WorldWideScience

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 ...

  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. ACHIEVEMENTS AND PECULIARITIES IN STUDIES OF ANCIENT DNA AND DNA FROM COMPLICATED FORENSIC SPECIMENS

    OpenAIRE

    Grigorenko, A.; Borinskaya, S.; Yankovsky, N.; E. Rogaev

    2009-01-01

    Studies of ancient DNA specimens started 25 years ago. At that time short mitochondrial DNA (mtDNA) fragments were the main targets in ancient DNA studies. The last three years were especially productive in the development of new methods of DNA purification and analysis. Complete mtDNA molecules and relatively large fragments of nuclear DNA are the targets of ancient DNA studies today. Ancient DNA studies allowed us to study organisms that went extinct more than ten thousand years ago, to rec...

  4. Comparative study of ancient DNA extraction methods for archaeological plant remains

    OpenAIRE

    Moore, Jason Nicholas

    2011-01-01

    Despite the potential for plant ancient DNA (aDNA) to address important archaeological questions, there are significantly fewer studies of plant aDNA compared to human and animal aDNA, partially due to a lack of research on DNA extraction methods for ancient plant remains. The current study uses heat to degrade modern corn, pea, and squash seeds to simulate degraded DNA associated with archaeological macro-botanical remains. I then compare DNA recovery efficiencies of three common DNA extract...

  5. Phylogenetic estimation of timescales using ancient DNA

    DEFF Research Database (Denmark)

    Molak, Martyna; Lorenzen, Eline; Shapiro, Beth;

    2013-01-01

    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...

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

    DEFF Research Database (Denmark)

    Sandoval Velasco, Marcela

    preservation, degradation and contamination, ancient DNA research presents significant limitations and challenges. Until recently, it was thought that DNA did not survive more than few hundred thousand years, and that it was impossible to retrieve whole genome data from ancient samples preserved under...... suboptimal conditions. However, experimental and analytical methods have been developed to overcome these limitations. Rigorous laboratory procedures, optimized capture enrichment methods coupled to high-throughput sequencing platforms, and expanding modern reference datasets have enabled the generation...... of complete ancient genomes from numerous extinct and extant species, including humans and hominins. In addition, the field has gradually opened the opportunity to study human populations through history. In this thesis I have applied, tested and investigated the performance of different ancient DNA...

  7. 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.

  8. Mitogenomic analyses from ancient DNA

    DEFF Research Database (Denmark)

    Paijmans, Johanna L.A.; Gilbert, M Thomas P; Hofreiter, Michael

    2013-01-01

    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....... To date, at least 124 partially or fully assembled mitogenomes from more than 20 species have been obtained, and, given the rapid progress in sequencing technology, this number is likely to dramatically increase in the future. The increased information content offered by analysing full mitogenomes has...

  9. Re-inventing ancient human DNA

    OpenAIRE

    Knapp, Michael; Lalueza-Fox, Carles; Hofreiter, M.

    2015-01-01

    For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, beca...

  10. Analysis of Ancient DNA in Microbial Ecology.

    Science.gov (United States)

    Gorgé, Olivier; Bennett, E Andrew; Massilani, Diyendo; Daligault, Julien; Pruvost, Melanie; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota. PMID:26791510

  11. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific.

    Science.gov (United States)

    Thomson, Vicki A; Lebrasseur, Ophélie; Austin, Jeremy J; Hunt, Terry L; Burney, David A; Denham, Tim; Rawlence, Nicolas J; Wood, Jamie R; Gongora, Jaime; Girdland Flink, Linus; Linderholm, Anna; Dobney, Keith; Larson, Greger; Cooper, Alan

    2014-04-01

    The human colonization of Remote Oceania remains one of the great feats of exploration in history, proceeding east from Asia across the vast expanse of the Pacific Ocean. Human commensal and domesticated species were widely transported as part of this diaspora, possibly as far as South America. We sequenced mitochondrial control region DNA from 122 modern and 22 ancient chicken specimens from Polynesia and Island Southeast Asia and used these together with Bayesian modeling methods to examine the human dispersal of chickens across this area. We show that specific techniques are essential to remove contaminating modern DNA from experiments, which appear to have impacted previous studies of Pacific chickens. In contrast to previous reports, we find that all ancient specimens and a high proportion of the modern chickens possess a group of unique, closely related haplotypes found only in the Pacific. This group of haplotypes appears to represent the authentic founding mitochondrial DNA chicken lineages transported across the Pacific, and allows the early dispersal of chickens across Micronesia and Polynesia to be modeled. Importantly, chickens carrying this genetic signature persist on several Pacific islands at high frequencies, suggesting that the original Polynesian chicken lineages may still survive. No early South American chicken samples have been detected with the diagnostic Polynesian mtDNA haplotypes, arguing against reports that chickens provide evidence of Polynesian contact with pre-European South America. Two modern specimens from the Philippines carry haplotypes similar to the ancient Pacific samples, providing clues about a potential homeland for the Polynesian chicken. PMID:24639505

  12. Ancient DNA in Greece. Problems and prospects

    International Nuclear Information System (INIS)

    The promise associated with early 'ancient DNA' results has not been translated into routine techniques of value to archaeologists. The reasons for this are partly technical - ancient DNA analysis is an extremely difficult technique - and partly practical - ancient DNA analysis is often an 'after thought' to an archaeological project. In this paper ancient human DNA analysis is briefly reviewed paying particular attention to specimens originating from Greek archaeological contexts. Problems commonly encountered during ancient DNA research are summarised and recommendations for future strategies in the application of ancient DNA in archaeology are proposed. (author)

  13. Fossil avian eggshell preserves ancient DNA

    DEFF Research Database (Denmark)

    Oskam, Charlotte L; Haile, James; 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...

  14. Detecting hybridization using ancient DNA.

    Science.gov (United States)

    Schaefer, Nathan K; Shapiro, Beth; Green, Richard E

    2016-06-01

    It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history.

  15. Use of RAPD and PCR double amplification in the study of ancient DNA

    Directory of Open Access Journals (Sweden)

    F. Balzano

    2011-01-01

    Full Text Available This project analysed the DNA extracted from bones of ancient sheep which have been brought to light in Sardinian different archaeological sites. In order to better analyse this highly fragmented DNA, a double amplification technique was chosen. The first approach consisted of RAPD-PCR abd the second one in classic PCR. The RAPD-PCR amplified random fragments and allowed the production of numerous amplicons. The products of RAPD amplification have been amplified, more specifically, by the second PCR using primers for a sequence of 176 bp of mitochondrial D-loop region. These DNA fragments have been sequenced and the sequence analysis has confirmed that it belonged to Ovis aries. Consequently, this provedure can be considered a valid tool to perform amplification of degraded DNA, such as ancient DNA.

  16. Ancient and modern environmental DNA

    DEFF Research Database (Denmark)

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

    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...... 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....

  17. Damage and repair of ancient DNA

    DEFF Research Database (Denmark)

    Mitchell, David; Willerslev, Eske; Hansen, Anders

    2005-01-01

    , and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived......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...... degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes...

  18. 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...... modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in...... paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes....

  19. 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.

  20. 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

    The use of wool derived from sheep (Ovis aries) hair shafts is widespread in ancient and historic textiles. Given that hair can represent a valuable source of ancient DNA, wool may represent a valuable genetic archive for studies on the domestication of the sheep. However, both the quality...... to considerable DNA degradation. Lastly, we demonstrate that mtDNA at least can be PCR-amplified, cloned and sequenced from a range of archaeological and historic Danish, Flemmish and Greenlandic wool textile samples. In summary, our data suggest that wool offers a promising source for future ancient...... mitochondrial DNA studies....

  1. 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)

  2. 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...... 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...... 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...

  3. Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

    OpenAIRE

    Rohland, Nadin; Harney, Eadaoin; Mallick, Swapan; Nordenfelt, Susanne; Reich, David

    2015-01-01

    The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popula...

  4. Preservation potential of ancient plankton DNA in Pleistocene marine sediments

    NARCIS (Netherlands)

    Boere, A.C.; Rijpstra, W.I.C.; de Lange, G.J.; Sinninghe Damsté, J.S.; Coolen, M.J.L.

    2011-01-01

    Recent studies have shown that ancient plankton DNA can be recovered from Holocene lacustrine and marine sediments, including from species that do not leave diagnostic microscopic fossils in the sediment record. Therefore, the analysis of this so-called fossil plankton DNA is a promising approach fo

  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.

  6. 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...... geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long...... 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....

  7. Unravelling the complexity of domestication: a case study using morphometrics and ancient DNA analyses of archaeological pigs from Romania.

    Science.gov (United States)

    Evin, Allowen; Flink, Linus Girdland; Bălăşescu, Adrian; Popovici, Dragomir; Andreescu, Radian; Bailey, Douglas; Mirea, Pavel; Lazăr, Cătălin; Boroneanţ, Adina; Bonsall, Clive; Vidarsdottir, Una Strand; Brehard, Stéphanie; Tresset, Anne; Cucchi, Thomas; Larson, Greger; Dobney, Keith

    2015-01-19

    Current evidence suggests that pigs were first domesticated in Eastern Anatolia during the ninth millennium cal BC before dispersing into Europe with Early Neolithic farmers from the beginning of the seventh millennium. Recent ancient DNA (aDNA) research also indicates the incorporation of European wild boar into domestic stock during the Neolithization process. In order to establish the timing of the arrival of domestic pigs into Europe, and to test hypotheses regarding the role European wild boar played in the domestication process, we combined a geometric morphometric analysis (allowing us to combine tooth size and shape) of 449 Romanian ancient teeth with aDNA analysis. Our results firstly substantiate claims that the first domestic pigs in Romania possessed the same mtDNA signatures found in Neolithic pigs in west and central Anatolia. Second, we identified a significant proportion of individuals with large molars whose tooth shape matched that of archaeological (likely) domestic pigs. These large 'domestic shape' specimens were present from the outset of the Romanian Neolithic (6100-5500 cal BC) through to later prehistory, suggesting a long history of admixture between introduced domestic pigs and local wild boar. Finally, we confirmed a turnover in mitochondrial lineages found in domestic pigs, possibly coincident with human migration into Anatolia and the Levant that occurred in later prehistory.

  8. Authenticity of Ancient-DNA Results: A Statistical Approach

    OpenAIRE

    Spencer, Matthew; Howe, Christopher J.

    2004-01-01

    Although there have been several papers recommending appropriate experimental designs for ancient-DNA studies, there have been few attempts at statistical analysis. We assume that we cannot decide whether a result is authentic simply by examining the sequence (e.g., when working with humans and domestic animals). We use a maximum-likelihood approach to estimate the probability that a positive result from a sample is (either partly or entirely) an amplification of DNA that was present in the s...

  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. Ancient DNA from marine mammals

    DEFF Research Database (Denmark)

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

    2012-01-01

    Marine mammals have long generation times and broad, difficult to sample distributions, which makes inferring evolutionary and demographic changes using field studies of extant populations challenging. However, molecular analyses from sub-fossil or historical materials of marine mammals such as b...

  11. Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The archaeological site of Sampula cemetery was located about 14 km to the southwest of the Luo County in Xinjiang Khotan, China, belonging to the ancient Yutian kingdom. 14C analysis showed that this cemetery was used from 217 B.C. to 283 A.D.Ancient DNA was analyzed by 364 bp of the mitochondrial DNA hypervariable region Ⅰ (mtDNA HVR-Ⅰ), and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region. We successfully extracted and sequenced intact stretches of maternally inherited mtDNA from 13 out of 16 ancient Sampula samples. The analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population with both European and Asian characteristics. Median joining network of U3 sub-haplogroup and multi-dimensional scaling analysis all showed that the ancient Sampula had maternal relationship with Ossetian and Iranian.

  12. The first attested extraction of ancient DNA in legumes (Fabaceae

    Directory of Open Access Journals (Sweden)

    Aleksandar M. Mikić

    2015-11-01

    Full Text Available Ancient DNA (aDNA is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analysing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum and bitter vetch (Vicia ervilia from Hissar, southeast Serbia, dated to 1,350 - 1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl-1 of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK and rbcL among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighbouring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide.

  13. The First Attested Extraction of Ancient DNA in Legumes (Fabaceae).

    Science.gov (United States)

    Mikić, Aleksandar M

    2015-01-01

    Ancient DNA (aDNA) is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae) are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analyzing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum) and bitter vetch (Vicia ervilia) from Hissar, southeast Serbia, dated to 1,350-1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB) method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl(-1) of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK, and rbcL) among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighboring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide. PMID:26635833

  14. Ancient mtDNA sequences from the First Australians revisited.

    Science.gov (United States)

    Heupink, Tim H; Subramanian, Sankar; Wright, Joanne L; Endicott, Phillip; Westaway, Michael Carrington; Huynen, Leon; Parson, Walther; Millar, Craig D; Willerslev, Eske; Lambert, David M

    2016-06-21

    The publication in 2001 by Adcock et al. [Adcock GJ, et al. (2001) Proc Natl Acad Sci USA 98(2):537-542] in PNAS reported the recovery of short mtDNA sequences from ancient Australians, including the 42,000-y-old Mungo Man [Willandra Lakes Hominid (WLH3)]. This landmark study in human ancient DNA suggested that an early modern human mitochondrial lineage emerged in Asia and that the theory of modern human origins could no longer be considered solely through the lens of the "Out of Africa" model. To evaluate these claims, we used second generation DNA sequencing and capture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same four Willandra Lakes and Kow Swamp 8 (KS8) remains studied in the work by Adcock et al. Two of the remains sampled contained no identifiable human DNA (WLH15 and WLH55), whereas the Mungo Man (WLH3) sample contained no Aboriginal Australian DNA. KS8 reveals human mitochondrial sequences that differ from the previously inferred sequence. Instead, we recover a total of five modern European contaminants from Mungo Man (WLH3). We show that the remaining sample (WLH4) contains ∼1.4% human DNA, from which we assembled two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian haplotype belonging to haplogroup S2 that we sequenced to a high coverage. The other was a contaminating modern European mitochondrial haplotype. Although none of the sequences that we recovered matched those reported by Adcock et al., except a contaminant, these findings show the feasibility of obtaining important information from ancient Aboriginal Australian remains. PMID:27274055

  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...

  16. Analysis of the three Yersinia pestis CRISPR loci provides new tools for phylogenetic studies and possibly for the investigation of ancient DNA.

    Science.gov (United States)

    Vergnaud, Gilles; Li, Yanjun; Gorgé, Olivier; Cui, Yujun; Song, Yajun; Zhou, Dongsheng; Grissa, Ibtissem; Dentovskaya, Svetlana V; Platonov, Mikhail E; Rakin, Alexander; Balakhonov, Sergey V; Neubauer, Heinrich; Pourcel, Christine; Anisimov, Andrey P; Yang, Ruifu

    2007-01-01

    The precise nature of the pathogen having caused early plague pandemics is uncertain. Although Yersinia pestis is a likely candidate for all three plague pandemics, the very rare direct evidence that can be deduced from ancient DNA (aDNA) analysis is controversial. Moreover, which of the three biovars, Antiqua, Medievalis or Orientalis, was associated with these pandemics is still debated. There is a need for phylogenetic analysis performed on Y. pestis strains isolated from countries from which plague probably arose and is still endemic. In addition there exist technical difficulties inherent to aDNA investigations and a lack of appropriate genetic targets. The recently described CRISPRs (clustered regularly interspaced short palindromic repeats) may represent such a target. CRISPR loci consist of a succession of highly conserved regions separated by specific "spacers" usually of viral origin. To be of use, data describing the mechanisms of evolution and diversity of CRISPRs in Y. pestis, its closest neighbors, and other species which might contaminate ancient DNA, are necessary. The investigation of closely related Y. pestis isolates has revealed recent mutation events in which elements constituting CRISPRs were acquired or lost, providing essential insight on their evolution. Rules deduced represent the basis for subsequent interpretation. In the present study, the CRISPR loci from representative Y. pestis and Yersinia pseudotuberculosis strains were investigated by PCR amplification and sequence analysis. The investigation of this wider panel of strains, including other subspecies or ecotypes within Y. pestis and also Y. pseudotuberculosis strains provides a database of the existing CRISPR spacers and helps predict the expected CRISPR structure of the Y. pestis ancestor. This knowledge will open the way to the development of a spoligotyping assay, in which spacers can be amplified even from highly degraded DNA samples. The data obtained show that CRISPR

  17. Pitfalls in the analysis of ancient human mtDNA

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The retrieval of DNA from ancient human specimens is not always successful owing to DNA deterioration and contamination although it is vital to provide new insights into the genetic structure of ancient people and to reconstruct the past history. Normally, only short DNA fragments can be retrieved from the ancient specimens. How to identify the authenticity of DNA obtained and to uncover the information it contained are difficult. We employed the ancient mtDNAs reported from Central Asia (including Xinjiang, China) as an example to discern potentially extraneous DNA contamination based on the updated mtDNA phylogeny derived from mtDNA control region, coding region, as well as complete sequence information. Our results demonstrated that many mtDNAs reported are more or less problematic. Starting from a reliable mtDNA phylogeney and combining the available modern data into analysis, one can ascertain the authenticity of the ancient DNA, distinguish the potential errors in a data set, and efficiently decipher the meager information it harbored. The reappraisal of the mtDNAs with the age of more than 2000 years from Central Asia gave support to the suggestion of extensively (pre)historical gene admixture in this region.

  18. 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

    Although ancient DNA from sediments (sedaDNA) has been used to investigate past ecosystems, the approach has never been directly compared with the traditional methods of pollen and macrofossil analysis. We conducted a comparative survey of 18 ancient permafrost samples spanning the Late Pleistocene...... (46-12.5 thousand years ago), from the Taymyr Peninsula in northern Siberia. The results show that pollen, macrofossils and sedaDNA are complementary rather than overlapping and, in combination, reveal more detailed information on plant palaeocommunities than can be achieved by each individual...... 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...

  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 conventio...

  20. Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus.

    Directory of Open Access Journals (Sweden)

    Stefan Prost

    Full Text Available BACKGROUND: Global temperature increased by approximately half a degree (Celsius within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus, which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. RESULTS: Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (Bølling/Allerød warming phase at 14.5 kyrs BP. CONCLUSION: Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population

  1. Reconstructing the evolutionary history of China: a caveat about inferences drawn from ancient DNA.

    Science.gov (United States)

    Yao, Yong-Gang; Kong, Qing-Peng; Man, Xiao-Yong; Bandelt, Hans-Jürgen; Zhang, Ya-Ping

    2003-02-01

    The decipherment of the meager information provided by short fragments of ancient mitochondrial DNA (mtDNA) is notoriously difficult but is regarded as a most promising way toward reconstructing the past from the genetic perspective. By haplogroup-specific hypervariable segment (HVS) motif search and matching or near-matching with available modern data sets, most of the ancient mtDNAs can be tentatively assigned to haplogroups, which are often subcontinent specific. Further typing for mtDNA haplogroup-diagnostic coding region polymorphisms, however, is indispensable for establishing the geographic/genetic affinities of ancient samples with less ambiguity. In the present study, we sequenced a fragment (approximately 982 bp) of the mtDNA control region in 76 Han individuals from Taian, Shandong, China, and we combined these data with previously reported samples from Zibo and Qingdao, Shandong. The reanalysis of two previously published ancient mtDNA population data sets from Linzi (same province) then indicates that the ancient populations had features in common with the modern populations from south China rather than any specific affinity to the European mtDNA pool. Our results highlight that ancient mtDNA data obtained under different sampling schemes and subject to potential contamination can easily create the impression of drastic spatiotemporal changes in the genetic structure of a regional population during the past few thousand years if inappropriate methods of data analysis are employed.

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

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2006-01-01

    ) report that direct sequencing of ancient microbial DNA produced a sequence resembling (for example) Treponerma pallidum (the causative agent of venereal syphilis) even in the absence of real T. pallidum, simply due to the presence of diverse bacterial DNA in the experiment. In addition, the limited...

  3. Analysis of Mitochondrial DNA from the Ancient Tombs of Turfan

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    MtDNA was successfully extracted from ten individual bones (femurs) in the tombs of ancient Jushi in Turfan basin, dated back to the year about 3 000-2 500 years ago. By means of four overlapping primers, we got nucleotide sequence of the 218bp length. Ancient mtDNA was analyzed by the sequencing of hypervariable region Ⅰ of the mtDNA control region. The result shows that 9 haplotypes with 24 polymorphic sites were obtained. The phylogenetic analysis indicated that Mongolians and Altai are the population genetically closest to the Jushi groups and Jushi mtDNA pool being an admixture of eastern Asian and European lineages. So our preliminary data imply that an ancient mingling of Euro-Asian population had existed in Turfan basin prior to the early Iron Age.

  4. 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.

  5. 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, A.; Orlando, L.;

    2013-01-01

    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...... 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 10,650calyrBP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less...

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

    Science.gov (United States)

    Wales, Nathan; Carøe, Christian; Sandoval-Velasco, Marcela; Gamba, Cristina; Barnett, Ross; Samaniego, José Alfredo; Madrigal, Jazmín Ramos; Orlando, Ludovic; Gilbert, M Thomas P

    2015-12-01

    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 DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size < 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method.

  7. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

    Directory of Open Access Journals (Sweden)

    Andaine Seguin-Orlando

    Full Text Available Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

  8. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

    Science.gov (United States)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel; Stagegaard, Julia; Alberdi, Maria T; Prado, José Luis; Prieto, Alfredo; Willerslev, Eske; Orlando, Ludovic

    2013-01-01

    Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.

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

    Science.gov (United States)

    DNA residues may preserve on ancient stone tools used to process animals. We studied 24 stone tools recovered from the Bugas-Holding site in northwestern Wyoming. Nine tools that yielded DNA included five bifaces, two side scrapers, one end scraper, and one utilized flake. The...

  10. 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

  11. Short sequence effect of ancient DNA on mammoth phylogenetic analyses

    Institute of Scientific and Technical Information of China (English)

    Guilian SHENG; Lianjuan WU; Xindong HOU; Junxia YUAN; Shenghong CHENG; Bojian ZHONG; Xulong LAI

    2009-01-01

    The evolution of Elephantidae has been intensively studied in the past few years, especially after 2006. The molecular approaches have made great contribution to the assumption that the extinct woolly mammoth has a close relationship with the Asian elephant instead of the African elephant. In this study, partial ancient DNA sequences of cytochrome b (cyt b) gene in mitochondrial genome were successfully retrieved from Late Pleistocene Mammuthus primigenius bones collected from Heilongjiang Province in Northeast China. Both the partial and complete homologous cyt b gene sequences and the whole mitochondrial genome sequences extracted from GenBank were aligned and used as datasets for phylogenetic analyses. All of the phylogenetic trees, based on either the partial or the complete cyt b gene, reject the relationship constructed by the whole mitochondrial genome, showing the occurrence of an effect of sequence length of cyt b gene on mammoth phylogenetic analyses.

  12. 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.

  13. Ancient DNA study of the remains of putative infanticide victims from the Yewden Roman villa site at Hambleden, England

    OpenAIRE

    Hassan, A; Brown, K; Eyers, J.; Brown, T; Mays, S.

    2014-01-01

    Previous analysis of the perinatal infant burials from Romano-British Yewden villa, Hambleden, indicated the practice of infanticide at that site. We attempted to determine whether this practice was specifically targeted at one sex or other by determining the sex of the infants using analysis of fragments of the amelogenin gene. We also analysed mtDNA in order to shed light on aspects of kinship. Thirty-three infants were analysed, and sex was successfully identified in 12. Seven were female,...

  14. Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA

    OpenAIRE

    Stiller, M.; Green, R. E.; Ronan, M.; Simons, J F; Du, L; He, W.; Egholm, M; Rothberg, J. M.; Keates, S.G.; Ovodov, N. D.; Antipina, E. E.; Baryshnikov, G. F.; Kuzmin, Y.V.; Vasilevski, A. A.; Wuenschell, G. E.

    2006-01-01

    Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. U...

  15. 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.

  16. Identification of ancient Olea europaea L. and Cornus mas L. seeds by DNA barcoding.

    Science.gov (United States)

    Gismondi, Angelo; Rolfo, Mario Federico; Leonardi, Donatella; Rickards, Olga; Canini, Antonella

    2012-07-01

    The analysis of ancient DNA (aDNA) provides archaeologists and anthropologists with innovative, scientific and accurate data to study and understand the past. In this work, ancient seeds, found in the "Mora Cavorso" archaeological site (Latium, Central Italy), were analyzed to increase information about Italian Neolithic populations (plant use, agriculture, diet, trades, customs and ecology). We performed morphological and genetic techniques to identify fossil botanical species. In particular, this study also suggests and emphasizes the use of DNA barcode method for ancient plant sample analysis. Scanning electron microscope (SEM) observations showed seed compact structure and irregular surface but they did not permit a precise nor empirical classification: so, a molecular approach was necessary. DNA was extracted from ancient seeds and then it was used, as template, for PCR amplifications of standardized barcode genes. Although aDNA could be highly degraded by the time, successful PCR products were obtained, sequenced and compared to nucleotide sequence databases. Positive outcomes (supported by morphological comparison with modern seeds, geographical distribution and historical data) indicated that seeds could be identified as belonging to two plant species: Olea europaea L. and Cornus mas L. PMID:22847014

  17. 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;

    2011-01-01

    . 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...

  18. 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...

  19. 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.

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

    OpenAIRE

    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...

  1. Characterization of ancient DNA supports long-term survival of Haloarchaea.

    Science.gov (United States)

    Sankaranarayanan, Krithivasan; Lowenstein, Tim K; Timofeeff, Michael N; Schubert, Brian A; Lum, J Koji

    2014-07-01

    Bacteria and archaea isolated from crystals of halite 10(4) to 10(8) years old suggest long-term survival of halophilic microorganisms, but the results are controversial. Independent verification of the authenticity of reputed living prokaryotes in ancient salt is required because of the high potential for environmental and laboratory contamination. Low success rates of prokaryote cultivation from ancient halite, however, hamper direct replication experiments. In such cases, culture-independent approaches that use the polymerase chain reaction (PCR) and sequencing of 16S ribosomal DNA are a robust alternative. Here, we use amplification, cloning, and sequencing of 16S ribosomal DNA to investigate the authenticity of halophilic archaea cultured from subsurface halite, Death Valley, California, 22,000 to 34,000 years old. We recovered 16S ribosomal DNA sequences that are identical, or nearly so (>99%), to two strains, Natronomonas DV462A and Halorubrum DV427, which were previously isolated from the same halite interval. These results provide the best independent support to date for the long-term survival of halophilic archaea in ancient halite. PCR-based approaches are sensitive to small amounts of DNA and could allow investigation of even older halites, 10(6) to 10(8) years old, from which microbial cultures have been reported. Such studies of microbial life in ancient salt are particularly important as we search for microbial signatures in similar deposits on Mars and elsewhere in the Solar System. PMID:24977469

  2. 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...

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

    OpenAIRE

    Ávila-Arcos, María C.; Enrico Cappellini; J. Alberto Romero-Navarro; Nathan Wales; J. Víctor Moreno-Mayar; Morten Rasmussen; Fordyce, Sarah L.; Rafael Montiel; Jean-Philippe Vielle-Calzada; Eske Willerslev; Gilbert, M. Thomas P.

    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. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing ...

  4. Optimization of the Phenol -Chloroform Silica DNA Extraction Method in Ancient Bones DNA Extraction

    Directory of Open Access Journals (Sweden)

    Morteza Sadeghi

    2014-04-01

    Full Text Available Introduction: DNA extraction from the ancient bones tissues is currently very difficult. Phenol chloroform silica method is one of the methods currently used for this aim. The purpose of this study was to optimize the assessment method. Methods: DNA of 62 bone tissues (average 3-11 years was first extracted with phenol chloroform silica methods and then with changing of some parameters of the methods the extracted DNA was amplified in eight polymorphisms area including FES, F13, D13S317, D16, D5S818, vWA and CD4. Results from samples gained by two methods were compared in acrylamide gel. Results: The average of PCR yield for new method and common method in eight polymorphism regions was 75%, 78%, 81%, 76%, 85%, 71%, 89%, 86% and 64%, 39%, 70%, 49%, 68%, 76%, 71% and 28% respectively. The average of DNA in optimized (in 35l silica density and common method were 267.5 µg/ml with 1.12 purity and 192.76 g/ml with 0.84 purity respectively. Conclusions: According to the findings of this study, it is estimated that longer EDTA attendance is an efficient agent in removing calcium and also adequate density of silica particles can be efficient in removal of PCR inhibitors.

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

    Science.gov (United States)

    Hansen, Anders J; Mitchell, David L; Wiuf, Carsten; Paniker, Lakshmi; Brand, Tina B; Binladen, Jonas; Gilichinsky, David A; Rønn, Regin; Willerslev, Eske

    2006-06-01

    Diagenesis was studied in DNA obtained from Siberian permafrost (permanently frozen soil) ranging from 10,000 to 400,000 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 approximately 100 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 sediments is to be significantly increased. Using the obtained rate constant for interstrand crosslinks the maximal survival time of amplifiable 120-bp fragments of bacterial 16S ribosomal DNA was estimated to be approximately 400,000 years. Additionally, a clear relationship was found between DNA damage and sample age, contradicting previously raised concerns about the possible leaching of free DNA molecules between permafrost layers.

  6. 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

    Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error...... 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...

  7. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

    OpenAIRE

    Briggs, A; Stenzel, U.; Meyer, M; Krause, J.; Kircher, M. (Manfred); Pääbo, S

    2010-01-01

    DNA sequences determined from ancient organisms have high error rates, primarily due to uracil bases created by cytosine deamination. We use synthetic oligonucleotides, as well as DNA extracted from mammoth and Neandertal remains, to show that treatment with uracil–DNA–glycosylase and endonuclease VIII removes uracil residues from ancient DNA and repairs most of the resulting abasic sites, leaving undamaged parts of the DNA fragments intact. Neandertal DNA sequences determined with this proto...

  8. 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. PMID:26169594

  9. Analyses of DNA from ancient bones of a pre-Columbian Cuban woman and a child

    Directory of Open Access Journals (Sweden)

    Ricardo Lleonart

    1999-09-01

    Full Text Available Molecular anthropology has brought new possibilities into the study of ancient human populations. Amplification of chromosomal short tandem repeat (STR loci and mitochondrial DNA (mtDNA has been successfully employed in analyses of ancient bone material. Although several studies have reported on continental Amerindian populations, none have addressed the ancient populations inhabiting the Caribbean islands. We used STR and mtDNA analyses to study the skeletal remains of a Cuban Ciboney female adult holding an infant. Results showed that for the STR analyzed the skeletal remains shared common alleles, suggesting a relationship. Mitochondrial DNA analysis showed sequence identity, thus corroborating a possible mother-child relationship. The mtDNA sequence grouped these remains into haplogroup A, commonly found in Amerindian populations. Based on these results, we speculated on a South American origin of pre-Columbian Antilles populations and possible infanticide practices in these populations. This constitutes the first report on DNA analysis of ancient pre-Columbian Cuban populations.A antropologia molecular trouxe novas possibilidades para o estudo de populações humanas antigas. A amplificação de loci em pequenos segmentos cromossômicos repetidos (short tandem repeat, STR e de DNA mitocondrial (mtDNA tem sido empregada com sucesso em análises de material ósseo antigo. Embora vários estudos tenham sido publicados a respeito de populações ameríndias continentais, nenhum estudou as populações antigas que habitavam as ilhas do Caribe. Nós usamos análise de STR e mtDNA para estudar os restos de ossos de uma mulher adulta da tribo Ciboney cubana carregando uma criança. Os resultados mostraram que para o STR analisado os restos ósseos compartilhavam alelos comuns, sugerindo um parentesco. A análise de mtDNA mostrou identidade de seqüência, corroborando assim uma possível relação mãe-filho. A seqüência de mtDNA alocou esses

  10. Phylogenetic Analysis of mtDNA from the Ancient Human of Yuan Dynasty in Inner Mongolia in China

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A study of the genetic structure of an ancient human excavated from the Yikeshu site of Yuanshangdu ancient city in Inner Mongolia and the relationships between the ancient population and the extant populations was carried out.Sequences of the control region and coding region of mtDNA from the ancient human were analyzed by using direct sequencing and restriction-fragment length polymorphism (RFLP) methods. Phylogenetic analysis and multidimensional scaling analysis were also performed on the mtDNA data of the ancient population and 12 extant populations. These results show that the ancient individuals of Yikeshu site can be assigned to D, G, B and Z haplogroups that are prevalent in Duars and Mongolians from Inner Mongolia. The ancient population is also closer to Duar and Mongolian populations in genetic distance than other compared populations. This study reveals that the ancient population from Yikeshu site in the Yuan Dynasty shares a common ancestor with Mongolic-speaking Daur and Mongolian tribes.

  11. 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

    2007-07-01

    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.

  12. Biomolecular identification of ancient mycobacterium tuberculosis complex DNA in human remains from Britain and continental Europe.

    OpenAIRE

    Müller, R.; Roberts, C A; Brown, T. A.

    2014-01-01

    Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st–19th centuries AD. We performed the work in dedicated ancient DNA facilities designe...

  13. Ancient DNA from 8400 Year-Old Catalhoyuk 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.

  14. mapDamage: testing for damage patterns in ancient DNA sequences

    DEFF Research Database (Denmark)

    Ginolhac, Aurelien; Rasmussen, Morten; Gilbert, M Thomas P;

    2011-01-01

    Ancient DNA extracts consist of a mixture of contaminant DNA molecules, most often originating from environmental microbes, and endogenous fragments exhibiting substantial levels of DNA damage. The latter introduce specific nucleotide misincorporations and DNA fragmentation signatures in sequenci...... of the SAMtools suite and R environment and has been validated on both GNU/Linux and MacOSX operating systems....

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

    OpenAIRE

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

    2009-01-01

    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 likeliho...

  16. 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......DNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine guanine and thymine --> cytosine) and type 2 transitions (cytosine --> thymine and guanine...

  17. Genetic features of ancient West Siberian people of the Middle Ages, revealed by mitochondrial DNA haplogroup analysis.

    Science.gov (United States)

    Sato, Takehiro; Razhev, Dmitry; Amano, Tetsuya; Masuda, Ryuichi

    2011-08-01

    In order to investigate the genetic features of ancient West Siberian people of the Middle Ages, we studied ancient DNA from bone remains excavated from two archeological sites in West Siberia: Saigatinsky 6 (eighth to eleventh centuries) and Zeleny Yar (thirteenth century). Polymerase chain reaction amplification and nucleotide sequencing of mitochondrial DNA (mtDNA) succeeded for 9 of 67 specimens examined, and the sequences were assigned to mtDNA haplogroups B4, C4, G2, H and U. This distribution pattern of mtDNA haplogroups in medieval West Siberian people was similar to those previously reported in modern populations living in West Siberia, such as the Mansi, Ket and Nganasan. Exact tests of population differentiation showed no significant differences between the medieval people and modern populations in West Siberia. The findings suggest that some medieval West Siberian people analyzed in the present study are included in direct ancestral lineages of modern populations native to West Siberia. PMID:21753768

  18. 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; Burger, Pamela A

    2016-06-14

    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

  19. 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; Burger, Pamela A

    2016-06-14

    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.

  20. 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

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

    DEFF Research Database (Denmark)

    Murray, D.C.; Pearson, S.G.; Fullagar, R.;

    2012-01-01

    of information regarding past environments and the nature of ecological fluctuations within arid zones. The application of ancient DNA (aDNA) techniques to hot, arid zone middens remains unexplored. This paper attempts to retrieve and characterise aDNA from four Southern Hemisphere fossil middens; three located...

  2. 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...

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

    Directory of Open Access Journals (Sweden)

    Alice A Storey

    Full Text Available 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.

  4. 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

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

    Directory of Open Access Journals (Sweden)

    Treena Swanston

    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.

  6. Highly Informative Ancient DNA ‘Snippets’ for New Zealand Moa

    OpenAIRE

    Jonathan McCallum; Samantha Hall; Iman Lissone; Jennifer Anderson; Leon Huynen; Lambert, David M

    2013-01-01

    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 targe...

  7. Absence of ancient DNA in sub-fossil insect inclusions preserved in 'Anthropocene' Colombian copal.

    Directory of Open Access Journals (Sweden)

    David Penney

    Full Text Available Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae preserved in 'Anthropocene' Colombian copal, dated to 'post-Bomb' and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal.

  8. Science in the Study of Ancient Egypt

    OpenAIRE

    Zakrzewski, Sonia; Shortland, Andrew; Rowland, Joanne

    2016-01-01

    Egyptology has been dominated by the large quantity of written and pictorial material available. This amazing archaeology has opened up a wonderful view of the ancient Egyptian world. The importance of hieroglyphics and texts, and their interpretation, has led to other areas of archaeology playing much less prominence in the study of Egypt. Perhaps most notable in this is relative lack of the application of analytical science to answer Egyptian questions. This problem has been compounded by d...

  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...... cores as well. Here, we present some future perspectives for DNA studies on polar ice cores in regard to molecular ecology, DNA damage and degradation, anabiosis and antibiotic resistance genes. Finally, we address some of the methodological problems connected to ancient DNA research....

  10. 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...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    We extracted DNA from 39 Danish aurochs specimens and successfully amplified and sequenced a 252 base pair long fragment of the multivariable region I of the mitochondrial control region from 11 specimens. The sequences from these specimens dated back to 9830-2865 14C yr BP and represent the first...... study of genetic variation of Danish aurochs. In addition, for all specimens we address correlations between the ability to obtain DNA sequences and various parameters such as the age of the sample, the collagen content, the museum storage period, Danish geography and whether the specimens were found...

  12. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.

