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Sample records for ancient dna authenticity

  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. 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...

  3. 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...

  4. 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...

  5. 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.

  6. 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...

  7. An Ancient Indian Board Game as a Tool for Authentication

    Directory of Open Access Journals (Sweden)

    Sreelatha Malempati

    2011-08-01

    Full Text Available User authentication is the first phase of information security. Users should remember their passwords and recall them for authentication. Text based passwords is the traditional method for authentication. Short and simple passwords are memorable and usable but not secure. Random and lengthy passwords are secure but not memorable and usable. Graphical password schemes are introduced as alternatives to text based schemes. Few grid based authentication techniques are also proposed. The purpose of this paper is to introduce a tool to enhance the memorability and security of passwords which also provides usability. The most popular ancient Indian board game “Snakes and Ladders” is used as a tool for authentication.

  8. 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.

  9. 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)

  10. 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...

  11. 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...

  12. 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....

  13. 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

  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. 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...

  16. 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...

  17. 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.

  18. 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....

  19. 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

  20. 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.

  1. 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.

  2. 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....

  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. 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.

  5. Forensics: Food Authentication Using MtDNA

    OpenAIRE

    Chandrika Murugaiah

    2015-01-01

    There is a clear trend in the food international market towards labelling products with information about their composition and quality. Due to the increase in international trade in seafood and seafood products, authentication has become a necessity. There is a need for suitable methods of identification to ensure compliance with the labelling regulations and thereby to prevent the substitution of fish species.

  6. 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

  7. 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...

  8. 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....

  9. 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...

  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. Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years.

    Directory of Open Access Journals (Sweden)

    Linea Melchior

    Full Text Available BACKGROUND: Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles. METHODOLOGY/PRINCIPAL FINDINGS: We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a "clean- laboratory" dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the "unhandled" teeth and there was no indication of contamination, while the latter was the case with half of the "handled" teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (<2% in modern Scandinavians supports our previous findings of a pronounced frequency of this haplogroup in Viking and Iron Age Danes. CONCLUSION: The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate

  12. Dipstick test for DNA-based food authentication. Application to coffee authenticity assessment.

    Science.gov (United States)

    Trantakis, Ioannis A; Spaniolas, Stelios; Kalaitzis, Panagiotis; Ioannou, Penelope C; Tucker, Gregory A; Christopoulos, Theodore K

    2012-01-25

    This paper reports DNA-based food authenticity assays, in which species identification is accomplished by the naked eye without the need of specialized instruments. Strongly colored nanoparticles (gold nanoparticles) are employed as reporters that enable visual detection. Furthermore, detection is performed in a low-cost, disposable, dipstick-type device that incorporates the required reagents in dry form, thereby avoiding multiple pipetting and incubation steps. Due to its simplicity, the method does not require highly qualified personnel. The procedure comprises the following steps: (i) PCR amplification of the DNA segment that flanks the unique SNP (species marker); (ii) a 15 min extension reaction in which DNA polymerase extends an allele-specific primer only if it is perfectly complementary with the target sequence; (iii) detection of the products of the extension reaction within a few minutes by the naked eye employing the dipstick. No purification is required prior to application of the extension products to the dipstick. The method is general and requires only a unique DNA sequence for species discrimination. The only instrument needed is a conventional thermocycler for PCR, which is common equipment in every DNA laboratory. As a model, the method was applied to the discrimination of Coffea robusta and arabica species in coffee authenticity assessment. As low as 5% of Robusta coffee can be detected in the presence of Arabica coffee.

  13. 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

  14. 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...

  15. 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

  16. 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...

  17. 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.

  18. Laser induced micro-photoluminescence of marble and application to authenticity testing of ancient objects

    Science.gov (United States)

    Polikreti, K.; Christofides, C.

    2008-02-01

    For the last 70 years, the authenticity of disputable marble objects has been tested by using a black light lamp. According to empirical observations “fresh marbles are purple while ancient ones are blue under the lamp”. This discrimination lacks scientific basis but is very popular because sculptured stone dating is impossible. This work aims to test the reliability of the “UV method” by studying the laser excited photoluminescence (PL) of marble surfaces. An argon ion laser beam was focused through a microscope objective onto the sample, offering a PL spatial resolution of 3 μm. Newly-cut marbles show an intense emission at 610 nm ascribed to Mn2+ and a less intense one at 390 nm. Excavated surfaces show the 610 nm emission and a broadband (380-530 nm) one. Similar broadband emissions due to humic (HAs) and fulvic acids (FAs) are typical in soil PL spectra and were observed in the spectra of samples taken from the soil surrounding the excavated surfaces. Additionally, electron paramagnetic resonance (EPR) spectra of excavated surfaces show a peak at g=2.0045, typical in calcite doped with humic acids. We presume that the 380-550 nm emission originates from HA and FA salts existing in the infiltrated soil or the recrystallised calcite developed in marble patinas. Finally, the application of the “UV method” on twelve ancient and modern surfaces proved that the technique is only partly reliable and should be used together with other analytical techniques.

  19. 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.

  20. 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.

  1. Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding.

    Science.gov (United States)

    Little, Damon P

    2014-09-01

    Ginkgo biloba L. (known as ginkgo or maidenhair tree) is a phylogenetically isolated, charismatic, gymnosperm tree. Herbal dietary supplements, prepared from G. biloba leaves, are consumed to boost cognitive capacity via improved blood perfusion and mitochondrial function. A novel DNA mini-barcode assay was designed and validated for the authentication of G. biloba in herbal dietary supplements (n = 22; sensitivity = 1.00, 95% CI = 0.59-1.00; specificity = 1.00, 95% CI = 0.64-1.00). This assay was further used to estimate the frequency of mislabeled ginkgo herbal dietary supplements on the market in the United States of America: DNA amenable to PCR could not be extracted from three (7.5%) of the 40 supplements sampled, 31 of 37 (83.8%) assayable supplements contained identifiable G. biloba DNA, and six supplements (16.2%) contained fillers without any detectable G. biloba DNA. It is hoped that this assay will be used by supplement manufacturers to ensure that their supplements contain G. biloba.

  2. 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.

  3. 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

  4. 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...

  5. 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...

  6. 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...

  7. 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

  8. 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

  9. 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.

  10. 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...

  11. 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 ...

  12. 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...

  13. 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...

  14. 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

  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. 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.

  17. 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.

  18. 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....

  19. 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...

  20. 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...

  1. 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.

  2. 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.

  3. 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...

  4. 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...

  5. 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...

  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. 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...

  8. 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.

  9. 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.

  10. DNA Barcode Authentication of Saw Palmetto Herbal Dietary Supplements

    OpenAIRE

    Little, Damon P.; Jeanson, Marc L.

    2013-01-01

    Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini–barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74–1.00); sensitivity = 1.00 (95% confidence interval = 0.66–1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini–barcodes were used to estimate the frequency of mis...

  11. 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.

  12. 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...

  13. 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...

  14. 论DNA证据的鉴真%Studies on the authentication of DNA evidence

    Institute of Scientific and Technical Information of China (English)

    王志刚

    2015-01-01

    DNA evidence has no natural features and unique marks, from the form of material evidence to be extracted and applied in courtroom as part of forensic examination opinion, it would experience multiple parts of a transfer process, which makes the DNA evidence easy to be replaced and its characters subject to change. From a practical point of view, DNA evidence has been given relatively strong probative value, and accurately using DNA evidence to identify the premise of facts of the case lies in the authenticity of DNA evidence, so it is necessary to do DNA evidence authentication. Through authentication, it can guarantee legitimate admissibility of DNA evidence in litigation while ensure the accuracy of fact-ifnding and prevent replacement or destroying evidence. The focus of DNA evidence authentication should be allocated in three aspects: a traceable extraction process, integrity in the chain of custody and a reliable identiifcation process.%DNA证据不具有独特的自然特征与标记,其从物证形态被提取到以鉴定意见形态应用于法庭要经历多环节的流转过程,这使得DNA证据易于被替换且性状也容易发生变化。从实践情况来看,DNA证据被赋予较强证明力,而准确运用DNA证据认定案件事实的前提在于DNA证据的真实性,因此,有必要对其进行鉴真。通过鉴真,可保障DNA证据在诉讼中的合法准入、确保事实认定的准确性以及防止证据替换或毁损。DNA证据鉴真的重点应放在提取过程的可回溯性、证据保管链的完整性和鉴定过程的可靠性三个方面。

  15. DNA Barcoding of Catfish: Species Authentication and Phylogenetic Assessment

    OpenAIRE

    Wong, Li Lian; Peatman, Eric; Lu, Jianguo; Kucuktas, Huseyin; He, Shunping; Zhou, Chuanjiang; Na-Nakorn, Uthairat; Liu, Zhanjiang

    2011-01-01

    As the global market for fisheries and aquaculture products expands, mislabeling of these products has become a growing concern in the food safety arena. Molecular species identification techniques hold the potential for rapid, accurate assessment of proper labeling. Here we developed and evaluated DNA barcodes for use in differentiating United States domestic and imported catfish species. First, we sequenced 651 base-pair barcodes from the cytochrome oxidase I (COI) gene from individuals of ...

