because porcelain differs from pottery on composition, structure and firing temperature. Besides, some complicated factors in the pre-dose technique would be the possible cause of the greater errors

  17. Application of nuclear analysis techniques in ancient chinese porcelain

    International Nuclear Information System (INIS)

    Feng Songlin; Xu Qing; Feng Xiangqian; Lei Yong; Cheng Lin; Wang Yanqing

    2005-01-01

    Ancient ceramic was fired with porcelain clay. It contains various provenance information and age characteristic. It is the scientific foundation of studying Chinese porcelain to analyze and research the ancient ceramic with modern analysis methods. According to the property of nuclear analysis technique, its function and application are discussed. (authors)

  18. The value of ancient architecture for educational program of masters of architectural space design

    OpenAIRE

    Prishchepa Aleksandr; Maidibor Olesya

    2017-01-01

    The existence of archaeological sites of ancient Greek colony-towns and medieval fortresses gives a real insight into the interaction of all spheres of human activity in ancient times. Ancient Greek Emporium is a vivid example of the architecture, art, archaeology and urban planning synthesis. Archaeological excavations provide an opportunity to study the artefacts of the ancient world belonging to several fields, such as sculpture, decorative arts, fashion design and household. Studying hist...

  19. DNA-binding studies of AV-153, an antimutagenic and DNA repair-stimulating derivative of 1,4-dihydropiridine.

    Science.gov (United States)

    Buraka, E; Chen, C Yu-Chian; Gavare, M; Grube, M; Makarenkova, G; Nikolajeva, V; Bisenieks, I; Brūvere, I; Bisenieks, E; Duburs, G; Sjakste, N

    2014-09-05

    The ability to intercalate between DNA strands determines the cytotoxic activity of numerous anticancer drugs. Strikingly, intercalating activity was also reported for some compounds considered to be antimutagenic. The aim of this study was to determine the mode of interaction of DNA with the antimutagenic and DNA repair-stimulating dihydropyridine (DHP) AV-153. DNA and AV-153 interactions were studied by means of UV/VIS spectroscopy, fluorimetry and infrared spectroscopy. Compound AV-153 is a 1,4 dihydropyridine with ethoxycarbonyl groups in positions 3 and 5. Computer modeling of AV-153 and DNA interactions suggested an ability of the compound to dock between DNA strands at a single strand break site in the vicinity of two pyrimidines, which was confirmed in the present study. AV-153 evidently interacted with DNA, as addition of DNA to AV-153 solutions resulted in pronounced hyperchromic and bathochromic effects on the spectra. Base modification in a plasmid by peroxynitrite only minimally changed binding affinity of the compound; however, induction of single-strand breaks using Fenton's reaction greatly increased binding affinity. The affinity did not change when the ionic strength of the solution was changed from 5 to 150 mM NaCl, although it increased somewhat at 300 mM. Neither was it influenced by temperature changes from 25 to 40°C, however, it decreased when the pH of the solution was changed from 7.4 to 4.7. AV-153 competed with EBr for intercalation sites in DNA: 116 mM of the compound caused a two-fold decrease in fluorescence intensity. FT-IR spectral data analyses indicated formation of complexes between DNA and AV-153. The second derivative spectra analyses indicated interaction of AV-153 with guanine, cytosine and thymine bases, but no interaction with adenine was detected. The antimutagenic substance AV-153 appears to intercalate between the DNA strands at the site of a DNA nick in the vicinity of two pyrimidines. Copyright © 2014 Elsevier

  20. Exploring Ancient Skies A Survey of Ancient and Cultural Astronomy

    CERN Document Server

    Kelley, David H

    2011-01-01

    Exploring Ancient Skies brings together the methods of archaeology and the insights of modern astronomy to explore the science of astronomy as it was practiced in various cultures prior to the invention of the telescope. The book reviews an enormous and growing body of literature on the cultures of the ancient Mediterranean, the Far East, and the New World (particularly Mesoamerica), putting the ancient astronomical materials into their archaeological and cultural contexts. The authors begin with an overview of the field and proceed to essential aspects of naked-eye astronomy, followed by an examination of specific cultures. The book concludes by taking into account the purposes of ancient astronomy: astrology, navigation, calendar regulation, and (not least) the understanding of our place and role in the universe. Skies are recreated to display critical events as they would have appeared to ancient observers—events such as the supernova of 1054 A.D., the "lion horoscope," and the Star of Bethlehem. Explori...