    Directory of Open Access Journals (Sweden)

    Susanna Sawyer

    Full Text Available DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5'-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments.

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

    Science.gov (United States)

    Murray, Dáithí C.; Pearson, Stuart G.; Fullagar, Richard; Chase, Brian M.; Houston, Jayne; Atchison, Jennifer; White, Nicole E.; Bellgard, Matthew I.; Clarke, Edward; Macphail, Mike; Gilbert, M. Thomas P.; Haile, James; Bunce, Michael

    2012-12-01

    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 source of information regarding past environments and the nature of ecological fluctuations within arid zones. The application of ancient DNA (aDNA) techniques to hot, arid zone middens remains unexplored. This paper attempts to retrieve and characterise aDNA from four Southern Hemisphere fossil middens; three located in hot, arid regions of Australia and one sample from South Africa's Western Cape province. The middens are dated to between 30,490 (±380) and 710 (±70) cal yr BP. The Brockman Ridge midden in this study is potentially the oldest sample from which aDNA has been successfully extracted in Australia. The application of high-throughput sequencing approaches to profile the biotic remains preserved in midden material has not been attempted to date and this study clearly demonstrates the potential of such a methodology. In addition to the taxa previously detected via macrofossil and palynological analyses, aDNA analysis identified unreported plant and animal taxa, some of which are locally extinct or endemic. The survival and preservation of DNA in hot, arid environments is a complex and poorly understood process that is both sporadic and rare, but the survival of DNA through desiccation may be important. Herbivore middens now present an important source of material for DNA metabarcoding studies of hot, arid palaeoenvironments and can potentially be used to analyse middens in these environments throughout Australia, Africa, the Americas and the Middle East.

  14. 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.

  15. Ancient mitochondrial DNA and morphology elucidate an extinct island radiation of Indian Ocean giant tortoises (Cylindraspis).

    OpenAIRE

    Austin, J. J.; Arnold, E. N.

    2001-01-01

    Ancient mitochondrial DNA sequences were used for investigating the evolution of an entire clade of extinct vertebrates, the endemic tortoises (Cylindraspis) of the Mascarene Islands in the Indian Ocean. Mitochondrial DNA corroborates morphological evidence that there were five species of tortoise with the following relationships: Cylindraspis triserrata ((Cylindraspis vosmaeri and Cylindraspis peltastes) (Cylindraspis inepta and Cylindraspis indica)). Phylogeny indicates that the ancestor of...

  16. 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.

  17. Study of ancient pottery from Slovakia

    International Nuclear Information System (INIS)

    Ancient pottery samples collected from south-west Slovakia were studied through subjective observation and by Moessbauer spectroscopy. This method is convenient for determining the provenance and the manufacture of pottery. Transformations, induced by firing the clay and characterized by Moessbauer spectroscopy, give valuable information regarding the manufacture as, for instance, the final temperature of firing in it. The relative abundance of Fe2+ and Fe3+ determines the atmosphere used to fire a pottery. It has been found that the determination of the firing atmosphere obtained through the subjective observation is in good agreement with that obtained using Moessbauer spectroscopy. An unfired and fired clay was also investigated. (orig.)

  18. 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.

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

    DEFF Research Database (Denmark)

    Mourier, Tobias; Ho, Simon; Gilbert, M Thomas P;

    2012-01-01

    quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuclear single-nucleotide polymorphisms (SNPs) to detect past population bottlenecks. Within our simulated framework, mitochondrial sequences have only limited power to detect subtle bottlenecks and/or fast...... 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...

  20. 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.

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

    OpenAIRE

    Iñiguez Alena M; Araújo Adauto; Ferreira Luiz Fernando; Vicente Ana Carolina P

    2003-01-01

    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 pre...

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

    Science.gov (United States)

    Ávila-Arcos, María C.; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Moreno-Mayar, J. Víctor; Rasmussen, Morten; Fordyce, Sarah L.; Montiel, Rafael; Vielle-Calzada, Jean-Philippe; Willerslev, Eske; Gilbert, M. Thomas P.

    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. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA. PMID:22355593

  3. 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

    The scope and ambition of biomolecular archaeology is undergoing rapid change due to the development of new ‘next generation’ sequencing (NGS) methods for analysis of ancient DNA in archaeological specimens. These methods have not yet been applied extensively to archaeobotanical material but thei......The scope and ambition of biomolecular archaeology is undergoing rapid change due to the development of new ‘next generation’ sequencing (NGS) methods for analysis of ancient DNA in archaeological specimens. These methods have not yet been applied extensively to archaeobotanical material...... the archaeobotanical research community....

  4. 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.

  5. 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

    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...... containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD...... 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...

  6. 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.

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

    OpenAIRE

    Sarit Suissa; Zhibo Wang; Jason Poole; Sharine Wittkopp; Jeanette Feder; Shutt, Timothy E.; Wallace, Douglas C.; Shadel, Gerald S.; Dan Mishmar

    2009-01-01

    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 transcri...

  8. Ancient diversification of eukaryotic MCM DNA replication proteins

    Directory of Open Access Journals (Sweden)

    Aves Stephen J

    2009-03-01

    Full Text Available Abstract Background Yeast and animal cells require six mini-chromosome maintenance proteins (Mcm2-7 for pre-replication complex formation, DNA replication initiation and DNA synthesis. These six individual MCM proteins form distinct heterogeneous subunits within a hexamer which is believed to form the replicative helicase and which associates with the essential but non-homologous Mcm10 protein during DNA replication. In contrast Archaea generally only possess one MCM homologue which forms a homohexameric MCM helicase. In some eukaryotes Mcm8 and Mcm9 paralogues also appear to be involved in DNA replication although their exact roles are unclear. Results We used comparative genomics and phylogenetics to reconstruct the diversification of the eukaryotic Mcm2-9 gene family, demonstrating that Mcm2-9 were formed by seven gene duplication events before the last common ancestor of the eukaryotes. Mcm2-7 protein paralogues were present in all eukaryote genomes studied suggesting that no gene loss or functional replacements have been tolerated during the evolutionary diversification of eukaryotes. Mcm8 and 9 are widely distributed in eukaryotes and group together on the MCM phylogenetic tree to the exclusion of all other MCM paralogues suggesting co-ancestry. Mcm8 and Mcm9 are absent in some taxa, including Trichomonas and Giardia, and appear to have been secondarily lost in some fungi and some animals. The presence and absence of Mcm8 and 9 is concordant in all taxa sampled with the exception of Drosophila species. Mcm10 is present in most eukaryotes sampled but shows no concordant pattern of presence or absence with Mcm8 or 9. Conclusion A multifaceted and heterogeneous Mcm2-7 hexamer evolved during the early evolution of the eukaryote cell in parallel with numerous other acquisitions in cell complexity and prior to the diversification of extant eukaryotes. The conservation of all six paralogues throughout the eukaryotes suggests that each Mcm2

  9. Study on Prohibitions of Ancient Chinese Costumes in Black Series

    OpenAIRE

    Xiaomeng Qu

    2013-01-01

    China is a historical country with extensive and profound civilization, in which the Chinese Costume has always been a brilliant feature. Black series occupies an important position in the color institution of ancient Chinese Costumes. The prohibition on black series costumes also has a significant meaning in ancient China. By discussing prohibitions related to black series in ancient Chinese costume institution, this paper studied two typical colors used by people of different classes as the...

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

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren

    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...... acquire functional genetic signatures of the deeper past. Moreover, not only can old DNA revert microbes to past genotypes, but damaged DNA can also produce new variants of already functional sequences. Besides, DNA fragments carry potential to combine functional domains in new ways. The identified novel...

  11. The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA

    Science.gov (United States)

    Giovannotti, Massimo; Negri, Alessandra; Ruggeri, Paolo; Olivieri, Luigi; Nisi Cerioni, Paola; Lorenzoni, Massimo; Caputo Barucchi, Vincenzo

    2016-01-01

    In this pilot study for the first time, ancient DNA has been extracted from bone remains of Salmo trutta. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples. Three haplotypes were observed: two (ADcs-1 and MEcs-1) already described in rivers from the Italian peninsula; one (ATcs-33) belonging to the southern Atlantic clade of the AT Salmo trutta mtDNA lineage (sensu Bernatchez). The prehistoric occurrence of this latter haplotype in the water courses of the Italian peninsula has been detected for the first time in this study. Finally, we observed a correspondence between frequency of trout remains and variation in haplotype diversity that we related with ecological and demographic changes resulting from a period of rapid cooling known as the Younger Dryas. PMID:27331397

  12. DNA extraction of ancient animal hard tissue samples via adsorption to silica particles.

    Science.gov (United States)

    Rohland, Nadin

    2012-01-01

    A large number of subfossil and more recent skeletal remains, many of which are stored in museums and private collections, are potentially accessible for DNA sequence analysis. In order to extract the small amount of DNA preserved in these specimens, an efficient DNA release and purification method is required. In this chapter, I describe an efficient and straightforward purification and concentration method that uses DNA adsorption to a solid surface of silica particles. Comparative analysis of extraction methods has shown that this method works reliably for ancient as well as younger, museum-preserved specimens.

  13. Technical note: improved DNA extraction from ancient bones using silica-based spin columns.

    Science.gov (United States)

    Yang, D Y; Eng, B; Waye, J S; Dudar, J C; Saunders, S R

    1998-04-01

    We describe a simple method for extracting polymerase chain reaction-amplifiable DNA from ancient bones without the use of organic solvents. Bone powders are digested with proteinase K, and the DNA is purified directly using silica-based spin columns (QIAquick3, QIAGEN). The efficiency of this protocol is demonstrated using human bone samples ranging in age from 15 to 5,000 years old.

  14. Palaeoceanographic changes in Hornsund Fjord (Spitsbergen, Svalbard) over the last millennium: new insights from ancient DNA

    Science.gov (United States)

    Pawłowska, Joanna; Zajączkowski, Marek; Łącka, Magdalena; Lejzerowicz, Franck; Esling, Philippe; Pawlowski, Jan

    2016-07-01

    This paper presents a reconstruction of climate-driven environmental changes over the last millennium in Hornsund Fjord (Svalbard), based on sedimentological and micropalaeontological records. Our palaeo-investigation was supported by an analysis of foraminiferal ancient DNA (aDNA), focusing on the non-fossilized monothalamous species. The main climatic fluctuations during the last millennium were the Medieval Warm Period (MWP, AD 1000-1600), the Little Ice Age (LIA, AD 1600-1900) and the modern warming (MW, AD 1900 to present). Our study indicates that the environmental conditions in Hornsund during the MWP and the early LIA (before ˜ AD 1800) were relatively stable. The beginning of the LIA (˜ AD 1600) was poorly evidenced by the micropalaeontological record but was well marked in the aDNA data by an increased proportion of monothalamous foraminifera, especially Bathysiphon sp. The early LIA (˜ 1600 to ˜ AD 1800) was marked by an increase in the abundance of sequences of Hippocrepinella hirudinea and Cedhagenia saltatus. In the late LIA (after ˜ AD 1800), the conditions in the fjord became glacier-proximal and were characterized by increased meltwater outflows, high sedimentation and a high calving rate. This coincided with an increase in the percentages of sequences of Micrometula sp. and Vellaria pellucidus. During the MW, the major glacier fronts retreated rapidly to the inner bays, which limited the iceberg discharge to the fjord's centre and caused a shift in the foraminiferal community that was reflected in both the fossil and aDNA records. The palaeoceanographic changes in the Hornsund fjord over the last millennium were driven mainly by the inflow of shelf-originated water masses and glacial activity. However, the environmental changes were poorly evidenced in the micropalaeontological record, but they were well documented in our aDNA data. We considerably increased the number of potential proxy species by including monothalamous foraminifera in the

  15. Studies of Ancient Lice Reveal Unsuspected Past Migrations of Vectors.

    Science.gov (United States)

    Drali, Rezak; Mumcuoglu, Kosta Y; Yesilyurt, Gonca; Raoult, Didier

    2015-09-01

    Lice are among the oldest parasites of humans representing an excellent marker of the evolution and migration of our species over time. Here, we analyzed by real-time polymerase chain reaction (RT-PCR) developed in this study the mitochondrial DNA of seven ancient head louse eggs found on hair remains recovered from two sites in Israel: 1) five nits dating from Chalcolithic period (4,000 bc) were found in the Cave of the Treasure located at Nahal Mishmar, in the Judean Desert and 2) two nits dating from Early Islamic Period (ad 650-810) were found in Nahal Omer in the Arava Valley (between Dead Sea and Red Sea). Our results suggest that these eggs belonged to people originating from west Africa based on identification of the louse mitochondrial sub-clade specific to that region. PMID:26078317

  16. 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.

  17. 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......, and that their water sources were pooled or stored water. Both mtDNA sequence data and Y SNP data hint at possible gene flow or a common ancestral population for both the Beothuk and the current day Mikmaq, but more importantly the data do not lend credence to the proposed idea that the Beothuk (specifically......, Nonosabasut) were of admixed (European-Native American) descent. We also analyzed patterns of DNA damage in the clones of authentic mtDNA sequences; there is no tendency for DNA damage to occur preferentially at previously defined mutational hotspots, suggesting that such mutational hotspots...

  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. Moessbauer effect study of ancient Egyptian pottery

    International Nuclear Information System (INIS)

    Moessbauer spectroscopy was used in examining ancient Egyptian pottery. From the values of Moessbauer parameters and the differences for the individual samples, conclusions could be drawn as to the temperature of baking and the kind of clay used in various archaeological periods. (A.K.)

  20. 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.

  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. PMID:23076995

  2. Origin of Chinese ancient glasses——study on the earliest Chinese ancient glasses

    Institute of Scientific and Technical Information of China (English)

    GAN Fuxi; CHENG Huansheng; LI Qinghui

    2006-01-01

    The earliest Chinese ancient glasses before the West Han Dynasty (200 BC) from different regions are studied. The glass samples were unearthed from Hunan, Hubei, Yunnan, Sichuan, Guizhou, Guangdong and Xinjiang of China. The chemical composition of these glasses samples is analyzed by proton induced X-ray emission (PIXE) technique, energy dispersive X-ray fluorescence (EDXRF) method and inductively coupled plasma atomic emission spectrometry (ICP-AES). It is shown that the glass chemical compositions belong to barium-lead silicate BaO-PbO-SiO2, potash soda lime silicate K2O (Na2O)-CaO-SiO2 (K2O/Na2O>1), soda potash lime silicate Na2O (K2O)-CaO-SiO2 (K2O/Na2O<1) and potash silicate K2O-SiO2 glass systems, respectively. The origins of the earliest Chinese ancient glasses are discussed from the archaeological and historical points of view. These four types of Chinese ancient glasses were all made in Chinese territory using local raw materials. The glass preparation technology was related to the Chinese ancient bronze metallurgy and proto-porcelain glaze technology. The glass technology relationship between the East and the West is analyzed at the same time.

  3. Fossil DNA as a Recorder of Ancient Microbial Communities and Palaeoenvironments

    Science.gov (United States)

    Coolen, M. J.; Boere, A.; Abbas, B.; Muyzer, G.; Overmann, J.; Wakeham, S. G.; Volkman, J. K.; Sinninghe Damste, J. S.

    2005-12-01

    Fossilized organic components provide an archive of ancient aquatic microbial communities and, hence, can be used to reconstruct climate-induced environmental changes and their impacts on biodiversity. However, the interpretation of these data is complicated by the limited source specificity of some traditional biomarkers, such as lipids and pigments. The ultimate biomarkers are genes encoding for ribosomal RNA (rDNA), which sequences provide information at the species level by phylogenetic comparison but until recently was only applied to identify extant species within environmental samples. With the exception of excellent preservation conditions prevailing in permafrost sediments (3), it was generally believed that DNA becomes rapidly degraded within fossil records. However, we have recently shown that especially in the presence of hydrogen sulfide, DNA can survive in the Holocene fossil record (1, 2). In this presentation we will show how, and to what extent, fossil DNA extracted from Holocene sediments of stratified lakes (the Canadian Mahoney Lake and the Antarctic Ace Lake) and the deep-sea (Black Sea) can be used as a novel proxy to reconstruct the ancient palaeodepositional environments and evolution of past microbial communities. In addition, we will discuss the fate of fossil DNA; quantitative stratigraphic analysis of lipid biomarkers and rDNA from the same biological precursors revealed information on the survival of fossil DNA in comparison to lipid biomarkers. It was shown that most of the DNA was degraded before dead cells reach the bottom but the remaining part was found to be well protected and even less prone to diagenetic alteration compared to certain lipid biomarkers. Base-pair compositions did not change during the Holocene, however, the fossil DNA became fragmented after several thousands of years of deposition but without significantly biasing the qualitative and quantitative molecular biological analysis of at least 10-ka-old fossil DNA

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

    Directory of Open Access Journals (Sweden)

    Fernando Racimo

    2016-04-01

    Full Text Available 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%.

  5. Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions

    Science.gov (United States)

    Brotherton, Paul; Endicott, Phillip; Sanchez, Juan J.; Beaumont, Mark; Barnett, Ross; Austin, Jeremy; Cooper, Alan

    2007-01-01

    Ancient DNA (aDNA) research has long depended on the power of PCR to amplify trace amounts of surviving genetic material from preserved specimens. While PCR permits specific loci to be targeted and amplified, in many ways it can be intrinsically unsuited to damaged and degraded aDNA templates. PCR amplification of aDNA can produce highly-skewed distributions with significant contributions from miscoding lesion damage and non-authentic sequence artefacts. As traditional PCR-based approaches have been unable to fully resolve the molecular nature of aDNA damage over many years, we have developed a novel single primer extension (SPEX)-based approach to generate more accurate sequence information. SPEX targets selected template strands at defined loci and can generate a quantifiable redundancy of coverage; providing new insights into the molecular nature of aDNA damage and fragmentation. SPEX sequence data reveals inherent limitations in both traditional and metagenomic PCR-based approaches to aDNA, which can make current damage analyses and correct genotyping of ancient specimens problematic. In contrast to previous aDNA studies, SPEX provides strong quantitative evidence that C > U-type base modifications are the sole cause of authentic endogenous damage-derived miscoding lesions. This new approach could allow ancient specimens to be genotyped with unprecedented accuracy. PMID:17715147

  6. 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.

  7. 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. PMID:26864783

  8. 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.

  9. PIXE study on ancient pottery from Chinese Shanghai area

    International Nuclear Information System (INIS)

    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

  10. 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

  11. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA

    OpenAIRE

    Susanna Sawyer; Johannes Krause; Katerina Guschanski; Vincent Savolainen; Svante Pääbo

    2012-01-01

    DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular f...

  12. 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)

  13. 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.

  14. Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA.

    Science.gov (United States)

    Zeyland, J; Wolko, L; Bocianowski, J; Szalata, M; Słomski, R; Dzieduszycki, A M; Ryba, M; Przystałowska, H; Lipiński, D

    2013-01-01

    Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon-dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.

  15. 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.

  16. 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.

  17. A review of Moessbauer spectroscopic studies of ancient pottery

    International Nuclear Information System (INIS)

    Moessbauer spectroscopy has proven itself to be invaluable to archaeologists by providing a means to classify pottery and to provide information on particular providences for various ancient pottery finds. The original firing atmospheres can often by deduced from the ratio of Fe2+ to Fe3+. The change in the quadrupole splitting and the magnetic hyperfine splittings allow for the determination of the original firing temperatures. Ancient pottery samples from many cultures have been studied and a number of general conclusions are possible. (Auth.)

  18. Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage.

    Science.gov (United States)

    Hervella, Montserrat; Rotea, Mihai; Izagirre, Neskuts; Constantinescu, Mihai; Alonso, Santos; Ioana, Mihai; Lazăr, Cătălin; Ridiche, Florin; Soficaru, Andrei Dorian; Netea, Mihai G; de-la-Rua, Concepcion

    2015-01-01

    The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations. PMID:26053041

  19. Optical dating of perennially frozen deposits associated with preserved ancient plant and animal DNA in north-central Siberia

    DEFF Research Database (Denmark)

    Arnold, L.J.; Roberts, R.G.; Macphee, R.D.E.;

    2008-01-01

    We present chronological constraints on a suite of permanently frozen fluvial deposits which contain ancient DNA (aDNA) from the Taimyr Peninsula of north-central Siberia. The luminescence phenomenology of these samples is first discussed, focusing on the optically stimulated luminescence (OSL) d...... of providing a reliable chronometric framework for sedimentary aDNA records in permafrost environments. (C) 2007 Elsevier Ltd. All rights reserved Udgivelsesdato: 2008...

  20. 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.

  1. Tech Talk for Social Studies Teachers: Ancient Egypt.

    Science.gov (United States)

    Pahl, Ronald H.

    1998-01-01

    Presents an annotated bibliography of 10 Web sites concerning ancient Egypt that have materials appropriate for social studies classes. Includes virtual tours of Egypt and specific temples, explorations of the pyramids, archaeological and geographic information, and information on the Egyptian "Book of the Dead." (MJP)

  2. Novel DNA Extraction Method Unveiled the Ancient Hot Deep Biosphere Concealed in Terrestrial Sedimentary Rocks

    Science.gov (United States)

    Kouduka, M.; Suko, T.; Okuzawa, K.; Fukuda, A.; Nanba, K.; Yamamoto, M.; Sakata, S.; Ito, K.; Suzuki, Y.

    2009-12-01

    thermophilic bacteria and the transformation of silica minerals in the deep subsurface. As intensive erosion is unlikely around the drilling site, a short period of hydrothermal activities rather than long-term burial at great depth caused high temperature conditions, which might explain the lack of maturity in hydrocarbon. A novel DNA-based approach coupled mineralogical and organic geochemical analyses has the potential to reconstruct ancient biogeochemical processes mediated in the deep subsurface as well as geothermal history. This study was supported by grants from the Nuclear and Industrial Safety Agency (NISA) and Japan Nuclear Energy Safety Organization (JNES).

  3. Ancient DNA from European early neolithic farmers reveals their near eastern affinities.

    Directory of Open Access Journals (Sweden)

    Wolfgang Haak

    Full Text Available 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

  4. 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...

  5. New ancient DNA sequences suggest high genetic diversity for the woolly mammoth (Mammuthus primigenius )

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Partial DNA sequences of cytochrome b gene (mtDNA) were successfully retrieved from Late Pleistocene fossil bone of Mammuthus primigenius collected from the Xiguitu County (Yakeshi), Inner Mongolia Autonomous Region and from Zhaodong, Harbin of Heilongjiang Province in northern China. Two ancient DNA fragments ( 109 bp and 124 bp) were authenticated by reproducible experiments in two different laboratories and by phylogenetic analysis with other Elephantidae taxa. Phylogenetic analysis using these sequences and published data in either separate or combined datasets indicate unstable relationship among the woolly mammoth and the two living elephants, Elephas and Loxodonta. In addition to the short sequences used to attempt the long independent evolution of Elephantidae terminal taxa, we suggest that a high intra-specific diversity existed in Mammuthus primigenius crossing both spatial and temporal ranges, resulting in a complex and divergent genetic background for DNA sequences so far recovered. The high genetic diversity in the extinct woolly mammoth can explain the apparent instability of Elephantidae taxa on the molecular phylogenetic trees and can reconcile the apparent paradox regarding the unresolved Elephantidae trichotomy.

  6. Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman

    Directory of Open Access Journals (Sweden)

    Egarter-Vigl Eduard

    2009-06-01

    Full Text Available Abstract Background Progress in the field of human ancient DNA studies has been severely restricted due to the myriad sources of potential contamination, and because of the pronounced difficulty in identifying authentic results. Improving the robustness of human aDNA results is a necessary pre-requisite to vigorously testing hypotheses about human evolution in Europe, including possible admixture with Neanderthals. This study approaches the problem of distinguishing between authentic and contaminating sequences from common European mtDNA haplogroups by applying a multiplexed Single-Base-Extension assay, containing both control and coding region sites, to DNA extracted from the Tyrolean Iceman. Results The multiplex assay developed for this study was able to confirm that the Iceman's mtDNA belongs to a new European mtDNA clade with a very limited distribution amongst modern data sets. Controlled contamination experiments show that the correct results are returned by the multiplex assay even in the presence of substantial amounts of exogenous DNA. The overall level of discrimination achieved by targeting both control and coding region polymorphisms in a single reaction provides a methodology capable of dealing with most cases of homoplasy prevalent in European haplogroups. Conclusion The new genotyping results for the Iceman confirm the extreme fallibility of human aDNA studies in general, even when authenticated by independent replication. The sensitivity and accuracy of the multiplex Single-Base-Extension methodology forms part of an emerging suite of alternative techniques for the accurate retrieval of ancient DNA sequences from both anatomically modern humans and Neanderthals. The contamination of laboratories remains a pressing concern in aDNA studies, both in the pre and post-PCR environments, and the adoption of a forensic style assessment of a priori risks would significantly improve the credibility of results.

  7. Ancient DNA Assessment of Tiger Salamander Population in Yellowstone National Park

    OpenAIRE

    McMenamin, Sarah K.; Hadly, Elizabeth A.

    2012-01-01

    Recent data indicates that blotched tiger salamanders (Ambystoma tigrinum melanostictum) in northern regions of Yellowstone National Park are declining due to climate-related habitat changes. In this study, we used ancient and modern mitochondrial haplotype diversity to model the effective size of this amphibian population through recent geological time and to assess past responses to climatic changes in the region. Using subfossils collected from a cave in northern Yellowstone, we analyzed >...

  8. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA.

    Science.gov (United States)

    Larson, Greger; Liu, Ranran; Zhao, Xingbo; Yuan, Jing; Fuller, Dorian; Barton, Loukas; Dobney, Keith; Fan, Qipeng; Gu, Zhiliang; Liu, Xiao-Hui; Luo, Yunbing; Lv, Peng; Andersson, Leif; Li, Ning

    2010-04-27

    The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.

  9. 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.

  10. 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.

  11. A conditional likelihood is required to estimate the selection coefficient in ancient DNA

    CERN Document Server

    Valleriani, Angelo

    2016-01-01

    Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to end anywhere. Based on the Moran model of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation ...

  12. 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.

  13. 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

  14. The moessbauer study on ancient pottery with known age

    International Nuclear Information System (INIS)

    It is of important scientific value in archaeology to study the age effect with Moessbauer effect. 13 samples of ancient pottery from different excavated places and with different technology of production have been measured by transmission Moessbauer technique at room temperature. The experimental results show that the paramagnetic Fe2+ Q.S. values for 11 samples linearly increase with the age of pottery and that the mangnetic component of pottery with very old age almost disappears

  15. Reconstructing ancient genomes and epigenomes

    DEFF Research Database (Denmark)

    Orlando, Ludovic Antoine Alexandre; Gilbert, M. Thomas P.; Willerslev, Eske

    2015-01-01

    DNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and...... contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes....

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

    Science.gov (United States)

    Bilgic, Hatice; Hakki, Erdogan E; Pandey, Anamika; Khan, Mohd Kamran; Akkaya, Mahinur S

    2016-01-01

    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.

  17. Of Amoebae and Men: Extracellular DNA Traps as an Ancient Cell-Intrinsic Defense Mechanism

    Science.gov (United States)

    Zhang, Xuezhi; Soldati, Thierry

    2016-01-01

    Since the discovery of the formation of DNA-based extracellular traps (ETs) by neutrophils as an innate immune defense mechanism (1), hundreds of articles describe the involvement of ETs in physiological and pathological human and animal conditions [reviewed in Ref. (2), and the previous Frontiers Research Topic on NETosis: http://www.frontiersin.org/books/NETosis_At_the_Intersection_of_Cell_Biology_Microbiology_and_Immunology/195]. Interestingly, a few reports reveal that ETs can be formed by immune cells of more ancient organisms, as far back as the common ancestor of vertebrates and invertebrates (3). Recently, we reported that the Sentinel cells of the multicellular slug of the social amoeba Dictyostelium discoideum also produce ETs to trap and kill slug-invading bacteria [see Box 1; and Figure 1 Ref. (4)]. This is a strong evidence that DNA-based cell-intrinsic defense mechanisms emerged much earlier than thought, about 1.3 billion years ago. Amazingly, using extrusion of DNA as a weapon to capture and kill uningestable microbes has its rationale. During the emergence of multicellularity, a primitive innate immune system developed in the form of a dedicated set of specialized phagocytic cells. This professionalization of immunity allowed the evolution of sophisticated defense mechanisms including the sacrifice of a small set of cells by a mechanism related to NETosis. This altruistic behavior likely emerged in steps, starting from the release of “dispensable” mitochondrial DNA by D. discoideum Sentinel cells. Grounded in this realization, one can anticipate that in the near future, many more examples of the invention and fine-tuning of ETs by early metazoan ancestors will be identified. Consequently, it can be expected that this more complete picture of the evolution of ETs will impact our views of the involvement and pathologies linked to ETs in human and animals. PMID:27458458

  18. Effect of X-ray irradiation on ancient DNA in sub-fossil bones – Guidelines for safe X-ray imaging

    Science.gov (United States)

    Immel, Alexander; Le Cabec, Adeline; Bonazzi, Marion; Herbig, Alexander; Temming, Heiko; Schuenemann, Verena J.; Bos, Kirsten I.; Langbein, Frauke; Harvati, Katerina; Bridault, Anne; Pion, Gilbert; Julien, Marie-Anne; Krotova, Oleksandra; Conard, Nicholas J.; Münzel, Susanne C.; Drucker, Dorothée G.; Viola, Bence; Hublin, Jean-Jacques; Tafforeau, Paul; Krause, Johannes

    2016-01-01

    Sub-fossilised remains may still contain highly degraded ancient DNA (aDNA) useful for palaeogenetic investigations. Whether X-ray computed [micro-] tomography ([μ]CT) imaging of these fossils may further damage aDNA remains debated. Although the effect of X-ray on DNA in living organisms is well documented, its impact on aDNA molecules is unexplored. Here we investigate the effects of synchrotron X-ray irradiation on aDNA from Pleistocene bones. A clear correlation appears between decreasing aDNA quantities and accumulating X-ray dose-levels above 2000 Gray (Gy). We further find that strong X-ray irradiation reduces the amount of nucleotide misincorporations at the aDNA molecule ends. No representative effect can be detected for doses below 200 Gy. Dosimetry shows that conventional μCT usually does not reach the risky dose level, while classical synchrotron imaging can degrade aDNA significantly. Optimised synchrotron protocols and simple rules introduced here are sufficient to ensure that fossils can be scanned without impairing future aDNA studies. PMID:27615365

  19. 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".

  20. Myth or relict: Does ancient DNA detect the enigmatic Upland seal?

    Science.gov (United States)

    Salis, Alexander T; Easton, Luke J; Robertson, Bruce C; Gemmell, Neil; Smith, Ian W G; Weisler, Marshall I; Waters, Jonathan M; Rawlence, Nicolas J

    2016-04-01

    The biological status of the so-called 'Upland seal' has remained contentious ever since historical records described a distinct seal from the uplands of New Zealand's (NZ) remote sub-Antarctic islands. Subsequent genetic surveys of the NZ fur seal (Arctocephalus forsteri) detected two highly-divergent mtDNA clades, hypothesized to represent a post-sealing hybrid swarm between 'mainland' (Australia-NZ; A. forsteri) and sub-Antarctic (putative 'Upland'; A. snaresensis) lineages. We present ancient-DNA analyses of prehistoric mainland NZ and sub-Antarctic fur seals, revealing that both of these genetic lineages were already widely distributed across the region at the time of human arrival. These findings indicate that anthropogenic factors did not contribute to the admixture of these lineages, and cast doubt on the validity of the Upland seal. Human-mediated impacts on Arctocephalus genetic diversity are instead highlighted by a dramatic temporal haplotype frequency-shift due to genetic drift in heavily bottlenecked populations following the cessation of industrial-scale harvesting. These extinction-recolonisation dynamics add to a growing picture of human-mediated change in NZ's coastal and marine ecosystems. PMID:26768113

  1. 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.

  2. 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

  3. 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

  4. Ancient DNA assessment of tiger salamander population in Yellowstone National Park.

    Directory of Open Access Journals (Sweden)

    Sarah K McMenamin

    Full Text Available Recent data indicates that blotched tiger salamanders (Ambystoma tigrinum melanostictum in northern regions of Yellowstone National Park are declining due to climate-related habitat changes. In this study, we used ancient and modern mitochondrial haplotype diversity to model the effective size of this amphibian population through recent geological time and to assess past responses to climatic changes in the region. Using subfossils collected from a cave in northern Yellowstone, we analyzed >700 base pairs of mitochondrial sequence from 16 samples ranging in age from 100 to 3300 years old and found that all shared an identical haplotype. Although mitochondrial diversity was extremely low within the living population, we still were able to detect geographic subdivision within the local area. Using serial coalescent modelling with Bayesian priors from both modern and ancient genetic data we simulated a range of probable population sizes and mutation rates through time. Our simulations suggest that regional mitochondrial diversity has remained relatively constant even through climatic fluctuations of recent millennia.

  5. 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...

  6. A conditional likelihood is required to estimate the selection coefficient in ancient DNA

    Science.gov (United States)

    Valleriani, Angelo

    2016-08-01

    Time-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to visit the available fitness landscape. Based on two models of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation whereas the unconditioned likelihood fails. Finally, we discuss the fact that the traditional, unconditioned likelihood always delivers an answer, which is often unfalsifiable and appears reasonable also when it is not correct.

  7. Geochemical Analyses of Macrophytes (Potamogeton sp.) and ancient DNA from Lake Karakul, Tajikistan

    Science.gov (United States)

    Heinecke, Liv; Epp, Laura S.; Mischke, Steffen; Reschke, Maria; Stoof-Leichsenring, Kathleen; Rajabov, Ilhomjon; Herzschuh, Ulrike

    2016-04-01

    Mountain ecosystems are very sensitive towards changes in moisture and temperature and therefore most likely to be affected by climate change. To be able to get a closer insight into the alpine system of the Pamir Mountains, a 11.25 m long core was retrieved from the eastern basin of Lake Karakul (3,929 m asl), Tajikistan, in 2012. In order to gain insights into changes in the paleo-productivity of Lake Karakul over the last 29 cal kyrs BP, we investigate temporal gradients of elemental content (TOC, TN) and stable isotopes (δ13C, δ15N) of macrophyte remains (Potamogeton sp.) and plant communities obtained from ancient sedimentary DNA along the core. For the geochemical analyses we make use of the ability of submerged macrophytes, such as Potamogeton, to use HCO3- for photosynthesis in times of CO2 shortage and implement our results in a transfer function for paleo-productivity inferences. No data are available from 20 to 7 cal kyrs BP as no macrophyte remains are preserved, indicating unfavourable conditions for plant growth at the coring site or poor preservation conditions during this time. Biogeochemical analyses show significant variations from core base until approx. 20 cal kyrs BP with TOCPotamogeton 25-45 %, TNPotamogeton 0.5 % - 1.5 %, δ13CPotamogeton below -9 ‰ and δ15NPotamogeton of below 3.5 ‰ suggesting a cooler climate and reflecting the last glacial maximum. Sediments in the upper 4.5 m (approx. 6.7 cal kyrs BP) are rich in macrophyte remains. TOCPotamogeton and TNPotamogeton values from this part of the core are higher, and an enrichment of heavier isotopes with δ13CPotamogeton up to -7 ‰ and δ15NPotamogeton up to 6 ‰ indicating a higher productivity within the lake due to more favourable conditions for macrophyte growths on the lake floor. We assume shifts towards a warmer climate and changes in lake level as the dominating causes. Ancient sedimentary DNA was extracted from selected sediment slices and a metabarcoding approach (using

  8. Neonate Human Remains: A Window of Opportunity to the Molecular Study of Ancient Syphilis

    Science.gov (United States)

    Montiel, Rafael; Solórzano, Eduvigis; Díaz, Nancy; Álvarez-Sandoval, Brenda A.; González-Ruiz, Mercedes; Cañadas, Mari Pau; Simões, Nelson; Isidro, Albert; Malgosa, Assumpció

    2012-01-01

    Ancient DNA (aDNA) analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of “La Ermita de la Soledad” (XVI–XVII centuries), located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals. PMID:22567153

  9. Neonate human remains: a window of opportunity to the molecular study of ancient syphilis.

    Directory of Open Access Journals (Sweden)

    Rafael Montiel

    Full Text Available Ancient DNA (aDNA analysis can be a useful tool in bacterial disease diagnosis in human remains. However, while the recovery of Mycobacterium spp. has been widely successful, several authors report unsuccessful results regarding ancient treponemal DNA, casting doubts on the usefulness of this technique for the diagnosis of ancient syphilis. Here, we present results from an analysis of four newborn specimens recovered from the crypt of "La Ermita de la Soledad" (XVI-XVII centuries, located in the province of Huelva in the southwest of Spain. We extracted and analyzed aDNA in three independent laboratories, following specific procedures generally practiced in the aDNA field, including cloning of the amplified DNA fragments and sequencing of several clones. This is the most ancient case, reported to date, from which detection of DNA from T. pallidum subspecies pallidum has been successful in more than one individual, and we put forward a hypothesis to explain this result, taking into account the course of the disease in neonate individuals.

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

    International Nuclear Information System (INIS)

    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 11000C in steps of 1000C 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 900-10000C. 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.)

  11. Studies of modern and ancient solar energetic particles

    Energy Technology Data Exchange (ETDEWEB)

    Reedy, R.C.

    1998-10-01

    Modern solar energetic particles (SEPs) have been studied for about 50 years by satellites and ground-based observations. These measurements indicate much about the nature of SEPs but cover too short a period to quantify the probabilities of very large solar particle events. Many SEPs have high enough energies to make nuclides in material in which they interact. Some nuclides measured in lunar samples have been used to extend the record about SEPs back several million years. Some new measurements of modern SEPs during the last solar cycle and new results for nuclides made by SEPs in lunar samples are presented and their implications discussed. Both the modern and ancient records need to be improved, and methods to get a better understanding of solar energetic particles are discussed. The SEP average fluxes from both sets of records are similar, and both sets can be used to show that huge fluxes of SEPs are very rare.