  16. DNA Barcode Authentication of Saw Palmetto Herbal Dietary Supplements

    Science.gov (United States)

    Little, Damon P.; Jeanson, Marc L.

    2013-01-01

    Herbal dietary supplements made from saw palmetto (Serenoa repens; Arecaceae) fruit are commonly consumed to ameliorate benign prostate hyperplasia. A novel DNA mini–barcode assay to accurately identify [specificity = 1.00 (95% confidence interval = 0.74–1.00); sensitivity = 1.00 (95% confidence interval = 0.66–1.00); n = 31] saw palmetto dietary supplements was designed from a DNA barcode reference library created for this purpose. The mini–barcodes were used to estimate the frequency of mislabeled saw palmetto herbal dietary supplements on the market in the United States of America. Of the 37 supplements examined, amplifiable DNA could be extracted from 34 (92%). Mini–barcode analysis of these supplements demonstrated that 29 (85%) contain saw palmetto and that 2 (6%) supplements contain related species that cannot be legally sold as herbal dietary supplements in the United States of America. The identity of 3 (9%) supplements could not be conclusively determined. PMID:24343362

  17. 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.

  18. 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.

  19. 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.

  20. 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...

  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. 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.

  6. 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...

  7. 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

  8. 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...

  9. 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...

  10. 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.

  11. 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...

  12. 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...

  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. 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.

  15. 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.

  16. 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...

  17. 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

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    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...

  19. 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.

  20. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market.

    Science.gov (United States)

    Mishra, Priyanka; Kumar, Amit; Nagireddy, Akshitha; Mani, Daya N; Shukla, Ashutosh K; Tiwari, Rakesh; Sundaresan, Velusamy

    2016-01-01

    The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics. PMID:26079154

  1. Determining the authenticity of athlete urine in doping control by DNA analysis.

    Science.gov (United States)

    Devesse, Laurence; Syndercombe Court, Denise; Cowan, David

    2015-10-01

    The integrity of urine samples collected from athletes for doping control is essential. The authenticity of samples may be contested, leading to the need for a robust sample identification method. DNA typing using short tandem repeats (STR) can be used for identification purposes, but its application to cellular DNA in urine has so far been limited. Here, a reliable and accurate method is reported for the successful identification of urine samples, using reduced final extraction volumes and the STR multiplex kit, Promega® PowerPlex ESI 17, with capillary electrophoretic characterisation of the alleles. Full DNA profiles were obtained for all samples (n = 20) stored for less than 2 days at 4 °C. The effect of different storage conditions on yield of cellular DNA and probability of obtaining a full profile were also investigated. Storage for 21 days at 4 °C resulted in allelic drop-out in some samples, but the random match probabilities obtained demonstrate the high power of discrimination achieved through targeting a large number of STRs. The best solution for long-term storage was centrifugation and removal of supernatant prior to freezing at -20 °C. The method is robust enough for incorporation into current anti-doping protocols, and was successfully applied to 44 athlete samples for anti-doping testing with 100% concordant typing.

  2. 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

  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. 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.

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

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    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%.

  6. A DNA microarray for the authentication of toxic traditional Chinese medicinal plants.

    Science.gov (United States)

    Carles, Maria; Cheung, Matthew Kin; Moganti, Shanti; Dong, Tina T; Tsim, Karl W; Ip, Nancy Y; Sucher, Nikolaus J

    2005-06-01

    A silicon-based DNA microarray was designed and fabricated for the identification of toxic traditional Chinese medicinal plants. Species-specific oligonucleotide probes were derived from the 5S ribosomal RNA gene of Aconitum carmichaeli, A. kusnezoffi, Alocasia macrorrhiza, Croton tiglium, Datura inoxia, D. metel, D. tatula, Dysosma pleiantha, Dy. versipellis, Euphorbia kansui, Hyoscyamus niger, Pinellia cordata, P. pedatisecta, P. ternata, Rhododendron molle, Strychnos nux-vomica, Typhonium divaricatum and T. giganteum and the leucine transfer RNA gene of Aconitum pendulum and Stellera chamaejasme. The probes were immobilized via dithiol linkage on a silicon chip. Genomic target sequences were amplified and fluorescently labeled by asymmetric polymerase chain reaction. Multiple toxic plant species were identified by parallel genotyping. Chip-based authentication of medicinal plants may be useful as inexpensive and rapid tool for quality control and safety monitoring of herbal pharmaceuticals and neutraceuticals. PMID:15971136

  7. 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...

  8. 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.

  9. 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

  10. Quantitative bioluminometric method for DNA-based species/varietal identification in food authenticity assessment.

    Science.gov (United States)

    Trantakis, Ioannis A; Christopoulos, Theodore K; Spaniolas, Stelios; Kalaitzis, Panagiotis; Ioannou, Penelope C; Tucker, Gregory A

    2012-02-01

    A method is reported for species quantification by exploiting single-nucleotide polymorphisms (SNPs). These single-base changes in DNA are particularly useful because they enable discrimination of closely related species and/or varieties. As a model, quantitative authentication studies were performed on coffee. These involved the determination of the percentage of Arabica and Robusta species based on a SNP in the chloroplastic trnL(UAA)-trnF(GAA) intraspacer region. Following polymerase chain reaction (PCR), the Robusta-specific and Arabica-specific fragments were subjected to 15 min extension reactions by DNA polymerase using species-specific primers carrying oligo(dA) tags. Biotin was incorporated into the extended strands. The products were captured in streptavidin-coated microtiter wells and quantified by using oligo(dT)-conjugated photoprotein aequorin. Aequorin was measured within 3 s via its characteristic flash-type bioluminescent reaction that was triggered by the addition of Ca(2+). Because of the close resemblance between the two DNA fragments, during PCR one species serves as an internal standard for the other. The percentage of the total luminescence signal obtained from a certain species was linearly related to the percent content of the sample with respect to this species. The method is accurate and reproducible. The microtiter well-based assay configuration allows high sample throughput and facilitates greatly the automation.

  11. Distinguishing authentic mitochondrial and plastid DNAs from similar DNA sequences in the nucleus using the polymerase chain reaction.

    Science.gov (United States)

    Kumar, Rachana A; Bendich, Arnold J

    2011-08-01

    DNA sequences similar to those in the organellar genomes are also found in the nucleus. These non-coding sequences may be co-amplified by PCR with the authentic organellar DNA sequences, leading to erroneous conclusions. To avoid this problem, we describe an experimental procedure to prevent amplification of this "promiscuous" DNA when total tissue DNA is used with PCR. First, primers are designed for organelle-specific sequences using a bioinformatics method. These primers are then tested using methylation-sensitive PCR. The method is demonstrated for both end-point and real-time PCR with Zea mays, where most of the DNA sequences in the organellar genomes are also present in the nucleus. We use this procedure to quantify those nuclear DNA sequences that are near-perfect replicas of organellar DNA. This method should be useful for applications including phylogenetic analysis, organellar DNA quantification and clinical testing.

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

    Science.gov (United States)

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

  13. 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.

  14. 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

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

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    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.

  16. 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.

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

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    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.

  18. 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.

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

    Science.gov (United States)

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

    2012-01-01

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

  20. 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

  1. 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

  2. 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...

  3. 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.

  4. 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.

  5. 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.

  6. An economic analysis of private incentives to adopt DNA barcoding technology for fish species authentication in Canada.

    Science.gov (United States)

    Ugochukwu, Albert I; Hobbs, Jill E; Phillips, Peter W B; Gray, Richard

    2015-12-01

    The increasing spate of species substitution and mislabelling in fish markets has become a concern to the public and a challenge to both the food industry and regulators. Species substitution and mislabelling within fish supply chains occurs because of price incentives to misrepresent products for economic gain. Emerging authenticity technologies, such as the DNA barcoding technology that has been used to identify plants and animal (particularly fish) species through DNA sequencing, offer a potential technological solution to this information problem. However, the adoption of these authenticity technologies depends also on economic factors. The present study uses economic welfare analysis to examine the effects of species substitution and mislabelling in fish markets, and examines the feasibility of the technology for a typical retail store in Canada. It is assumed that increased accuracy of the technology in detecting fraud and enforcement of legal penalties and other associated costs would be likely to discourage cheating. Empirical results suggest that DNA barcoding technology would be feasible presently for a typical retail store only if authentication is done in a third party laboratory, as it may not be feasible on an individual retail store level once fixed and other associated costs of the technology are considered.