  1. Studies of the silencing of Baculovirus DNA binding protein

    NARCIS (Netherlands)

    Quadt, I.; Lent, van J.W.M.; Knebel-Morsdorf, D.

    2007-01-01

    Baculovirus DNA binding protein (DBP) binds preferentially single-stranded DNA in vitro and colocalizes with viral DNA replication sites. Here, its putative role as viral replication factor has been addressed by RNA interference. Silencing of DBP in Autographa californica multiple

  2. Bioinformatical approaches to RNA structure prediction & Sequencing of an ancient human genome

    DEFF Research Database (Denmark)

    Lindgreen, Stinus

    in the publication of the first genome of an ancient human individual, where close to the theoretical maximum of the genome sequence was recovered with high confidence. Part of the project was the development of the program SNPest for genotyping and SNP calling that models various sources of error and predicts...... tools that exist. The second part has been focused on the mapping and genotyping of ancient genomic DNA. The development of next generation sequencing technologies combined with the use of ancient DNA material present the researchers with some special challenges in the analyses. This work resulted...

  3. DNA adsorption and desorption on mica surface studied by atomic force microscopy

    International Nuclear Information System (INIS)

    Sun Lanlan; Zhao Dongxu; Zhang Yue; Xu Fugang; Li Zhuang

    2011-01-01

    The adsorption of DNA molecules on mica surface and the following desorption of DNA molecules at ethanol-mica interface were studied using atomic force microscopy. By changing DNA concentration, different morphologies on mica surface have been observed. A very uniform and orderly monolayer of DNA molecules was constructed on the mica surface with a DNA concentration of 30 ng/μL. When the samples were immersed into ethanol for about 15 min, various desorption degree of DNA from mica (0-99%) was achieved. It was found that with the increase of DNA concentration, the desorption degree of DNA from the mica at ethanol-mica interface decreased. And when the uniform and orderly DNA monolayers were formed on the mica surface, almost no DNA molecule desorbed from the mica surface in this process. The results indicated that the uniform and orderly DNA monolayer is one of the most stable DNA structures formed on the mica surface. In addition, we have studied the structure change of DNA molecules after desorbed from the mica surface with atomic force microscopy, and found that the desorption might be ascribed to the ethanol-induced DNA condensation.

  4. LD Students and the Ancient Mariner.

    Science.gov (United States)

    Cohen, Barbara L.

    1988-01-01

    Synectics, the making of analogies, was used with learning disabled high school seniors to provide them with a creative process that aids in developing a deeper understanding of literature. After studying Coleridge's "Rime of the Ancient Mariner," the students completed a six-step process and produced a short writing assignment. (VW)

  5. The Challenges of Qualitatively Coding Ancient Texts

    Science.gov (United States)

    Slingerland, Edward; Chudek, Maciej

    2012-01-01

    We respond to several important and valid concerns about our study ("The Prevalence of Folk Dualism in Early China," "Cognitive Science" 35: 997-1007) by Klein and Klein, defending our interpretation of our data. We also argue that, despite the undeniable challenges involved in qualitatively coding texts from ancient cultures,…

  6. Optical tweezers studies of viral DNA packaging: Motor function and DNA confinement in Bacteriophages phi29, lambda, and T4

    Science.gov (United States)

    Smith, Douglas

    2007-03-01

    In the assembly of many viruses a powerful molecular motor translocates the genome into a pre-assembled capsid. We use optical tweezers to directly measure translocation of a single DNA molecule into the viral capsid. Improved techniques allow us to measure initiation and early stages of packaging. With phi29 the DNA terminal protein was found to cause large variations in the starting point of packaging. Removal of this protein results in terminal initiation, permitting more accurate assessment of motor function and DNA confinement forces. We investigated the role of electrostatic repulsion by varying ionic screening of the DNA. The observed trends are in accord with those theoretically expected considering counter-ion competition; however the forces are larger than expected in comparison with recent theories and DNA ejection measurements. We have recently succeeded in extending our methods to study two other phages: lambda and T4. These systems have unique structural and functional features, presenting an opportunity for comparative studies in this family of molecular motors. Initial measurements show that lambda and T4 translocate DNA several times faster than the phi29 motor, but are more sensitive to applied load.

  7. Structure study for the complex of HU protein and DNA

    International Nuclear Information System (INIS)

    Tanaka, Ichiro; Niimura, Nobuo; Tanaka, Isao; Kataoka, Mikio; Mihara, Ken-ichi; Tokunaga, Fumio; Mita, Kazuei.