  12. 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

  13. 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…

  14. Characterization of Ancient DNA Supports Long-Term Survival of Haloarchaea

    OpenAIRE

    Sankaranarayanan, Krithivasan; Lowenstein, Tim K.; Timofeeff, Michael N.; Schubert, Brian A.; Lum, J. Koji

    2014-01-01

    Bacteria and archaea isolated from crystals of halite 104 to 108 years old suggest long-term survival of halophilic microorganisms, but the results are controversial. Independent verification of the authenticity of reputed living prokaryotes in ancient salt is required because of the high potential for environmental and laboratory contamination. Low success rates of prokaryote cultivation from ancient halite, however, hamper direct replication experiments. In such cases, culture-independent a...

  15. Studies in Continuity and Change: A Comparative Study of the Mother Goddess in Ancient India and Ancient Egypt.

    Science.gov (United States)

    Hardiman, W. J.

    Visiting the Temple of Kali in Calcutta, India, one understands the importance of an Afro-centric methodology in describing the complex nature of the Mother Goddess in ancient India. Discoveries of ancient female figurines indicate an early Indian concept of the female role in the creation of civilization and culture and of the notion of the…

  16. Ancient genomics

    DEFF Research Database (Denmark)

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

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  17. Pig domestication and human-mediated dispersal in western Eurasia revealed through ancient DNA and geometric morphometrics.

    Science.gov (United States)

    Ottoni, Claudio; Flink, Linus Girdland; Evin, Allowen; Geörg, Christina; De Cupere, Bea; Van Neer, Wim; Bartosiewicz, László; Linderholm, Anna; Barnett, Ross; Peters, Joris; Decorte, Ronny; Waelkens, Marc; Vanderheyden, Nancy; Ricaut, François-Xavier; Cakirlar, Canan; Cevik, Ozlem; Hoelzel, A Rus; Mashkour, Marjan; Karimlu, Azadeh Fatemeh Mohaseb; Seno, Shiva Sheikhi; Daujat, Julie; Brock, Fiona; Pinhasi, Ron; Hongo, Hitomi; Perez-Enciso, Miguel; Rasmussen, Morten; Frantz, Laurent; Megens, Hendrik-Jan; Crooijmans, Richard; Groenen, Martien; Arbuckle, Benjamin; Benecke, Nobert; Vidarsdottir, Una Strand; Burger, Joachim; Cucchi, Thomas; Dobney, Keith; Larson, Greger

    2013-04-01

    Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ~8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.

  18. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    Science.gov (United States)

    Der Sarkissian, Clio; Balanovsky, Oleg; Brandt, Guido; Khartanovich, Valery; Buzhilova, Alexandra; Koshel, Sergey; Zaporozhchenko, Valery; Gronenborn, Detlef; Moiseyev, Vyacheslav; Kolpakov, Eugen; Shumkin, Vladimir; Alt, Kurt W; Balanovska, Elena; Cooper, Alan; Haak, Wolfgang

    2013-01-01

    North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present). We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses) and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a), a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population movements across

  19. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    Directory of Open Access Journals (Sweden)

    Clio Der Sarkissian

    Full Text Available North East Europe harbors a high diversity of cultures and languages, suggesting a complex genetic history. Archaeological, anthropological, and genetic research has revealed a series of influences from Western and Eastern Eurasia in the past. While genetic data from modern-day populations is commonly used to make inferences about their origins and past migrations, ancient DNA provides a powerful test of such hypotheses by giving a snapshot of the past genetic diversity. In order to better understand the dynamics that have shaped the gene pool of North East Europeans, we generated and analyzed 34 mitochondrial genotypes from the skeletal remains of three archaeological sites in northwest Russia. These sites were dated to the Mesolithic and the Early Metal Age (7,500 and 3,500 uncalibrated years Before Present. We applied a suite of population genetic analyses (principal component analysis, genetic distance mapping, haplotype sharing analyses and compared past demographic models through coalescent simulations using Bayesian Serial SimCoal and Approximate Bayesian Computation. Comparisons of genetic data from ancient and modern-day populations revealed significant changes in the mitochondrial makeup of North East Europeans through time. Mesolithic foragers showed high frequencies and diversity of haplogroups U (U2e, U4, U5a, a pattern observed previously in European hunter-gatherers from Iberia to Scandinavia. In contrast, the presence of mitochondrial DNA haplogroups C, D, and Z in Early Metal Age individuals suggested discontinuity with Mesolithic hunter-gatherers and genetic influx from central/eastern Siberia. We identified remarkable genetic dissimilarities between prehistoric and modern-day North East Europeans/Saami, which suggests an important role of post-Mesolithic migrations from Western Europe and subsequent population replacement/extinctions. This work demonstrates how ancient DNA can improve our understanding of human population

  20. A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages

    Science.gov (United States)

    Grealy, Alicia C.; McDowell, Matthew C.; Scofield, Paul; Murray, Dáithí C.; Fusco, Diana A.; Haile, James; Prideaux, Gavin J.; Bunce, Michael

    2015-11-01

    When pooled for extraction as a bulk sample, the DNA within morphologically unidentifiable fossil bones can, using next-generation sequencing, yield valuable taxonomic data. This method has been proposed as a means to rapidly and cost-effectively assess general ancient DNA preservation at a site, and to investigate temporal and spatial changes in biodiversity; however, several caveats have yet to be considered. We critically evaluated the bulk bone metabarcoding (BBM) method in terms of its: (i) repeatability, by quantifying sampling and technical variance through a nested experimental design containing sub-samples and replicates at several stages; (ii) accuracy, by comparing morphological and molecular family-level identifications; and (iii) overall utility, by applying the approach to two independent Holocene fossil deposits, Bat Cave (Kangaroo Island, Australia) and Finsch's Folly (Canterbury, New Zealand). For both sites, bone and bone powder sub-sampling were found to contribute significantly to variance in molecularly identified family assemblage, while the contribution of library preparation and sequencing was almost negligible. Nevertheless, total variance was small. Sampling over 80% fewer bones than was required to morphologically identify the taxonomic assemblages, we found that the families identified molecularly are a subset of the families identified morphologically and, for the most part, represent the most abundant families in the fossil record. In addition, we detected a range of extinct, extant and endangered taxa, including some that are rare in the fossil record. Given the relatively low sampling effort of the BBM approach compared with morphological approaches, these results suggest that BBM is largely consistent, accurate, sensitive, and therefore widely applicable. Furthermore, we assessed the overall benefits and caveats of the method, and suggest a workflow for palaeontologists, archaeologists, and geneticists that will help mitigate these

  1. Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas.

    Science.gov (United States)

    Llamas, Bastien; Fehren-Schmitz, Lars; Valverde, Guido; Soubrier, Julien; Mallick, Swapan; Rohland, Nadin; Nordenfelt, Susanne; Valdiosera, Cristina; Richards, Stephen M; Rohrlach, Adam; Romero, Maria Inés Barreto; Espinoza, Isabel Flores; Cagigao, Elsa Tomasto; Jiménez, Lucía Watson; Makowski, Krzysztof; Reyna, Ilán Santiago Leboreiro; Lory, Josefina Mansilla; Torrez, Julio Alejandro Ballivián; Rivera, Mario A; Burger, Richard L; Ceruti, Maria Constanza; Reinhard, Johan; Wells, R Spencer; Politis, Gustavo; Santoro, Calogero M; Standen, Vivien G; Smith, Colin; Reich, David; Ho, Simon Y W; Cooper, Alan; Haak, Wolfgang

    2016-04-01

    The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages. PMID:27051878

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

    Directory of Open Access Journals (Sweden)

    Sevgin Demirci

    Full Text Available 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.

  3. 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). PMID:24349158

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

    DEFF Research Database (Denmark)

    Bellemain, E.; Davey, M.L.; Kauserud, H.;

    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...

  5. 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.

  6. New high through put approach to study ancient microbial phylogenetic diversity in permafrost

    Science.gov (United States)

    Spirina, E.; Cole, J.; Chai, B.; Gilichinksy, D.; Tiedje, J.

    2003-04-01

    The study of microbial diversity in the deep ancient permafrost can help to answer many questions: (1) what kind of mechanisms keeps microbial cells alive, (2) how many of phylogenetic groups exist in situ and never had been cultivated, (3) what is the difference between modern and ancient microorganisms? From this point, distinct environments were examined: Arctic and Antarctic modern soil and permafrost. 16S rDNA genes were amplified from genomic DNA extracted from both original frozen samples and the same samples incubated at 10oC for 8 weeks under both aerobic and anaerobic conditions to determine those capable to grow. High throughput DNA sequencing was performed on the cloned PCR products to obtain partial 16S rDNA gene sequences. The unique script was written to automatically compare over 2,000 partial sequences with those rrn sequences in the Ribosomal Database Project (RDP) release 8.1 using the SEQUENCE MATCH. Sequences were grouped into categories from the RDPs phylogenetic hierarchy based on the closest database matches. Investigation revealed significant microbial diversity; two phylogenetic groups were predominant in all samples: Proteobacteria and Gram Positive Bacteria. Microbial community composition within those groups is different from sample to sample. However, similar genera, such as Arthrobacter, Bacillus, Citrobacter, Caulobacter, Comamonas, Flavobacterium, Nocardioides, Pseudomonas, Rhodocyclus, Rhodococcus, Sphingobacterium, Sphingomonas, Streptococcus, Terrabacter appeared in both polar regions. The greatest microbial diversity was detected in Arctic surface samples. According to RDPs phylogenetic hierarchy those organisms are related to Proteobacteria_SD, Gram Positive Bacteria_SD, Leptospirillum-Nitrospira, Nitrospina_SD, Flexibacter-Cytophaga-Bacteroides, Planctomyces and Relatives. Both the aerobic and anaerobic low temperatures soil incubation yielded some microbes not detected in the original samples. It should be possible, using

  7. 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

  8. 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

    the reliability of one of the proposed criteria, that of appropriate molecular behavior. Using real-time polymerase chain reaction (PCR) and pyrosequencing, we have quantified the relative levels of authentic aDNA and contaminant human DNA sequences recovered from archaeological dog and cattle remains. In doing....... Furthermore, we find that there is a substantial increase in the relative proportions of authentic DNA to contaminant DNA as the PCR target fragment size is decreased. We therefore conclude that the degradation pattern in aDNA provides a quantifiable difference between authentic aDNA and modern contamination...

  9. Raman spectroscopic study of ancient South African domestic clay pottery.

    Science.gov (United States)

    Legodi, M A; de Waal, D

    2007-01-01

    The technique of Raman spectroscopy was used to examine the composition of ancient African domestic clay pottery of South African origin. One sample from each of four archaeological sites including Rooiwal, Lydenburg, Makahane and Graskop was studied. Normal dispersive Raman spectroscopy was found to be the most effective analytical technique in this study. XRF, XRD and FT-IR spectroscopy were used as complementary techniques. All representative samples contained common features, which were characterised by kaolin (Al2Si2O5(OH)5), illite (KAl4(Si7AlO20)(OH)4), feldspar (K- and NaAlSi3O8), quartz (alpha-SiO2), hematite (alpha-Fe2O3), montmorillonite (Mg3(Si,Al)4(OH)2 x 4.5 5H(2)O[Mg]0.35), and calcium silicate (CaSiO3). Gypsum (CaSO4 x 2H2O) and calcium carbonates (most likely calcite, CaCO3) were detected by Raman spectroscopy in Lydenburg, Makahane and Graskop shards. Amorphous carbon (with accompanying phosphates) was observed in the Raman spectra of Lydenburg, Rooiwal and Makahane shards, while rutile (TiO(2)) appeared only in Makahane shard. The Raman spectra of Lydenburg and Rooiwal shards further showed the presence of anhydrite (CaSO4). The results showed that South African potters used a mixture of clays as raw materials. The firing temperature for most samples did not exceed 800 degrees C, which suggests the use of open fire. The reddish brown and grayish black colours were likely due to hematite and amorphous carbon, respectively. PMID:16839805

  10. Compositional Studies of Ancient Copper from Romanian Territories

    CERN Document Server

    Olariu, A; Belc, M; Popescu, I V; Badica, T; Lazarovici, G; Olariu, Agata; Lazarovici, Gh.

    1999-01-01

    Ancient copper objects from Romanian Territories have been analyzed by neutron activation analysis. A series of elements is determined: Au, Ag, As, Co, Cr, Fe, Hg, Ni, Zn, Sb, Sc, Se, Sn. Using mathematical dendograms some classifications and correlation have been established.

  11. 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.

  12. PIXE and INAA studies on ancient potteries from Guangfulin relics in Shanghai

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper reports the study of ancient potteries unearthed from the Guangfulin site in Shanghai. From the external features of these potteries, archeologists can classify them into two different cultural types: Liangzhu culture (local culture) and a new culture which might be derived elsewhere, but they can not recognize whether they were produced in the same place. Proton induced X-ray emission (PIXE) and instrumental neutron activation analysis (INAA) were used to measure the chemical compositions of the samples and the results were analyzed using multivariate statistics. We found that the two methods can complement each other and their database can be mutually referenced in the study of ancient potteries. Experimental results show that the compositions of the potteries from the two cultural types are different, which means that the materials for ancient potteries of new culture originate from elsewhere. This supports the archaeologists' speculation that a group of ancient people migrated to Shanghai from some other places 4000 years ago.

  13. 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.

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

    Science.gov (United States)

    Valverde, Guido; Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars; Llamas, Bastien; Haak, Wolfgang

    2016-01-01

    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. PMID:27248693

  15. Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family

    Directory of Open Access Journals (Sweden)

    Rothblatt Jonathan

    2008-07-01

    transcriptional induction of BH3 domain proteins is likely to be an ancient DNA damage response function of the p53 family. Interestingly, although the apoptotic response to DNA damage is regulated through the transcriptional activity of CEP-1, other DNA damage responses do not appear to be regulated on the transcriptional level and do not require the p53 like gene cep-1.

  16. The provenance study of Chinese ancient color glaze from Shanxi by INAA and factor analysis

    International Nuclear Information System (INIS)

    This paper reports the results of the provenance study of Chinese ancient color glaze in Shanxi. The minor and trace elements of body of color glaze in different dynasty from Xiyue temper kiln and that of Lidipo kiln in Ming Dynasty determined by INAA, some of ancient porcelain from Lidipo kiln were measured, also. The factor analysis showed that provenances of the ancient color glazes from Xiyue Temple that were produced during Song Dynasty to the early Qing Dynasty were in the place of the Xiyue kiln, and body material of ancient color have little been changed, on the other hand, that of Later Qing Dynasty were-produced from Lidipo kiln. Different color glazes were measured by SRXRF and it proved the colored elements were Fe and Cu.

  17. Paleo-oncology: the role of ancient remains in the study of cancer.

    Science.gov (United States)

    Halperin, Edward C

    2004-01-01

    Paleo-oncology is the study of carcinomas and sarcomas in ancient human populations and their hominid precursors. These populations are informative concerning the possible influences on cancer of morphologic and functional evolution, diet, lifestyle, and other environmental factors. The prevalence of cancer in ancient populations might have differed from that in modern humans, because of substantial differences in tobacco and alcohol use, diet, life expectancy, and the availability of treatment. The available physical data concerning cancer in antiquity includes evidence of its existence in animal fossils and ancient humans and their precursors. The difficulties of paleo-oncologic research include a limited soft tissue record. In evaluating cancer in ancient remains, one must also deal with the problem of pseudopathology: whether an observed tissue change is all antemortem pathologic lesion or a postmortem artifact. Future archeological discoveries and the application of improved diagnostic techniques may enable paleo-oncology to make further contributions to our understanding of cancer. PMID:15061165

  18. Paleo-oncology: the role of ancient remains in the study of cancer.

    Science.gov (United States)

    Halperin, Edward C

    2004-01-01

    Paleo-oncology is the study of carcinomas and sarcomas in ancient human populations and their hominid precursors. These populations are informative concerning the possible influences on cancer of morphologic and functional evolution, diet, lifestyle, and other environmental factors. The prevalence of cancer in ancient populations might have differed from that in modern humans, because of substantial differences in tobacco and alcohol use, diet, life expectancy, and the availability of treatment. The available physical data concerning cancer in antiquity includes evidence of its existence in animal fossils and ancient humans and their precursors. The difficulties of paleo-oncologic research include a limited soft tissue record. In evaluating cancer in ancient remains, one must also deal with the problem of pseudopathology: whether an observed tissue change is all antemortem pathologic lesion or a postmortem artifact. Future archeological discoveries and the application of improved diagnostic techniques may enable paleo-oncology to make further contributions to our understanding of cancer.

  19. 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.

  20. Ancient DNA analyses of early archaeological sites in New Zealand reveal extreme exploitation of moa (Aves: Dinornithiformes) at all life stages

    Science.gov (United States)

    Oskam, Charlotte L.; Allentoft, Morten E.; Walter, Richard; Scofield, R. Paul; Haile, James; Holdaway, Richard N.; Bunce, Michael; Jacomb, Chris

    2012-10-01

    The human colonisation of New Zealand in the late thirteenth century AD led to catastrophic impacts on the local biota and is among the most compelling examples of human over-exploitation of native fauna, including megafauna. Nearly half of the species in New Zealand' s pre-human avifauna are now extinct, including all nine species of large, flightless moa (Aves: Dinornithiformes). The abundance of moa in early archaeological sites demonstrates the significance of these megaherbivores in the diet of the first New Zealanders. Combining moa assemblage data, based on DNA identification of eggshell and bone, with morphological identification of bone (literature and museum catalogued specimens), we present the most comprehensive audit of moa to date from several significant 13th-15th century AD archaeological deposits across the east coast of the South Island. Mitochondrial DNA (mtDNA) was amplified from 251 of 323 (78%) eggshell fragments and 22 of 27 (88%) bone samples, and the analyses revealed the presence of four moa species: Anomalopteryx didiformis; Dinornis robustus; Emeus crassus and Euryapteryx curtus. The mtDNA, along with polymorphic microsatellite markers, enabled an estimate of the minimum number of individual eggs consumed at each site. Remarkably, in one deposit over 50 individual eggs were identified - a number that likely represents a considerable proportion of the total reproductive output of moa in the area and emphasises that human predation of all life stages of moa was intense. Molecular sexing was conducted on bones (n = 11). Contrary to previous ancient DNA studies from natural sites that consistently report an excess of female moa, we observed an excess of males (2.7:1), suggestive that males were preferential targets. This could be related to different behaviour between the two highly size-dimorphic sexes in moa. Lastly, we investigated the moa species from recovered skeletal and eggshell remains from seven Wairau Bar burials, and identified

  1. mtDNA haplogroup X: An ancient link between Europe/Western Asia and North America?

    OpenAIRE

    Brown, M. D.; Hosseini, S H; Torroni, A.; Bandelt, H. J.; Allen, J C; Schurr, T. G.; Scozzari, R; Cruciani, F; Wallace, D C

    1998-01-01

    On the basis of comprehensive RFLP analysis, it has been inferred that approximately 97% of Native American mtDNAs belong to one of four major founding mtDNA lineages, designated haplogroups "A"-"D." It has been proposed that a fifth mtDNA haplogroup (haplogroup X) represents a minor founding lineage in Native Americans. Unlike haplogroups A-D, haplogroup X is also found at low frequencies in modern European populations. To investigate the origins, diversity, and continental relationships of ...

  2. 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.

  3. Some new results of PIXE study on Chinese ancient porcelain

    International Nuclear Information System (INIS)

    This paper reports some new results obtained by PIXE on Chinese ancient porcelain. The first results concern the provenance of blue and white porcelain made during the Tang Dynasty (AD618-907), which are the earliest products found in China. The PIXE experimental results show that they were fired in Huangye Kiln, Gongyi, Henan Province. The chemical composition of the body, white glaze and of the cobalt pigment will be reported. This paper also reports the results for early Chinese blue and white porcelain made under the Yuan dynasty (AD1206-1368) in Jingdezhen, Jiangxi Province. Experimental results show that the chemical composition of the cobalt pigment used by officers and popular are similar. These materials were imported from another country. The local asbolite was used as cobalt pigment material since the early Ming Dynasty (AD1368-1644) in Jingdezhen at folk kiln, and it was used at official kiln until the 16th century

  4. Some new results of PIXE study on Chinese ancient porcelain

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, H.S. [Institute of Modern Physics, Fudan University, Shanghai 200433 (China)]. E-mail: hscheng@fudan.edu.cn; Zhang, B. [Institute of Modern Physics, Fudan University, Shanghai 200433 (China); Zhu, D. [Institute of Modern Physics, Fudan University, Shanghai 200433 (China); Yang, F.J. [Institute of Modern Physics, Fudan University, Shanghai 200433 (China); Sun, X.M. [Cultural Relics and Archaeology Research Institute of Henan Province, Zheng Zhou 450000 (China); Guo, M.S. [Cultural Relics and Archaeology Research Institute of Henan Province, Zheng Zhou 450000 (China)

    2005-10-15

    This paper reports some new results obtained by PIXE on Chinese ancient porcelain. The first results concern the provenance of blue and white porcelain made during the Tang Dynasty (AD618-907), which are the earliest products found in China. The PIXE experimental results show that they were fired in Huangye Kiln, Gongyi, Henan Province. The chemical composition of the body, white glaze and of the cobalt pigment will be reported. This paper also reports the results for early Chinese blue and white porcelain made under the Yuan dynasty (AD1206-1368) in Jingdezhen, Jiangxi Province. Experimental results show that the chemical composition of the cobalt pigment used by officers and popular are similar. These materials were imported from another country. The local asbolite was used as cobalt pigment material since the early Ming Dynasty (AD1368-1644) in Jingdezhen at folk kiln, and it was used at official kiln until the 16th century.

  5. 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.

  6. Highly skewed sex ratios and biased fossil deposition of moa: ancient DNA provides new insight on New Zealand's extinct megafauna

    Science.gov (United States)

    Allentoft, Morten E.; Bunce, Michael; Scofield, R. Paul; Hale, Marie L.; Holdaway, Richard N.

    2010-03-01

    Ancient DNA was isolated from the bones of 267 individuals of the extinct New Zealand moa (Aves: Dinornithiformes) from two late Holocene deposits [Pyramid Valley (PV) and Bell Hill Vineyard (BHV)] located 5.7 km apart in North Canterbury, South Island. The two sites' combined fossil record cover the last 3000 years of pre-human New Zealand and mitochondrial DNA confirmed that four species ( Dinornis robustus, Euryapteryx curtus, Emeus crassus, and Pachyornis elephantopus) were sympatric in the region. However, the relative species compositions in the two deposits differed significantly with D. robustus and E. crassus being most abundant at PV while E. curtus outnumbered the other three moa taxa combined at BHV. A subsample of 227 individuals had sufficient nuclear DNA preservation to warrant the use of molecular sexing techniques, and the analyses uncovered a remarkable excess of females in both deposits with an overall male to female ratio of 1:5.1. Among juveniles of E. curtus, the only species which was represented by a substantial fraction of juveniles, the sex ratio was not skewed (10 ♂, 10 ♀), suggesting that the observed imbalance arose as a result of differential mortality during maturation. Surprisingly, sex ratios proved significantly different between sites with a 1:2.2 ratio at BHV ( n = 90) and 1:14.2 at PV ( n = 137). Given the mobility of large ratites, and the proximity of the two fossil assemblages in space and time, these differences in taxonomic and gender composition indicate that moa biology and the local environment have affected the fossil representation dramatically and several possible explanations are offered. Apart from adding to our understanding of moa biology, these discoveries reinforce the need for caution when basing interpretation of the fossil record on material from a single site.

  7. Moa's Ark or volant ghosts of Gondwana? Insights from nineteen years of ancient DNA research on the extinct moa (Aves: Dinornithiformes) of New Zealand.

    Science.gov (United States)

    Allentoft, Morten E; Rawlence, Nicolas J

    2012-01-20

    The moa (Aves: Dinornithiformes) of New Zealand represent one of the extinct iconic taxa that define the field of ancient DNA (aDNA), and after almost two decades of genetic scrutiny of bones, feathers, coprolites, mummified tissue, eggshell, and sediments, our knowledge of these prehistoric giants has increased significantly. Thanks to molecular and morphological-based research, the insights that have been obtained into moa phylogenetics, phylogeography, and palaeobiology exceeds that of any other extinct taxon. This review documents the strengths of applying a multidisciplinary approach when studying extinct taxa but also shows that cross-disciplinary controversies still remain at the most fundamental levels, with highly conflicting interpretations derived from aDNA and morphology. Moa species diversity, for example, is still heavily debated, as well as their relationship with other ratites and the mode of radiation. In addition to increasing our knowledge on a lineage of extinct birds, further insights into these aspects can clarify some of the basal splits in avian evolution, and the evolutionary implications of the breakup of the prehistoric supercontinent Gondwana. Did a flightless moa ancestor drift away on proto New Zealand (Moa's Ark) or did a volant ancestor arrive by flight? Here we provide an overview of 19 years of aDNA research on moa, critically assess the attempts and controversies in placing the moa lineage among palaeognath birds, and discuss the factors that facilitated the extensive radiation of moa. Finally, we identify the most obvious gaps in the current knowledge to address the future potential research areas in moa genetics.

  8. Ancient DNA reveals late survival of mammoth and horse in interior Alaska

    DEFF Research Database (Denmark)

    Haile, James; Froese, Duane G; Macphee, Ross D E;

    2009-01-01

    of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000-13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct...... perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than...... indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people...

  9. 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.

  10. Adsorption of DNA on biomimetic apatites: Toward the understanding of the role of bone and tooth mineral on the preservation of ancient DNA

    OpenAIRE

    Grunenwald, Anne; Keyser, Christine; Sautereau, Anne-Marie; Crubézy, Eric; Ludes, Bertrand; Drouet, Christophe

    2014-01-01

    International audience In order to shed some light on DNA preservation over time in skeletal remains from a physicochemicalviewpoint, adsorption and desorption of DNA on a well characterized synthetic apatite mimicking boneand dentin biominerals were studied. Batch adsorption experiments have been carried out to determinethe effect of contact time (kinetics), DNA concentration (isotherms) and environmentally relevant factorssuch as temperature, ionic strength and pH on the adsorption behav...

  11. Ancient "Red Cliff" battlefield: a historical-geographic study

    Institute of Scientific and Technical Information of China (English)

    Zhang Xiugui

    2006-01-01

    The famous battle of Chibi,or "battle of Red Cliff",took place in 208 CE,the 13th year of the Jian'an period of the Eastern Han dynasty.This paper holds that the whole battle consisted of three inseparable stages,namely the initial clash at Chibi,the chase battle to Wulin,and Cao Cao's disorganized escape along Huarong Road.The Red Cliff battlefield thus extended across a distance of more than 300 li (150km).Even if the Chibi where the initial military engagement took place (that is,Chiji Hill,southwest of Wuchang in modern Wuhan City) has already disappeared,it should be restored to its proper historical position.The chase battle along the Yangzi River came to an end at Wulin,across the river is Chibi Hill in today's Chibi City.Although this Chibi is not the Chibi where the initial combat took place,it nonetheless forms an integral part of the ancient Chibi battlefield as a whole.The Huarong Road along which Cao Cao escaped runs through the middle of today's Jianghan Plain.Finally,the text aims to show that Chibi (Red Nose)1 Hill in modern Huangzhou City has nothing to do with the Chibi of the "battle of Red Cliff."

  12. Study and progress of the thermoluminescence dating of the ancient pottery and porcelain

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Two standard methods,the "fine-grain technique" and the "quartz inclusion technique",and a new method,the pre-dose saturation exponential technique in thermoluminescence(TL)dating of ancient pottery and porcelain were reviewed,especially for the measurement of the paleodose and the annual dose.The two standard methods have been acknowledged in domain of TL dating and are used widely for age determination in archaeology and geology.As a dating tool the TL technique has been of great success in authentication of ancient ceramic art objects.However,a few complicated factors limit the precision and accuracy in age determination.These complicated factors are analyzed and discussed.Therefore,although ceramic TL dating can in general solve the problem of authentication of ancient ceramics,there are still complexities that require further research and study.

  13. Study and progress of the thermoluminescence dating of the ancient pottery and porcelain

    Institute of Scientific and Technical Information of China (English)

    WANG WeiDa

    2009-01-01

    Two standard methods, the "fine-grain technique" and the "quartz inclusion technique", and a new method, the pre-dose saturation exponential technique in thermoluminescence (TL) dating of ancient pottery and porcelain were reviewed, especially for the measurement of the paleodose and the annual dose. The two standard methods have been acknowledged in domain of TL dating and are used widely for age determination in archaeology and geology. As a dating tool the TL technique has been of great success in authentication of ancient ceramic art objects. However, a few complicated factors limit the precision and accuracy in age determination. These complicated factors are analyzed and discussed. Therefore, although ceramic TL dating can in general solve the problem of authentication of ancient ceramics, there are still complexities that require further research and study.

  14. Ancient mitogenomics

    DEFF Research Database (Denmark)

    Ho, Simon Y W; Gilbert, M Thomas P

    2010-01-01

    the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field....

  15. 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.

  16. Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

    Science.gov (United States)

    Larson, Greger; Cucchi, Thomas; Fujita, Masakatsu; Matisoo-Smith, Elizabeth; Robins, Judith; Anderson, Atholl; Rolett, Barry; Spriggs, Matthew; Dolman, Gaynor; Kim, Tae-Hun; Thuy, Nguyen Thi Dieu; Randi, Ettore; Doherty, Moira; Due, Rokus Awe; Bollt, Robert; Djubiantono, Tony; Griffin, Bion; Intoh, Michiko; Keane, Emile; Kirch, Patrick; Li, Kuang-Ti; Morwood, Michael; Pedriña, Lolita M.; Piper, Philip J.; Rabett, Ryan J.; Shooter, Peter; Van den Bergh, Gert; West, Eric; Wickler, Stephen; Yuan, Jing; Cooper, Alan; Dobney, Keith

    2007-01-01

    Human settlement of Oceania marked the culmination of a global colonization process that began when humans first left Africa at least 90,000 years ago. The precise origins and dispersal routes of the Austronesian peoples and the associated Lapita culture remain contentious, and numerous disparate models of dispersal (based primarily on linguistic, genetic, and archeological data) have been proposed. Here, through the use of mtDNA from 781 modern and ancient Sus specimens, we provide evidence for an early human-mediated translocation of the Sulawesi warty pig (Sus celebensis) to Flores and Timor and two later separate human-mediated dispersals of domestic pig (Sus scrofa) through Island Southeast Asia into Oceania. Of the later dispersal routes, one is unequivocally associated with the Neolithic (Lapita) and later Polynesian migrations and links modern and archeological Javan, Sumatran, Wallacean, and Oceanic pigs with mainland Southeast Asian S. scrofa. Archeological and genetic evidence shows these pigs were certainly introduced to islands east of the Wallace Line, including New Guinea, and that so-called “wild” pigs within this region are most likely feral descendants of domestic pigs introduced by early agriculturalists. The other later pig dispersal links mainland East Asian pigs to western Micronesia, Taiwan, and the Philippines. These results provide important data with which to test current models for human dispersal in the region. PMID:17360400

  17. Adsorption of DNA on biomimetic apatites: Toward the understanding of the role of bone and tooth mineral on the preservation of ancient DNA

    Science.gov (United States)

    Grunenwald, A.; Keyser, C.; Sautereau, A. M.; Crubézy, E.; Ludes, B.; Drouet, C.

    2014-02-01

    In order to shed some light on DNA preservation over time in skeletal remains from a physicochemical viewpoint, adsorption and desorption of DNA on a well characterized synthetic apatite mimicking bone and dentin biominerals were studied. Batch adsorption experiments have been carried out to determine the effect of contact time (kinetics), DNA concentration (isotherms) and environmentally relevant factors such as temperature, ionic strength and pH on the adsorption behavior. The analogy of the nanocrystalline carbonated apatite used in this work with biological apatite was first demonstrated by XRD, FTIR, and chemical analyses. Then, DNA adsorption kinetics was fitted with the pseudo-first order, pseudo-second order, Elovich, Ritchie and double exponential models. The best results were achieved with the Elovich kinetic model. The adsorption isotherms of partially sheared calf thymus DNA conformed satisfactorily to Temkin's equation which is often used to describe heterogeneous adsorption behavior involving polyelectrolytes. For the first time, the irreversibility of DNA adsorption toward dilution and significant phosphate-promoted DNA desorption were evidenced, suggesting that a concomitant ion exchange process between phosphate anionic groups of DNA backbone and labile non-apatitic hydrogenphosphate ions potentially released from the hydrated layer of apatite crystals. This work should prove helpful for a better understanding of diagenetic processes related to DNA preservation in calcified tissues.

  18. 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.

  19. 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.

  20. Bio-Anthropological Studies on Human Skeletons from the 6th Century Tomb of Ancient Silla Kingdom in South Korea

    Science.gov (United States)

    Lee, Won-Joon; Woo, Eun Jin; Oh, Chang Seok; Yoo, Jeong A.; Kim, Yi-Suk; Hong, Jong Ha; Yoon, A. Young; Wilkinson, Caroline M.; Ju, Jin Og; Choi, Soon Jo; Lee, Soong Doek; Shin, Dong Hoon

    2016-01-01

    In November and December 2013, unidentified human skeletal remains buried in a mokgwakmyo (a traditional wooden coffin) were unearthed while conducting an archaeological investigation near Gyeongju, which was the capital of the Silla Kingdom (57 BCE– 660 CE) of ancient Korea. The human skeletal remains were preserved in relatively intact condition. In an attempt to obtain biological information on the skeleton, physical anthropological, mitochondrial DNA, stable isotope and craniofacial analyses were carried out. The results indicated that the individual was a female from the Silla period, of 155 ± 5 cm height, who died in her late thirties. The maternal lineage belonged to the haplogroup F1b1a, typical for East Asia, and the diet had been more C3- (wheat, rice and potatoes) than C4-based (maize, millet and other tropical grains). Finally, the face of the individual was reconstructed utilizing the skull (restored from osseous fragments) and three-dimensional computerized modeling system. This study, applying multi-dimensional approaches within an overall bio-anthropological analysis, was the first attempt to collect holistic biological information on human skeletal remains dating to the Silla Kingdom period of ancient Korea. PMID:27249220

  1. Bio-Anthropological Studies on Human Skeletons from the 6th Century Tomb of Ancient Silla Kingdom in South Korea.

    Science.gov (United States)

    Lee, Won-Joon; Woo, Eun Jin; Oh, Chang Seok; Yoo, Jeong A; Kim, Yi-Suk; Hong, Jong Ha; Yoon, A Young; Wilkinson, Caroline M; Ju, Jin Og; Choi, Soon Jo; Lee, Soong Doek; Shin, Dong Hoon

    2016-01-01

    In November and December 2013, unidentified human skeletal remains buried in a mokgwakmyo (a traditional wooden coffin) were unearthed while conducting an archaeological investigation near Gyeongju, which was the capital of the Silla Kingdom (57 BCE- 660 CE) of ancient Korea. The human skeletal remains were preserved in relatively intact condition. In an attempt to obtain biological information on the skeleton, physical anthropological, mitochondrial DNA, stable isotope and craniofacial analyses were carried out. The results indicated that the individual was a female from the Silla period, of 155 ± 5 cm height, who died in her late thirties. The maternal lineage belonged to the haplogroup F1b1a, typical for East Asia, and the diet had been more C3- (wheat, rice and potatoes) than C4-based (maize, millet and other tropical grains). Finally, the face of the individual was reconstructed utilizing the skull (restored from osseous fragments) and three-dimensional computerized modeling system. This study, applying multi-dimensional approaches within an overall bio-anthropological analysis, was the first attempt to collect holistic biological information on human skeletal remains dating to the Silla Kingdom period of ancient Korea. PMID:27249220

  2. Bio-Anthropological Studies on Human Skeletons from the 6th Century Tomb of Ancient Silla Kingdom in South Korea.

    Directory of Open Access Journals (Sweden)

    Won-Joon Lee

    Full Text Available In November and December 2013, unidentified human skeletal remains buried in a mokgwakmyo (a traditional wooden coffin were unearthed while conducting an archaeological investigation near Gyeongju, which was the capital of the Silla Kingdom (57 BCE- 660 CE of ancient Korea. The human skeletal remains were preserved in relatively intact condition. In an attempt to obtain biological information on the skeleton, physical anthropological, mitochondrial DNA, stable isotope and craniofacial analyses were carried out. The results indicated that the individual was a female from the Silla period, of 155 ± 5 cm height, who died in her late thirties. The maternal lineage belonged to the haplogroup F1b1a, typical for East Asia, and the diet had been more C3- (wheat, rice and potatoes than C4-based (maize, millet and other tropical grains. Finally, the face of the individual was reconstructed utilizing the skull (restored from osseous fragments and three-dimensional computerized modeling system. This study, applying multi-dimensional approaches within an overall bio-anthropological analysis, was the first attempt to collect holistic biological information on human skeletal remains dating to the Silla Kingdom period of ancient Korea.

  3. Ancient Tibetan Manuscripts of the Tubo Period Recoverd form Dunhuang: Its Historical-Material Value in the Tibetan Studies

    Institute of Scientific and Technical Information of China (English)

    KalzangGyal

    2004-01-01

    Ancient Tibetan documents of the Tubo period are amongst those discovered in the Mogao Grottoes at Dunhuang in i9oo. As handwritten documents in the ancient Tibetan language of the Tubo period, they are an important part of the international Dunhuang study and indispensable to Tibetology. Incomplete statistics

  4. Ancient DNA reveals genetic stability despite demographic decline: 3,000 years of population history in the endemic Hawaiian petrel.