  7. An economic analysis of private incentives to adopt DNA barcoding technology for fish species authentication in Canada.

    Science.gov (United States)

    Ugochukwu, Albert I; Hobbs, Jill E; Phillips, Peter W B; Gray, Richard

    2015-12-01

    The increasing spate of species substitution and mislabelling in fish markets has become a concern to the public and a challenge to both the food industry and regulators. Species substitution and mislabelling within fish supply chains occurs because of price incentives to misrepresent products for economic gain. Emerging authenticity technologies, such as the DNA barcoding technology that has been used to identify plants and animal (particularly fish) species through DNA sequencing, offer a potential technological solution to this information problem. However, the adoption of these authenticity technologies depends also on economic factors. The present study uses economic welfare analysis to examine the effects of species substitution and mislabelling in fish markets, and examines the feasibility of the technology for a typical retail store in Canada. It is assumed that increased accuracy of the technology in detecting fraud and enforcement of legal penalties and other associated costs would be likely to discourage cheating. Empirical results suggest that DNA barcoding technology would be feasible presently for a typical retail store only if authentication is done in a third party laboratory, as it may not be feasible on an individual retail store level once fixed and other associated costs of the technology are considered. PMID:26577715

  8. 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...

  9. 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.

  10. 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...

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 古城文化型景区旅游真实性实证研究——以丽江古城为例%Empirical Research on Tourism Authenticity of Ancient Cultural City

    Institute of Scientific and Technical Information of China (English)

    王秀红

    2011-01-01

    基于旅游真实性理论和对丽江古城文化型景区进行的田野调查分析,探索我国古城文化型景区旅游者的旅游真实性结构情况,并进一步挖掘了古城文化型景区旅游真实性和旅游动机的内在联系.研究发现古城文化型景区旅游真实性总体上表现为客观真实性最高,依次为存在真实性、建构真实性和后现代真实性.古城文化型景区旅游真实性和旅游动机相关性总体上表现为“知识功能”动机、“奖励最大化”动机、“最小化惩罚”动机、“自尊”动机和“自我实现”动机逐步递减趋势;4类不同的旅游真实性与5类不同类型的旅游动机之间的相关性也表现出各自不同的特点.从理论上丰富了国内有关旅游真实性实证定量研究的成果,从实践上对现实的旅游市场研究和基于旅游者的规划活动极具应用价值.%On the basis of tourism authenticity theory and field investigation and analysis of Lijiang ancient city, the paper had explored tour ists ' authenticity, and further revealed the inner relation between tourism authenticity and tourism motivation of ancient cultural cities. It was found that ancient cultural cities generally had the highest objective authenticity, followed by existential, constructive and post-modem authen ticity. As for tourism motivation, motivation of knowledge function, of reward maximization, of punishment minimization, of self-esteem and of self-fulfillment presented to diminish progressively. Relationships between four types of tourism authenticity and five types of tourism motiva tions also varied from each other. It had enriched empirical quantitative research results of domestic tourism authenticity in theory, and provid ed application value for research on realistic tourism market and planning activity based on tourists in practice.

  18. Molecular authentication of the medicinal herb Ruta graveolens (Rutaceae) and an adulterant using nuclear and chloroplast DNA markers.

    Science.gov (United States)

    Al-Qurainy, F; Khan, S; Tarroum, M; Al-Hemaid, F M; Ali, M A

    2011-11-10

    Dried parts of different plant species often look alike, especially in powdered form, making them very difficult to identify. Ruta graveolens, sold as a dried medicinal herb, can be adulterated with Euphorbia dracunculoides. The genomic DNA was isolated from the leaf powder (100 mg each) using the modified CTAB method. Internal transcribed spacer sequences of nuclear ribosomal DNA (nrDNA-ITS), and chloroplast spacer sequences (rpoB and rpoC1) are regarded as potential genes for plant DNA barcoding. We amplified and sequenced these spacer sequences and confirmed the sequences with a BLAST search. Sequence alignment was performed using ClustalX to look for differences in the sequences. A DNA marker was developed based on rpoB and rpoC1 of the nrDNA-ITS for the identification of the adulterant E. dracunculoides in samples of R. graveolens that are sold in local herbal markets. Sequence-characterized amplified region markers of 289 and 264 bp for R. graveolens and 424 bp for E. dracunculoides were developed from dissimilar sequences of this nrDNA-ITS to speed up the authentication process. This marker successfully distinguished these species in extracted samples with as little as 5 ng DNA/μL extract.

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

    Science.gov (United States)

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

    2015-03-01

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

  20. 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 ...

  1. 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

  2. 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.

  3. 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

  4. Authentication of Cordyceps sinensis by DNA Analyses: Comparison of ITS Sequence Analysis and RAPD-Derived Molecular Markers.

    Science.gov (United States)

    Lam, Kelly Y C; Chan, Gallant K L; Xin, Gui-Zhong; Xu, Hong; Ku, Chuen-Fai; Chen, Jian-Ping; Yao, Ping; Lin, Huang-Quan; Dong, Tina T X; Tsim, Karl W K

    2015-01-01

    Cordyceps sinensis is an endoparasitic fungus widely used as a tonic and medicinal food in the practice of traditional Chinese medicine (TCM). In historical usage, Cordyceps specifically is referring to the species of C. sinensis. However, a number of closely related species are named themselves as Cordyceps, and they are sold commonly as C. sinensis. The substitutes and adulterants of C. sinensis are often introduced either intentionally or accidentally in the herbal market, which seriously affects the therapeutic effects or even leads to life-threatening poisoning. Here, we aim to identify Cordyceps by DNA sequencing technology. Two different DNA-based approaches were compared. The internal transcribed spacer (ITS) sequences and the random amplified polymorphic DNA (RAPD)-sequence characterized amplified region (SCAR) were developed here to authenticate different species of Cordyceps. Both approaches generally enabled discrimination of C. sinensis from others. The application of the two methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, the SCAR markers derived from the RAPD results provide a new method for quick authentication of Cordyceps. PMID:26694332

  5. Authentication of Cordyceps sinensis by DNA Analyses: Comparison of ITS Sequence Analysis and RAPD-Derived Molecular Markers

    Directory of Open Access Journals (Sweden)

    Kelly Y. C. Lam

    2015-12-01

    Full Text Available Cordyceps sinensis is an endoparasitic fungus widely used as a tonic and medicinal food in the practice of traditional Chinese medicine (TCM. In historical usage, Cordyceps specifically is referring to the species of C. sinensis. However, a number of closely related species are named themselves as Cordyceps, and they are sold commonly as C. sinensis. The substitutes and adulterants of C. sinensis are often introduced either intentionally or accidentally in the herbal market, which seriously affects the therapeutic effects or even leads to life-threatening poisoning. Here, we aim to identify Cordyceps by DNA sequencing technology. Two different DNA-based approaches were compared. The internal transcribed spacer (ITS sequences and the random amplified polymorphic DNA (RAPD-sequence characterized amplified region (SCAR were developed here to authenticate different species of Cordyceps. Both approaches generally enabled discrimination of C. sinensis from others. The application of the two methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, the SCAR markers derived from the RAPD results provide a new method for quick authentication of Cordyceps.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. Evidence of authentic DNA from Danish Viking Age skeletons untouched by humans for 1,000 years

    DEFF Research Database (Denmark)

    Melchior, Linea; Kivisild, Toomas; Lynnerup, Niels;

    2008-01-01

    , pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles. METHODOLOGY/PRINCIPAL FINDINGS: We avoided some of these obstacles by analyzing DNA from ten Viking...... Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre...... with the "unhandled" teeth and there was no indication of contamination, while the latter was the case with half of the "handled" teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree...

  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. DNA Profiling in Authentication of Panax Plants and Drugs: A New Approach to Old Problems

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@INTRODUCTION Ginseng is one of the famous herbs of all used by mankind as it has been valued for its remarkable therapeutic benefits as an energy tonic by the oriental people since the dawn of their civilization and has a rich and extensive history. Now Ginseng is becoming widely known and used in the West, and like any other Chinese drugs, the authentication of Ginseng must be understood in order to use it widely and appropriately.

  16. 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...

  17. 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.