    1993-01-01

    The small angle X-ray and neutron scattering experiments have revealed the structure of the complex of DNA-binding protein HU and DNA with 20 base pair long in solution. By comparing observed Rg(Radius of gyration) of the complex with calculated Rg of the model, we have concluded that HU protein binds DNA in such a manner that the protein bends the rod-like DNA, and that the binding is rather cooperative. This is the first evidence on the structure of HU-DNA complex obtained by the diffractive method in vitro. These findings give us the view that HU protein might facilitate the DNA's dynamical reactions in a cell by winding DNA like an enzyme, and that there might been a possibility that cells turn on and off the enzymatic actions by changing the concentration of HU protein. (author)

  8. Studies on the fate of homologous DNA applied to seedlings of Matthiola incana.

    Science.gov (United States)

    Hemleben, V; Ermisch, N; Kimmich, D; Leber, B; Peter, G

    1975-08-15

    Seedlings of Matthiola incana (crucifer) are able to take up exogenous homologous DNA by the roots. DNA homogenously labelled with [3H]adenine and 5-bromodeoxyuridine is incorporated into the plants in a macromolecular form. Intact donor DNA and a fraction with a buoyant density intermediate between that of the donor and the recipient DNA can be recovered. Analysis of this intermediate fraction by ultrasonication and alkali treatment allows the suggestion that homologous DNA is integrated as a double-stranded DNA which becomes covalently linked to the recipient DNA. Control experiments in which seedlings were incubated in a mixture simulating donor DNA degradation products in the presence and absence of unlabelled competitors suggest that these results are not due to the breakdown of donor DNA and reincorporation of the products during DNA synthesis in the recipient plants. When ultrasonicated or thermally denatured DNA is applied to the plants it may be degraded and reused for recipient DNA synthesis but it is not recovered in a macromolecular form. The possibility that the intermediate DNA fraction arises by bacterial contamination of the plants can be excluded by several arguments. Autoradiographic studies show that at least part of the radioactivity of the donor DNA taken up by the plants is associated with the cell nucleus.

  9. Finding the founder of Stockholm - A kinship study based on Y-chromosomal, autosomal and mitochondrial DNA

    DEFF Research Database (Denmark)

    Malmström, Helena; Vretemark, Maria; Tillmar, Andreas

    2012-01-01

    these conclusions, ultimately leading to the reopening and reexamination of the grave in 2002. Ancient DNA-analyses were performed to investigate if the relationship between the three individuals matched what we would expect if the individuals were Birger, Erik and Mechtild. We used pyrosequencing of Y......-chromosomal and autosomal SNPs and compared the results with haplogroup frequencies of modern Swedes to investigate paternal relations. Possible maternal kinship was investigated by deep FLX-sequencing of overlapping mtDNA amplicons. The authenticity of the sequences was examined using data from independent extractions...

  10. Localized surface plasmon resonance (LSPR) study of DNA hybridization at single nanoparticle transducers

    International Nuclear Information System (INIS)

    Schneider, T.; Jahr, N.; Jatschka, J.; Csaki, A.; Stranik, O.; Fritzsche, W.

    2013-01-01

    The effect of DNA–DNA interaction on the localized surface plasmon resonance of single 80 nm gold nanoparticles is studied. Therefore, both the attachment of the capture DNA strands at the particle surface and the sequence-specific DNA binding (hybridization) of analyte DNA to the immobilized capture DNA is subject of investigations. The influence of substrate attachment chemistry, the packing density of DNA as controlled by an assisting layer of smaller molecules, and the distance as increased by a linker on the LSPR efficiency is investigated. The resulting changes in signal can be related to a higher hybridization efficiency of the analyte DNA to the immobilized capture DNA. The subsequent attachment of additional DNA strands to this system is studied, which allows for a multiple step detection of binding and an elucidation of the resulting resonance shifts. The detection limit was determined for the utilized DNA system by incubation with various concentration of analyte DNA. Although the method allows for a marker-free detection, we show that additional markers such as 20 nm gold particle labels increase the signal and thereby the sensitivity significantly. The study of resonance shift for various DNA lengths revealed that the resonance shift per base is stronger for shorter DNA molecules (20 bases) as compared to longer ones (46 bases).

  11. Ancient Greek new music

    Directory of Open Access Journals (Sweden)

    Martin Žužek

    2000-12-01

    Full Text Available In this article I use a contextual approach to questions about the revolutionary »new music« in ancient Greece. This view is different from the nowadays most common formalistk view. Rather than analyze textual sources stylistically, I will try to present the available lata in the context of the structure and events of the Athenian society at a tirne when a wave of »new« poetics appeared. In the following discussion it is argued that the »new music« and the phenomena of the destruction of mousiké connected with it are not an esthetical novum, but more a consequence of the change of the discursive practice, where a musical poetry became less important and needless.