    Science.gov (United States)

    Welch, Andreanna J; Wiley, Anne E; James, Helen F; Ostrom, Peggy H; Stafford, Thomas W; Fleischer, Robert C

    2012-12-01

    In the Hawaiian Islands, human colonization, which began approximately 1,200 to 800 years ago, marks the beginning of a period in which nearly 75% of the endemic avifauna became extinct and the population size and range of many additional species declined. It remains unclear why some species persisted whereas others did not. The endemic Hawaiian petrel (Pterodroma sandwichensis) has escaped extinction, but colonies on two islands have been extirpated and populations on remaining islands have contracted. We obtained mitochondrial DNA sequences from 100 subfossil bones, 28 museum specimens, and 289 modern samples to investigate patterns of gene flow and temporal changes in the genetic diversity of this endangered species over the last 3,000 years, as Polynesians and then Europeans colonized the Hawaiian Islands. Genetic differentiation was found to be high between both modern and ancient petrel populations. However, gene flow was substantial between the extirpated colonies on Oahu and Molokai and modern birds from the island of Lanai. No significant reductions in genetic diversity occurred over this period, despite fears in the mid-1900s that this species may have been extinct. Simulations show that even a decline to a stable effective population size of 100 individuals would result in the loss of only 5% of the expected heterozygosity. Simulations also show that high levels of genetic diversity may be retained due to the long generation time of this species. Such decoupling between population size and genetic diversity in long-lived species can have important conservation implications. It appears that a pattern of dispersal from declining colonies, in addition to long generation time, may have allowed the Hawaiian petrel to escape a severe genetic bottleneck, and the associated extinction vortex, and persist despite a large population decline after human colonization. PMID:22844071

  5. 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.

  6. Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

    DEFF Research Database (Denmark)

    Foote, Andrew D; Kaschner, Kristin; Schultze, Sebastian E;

    2013-01-01

    that a true Arctic species, the bowhead whale (Balaena mysticetus), shifted its range and tracked its core suitable habitat northwards during the rapid climate change of the Pleistocene-Holocene transition. Late Pleistocene lineages survived into the Holocene and effective female population size increased...... rapidly, concurrent with a threefold increase in core suitable habitat. This study highlights that responses to climate change are likely to be species specific and difficult to predict. We estimate that the core suitable habitat of bowhead whales will be almost halved by the end of this century...

  7. Reflection and Prospective Symposium of the Centennial Studies of Ancient Chinese Philology%新书籍史对古文献学研究的启示

    Institute of Scientific and Technical Information of China (English)

    张升

    2013-01-01

    Editor's note:It is both an important task and optimal subject of the 21st century philology to summarize the achievements of centen-nial ancient philology, reflect the current issues, grasp the development trend of ancient literature studies, expand research space, enrich the research contents, and put forward farsighted countermeasures for inhering and innovating Chinese culture, establishing ancient philology, and promoting academic development. To solve these problems, we organized a symposium of three articles. Professor Zhou Shaochuan's article clarifies the significance of centennial Chinese ancient books and ancient philology, pointing out two aspects of China's ancient books in the 20th century and the ancient literature studies: diachronic investigation following two main lines of collection of ancient books and establishment of ancient philology, and synchronic analysis from four aspects, that is, basic historical facts, methodology, basic principles, and scientific theorizing, in order to explore the development law of collection of ancient books and ancient philology, and specify the direction of ancient philology. Professor Wang Jilu's article discusses five urgent issues in ancient philology of the 21st century: theoretical system and research paradigm, philological heritages, the position of philology of ethnic minorities, comparative study of Chinese and Western philology, theories and methods in digitalization of ancient books, etc. Professor Zhang Sheng's article discusses the implication of Western new history of books for ancient philology, and argues that new history of books expands the horizon and scope of ancient philology. The introduction of methodology of social history and cultural history makes it clear that philology has social and cultural significance. Ancient philology should become solid and draw on interdisciplinary methods to enrich the content of its own research.

  8. 新书籍史对古文献学研究的启示%Reflection and Prospective Symposium of the Centennial Studies of Ancient Chinese Philology

    Institute of Scientific and Technical Information of China (English)

    张升

    2013-01-01

    Editor's note:It is both an important task and optimal subject of the 21st century philology to summarize the achievements of centen-nial ancient philology, reflect the current issues, grasp the development trend of ancient literature studies, expand research space, enrich the research contents, and put forward farsighted countermeasures for inhering and innovating Chinese culture, establishing ancient philology, and promoting academic development. To solve these problems, we organized a symposium of three articles. Professor Zhou Shaochuan's article clarifies the significance of centennial Chinese ancient books and ancient philology, pointing out two aspects of China's ancient books in the 20th century and the ancient literature studies: diachronic investigation following two main lines of collection of ancient books and establishment of ancient philology, and synchronic analysis from four aspects, that is, basic historical facts, methodology, basic principles, and scientific theorizing, in order to explore the development law of collection of ancient books and ancient philology, and specify the direction of ancient philology. Professor Wang Jilu's article discusses five urgent issues in ancient philology of the 21st century: theoretical system and research paradigm, philological heritages, the position of philology of ethnic minorities, comparative study of Chinese and Western philology, theories and methods in digitalization of ancient books, etc. Professor Zhang Sheng's article discusses the implication of Western new history of books for ancient philology, and argues that new history of books expands the horizon and scope of ancient philology. The introduction of methodology of social history and cultural history makes it clear that philology has social and cultural significance. Ancient philology should become solid and draw on interdisciplinary methods to enrich the content of its own research.

  9. Calcium in ancient glazes and glasses: a XAFS study

    International Nuclear Information System (INIS)

    Ceramic tiles used to manufacture artistic panels during the XVI to the XVIII centuries were decorated with high-lead soda-lime glazes, incorporating a diversity of chromophore cations, as ascertained by SRXRF (synchrotron radiation X-ray fluorescence). Previous X-ray absorption spectroscopy (XAS) studies have shown that sodium and lead are hosted by the glassy matrix in those glazes. However, the possible role of calcium as a modifier of the tetrahedral silica network is not fully clarified, despite being recognized that calcium cations alter some fundamental properties of glazes, namely transparency. An X-ray absorption fine structure (XAFS) study of glazes with varied colorings was therefore undertaken at Ca K- and L-edges. Well crystallized oxide minerals were used to model distinct coordination environments by oxygen atoms - close to octahedral geometry in calcite and dodecahedral in gypsum - while fluorite was chosen to mimic ideal cubic coordination. A first XAS approach suggested a minor variation in the energy separation between L2-L3 absorption edges when comparing blue and yellow glazes, irrespective of the period of manufacture. A further study on the X-ray absorption near-edge structure (XANES) carried out at the K-edge corroborated this difference and, along with the theoretical spectra modeling performed with the FEFF code, allowed interpreting of the Ca 1s absorption spectra of glazes as arising from a non-regular high-coordination environment within the silica matrix. (orig.)

  10. Revaluation of Xihuang Pill on tumor treatment:from ancient literatures to modern studies

    Institute of Scientific and Technical Information of China (English)

    Xue Yang; Xiong-ZhiWu

    2016-01-01

    Xihuang Pill (XHP), an old prescription since the 18th century to treat various diseases, including breast cancer, is used widely for tumor therapy alone or in combination with chemotherapy and/or radiotherapy. XHP is composed of Niu Huang (Calculus bovis), She Xiang (Moschus), Ru Xiang (Olibanum), and Mo Yao (Myrrha). XHP was recorded to have effects on treating breast cancer, intestinal cancer, lymphomas, ovarian cancer. Modern studies indicate that XHP can inhibit tumor cells proliferation, migration, angiogenesis and regulate tumor microenvironment. In this review, we firstly introduced the application of XHP on tumor therapy in ancient literatures. Then, the antitumor studies of XHP in both clinical and basic aspects were summarized and we also discussed the antitumor material basis and mechanisms of Calculus Bovis, Moschus, Olibanum and Myrrha. In addition, with the development of time, the dosage form of XHP, source and dose of herbs and processing methods of Olibanum and Myrrha have been changed and we also evaluated the advantage and disadvantage of these changes of XHP. Taken together, XHP has various antitumor active ingredients, which is multi-target. Moreover, beneficial technology improvement has been made in modern XHP compared to the ancient prescription. Here, we aimed to put forward a new method to revaluating XHP on its application from ancient literatures to modern studies and from pharmacy to medicine.

  11. PIXE study on ancient pottery from Chinese Sanxia area

    International Nuclear Information System (INIS)

    Thirty-nine pieces of Neolithic pottery, made about 4500 years ago, were collected from Maliutuo, Maliuwan and Suheping village sites in Chinese Sanxia area. Nine pieces of pottery in the Shang Dynasty (1600-1100 BC) and ten pieces of pottery in the Eastern Zhou Dynasty (770-256 BC) were also collected from Maliutuo. PIXE and factor analysis were used to study interchange of the Neolithic pottery between these three sites. The source of raw material of pottery from Maliutuo was simultaneously studied. The major and trace element contents in pottery were determined by PIXE. Factor analysis was employed to classify these pieces of pottery. The results showed that the trace element contents were more useful to distinguish these pieces of pottery than the major element contents. In about 2500 BC, no interchange of pottery occurred between the three villages. Although Maliutuo was close to Maliuwan, the pottery products used in daily life in the two villages were independently made and not exchanged. In the source of raw material, the Neolithic pottery samples from Maliutuo were identical with those in the Shang Dynasty, but different from those in the Eastern Zhou Dynasty

  12. PIXE study on ancient pottery from Chinese Sanxia area

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, B.; Pan, B.H.; Zhang, Z.Q.; Cheng, H.S. E-mail: hscheng@fudan.edu.cn; Gao, M.H.; Yang, F.J.; Peng, X.B

    2004-06-01

    Thirty-nine pieces of Neolithic pottery, made about 4500 years ago, were collected from Maliutuo, Maliuwan and Suheping village sites in Chinese Sanxia area. Nine pieces of pottery in the Shang Dynasty (1600-1100 BC) and ten pieces of pottery in the Eastern Zhou Dynasty (770-256 BC) were also collected from Maliutuo. PIXE and factor analysis were used to study interchange of the Neolithic pottery between these three sites. The source of raw material of pottery from Maliutuo was simultaneously studied. The major and trace element contents in pottery were determined by PIXE. Factor analysis was employed to classify these pieces of pottery. The results showed that the trace element contents were more useful to distinguish these pieces of pottery than the major element contents. In about 2500 BC, no interchange of pottery occurred between the three villages. Although Maliutuo was close to Maliuwan, the pottery products used in daily life in the two villages were independently made and not exchanged. In the source of raw material, the Neolithic pottery samples from Maliutuo were identical with those in the Shang Dynasty, but different from those in the Eastern Zhou Dynasty.

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

    International Nuclear Information System (INIS)

    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.)

  14. Rise and fall of Kantu: A historical study of an ancient Tibeto-Burmese speaking group

    Institute of Scientific and Technical Information of China (English)

    He Ping

    2006-01-01

    On the basis of Chinese records and previous academic achievements in and outside China,the author makes a deeper study on the history of Kantu.As an ancient Tibeto-Burmese speaking group,Kantu was likely to have developed from the Qiongdu(Kontu)of Xinan yi(ancient ethnic groups in southwestern China).During the 12th-13th centuries,the Kantu group resided in an extensive area expanding from the border area between present Sichuan and Yunnan provinces of China to Burma.In the late 13th century,the Yuan troops occupied the area of Kantu.Since then,there have been no more record about Kantu in Chinese annals,and they were likely merged into the groups of"Luoluo"(Lolo).In Burma,most of the Kantu people had been merged into the local peoples,with only a few remaining in remote mountain forests of northern Burma and still keeping their own name and customs.Thus,these people ale lust the living sources for our studies on ancient Kantu.

  15. Agricola's Ukko in the light of archaeology: a chronological and interpretative study of ancient Finnish religion

    Directory of Open Access Journals (Sweden)

    Unto Salo

    1990-01-01

    Full Text Available No written sources of ancient Finnish religion have been preserved from the pre-Christian period. Study of the subject is thus based on later historical data, folk poetry and other recorded national traditions, supplemented by etymology and onomastics. A valuable basis for study is provided by the verses of Mikael Agricola in the preface to his Psalms of David from 1551. Here Agricola lists the gods of Karelia and Häme. He admittedly subjects them to Christian censure, but he is also in these verses the first systematizer and the first theologian of our ancient religion. He created twin Olympuses of the old religion, two anthropomorphic god-worlds, the sub-structure of which includes the worship of spirits, animals and the dead. From the point of view of archaeology, Agricola's Ukko, 'old man', is one of the most interesting figures in ancient religion. According to Agricola, Ukko was (only a Karelian god, but scholars have long considered that he was referring to the universally feared Ukko, Ukkonen, the god of thunder, who would have fitted equally well among the gods of Häme (Tavastland.

  16. 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 (RHstrategies for scheduling routine maintenance and designing suitable layouts for their preservation. In this work we present the results of a carefully planned thermo-hygrometric monitoring campaign conducted in a peculiar Roman building (130CE), the "Casa di Diana" Mithraeum, sited in Ostia Antica (archaeological site, Rome-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. PMID:27232960

  17. 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

  18. Smoking Leaves Lasting Marks on DNA: Study

    Science.gov (United States)

    ... fullstory_161060.html Smoking Leaves Lasting Marks on DNA: Study Changes related to disease found in more ... cigarettes can leave a lasting imprint on human DNA, altering more than 7,000 genes in ways ...

  19. Studies on Interaction Between Gallocyanine and DNA

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The interaction of Gallocyanine(Gal) with DNA was studied by using UV spectra and circular dichroism(CD) spectrum methods. Gal and DNA strongly interacted on each other in acid solutions. The intrinsic binding constant(K) and the binding numbers(CDNA/Cgal) of Gal and DNA are 2.25×104 mol-1 and 2.5, respectively. The influence of pH on the interaction of Gal and DNA was also studied.

  20. Are Ancient Durum Wheats Less Toxic to Celiac Patients? A Study of α-Gliadin from Graziella Ra and Kamut

    OpenAIRE

    M. Stella Colomba; Armando Gregorini

    2012-01-01

    In the present paper, the controversial hypothesis suggesting ancient grains might show lower immunogenic properties and therefore the possibility to introduce them in the diet of wheat-sensitive people, including celiac patients, was investigated. The immunogenic potential of the ancient durum wheats Graziella Ra and Kamut was studied by comparison to the durum accessions Cappelli, Flaminio, Grazia and Svevo. Experiments were carried out with two monoclonal antibodies (mAbs) raised against α...

  1. [Application of studies on popular words in the systematization of ancient medical books].

    Science.gov (United States)

    Fan, D; Lai, W

    2000-07-01

    Based on the arrangement of Renho Temple edition of Taisu (Extremely Plain), as an example, it can be seen that by correcting the wrong popular words in ancient medical books, the causes of mistakes of ancient editions and solution for annotations of difficult terms of ancient words in the medical books are of significance.

  2. 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;

    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...... of parasite an egg originates from. This is impossible solely using morphological examination. One example is the whipworm, Trichuris spp. that is known to have narrow host ranges, which makes it particularly suited to determine from which host an egg originates. A case study will be presented, in which...

  3. 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.

  4. XAS study on copper red in ancient glass beads from Thailand.

    Science.gov (United States)

    Klysubun, Wantana; Thongkam, Yatima; Pongkrapan, Sorapong; Won-in, Krit; T-Thienprasert, Jiraroj; Dararutana, Pisutti

    2011-03-01

    Glass has been used in ornaments and decorations in Thailand for thousands of years, being discovered in several archeological sites and preserved in museums throughout the country. To date only a few of them have been examined by conventional methods for their compositions and colorations. In this work we report for the first time an advanced structural analysis of Thai ancient glass beads using synchrotron X-ray absorption spectroscopy (XAS) and energy-dispersive X-ray (EDX) spectrometry. Four samples of ancient glass beads were selected from four different archeological sites in three southern provinces (Ranong, Krabi and Pang-nga) of Thailand. Archaeological dating indicated that they were made more than 1,300 years ago. A historically known method for obtaining a red color is to add compounds containing transition elements such as gold, copper, and chromium. For our samples, EDX spectrometry data revealed existing fractions of iron, copper, zinc, and chromium in ascending order. Thus, copper was selectively studied by XAS as being potentially responsible for the red color in the glass beads. K-shell X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) of copper were recorded in fluorescence mode using an advanced 13-element germanium detector. Comparisons with XANES spectra of reference compounds identified two major forms of copper, monovalent copper and a metallic cluster, dispersed in the glass matrix. The cluster dimension was approximated on the basis of structural modeling and a theoretical XANES calculation. As a complement, EXAFS spectra were analyzed to determine the first-shell coordination around copper. XAS was proven to be an outstanding, advanced technique that can be applied to study nondestructively archaeological objects to understand their characteristics and how they were produced in ancient times.

  5. 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...

  6. 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.

  7. Studies of DNA-carbon nanotube interactions

    Science.gov (United States)

    Hughes, Mary Elizabeth

    2008-10-01

    Recently a new biomaterial consisting of a DNA-wrapped single-walled carbon nanotube, and known as a DNA/SWNT, has been discovered. The possible applications of this hybrid are varied and range from genomic sequencing to nanoscale electronics to molecular delivery. The realization of these potential applications requires more knowledge about the microscopic properties of this material. In this thesis, I present studies of: the orientation of nucleobases on the nanotube sidewall; the sequence and length dependence of the DNA-nanotube interaction; and solution conditions to manipulate the DNA/SWNT hybrid. The measurement of the UV optical absorbance of DNA/SWNT and the nucleotide absorbance from DNA/SWNT provide the first experimental confirmation that DNA binds to nanotubes through pi-stacking. Because the hypochromic absorbance typical of pi-stacked structures are expected to occur primarily for DNA dipole transitions that lie along the axis of the optically anisotropic SWNTs, the absorbance changes following binding of DNA to the nanotubes reveals the preferred orientation assumed by each of the four bound nucleotides with respect to the nanotube's long axis. The first observations of pronounced sequence- and length-dependent variations in the binding between ssDNA and SWNTs in aqueous solution are presented. These observations rely on the discovery that there exists a range of DNA lengths able to hybridize with SWNTs that can nevertheless be dissociated at temperatures below the boiling point of water. Quantitative results comparing the isochronal dissociation temperatures and binding energies of DNA/SWNT composed of differing DNA sequences and lengths are given. These results indicate variability and complexity in the binding mechanism responsible for the stability of the hybrid system that transcends simple models based on the sum of independent base-nanotube interactions. Binding energies between a DNA base and nanotube (0.05 to 0.09 eV per base) are similar

  8. Experimental study of oxidative DNA damage

    DEFF Research Database (Denmark)

    Loft, S; Deng, Xiaohong; Tuo, J;

    1998-01-01

    of dative DNA damage and tumour formation. In principle the level of oxidative DNA damage in an organ or cell may be studied by measurement of modified bases in extracted DNA by immunohistochemical visualisation, and from assays of strand breakage before and after treatment with repair enzymes. However......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...... to induce oxidative DNA damage in experimental animals. The hepatocarcinogen 2-nitropropane induces up to 10-fold increases in 8-oxodG levels in rat liver DNA. The level of 8-oxodG is also increased in kidneys and bone marrow but not in the testis. By means of 2-nitropropane we have shown correspondence...

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

    Science.gov (United States)

    Barreto Romero, María Inés; Flores Espinoza, Isabel; Cooper, Alan; Fehren-Schmitz, Lars

    2016-01-01

    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. PMID:27248693

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

    International Nuclear Information System (INIS)

    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

  11. Molecular confirmation of Schistosoma and family relationship in two ancient Egyptian mummies

    OpenAIRE

    Matheson, C. D.; David, R; Spigelman, M.; Donoghue, H. D.

    2014-01-01

    Egg morphology and immunocytochemistry have identified schistosomiasis in ancient Egypt. Our study aimedbto detect and characterize schistosomal DNA in mummified human tissue. Liver samples from the mummy Nekht-Ankh (c. 3900 BP) and intestinal samples from Khnum-Nakht, possibly his brother, were analyzed using PCR primers suitable for fragmented ancient DNA, specific for either Schistosoma mansoni or Schistosoma haematobium. Mitochondrial primers examined any relationship between the supposed...

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

    International Nuclear Information System (INIS)

    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.

  13. Study of Yue kiln ancient celadon by SRXRF and statistic analysis

    International Nuclear Information System (INIS)

    20 elements of eighty ancient celadon samples were analyzed by using synchrotron radiation X-ray fluorescence (SRXRF). V, Ni, Zn and Mn display variable dynastic orderliness. Results of statistic analysis show that Yue kiln ancient celadon has distinctively born character on different dynasty and kiln. The statistic analysis results of SRXRF and NAA are similar

  14. DNA Interaction Studies of Selected Polyamine Conjugates

    Science.gov (United States)

    Szumilak, Marta; Merecz, Anna; Strek, Malgorzata; Stanczak, Andrzej; Inglot, Tadeusz W.; Karwowski, Boleslaw T.

    2016-01-01

    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. PMID:27657041

  15. Neon isotope studies of Fayetteville and Kapoeta meteorites and clues to ancient solar activity

    Science.gov (United States)

    Padia, J. T.; Rao, M. N.

    1989-01-01

    Under the assumption that the solar-flare bombardment of the irradiated grains of gas-rich meteorites occurred about 4.5 b.y. ago on the parent body regoliths at 3 A.U., an estimate of the solar cosmic ray-produced Ne-21 is made by studying etched pyroxene minera separates from both light and dark portions of the gas-rich meteorites Fayetteville and Kapoeta. Excesses of solar cosmic ray Ne-21 were observed in dark portions of these meteorites, after accounting for their galactic cosmic ray Ne-21 production and solar flare Ne-21. In order to produce the estimated solar cosmic ray Ne-21 in the present samples, highly enhanced solar cosmic ray proton fluxes from the ancient sun are required.

  16. 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…

  17. Molecular genetic analysis of Dongzhou-period ancient human of Helingeer in Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The mtDNA hypervariable region I (HVR-I) of 10 ancient individuals from Dongzhou-period ancient human populations in Helingeer county of Inner Mongolia were amplified and sequenced to investigate the genetic structure. The relationships between the ancient population and related extant populations, as well as its possible origin at the molecular level, were also studied. Moreover, phylogenetic analysis and multi-dimensional scaling analysis were also performed based on the mtDNA data of the ancient population in Helingeer and the related Eurasian population. The results showed that the ancient population in Helingeer were closer to the northern Asian populations than to the other compared populations in matrilineal lineage. Combining the research results of archaeology and anthropology as well as molecular biology, we inferred that they were nomads who migrated from Mongolia plateau and cis-Baikal region to Helingeer in Inner Mongolia, China.

  18. 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.

  19. Identification of Photosynthetic Plankton Communities Using Sedimentary Ancient DNA and Their Response to late-Holocene Climate Change on the Tibetan Plateau

    Science.gov (United States)

    Hou, Weiguo; Dong, Hailiang; Li, Gaoyuan; Yang, Jian; Coolen, Marco J. L.; Liu, Xingqi; Wang, Shang; Jiang, Hongchen; Wu, Xia; Xiao, Haiyi; Lian, Bin; Wan, Yunyang

    2014-10-01

    Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.

  20. Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-Holocene climate change on the Tibetan Plateau.

    Science.gov (United States)

    Hou, Weiguo; Dong, Hailiang; Li, Gaoyuan; Yang, Jian; Coolen, Marco J L; Liu, Xingqi; Wang, Shang; Jiang, Hongchen; Wu, Xia; Xiao, Haiyi; Lian, Bin; Wan, Yunyang

    2014-10-17

    Sediments from Tibetan lakes in NW China are potentially sensitive recorders of climate change and its impact on ecosystem function. However, the important plankton members in many Tibetan Lakes do not make and leave microscopically diagnostic features in the sedimentary record. Here we established a taxon-specific molecular approach to specifically identify and quantify sedimentary ancient DNA (sedaDNA) of non-fossilized planktonic organisms preserved in a 5-m sediment core from Kusai Lake spanning the last 3100 years. The reliability of the approach was validated with multiple independent genetic markers. Parallel analyses of the geochemistry of the core and paleo-climate proxies revealed that Monsoon strength-driven changes in nutrient availability, temperature, and salinity as well as orbitally-driven changes in light intensity were all responsible for the observed temporal changes in the abundance of two dominant phytoplankton groups in the lake, Synechococcus (cyanobacteria) and Isochrysis (haptophyte algae). Collectively our data show that global and regional climatic events exhibited a strong influence on the paleoecology of phototrophic plankton in Kusai Lake.

  1. DNA hydration studied by neutron fiber diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J. [Keele Univ. (United Kingdom)] [and others

    1994-12-31

    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.

  2. Deep sequencing of RNA from ancient maize kernels.

    Directory of Open Access Journals (Sweden)

    Sarah L Fordyce

    Full Text Available 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.

  3. Transcriptional profiling in C. elegans suggests DNA damage dependent apoptosis as an ancient function of the p53 family

    NARCIS (Netherlands)

    S. Greiss (Sebastian); B. Schumacher (Björn); K. Grandien (Kaj); J. Rothblatt (Jonathan); A. Gartner (Anton)

    2008-01-01

    textabstractBackground: In contrast to the three mammalian p53 family members, p53, which is generally involved in DNA damage responses, and p63 and p73 which are primarily needed for developmental regulation, cep-1 encodes for the single C. elegans p53-like gene. cep-1 acts as a transcription activ

  4. [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.

  5. [The Dynamics of the Composition of mtDNA Haplotypes of the Ancient Population of the Altai Mountains from the Early Bronze Age (3rd Millennium BC) to the Iron Age (2nd-1st Centuries BC)].

    Science.gov (United States)

    Gubina, M A; Kulikov, I V; Babenko, V N; Chikisheva, T A; Romaschenko, A G; Voevoda, M I; Molodin, V I

    2016-01-01

    The mtDNA polymorphism in representatives of various archaeological cultures of the Developed Bronze Age, Early Scythian, and Hunnish-Sarmatian periods was analyzed (N = 34). It detected the dominance of Western-Eurasian haplotypes (70.6%) in mtDNA samples from the representatives of the ancient population of the Early Bronze Age--Iron Age on the territory of Altai Mountains. Since the 8th to the 7th centuries BC, a sharp increase was revealed in the Eastern-Eurasian haplogroups A, D, C, andZ (43.75%) as compared to previous cultures (16.7%). The presence of haplotype 223-242-290-319 of haplogroup A8 in Dolgans, Itelmens, Evens, Koryaks, and Yakuts indicates the possible long-term presence of its carriers in areas inhabited by these populations. The prevalence of Western-Eurasian haplotypes is observed not only in the Altai Mountains but also in Central Asia (Kazakhstan) and the South of the Krasnoyarsk Krai. All of the three studied samples from the Western-Eurasian haplogroups were revealed to contain U, H, T, and HV. The ubiquitous presence of haplotypes of haplogroup H and some haplogroups of cluster U (U5al, U4, U2e, and K) in the vast territory from the Yenisei River basin to the Atlantic Ocean may indicate the direction of human settlement, which most likely occurred in the Paleolithic Period from Central Asia. PMID:27183799

  6. STUDY ON GMA-DNA ADDUCTS

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Objective. DNA modification fixed as mutations in the cells may be an essential factor in the initiation step of chemical carcinogenesis. In order to explore the mechanism of gene mutation and cell transformation induced by glycidyl methacrylate (GMA), the current test studied the characteristics of GMA-DNA adducts formation in vitro.Methods. In vitro test, dAMP, dCMP, dGMP, dTMP and calf thymus DNA were allowed to react with GMA (Glycidyl Methacrylate). After the reaction, the mixtures were detected by UV and subjected to reversed-phase HPLC on ultrasphere ODS reversed-phase column, the reaction products were eluted with a linear gradients of methanol (solvent A) and 10mmol/L ammonium formate, pH5.0 (solvent B). The synthesized adducts were then characterized by UV spectroscopy in acid (pH1.0), neutral (pH7.2), alkaline (pH11.0) and by mass spectroscopy.Results. The results showed that GMA could bind with dAMP, dCMP, dGMP and calf thymus DNA by covalent bond, and the binding sites were specific (N6 of adenine, N3 of cytosine). Meanwhile, a main GMA-DNA adduct in the reaction of GMA with calf thymus DNA was confirmed as N3-methacrylate-2-hydroxypropy1-dCMP.Conclusions. GMA can react with DNA and /or deoxynucleotide monophosphate and generate some adducts such as N6-methacrylate-2-hydroxypropyl-dAMP and N3-methacrylate-2-hydroxypropyl-dCMP, ets. Formation of GMA-DNA adducts is an important molecular event in gene mutation and cell transformation induced by GMA.

  7. Application of ICP-MS trace element analysis in study of ancient Chinese ceramics

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Thirty-nine trace elements of the Song-Yuan period (960-1368 AD) porcelain bodies from Cizhou, Jizhou and Longquanwu kilns were analyzed with ICP-MS, a technique rarely used in Chinese archaeometry, to investigate its potential application in such studies. Trace element compositions clearly reflect the distinctive raw materials and their mineralogy at the three kilns and allow their products to be distinguished. Significant chemical variations are also observed between Yuan and Song-Jing dynasties samples from Cizhou as well as fine and coarse porcelain bodies from Longquanwu. In Cizhou, porcelains of better quality which imitate the famous Ding kiln have trace element features distinctive from ordinary Cizhou products, that indicates geochemically distinctive raw materials were used and which possibly also underwent extra refining prior to use. The distinct trace element features of different kilns and the various types of porcelains from an individual kiln can be interpreted from a geochemical perspective. ICP-MS can provide a large amount of valuable information about ancient Chinese ceramics as it is capable of analyzing >40 elements with a typical of precision < 2%.

  8. 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. PMID:25998639

  9. Use of x-ray fluorescence and diffraction techniques in studying ancient ceramics of Sri Lanka

    International Nuclear Information System (INIS)

    Ceramics were produced for centuries in Sri Lanka for various purposes. Ancient ceramic articles such as pottery, bricks, tiles, sewer pipes, etc, were made from naturally occurring raw materials. Use of X-ray fluorescence (XRF), X-ray diffraction (XRD) and Scanning Electron Microscopy (SEM) in characterizing of two ancient ceramic samples from two different archaeological sites in Sri Lanka is presented. The information obtained in this manner is used to figure out the ancient ceramic technology, particularly to learn about the raw materials used, the source of raw materials, processing parameters such as firing temperature or binders used in ceramic production. This information then can be used to explore the archaeometric background such as the nature and extent of cultural and technological interaction between different periods of history in Sri Lanka.

  10. Use of x-ray fluorescence and diffraction techniques in studying ancient ceramics of Sri Lanka

    Science.gov (United States)

    Karunaratne, B. S. B.

    2012-07-01

    Ceramics were produced for centuries in Sri Lanka for various purposes. Ancient ceramic articles such as pottery, bricks, tiles, sewer pipes, etc, were made from naturally occurring raw materials. Use of X-ray fluorescence (XRF), X-ray diffraction (XRD) and Scanning Electron Microscopy (SEM) in characterizing of two ancient ceramic samples from two different archaeological sites in Sri Lanka is presented. The information obtained in this manner is used to figure out the ancient ceramic technology, particularly to learn about the raw materials used, the source of raw materials, processing parameters such as firing temperature or binders used in ceramic production. This information then can be used to explore the archaeometric background such as the nature and extent of cultural and technological interaction between different periods of history in Sri Lanka.

  11. 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...... that is required before being able to make inferences from the data introduces multiple levels of uncertainty, especially for low-depth data. Therefore methods that take into account the inherent uncertainty are needed for being able to make robust inferences in the downstream analysis of such data. This poses...... data. These methods are all based on the concept of genotype likelihoods, which provides a degree of uncertainty of the data, and we show, both through simulations and with proper high-throughput sequencing data, that for low-depth data our methods outperform existing approaches, which are based...

  12. Do All Hemochromatosis Patients Have the Same Origin? A Pilot Study of Mitochondrial DNA and Y-DNA

    Directory of Open Access Journals (Sweden)

    Caitlin J Symonette

    2011-01-01

    Full Text Available BACKGROUND: Mitochondrial DNA (mtDNA and Y-DNA analysis have been widely used to predict ancestral origin. Genetic anthropologists predict that human civilizations may have originated in central Africa one to two million years previously. Primary iron overload is not a common diagnosis among indigenous people of northern Africa, but hereditary hemochromatosis is present in approximately one in 200 people in northern Europe. MtDNA analysis has the potential to determine whether contemporary hemochromatosis patients have an ancient ancestral linkage.

  13. A Study of Ancient Man’s Diet%古人类食物结构研究

    Institute of Scientific and Technical Information of China (English)

    张雪莲; 王金霞; 冼自强; 仇士华

    2003-01-01

    This is a study of ancient man's diet by means of the isotopes 13C and 15N analysis method.A set of experiment conditions for N2 collection with the element analyser has been established through experiments, which brought initial results to the application of the method in archaeology. A preliminary analysis on the relative situation of ancient man's meat eating has been made for some archaeological sites, such as Inner-Mongolia Xinglongwa, Qinghai Shangsunjia and Xingjiang Yanbulake. It is the first example of this research.Meanwhile, results of 13C analysis have also been acquired for the first time from a series of sites, including the Yin Ruins, Western Zhou Liulihe, Kayao culture Shangsunjia,Xinglongwa, and Zhejiang Hemudu. This froms a basis for studying the components of the then people's staple food.

  14. Single gene retrieval from thermally degraded DNA

    Indian Academy of Sciences (India)

    Lianwen Zhang; Lianwen Zhang

    2005-12-01

    To simulate single gene retrieval from ancient DNA, several related factors have been investigated. By monitoring a 889 bp polymerase chain reaction (PCR) product and genomic DNA degradation, we find that heat and oxygen (especially heat) are both crucial factors influencing DNA degradation. The heat influence, mainly represented by temperature and heating time, affects the DNA degradation via DNA depurination followed by cleavage of nearby phosphodiesters. The heating time influence is temperature-dependent. By reactive oxygen species (ROS) scavenging and 1,3-diphenyl-isobenzofuran (DPBF) bleaching experiments the influence of oxygen on DNA thermal degradation was shown to occur via a singlet oxygen pathway. A comparative study of the thermal degradation of cellular DNA and isolated DNA showed that cellular lipids can aggravate DNA thermal degradation. These results confirm the possibility of gene amplification from thermally degraded DNA. They can be used to evaluate the feasibility of the retrieval of single gene from ancient remains.

  15. An Experimental Study on the Sound and Frequency of the Chinese Ancient Variable Bell

    Science.gov (United States)

    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…

  16. Hgis and Archive Researches: a Tool for the Study of the Ancient Mill Channel of Cesena (italy)

    Science.gov (United States)

    Bitelli, G.; Bartolini, F.; Gatta, G.

    2016-06-01

    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.

  17. Testing the applicability of morphometric characterisation in discordant catchments to ancient landscapes: A case study from southern Africa

    Science.gov (United States)

    Richardson, J. C.; Hodgson, D. M.; Wilson, A.; Carrivick, J. L.; Lang, A.

    2016-05-01

    The ancient landscapes south of the Great Escarpment in southern Africa preserve large-scale geomorphological features despite their antiquity. This study applies and evaluates morphometric indices (such as hypsometry, long profile analysis, stream gradient index, and linear/areal catchment characteristics) to the Gouritz catchment, a large discordant catchment in the Western Cape. Spatial variation of morphometric indices were assessed across catchment (trunk rivers) and subcatchment scales. The hypsometric curve of the catchment is sinusoidal, and a range of curve profiles are evident at subcatchment scale. Hypsometric integrals do not correlate to catchment properties such as area, circularity, relief, and dissection; and stream length gradients do not follow expected patterns, with the highest values seen in the mid-catchment areas. Rock type variation is interpreted to be the key control on morphometric indices within the Gouritz catchment, especially hypsometry and stream length gradient. External controls, such as tectonics and climate, were likely diminished because of the long duration of catchment development in this location. While morphometric indices can be a useful procedure in the evaluation of landscape evolution, this study shows that care must be taken in the application of morphometric indices to constrain tectonic or climatic variation in ancient landscapes because of inherited tectonic structures and signal shredding. More widely, we consider that ancient landscapes offer a valuable insight into long-term environmental change, but refinements to geomorphometric approaches are needed.

  18. Are Ancient Durum Wheats Less Toxic to Celiac Patients? A Study of α-Gliadin from Graziella Ra and Kamut

    Directory of Open Access Journals (Sweden)

    M. Stella Colomba

    2012-01-01

    Full Text Available In the present paper, the controversial hypothesis suggesting ancient grains might show lower immunogenic properties and therefore the possibility to introduce them in the diet of wheat-sensitive people, including celiac patients, was investigated. The immunogenic potential of the ancient durum wheats Graziella Ra and Kamut was studied by comparison to the durum accessions Cappelli, Flaminio, Grazia and Svevo. Experiments were carried out with two monoclonal antibodies (mAbs raised against α-gliadin peptides p31–49 and p56–75 (the latter containing the overlapping DQ2-Glia-α1 and DQ2-Glia-α2 epitopes, toxic for celiac patients. For all accessions, a few α-gliadin alleles were also cloned, sequenced and translated into aminoacid sequences. Several aminoacid substitutions or deletions were detected in p31–49, DQ2-Glia-α1 and DQ2-Glia-α2 epitopes, nevertheless, ELISA constantly showed antibody-antigen positive reactions which led us to suggest that mAbs binding was not apparently affected by polymorphisms. Moreover, a few substitutions were also observed in DQ2-Glia-α3 and DQ8-Glia-α1 epitopes. Although some DQ2-Glia-α1 and DQ2-Glia-α2 variants evidenced herein were previously reported to have a diminished or abolished T cell stimulatory capacity, present results cannot confirm that ancient durum wheats would be less CD-toxic. In conclusion, we strongly advice celiac patients from consuming ancient wheats including Graziella Ra or Kamut.