  18. 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

  19. DNA Barcode Authentication of Wood Samples of Threatened and Commercial Timber Trees within the Tropical Dry Evergreen Forest of India

    Science.gov (United States)

    Nithaniyal, Stalin; Newmaster, Steven G.; Ragupathy, Subramanyam; Krishnamoorthy, Devanathan; Vassou, Sophie Lorraine; Parani, Madasamy

    2014-01-01

    Background India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. Methodology/Principal Findings We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. Conclusions We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value. PMID:25259794

  20. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India.

    Directory of Open Access Journals (Sweden)

    Stalin Nithaniyal

    Full Text Available BACKGROUND: India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. METHODOLOGY/PRINCIPAL FINDINGS: We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK correctly identified 136 out of 143 species (95%. This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. CONCLUSIONS: We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.

  1. 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).

  2. 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

  3. 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.

  4. DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market.

    Science.gov (United States)

    Lee, Shiou Yih; Ng, Wei Lun; Mahat, Mohd Noor; Nazre, Mohd; Mohamed, Rozi

    2016-01-01

    The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.

  5. Detection of porcine DNA in gelatine and gelatine-containing processed food products-Halal/Kosher authentication.

    Science.gov (United States)

    Demirhan, Yasemin; Ulca, Pelin; Senyuva, Hamide Z

    2012-03-01

    A commercially available real-time PCR, based on a multi-copy target cytochrome b (cyt b) using porcine specific primers, has been validated for the Halal/Kosher authentication of gelatine. Extraction and purification of DNA from gelatine were successfully achieved using the SureFood® PREP Animal system, and real-time PCR was carried out using SureFood® Animal ID Pork Sens kit. The minimum level of adulteration that could be detected was 1.0% w/w for marshmallows and gum drops. A small survey was undertaken of processed food products such as gum drops, marshmallows and Turkish delight, believed to contain gelatine. Of fourteen food products from Germany, two samples were found to contain porcine gelatine, whereas of twenty-nine samples from Turkey twenty-eight were negative. However, one product from Turkey contained porcine DNA and thus was not Halal, and neither was the use of porcine gelatine indicated on the product label.

  6. 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...

  7. 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.

  8. 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

  9. 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

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. DNA Barcode-Based PCR-RFLP and Diagnostic PCR for Authentication of Jinqian Baihua She (Bungarus Parvus

    Directory of Open Access Journals (Sweden)

    Xiaolei Li

    2015-01-01

    Full Text Available We established polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP and diagnostic PCR based on cytochrome C oxidase subunit I (COI barcodes of Bungarus multicinctus, genuine Jinqian Baihua She (JBS, and adulterant snake species. The PCR-RFLP system utilizes the specific restriction sites of SpeI and BstEII in the COI sequence of B. multicinctus to allow its cleavage into 3 fragments (120 bp, 230 bp, and 340 bp; the COI sequences of the adulterants do not contain these restriction sites and therefore remained intact after digestion with SpeI and BstEII (except for that of Zaocys dhumnades, which could be cleaved into a 120 bp and a 570 bp fragment. For diagnostic PCR, a pair of species-specific primers (COI37 and COI337 was designed to amplify a specific 300 bp amplicon from the genomic DNA of B. multicinctus; no such amplicons were found in other allied species. We tested the two methods using 11 commercial JBS samples, and the results demonstrated that barcode-based PCR-RFLP and diagnostic PCR both allowed effective and accurate authentication of JBS.

  16. An authenticity survey of herbal medicines from markets in China using DNA barcoding.

    Science.gov (United States)

    Han, Jianping; Pang, Xiaohui; Liao, Baosheng; Yao, Hui; Song, Jingyuan; Chen, Shilin

    2016-01-07

    Adulterant herbal materials are a threat to consumer safety. In this study, we used DNA barcoding to investigate the proportions and varieties of adulterant species in traditional Chinese medicine (TCM) markets. We used a DNA barcode database of TCM (TCMD) that was established by our group to investigate 1436 samples representing 295 medicinal species from 7 primary TCM markets in China. The results indicate that ITS2 barcodes could be generated for most of the samples (87.7%) using a standard protocol. Of the 1260 samples, approximately 4.2% were identified as adulterants. The adulterant focused on medicinal species such as Ginseng Radix et Rhizoma (Renshen), Radix Rubi Parvifolii (Maomeigen), Dalbergiae odoriferae Lignum (Jiangxiang), Acori Tatarinowii Rhizoma (Shichangpu), Inulae Flos (Xuanfuhua), Lonicerae Japonicae Flos (Jinyinhua), Acanthopanacis Cortex (Wujiapi) and Bupleuri Radix (Chaihu). The survey revealed that adulterant species are present in the Chinese market, and these adulterants pose a risk to consumer health. Thus, regulatory measures should be adopted immediately. We suggest that a traceable platform based on DNA barcode sequences be established for TCM market supervision.

  17. Authentication of ruta graveolens and its adulterant using internal transcribed spacer (its) sequences of nuclear ribosomal DNA

    International Nuclear Information System (INIS)

    Ruta graveolens L. (Rutaceae) is commonly known as 'Sudab' which is well known for hippocratic medicine and is commonly used in indigenous health-care system in India. Euphorbia dracunculoides Lam. (Euphorbiaceae) in raw drug trading has almost similar morphology to R. graveolens in dried state, is being sold locally or used clinically as an adulterant of R. graveolens (genuine) at a relatively low price under the same name 'Sudab' which has ultimately reduced the efficacy and quality of this herb. The internal transcribed spacer (ITS) sequence of nuclear ribosomal DNA gene of genuine and adulterant were sequenced and analyzed to assess species admixture in raw drug trading of genuine herbal drug. The BLAST search results of ITS sequence of genuine sample of 'Sudab' i.e., R. graveolens showed 99% similarity to the sequence of R. graveolens, however, E. dracunculoides showed 100% similarity to the species of Euphorbia and did not show any similarity with R. graveolens. The sequence alignment of both species was entirely different to each other. Phylogenetic analysis based on ITS sequence of adulterant sample i.e., E. dracunculoides together with sequences of Euphorbia species available in the GenBank has also clearly showed its nesting within the Euphorbia tree. The generated ITS sequences of both samples in the present study may be referred hereafter as species-specific DNA barcode signature, which can be used in authenticating and validating the exact species identities to discriminate the genuine sample of 'Sudab' from its adulterants if any available to guarantee the quality and purity of this drug in the herbal drug market. (author)

  18. Authentication of shankhpushpi by RAPD markers

    Directory of Open Access Journals (Sweden)

    Showkat Hussain Ganie

    2012-05-01

    Full Text Available Background: “Shankhpushpi”, an important indigenous drug of Ayurveda, an ancient system of Indian medicine, improves memory power and intellect. It is used in many Ayurvedic formulations, either singly or in combination with other herbs, meant for sleeplessness, epilepsy, hallucinations and anxiety. At least three different plant species viz., Clitoria ternatea, Convolvulus pluricaulis and Evolvulus alsinoides are as the source of this drug in the different parts of the country. Because of increased demand and high price, shankhpushpi is often adulterated in the trade by other related species. Therefore, a reliable authentication method is needed to facilitate differentiation/identification of the genuine material from its adulterants. The present study was aimed at developing RAPD-based markers for identification of C. pluricaulis, E. alsinoides and C. ternatea, and analyzing the market samples of the drug to ascertain their authenticity. Material and Methods: Fresh samples of source plants of shankhpushpi were collected from Ghaziabad and Delhi. The market samples were procured from the crude-drug markets of different geographical regions of India. The amplified polymorphic DNA (RAPD technique was employed for characterization of genuine and market samples. Twenty-five 11-mer oligonucleotide primers were used to amplify the DNA isolated. Results: Out of 25 primers, only four (OPN-03, OPN-04, OPN-05 and OPN-06 yielded amplification products that produced clear and reproducible bands, which were used to characterize the market samples. RAPD profile of some market samples did not match with the authentic samples, indicating that these samples were either adulterated or spurious. Conclusion: The RAPD markers developed in this study may provide guidance for the authentication of plant materials traded as shankhpushpi.

  19. 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...

  20. 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 >...

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

    Science.gov (United States)

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

    2016-01-01

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

  2. 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.

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

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    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.

  4. 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

  5. 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.

  6. DNA barcoding for species identification from dried and powdered plant parts: a case study with authentication of the raw drug market samples of Sida cordifolia.