  12. Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy

    Science.gov (United States)

    Chikira, Makoto; Ng, Chew Hee; Palaniandavar, Mallayan

    2015-01-01

    The interaction of simple and ternary Cu(II) complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II) complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR) spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements. PMID:26402668

  13. Illuminating the evolution of equids and rodents with next-generation sequencing of ancient specimens

    DEFF Research Database (Denmark)

    Mouatt, Julia Thidamarth Vilstrup

    The sequencing of ancient DNA provides perspectives on the genetic history of past populations and extinct species. However, ancient DNA research presents specific limitations mostly due to DNA survival, damage and contamination. Yet with stringent laboratory procedures, the sensitivity of target...... enrichment methods and the massive throughput and latest advances within DNA sequencing, the field of ancient DNA has flourished in later years. Those advances have even enabled the sequencing of complete genomes from the past, moving the field into genomic sciences. In this thesis we have used these latest...... ial genomes of extant and extinct taxa, and dated major radiation events within Equidae. We have also revealed the phylogenetic origins of hutias, a group of capromyid rodents from the West Indies using museum specimens and a museomic approach, and at the other end of the spectrum, characterized...

  14. Ancient and Medieval Cosmology in Armenian Highland

    Science.gov (United States)

    Farmanyan, Sona V.; Mickaelian, Areg M.

    2016-12-01

    Humankind has always sought to recognize the nature of various sky related phenomena and tried to give them explanations. It is especially vivid in ancient cultures, many of which are related to the Middle East. The purpose of this study is to identify ancient Armenian's pantheistic and cosmological perceptions, world view, notions and beliefs. By this study we answer the question "How did the Universe work in Ancient Armenian Highland?" The paper focuses on the structure of the Universe and many phenomena of nature that have always had major influence on ancient Armenians thinking. Here we weave together astronomy, anthropology and mythology of Armenia, and scientific thinking revealed in local astronomy traditions. The initial review of the study covers Moses of Khoren, Yeznik of Koghb, Anania Shirakatsi and other 5th-7th centuries historians' and scientists' records about the Universe related superstitious beliefs and cosmological understanding. By discussing and comparing Universe structure in various regional traditions, myths, folk songs and phraseological units we very often came across "seven worlds", "seven earths" and "seven layers" concepts. We draw parallels between scientific and mythological Earth and Heaven and thus find similar number of layers on both of the ancient and modern thinking. In the article we also give some details about the tripartite structure of the Universe and how these parts are connected with axis. This axis is either a column or a Cosmic Tree (Kenatz Tsar). In Armenian culture the preliminary meanings of the Kenatz Tsar are more vivid in folk songs (Jan gyulums), plays, epic, and so on, which was subsequently mixed with religious and spiritual views. We conclude that the perception of the Universe structure and celestial objects had a significant impact on culture and worldview of the people of the Armenian Highland; particularly it was one of the bases of the regional cultural diversity.

  15. The study of electrical conductivity of DNA molecules by scanning tunneling spectroscopy

    Science.gov (United States)

    Sharipov, T. I.; Bakhtizin, R. Z.

    2017-10-01

    An interest to the processes of charge transport in DNA molecules is very high, due to perspective of their using in nanoelectronics. The original sample preparation for studying electrical conductivity of DNA molecules by scanning tunneling spectroscopy has been proposed and tested. The DNA molecules immobilized on gold surface have been imaged clearly and their current-voltage curves have been measured.

  16. Polymerase chain reaction-mediated DNA fingerprinting for epidemiological studies on Campylobacter spp

    NARCIS (Netherlands)

    Giesendorf, B A; Goossens, H; Niesters, H G; Van Belkum, A; Koeken, A; Endtz, H P; Stegeman, H; Quint, W G

    The applicability of polymerase chain reaction (PCR)-mediated DNA typing, with primers complementary to dispersed repetitive DNA sequences and arbitrarily chosen DNA motifs, to study the epidemiology of campylobacter infection was evaluated. With a single PCR reaction and simple gel electrophoresis,

  17. Spectroscopic and molecular docking studies on the interaction of antiviral drug nevirapine with calf thymus DNA.

    Science.gov (United States)

    Moghadam, Neda Hosseinpour; Salehzadeh, Sadegh; Shahabadi, Nahid

    2017-09-02

    The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations. The molecular docking results suggested that nevirapine prefers to bind on the minor groove of ct-DNA.