  19. DNA oligonucleotide conformations: high resolution NMR studies

    International Nuclear Information System (INIS)

    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 1H 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 1H NMR spectrum of a DNA tetramer, d(TAAT). Preliminary conformational data derived from the spectral parameters recorded at 27 0C are given. A more detailed analysis employing temperature-dependence studies is given in Chapter 4. (Auth.)

  20. 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.

  1. 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.

  2. Methodological proposals for the study of ancient rural landscapes in the central area of the Contestania

    OpenAIRE

    Grau Mira, Ignasi; César CARRERAS; Jaime MOLINA; Pau DE SOTO; Josep María SEGURA

    2013-01-01

    In this paper we have two main objectives. The first is the presentation of fieldwork and geophysics assisted with GPS, GIS and other Spatial Technologies applied to archaeological research. The advantage of this approach is the scarce aggression to soils and environment and the request of smaller economic and temporary resources than other archaeological fieldwork. The second objective is to reflect on ancient land uses, the diachronic sequence and structure of a complex Iberian Iron Age and...

  3. Research on residents' perceptions on tourism impacts and attitudes: a case study of Pingyao Ancient City

    OpenAIRE

    Zhang, Min; Xiaoli, Pan; Bihu, Wu

    2012-01-01

    Residents’ perceptions on tourism impacts and attitudes towards tourism development have a great influence on tourism sustainable development. But the measuring factors of research on residents’ perceptions on tourism impacts are not unified. This paper takes Pingyao ancient city as a case and employs interviewing method, and it analyzes residents’ perceptions on tourism economic impacts, socio-cultural impacts and environmental impacts. Furthermore, the paper examines the signifi...

  4. [Psychiatry in ancient Mexico].

    Science.gov (United States)

    Calderón Narváez, G

    1992-12-01

    Using studies on prehispanic and early post-conquest documents of Ancient Mexico--such as the Badianus Manuscript, also known as Libellus de Medicinalibus Indorum Herbis, and Brother Bernardino de Sahagún's famous work History of the Things of the New Spain, a description of some existing medical and psychiatric problems, and treatments Ancient Aztecs resorted to, is presented. The structure of the Aztec family, their problems with the excessive ingestion of alcoholic beverages, and the punishments native authorities had implemented in order to check alcoholism up are also described. PMID:1341125

  5. Triplex technology in studies of DNA damage, DNA repair, and mutagenesis.

    Science.gov (United States)

    Mukherjee, Anirban; Vasquez, Karen M

    2011-08-01

    Triplex-forming oligonucleotides (TFOs) can bind to the major groove of homopurine-homopyrimidine stretches of double-stranded DNA in a sequence-specific manner through Hoogsteen hydrogen bonding to form DNA triplexes. TFOs by themselves or conjugated to reactive molecules can be used to direct sequence-specific DNA damage, which in turn results in the induction of several DNA metabolic activities. Triplex technology is highly utilized as a tool to study gene regulation, molecular mechanisms of DNA repair, recombination, and mutagenesis. In addition, TFO targeting of specific genes has been exploited in the development of therapeutic strategies to modulate DNA structure and function. In this review, we discuss advances made in studies of DNA damage, DNA repair, recombination, and mutagenesis by using triplex technology to target specific DNA sequences. PMID:21501652

  6. 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.

  7. [Study on rules of acupoints selection for vertigo in ancient acupuncture].

    Science.gov (United States)

    Zhan, Qiana; Chen, Hua-De

    2014-04-01

    The characteristics of selection and matching acupoint and application rules of meridians in ancient acupuncture literature for vertigo were explored. The data were collected from literature regarding acupuncture for vertigo from the pre-Qin period to Qing dynasty and then database was established. Frequency statistics method and comparison of support degree were applied to analyze and explore application rules of acupoints and meridians, while association rules in data mining was used to extract combinations of acupoints. As a result, for treatment of vertigo, according to frequency of use and support degree, generally the most selected acupoints, in turn, were Fengchi (GB 20), Shangxing (GV 23), Yanggu (SI 5), Jiexi (ST 41), Zulinqi (GB 41) and Shenting (GV 24), etc.; the most methods for matching acupoint were combination of adjacent acupoints, combination of same-meridian acupoints, combination of the superior-inferior acupoints, combination of yang-meridian and yang-meridian acupoints and combination of child-mother meridians acupoints; the most selected meridians were bladder meridian of foot-taiyang, gallbladder meridian of foot-shaoyang and governor vessel. Compared between the ancient and modern literature, it was found out that the ancient and modern clinic has same points in selection of acupoint-meridian and matching acupoints methods. However, the use of Yanggu (SI 5), Jiexi (ST 41) and Feiyang (BL 58) as well as combination of child-mother meridians acupoints were less seen in modern clinic, which could provide new reference.

  8. [Study on rules of acupoints selection for vertigo in ancient acupuncture].

    Science.gov (United States)

    Zhan, Qiana; Chen, Hua-De

    2014-04-01

    The characteristics of selection and matching acupoint and application rules of meridians in ancient acupuncture literature for vertigo were explored. The data were collected from literature regarding acupuncture for vertigo from the pre-Qin period to Qing dynasty and then database was established. Frequency statistics method and comparison of support degree were applied to analyze and explore application rules of acupoints and meridians, while association rules in data mining was used to extract combinations of acupoints. As a result, for treatment of vertigo, according to frequency of use and support degree, generally the most selected acupoints, in turn, were Fengchi (GB 20), Shangxing (GV 23), Yanggu (SI 5), Jiexi (ST 41), Zulinqi (GB 41) and Shenting (GV 24), etc.; the most methods for matching acupoint were combination of adjacent acupoints, combination of same-meridian acupoints, combination of the superior-inferior acupoints, combination of yang-meridian and yang-meridian acupoints and combination of child-mother meridians acupoints; the most selected meridians were bladder meridian of foot-taiyang, gallbladder meridian of foot-shaoyang and governor vessel. Compared between the ancient and modern literature, it was found out that the ancient and modern clinic has same points in selection of acupoint-meridian and matching acupoints methods. However, the use of Yanggu (SI 5), Jiexi (ST 41) and Feiyang (BL 58) as well as combination of child-mother meridians acupoints were less seen in modern clinic, which could provide new reference. PMID:24946637

  9. 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 c

  10. 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 of the e......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......, that is, the observation that small structural changes in oligonucleotide composition may lead to dramatic shifts in phenotypes. These observations should be taken into account in future oligonucleotide drug discovery, and by focusing more on non RNA target interactions it should be possible to utilize...

  11. 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

    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...

  12. 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.

  13. Ancient DNA from the extinct South American giant glyptodont Doedicurus sp. (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos.

    Science.gov (United States)

    Mitchell, Kieren J; Scanferla, Agustin; Soibelzon, Esteban; Bonini, Ricardo; Ochoa, Javier; Cooper, Alan

    2016-07-01

    Glyptodonts were giant (some of them up to ~2400 kg), heavily armoured relatives of living armadillos, which became extinct during the Late Pleistocene/early Holocene alongside much of the South American megafauna. Although glyptodonts were an important component of Cenozoic South American faunas, their early evolution and phylogenetic affinities within the order Cingulata (armoured New World placental mammals) remain controversial. In this study, we used hybridization enrichment and high-throughput sequencing to obtain a partial mitochondrial genome from Doedicurus sp., the largest (1.5 m tall, and 4 m long) and one of the last surviving glyptodonts. Our molecular phylogenetic analyses revealed that glyptodonts fall within the diversity of living armadillos. Reanalysis of morphological data using a molecular 'backbone constraint' revealed several morphological characters that supported a close relationship between glyptodonts and the tiny extant fairy armadillos (Chlamyphorinae). This is surprising as these taxa are among the most derived cingulates: glyptodonts were generally large-bodied and heavily armoured, while the fairy armadillos are tiny (~9-17 cm) and adapted for burrowing. Calibration of our phylogeny with the first appearance of glyptodonts in the Eocene resulted in a more precise timeline for xenarthran evolution. The osteological novelties of glyptodonts and their specialization for grazing appear to have evolved rapidly during the Late Eocene to Early Miocene, coincident with global temperature decreases and a shift from wet closed forest towards drier open woodland and grassland across much of South America. This environmental change may have driven the evolution of glyptodonts, culminating in the bizarre giant forms of the Pleistocene. PMID:27158910

  14. A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences

    OpenAIRE

    David Caramelli; Lucio Milani; Stefania Vai; Alessandra Modi; Elena Pecchioli; Matteo Girardi; Elena Pilli; Martina Lari; Barbara Lippi; Annamaria Ronchitelli; Francesco Mallegni; Antonella Casoli; Giorgio Bertorelle; Guido Barbujani

    2008-01-01

    Background: DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans. Methodology/Principal Findings: We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28...

  15. 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.

  16. Preclinical and clinical safety studies on DNA vaccines.

    OpenAIRE

    Schalk, Johanna A C; Mooi, Frits R.; Berbers, Guy A M; Aerts, Leon A G J M van; Ovelgönne, Hans; Kimman, Tjeerd G.

    2007-01-01

    DNA vaccines are based on the transfer of genetic material, encoding an antigen, to the cells of the vaccine recipient. Despite high expectations of DNA vaccines as a result of promising preclinical data their clinical utility remains unproven. However, much data is gathered in preclinical and clinical studies about the safety of DNA vaccines. Here we review current knowledge about the safety of DNA vaccines. Safety concerns of DNA vaccines relate to genetic, immunologic, toxic, and environme...

  17. Methodological proposals for the study of ancient rural landscapes in the central area of the Contestania

    Directory of Open Access Journals (Sweden)

    Ignasi GRAU MIRA

    2013-01-01

    Full Text Available In this paper we have two main objectives. The first is the presentation of fieldwork and geophysics assisted with GPS, GIS and other Spatial Technologies applied to archaeological research. The advantage of this approach is the scarce aggression to soils and environment and the request of smaller economic and temporary resources than other archaeological fieldwork. The second objective is to reflect on ancient land uses, the diachronic sequence and structure of a complex Iberian Iron Age and Roman site of long duration (3rd cent. BC to 7th cent. AD. The accurate mapping of dispersion of the archaeological record allows this kind of historical analysis.

  18. Late Paleocene high Laramide ranges in northeast Wyoming: Oxygen isotope study of ancient river water

    Science.gov (United States)

    Fan, Majie; Dettman, David L.

    2009-08-01

    The distribution and initial timing of the establishment of high surface elevations in the Rocky Mountains during the Early Cenozoic remain controversial despite the importance of these data in testing tectonic models for this region. We track the timing and distribution of high elevation in the Rocky Mountains during the Late Cretaceous-Early Eocene by examining annual and seasonal δ18O values of the ancient river water, which are calculated from the δ18O values of well-preserved freshwater bivalve shells. In the Powder River basin of the eastern Laramide province, the δ18O values of the ancient river water vary between - 23.0‰ and - 8.0‰ SMOW in both seasonal and annual records in the Late Paleocene-Early Eocene. The large variation suggests that the ancient rivers were fed yearly or seasonally by snowmelt from highlands of 4.5 ± 1.3 km. This can be explained by the existence of the Bighorn Mountains and Black Hills with a drainage pattern similar to the present in northeast Wyoming. The δ18O values of ancient river water along the front of the Sevier thrust belt generally follow a trend from lower values in north, - 14.2 ± 1.4‰ in the Early Paleocene Crazy Mountains basin, to higher values in south, - 11.1 ± 0.8‰ in the Late Paleocene Bighorn basin, and - 7.1 ± 1.6‰ in the Early Eocene Washakie basin. The variations within each basin are relatively small. These rivers most likely rise in the Sevier thrust belt, and may reflect highland elevation of 1-2 km. The δ18O values in the Alberta foreland and Williston basin are very low (- 20.5‰) in the Late Cretaceous, indicating the rivers were fed by snowmelt from the Canadian Rocky Mountains of 4.3 ± 1.0 km high. The attainment of high elevation in the eastern Laramide province prior to the western province could be explained by southwestward progression of back-thrusts soled into an earlier east-directed master detachment, which may be formed by the westward rollback of subducted shallow slab.

  19. Emanation Study of Gas Radon on the Ancient Cuexcomate Geyser in Puebla City, Mexico

    Directory of Open Access Journals (Sweden)

    J. A. Monarca Serrano

    2016-08-01

    Full Text Available Radon measurements were collected over a period of nine months in the area of the ancient Cuexcomate geyser, in Puebla City. For measuring radon, the passive method of nuclear tracks in solids was used, using polycarbonate CR-39 as radiation sensitive material. Radon concentrations varied in strong anti-correlation with the rainfall intensity. And are lower compared to other locations, in concordance with the stratigraphic composition, as travertine and deposits of volcanic origin, corresponding to the geyser chemical composition and the active environment in the north part of the Trans-Mexican Volcanic Belt with an andesitic and basalt composition.

  20. Triplex technology in studies of DNA damage, DNA repair, and mutagenesis

    OpenAIRE

    Mukherjee, Anirban; Vasquez, Karen M.

    2011-01-01

    Triplex-forming oligonucleotides (TFOs) can bind to the major groove of homopurine-homopyrimidine stretches of double-stranded DNA in a sequence-specific manner through Hoogsteen hydrogen bonding to form DNA triplexes. TFOs by themselves or conjugated to reactive molecules can be used to direct sequence-specific DNA damage, which in turn results in the induction of several DNA metabolic activities. Triplex technology is highly utilized as a tool to study gene regulation, molecular mechanisms ...

  1. A Survey of the Studies on White Tiger Shaking Head Method Described by Ancient and Modern Physicians

    Institute of Scientific and Technical Information of China (English)

    YUE Gong-lei; WANG Fu-chun; YAN Bing; HONG Jie

    2009-01-01

    @@ Having studied white tiger shaking head method described by ancient and modem physicians, and analyzed and compared its manipulation techniques, the authors believe that the core of white tiger shaking head method originating from Zhenjiu Daquan (针灸大全Complete Book of Acupuncture-Moxibustion) by XU Feng lies in the techniques of "squarely withdrawing and circularly inserting" and "shaking and vibrating",and the manipulation factor is "circularly inserting and shaking, and squarely withdrawing and vibrating".Physicians such as WANG Ji (his second method), YANG Ji-zhou, LU Shou-kang and ZHENG Kui-shan inherited and developed white tiger shaking head method.

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

    Institute of Scientific and Technical Information of China (English)

    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 different ways,with characteristics of tourism resources such as long history and ancient folklore. It should seize the historical opportunity of China vigorously developing rural tourism based on the construction of the new socialist countryside,to make characteristic agricultural economy gain ground; assume the leading role to drive the development of tourism economy in surrounding areas; correctly handle the relationship between development and protection to walk the path of sustainable development of tourism.

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

    International Nuclear Information System (INIS)

    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

  4. 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

  5. 古村落保护性开发研究--以佛山大旗头古村落为例%Study on the Protective Development of Ancient Village:Taking Foshan Daqitou Ancient Village for Example

    Institute of Scientific and Technical Information of China (English)

    余琳; 张智威

    2014-01-01

    Ancient villages in China are crystallizations of Chinese thousand-year old farming cultures, concentrations of historical, scientific and artistic values and demonstrations of ethnic and regional characteristics. Unfortunately, due to insufficient protection and development, a majority of them gradually show declining state, and protection and development are imminent. This study analyzes the main reasons why ancient villages declining state by conducting a case study of Daqitou Ancient Village in foshan and proposes several practices such as document management, functional replacement and widening of investment channels to use the resources in ancient villages effectively and efficiently for a positive loop between development and protection.%古村落是我国数千年农耕文化的结晶,它凝聚着丰富的历史、科学和艺术价值,直接表达了民族、地域的个性特征。但目前由于没有受到应有的保护和发展,很多古村落渐显的颓态,保护与发展迫在眉睫。本文以佛山大旗头古村落为例,分析古村落凸显颓态的主要原因,同时,根据实际提出实施建档管理、功能置换拓宽资金投入渠道等措施,对古村落的资源进行合理有效的利用和开发,从而形成保护与开发的良性循环。

  6. 国学及其研究方法%Studies of Chinese Ancient Civilization and Research Methods

    Institute of Scientific and Technical Information of China (English)

    张崇琛

    2015-01-01

    “国学”是中国固有的学术,是研究中国传统的典籍、学术与文化的学问。国学既是文献的学问,又是德性的学问,更是养成完美人格和延续民族文化传统的学问。对待国学,不但要准确理解,大力弘扬;同时也要联系实际,付诸实施,并使其常新。%The studies of Chinese ancient civilization is China's inherent academic. It is the knowledge about Chinese traditional records, academic and culture. It is not only the literature knowledge and the virtue knowledge, but also the knowledge to develop the perfect personality and to continue the traditional ethnic culture. For the studies of Chinese ancient civilization we should not only understand accurately and promote vigorously, at the same time we should practice, implement and keep it fresh.

  7. [Xeroradiography and digital luminescence radiography in the study of the technics of manufacturing ancient ceramics. The advantages and limits].

    Science.gov (United States)

    Meduri, A; Pirronti, T; Calicchio, D; Rispoli, F; Vidale, M; Marano, P

    1993-01-01

    This paper reports on the cooperative work of the Department of Radiology of the Catholic University, Rome, and of the Italian Institute for Middle and Far East. The study was aimed at using xeroradiography and digital luminescence radiography for the archeometric evaluation of ancient ceramics and at assessing the imaging potentials of the two techniques. Some manufacturing techniques are reported which were used in the ancient world and societies for pottery making--i.e., coil building (the superimposition of clay rings), paddle and anvil beating and throwing of the wheel. Such techniques leave, on the vessel's wall, clear traces which can be detected by X-ray imaging. After discussing the main semiologic features, we present 4 case studies from the project archive. Each vase underwent xeroradiography and digital luminescence radiography. The former technique was useful in detailing minor phase transitions--e.g., pores and inclusions--while the latter, thanks to both its wide dynamic range and its image processing potentials, was optimal in defining very gradual thickness transitions due to the different techniques used to join the clay parts. By combining the two techniques, the manufacturing technology of the artifacts could be defined. The interactive processing of radiographic images at the system console was seen to be of major importance: it allowed the best results to be obtained thanks to the integration of the radiologists' and archeologists' know-how during the actual analytical stages.

  8. DNA-Based Vaccine Guards Against Zika in Monkey Study

    Science.gov (United States)

    ... page: https://medlineplus.gov/news/fullstory_161106.html DNA-Based Vaccine Guards Against Zika in Monkey Study ... THURSDAY, Sept. 22, 2016 (HealthDay News) -- An experimental DNA-based vaccine protected monkeys from infection with the ...

  9. Ancient DNA analysis of mid-holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes.

    Directory of Open Access Journals (Sweden)

    Yinqiu Cui

    Full Text Available 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.

  10. Study on provenance of ancient Yaozhou porcelain bodies by fingerprint elements scatter analysis

    International Nuclear Information System (INIS)

    25 samples of Yaozhou porcelain bodies, 3 samples of the tri-color pottery bodies during the Tang Dynasty, 1 samples of Saggar material during Song Dynasty and 4 samples of clay mineral taken from the place near Yaozhou Kiln Museum was selected. The technique of neutron activation analysis (NAA) has been employed to measure the content of 29 kinds of elements in the samples. 8 elements of them were selected as fingerprint elements to make scatter analysis. The conclusion is that the ancient Yaozhou porcelain bodies produced by different kilns have long shared a stable and concentrated raw material sources. Both the tri-colored pottery bodies made in Yaozhou Kilns during the Tang Dynasty and the Yaozhou porcelain bodies are from the same provenance. (authors)

  11. A Date Recovery System launched for chronological studies in ancient China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Benefited from the performance of the Xia-Shang-Zhou Chronology Project (XSZP) in China and our new astronomical chronology method designed and processed for Chinese particular 60-day-cycle Ganzhi (the heavenly stems and earthly branches) date records, we launch a Date Recovery System (DRS) for ancient China. Of high analysis function, this software can recover and convert the complete or incomplete date information originally from Ganzhi style in the historical period of China to the Gregorian Calendar System, which may have wide applications in the area of literary history, archaeology and cultural relic, etc., and solve the Goldbach Puzzles of Chinese nations. As an example, we give the detailed process for the sculptures on four bronze wares with the Ganzhi data and afterwards employ this software and provide their possible dates corresponding to Gregorian system.

  12. A Date Recovery System launched for chronological studies in ancient China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Benefited from the performance of the Xia-Shang-Zhou Chronology Project(XSZP) in China and our new astronomical chronology method designed and processed for Chinese particular 60-day-cycle Ganzhi(the heavenly stems and earthly branches)date records,we launch a Date Recovery System(DRS)for ancient China. Of high analysis function,this software can recover and convert the complete or incomplete date information originally from Ganzhi style in the historical period of China to the Gregorian Calendar System,which may have wide applications in the area of literary history,archaeology and cultural relic,etc.,and solve the Goldbach Puzzles of Chinese nations.As an example,we give the detailed process for the sculptures on four bronze wares with the Ganzhi data and afterwards employ this software and provide their possible dates corresponding to Gregorian system.

  13. Serious games for disseminating the knowledge of ancient manuscripts: a case study

    Directory of Open Access Journals (Sweden)

    Cristian Lorenzini

    2014-07-01

    Full Text Available En In this paper we present a Digital Serious Game set in a medieval alchemical laboratory, aimed at disseminating the ancient knowledge of medicine distillation contained in the famous Adam Lonicer's Kreuterbuch (1569 treatise. The application is  based on interactive Virtual Environments and available on multiple visualization technologies, ranging from simple touch-based tablet up to immersive environments such as CAVEs or Oculus Rift.  The game comes as the latest development level of a larger international multidisciplinary project meant to explore novel methodologies to raise the awareness about ancient books, in particular the collection of the Gunnerus Library of Trondheim, with a special attention to the public of youngsters. ItIn questo articolo viene presentato un Digital Serious Game ambientato in un laboratorio alchemico medievale, realizzato al fine di facilitare la trasmissione della conoscenza relativa alle antiche tecniche di distillazione medicinale così come illustrate nel famoso trattato Kreuterbuch di Adam Lonicer (1569. L'applicazione è stata realizzata utilizzando tecnologie di ambienti virtuali interattivi ed è fruibile su un vasto panorama di dispositivi di visualizzazione, a partire da semplici PC touch-screen fino a sistemi immersivi come il CAVE o il recente Oculus Rift. Il gioco rappresenta il terzo livello di sviluppo di un più grande progetto di ricerca multidisciplinare avente come obiettivo l'esplorazione di nuove metodologie per stimolare e  promuovere l'interesse  per i libri antichi, in particolare la collezione della Gunnery Library di Trondheim, con una speciale attenzione al pubblico dei giovani.

  14. 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).

  15. 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...

  16. 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.

  17. Survey on Farming Culture of Ancient Villages and Tourism Development: A Case Study of Hongjiang City in Hunan Province

    Institute of Scientific and Technical Information of China (English)

    Lei; FANG

    2014-01-01

    The origin of human civilization is based on agriculture and settlement,and the ancient villages preserved up to now can be rated as " museum and historical library of rural lifestyle and rural culture",which are of important historical and cultural value. Through the field survey of farming culture resources of ancient villages in Hongjiang City of Hunan Province,this article classifies and evaluates the farming culture and ancient village resources,and sets forth the following recommendations for the development of ancient village tourism: strengthening the product differentiation development; focusing on the cultivation and integration of resources; enhancing the village environmental remediation.

  18. Interaction studies of Epirubicin with DNA using spectroscopic techniques

    Science.gov (United States)

    Charak, Sonika; Jangir, Deepak K.; Tyagi, Gunjan; Mehrotra, Ranjana

    2011-08-01

    Epirubicin (EPR) is an anticancer chemotherapeutic drug which exerts its cytotoxic effect by inhibiting DNA synthesis and DNA replication. We report the structural and conformational effect of EPR binding on DNA duplex under physiological conditions. Fourier transform infrared spectroscopy (FTIR), ultraviolet-visible (UV-visible) spectroscopy and circular dichroism (CD) spectroscopy were used to determine the binding mode and binding constant of EPR with DNA. The effect of EPR-DNA complexation on stability and secondary structure of DNA was studied. FTIR measurements showed that EPR-DNA interaction occurs through guanine and cytosine bases. External binding of EPR with DNA was observed through phosphate backbone. UV-visible measurements revealed the intercalative mode of binding of EPR with DNA. The binding constant was estimated to be K = 3.4 × 10 4 which is indicative of moderate binding between EPR and DNA helix. FTIR and CD studies suggested partial transition from B-conformation of DNA to A-conformation of DNA after EPR binding to DNA duplex.

  19. 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. PMID:22674514

  20. 中国古代个性心理测量的研究%A Study on Personality Assessment In Ancient China

    Institute of Scientific and Technical Information of China (English)

    章竞思; 张秀琴

    2001-01-01

    该文从四个方面对古代个性心理测量进行了全面论述。首先介绍了中国古代个性心理测量研究的发展过程;接着讨论了中国古代个性心理测量研究运用的各种方法,如观察法、访谈法、自然实验法等;然后本文归纳总结了中国古代个性心理测量的特点;最后探讨了研究中国古代个性心理测量的理论和现实意义。%This thesis gives a thorough discussion of the personality assessment in ancient China from four aspects.Firstly,it introduces the developing process of personality assessment in ancient China,then studies the kinds of methods that were used in the analysis of personality assessment in ancient China,such as observation method,interview method and experiment under natural conditions;then the thesis concluded the characteristics of personality assessment in ancient China,Lastly,the thesis inquired into theoretical and practical signficance of studying personality assessment in ancient China.

  1. Pyrite Framboids: A Possible Biosignature For the Study of Ancient Sediments

    Science.gov (United States)

    Schelble, R. T.; Popa, R.; Douglas, S.; Nealson, K. H.

    2003-12-01

    Framboids are 0.5-100 μ m-sized, raspberry-like, spheroidal accumulations of 10-109 microcrystallites. These structures are predominantly composed of pyrite (FeS2), although other minerals such as greigite (Fe3S4), magnetite (Fe3O4), and limonite (FeO.OH.nH2O) have also been identified. Modern framboids are present in a variety of natural environments (soils, sediments, microbial mats), and can also be produced artificially in the laboratory. Even though numerous cases of framboids have been cited from the geological record, little is known about their mechanisms of formation, and biogenicity. Understanding the effects of the conditions of formation upon framboid characteristics from modern environments (e.g. size distribution, microtexture, composition, and mineralogy) will allow us to better understand what pyrite framboids can tell us about sediments from the geological record. The purpose of this project was to determine whether pyrite framboids can be used as a biosignature within ancient sediments. Microbial mats rich in pyrite framboids were collected from the Buncar Springs in Mangalia aquifer (Romania). The pyrite framboid rich microbial mats are formed underground at the anaerobic water-gas (90-95% methane, 5-10% CO2) interface. Neoproterozoic (750-600 Ma) manganese carbonate deposits containing fossilized pyrite framboids were collected from a mine near the city of Ming Lo, Hunan Province, China. Synthetic framboids were made in the laboratory by a modification of the protocol provided by Sweeney and Kaplan (1973). The morphology of framboids formed within modern microbial mats, within ancient sediments, and those synthesized abiotically in the laboratory were compared, and then correlated with their biogenicity. Images were obtained using environmental scanning electron microscopy and the microtextures were analyzed using shape-analysis tools providing information about the overall size distribution of framboids, number of microcrystallites per unit

  2. Fluorescence Study on the Interaction between Naproxen and Yeast DNA

    Institute of Scientific and Technical Information of China (English)

    叶宝芬; 张志洁; 鞠熀先

    2005-01-01

    The interaction between naproxen and yeast DNA was studied using fluorescence spectrometry and ultra-violet (UV) spectrometry. The addition of yeast dsDNA to naproxen solution resulted in a strong fluorescence quenching. Both the Stern-Volmer and the Scatchard plots of the fluorescence quenching showed a curve with two slopes and a threshold DNA concentration of about 100 μtmol·L-1. The interaction between naproxen and the dsDNA was found to be a groove binding mode by UV spectra, the influence of ion strength and I- quenching effect. This mode was independent on DNA concentration. However, the increase in DNA concentration changed the binding constant K of naproxen to yeast dsDNA and the number of binding sites in DNA base pairs (n).

  3. Electrochemical Study on the Interaction Betwwen Neutral Red and DNA

    Institute of Scientific and Technical Information of China (English)

    NIU Shu-yan; ZHANG Shu-sheng; SHI Xin; JIAO Kui

    2005-01-01

    A voltammetric study of the interaction of neutral Red(NR) with DNA at a gold electrode in a phosphate buffer solution is described. After adding DNA in an NR solution, the reduction peak current of NR decreases. The binding mechahisms of NR to DNA in different pH ranges are different. The reduction peak potential of NR in a pH 7.0 phosphate buffer solution in the presence of DNA shifts positively, indicating that the binding of NR to DNA is intercalation action, but at pH=6.0 the reduction peak potential of NR shifts negatively, indicating that the binding of NR to DNA is electrostatic action. The formed complexes are DNA-NR when [NR]/[DNA]0.35, respectively.

  4. Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.

    Directory of Open Access Journals (Sweden)

    Catherine Thèves

    Full Text Available Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th to the 19(th century, we propose a methodology that includes the: 1 amplification of all 16S rDNA gene sequences present in each sample; 2 identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3 identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4 establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1 the correct identification of bacterial molecular sequence signatures by quality criteria; 2 the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3 the distribution of bacterial species for each subject and for each burial; and 4 the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th century to the early 18(th century.

  5. A Comparative Study of The Regular Pattern of Syndrome and Treatment of Lung-intestine Related Diseases in Ancient and Modern Medical Cases Based on Data Mining

    Institute of Scientific and Technical Information of China (English)

    Fang-Fang Mo; Le-Peng Wang; Si-Hua Gao

    2016-01-01

    Objective: To analyze the similarities and differences of the applications of “the lung and large intestine being interior-exteriorly related”between the ancient and modern clinical practices, and to reveal the theory meaning. Method: Based on the ancient and modern medical cases database, 245 ancient medical records and 373 modern medical records were studied with the general statistical description and analysis of association rules, and the results were compared to summarize the similarities and differences of the regular pattern of syndrome and treatment on lung-large intestine related diseases in ancient and modern medical records. Results: In modern medical cases, intestinal diseases appeared with the main symptom of constipation due to deficiency of lung qi and qi stagnation of large intestine were always treated by purgation together with replenishing and restoring lung qi. In ancient medical cases, large intestine heat was always caused by lung heat and a variety of diarrhea symptoms appeared. They were always treated by clearing heat and moistening lungs. In addition, the symptom of bound stool caused by qi stagnation of large intestine due to lung qi stagnation was always treated by lowering lung qi to regulate and smooth large intestine qi. And Armeniae Amarum Semen was used by both as a core medicinal herb. Conclusion: Ascending-descending of qi movement is the core of the lung and large intestine relationship. In other words, the lung and the large intestine communicate through qi.

  6. Study on ancient porcelain of Loulinpo Kiln Site by nuclear analysis technology

    International Nuclear Information System (INIS)

    Yaozhou Kiln located at Tongchuan of Shanxi Province has lasted continuous history of firing celadon porcelain from Tang Dynasty (618-907A.D.) to Yuan Dynasty (1234-1368A.D.), The firing technology has had important effect for celadon porcelain of many kilns in ancient China. In Jin Dynasty (1127-1234A.D.) and Yuan Dynasty, because of lacking of raw material resources, the central site of Yaozhou Kiln moved from Tongchuan to Lidipo, Shangdian and Chenlu area. Luolinpo site belongs to Yaozhou Kiln series and is one kiln of Shangdian area. The bowl sherds samples of Yuan dynasty stratum excavated in recent year. The glaze color is celadon, black, dark brown and dark reddish brown respectively. Ten pieces of sherds of each glaze color were selected. The main chemical compositions of theses samples were analyzed by XRF and the trace elemental contents were determined by NAA. The result shown that the content of Fe2O3 can decide the kind of glaze color will be. The concentration of CaO, Na2O and K2O can be used to explain the developing process of firing techniques. Except samples of dark brown glaze, the contents of Fe2O3 and CaO change in small range. The proportions of these main chemical compositions of the porcelain with glaze color of black, celadon and dark reddish brown have little variation. But it was very different form some samples of dark brown glaze.

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

    International Nuclear Information System (INIS)

    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.

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

    International Nuclear Information System (INIS)

    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 K2O-SiO2, PbO-BaO-SiO2, PbO-SiO2, Na2O-K2O-PbO-SiO2 and (Na2O)K2O-CaO-SiO2. But most of the samples belong to K2O-SiO2 system glass. Due to the surface corrosion, the flux K2O in the surface of the K2O-SiO2 glass was lost, but with the relative enrichment of the SiO2. 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 K2O-SiO2 glass in China was influenced by the technique related to the PbO-BaO-SiO2 glass from abroad. (authors)

  9. 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.

  10. Integration of μ-XRF, and u-Raman techniques to study ancient Islamic manuscripts

    Science.gov (United States)

    Hamdan, N. M.; Alawadhi, H.; Jisrawi, N.

    2012-07-01

    Systematic characterizations of inks used in three ancient Arabic manuscripts were performed using energy dispersive X-ray fluorescence (EDXRF) and RAMAN spectroscopy. Spatially resolved element distributions obtained by area scans in addition to spot analysis provided detailed information about the manuscripts. RAMAN spectroscopy, on the other hand provided decisive information about the compounds used in various color pigments. Different compounds were found in the red ink in each manuscript: HgS (cinnabar) in one manuscript, red lead Pb304 (minium) in the second, and a mixture of the two in the third manuscript. The green pigment was Cu based and it is probably malachite (Cu2CO3(OH)2), while the black ink pigment in the three manuscripts is iron gall (Fe2SO4 plus gallottanic acid). Analytical results and the context of the manuscripts were used to extract information about the authenticity and origin of the manuscripts. For example, the use of cinnabar as a red ink pigment found in the third manuscript reveals that this manuscript attributed to Al-Gazali (11th century) is probably a copy from a later period, because cinnabar was first introduced in the 16th century.

  11. Listening in the Pakal controversy: a matter of care in Ancient Maya studies.

    Science.gov (United States)

    Watson, Matthew C

    2014-12-01

    This article explores the fraught historical politics of a 20th-century controversy over a Classic Maya king. The controversy ostensibly concerned the age at death of a ruler discovered in 1952 in an elaborate sarcophagus at the Mexican site of Palenque. Combining osteological and epigraphic techniques, Mexican scholars estimated that the ruler died at about 40 or 50years of age. Two decades later, an emerging collective of US hieroglyph experts claimed to have determined the grammatical structure of Maya glyphs for the first time and reevaluated the sarcophagus inscriptions. They concluded that the king, given the name 'Pakal', lived a remarkably long life of 80years (603-683 CE). This reading sparked a controversy that would persist until 1999. At stake was not just how to tell the story of an ancient Maya lord, but who could tell it, with what evidence, and with what degree of certainty. The inclination of some Mexican archaeologists to adopt nationalist and Marxist orientations came into palpable tension with foreign scholars' liberal, universalist knowledge practices. To address this problem, I rethink Pakal's material mediation through bones and inscriptions as a 'matter of concern' (Bruno Latour) and 'matter of care' (Maria Puig de la Bellacasa). I show how these concepts facilitate the reconsideration of contradictory historical propositions as potential sites of coexistence among actors temporarily ill equipped to listen to each other's claims. Ultimately, I present 'listening' as a technique of cosmopolitical care that complements the extensive emphasis on speech and spokespersonship in Latourian cosmopolitics.

  12. SINCRETIC SEMIOTIC THE ANCIENT INDONESIAN MOSQUE TOMBHOUSE Case study SENDANG DUWUR-EAST JAVA

    Directory of Open Access Journals (Sweden)

    Wiranto Wiranto

    2002-01-01

    Full Text Available Mosque is a place for worship, spirit, contemplation, but above all, Mosque is "a gate way". Sendang Duwur Mosque and Tombhouse is an Islamic antiquity as the product of syncretism process between traditional Javanese architecture - Hindunese/Budhanese - foreign Islamic which born early Mosque in Java. The semiotic and syncretic of Indonesian Mosque and Tombhouse also integrated some principles of the Javanese cosmology blend with the concept of Islamic Architecture, which resulted a symthesis of both traditional and new idea. It manifested in the type of ancient Mosque and tombhouse Sendang Duwur,which is original types ,specific with identity. Abstract in Bahasa Indonesia : Pada hakekatnya peran suatu Masjid adalah sebagai tempat beribadat, tempat menemukan kekuatan bathin ,tempat samadi, namun diatas itu semua peran Masjid adalah sebagai suatu "gerbang". Masjid makam Sunan Sendang Duwur adalah bangunan purbakala sebagai salah satu produk proses sinkretisme arsitektur Tradisional Jawa - Hindu/Budha - dan Islam .yang selanjutnya melahirkan wujud awal Masjid utama diJawa. Semiotic dan sinkretis Masjid makam di Indonesia juga mengintegrasikan beberapa prinsip Kosmologi Jawa yang diramu secara harmonis dengan konsep arsitektur Islam ,yang selanjutnya menghasilkan suatu sinthesa tradisional sebagai ide baru. Jabaran tersebut terlihat pada Masjid makam Sunan Sendang Duwur yang menampilkan type yang aseli, spesifik dan beridentitas. Kata kunci: sinkretisme, semiotic, Masjid, Gapura, Nilai.