    Science.gov (United States)

    Vassou, Sophie Lorraine; Kusuma, G; Parani, Madasamy

    2015-03-15

    The majority of the plant materials used in herbal medicine is procured from the markets in the form of dried or powdered plant parts. It is essential to use authentic plant materials to derive the benefits of herbal medicine. However, establishing the identity of these plant materials by conventional taxonomy is extremely difficult. Here we report a case study in which the species identification of the market samples of Sida cordifolia was done by DNA barcoding. As a prelude to species identification by DNA barcoding, 13 species of Sida were collected, and a reference DNA barcode library was developed using rbcL, matK, psbA-trnH and ITS2 markers. Based on the intra-species and inter-species divergence observed, psbA-trnH and ITS2 were found to be the best two-marker combination for species identification of the market samples. The study showed that none of the market samples belonged to the authentic species, S. cordifolia. Seventy-six per cent of the market samples belonged to other species of Sida. The predominant one was Sida acuta (36%) followed by S. spinosa (20%), S. alnifolia (12%), S. scabrida (4%) and S. ravii (4%). Such substitutions may not only fail to give the expected therapeutic effect, but may also give undesirable effects as in case of S. acuta which contains a 6-fold higher amount of ephedrine compared to the roots of S. cordifolia. The remaining 24% of the samples were from other genera such as Abutilon sp. (8%), Ixonanthes sp., Terminalia sp., Fagonia sp., and Tephrosia sp. (4% each). This observation is in contrast to the belief that medicinal plants are generally substituted or adulterated with closely related species. The current study strongly suggests that the raw drug market samples of herbal medicines need to be properly authenticated before use, and DNA barcoding has been found to be suitable for this purpose.

  7. Authentic Creation of Imitative Ancient Town Tourism: A Case Study of Yi Ancient Town of Chuxiong Prefecture, Yunnan Province%模仿式古镇旅游的真实性创造——以云南省楚雄州彝人古镇为例

    Institute of Scientific and Technical Information of China (English)

    张文芬

    2012-01-01

    随着旅游多样化发展,传统旅游资源已难以满足现代旅游者的需求,以彝人古镇为例,模仿式旅游资源随之应运而生。对旅游古镇的研究,虽然已有的研究内容及视角等都具有多样性,但从真实性视角对新出现的模仿式古镇进行的研究却知之甚少。彝人古镇是模仿式的,它没有原生文化系统却以彝族文化为依托,不是真实的传统古镇却给游客真实的旅游体验,所以,模仿式古镇的开发是值得倡导的,只是在开发时必须遵循文化的本质,避免文化因旅游而变迁或遗失。%With the development of tourism diversification, traditional tourism resources are difficult to meet the demand of modem tourists. Imitative tourism resources such as Yi Ancient Town have been built. Although the content and the perspective of the current study on ancient tourism town are very diverse, the study on new emerging imitative ancient town in the view of authenticity is little known. Yi Ancient Town is a style of imitation without native cultural system, but based on the culture of Yi people, which is not a traditional town in the true sense, but visitors who can enjoy a real experience for themselves in the town. Therefore, it is worth advocating the development of the imitative ancient town, but its development should follow the cultural nature and avoid the' changes or the losses of its culture.

  8. 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.

  9. DNA barcoding of authentic and substitute samples of herb of the family Asparagaceae and Asclepiadaceae based on the ITS2 region

    Directory of Open Access Journals (Sweden)

    Padmalatha S Rai

    2012-01-01

    Full Text Available Background : Herbal drugs used to treat illness according to Ayurveda are often misidentified or adulterated with similar plant materials. Objective: To aid taxonomical identification, we used DNA barcoding to evaluate authentic and substitute samples of herb and phylogenetic relationship of four medicinal plants of family Asparagaceace and Asclepiadaceae. Materials and Methods : DNA extracted from dry root samples of two authentic and two substitutes of four specimens belonging to four species were subjected to polymerase chain reaction (PCR and DNA sequencing. Primers for nuclear DNA (nu ITS2 and plastid DNA (matK and rpoC1 were used for PCR and sequence analysis was performed by Clustal W. The intraspecific variation and interspecific divergence were calculated using MEGA V 4.0. Statistical Analysis : Kimura′s two parameter model, neighbor joining and bootstrapping methods were used in this work. Results: The result indicates the efficiency of amplification for ITS2 candidate DNA barcodes was 100% for four species tested. The average interspecific divergence is 0.12 and intraspecific variation was 0.232 in the case of two Asparagaceae species. In two Asclepiadaceae species, average interspecific divergence and intraspecific variation were 0.178 and 0.004 respectively. Conclusions: Our findings show that the ITS2 region can effectively discriminate Asparagus racemosus and Hemidesmus indicus from its substitute samples and hence can resolve species admixtures in raw samples. The ITS2 region may be used as one of the standard DNA barcodes to identify closely related species of family Asclepiadaceae but was noninformative for Asparagaceae species suggesting a need for the development of new markers for each family. More detailed studies involving more species and substitutes are warranted.

  10. 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 ...

  11. Aplication of authenticity criteria in mitochondrial studies on archaic bone remains from a prehispanic Muisca population

    Directory of Open Access Journals (Sweden)

    Mónica Díaz

    2011-01-01

    Full Text Available Introduction: Ancient DNA (aDNAstudies can support hypotheses regarding ancient populations; molecular studies can analyze the local population’s genetic composition, minimizing biases introduced by later migrations, demographic expansions, mutations, and bottleneck effects. These analyses must be performed with special care because of the low DNA concentrations and contamination risk; therefore, it is necessary to establish protocols to guarantee the reproducibility and veracity of results. Objective: The present study aims to establish a protocol to obtain ancient DNA from 16 pre-Columbian bone samples found in an excavation performed in the area «Candelaria La Nueva» in Bogota, Colombia, dated in the period «Muisca Tardio». Methods: Four founder mitochondrial DNA Amerindian haplotypes were analyzed by high resolution restriction enzyme analyses, obtaining fragments between 121 and 186 base pairs (bp. Different analyses were performed following a strict control of authenticity criteria regarding laboratory conditions, including: positive and negative controls, reproducibility of results, and verification of particular characteristics present in ancient DNA. Results: Results obtained from the bone samples showed the exclusive presence of haplogroup A in the population studied. This data support the statement of the archaeologists of a single biological population in space and time. The distribution of this haplogroup in a 100% frequency supports the hypothesis of Chibcha genetic affiliation. Conclusion: The present study is a contribution to the study of genetic diversity in archaic American populations, allowing the integration of geographic and historic data with genetic characterization techniques associated with linguistic, ethnographic, and glottochronology patterns. Following the protocol proposed in the present study allows fulfilling authenticity criteria for ancient samples with the available techniques.

  12. 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.

  13. 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...

  14. 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

  15. 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.

  16. 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...

  17. Geospatial Authentication

    Science.gov (United States)

    Lyle, Stacey D.

    2009-01-01

    A software package that has been designed to allow authentication for determining if the rover(s) is/are within a set of boundaries or a specific area to access critical geospatial information by using GPS signal structures as a means to authenticate mobile devices into a network wirelessly and in real-time has been developed. The advantage lies in that the system only allows those with designated geospatial boundaries or areas into the server. The Geospatial Authentication software has two parts Server and Client. The server software is a virtual private network (VPN) developed in Linux operating system using Perl programming language. The server can be a stand-alone VPN server or can be combined with other applications and services. The client software is a GUI Windows CE software, or Mobile Graphical Software, that allows users to authenticate into a network. The purpose of the client software is to pass the needed satellite information to the server for authentication.

  18. 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

  19. 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

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

    Directory of Open Access Journals (Sweden)

    Alcover Josep Antoni

    2005-12-01

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

  1. 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.

  2. 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

  3. Speaker Authentication

    CERN Document Server

    Li, Qi (Peter)

    2012-01-01

    This book focuses on use of voice as a biometric measure for personal authentication. In particular, "Speaker Recognition" covers two approaches in speaker authentication: speaker verification (SV) and verbal information verification (VIV). The SV approach attempts to verify a speaker’s identity based on his/her voice characteristics while the VIV approach validates a speaker’s identity through verification of the content of his/her utterance(s). SV and VIV can be combined for new applications. This is still a new research topic with significant potential applications. The book provides with a broad overview of the recent advances in speaker authentication while giving enough attention to advanced and useful algorithms and techniques. It also provides a step by step introduction to the current state of the speaker authentication technology, from the fundamental concepts to advanced algorithms. We will also present major design methodologies and share our experience in developing real and successful speake...

  4. Experimental Review of DNA-Based Methods for Wine Traceability and Development of a Single-Nucleotide Polymorphism (SNP) Genotyping Assay for Quantitative Varietal Authentication.