  18. Ancient Egypt in our Cultural Heritage?

    Directory of Open Access Journals (Sweden)

    Vera Vasiljević

    2016-02-01

    Full Text Available Inspiration derived from ancient Egypt is usually expressed through the Egyptian motifs in arts and popular culture of the 19th and 20th centuries, as well as through the non-scientific interpretations of the culture, very much based upon the Renaissance ones. The number and variety of material and non-material traces of this fascination are most expressed in the countries where, along with the early support for the institutional development of Egyptology, there existed economically potent educated middle classes (Western and Central Europe, USA, but may also be traced elsewhere. The public fascination by ancient Egypt has not ceased by the times of foundation of Egyptology, marked by the decipherment of the hieroglyphic script in 1822. Until the end of the 20th century Egyptologists have rarely dealt with the prelude to their discipline, limiting their interest to the critical approach to ancient sources and to noting the attempts to interpret the hieroglyphic script and the function of pyramids. However, the rising importance of the reception studies in other disciplines raised the interest of Egyptologists for the "fascination of Egypt", thus changing the status of various modes of expressing "Egyptomania" – they have thus become a part of the cultural heritage, registered, documented, preserved and studied. The research of this kind is only beginning in Serbia. The line of inquiry enhances the knowledge of the scope, manifestations and roles of the interest in Egypt, not limited by the national or political borders. On the other hand, the existence of the cultural heritage similar to the wider European view of ancient Egypt – short remarks by Jerotej Račanin, Kandor by Atanasije Stojković, the usage of architectural motifs derived from Egypt, the emergence of small private collections, to mention several early examples – all show that the research into the reception of ancient Egypt may contribute to the knowledge about the history

  19. Molecular studies of fibroblasts transfected with hepatitis B virus DNA

    International Nuclear Information System (INIS)

    Chen, M.L.; Hood, A.; Thung, S.N.; Gerber, M.A.

    1987-01-01

    Two subclones (D7 and F8) derived from an NIH 3T3 mouse fibroblast cell line after transfection with hepatitis B virus (HBV) genomes, secreted significantly different amounts of HBsAg and HBeAg. DNA extracted from the subclones revealed only integrated and no extrachromosomal HBV DNA sequences as determined by the Southern blot technique with a /sup 32/P-labeled full length HBV DNA probe. The amount and integration sites of HBV sequences were significantly different in the two subclones. HBV DNA sequences coding for HBsAg and HBcAg were detected by alkaline phosphatase-conjugated, single-stranded synthetic gene-specific oligonucleotide probes revealing a larger number of copies in D7 DNA than in F8 DNA. Using a biotinylated probe for in situ hybridization, HBV DNA was found in the nuclei of all D7 cells with predominant localization to a single chromsome, but only in 10-20% of F8 cells. These observations demonstrate different integration patterns of HBV and DNA in two subclones derived from a transfected cell line and suggest that the amount of integrated HBV DNA is proportional to the amount of HBV antigens produced

  20. Fast characterization of C-glycoside acetophenones in Medemia argun male racemes (an Ancient Egyptian palm) using LC-MS analyses and computational study with their antioxidant effect

    Science.gov (United States)

    Ben Said, Ridha; Hamed, Arafa I.; Essalah, Khaled; Al-Ayed, Abdullah S.; Boughdiri, Salima; Tangour, Bahoueddine; Kowalczyk, Mariusz; Moldoch, Jaroslaw; Mahalel, Usama A.; Olezek, Wolesow; Stochmal, Anna

    2017-10-01

    Medemia argun is an ancient endemic palm growing in Nubian Desert of Egypt and Sudan. Liquid chromatography coupled with mass spectrometry in negative ion mode (LC/ESI-MS) has proved to be a potent tool for rapid identification and characterization of complex phytochemicals in male racemes of M. argun. A total of seven compounds were tentatively identified comprising of two C-glycoside acetophenones, along with the known compounds one stilbene derivative and four known flavonol derivatives from 40% methanolic portion. The product ions of acetophenone derivatives [M-H]- were shown to be cross-ring cleavages of the hexoside moiety [M-(90/120)-H]- characteristic for C-glycoside linkage. The position of Csbnd C-linkage was elucidated by DFT study using the Fukui functions and descriptors. The results revealed that hexose was conjugated with aglycones at C3 or C5. In addition, the theoretical antioxidant activity of compounds 6 and 7 was evaluated by using Bond Dissociation Enthalpy (BDE).