  13. Integration of μ-XRF, and u-Raman techniques to study ancient Islamic manuscripts

    International Nuclear Information System (INIS)

    Systematic characterizations of inks used in three ancient Arabic manuscripts were performed using energy dispersive X-ray fluorescence (EDXRF) and RAMAN spectroscopy. Spatially resolved element distributions obtained by area scans in addition to spot analysis provided detailed information about the manuscripts. RAMAN spectroscopy, on the other hand provided decisive information about the compounds used in various color pigments. Different compounds were found in the red ink in each manuscript: HgS (cinnabar) in one manuscript, red lead Pb304 (minium) in the second, and a mixture of the two in the third manuscript. The green pigment was Cu based and it is probably malachite (Cu2CO3(OH)2), while the black ink pigment in the three manuscripts is iron gall (Fe2SO4 plus gallottanic acid). Analytical results and the context of the manuscripts were used to extract information about the authenticity and origin of the manuscripts. For example, the use of cinnabar as a red ink pigment found in the third manuscript reveals that this manuscript attributed to Al-Gazali (11th century) is probably a copy from a later period, because cinnabar was first introduced in the 16th century.

  14. A multi-analytical approach to gold in Ancient Egypt: Studies on provenance and corrosion

    Science.gov (United States)

    Tissot, I.; Troalen, L. G.; Manso, M.; Ponting, M.; Radtke, M.; Reinholz, U.; Barreiros, M. A.; Shaw, I.; Carvalho, M. L.; Guerra, M. F.

    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 (D2XRF). 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.

  15. Spectroscopic Electrochemical Studies of Interaction Between Fuchsin Basic DNA

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Visible spectroscopic and electrochemical methods were used to study the interactions between DNA and fuchsin basic(FB). FB has an irreversible electro-oxidation peak in 5 mmol/L Tris-HCl buffer solution at pH = 7.4 on a glassy carbon electrode(GCE). After adding certain concentration of dsDNA, the oxidation peak current of FB decreases, but the peak potential hardly changs. The visible absorption spectroscopic study shows that the binding mode of FB to dsDNA is intercalative binding and electrostatic binding when the ratio of the concentration of dsDNA to FB is smaller than 0. 2, and a new substance, which produces a new absorption peak, is obtained via a covalent binding between dsDNA and FB apart from intercalative binding and electrostatic binding when the ratio of the concentration of dsDNA to FB is larger than 0. 2. The visible absorption spectra varies no longer when the ratio of the concentration of dsDNA to FB is larger than 1.5. A mean binding ratio of dsDNA to FB was determined to be 1.4: 1,suggesting that two complexes FB-dsDNA and FB-2dsDNA be formed. The interaction between FB and ssDNA was only electrostatic binding. The more powerful interaction of FB with dsDNA than with ssDNA may be applied for the recognition of dsDNA and ssDNA, and in DNA biosensor as hybridization indicator.

  16. Ancient human microbiomes

    Science.gov (United States)

    Warinner, Christina; Speller, Camilla; Collins, Matthew J.; Lewis, Cecil M.

    2015-01-01

    Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and therefore, we lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today. PMID:25559298

  17. Studies of interaction between two alkaloids and double helix DNA

    International Nuclear Information System (INIS)

    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 (KA) 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

  18. Studies of interaction between two alkaloids and double helix DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Yantao [Key Laboratory of Preparation and Applications of Environmentally Friendly Materials (Jilin Normal University), Ministry of Education China, Siping 136000 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China); Peng, Tingting [College of Chemistry, Jilin Normal University, Siping 136000 (China); College of Chemistry, Baicheng Normal University, Baicheng, 130032 (China); Zhao, Lei [Siping Institute for Food and Drug Control, Siping 136000 (China); Jiang, Dayu [Key Laboratory of Preparation and Applications of Environmentally Friendly Materials (Jilin Normal University), Ministry of Education China, Siping 136000 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China); Cui, Yuncheng, E-mail: 1979yanzi@163.com [Key Laboratory of Preparation and Applications of Environmentally Friendly Materials (Jilin Normal University), Ministry of Education China, Siping 136000 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China)

    2014-12-15

    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{sub 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.

  19. Theoretical study of electron transport in DNA

    Science.gov (United States)

    Tan, Bikan; Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry

    2013-03-01

    Many experiments have observed high conductivity of DNA, but its origin has not yet been satisfactorily explained. In this work, we explore the dynamics of solvated B-DNA sandwiched between metallic nanotubes and connected via alkane linkers. The geometries are relaxed using the CHARMM force field. Conductivities of different snapshots of the system are calculated using the non-equilibrium Green's function method within density-functional theory. Our results show that in certain geometries, the DNA conducts significantly better than in others. For the highest conductivity configuration, a HOMO state extends across DNA's guanine sites to the alkane linkers. In general, we find that the conformational changes strongly affect the energy alignment of HOMO states of the DNA and the linker, and thus have a major effect on the conductivity of the entire system.

  20. Pairing Mismatched ssDNA to dsDNA Studied with Reflectometric Interference Spectroscopy Sensor

    Institute of Scientific and Technical Information of China (English)

    Qing-Qing Wu; Kai-Ge Wang; Dan Sun; Shuang Wang; Chen Zhang; Wei Zhao

    2016-01-01

    The interaction between two single-stranded DNA (ssDNA) molecules as pairing to a double-stranded DNA (dsDNA) molecule is studied by the reflectometric interference spectroscopy (RIFS) technology.A nano-porous anode alumina membrane coated an Au layer is employed as the sensor substrate.The results indicate that when there are mismatched nucleotide bases,the effective optical thicknesses (OTeff) have obvious difference,and the changes of OTeff are connected with the sensor layer thickness and the effective refractive index.It is also demonstrated that the RIFS technique can be used to precisely detect the ssDNA molecules with individual base mismatched as pairing to dsDNA.

  1. Archaeological reconstruction of medieval lead production: Implications for ancient metal provenance studies and paleopollution tracing by Pb isotopes

    International Nuclear Information System (INIS)

    The identification of metal provenance is often based on chemical and Pb isotope analyses of materials from the operating chain, mainly ores and metallic artefacts. Such analyses, however, have their limits. Some studies are unable to trace metallic artefacts or ingots to their ore sources, even in well-constrained archaeological contexts. Possible reasons for this difficulty are to be found among a variety of limiting factors: (i) problems of ore signatures, (ii) mixing of different ores (alloys), (iii) the use of additives during the metallurgical process, (iv) metal recycling and (v) possible Pb isotopic fractionation during metal production. This paper focuses on the issue of Pb isotope fractionation during smelting to address the issue of metal provenance. Through an experimental reconstruction of argentiferous Pb production in the medieval period, an attempt was made to better understand and interpret the Pb isotopic composition of ore smelting products. It is shown that the measured differences (outside the total external uncertainties of 0.005 (2*sd) for 206Pb/204Pb ratios) in Pb signatures measured between ores, slag and smoke are not due to Pb mass fractionation processes, but to (1) ore heterogeneity (Δ206Pb/204Pbslag-ores = 0.066) and (2) the use of additives during the metallurgical process (Δ206Pb/204Pbslag-ores = 0.083). Even if these differences are due to causes (1) and/or (2), smoke from the ore reduction appears to reflect the ore mining area without a significant disturbance of its Pb signature for all the isotopic ratios (Δ206Pb/204Pbsmokes-ores = 0.026). Thus, because the isotopic heterogeneity of the mining district and additives is averaged in slags, slag appears as the most relevant product to identify ancient metal provenance. Whereas aiming at identifying a given mine seems beyond the possibilities provided by the method, searching for the mining district through analysis of the smelting workshop materials should provide a more

  2. Incorporation of Trace Elements in Ancient and Modern Human Bone: An X-Ray Absorption Spectroscopy Study

    Science.gov (United States)

    Pingitore, N. E.; Cruz-Jimenez, G.; Price, T. D.

    2001-12-01

    X-ray absorption spectroscopy (XAS) affords the opportunity to probe the atomic environment of trace elements in human bone. We are using XAS to investigate the mode(s) of incorporation of Sr, Zn, Pb, and Ba in both modern and ancient (and thus possibly altered) human and animal bone. Because burial and diagenesis may add trace elements to bone, we performed XAS analysis on samples of pristine contemporary and ancient, buried human and animal bone. We assume that deposition of these elements during burial occurs by processes distinct from those in vivo, and this will be reflected in their atomic environments. Archaeologists measure strontium in human and animal bone as a guide to diet. Carnivores show lower Sr/Ca ratios than their herbivore prey due to discrimination against Sr relative to Ca up the food chain. In an initial sample suite no difference was observed between modern and buried bone. Analysis of additional buried samples, using a more sensitive detector, revealed significant differences in the distance to the second and third neighbors of the Sr in some of the buried samples. Distances to the first neighbor, oxygen, were similar in all samples. Zinc is also used in paleo-diet studies. Initial x-ray absorption spectroscopy of a limited suite of bones did not reveal any differences between modern and buried samples. This may reflect the limited number of samples examined or the low levels of Zn in typical aqueous solutions in soils. Signals from barium and lead were too low to record useful XAS spectra. Additional samples will be studied for Zn, Ba, and Pb. We conducted our XAS experiments on beam lines 4-1 and 4-3 at the Stanford Synchrotron Radiation Laboratory. Data were collected in the fluorescence mode, using a Lytle detector and appropriate filter, and a solid state, 13-element Ge-detector.

  3. 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.

  4. Single-molecule studies of DNA by molecular combing

    Institute of Scientific and Technical Information of China (English)

    Liu Yuying; Wang Pengye; Dou Shuoxing

    2007-01-01

    Molecular combing is a powerful method for aligning a large array of DNA molecules onto a surface. It is a process whereby DNA molecules are stretched and aligned on a glass surface by the force via fluid flow. The ability to comb up to several hundred DNAs on a single cover slip allows for a statistically significant number of measurements to be made. These features make molecular combing an attractive tool for genomic studies, such as DNA replication, DNA transcription, DNA-protein interaction and so on. In this review article, we discuss the molecular combing principle, method and its applications.

  5. Life without mitochondrial DNA : studies of transgenic mice

    OpenAIRE

    Wang, Jianming

    2000-01-01

    Mitochondrial DNA (mtDNA) is a closed circular DNA genome that resides in the mitochondrial network. Mutations of mtDNA cause spontaneous and hereditary disorders known as mitochondrial diseases. Mitochondrial transcription factor A (Tfam) is a key factor for transcription of mtDNA in vitro. We disrupted the mouse Tfam gene by using the cre-loxP recombination system to study the in vivo roles of Tfam. This thesis focuses on the analyses of germline knockout mice and the c...

  6. 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.

  7. 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.

  8. A multi-analytical approach to gold in Ancient Egypt: Studies on provenance and corrosion

    International Nuclear Information System (INIS)

    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 (D2XRF). 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 D2XRF 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

  9. Initiation of bacteriophage Φ29 DNA packaging studied by optical tweezers manipulation of single DNA molecules

    Science.gov (United States)

    Rickgauer, John Peter; Fuller, Derek N.; Hu, Bo; Grimes, Shelley; Jardine, Paul J.; Anderson, Dwight L.; Smith, Douglas E.

    2006-08-01

    A key step in the life cycle of many viruses, including bacteriophages, adenoviruses, and herpesviruses, is the packaging of replicated viral genomes into pre-assembled proheads by the action of ATP-dependent portal motor complexes. Here we present a method that allows the initiation of packaging by single complexes to be studied using optical tweezers. A procedure is developed for assembling phage Φ29 prohead-motor complexes, which are demonstrated to bind and begin translocation of a target DNA molecule within only a few seconds. We show that the Φ29 DNA terminal protein (gene product 3), which functions to prime DNA replication, also has a dramatic effect on packaging. The DNA tether length measured immediately after binding varied from ~30-100% of the full length, yet shortened monotonically, indicating that packaging does not strictly begin at the terminal end of the DNA. Removal of the terminal protein eliminated this variability, causing packaging to initiate at or very near the end of the DNA. These findings, taken together with electron microscopy data, suggest that rather than simply threading into the portal, the motor captures and dynamically tensions a DNA loop, and that the function of the terminal protein is to load DNA segments on both sides of the loop junction onto separate DNA translocating units.

  10. Single-molecule fluorescence studies on DNA looping.

    Science.gov (United States)

    Jeong, Jiyoun; Le, Tung T; Kim, Harold D

    2016-08-01

    Structure and dynamics of DNA impact how the genetic code is processed and maintained. In addition to its biological importance, DNA has been utilized as building blocks of various nanomachines and nanostructures. Thus, understanding the physical properties of DNA is of fundamental importance to basic sciences and engineering applications. DNA can undergo various physical changes. Among them, DNA looping is unique in that it can bring two distal sites together, and thus can be used to mediate interactions over long distances. In this paper, we introduce a FRET-based experimental tool to study DNA looping at the single molecule level. We explain the connection between experimental measurables and a theoretical concept known as the J factor with the intent of raising awareness of subtle theoretical details that should be considered when drawing conclusions. We also explore DNA looping-assisted protein diffusion mechanism called intersegmental transfer using protein induced fluorescence enhancement (PIFE). We present some preliminary results and future outlooks. PMID:27064000

  11. Kinetic study for hopping conduction through DNA molecules

    OpenAIRE

    Yang, Yong-Gang; Yin, Peng-Gang; Yan, Xin-Qi Li anf YiJing

    2004-01-01

    Recent experiments indicated that disorder effect in DNA may lead to a transition of the charge transport mechanism from band resonant tunnelling to thermal activated hopping. In this letter, based on Mott's variable-range hopping theory we present a kinetic study for the charge transport properties of DNA molecules. Beyond the conventional argument in large-scale systems, our numerical study for finite-size DNA molecules reveals a number of unique features for (i) the I-V characteristics, (i...

  12. Gold nanoparticle DNA damage in radiotherapy: A Monte Carlo study

    Directory of Open Access Journals (Sweden)

    Chun He

    2016-07-01

    Full Text Available This study investigated the DNA damage due to the dose enhancement of using gold nanoparticles (GNPs as a radiation sensitizer in radiotherapy. Nanodosimetry of a photon irradiated GNP was performed with Monte Carlo simulations using Geant4-DNA (ver. 10.2 in the nanometer scale. In the simulation model, GNP spheres (with diameters of 30, 50, and 100 nm and a DNA model were placed in a water cube (1 µm3. The GNPs were irradiated by photon beams with varying energies (50, 100, and 150 keV, which produced secondary electrons, enhancing the dose to the DNA. To investigate the dose enhancement effect at the DNA level, energy deposition to the DNA with and without the GNP were determined in simulations for calculation of the dose enhancement ratio (DER. The distance between the GNP and the DNA molecule was varied to determine its effect on the DER. Monte Carlo results were collected for three variables; GNP size, distances between the GNP and DNA molecule, and the photon beam energy. The DER was found to increase with the size of GNP and decrease with the distance between the GNP and DNA molecule. The largest DER was found to be 3.7 when a GNP (100 nm diameter was irradiated by a 150 keV photon beam set at 30 nm from the DNA molecule. We conclude that there is significant dependency of the DER on GNP size, distance to the DNA and photon energy and have simulated those relationships.

  13. Genetic diversity among ancient Nordic populations.

    Science.gov (United States)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R; Kivisild, Toomas; Dissing, Jørgen

    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, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among 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 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 for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  14. 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

    and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate...... 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...

  15. 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…

  16. 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

  17. 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

  18. AFM studies of nonspecific binding of enzyme on DNA

    Institute of Scientific and Technical Information of China (English)

    张益; 谢恒月; 等

    1996-01-01

    Atomic force microscope(AFM) is used to study restriction endonuclease digestion of plasmid DNA,pWRr plasmid DNA is digested by Hind Ⅲ,and the specific and the nonspecific binding of the restriction endonuclease are imaged,and the biological function of the enzyme binding to nonspecific sites is discussed.In addition,it is found that nonspecific binding of Hind ǚ could not induce the DNA characteristic bending angle.

  19. 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.

  20. 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...

  1. NMR studies of DNA structures in solution

    International Nuclear Information System (INIS)

    This thesis describes the conformational analysis of some polynucleotides in aqueous solution. A new graphical method is presented as an aid in the pseudorotational analysis of the sugar rings in DNA by means of sums of proton-proton coupling constants. (Auth.)

  2. A 150-year record of ancient DNA, lipid biomarkers and hydrogen isotopes, tracing the microbial-planktonic community succession controlled by (hydro)climatic variability in a tropical lake

    Science.gov (United States)

    Smittenberg, Rienk; Yamoah, Kweku; Callac, Nolwenn; Fru, Ernest Chi; Chabangborn, Akkaneewut; Rattray, Jayne; Wohlfarth, Barbara

    2016-04-01

    We investigated the decadal variations in phytoplankton communities, and their response to environmental and climatic conditions, from a ˜150 year long sedimentary archive of Lake Nong Thale Prong (NTP), southern Thailand. We applied a combination of analyses: lipid biomarkers, compound-specific hydrogen isotopes, bulk carbon and nitrogen concentrations and isotopes, environmental SEM, and fossil DNA using qPCR targeted to specific taxa. Past hydrological conditions were reconstructed using the hydrogen isotopic composition of leaf wax n-alkanes. Temperatures were reconstructed using the tetraether-based MBT/CBT index, measured using a new and efficient reverse-phase HPLC-MS method. The climatological data compared well with meteorological data from the last decades. Reconstructed drier and warmer conditions from ˜1857-1916 Common Era (CE) coincided with oligotrophic lake water conditions and dominance of the green algae Botryococcus braunii - evidenced by a combination of both fossil DNA and the occurrence of characteristic botryococcene lipids. A change to higher silica (Si) input ˜1916 CE was related to increased rainfall and lower temperatures concurring with an abrupt takeover by diatom blooms lasting for 50 years - as evidenced by ancient DNA, characteristic highly branched isoprenoid lipids, and SEM. From the 1970s onwards, more eutrophic conditions prevailed, and these were likely caused by increased levels of anthropogenic phosphate (P), aided by stronger lake stratification caused by dryer and warmer conditions. The eutrophic conditions led to increased primary productivity in the lake, consisting again of a Botryococcus sp., although this time not producing botryococcene lipids. Moreover, Cyanobacteria became dominant - again evidenced by ancient DNA and the characteristic C19 alkane. Throughout the record, stratification and primary production could be linked to the intensity of methane cycling, by targeting and quantifying the mcrA gene that is used

  3. Electrochemical studies of reaction of ciprofloxcin and DNA

    Institute of Scientific and Technical Information of China (English)

    Qiaocui SHI; Sufen WANG; Bin ZHU; Min JI

    2008-01-01

    The electrochemical behavior of ciprofloxacin (CFX) and its interaction with the natural calf thymus DNA (ctDNA) is studied by using pulse difference voltammetry on a carbon electrode. CFX shows a well-defined oxidative peak at+0.88 V. As a result of reaction with ctDNA,the oxidative peak of CFX decreased markedly. According to the electrochemical equation deduced in this paper, the binding constant of 1.36 × 105 (mol/L)-1 and the binding size of 1.94 (base pairs) of CFX with ctDNA were obtained by nonlinear fit analysis of the electrochemical data. The mechanism of the interaction was explored.

  4. In vitro DNA binding studies of Aspartame, an artificial sweetener.

    Science.gov (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Kheirdoosh, Fahimeh

    2013-03-01

    A number of small molecules bind directly and selectively to DNA, by inhibiting replication, transcription or topoisomerase activity. In this work the interaction of native calf thymus DNA (CT-DNA) with Aspartame (APM), an artificial sweeteners was studied at physiological pH. DNA binding study of APM is useful to understand APM-DNA interaction mechanism and to provide guidance for the application and design of new and safer artificial sweeteners. The interaction was investigated using spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD). Hypochromism and red shift are shown in UV absorption band of APM. A strong fluorescence quenching reaction of DNA to APM was observed and the binding constants (Kf) of DNA with APM and corresponding number of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be +181kJmol(-1) and +681Jmol(-1)K(-1) according to Van't Hoff equation, which indicated that reaction is predominantly entropically driven. Moreover, spectrofluorometric competition experiment and circular dichroism (CD) results are indicative of non-intercalative DNA binding nature of APM. We suggest that APM interacts with calf thymus DNA via groove binding mode with an intrinsic binding constant of 5×10(+4)M(-1).

  5. 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.

  6. Nuclear and mitochondrial DNA sequence data reveal the evolutionary history of Barbus (Cyprinidae) in the ancient lake systems of the Balkans.

    Science.gov (United States)

    Marková, Silvia; Sanda, Radek; Crivelli, Alain; Shumka, Spase; Wilson, Iain F; Vukić, Jasna; Berrebi, Patrick; Kotlík, Petr

    2010-05-01

    Freshwater fauna of ancient lakes frequently contain endemic taxa thought to have originated during the long existence of these lakes, yet uncertainties remain as to whether they represent distinct genetic lineages with respect to more widespread relatives and to the relative roles of isolation and dispersal in their evolution. Phylogenetic analyses of sequence variation at nuclear and mitochondrial genes were used to examine these issues for the freshwater fish genus Barbus in two European ancient lake systems on the Balkan Peninsula. The nuclear and mitochondrial data yielded concordant phylogeographic patterns though incomplete sorting of nuclear haplotypes between some mitochondrial clades was detected. The distributions of two currently recognized species investigated here do not match the distributions of evolutionary lineages revealed by phylogenetic analyses. The Prespa barbel, Barbus prespensis, is not endemic to the lakes Prespa as previously thought but is instead found to be widespread in the south-eastern Adriatic Sea basin, with a distribution largely corresponding to the basin of the now extinct Lake Maliq historically connected with Lake Prespa. On the other hand, a cryptic phylogenetic subdivision in a widespread species, B. rebeli, was discovered to be more distant from B. rebeli than from other Barbus species and to be endemic to the system of connected lakes Ohrid and Shkodra. The division coincides with the hydrogeographical boundary delimiting distributions of other freshwater fishes, and we suggest that this newly discovered evolutionary lineage represents a distinct species. These findings support the emerging pattern that endemic taxa have evolved not through isolation of individual lakes, but in systems of currently and historically interconnected lakes and their wider basins. PMID:20139017

  7. DNA AND PROTEIN RECOVERY FROM WASHED EXPERIMENTAL STONE TOOLS

    Science.gov (United States)

    DNA residues may preserve on ancient stone tools used to process animals. We studied 24 stone tools recovered from the Bugas-Holding site in northwestern Wyoming. Nine tools that yielded DNA included five bifaces, two side scrapers, one end scraper, and one utilized flake. The...

  8. A Preliminary Study of Guizhou’s Ethnic Ancient Books Personnel Training Modes%贵州省民族古籍人才培养模式初探

    Institute of Scientific and Technical Information of China (English)

    欧阳伟华

    2015-01-01

    The number and quality of competent persons has decisive effcct on the thriving of the country or a nation. Since 1980 s Guizhou province has achieved a lot in rescuing ancent books. But for the further devel-opment of ethnic ancient books business, it is necessary to sort out in the national translation and study of an-cient books, which requires a large number of ethnic ancient books professionals, the current national ancient talent far cannot satisfy the need, thus strengthen the cultivation of ethnic ancient books professionals is a daunting task for a long time. Through higher education training, on-the-job training, cultivation and master apprentice training , we can caltivate more professional in this field .%一个国家或民族人才的多寡优劣直接决定着这个国家或民族的兴衰存亡。20世纪80年代以来贵州省在民族古籍的抢救、普查和整理等方面取得了累累硕果,但要让民族古籍事业向纵深发展,必须对已经整理出来的民族古籍翻译和研究,这就需要大量的民族古籍专业人才,目前的民族古籍人才远远不能满足需要,因此加强民族古籍专业人才的培养是一项艰巨而长期的任务。可以采取高等教育培养、在职培训培养和师傅带徒弟培养等多渠道、多层次、灵活多变的方式来培养民族古籍人才。

  9. Molecular study of DNA radioprotection by thiols

    Energy Technology Data Exchange (ETDEWEB)

    Savoye, C.; Charlier, M.; Spotheim-Maurizot, M. [Centre National de la Recherche Scientifique (CNRS), 45 - Orleans-la-Source (France); Swenberg, C. [ACRD, Armed Forces Radiobiology Research Institute, Bethesda (United States); Sabattier, R. [Centre Hospitalier Regional d`Orleans, 45 (France)

    1997-03-01

    Polyamines (PA) are natural components of mammalian cells, essential for growth processes. Since a decrease of the cellular level of PA increases the effect of radiotherapy on tumour cells, we have supposed that PA may act as DNA radioprotectors. The search of non-toxic agents that protect specifically normal cells led to the discovery of the agent WR-2721 used now in cancer cancer therapy under the name Ethyol (Amifostine) and of the agent WR-151327. Both have a chemical structure close to that of natural PA. The main radioprotective metabolites of these agents are the thiols WR>61065 and WR-151326. We have compared here here the protective effects of these thiols to those of another simpler thiol, the cysteamine, and of a related PA, the putrescine, on the number and location of fast neutrons-induced DNA strand breaks. (authors)

  10. 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

    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.

  11. 水芹的本草考证%Textual study on Oenanthe javanica documented in ancient Chinese medicinal literatures

    Institute of Scientific and Technical Information of China (English)

    黄正明; 杨新波; 曹文斌

    2001-01-01

    Object To obtain a deeper understanding of the origin andvarieties of Oenanthe javanica (Bl.) DC. for therapeutic use. Methods Literatures documented through generations of practical experiences were retrieved with simultaneous field study and laboratory identification of chemical constituents and pharmacological actions for comparison. Results The growth pattern and its therapeutic efficacy in different indications as recorded in the ancient literatures were found to be basically identical to that obtained by modern scientific research. Conclusion Only Oenanthe javanica (BL.) DC. of the Umbelliferae family can be considered as the orthodox product for therapeutic use.%目的 通过对水芹的本草学研究,考证其基源及药用品种。方法 查阅有关历代文献,实地考察和应用现代科学技术对水芹的化学成分和药理作用等进行研究。结果 表明历代本草文献中所记载水芹的生长特征及其功能主治与现代研究结果基本一致。结论 水芹基源仅伞形科水芹属植物水芹Oenanthejavanica(B1.)DC.为药用正品。

  12. Study and characterization of an ancient European flint white maize rich in anthocyanins: Millo Corvo from Galicia.

    Directory of Open Access Journals (Sweden)

    Chiara Lago

    Full Text Available 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.

  13. XRF study of archaeological and metallurgical material from an ancient copper-smelting site near Ein-Yahav, Israel.

    Science.gov (United States)

    Shalev, S; Shilstein, S Sh; Yekutieli, Yu

    2006-12-15

    A movable XRF instrument (a bench-top designed machine modified to work in the field for archaeological purposes) was used for analysis of artifacts and sediments during the field study (01-07 April 2003) of a small copper-smelting site in the Negev (about 30km west of the Feinan complex of ancient copper mines and smelting sites in Jordan). The site consists of a relatively small hill with blackened slopes, covered mainly by crushed copper slag. The surface collection of datable objects (i.e. pottery shards and stone tools) indicated that the site had functioned at the end of the Early Bronze Age and during the Roman/Byzantine time. The analysis of Cu concentration in the ash and in the ground as well as the analysis of ore and slag, were used as markers for the identification of the operation centers and for locating the remains of the smelting devices used at the end of the Early Bronze Age for smelting copper. The ore in use typically contained 35-45% Cu, up to 1% Mn and up to several percent Fe. The slag contained 13-20% Mn and 1-5% Cu and Fe. From these results we are able to estimate the Cu production scale during the first and most active period on this site, at the end of the Early Bronze Age. PMID:18970859

  14. Cytotoxic, DNA binding, DNA cleavage and antibacterial studies of ruthenium-fluoroquinolone complexes

    Indian Academy of Sciences (India)

    Mohan N Patel; Hardik N Joshi; Chintan R Patel

    2014-05-01

    Six new Ru(II) and Ru(III) complexes have been synthesized and characterized by elemental analysis, LC-MS, electronic spectra, IR spectra and magnetic moment measurements. 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 electrophoresis. The experimental results show that all the complexes can bind to DNA via partial intercalative mode. The b values of complexes were found in the range 2.14 × 104 to 2.70 × 105 M-1. 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 g mL-1.

  15. 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.

  16. Genome-wide patterns of selection in 230 ancient Eurasians.

    Science.gov (United States)

    Mathieson, Iain; Lazaridis, Iosif; Rohland, Nadin; Mallick, Swapan; Patterson, Nick; Roodenberg, Songül Alpaslan; Harney, Eadaoin; Stewardson, Kristin; Fernandes, Daniel; Novak, Mario; Sirak, Kendra; Gamba, Cristina; Jones, Eppie R; Llamas, Bastien; Dryomov, Stanislav; Pickrell, Joseph; Arsuaga, Juan Luís; de Castro, José María Bermúdez; Carbonell, Eudald; Gerritsen, Fokke; Khokhlov, Aleksandr; Kuznetsov, Pavel; Lozano, Marina; Meller, Harald; Mochalov, Oleg; Moiseyev, Vyacheslav; Guerra, Manuel A Rojo; Roodenberg, Jacob; Vergès, Josep Maria; Krause, Johannes; Cooper, Alan; Alt, Kurt W; Brown, Dorcas; Anthony, David; Lalueza-Fox, Carles; Haak, Wolfgang; Pinhasi, Ron; Reich, David

    2015-12-24

    Ancient DNA makes it possible to observe natural selection directly by analysing samples from populations before, during and after adaptation events. Here we report a genome-wide scan for selection using ancient DNA, capitalizing on the largest ancient DNA data set yet assembled: 230 West Eurasians who lived between 6500 and 300 bc, including 163 with newly reported data. The new samples include, to our knowledge, the first genome-wide ancient DNA from Anatolian Neolithic farmers, whose genetic material we obtained by extracting from petrous bones, and who we show were members of the population that was the source of Europe's first farmers. We also report a transect of the steppe region in Samara between 5600 and 300 bc, which allows us to identify admixture into the steppe from at least two external sources. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. PMID:26595274

  17. From Mexico to Brazil, from Ancient China to New Confucianism: Sinological Studies in Latin America

    Directory of Open Access Journals (Sweden)

    Barbara Pihler Ciglič

    2016-05-01

    Full Text Available The paper presents a general framework of the beginnings and development of sinological studies in geographically, politically and culturally very diverse Latin America, and highlights current issues and trends therein. In the 21st century the fast- growing relationship between China and Latin America is reflected in the accelerated creation of diverse economic-political, academic and educational institutions, publications and in the organization of numerous international conferences and scientific symposia. The study analyses the development of Confucian Studies – first, through reviewing the most important translations and publications of the 20th century in connection with “the intellectual movement” in Latin America, and, second, through an illustrative commentary on the most renowned scientific articles and monographs. The study initially focuses on Mexico, the country with the longest sinological tradition in Latin America, where the Centro de Estudios de Asia y África at El Colegio de México is still regarded to be one of the most prominent Latin American centres for Asian and African Studies. The focus then shifts to Brazil, which seems, of all the countries in Latin America, to have the least well-established tradition in Chinese studies and Confucianism. The central premise of sinological and Confucian studies in these two countries is presented through the prism of major studies of two modern sinologists, Chen Yong (El Colegio de México and André Bueno (Universidade do Estado de Rio de Janeiro.

  18. Study of post traumatic stress disorder among inhabitants of ancient Οlympia exposed to 2007 fire

    Directory of Open Access Journals (Sweden)

    Gritzani I.

    2013-07-01

    Full Text Available Introduction: Post Traumatic Stress Disorder (PTSD is the most often studied and most frequent and debilitating psychological disturbance that occurs after natural disasters. The aim of this study was to investigate the role of fire on post traumatic stress, psychopathology and hostility among individuals who had been exposed to, and to evaluate the differences of the above psychological parameters, in contrast to those who had not experienced.Material and Method: 174 healthy individuals participated to the present study. Subjects were classified into two groups- inhabitants of ancient Olympia exposed to fire disaster and not being exposed in fire residents of Nauplio- based on their personal statements. The first group constituted of 83 individuals who reported being exposed to the fire, while the other group constituted of 91 individuals who reported not being exposed to such a traumatic experience. The questionnaire PTSD Checklist Civilian Version (PCL (Weathers, Litz, Huska & Keane, 1994, the questionnaire (SCL-90 (Derogatis, 1977 and the questionnaire (HDHQ(Caine et al. 1967 were used to gather the data. Results: Higher levels of post traumatic stress and a tendency to develop a extrapunitiveness hostile attitude were observed among participants who had reported being exposed to fire natural disaster. Psychopathology in those participants was not proved, apart from the depression subscale. Demographic factors such as middle age and female gender seemed to be correlated with PTSD, psychopathology and hostility after fire. Conclusion: Findings illustrated the multidimensional nature of natural disasters. Longitudinal studies are needed to examine the range of factors associated with the development and/or persistence of PTSD or related disorders from the chronic phase of psychological reactivity.

  19. Studies on the interaction of cupric isonicotinohydrazide with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Divakar, S.; Vasudevachari, M.B.; Antony, A.; Easwaran, K.R.K.

    1987-06-30

    The interaction of cupric isonicotinohydrazide (Cu/sup II/INH), antiviral compound, with calf thymus DNA was investigated by circular dichroism (CD) and nuclear magnetic resonance (NMR). Gel electrophoresis of DNA incubated with Cu/sup II/INH showed cleavage of DNA to various extents. This cleavage was found to be time and concentration dependent. In the presence of Cu/sup II/INH the positive CD band at 274 nm disappeared and the negative band at 246 nm showed a decrease in the mean residual ellipticity value, indicating binding of Cu/sup II/INH to DNA. /sup 31/P NMR studies indicated that the binding of copper in Cu/sup II/INH is to the phosphate oxygen of the DNA backbone. The binding of Cu/sup II/INH was also found to be reversible. Addition of ethylenediaminetetraacetic acid to the Cu/sup II/INH-DNA complex resulted in breaking of the complex and restoring the original structure features of the B family of DNA in the resulting fragments. At the concentration level of Cu/sup II/INH employed, both CuSO/sub 4/ and INH independently did not show any interaction with DNA.

  20. Ancient DNA of the extinct lava shearwater (Puffinus olsoni from the Canary Islands reveals incipient differentiation within the P. puffinus complex.

    Directory of Open Access Journals (Sweden)

    Oscar Ramirez

    Full Text Available BACKGROUND: The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands. METHODOLOGY/PRINCIPAL FINDINGS: We used bones of the two extinct Canary shearwaters (P. olsoni and P. holeae to obtain genetic data, for use in providing insights into the differentiation process within the genus Puffinus. Although mitochondrial DNA (mtDNA cytochrome b sequences were successfully retrieved from four Holocene specimens of the extinct Lava shearwater (P. olsoni from Fuerteventura (Canary Islands, the P. holeae specimens yielded no DNA. Only one haplotype was detected in P. olsoni, suggesting a low genetic diversity within this species. CONCLUSIONS: The phylogenetic analyses based on the DNA data reveal that: (i the "Puffinus puffinus complex", an assemblage of species defined using osteological characteristics (P. puffinus, P. olsoni, P. mauretanicus, P. yelkouan and probably P. holeae, shows unresolved phylogenetic relationships; (ii despite the differences in body size and proportions, P. olsoni and the extant P. puffinus are sister species. Several hypotheses can be considered to explain the incipient differentiation between P. olsoni and P. puffinus.

  1. 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.

  2. A comparative study between wild ancient tea and tea garden tea%野生古茶树茶与茶园茶的比较研究

    Institute of Scientific and Technical Information of China (English)

    鲍晓华; 董玄; 潘思轶

    2012-01-01

    The appearance, liquor color, taste and aroma of wild ancient tea and tea garden tea were evaluated and determined by sensory evaluation and chemical analysis method. Both of the appearances were stripy. The color of ,dried wild ancient tea was red-yellow and liquor color is yellow-red, while the dried tea garden tea was green-black and liquor color was green-yellow. The wild ancient tea tasted soft, sweet, and a little bitter, while the tea garden tea was much bitter and slightly sweet at the beginning. The contents of tea polyphenols and flavonoid compounds of both were the same, which were about 28. 9% and 7%. The five kinds of catechins which were determined in wild ancient tea were two times more of that in tea garden tea. The tea garden tea's caffeine content was nearly two times more than wild ancient tea. The content of free amino acids ( Aas) in wild ancient tea was higher, while the tea garden tea had a higher content (4. 60% ) than wild ancient tea (3. 82% ) in soluble sugar. Fifty-eight kinds of aroma compounds were measured in wild ancient tea and 74 kinds of aroma compounds in tea garden tea, and there were 12 common components in both. In all, the wild ancient tea was far superior to the tea garden tea, but the effects of catechins and aroma compounds on the human body needed to be further studied.%采用感官审评和化学分析手段,对野生古茶树茶和茶园茶的外形、颜色、滋味、香气等进行审评、测定和比较.两者都为条索,在颜色方面,野生古茶树茶的干品偏向红黄,汤色黄红,茶园茶的干品呈绿黑,茶汤绿黄色;滋味方面,野生古茶树茶苦涩味较淡,醇和,回甘,茶园茶苦涩味比之更盛,味微短,入口略甜.茶多酚、黄酮类化合物两者基本一样,分别是28.9%左右和7%左右,测定的5种儿茶素,茶园茶是野生古茶树茶的两倍多,咖啡碱茶园茶是野生古茶树茶的约两倍,游离氨基酸野生古茶树茶比茶园茶高,

  3. 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...