    Science.gov (United States)

    Catalano, Valentina; Moreno-Sanz, Paula; Lorenzi, Silvia; Grando, Maria Stella

    2016-09-21

    The genetic varietal authentication of wine was investigated according to DNA isolation procedures reported for enological matrices and also by testing 11 commercial extraction kits and various protocol modifications. Samples were collected at different stages of the winemaking process of renowned Italian wines Brunello di Montalcino, Lambruschi Modenesi, and Trento DOC. Results demonstrated not only that grape DNA loss is produced by the fermentation process but also that clarification and stabilization operations contribute to the reduction of double-stranded DNA content on wine. Despite the presence of inhibitors, downstream PCR genotyping yielded reliable nuclear and chloroplast SSR markers for must samples, whereas no amplification or inconsistent results were obtained at later stages of the vinification. In addition, a TaqMan genotyping assay based on cultivar-specific single-nucleotide polymorphisms (SNPs) was designed, which allowed assessment of grapevine DNA mixtures. Once the wine matrix limitations are overcome, this sensitive tool may be implemented for the relative quantification of cultivars used for blend wines or frauds. PMID:27573905

  5. 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

  6. 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.

  7. 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

  8. 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

  9. Authenticating cache.

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Tyler Barratt; Urrea, Jorge Mario

    2012-06-01

    The aim of the Authenticating Cache architecture is to ensure that machine instructions in a Read Only Memory (ROM) are legitimate from the time the ROM image is signed (immediately after compilation) to the time they are placed in the cache for the processor to consume. The proposed architecture allows the detection of ROM image modifications during distribution or when it is loaded into memory. It also ensures that modified instructions will not execute in the processor-as the cache will not be loaded with a page that fails an integrity check. The authenticity of the instruction stream can also be verified in this architecture. The combination of integrity and authenticity assurance greatly improves the security profile of a system.

  10. 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.

  11. 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

  12. 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

  13. System and method for authentication

    Energy Technology Data Exchange (ETDEWEB)

    Duerksen, Gary L.; Miller, Seth A.

    2015-12-29

    Described are methods and systems for determining authenticity. For example, the method may include providing an object of authentication, capturing characteristic data from the object of authentication, deriving authentication data from the characteristic data of the object of authentication, and comparing the authentication data with an electronic database comprising reference authentication data to provide an authenticity score for the object of authentication. The reference authentication data may correspond to one or more reference objects of authentication other than the object of authentication.

  14. Authentication of Curcuma species (Zingiberaceae) based on nuclear 18S rDNA and plastid trnK sequences.

    Science.gov (United States)

    Cao, Hui; Sasaki, Yohei; Fushimi, Hirotoshi; Komatsu, Katsuko

    2010-07-01

    Curcuma drugs have been used discriminatingly for invigorating blood circulation, promoting digestion, and as a cholagogic in China. However, there is confusion about the drug's botanical origins and clinical uses because of morphological similarity of Curcuma plants and drugs. Comparative sequencing of the 18S rRNA gene in nuclear ribosomal DNA (rDNA) and trnK gene in chloroplast DNA (cpDNA) was carried out in order to examine interspecies phylogeny and to identify ultimately Curcuma species. A total of a hundred of accessions of eighteen species were analyzed. This resulted in an aligned matrix of 1810 bp for 18S rDNA and 2 800 bp for trnK. 18S rDNA sequence divergence within the ingroup ranged from 0-0.05%, trnK ranged from 0-0.19%. One base transversion-substituted site (from cytosine to thymine) was observed from the upstream of 18S rDNA at nucleotide position 234 in C. kwangsiensis and Japanese population of C. zedoaria which have separated genetic distance to other Curcuma taxa. Two noncoding regions embedded in trnK intron showed higher variability, including nucleotide substitutions, repeat insertion and deletions. Based on consensus of relationship, eighteen major lineages within Curcuma are recognized at the species level. The results suggest that Curcuma is monophyletic with 100% bootstrap support and sister to the genera Hedychium and Zingiber. The trnK sequences showed considerable variations between Curcuma species and thus were revealed as a promising candidate for barcoding of Curcuma species, which provide valuable characters for inferring relationship within species but are insufficient to resolve relationships among closely related taxa.

  15. 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.

  16. 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

  17. Tibetan Interpretations of Authenticity

    DEFF Research Database (Denmark)

    Sobisch, Jan-Ulrich

    2015-01-01

    The four means of authentication are arguments for the authentication of Buddhist teachings in a Tibetan tradition. Different traditions emphasize different means of authentication. These reveal interesting facts about the self-image of these traditions....

  18. 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....

  19. 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.

  20. 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

  1. AIS authentication

    CERN Multimedia

    2006-01-01

    Users are invited to use the NICE password for AIS authentication. As announced in CNL June-August 2006 (see http://www.cerncourier.com/articles/cnl/3/6/14/1) it is possible to use the NICE username and password to log on to AIS. The procedure is now fully operational and users can themselves reset the AIS password such that the NICE password will be used for authentication required by AIS applications. We strongly recommend CERN users who have a NICE account (this is the case of most users) to do this, with the objective to reduce the number of passwords they need to remember. This can be achieved very easily, directly from the Change Password option on the AIS login (https://aislogin.cern.ch/). Users should just select the '[Change Password]' option displayed at the bottom of the page, provide the 'Old Password' and then click on the button 'Use Nice password' followed by 'Submit'. Change Password option on the AIS login windowSetting the AIS password - Use Nice Password It should be noted that the proce...

  2. 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

  3. Post-Session Authentication

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    2012-01-01

    Entity authentication provides confidence in the claimed identity of a peer entity, but the manner in which this goal is achieved results in different types of authentication. An important factor in this regard is the order between authentication and the execution of the associated session....... In this paper, we consider the case of post-session authentication, where parties authenticate each other at the end of their interactive session. This use of authentication is different from session-less authentication (e.g., in RFID) and pre-session authentication (e.g., for access control.) Post......-session authentication, although a new term, is not a new concept; it is the basis of at least a few practical schemes. We, for the first time, systematically study it and present the underlying authentication model. Further, we show that an important class of problems is solvable using post-session authentication...

  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. 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…

  6. 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

  7. Fingerprint Recognition on Various Authentication Sensors

    Institute of Scientific and Technical Information of China (English)

    A.Tirupathi Rao; N.Pattabhi Ramaiah; C.Krishna Mohan

    2014-01-01

    Fingerprint is a very popular and an ancient biometric technology to uniquely identify a person. In this paper, a fingerprint matcher is proposed which uses the global and local adaptive binarization and global minutia features. The fingerprint data is collected using three different authentication devices based on optical sensors. The experimental results are compared with the National Institute of Standards and Technology (NIST) Bozorth algorithm and various authentication fingerprint sensors. The accuracy of the proposed algorithm has been improved significantly compared with that of the NIST Bozorth algorithm.

  8. 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.

  9. Authenticating Performances

    DEFF Research Database (Denmark)

    Rudolph, Michael

    2015-01-01

    Adherents of performance theory emphasize the constitutive and transformative potential of rituals with respect to patterns of social organization and authority. For them, rituals “not only mean something, but also do something, particularly the way they construct and inscribe power relationships......” (Bell 1997). This contribution focuses on the role of ritual in postcolonial identity constitution and the performative authentication of political power and social authority in Taiwan. Since the middle of the 1990s, traditionalist performances have been on the rise on the island. Generously subsidized...... at the contemporary rituals of the Taroko and Ami, which are characterized by the above mentioned dynamics, I argue that rituals publicly performed by aborigines today amalgamate different levels of meaning. While they articulate and negotiate the identity needs and social exigencies of the respective social group...

  10. Should Teachers Be Authentic?

    Science.gov (United States)

    Bialystok, Lauren

    2015-01-01

    Authenticity is often touted as an important virtue for teachers. But what do we mean when we say that a teacher ought to be "authentic"? Research shows that discussions of teacher authenticity frequently refer to other character traits or simply to teacher effectiveness, but authenticity is a unique concept with a long philosophical…

  11. Definition of Entity Authentication

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    2010-01-01

    Authentication is considered a pre-requisite for communication security, but the definition of authentication is generally not agreed upon. Many attacks on authentication protocols are the result of misunderstanding of the goals of authentication. This state of affairs indicate limitations in the...

  12. 基于ITS序列分析对紫花地丁的分子鉴别%Molecular authentication of Viola yedoensis Makino and adulterants by analysis of rDNA ITS sequences

    Institute of Scientific and Technical Information of China (English)

    朱烨; 张春; 庄元春; 税丕先

    2013-01-01

    Objective: The rDNA ITS sequences of Viola yedoensis Makino and the adulterants were analyzed to establish the molecular biological method for authentication of Viola yedoensis Makino and the adulterants. Methods: Total DNA of Viola yedoensis Makino and the adulterants were extracted. The ITS sequence was amplified by universal primer. The PCR products were directly sequenced and both directions were sequenced. Results: 8 specific authenticate sites were found in the ITS1 and ITS2 region. Conclusion: The rDNA ITS sequence can be used as good marker for authenticating Viola yedoensis Makino from the adulterants.%目的:通过研究比较紫花地丁与其易混中药材ITS序列的差异和规律,建立紫花地丁与其易混药材之间的分子鉴别方法.方法:分别从紫花地丁和易混品中提取总DNA,用ITS序列通用引物扩增,扩增产物双向测序.结果:紫花地丁与其他易混品在ITS1和ITS2区段存在特异鉴别位点共8个.结论:根据ITS序列特征,能有效区分紫花地丁和其他易混中药材.ITS序列是紫花地丁鉴定的有效的分子标记.

  13. Authenticating the Leader

    DEFF Research Database (Denmark)

    Johnsen, Christian Garmann

    As authentic leadership, with its dictum of being true to the self, has become increasingly influential among practitioners and mainstream leadership scholars, critical writers have drawn attention to the negative consequences of this development. Yet, few scholars have investigated the problem...... of authentication within discourse of authentic leadership. If authentic leadership is to make any sense, it is necessary to be able to distinguish the authentic from the inauthentic leader – in other words, it is necessary to authenticate the leader. This paper uses Gilles Deleuze’s reading of Plato as the point...... of departure for discussing the problem of authentication – separating the authentic leader form the inauthentic one – in the leadership guru Bill George’s model of authentic leadership. By doing so, the paper offers a way of conceptualizing the problem of authenticating leaders, as well as challenging...

  14. 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...

  15. 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.

  16. Transparent User Authentication

    CERN Document Server

    Clarke, Nathan

    2011-01-01

    This groundbreaking text examines the problem of user authentication from a completely new viewpoint. Rather than describing the requirements, technologies and implementation issues of designing point-of-entry authentication, the book introduces and investigates the technological requirements of implementing transparent user authentication -- where authentication credentials are captured during a user's normal interaction with a system. This approach would transform user authentication from a binary point-of-entry decision to a continuous identity confidence measure. Topics and features: discu

  17. 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.

  18. 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.

  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. Authenticating the Leader

    DEFF Research Database (Denmark)

    Garmann Johnsen, Christian

    2015-01-01

    In the wake of a series of corporate scandals, there has been a growing call for authentic leadership in order to ensure ethical conduct in contemporary organizations. Authentic leadership, however, depends upon the ability to draw a distinction between the authentic and inauthentic leader....... This paper uses Deleuze’s discussion of Platonism as a point of departure for critically scrutinizing the problem of authenticating the leader - drawing a distinction between authentic and inauthentic leaders. This will be done through a reading of Bill George’s book Authentic Leadership. Informed by Deleuze......’s inverted Platonism, the paper challenges the practice by which authentic leaders are distinguished from inauthentic leaders. In conclusion, the paper suggests that an adequate concept of authentic leadership should consider how ethics can occur when the authentic leader is able to critically reflect his...

  2. 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

  3. 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...

  4. 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,...

  5. Vein matching using artificial neural network in vein authentication systems

    Science.gov (United States)

    Noori Hoshyar, Azadeh; Sulaiman, Riza

    2011-10-01

    Personal identification technology as security systems is developing rapidly. Traditional authentication modes like key; password; card are not safe enough because they could be stolen or easily forgotten. Biometric as developed technology has been applied to a wide range of systems. According to different researchers, vein biometric is a good candidate among other biometric traits such as fingerprint, hand geometry, voice, DNA and etc for authentication systems. Vein authentication systems can be designed by different methodologies. All the methodologies consist of matching stage which is too important for final verification of the system. Neural Network is an effective methodology for matching and recognizing individuals in authentication systems. Therefore, this paper explains and implements the Neural Network methodology for finger vein authentication system. Neural Network is trained in Matlab to match the vein features of authentication system. The Network simulation shows the quality of matching as 95% which is a good performance for authentication system matching.

  6. The Recognizability of Authenticity

    OpenAIRE

    Henderson, Madeleine; Gabora, Liane

    2013-01-01

    The goals of this research were to (1) determine if there is agreement both amongst viewers, and between viewers and the performer, about the extent to which performances are authentic, and (2) ascertain whether or not performers and/or viewers can distinguish between authenticity and skill. An authentic performance is one that is natural or genuine, while an inauthentic performance feels faked, forced, or imitative. Study participants were asked to rate the authenticity and skill level of a ...

  7. 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...

  8. Authenticity in Adult Learning

    Science.gov (United States)

    Ashton, Sam

    2010-01-01

    This paper is concerned with the relationship between authenticity and adult learning and prompted by some studies in which adult "authentic learning" is a central concept. The implication revealed by them is that real-worldness of learning contexts, learning content and learning tasks is perceived as conferring authenticity on learning. Here,…

  9. Authentication Assurance Levels

    International Nuclear Information System (INIS)

    This Common Criteria approach has been applied to create a definition of Authentication Assurance Levels that can quantify the level of assurance reached for a system subject to a set of authentication procedures. The arms-control authentication application of the Common Criteria expands on more typical information security evaluations in that it must contend with information barriers and preclude sophisticated intentional subversion attempts.

  10. 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.

  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. 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....

  13. Multi-factor authentication

    Energy Technology Data Exchange (ETDEWEB)

    Hamlet, Jason R; Pierson, Lyndon G

    2014-10-21

    Detection and deterrence of spoofing of user authentication may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a user of the hardware device. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a PUF value. Combining logic is coupled to receive the PUF value, combines the PUF value with one or more other authentication factors to generate a multi-factor authentication value. A key generator is coupled to generate a private key and a public key based on the multi-factor authentication value while a decryptor is coupled to receive an authentication challenge posed to the hardware device and encrypted with the public key and coupled to output a response to the authentication challenge decrypted with the private key.

  14. Authenticity in Employment Relations

    DEFF Research Database (Denmark)

    Tackney, Charles Thomas

    , it becomes possible to specify employment relations parameters between the indirect and direct employer and employees in a manner that will ensure working conditions consistent with these traditions, substantially enhancing the prospect of authenticity in employment relations. This theology of the workplace...... analysis should complement and support corporate social responsibility, management spirituality, authentic leadership / authentic follower, and other secular research by offering a research methods bridge between empirically grounded theology and secular studies, with the common goal of improving workplace...

  15. SECURE REMOTE CLIENT AUTHENTICATION

    Directory of Open Access Journals (Sweden)

    K.Pradeep,

    2010-10-01

    Full Text Available This paper discusses an application of Secure Remote Client Authentication. It presents a Smart Cards and Digitally certification from third party vendors, Smart cards are based on algorithm to provide secure Remote client Authentication. These schemes vary significantly.In relation to today’s security challenges, which includephishing, man-in-the-middle attacks and malicious software. Secure Remote Client authentication plays a key role.

  16. SECURE REMOTE CLIENT AUTHENTICATION

    OpenAIRE

    K.Pradeep,; R.Usha Rani; E.Ravi Kumar; K.Nikhila,; Vijay Sankar

    2010-01-01

    This paper discusses an application of Secure Remote Client Authentication. It presents a Smart Cards and Digitally certification from third party vendors, Smart cards are based on algorithm to provide secure Remote client Authentication. These schemes vary significantly.In relation to today’s security challenges, which includephishing, man-in-the-middle attacks and malicious software. Secure Remote Client authentication plays a key role.

  17. Sport and Authenticity

    OpenAIRE

    Bednář, Miloš

    2014-01-01

    This article focuses on the concept of authenticity as understood by Heidegger, Taylor, and Ferrara and its relationship to sport. I divide Heidegger’s unusual terms (existentiales) from “Being and time” into the categories of authenticity and inauthenticity and provide examples of each from the field of sport. In further I analyse the ethical standpoint of authenticity which is in the centre of both ethical and sociological discourse today. Taylor´s conceptions of moral ideal and culture of ...

  18. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens.

    Science.gov (United States)

    Weiß, Clemens L; Schuenemann, Verena J; Devos, Jane; Shirsekar, Gautam; Reiter, Ella; Gould, Billie A; Stinchcombe, John R; Krause, Johannes; Burbano, Hernán A

    2016-06-01

    Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens. PMID:27429780

  19. 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.

  20. 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...