  4. 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...

  5. Moessbauer spectroscopy and x-ray fluorescence study of ancient pottery from the New Kingdom excavated at Mit-Rahina (Memphis)

    International Nuclear Information System (INIS)

    Ancient pottery sherds from excavations at Mit Rahina Region from the New Kingdom were studied by Moessbauer and x-ray fluorescence spectroscopy. Based on the data the provenance of the clay used for the production of each type of these potteries and the manufacturing technology were determined. A group of potteries was found which had been imported from the neighbouring region. (author) 8 refs.; 7 figs.; 2 tabs

  6. A Moessbauer study of an ancient pottery figure (Western-Han Dynasty)

    International Nuclear Information System (INIS)

    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.)

  7. 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…

  8. A Stylistic Study into the Musicality of the English Translation of the An-cient Chinese Poem“Jianjia”

    Institute of Scientific and Technical Information of China (English)

    HUANG Qiu-yue

    2014-01-01

    “Jianjia”(“蒹葭”),one of the most famous poems in Shijing (《诗经》), is characterized by balanced sound patterns and euphonious rhythm. Investigation into the stylistic elements in both the source text and the English translation of“Jianjia”shows us the musicality in ancient Chinese poetry and its limits of translatability.

  9. Scattered organic matter of ancient black shale masses and technique for studying it. [USSR

    Energy Technology Data Exchange (ETDEWEB)

    Volkova, I.B.; Bogdanova, M.V.

    1981-01-01

    Methods of carbon petrographic and carbon chemical investigation of the insoluble part of scattered organic matter with the use of isotope, thermal, x-ray structural analyses and scanning electron microscopy are employed to show the biogenic primary-sedimentary origin of the carboniferous substance. Its degree of transformation is studied. For the first time descriptions are made of the residue of algae in the polished lump section in the schungite-bearing rocks of Kareliya and shales of the Kola Peninsula. The degree of metamorphic transformattion of organic matter of black shales is defined according to the scale developed for humus coal.

  10. PIXE/RBS Studies on Ancient Pottery from Jinsha Ruins Site of Chengdu

    International Nuclear Information System (INIS)

    Jinsha Ruins Site, Chengdu, China, spanned the age from late Shang Dynasty to Western Zhou Dynasty (B.C.1200-B.C.650), was generally considered as the inheritance of Sanxingdui Culture. This paper focuses on the studies of the pottery unearthed from Jinsha. PIXE and RBS experimental setup was preliminarily established and these techniques were employed to find the elemental composition of those collected shards. From the results of factor analysis,the differences can be seen among pottery shards from different stratums, which may suggest that the clay gathered from different sites was used in different periods. The authors also found that there was no obvious assemblage phenomenon in the factor analysis among the pottery shards from different pits, this may be the evidence for 'no special clay for special use'. (authors)

  11. Study of ancient Islamic gilded pieces combining PIXE-RBS on external microprobe with sem images

    Energy Technology Data Exchange (ETDEWEB)

    Ynsa, M.D.; Gutierrez, P.C.; Enguita, O. [Universidad Autonoma de Madrid, Centro de Micro-Analisis de Materiales (CMAM), Madrid (Spain); Chamon, J.; Pardo, A.I.; Arroyo, M.; Barrio, J. [Universidad Autonoma de Madrid, Dpto. Prehistoria y Arqueologia, Madrid (Spain); Gomez-Morilla, I. [Technische Universitaet Dresden, Institute fuer Stroemungsmechanik, Dresden (Germany); Ferretti, M. [CNR - Istituto per le Tecnologie Aplicate ai Beni Culturali, Monterotondo St., Roma (Italy); Climent-Font, A. [Universidad Autonoma de Madrid, Centro de Micro-Analisis de Materiales (CMAM), Madrid (Spain); Universidad Autonoma de Madrid, Dpto. Fisica Aplicada C-12, Madrid (Spain)

    2008-07-15

    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.)

  12. 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

    Recovering detailed morphological information from archaeological or paleontological material requires extensive hands-on time. Creating 3D scans based on e.g. computed tomography (CT) will recover the geometry of the specimen, but can inflict bimolecular degradation. Instead, we propose a fast......, 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...

  13. ARCHAEOMETRICAL STUDIES ON WALL PAINTINGS OF ZEUGMA (GAZİANTEP ANCIENT SITEABSTRACT

    Directory of Open Access Journals (Sweden)

    Şahinde DEMİRCİ

    2011-06-01

    Full Text Available In this study, Zeugma wall paintings and related materials including sediment and stone/rock had been examined. Samples were examined to get their raw material characteristics, mineralogical and chemical compositions, and microstructural properties using various analytical techniques. Sediments were calcereous soils of Eocene. Rock types of stones were mainly limestone which had 3 subgroups: micritic, biomicritic and recrytallised micritic limestones. The source of the limestones should be from the local formation. Binder of mortar samples were lime, aggregate materials come from the river deposites of Euphrates. Mural painting samples have different layers; pigment layer at the top, intonaco layer underneat, and single or double rather coarse grained arriccio layer(s below intonaco layer. The mural painting technique was fresco technique. Calcite was common mineral identified for all pigments of different colours. The sources of white, black and green coloured pigments were found as vaterite, graphite and malachite respectively. The sources of yellow coloured pigments were identified as ankerite, siderite and goethite. The red colours were identified as hematite, jasper and red earth/ochre. Jasper and vaterite, jasper and calcite, red earth/ochre and calcite, and hematite were the colour forming minerals of pink coloured pigments.

  14. 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.

  15. 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...

  16. Numerical study on a disordered model for DNA denaturation transition

    OpenAIRE

    Coluzzi, Barbara

    2005-01-01

    We study numerically a disordered version of the model for DNA denaturation transition (DSAW-DNA) consisting of two interacting SAWs in 3d, which undergoes a first order transition in the homogeneous case. The two possible values eAT and eGC of the interactions between base pairs are taken as quenched random variables distributed with equal probability along the chain. We measure quantities averaged over disorder such as the energy density, the specific heat and the probability distribution o...

  17. 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.

  18. 古代时期中国地名的英译研究%Studies on English Translation of Chinese Place Names in Ancient Times

    Institute of Scientific and Technical Information of China (English)

    陈剑

    2014-01-01

    Nowadays,the systematic research in mainland China on the English translation of Chinese place names in ancient times (from Song and Yuan dynasty to early Qing dynasty)is relatively rare.The paper mainly analyzes and studies on Chinese ancient maps in English version existing in China and abroad.The English translation of Chinese place names in ancient times is mainly based on the transliteration of local dialects,while the spelling method is gradually in the transition from copying the translation of other languages to spelling with the language factors and characteristics of English.The relatively full English translation method of Chinese place names in ancient times is initially formed.%现阶段国内对古代时期(宋元时期至清早期)中国地名英译的系统性研究相对较少。通过对国内外现有英文版中国古地图资料进行分析和研究,发现古代时期我国地名的英译以对各地方言的音译为主,拼写方法由最初照搬其他语系、语族语言的译名,逐步向以英语自身的语言因素和特点进行拼写过渡,最终形成了比较完整的古代时期我国地名英文翻译方法。

  19. Stretching and imaging studies of single DNA molecules

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    DNA molecules were stretched on silanized mica surface with the molecular combing technique, and detected with fluorescence microscopy and atomic force microscopy. Meantime, DNA molecules were stretched with a modified dynamic molecular combing technique and studied with atomic force microscopy. The results indicate that, compared with the dynamic molecular combing technique, the modified dynamic molecular combing technique has advantages of less-sample demand and less contamination to sample; as compared with the molecular combing technique, it has better aligning effect and reproducibility. Combination of this kind of DNA molecular manipulating technique with the single DNA molecule detecting technique by atomic force microscopy and fluorescence microscopy will play an important role in the basic research of molecular dynamics and the application of gene research.

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

    OpenAIRE

    Eveson J Paige; Deagle Bruce E; Jarman Simon N

    2006-01-01

    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 quantitativ...

  1. 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.

  2. 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.

  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. Electrochemical behavior of antioxidants: Part 3. Electrochemical studies of caffeic Acid–DNA interaction and DNA/carbon nanotube biosensor for DNA damage and protection

    Directory of Open Access Journals (Sweden)

    Refat Abdel-Hamid

    2016-05-01

    Full Text Available Multi-walled carbon nanotubes-modified glassy carbon electrode biosensor was used for electrochemical studies of caffeic acid–dsDNA interaction in phosphate buffer solution at pH 2.12. Caffeic acid, CAF, shows a well-defined cyclic voltammetric wave. Its anodic peak current decreases and the peak potential shifts positively on the addition of dsDNA. This behavior was ascribed to an interaction of CAF with dsDNA giving CAF–dsDNA complex by intercalative binding mode. The apparent binding constant of CAF–dsDNA complex was determined using amperometric titrations. The oxidative damage caused to DNA was detected using the biosensor. The damage caused by the reactive oxygen species, hydroxyl radical (·−OH generated by the Fenton system on the DNA-biosensor was detected. It was found that CAF has the capability of scavenging the hydroxide radical and protecting the DNA immobilized on the GCE surface.

  5. Genetic diversity among ancient Nordic populations.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available 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, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among 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 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 for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

  6. 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...

  7. The ginseng of ancient herbalism research study%古之人参的本草学考证的研究

    Institute of Scientific and Technical Information of China (English)

    方琪; 毛泽玲

    2015-01-01

    From the ginseng of ancient origin and ginseng in literature are summarized, in order to solve the ginseng campanulaceae codonopsis or five plus families and ginseng.%从人参的古今产地及人参的文献资料中进行了综述,以期能够解决人参是桔梗科党参还是五加科人参之争。

  8. Sounds of Gǝʿǝz – How to Study the Phonetics and Phonology of an Ancient Language

    OpenAIRE

    Weninger, Stefan

    2011-01-01

    The phonology belongs to the basic structures of a language. Knowing the sounds of the phonemes of a language is essential for the grammar, etymology or classification of a given language. For ancient languages (extinct or classical), phonology is always problematic, for obvious reasons. In this paper, various approaches are evaluated and combined that can shed light on how Gəʿəz might have sounded in Aksumite times: transcriptions in contemporary language, transcriptions and loanwords from c...

  9. Time of flight Laue fiber diffraction studies of perdeuterated DNA

    Energy Technology Data Exchange (ETDEWEB)

    Forsyth, V.T.; Whalley, M.A.; Mahendrasingam, A.; Fuller, W. [Keele Univ. (United Kingdom)] [and others

    1994-12-31

    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.

  10. 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

  11. 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.

  12. TYPES OF DNA USED IN SPECIATION AND PHYLOGENY STUDIES

    Directory of Open Access Journals (Sweden)

    Laura Buburuzan

    2007-12-01

    Full Text Available The present paper represents a synthesis of the main types of molecular markers used in contemporary phylogeny and phylogeography studies. Our purpose is also to reveal the recent discovered role of nuclear DNA polymorphic loci in the studies of filiation.

  13. Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia.

    Science.gov (United States)

    Rannamäe, E; Lõugas, L; Niemi, M; Kantanen, J; Maldre, L; Kadõrova, N; Saarma, U

    2016-04-01

    Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations. PMID:26805771

  14. 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

  15. Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

    International Nuclear Information System (INIS)

    Highlights: • Energetics of the interaction of proflavine with DNA has been studied. • The binding reaction was favored by both negative enthalpy and positive entropy. • Enthalpy–entropy compensation phenomenon was observed. • Non-polyelectrolytic forces played a dominant role in the binding process. • Proflavine enhanced the thermal stability of DNA remarkably. - Abstract: The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 105 · M−1 at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation

  16. Molecular analysis of ancient caries.

    Science.gov (United States)

    Simón, Marc; Montiel, Rafael; Smerling, Andrea; Solórzano, Eduvigis; Díaz, Nancy; Álvarez-Sandoval, Brenda A; Jiménez-Marín, Andrea R; Malgosa, Assumpció

    2014-09-01

    An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains.

  17. A Theoretical and Experimental Study of DNA Self-assembly

    Science.gov (United States)

    Chandran, Harish

    The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation. A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible. We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. We simulate DNA circuits by

  18. Esotericism Ancient and Modern

    OpenAIRE

    Frazer, Michael

    2006-01-01

    Leo Strauss presents at least two distinct accounts of the idea that the authors in the political-philosophical canon have often masked their true teachings. A weaker account of esotericism, dependent on the contingent fact of persecution, is attributed to the moderns, while a stronger account, stemming from a necessary conflict between philosophy and society, is attributed to the ancients. Although most interpreters agree that Strauss here sides with the ancients, this view fails to consider...

  19. Ionic mobility in DNA films studied by dielectric spectroscopy.

    Science.gov (United States)

    Kahouli, Abdelkader; Valle-Orero, Jessica; Garden, Jean-Luc; Peyrard, Michel

    2014-09-01

    Double-helix DNA molecules can be found under different conformational structures driven by ionic and hydration surroundings. Usually, only the B-form of DNA, which is the only form stable in aqueous solution, can be studied by dielectric measurements. Here, the dielectric responses of DNA molecules in the A- and B-form, oriented co-linearly within fibres assembled in a film have been analyzed. The dielectric dispersion, permittivity and dissipation factor, have been measured as a function of frequency, strength voltage, time, temperature and nature of the counter-ions. Besides a high electrode polarization component, two relaxation peaks have been observed and fitted by two Cole-Cole relaxation terms. In the frequency range that we investigated (0.1 Hz to 5 ·10(6) Hz) the dielectric properties are dominated by the mobility and diffusivity of the counter-ions and their interactions with the DNA molecules, which can therefore be characterized for the A- and B-forms of DNA.

  20. Ancient human genomics: the methodology behind reconstructing evolutionary pathways.

    Science.gov (United States)

    Marciniak, Stephanie; Klunk, Jennifer; Devault, Alison; Enk, Jacob; Poinar, Hendrik N

    2015-02-01

    High-throughput sequencing (HTS) has radically altered approaches to human evolutionary research. Recent contributions highlight that HTS is able to reach depths of the human lineage previously thought to be impossible. In this paper, we outline the methodological advances afforded by recent developments in DNA recovery, data output, scalability, speed, and resolution of the current sequencing technology. We review and critically evaluate the 'DNA pipeline' for ancient samples: from DNA extraction, to constructing immortalized sequence libraries, to enrichment strategies (e.g., polymerase chain reaction [PCR] and hybridization capture), and finally, to bioinformatic analyses of sequence data. We argue that continued evaluations and improvements to this process are essential to ensure sequence data validity. Also, we highlight the role of contamination and authentication in ancient DNA-HTS, which is particularly relevant to ancient human genomics, since sequencing the genomes of hominins such as Homo erectus and Homo heidelbergensis may soon be within the realm of possibility. PMID:25601038

  1. Radioautographic DNA synthesis study on mice Mus musculus gingival epithelium

    International Nuclear Information System (INIS)

    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.)

  2. Identification of DNA polymerase molecules repairing DNA irradiated damage and molecular biological study on modified factors of mutation rate

    Energy Technology Data Exchange (ETDEWEB)

    Yamada, Koichi; Inoue, Shuji [National Inst. of Healthand Nutrition, Tokyo (Japan)

    1999-02-01

    DNA repairing polymerase has not been identified in human culture cells because the specificities of enzyme inhibitors used in previous studies were not so high. In this study, anti-sense oligonucleotides were transfected into human fibroblast cells by electroporation and several clones selected by geneticin treatment were found to express the RNA of the incorporated DNA. However, the expression was not significant and its reproducibility was poor. Then, a study on repairing mechanism was made using XP30 RO and XP 115 LO cells which are variant cells of xeroderma pigmentosum, a human hereditary disease aiming to identify the DNA polymerase related to the disease. There were abnormalities in DNA polymerase subunit {delta} or {epsilon} which consists DNA replication complex. Thus, it was suggested that the DNA replication of these mutant cells might terminate at the site containing such abnormality. (M.N.)

  3. Identification of DNA polymerase molecules repairing DNA irradiated damage and molecular biological study on modified factors of mutation rate

    International Nuclear Information System (INIS)

    DNA repairing polymerase has not been identified in human culture cells because the specificities of enzyme inhibitors used in previous studies were not so high. In this study, anti-sense oligonucleotides were transfected into human fibroblast cells by electroporation and several clones selected by geneticin treatment were found to express the RNA of the incorporated DNA. However, the expression was not significant and its reproducibility was poor. Then, a study on repairing mechanism was made using XP30 RO and XP 115 LO cells which are variant cells of xeroderma pigmentosum, a human hereditary disease aiming to identify the DNA polymerase related to the disease. There were abnormalities in DNA polymerase subunit δ or ε which consists DNA replication complex. Thus, it was suggested that the DNA replication of these mutant cells might terminate at the site containing such abnormality. (M.N.)

  4. Correlation between chemical composition of dental calculus and bone samples in ancient human burials: perspectives in paleonutritional studies

    International Nuclear Information System (INIS)

    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

  5. ANCIENT BREAD STAMPS FROM JORDAN

    OpenAIRE

    Kakish, Randa

    2014-01-01

    Marking bread was an old practice performed in different parts of the old world. It was done for religious, magical, economic and identification purposes. Bread stamps differ from other groups of stamps. Accordingly, the aim of this article is to identify such stamps, displayed or stored, in a number of Jordanian Archaeological Museums. A col-lection of twelve ancient bread stamps were identified and studied. Two of the stamps were of unknown provenance while the others came from al-Shuneh, D...

  6. Physico-chemical characterization of mortars as a tool in studying specific hydraulic components: application to the study of ancient Naxos aqueduct

    Science.gov (United States)

    Maravelaki-Kalaitzaki, P.; Galanos, A.; Doganis, I.; Kallithrakas-Kontos, N.

    2011-07-01

    Mortars and plasters from the ancient aqueduct on the island of Naxos, Greece, were studied with regard to mineralogical and chemical composition, grain size distribution, raw materials and hydraulic properties, in order to assess their characteristics and design compatible repair mortars. The authentic materials contained lime, crushed-brick, siliceous and calcitic aggregates, in different proportions according to mortar type. Crushed-bricks fired at low temperatures and lightweight volcanic aggregates contained amorphous phases, which upon reaction with lime yielded hydraulic components capable of protecting the construction from the continuous presence of water. Hydraulic calcium silicate/aluminate hydrates, the proportions and the perfect packing of the raw materials, along with the diligent application justify the longevity and durability of the studied samples. The hydraulic properties of samples were pointed out through (a) the well-established CO2/H2O ratio derived from the thermogravimetric analysis and (b) by introducing two powerful indices issued from the chemical analysis, namely CaOhydr and soluble SiO2 hydr. These indices improved the clustering of hydraulic mortars and provided better correlation between mortars, plasters and their binders. By comparing grain size distribution and hydraulicity indices it was possible to distinguish among the construction phases. Based on this study, repair mortars were formulated by hydraulic lime, siliceous sand, calcareous and crushed-brick aggregates, with the optimal water content, ensuring optimum workability and compatible appearance with the authentic ones.

  7. Accounting for population stratification in DNA methylation studies.

    Science.gov (United States)

    Barfield, Richard T; Almli, Lynn M; Kilaru, Varun; Smith, Alicia K; Mercer, Kristina B; Duncan, Richard; Klengel, Torsten; Mehta, Divya; Binder, Elisabeth B; Epstein, Michael P; Ressler, Kerry J; Conneely, Karen N

    2014-04-01

    DNA methylation is an important epigenetic mechanism that has been linked to complex diseases and is of great interest to researchers as a potential link between genome, environment, and disease. As the scale of DNA methylation association studies approaches that of genome-wide association studies, issues such as population stratification will need to be addressed. It is well-documented that failure to adjust for population stratification can lead to false positives in genetic association studies, but population stratification is often unaccounted for in DNA methylation studies. Here, we propose several approaches to correct for population stratification using principal components (PCs) from different subsets of genome-wide methylation data. We first illustrate the potential for confounding due to population stratification by demonstrating widespread associations between DNA methylation and race in 388 individuals (365 African American and 23 Caucasian). We subsequently evaluate the performance of our PC-based approaches and other methods in adjusting for confounding due to population stratification. Our simulations show that (1) all of the methods considered are effective at removing inflation due to population stratification, and (2) maximum power can be obtained with single-nucleotide polymorphism (SNP)-based PCs, followed by methylation-based PCs, which outperform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based PCs, we find that PCs based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjust for population stratification in DNA methylation studies when genome-wide SNP data are unavailable.

  8. Accounting for population stratification in DNA methylation studies.

    Science.gov (United States)

    Barfield, Richard T; Almli, Lynn M; Kilaru, Varun; Smith, Alicia K; Mercer, Kristina B; Duncan, Richard; Klengel, Torsten; Mehta, Divya; Binder, Elisabeth B; Epstein, Michael P; Ressler, Kerry J; Conneely, Karen N

    2014-04-01

    DNA methylation is an important epigenetic mechanism that has been linked to complex diseases and is of great interest to researchers as a potential link between genome, environment, and disease. As the scale of DNA methylation association studies approaches that of genome-wide association studies, issues such as population stratification will need to be addressed. It is well-documented that failure to adjust for population stratification can lead to false positives in genetic association studies, but population stratification is often unaccounted for in DNA methylation studies. Here, we propose several approaches to correct for population stratification using principal components (PCs) from different subsets of genome-wide methylation data. We first illustrate the potential for confounding due to population stratification by demonstrating widespread associations between DNA methylation and race in 388 individuals (365 African American and 23 Caucasian). We subsequently evaluate the performance of our PC-based approaches and other methods in adjusting for confounding due to population stratification. Our simulations show that (1) all of the methods considered are effective at removing inflation due to population stratification, and (2) maximum power can be obtained with single-nucleotide polymorphism (SNP)-based PCs, followed by methylation-based PCs, which outperform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based PCs, we find that PCs based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjust for population stratification in DNA methylation studies when genome-wide SNP data are unavailable. PMID:24478250

  9. Study on Architectural Landscape in Ancient Townships of West Sichuan%川西古镇建筑景观研究——以黄龙溪为例

    Institute of Scientific and Technical Information of China (English)

    杨上清; 蒋玉川; 邓强

    2012-01-01

    Through the field investigation of a typical ancient town in West Sichuan, Huanglongxi Township in Shuangliu County of Chengdu City, Fengshui orientations, characteristics of folk dwellings, the Hakka buildings and stilt-building culture in the study area were analyzed from the perspectives of geographical location, overall layout and residential culture. Representative layouts of ancient Fengshui doctrines were stressed, such as "carrying yin at back and embracing yang in front, backing on mountains and facing water" , "four gods at four directions" ( Azure Dragon in the east, White Tiger in the west, Black Tortoise in the North and Vermilion Bird in the south). Moreover, primitive architectural style and rhythm of the continuous rows of buildings, "seven streets and nine lanes" , and overhanging eaves in the ancient Huanglongxi Township were demonstrated. The study is of great referential values for the research on architectural landscapes of ancient towns hips in West Sichuan, and modern architectural landscape design.%通过对川西典型古镇成都市双流县黄龙溪的现场调研,从地理位置、整体布局、居住文化等方面,简要剖析了黄龙溪古镇的风水朝向、民居特色、客家建筑和干栏文化,强调了古代风水学上“负阴抱阳,背山面水”以及“四砂神”(即左青龙、右白虎、前朱雀、后玄武)的绝妙格局,展现了黄龙溪古镇朴实飘逸的建筑风格,“七街九镇”的建筑布局,飞檐翘角、鳞次栉比的民居韵律.对川西古镇建筑景观的研究和当今景观建筑设计具有较大的参考价值.

  10. A study of the correlation between physical activities and ancient Yi characters%身体活动与古彝文字的相关性研究

    Institute of Scientific and Technical Information of China (English)

    孙德朝

    2016-01-01

    应用人类学研究的大小传统感通思维方式,从古彝文字中筛选出24个与身体活动相关的文字,提炼出古彝文字中的身体活动元素。研究认为:古彝文字蕴含着彝族尚武民族性格气质特征、彝族个体身体活动式样、人畜和谐共有的运动式样、毕摩作毕时对身体关怀的“显隐”身体活动文化内涵、原生态竞技游艺元素、教育传承元素。身体活动不仅对人类文化和文明具有重要的语言和思想传承属性,也对文字的形成具有重要的认知特征。%By applying traditional magnitude perception thinking mode used in anthropological study, the author screened out 24 physical activity related characters from ancient Yi characters, extracted physical activity ele-ments in ancient Yi characters, and put forward the following opinions: ancient Yi characters contain the charac-teristics of martial temperament of the Yi nationality, patterns of individual physical activities of the Yi national-ity, patterns of movement harmoniously own by human beings and animals, cultural connotations of “implicit” physical activities in Bimozuobi’s care for the human body, original ecological competition and game elements, and education inheritance elements; physical activities are provided not only with important language and thought inheritance attributes for human culture and civilization, but also with important cognitive characteristics for character formation.

  11. A DNA barcoding approach in the study of tardigrades

    Directory of Open Access Journals (Sweden)

    Michele Cesari

    2013-05-01

    Full Text Available DNA barcoding is a technique proposed by Hebert and co-workers in 2003 for discriminating species through analysis of a single gene barcode locus. It aims to obtain a better taxonomic resolution than that achieved through morphological studies, and to avoid the decline in taxonomic knowledge. Today DNA barcoding is a global enterprise, and the implementation of the idea has seen a rapid rise (more than 1900 papers published to date on different organisms. Nonetheless, controversy still arises regarding barcoding and taxonomy. It is important to note that DNA barcoding does not focus on building a tree-of-life or on doing DNA taxonomy, even though sometimes it has been used for these purposes. DNA barcoding rather focuses on producing a universal molecular identification key based on strong taxonomic knowledge that should be included in the barcode reference library. In the phylum Tardigrada, DNA barcoding represents a recent approach to species identification and to help in solving taxonomic problems, especially considering the diminutive size of these animals and the paucity of morphological characters useful for taxonomy. In the framework of the MoDNA Project (Morphology and DNA, carried out by our research group in collaboration with several colleagues, we are combining the study of a fragment of the mitochondrial cytochrome c oxidase subunit I gene (cox1 with morphological data, in a wide sense (cuticular structures, chromosomes, data on sex ratio and reproduction, to form an integrative taxonomy approach for tardigrade species identification. We believe that without verified reference sequences from voucher specimens that have been authenticated by qualified taxonomists, there is no reliable library for newly generated sequences with which to be compared. Methods and protocols for standardized results are focused on obtaining tight correspondence between tardigrade morphology (and egg shell morphology, when useful, possibly both light and

  12. Correlation of DNA methylation levels in blood and saliva DNA in young girls of the LEGACY Girls study.

    Science.gov (United States)

    Wu, Hui-Chen; Wang, Qiao; Chung, Wendy K; Andrulis, Irene L; Daly, Mary B; John, Esther M; Keegan, Theresa H M; Knight, Julia; Bradbury, Angela R; Kappil, Maya A; Gurvich, Irina; Santella, Regina M; Terry, Mary Beth

    2014-07-01

    Many epidemiologic studies of environmental exposures and disease susceptibility measure DNA methylation in white blood cells (WBC). Some studies are also starting to use saliva DNA as it is usually more readily available in large epidemiologic studies. However, little is known about the correlation of methylation between WBC and saliva DNA. We examined DNA methylation in three repetitive elements, Sat2, Alu, and LINE-1, and in four CpG sites, including AHRR (cg23576855, cg05575921), cg05951221 at 2q37.1, and cg11924019 at CYP1A1, in 57 girls aged 6-15 years with blood and saliva collected on the same day. We measured all DNA methylation markers by bisulfite-pyrosequencing, except for Sat2 and Alu, which were measured by the MethyLight assay. Methylation levels measured in saliva DNA were lower than those in WBC DNA, with differences ranging from 2.8% for Alu to 14.1% for cg05575921. Methylation levels for the three repetitive elements measured in saliva DNA were all positively correlated with those in WBC DNA. However, there was a wide range in the Spearman correlations, with the smallest correlation found for Alu (0.24) and the strongest correlation found for LINE-1 (0.73). Spearman correlations for cg05575921, cg05951221, and cg11924019 were 0.33, 0.42, and 0.79, respectively. If these findings are replicated in larger studies, they suggest that, for selected methylation markers (e.g., LINE-1), methylation levels may be highly correlated between blood and saliva, while for others methylation markers, the levels may be more tissue specific. Thus, in studies that differ by DNA source, each interrogated site should be separately examined in order to evaluate the correlation in DNA methylation levels across DNA sources.

  13. Models of ancient sound vases

    Science.gov (United States)

    Bruel, Per V.

    2002-11-01

    Models were made of vases described by Vitruvius in Rome in about the year 70 A.D. and of sound vases (lydpotter) placed in Danish churches from 1100-1300 A.D. Measurements of vase's resonant frequencies and damping (reradiation) verified that the model vases obeyed expected physical rules. It was concluded that the excellent acoustical quality of many ancient Greek and Roman theaters cannot be ascribed to the vases placed under their seats. This study also found that sound vases placed in Nordic churches could not have shortened the reverberation time because there are far too few of them. Moreover, they could not have covered a broad frequency range. It remains a mystery why vases were installed under the seats of ancient Greek theaters and why, 1000 years later, Danes placed vases in their churches.

  14. Deep Sequencing of RNA from Ancient Maize Kernels

    OpenAIRE

    Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen; Rasmussen, Morten; CAPPELLINI, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Alquezar Planas, David Eugenio; Penfield, Steven; Brown, Terence A.; Vielle-Calzada, Jean-Philippe; Montiel, Rafael; Jørgensen, Tina; Odegaard, Nancy; Jacobs, Michael; Arriaza, Bernardo

    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 v...

  15. Influence of a 10-Day Mimic of Our Ancient Lifestyle on Anthropometrics and Parameters of Metabolism and Inflammation: The "Study of Origin".

    Science.gov (United States)

    Pruimboom, Leo; Ruiz-Núñez, Begoña; Raison, Charles L; Muskiet, Frits A J

    2016-01-01

    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. PMID:27366752

  16. 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.

  17. 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...

  18. Progress in the study of the pottery belonging to the Ancient Advanced Neolithic of Los Castillejos (Montefrío, Granada

    Directory of Open Access Journals (Sweden)

    María Teresa Blázquez González

    2011-06-01

    Full Text Available The content of this article is an advance of the study that is being realized about the decorated ceramics belonging to the first four phases of the period I of the stratigraphy of the site known as Los Castillejos (Montefrio, Granada, ie, of the phase that has been dated in the Ancient Advanced Neolithic (5400-5150 cal BC. This study began motivated by the interest in analyzing the ceramics belonging to this stage that were excavated between 1991 and 1994, and that had remained unpublished until recently. To this end and to study the ceramic technology it has been used a methodology that includes the historiographical study of the site, the location, quantification and the weight of the pieces, the scanning and design of the ceramics, the study of the decorations and other characteristics of the ceramics and of the pieces, and laboratory analytical which results will be published in the future.

  19. Image of Landscapes in Ancient Water Towns——Case Study on Zhouzhuang and Tongli of Jiangsu Province

    Institute of Scientific and Technical Information of China (English)

    LI Yabing; ZHANG Jie; CHEN Youjun

    2006-01-01

    Researchers in several disciplines and fields agree that the image establishing has both perceptual and affective evaluations. The paper comparatively analyzes the image of landscapes in ancient water towns held by 1619 tourists after the investigations of Zhouzhuang and Tongli of Jiangsu Province. Based on the elements of the image of urban landscapes, the perceptual/cognitive image of tourist landscapes in water towns is developed including path, node,landmark, important courtyard, district and edge. Particularly the important courtyard plays the great role on the perceptive image of tourists, however, the perceptual/cognitive images of the district and the edge are obviously weak.Meanwhile, the finding showed that the affective images of tourist landscapes in Zhouzhuang differ with those of Tongli by the method of paired comparison. The main reason is that the affective images are influenced by the impressive scenery spots. Furthermore, the commercialization of streets and pollution of rivers are easy to be functioned negatively.

  20. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    International Nuclear Information System (INIS)

    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

  1. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Myungkoo

    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 7{beta}, 8{alpha}-dihydoxy-9{alpha}, l0{alpha}-epoxy-7,8,9, 10-tetrahydrobenzo[{alpha}]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, ({minus})-trans-, (+)-cis- and ({minus})-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 ( {approximately} 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant {pi}-{pi} 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{sub 2} or G{sub 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{sup 2}-dG in DNA isolated from the skin of mice treated topically with benzo[{alpha}]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{sup 2}-dG.

  2. Mechanism study of goldenseal-associated DNA damage.

    Science.gov (United States)

    Chen, Si; Wan, Liqing; Couch, Letha; Lin, Haixia; Li, Yan; Dobrovolsky, Vasily N; Mei, Nan; Guo, Lei

    2013-07-31

    Goldenseal has been used for the treatment of a wide variety of ailments including gastrointestinal disturbances, urinary tract disorders, and inflammation. The five major alkaloid constituents in goldenseal are berberine, palmatine, hydrastine, hydrastinine, and canadine. When goldenseal was evaluated by the National Toxicology Program (NTP) in the standard 2-year bioassay, goldenseal induced an increase in liver tumors in rats and mice; however, the mechanism of goldenseal-associated liver carcinogenicity remains unknown. In this study, the toxicity of the five goldenseal alkaloid constituents was characterized, and their toxic potencies were compared. As measured by the Comet assay and the expression of γ-H2A.X, berberine, followed by palmatine, appeared to be the most potent DNA damage inducer in human hepatoma HepG2 cells. Berberine and palmatine suppressed the activities of both topoisomerase (Topo) I and II. In berberine-treated cells, DNA damage was shown to be directly associated with the inhibitory effect of Topo II, but not Topo I by silencing gene of Topo I or Topo II. In addition, DNA damage was also observed when cells were treated with commercially available goldenseal extracts and the extent of DNA damage was positively correlated to the berberine content. Our findings suggest that the Topo II inhibitory effect may contribute to berberine- and goldenseal-induced genotoxicity and tumorigenicity.

  3. Studies on Aujeszky's disease using recombinant DNA technology

    International Nuclear Information System (INIS)

    The paper summarizes the results of studies carried out on the occurrence and physical state of Pseudorabies virus (PRV; Suid herpes virus 1) DNA in latently infected swine. During latency (between 7 and 52 weeks post-infection) 0.05 to 0.3 genome copies per cell were detected in different neural areas and extraneural cells of swine. During the latent state the predominant form of the PRV genome was found to represent linear, unit-length DNA. In some cases, two types of viral DNA alteration were found in the latently infected organ cells: (a) deletion of about 750 base pairs had occurred in the unique short region of PRV DNA, and (b) the abundant presence of limited portions of the viral genome. Results are also presented on the influence of a PRV glycoprotein (gI) in possibly controlling viral virulence. Avirulent PRV vaccine strains were shown not to express gI or its precursor protein. Analysis of the gI expression was further extended to other virus isolates obtained in vitro and in vivo. These data show a highly variable expression of gI in PRV, both qualitatively and quantitatively, leading to a loss of in vitro neutralization, with anti-gI monoclonal antibodies in some cases. (author)

  4. Illuminating the evolution of equids and rodents with next-generation sequencing of ancient specimens

    DEFF Research Database (Denmark)

    Mouatt, Julia Thidamarth Vilstrup

    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......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...... developments within ancient DNA research, including target enrichment capture and Next-Generation Sequencing, to address a range of evolutionary questions related to two major mammalian groups, equids and rodents. In particular we have resolved phylogenetic relationships within equids using complete mitochond...

  5. A Study on Chinese Ancient Theories of Painting and Easel Painting%中国古代画论与架上绘画研究

    Institute of Scientific and Technical Information of China (English)

    王军; 宋力

    2011-01-01

    To extend the spirit of modern art,it is necessary to have a clear knowledge and a proper understanding of traditional spirit,for the spirit of modern art is the inheritance and development of the spirit of classical art.This article summarizes the development course of Chinese ancient theories of painting and points out its most valuable part.Through the study of Chinese ancient theories of painting,artist is able to make Chinese artistic spirit and Chinese profound tradition of aesthetics embodied in their paintings.%现代艺术精神是古典艺术精神的承传与发展,要拓展现代艺术精神,需要对传统精神有一个清晰的认识和正确的理解。本文概述中国古代画论的发展历程,并指出其中最具价值的部分。艺术家通过对中国古代画论的学习,将有助于在绘画中体现中国艺术的精神、反映中国美学的深厚传统。

  6. Application of Analytic Signal and Euler Deconvolution in Archaeo-Magnetic Prospection for Buried Ruins at the Ancient City of Pelusium, NW Sinai, Egypt: A Case Study

    Science.gov (United States)

    Aziz, Akram Mekhael; Sauck, William August; Shendi, El-Arabi Hendi; Rashed, Mohamed Ahmed; Abd El-Maksoud, Mohamed

    2013-07-01

    Progress in the past three decades in geophysical data processing and interpretation techniques was particularly focused in the field of aero-geophysics. The present study is to demonstrate the application of some of these techniques, including Analytic Signal, Located Euler Deconvolution, Standard Euler Deconvolution, and 2D inverse modelling, to help in enhancing and interpreting the archeo-magnetic measurements. A high-resolution total magnetic field survey was conducted at the ancient city of Pelusium (name derived from the ancient Pelusiac branch of the Nile, and recently called Tell el-Farama), located in the northwestern corner of the Sinai Peninsula. The historical city had served as a harbour throughout the Egyptian history. Different ruins at the site have been dated back to late Pharaonic, Graeco-Roman, Byzantine, Coptic, and Islamic periods. An area of 10,000 m2, to the west of the famous huge red brick citadel of Pelusium, was surveyed using the magnetic method. The chosen location was recommended by the Egyptian archaeologists, where they suspected the presence of buried foundations of a temple to the gods Zeus and Kasios. The interpretation of the results revealed interesting shallow-buried features, which may represent the Temple's outer walls. These walls are elongated in the same azimuth as the northern wall of the citadel, which supports the hypothesis of a controlling feature such as a former seacoast or shore of a distributary channel.

  7. Study on the language of the ancient books of Yi culture%研究彝文古籍发扬彝族文化

    Institute of Scientific and Technical Information of China (English)

    梁丽娟

    2013-01-01

      彝文古籍是集民族学、民俗学、原始宗教学、历史学、文学、地理学、地名学、哲学、伦理学、修辞艺术等于一身的多学科书籍。通过对彝文古籍的价值进行研究,可以进一步发扬彝族文化,同时激发彝族人民的爱国主义精神,振兴中华文化。%The language of the ancient books is a set of ethnology, folklore, the original religion, history, literature, ge-ography, philosophy, ethics, toponymy, the art of rhetoric is a multidisciplinary books. Through the study of the language of the ancient books of value, can further promote the Yi culture, and stimulate the Yi People's spirit of patriotism, of promoting Chinese culture.

  8. Ab initio Study of Naptho-Homologated DNA Bases

    Energy Technology Data Exchange (ETDEWEB)

    Sumpter, Bobby G [ORNL; Vazquez-Mayagoitia, Alvaro [ORNL; Huertas, Oscar [Universitat de Barcelona; Fuentes-Cabrera, Miguel A [ORNL; Orozco, Modesto [Institut de Recerca Biomedica, Parc Cientific de Barcelona, Barcelona, Spain; Luque, Javier [Universitat de Barcelona

    2008-01-01

    Naptho-homologated DNA bases have been recently used to build a new type of size expanded DNA known as yyDNA. We have used theoretical techniques to investigate the structure, tautomeric preferences, base-pairing ability, stacking interactions, and HOMO-LUMO gaps of the naptho-bases. The structure of these bases is found to be similar to that of the benzo-fused predecessors (y-bases) with respect to the planarity of the aromatic rings and amino groups. Tautomeric studies reveal that the canonical-like form of naptho-thymine (yyT) and naptho-adenine (yyA) are the most stable tautomers, leading to hydrogen-bonded dimers with the corresponding natural nucleobases that mimic the Watson-Crick pairing. However, the canonical-like species of naptho-guanine (yyG) and naptho-cytosine (yyC) are not the most stable tautomers, and the most favorable hydrogen-bonded dimers involve wobble-like pairings. The expanded size of the naphto-bases leads to stacking interactions notably larger than those found for the natural bases, and they should presumably play a dominant contribution in modulating the structure of yyDNA duplexes. Finally, the HOMO-LUMO gap of the naptho-bases is smaller than that of their benzo-base counterparts, indicating that size-expansion of DNA bases is an efficient way of reducing their HOMO-LUMO gap. These results are examined in light of the available experimental evidence reported for yyT and yyC.

  9. Synthesis, Characterization, and DNA Binding Studies of Nanoplumbagin

    Directory of Open Access Journals (Sweden)

    Sheik Dawood Shahida Parveen

    2014-01-01

    Full Text Available The traditional anticancer medicine plumbagin (PLN was prepared as nanostructured material (nanoplumbagin, NPn1 from its commercial counterparts, simultaneously coencapsulating with cetyltrimethylammonium bromide or cyclodextrin as stabilizers using ultrasonication technique. Surface morphology of NPn analysed from atomic force microscopy (AFM indicates that NPn has tunable size between 75 nm and 100 nm with narrow particle size distribution. Its binding efficiency with herring sperm DNA was studied using spectral and electrochemical techniques and its efficiency was found to be more compared to the commercial microcrystalline plumbagin (PLN. DNA cleavage was also studied by gel electrophoresis. The observed results indicate that NPn1 has better solubility in aqueous medium and hence showed better bioavailability compared to its commercial counterparts.

  10. DNA interaction, antibacterial and antifungal studies of 3-nitrophenylferrocene

    International Nuclear Information System (INIS)

    We report herein DNA interactions and antimicrobial studies of 3-nitrophenylferrocene (NPF) ((eta /sup 5/-C/sub 5/H/sub 5/FeC/sub 5/H/sub 4/)C/sub 6/H/sub 5/NO/sub 2/). The DNA binding studies were carried out by using cyclic voltammetric and UV-Vis spectroscopic titrations along with viscosity measurements. The mode of interaction of the title compound was proved to be electrostatic interactions. The binding parameters like binding constant and free binding energy were determined from cyclic voltammetric and UV-Vis spectroscopic measurements showed significant interactions. The antimicrobial activity of title compound against Gram-positive bacteria (Staphylococcus aureus, Micrococcus luteus) and Gram-negative bacteria (Escherichia coli, Klebsiella pneumoniae) and fungal strains (Aspergillus niger and Aspergillus flavus) demonstrated significant activity. (author)

  11. 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

  12. 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.

  13. 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...

  14. A convenient method to generate methylated and un-methylated control DNA in methylation studies

    Directory of Open Access Journals (Sweden)

    Mehdi Manoochehri

    2013-09-01

    Full Text Available Methylated and un-methylated control DNA is an important part of DNA methylation studies. Although human and mouse DNA methylation control sets are commercially available, in case of methylation studies on other species such as animals, plants, and bacteria, control sets need to be prepared. In this paper a simple method of generating methylated and un-methylated control DNA is described. Whole genome amplification and enzymatic methylation were performed to generate un-methylated and methylated DNA. The generated DNA were confirmed using methylation sensitive/dependant enzymes, and methylation specific PCR. Control reaction assays confirmed the generated methylated and un-methylated DNA.

  15. Optimization of DNA recovery and amplification from non-carbonized archaeobotanical remains.

    Directory of Open Access Journals (Sweden)

    Nathan Wales

    Full Text Available Ancient DNA (aDNA recovered from archaeobotanical remains can provide key insights into many prominent archaeological research questions, including processes of domestication, past subsistence strategies, and human interactions with the environment. However, it is often difficult to isolate aDNA from ancient plant materials, and furthermore, such DNA extracts frequently contain inhibitory substances that preclude successful PCR amplification. In the age of high-throughput sequencing, this problem is even more significant because each additional endogenous aDNA molecule improves analytical resolution. Therefore, in this paper, we compare a variety of DNA extraction techniques on primarily desiccated archaeobotanical remains and identify which method consistently yields the greatest amount of purified DNA. In addition, we test five DNA polymerases to determine how well they replicate DNA extracted from non-charred ancient plant remains. Based upon the criteria of resistance to enzymatic inhibition, behavior in quantitative real-time PCR, replication fidelity, and compatibility with aDNA damage, we conclude these polymerases have nuanced properties, requiring researchers to make educated decisions as to which one to use for a given task. The experimental findings should prove useful to the aDNA and archaeological communities by guiding future research methodologies and ensuring precious archaeobotanical remains are studied in optimal ways, and may thereby yield important new perspectives on the interactions between humans and past plant communities.

  16. Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine-DNA adduct formation.

    Science.gov (United States)

    Agarwal, Shweta; Chadha, Deepti; Mehrotra, Ranjana

    2015-01-01

    Chloroethyl nitrosoureas constitute an important family of cancer chemotherapeutic agents, used in the treatment of various types of cancer. They exert antitumor activity by inducing DNA interstrand cross-links. Semustine, a chloroethyl nitrosourea, is a 4-methyl derivative of lomustine. There exist some interesting reports dealing with DNA-binding properties of chloroethyl nitrosoureas; however, underlying mechanism of cytotoxicity caused by semustine has not been precisely and completely delineated. The present work focuses on understanding semustine-DNA interaction to comprehend its anti-proliferative action at molecular level using various spectroscopic techniques. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy is used to determine the binding site of semustine on DNA. Conformational transition in DNA after semustine complexation is investigated using circular dichroism (CD) spectroscopy. Stability of semustine-DNA complexes is determined using absorption spectroscopy. Results of the present study demonstrate that semustine performs major-groove-directed DNA alkylation at guanine residues in an incubation-time-drug-concentration-dependent manner. CD spectral outcomes suggest partial transition of DNA from native B-conformation to C-form. Calculated binding constants (Ka) for semustine and lomustine interactions with DNA are 1.53 × 10(3) M(-1) and 8.12 × 10(3) M(-1), respectively. Moreover, molecular modeling simulation is performed to predict preferential binding orientation of semustine with DNA that corroborates well with spectral outcomes. Results based on comparative study of DNA-binding properties of semustine and lomustine, presented here, may establish a correlation between molecular structure and cytotoxicity of chloroethyl nitrosoureas that may be instrumental in the designing and synthesis of new nitrosourea therapeutics possessing better efficacy and fewer side effects. PMID:25350567

  17. A case study of ancient mortars and concretes from Umm al-Jimal, Jordan with implications for archaeological site conservation

    Science.gov (United States)

    Dunn, Edith Ann

    The excavation at Umm al-Jimal, a Late Roman-Byzantine site in northeast Jordan, yielded large amounts of fragmented mortar and concrete. These materials are relevant both to the archaeological context and to the continued care and management of the site. An analysis of the mortars and concretes can reveal the geologic origin of the raw materials, how they were processed, and how technology changed over time. This information, when viewed within the context of the inhabitational history of the site, contributes to an understanding of the site's historic development. It may also shed light on various social, economic and technological aspects of the people who manufactured these materials. The management of archaeological sites is usually designed as an afterthought to archaeological research. Unfortunately one result is that valuable information can be lost or remain uncollected. There is often a great deal of useful information present in the archaeological record which could be helpful to archaeological site conservators, engineers and planners. Specifically, a complete understanding of the site's original architectural materials provides a basis for decisions regarding the preservation and management of existing site features. Stabilization of existing standing structures cannot be accomplished without an understanding of the original materials used in their construction. In order to maximize the information available to archaeological site managers, a comprehensive site management plan must be an integral component of the archaeological research design and implementation. This requires integrating an investigation of construction materials into the original archaeological research model. The origin, manufacture, use and subsequent deterioration of these materials, as well as their archaeological context are important to the conservation plan. Ancient mortars and concretes from Umm al-Jimal proved to be complex mixtures containing both raw geologic, biological

  18. Collecting and analyzing DNA evidence from fingernails: a comparative study.

    Science.gov (United States)

    Hebda, Lisa M; Doran, Ashley E; Foran, David R

    2014-09-01

    Forensic practitioners and crime laboratories regularly collect and analyze fingernail evidence; however, the best techniques for processing such evidence have not been established. In this study, numerous aspects of fingernail evidence processing-collection of exogenous cells, transportation, purification of DNA, and STR analysis-were analyzed using fingernails harboring applied blood or epithelial cells from scratchings. Autosomal STR mixtures resulted when fingernails were soaked or swabbed, while scrapings rarely generated mixtures but exhibited allelic dropout. Y-STRs yielded single source profiles, with scrapings again showing dropout. A silica-based kit extraction recovered significantly more exogenous DNA than did organic extraction, neither of which was affected by nail polish. Swabbing nails in succession resulted in some cross-contamination from exogenous material, while transporting nails together did not, although there was loss of exogenous cells. Optimized nail processing produced complete Y-STR profiles of male volunteers from female fingernails following scratchings.

  19. Preliminary Study on Cordycepin-DNA Interaction by Raman Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    Jian Ya LING; Qin Zheng YANG; Shan Shan LUO; Yan LI; Chang Kai ZHANG

    2005-01-01

    The interaction of cordycepin with calf thymus DNA was investigated at physiological pH with drug/DNA molar ratio of 8. The Raman spectroscopy results indicated that the intercalation of high concentration cordycepin and the interaction of cordycepin with PO2 group led to a major reduction of B-form DNA structure in favor of A-form DNA.

  20. Methods for High-throughput Characterisation of Environmental DNA

    DEFF Research Database (Denmark)

    Andersen, Kenneth

    three, a study is designed to test the performance of alternative DNA extraction protocols, in order to maximise DNA yields from plant macrofossils. Furthermore, the precision and efficiency of PCR amplification of ancient DNA is tested for alternative DNA polymerase enzymes, under influence of PCR...... inhibition. In chapter four, alternative DNA extraction protocols and pipelines for characterising plant eDNA are tested on samples from contrasting environments including modern, Holocene and Pleistocene sediment samples. These results are compared to pollen and macrofossil records described from earlier......This PhD thesis examines the potential of describing biodiversity of green plants (Viridiplantae), birds (Aves) and mammals (Mammalia), in the context of next-generation sequencing, from the DNA that all organisms segregate into the environment (eDNA). The research is based on case studies...

  1. Adoption in ancient times

    OpenAIRE

    Bisha Eugena

    2015-01-01

    Since in ancient times, in all human cultures, children transfered from biological parents to parents that want them to create family, for political alliances, for inheritance, for a future marriage, or to care for elderly parents. The practice of adoption was fairly common in different places and periods. Adoption is mention on Bible and Quran. Greeks, Romans, Egyptians and Babylonians had adoption systems.

  2. 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...

  3. 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.

  4. 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…

  5. 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…

  6. Ancient Egyptian surgical heritage.

    Science.gov (United States)

    Saber, Aly

    2010-12-01

    Egyptian medicine influenced the medicine of neighboring cultures, including the culture of ancient Greece. From Greece, its influence spread onward, thereby affecting Western civilization significantly. The oldest extant Egyptian medical texts are six papyri: The Edwin Smith Surgical Papyrus and the Ebers Medical Papyrus are famous. PMID:21208098

  7. 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 course…

  8. 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…

  9. A Vibrant Ancient City

    Institute of Scientific and Technical Information of China (English)

    WANGTONG

    2004-01-01

    LIJIANG is a small city onthe Yunnan-Guizhou Plateau in southern Chinawith an 800-year history.Word of its ancient language and music, and unique natural scenery has spread over the decades, and Lijiang is now known throughout the world. It was added

  10. Study on the Interaction between Antitumor Drug Daunomycin and DNA

    Institute of Scientific and Technical Information of China (English)

    CHENG Gui-Fang; ZHAO Jie; TU Yong-Hua; HE Pin-Gang; FANG Yu-Zhi

    2005-01-01

    A detection of anthracycline antitumor drug daunomycin (DNR) reacting with DNA in simulate metabolism in vitro has been made. It was found that DNR could react with DNA to form DNR-DNA adducts. The adduct compositions of DNR with fish sperm DNA and thermally denaturated DNA were determined. The equilibrium association constant K of DNR with fish sperm DNA is 1.98 × 105 L/mol and that of DNR with denaturated DNA is 2.29 × 104 L/mol. Semiquinone free radicals, metabolic products of DNR, can destroy both fish sperm DNA and its thermally denaturated DNA. It is verified by hyperchromic effect increase observed in UV spectrum and AFM experiments. The mechanism of DNA degradation has also been investigated. Results obtained allow one to explain the reason of side effect of anthracycline drug and give the way to depress, which were of clinical significance.

  11. Advances in structural mechanics of Chinese ancient architectures

    Institute of Scientific and Technical Information of China (English)

    Maohong YU; Yoshiya ODA; Dongping FANG; Junhai ZHAO

    2008-01-01

    Chinese ancient architectures are valuable heritage of ancient culture of China. Many historical building have been preserved up to now. The researches on the structural mechanics of ancient architectures show the different aspects of structure and mechanics. Systematical studies on the structural mechanics of ancient architectures have been carried out at Xi'an Jiaotong University since 1982. It is related with the need of repair of some national preservation relics in Xi'an. These studies include: 1) Ancient wooden structures including three national preservation relics Arrow Tower at North City Gate, City Tower at East City Gate, and Baogao Temple in Ningbao, Zhejiang province. 2) Ancient tall masonry building, the Big Goose Pagoda and Small Goose Pagoda in Xi'an. 3) Mechanical characteristics of ancient soil under foundation and city wall; the influence of caves in and under the ancient City Wall on the stability of the wall. 4) The typical Chinese ancient building at the center of city: the Bell Tower and Drum tower. 5) The behavior of Dou-Gong and Joggle joint of Chinese ancient wooden structure. 6) The mechanical behavior of ancient soils under complex stress state. A new systematical strength theory, the unified strength theory, is used to analyze the stability of ancient city wall in Xi'an and foundation of tall pagoda built in Tang dynasty. These researches also concern differential settlements of Arrow Tower and resistance to earthquake of these historical architecture heritages. Some other studies are also introduced. This paper gives a summary of these researches. Preservation and research are nowadays an essential requirement for the famous monuments, buildings, towers and others. Our society is more and more conscious of this necessity, which involves increasing activities of restoration, and then sometimes also of repair, mechanical strengthening and seismic retrofitting. Many historical buildings have in fact problems of structural strength and

  12. A study on ancient glass of Western Han Dynasty from Tangpai, Hepu, Guangxi by the lead isotopic technique

    International Nuclear Information System (INIS)

    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 SiO2, K2O, CaO, Al2O3, MgO and Na2O 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 207Pb/206Pb and 208Pb/206Pb 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

  13. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry

    Science.gov (United States)

    Flegontov, Pavel; Changmai, Piya; Zidkova, Anastassiya; Logacheva, Maria D.; Altınışık, N. Ezgi; Flegontova, Olga; Gelfand, Mikhail S.; Gerasimov, Evgeny S.; Khrameeva, Ekaterina E.; Konovalova, Olga P.; Neretina, Tatiana; Nikolsky, Yuri V.; Starostin, George; Stepanova, Vita V.; Travinsky, Igor V.; Tříska, Martin; Tříska, Petr; Tatarinova, Tatiana V.

    2016-01-01

    The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal’ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal’ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed. PMID:26865217

  14. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry.

    Science.gov (United States)

    Flegontov, Pavel; Changmai, Piya; Zidkova, Anastassiya; Logacheva, Maria D; Altınışık, N Ezgi; Flegontova, Olga; Gelfand, Mikhail S; Gerasimov, Evgeny S; Khrameeva, Ekaterina E; Konovalova, Olga P; Neretina, Tatiana; Nikolsky, Yuri V; Starostin, George; Stepanova, Vita V; Travinsky, Igor V; Tříska, Martin; Tříska, Petr; Tatarinova, Tatiana V

    2016-01-01

    The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed. PMID:26865217

  15. Comparative Study on the Immunogenicity between Hsp70 DNA Vaccine and Hsp65 DNA Vaccine in Human Mycobacterium Tuberculosis

    Institute of Scientific and Technical Information of China (English)

    DAI; Wuxing; HUANG; Hailang; YUAN; Ye; HU; Jiajie; HUANGFU; Yongmu

    2001-01-01

    The BALB/c mice were immunized with Hsp70 DNA and Hsp65 DNA vaccines in human Mycobacterium tuberculosis. Eight weeks after immunization, the eyeballs were removed, blood and spleen taken, and intraperitoneal macrophages were harvested. The lymphocytic stimulating index(SI) was used to measure the cellular proliferating ability and NO release to measure the phagocytic activity of the macrophages. With ELISA kit, the levels of interleukin-2 (IL-2) and interferon-γ(IFN-γ) in serum and the splenic lymphocytic cultured supernatant were detected. The results showed that after the mice were immunized with 100 μg/mouse of Hsp70 DNA vaccine intramuscularly, the splenic lymphocytic proliferating ability in the mice was significantly increased as compared with that in the control group, vector group and Hsp65 DNA vaccine group (P<0. 01); The contents of NO in the intraperitoneal macrophages of the mice were significantly lower than in the control group and Hsp65 DNA vaccine group (P<0. 01); The levels of serum IL-2 in the mice were significantly higher than in the control group, but there was no statistical difference between Hsp65 DNA group and vector group (P>0. 05); The contents of serum IFN-γ in the mice were significantly higher than in the control group, but significantly lower than in the Hsp65 DNA vaccine group (P<0. 05). It was indicated that immunization with Hsp70 DNA vaccine could obviously enhance the immune response, but its intensity seemed inferior to Hsp65 DNA vaccine. The anti-infection mechanisms and clinical use in the future of the vaccines of Hsp70 DNA and Hsp65 DNA are worth further studying.

  16. DNA barcoding in diverse educational settings: five case studies

    Science.gov (United States)

    Imondi, Ralph; James, Karen; Spencer, Diana; Steinke, Dirk

    2016-01-01

    Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5–18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481792

  17. DNA barcoding in diverse educational settings: five case studies.

    Science.gov (United States)

    Henter, Heather J; Imondi, Ralph; James, Karen; Spencer, Diana; Steinke, Dirk

    2016-09-01

    Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5-18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481792

  18. DNA barcoding in diverse educational settings: five case studies.

    Science.gov (United States)

    Henter, Heather J; Imondi, Ralph; James, Karen; Spencer, Diana; Steinke, Dirk

    2016-09-01

    Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5-18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.This article is part of the themed issue 'From DNA barcodes to biomes'.

  19. Identification of DNA polymerase molecules repairing DNA irradiated damage and molecular biological study on modified factors of mutation rate

    International Nuclear Information System (INIS)

    To explain the development mechanism of mutation by radiation, DNA polymerase molecules repairing DNA should be identified. In this study, plasmid was constructed in order to express anti sense DNA of DNA polymerase in the cell and it was introduced into the cell by the calcium phosphate method. Polyclonal antibody of DNA polymerase δ and ε were produced so as to prove no existence of specific polymerase molecules in the cell. When center part of polymerase ε was immunized, antiserum with high antibody titer was obtained. Near terminal C of polymerase δ was immunized, then antiserum was obtained. We discovered very interesting fact that base sequence of polymerase ε published by Syvaoja was not correct. (S.Y.)

  20. Studies on bleomycin-induced repair DNA synthesis in permeable mouse ascites sarcoma cells.

    Directory of Open Access Journals (Sweden)

    Mori,Shigeru

    1989-04-01

    Full Text Available To study the mechanism of DNA excision repair, a DNA repair system employing permeable mouse sarcoma (SR-C3H/He cells was established and characterized. SR-C3H/He cells were permeabilized with a 0.0175% Triton X-100 solution. The permeable cells were treated with 1 mM ATP and 0.11 mM bleomycin, and then washed thoroughly to remove ATP and bleomycin. Repair DNA synthesis occurred in the bleomycin-damaged, permeable SR-C3H/He cells when incubated with ATP and four deoxyribonucleoside triphosphates. The repair nature of the DNA synthesis was confirmed by the BrdUMP density shift technique, and by the reduced sensitivity of the newly synthesized DNA to Escherichia coli exonuclease III. The DNA synthesis was optimally enhanced by addition of 0.08 M NaCl. Studies using selective inhibitors of DNA synthesis showed that aphidicolin-sensitive DNA polymerase (DNA polymerase alpha and/or delta and DNA polymerase beta were involved in the repair process. The present DNA repair system is thought to be useful to study nuclear DNA damage by bleomycin, removal of the damaged ends by an exonuclease, repair DNA synthesis by DNA polymerases and repair patch ligation by DNA ligase(s.

  1. 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.

  2. A Novel SERRS Sandwich-Hybridization Assay to Detect Specific DNA Target

    OpenAIRE

    Cécile Feuillie; Maxime Mohamad Merheb; Benjamin Gillet; Gilles Montagnac; Isabelle Daniel; Catherine Hänni

    2011-01-01

    International audience In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to ...

  3. 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.

  4. Studies on the formation and stability of triplex DNA using fluorescence correlation spectroscopy.

    Science.gov (United States)

    Hu, Hongyan; Huang, Xiangyi; Ren, Jicun

    2016-05-01

    Triplex DNA has become one of the most useful recognition motifs in the design of new molecular biology tools, therapeutic agents and sophisticated DNA-based nanomaterials because of its direct recognition of natural double-stranded DNA. In this paper, we developed a sensitive and microscale method to study the formation and stability characterization of triplex DNA using fluorescence correlation spectroscopy (FCS). The principle of this method is mainly based on the excellent capacity of FCS for sensitively distinguishing between free single-strand DNA (ssDNA) fluorescent probes and fluorescent probe-double-strand DNA (dsDNA) hybridized complexes. First, we systematically investigated the experimental conditions of triplex DNA formation. Then, we evaluated the equilibrium association constants (Ka ) under different ssDNA probe lengths, composition and pH. Finally, we used FCS to measure the hybridization fraction of a 20-mer perfectly matched ssDNA probe and three single-base mismatched ssDNA probes with 146-mer dsDNA. Our data illustrated that FCS is a useful tool for the direct determination of the thermodynamic parameters of triplex DNA formation and discrimination of a single-base mismatch of triplex DNA without denaturation. Compared with current methods, our method is characterized by high sensitivity, good universality and small sample and reagent requirements. More importantly, our method has the potential to become a platform for triplex DNA research in vitro. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26377428

  5. The impact of pyrogenic C on soil functioning : a study using ancient killn soil as a model system

    Science.gov (United States)

    Rumpel, Cornelia; Naisse, Christophe; Thi Ngo, Phuong; Davasse, Bernard; Girardin, Cyril; Chabbi, Abad

    2016-04-01

    The long-term effect of pyrogenic C on the physicochemical and biological functioning of soils is poorly understood. We used ancient killn soils as model systems in order to investigate soil properties after four centuries of pyrogenic C addition. In particular we were interested in the effect of the pyrogenic C amendment on the (micro-)biological functioning of the soil. We analysed for physicochemical properties, C mineralisation as well as C dynamics following input of 13C labelled charcoal and plant residues. Our results show compared to soil without any addition, that pyrogenic C amendment led in the long term to more rapid decomposition of the new materials. The decomposition rate was increased by about 17%. In contrast,a negative priming effect reduced soil organic carbon mineralization by about 30%. Soil physicochemical poperties, i.e. clay content, cation exchange and nutrient availability were durably improved in soil amended with pyrogenic C four centuries ago. These changes probably promoted higher microbial activity and thus intense mineralization when new plant litter was added. On the contrary, charcoal was degraded at a similar rate compared to soil without pyrogenic C amendment. Thus no specific adaptation of microorganism to charcoal degradation was observed even after several centuries. The negative priming effect induced by charcoal additiion can be due to a physical protection of the soluble carbon fraction at the surfaces of new charcoal. In contrast, the negative priming effect induced by plant residue input may be more likely due to a shift of substrate utilisation by microbial communities evolving in a nutrient-rich environment. Our results demonstrate that pyrogenic C addition modifies the carbon dynamic of soils in the long-term. We propose a conceptual model accounting for the alterations of soil functioning in the long term after pyrogenic C addition.

  6. 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...

  7. Triplex and quadruplex DNA structures studied by electrospray mass spectrometry

    OpenAIRE

    Rosu, Frédéric; Gabelica, Valérie; Houssier, Claude; Colson, Pierre; De Pauw, Edwin

    2002-01-01

    DNA triplex and quadruplex structures have been successfully detected by electrospray ionization mass spectrometry (ESI-MS). Circular dichroism and UV-melting experiments show that these structures are stable in 150 mM ammonium acetate at pH 7 for the quadruplexes and pH 5.5 for the triplexes. The studied quadruplexes were the tetramer [d(TGGGGT)](4), the dimer [d(GGGGTTTTGGGG)](2), and the intramolecular folded strand dGGG(TTAGGG)(3), which is an analog of the human telomeric sequence. The a...

  8. Design a Book: A Quest in Ancient Egypt

    Science.gov (United States)

    Cooper, David

    2005-01-01

    This article describes a classroom project that combines creative writing, basic book design, and social studies content. During this project, the authors' seventh grade students research a variety of ancient Egyptian archaeological sites while reviewing course material from a unit of study on ancient Egypt, practice project management skills…

  9. Studies on the mechanism of replication of adenovirus DNA. IV. Discontinuous DNA chain propagation

    NARCIS (Netherlands)

    Vlak, J.M.; Rozijn, Th.H.; Sussenbach, J.S.

    1975-01-01

    The replication of adenovirus type 5 DNA occurs by discontinuous chain propagation via short pieces of DNA. These pieces accumulate if the infected cells are treated with hydroxyurea. They have a sedimentation coefficient of 11 S corresponding to a molecular weight of about 700,000, and they contain

  10. A Study on Memes of Culture in Translating Ancient Chinese Poems into English%古汉诗英译的文化模因研究

    Institute of Scientific and Technical Information of China (English)

    黄跃进

    2012-01-01

      从模因理论原理出发,研究汉诗英译的文化模因特征,认为古诗翻译具有形神相似模因、形似神不似模因、形不似神似模因和形神不相似模因等,在诗歌翻译的文化传播过程中,译者要更多地采用形神相似或者形不似神似模因,避免形似神不似或形神不相似模因的出现,只有这样,才能最大限度地将中国文化的精髓传递给外国读者。%  The author will study on memes of culture in translating ancient Chinese poems into English from memetic perspective and holds that translating ancient Chinese poems possess memes of meaning and spiritual conformity, meaning conformity but spiritual inconformity, meaning inconformity but spiritual conformity, as well as meaning and spiritual inconformity. The translator should employ more memes of meaning and spiritual conformity or meaning inconformity but spiritual conformity, avoiding memes of meaning and spiritual inconformity or meaning conformity but spiritual inconformity in the course of poetry translation;only in this way can the essence of Chinese culture be delivered to foreign readers to its full play.

  11. Study on the Design Concept of Ancient Peking City%古代北京城市设计意匠探微

    Institute of Scientific and Technical Information of China (English)

    李震

    2014-01-01

    元、明、清三代的北京城及其内部主要宫殿、坛庙的选址、规划与建筑设计具有明显的特征。城市的“外局-大地景观”,“内局-皇城与宫城”和“堂局-紫禁城建筑群”三个层面的设计中运用了中国传统的风水与礼制思想方法,城市及其内部主要建筑群的位置、形态与尺度的确定具有深刻的含义。归纳并总结这一古代优秀城市与建筑的设计意匠,将为当代全球化加剧背景下我国城市与建筑设计特色的建构带来启示和借鉴,具有重要意义。%There were distinctive features of site selection, layout and architecture design in ancient Peking city and its main palaces and temples in Yuan/Ming/Qing dynasty. The methods of Chinese traditional Fengshui and set of etiquette concepts had been applied in the designs of “landscape architecture”, “ imperial city and imperial palace ” and “building group in the forbidden city” , and the site, form and scale decision of the city and the main buildings had profound meanings. To analyze and summarize the design concept of this excellent ancient city and its buildings, the study has important significance and will bring inspirations and references to construct unique feature of city and architecture design in our country under the background of globalization.

  12. 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.

  13. Genetic and environmental influence on DNA strand break repair: a twin study

    DEFF Research Database (Denmark)

    Garm, Christian; Moreno-Villanueva, Maria; Bürkle, Alexander;

    2013-01-01

    Accumulation of DNA damage deriving from exogenous and endogenous sources has significant consequences for cellular survival, and is implicated in aging, cancer, and neurological diseases. Different DNA repair pathways have evolved in order to maintain genomic stability. Genetic and environmental...... factors are likely to influence DNA repair capacity. In order to gain more insight into the genetic and environmental contribution to the molecular basis of DNA repair, we have performed a human twin study, where we focused on the consequences of some of the most abundant types of DNA damage (single...... dizygotic). We did not detect genetic effects on the DNA-strand break variables in our study....

  14. Comets in ancient India

    CERN Document Server

    Gupta, Patrick Das

    2014-01-01

    The Indo-aryans of ancient India observed stars and constellations for ascertaining auspicious times for sacrificial rites ordained by vedas. It is but natural that they would have recounted in the vedic texts about comets. In Rigveda ($\\sim $ 1700 - 1500 BC) and Atharvaveda ($\\sim $ 1150 BC), there are references to dhumaketus and ketus, which stand for comets in Sanskrit. Varahamihira in 550 AD and Ballala Sena ($\\sim $ 1100 - 1200 AD) have described a large number of comets recorded by ancient seers such as Parashara, Vriddha Garga, Narada, Garga, etc. In this article, I conjecture that an episode narrated in Mahabharata of a radiant king, Nahusha, ruling the heavens, and later turning into a serpent after he had kicked the seer Agastya (also the star Canopus), is a mythological retelling of a cometary event.

  15. Studying DNA translocation in nanocapillaries using single molecule fluorescence

    CERN Document Server

    Thacker, Vivek V; Hernández-Ainsa, Silvia; Bell, Nicholas A W; Keyser, Ulrich F; 10.1063/1.4768929

    2013-01-01

    We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the accompanying characteristic ionic current blockage. By tracking the motion of individual DNA molecules in the nanocapillary perpendicular to the optical axis and using a model, we can extract an effective mobility constant for DNA in our geometry under high electric fields.

  16. 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 nucleopolyhedrovir

  17. Spectroscopic and molecular docking studies on the interaction of troxerutin with DNA.

    Science.gov (United States)

    Subastri, A; Ramamurthy, C H; Suyavaran, A; Mareeswaran, R; Lokeswara Rao, P; Harikrishna, M; Suresh Kumar, M; Sujatha, V; Thirunavukkarasu, C

    2015-01-01

    Troxerutin (TXER) is a derivative of naturally occurring bioflavonoid rutin. It possesses different biological activities in rising clinical world. The biological activity possessed by most of the drugs mainly targets on macromolecules. Hence, in the current study we have examined the interaction mechanism of TXER with calf thymus DNA (CT-DNA) by using various spectroscopic methods, isothermal titration calorimetry (ITC) and molecular docking studies. Further, DNA cleavage study was carried out to find the DNA protection activity of TXER. UV-absorption and emission spectroscopy showed low binding constant values via groove binding. Circular dichroism study indicates that TXER does not modify native B-form of DNA, and it retains the native B-conformation. Furthermore, no effective positive potential peak shift was observed in TXER-DNA complex during electrochemical analysis by which it represents an interaction of TXER with DNA through groove binding. Molecular docking study showed thymine guanine based interaction with docking score -7.09 kcal/mol. This result was compared to experimental ITC value. The DNA cleavage study illustrates that TXER does not cause any DNA damage as well as TXER showed DNA protection against hydroxyl radical induced DNA damage. From this study, we conclude that TXER interacts with DNA by fashion of groove binding.

  18. [DNA in koilocytotic dysplasia of the cervix uteri, cytophotometric studies].

    Science.gov (United States)

    Christov, K; Karageosov, I; Makaveeva, V; Kristeva, K

    1987-01-01

    In koilocytotic dysplasia of the uterine cervix the DNA content in squamous cells was quantitated by cytophotometry in histological preparations stained according to Feulgen. Three patterns of DNA distribution in the squamous cells were found. In type one (21.4%) the cells had DNA content in the diploid and paradiploid zone of the histogram. In type two (35.7%) cells with triploid and tetraploid DNA values were found, but with a conspicuous modal class of cells. In type three no modal class cells were found (42.9%). The quantitative DNA changes in squamous cells show that some of the HPV induced alterations may be regarded as precancerous.

  19. Detecting Rare Triple Heteroplasmic Substitutions in the Mitochondrial DNA Control Region:A Potential Concern for Forensic DNA Studies

    Directory of Open Access Journals (Sweden)

    Saeid Morovvati

    2011-01-01

    Full Text Available Objective: Mitochondrial DNA (mtDNA is a useful tool for population studies, identificationof humans and forensic DNA studies. The existence of several hundreds copies ofmtDNA per cell permit its extraction from minute or degraded samples. In addition, thelevel of polymorphism in the hypervariable (HV region is high enough to permit its usein human identity testing. However, the presence of several heteroplasmy might lead toambiguous results.Materials and Methods: This study was an experiental study. This study evaluated heteroplasmyin the HV region of mtDNA in blood samples of 30 Iranians who belonged to tenunrelated families from three sequential generations (grandmother, mother and daughter.Results: There were no heteroplasmic substitutions in the HV1 region, but analysis ofHV2 showed heteroplasmic substitutions in two out ten families. In the first family thegrandmother showed heteroplasmy (T/C in nucleotide positions 146 and 151, howeverit was not detected in the mother and daughter. In second family, a triple heteroplasmy(T/C was detected in the daughter in nucleotide positions 146, 151 and 295, but theseheteroplasmic substitutions were not obvious in the grandmother and mother.Conclusion: Heteroplasmy in mtDNA is not a rare phenomenon and probably exists ineveryone, but a triple heteroplasmy in one family member is a novel finding. Our resultsdemonstrate that one or two sequence differences between samples in mtDNA do notwarrant exclusion. In our study, the average nucleotide difference between unrelated personsin the HV2 region was 2.8 nucleotides, whereas there was a triple heteroplasmy inone person which was not obvious in her family.

  20. [Ancient history of Indian pharmacy].

    Science.gov (United States)

    Okuda, Jun; Natsume, Yohko

    2010-01-01

    The study of the ancient history of Indian medicine has recently been revived due to the publication of polyglot translations. However, little is known of ancient Indian pharmacy. Archaeological evidence suggests the Indus people lived a settled life approximately in 2500 B.C. Their cities were enjoying the cleanest and most hygienic daily life with elaborate civic sanitation systems. The whole conception shows a remarkable concern for health. Then, the early Aryans invaded India about 1500 B.C. and the Vedic age started. The Rgveda texts contain the hymns for Soma and those for herbs. The term Ayurveda (i.e., science of life) is found in some old versions of both Ramāyana and Mahābhārata and in the Atharvaveda. Suśruta had the credit of making a breakthrough in the field of surgery. The Ayurveda, a work on internal medicine, gives the following transmission of sages: Brahmā-->Daksa-->Prajāpati-->Aśivinau-->Indra-->Caraka. On the other hand, the Suśruta-samhitā, which deals mainly with surgical medicine, explains it as follows; Indra-->Dhanvantari-->Suśruta Both Caraka and Suśruta were medical doctors as well as pharmacists, so they studied more than 1000 herbs thoroughly. The Ayurveda had been used by his devotees for medical purposes. It eventually spread over Asia with the advanced evolution of Buddhism.