  1. Single password authentication

    OpenAIRE

    Küpçü, Alptekin; Acar, Tolga; Belenkiy, Mira

    2013-01-01

    Single Password Authentication Tolga Acar∗ Intel Corporation, Bellevue, WA, USA Mira Belenkiy Microsoft Research, Redmond, WA, USA Alptekin K up c u† Ko c University, _Istanbul, TURKEY May 11, 2013 Abstract Users frequently reuse their passwords when authenticating to various online services. Com-bined with the use of weak passwords or honeypot/phishing attacks, this brings high risks to th...

  2. Authenticity and Imagination

    Science.gov (United States)

    Dirkx, John M.

    2006-01-01

    Central to development of authenticity in teaching is self-understanding and self-awareness. Using a Jungian perspective, the author suggests that the imaginative dimensions of the self play a critical role in our journey and experience as teachers, and in developing self-awareness and authenticity in our teaching.

  3. Brand new authentic places

    DEFF Research Database (Denmark)

    Stender, Marie

    How are places and material surroundings ascribed with meaning when new residential neighbourhoods are designed, branded and taken into use? Existing research on housing, neighbourhoods and urban design tends to take the perspective of either the architect or the user rather than to explore...... the relation and interplay between the two. This study strives to fill this gap by ethnographically tracing the process from design to occupancy including the role of branding as a means to create authenticity. The concept of authenticity is often associated with old houses and neighbourhoods, but also in new...... of community. The project explores the inherent paradox of such staging of authenticity by way of three research questions: 1) How are new houses and areas made authentic through stories told through material design and branding? 2) What different concepts of authenticity are at stake? 3) How are the stories...

  4. AUTHENTICITY IN THE BLOGOSPHERE

    Directory of Open Access Journals (Sweden)

    Waclaw Branicki

    2010-01-01

    Full Text Available The primary purpose of this article is to answer the question of whether writing a blog defined as a personal diary can help to better understand himself. Self-awareness is a prerequisite for authentic existence. In the first part analyzed the concept of authenticity. Pointed out the relationship of authenticity to the categories of freedom, truth and responsibility. The second part presents the relationship between authentic existence and the process of self-disclosure, which may take place in the blogosphere. In the third part presents the question whether a writing blog affects the level authenticity of existence. It was recognized that a key element of this phenomenon is the sense of responsibility.

  5. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.

    Science.gov (United States)

    Dabney, Jesse; Knapp, Michael; Glocke, Isabelle; Gansauge, Marie-Theres; Weihmann, Antje; Nickel, Birgit; Valdiosera, Cristina; García, Nuria; Pääbo, Svante; Arsuaga, Juan-Luis; Meyer, Matthias

    2013-09-24

    Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp. PMID:24019490

  6. Discovering your authentic leadership.

    Science.gov (United States)

    George, Bill; Sims, Peter; McLean, Andrew N; Mayer, Diana

    2007-02-01

    The ongoing problems in business leadership over the past five years have underscored the need for a new kind of leader in the twenty-first century: the authentic leader. Author Bill George, a Harvard Business School professor and the former chairman and CEO of Medtronic, and his colleagues, conducted the largest leadership development study ever undertaken. They interviewed 125 business leaders from different racial, religious, national, and socioeconomic backgrounds to understand how leaders become and remain authentic. Their interviews showed that you do not have to be born with any particular characteristics or traits to lead. You also do not have to be at the top of your organization. Anyone can learn to be an authentic leader. The journey begins with leaders understanding their life stories. Authentic leaders frame their stories in ways that allow them to see themselves not as passive observers but as individuals who learn from their experiences. These leaders make time to examine their experiences and to reflect on them, and in doing so they grow as individuals and as leaders. Authentic leaders also work hard at developing self-awareness through persistent and often courageous self-exploration. Denial can be the greatest hurdle that leaders face in becoming self-aware, but authentic leaders ask for, and listen to, honest feedback. They also use formal and informal support networks to help them stay grounded and lead integrated lives. The authors argue that achieving business results over a sustained period of time is the ultimate mark of authentic leadership. It may be possible to drive short-term outcomes without being authentic, but authentic leadership is the only way to create long-term results. PMID:17345686

  7. Richard Peters and Valuing Authenticity

    Science.gov (United States)

    Degenhardt, M. A. B.

    2009-01-01

    Richard Peters has been praised for the authenticity of his philosophy, and inquiry into aspects of the development of his philosophy reveals a profound authenticity. Yet authenticity is something he seems not to favour. The apparent paradox is resolved by observing historical changes in the understanding of authenticity as an important value.…

  8. Data Authentication Using Cryptography

    Directory of Open Access Journals (Sweden)

    Sagar Chouksey

    2013-06-01

    Full Text Available We present a novel approach using cryptographyfor data authentication. The key idea is to provide aencoded quantized data projection as authenticationdata. This can be correctly decoded with the help ofan authentic data using as side information.Cryptography source coding provides the desiredrobustness against legitimate variations whiledetecting illegitimate modification. Additionaladjustments might not change the meaning of thecontent, but could be misclassified as tampering.Users might also beinterested in localizingtampered regions. Distinguishing legitimateencodings with possible adjustments fromtampering and localizing tampering are thechallenges addressed in this paper. We applycryptography source coding and statistical methodsto solve the data authentication problem.Experimental results have been presented for dataauthentication.

  9. STUDENTS’ POTENTIAL FOR AUTHENTIC LEADERSHIP

    OpenAIRE

    Djurdja Solesa-Grijak; Dragan Solesa; Nedjo Kojic

    2015-01-01

    To know yourself and to act accordingly has been seen as a moral imperative throughout history. The aim of this research was to determine potential of students for authentic leadership and relation between their authentic personality and potential for authentic leadership. The sample consisted of students (N=133) from Serbia (male – 59% and female – 41%). The average age of students was M=21.9. Instruments used were Authenticity Scale (Wood et al., 2008) and Authentic Leadership Self-Assessme...

  10. 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

  11. Authentication of quantum messages.

    Energy Technology Data Exchange (ETDEWEB)

    Barnum, Howard; Crépeau, Jean-Claude; Gottesman, D. (Daniel); Smith, A. (Adam); Tapp, Alan

    2001-01-01

    Authentication is a well-studied area of classical cryptography: a sender A and a receiver B sharing a classical private key want to exchange a classical message with the guarantee that the message has not been modified or replaced by a dishonest party with control of the communication line. In this paper we study the authentication of messages composed of quantum states. We give a formal definition of authentication in the quantum setting. Assuming A and B have access to an insecure quantum channel and share a private, classical random key, we provide a non-interactive scheme that both enables A to encrypt and authenticate (with unconditional security) an m qubit message by encoding it into m + s qubits, where the probability decreases exponentially in the security parameter s. The scheme requires a private key of size 2m + O(s). To achieve this, we give a highly efficient protocol for testing the purity of shared EPR pairs. It has long been known that learning information about a general quantum state will necessarily disturb it. We refine this result to show that such a disturbance can be done with few side effects, allowing it to circumvent cryptographic protections. Consequently, any scheme to authenticate quantum messages must also encrypt them. In contrast, no such constraint exists classically: authentication and encryption are independent tasks, and one can authenticate a message while leaving it publicly readable. This reasoning has two important consequences: On one hand, it allows us to give a lower bound of 2m key bits for authenticating m qubits, which makes our protocol asymptotically optimal. On the other hand, we use it to show that digitally signing quantum states is impossible, even with only computational security.

  12. National Authentication Systems

    OpenAIRE

    Sandnes, Are Haugen

    2012-01-01

    Information security has to adapt to an ever-changing environment. Recently there has been a significant increase in the use of smartphones and other mobile devices to access services on the Internet that originally is designed for desktop computers.This thesis examines authentication systems on the Internet aimed at large user groups in light of the evolving threats due to increased use of mobile devices. It examines these authentication systems from the perspective of the end user and inves...

  13. DNA-Based Authentication of Botanicals and Plant-Derived Dietary Supplements: Where Have We Been and Where Are We Going?

    Science.gov (United States)

    Coutinho Moraes, Denise F; Still, David W; Lum, Michelle R; Hirsch, Ann M

    2015-06-01

    Herbal medicines and botanicals have long been used as sole or additional medical aids worldwide. Currently, billions of dollars are spent on botanicals and related products, but minimal regulation exists regarding their purity, integrity, and efficacy. Cases of adulteration and contamination have led to severe illness and even death in some cases. Identifying the plant material in botanicals and phytomedicines using organoleptic means or through microscopic observation of plant parts is not trivial, and plants are often misidentified. Recently, DNA-based methods have been applied to these products because DNA is not changed by growth conditions unlike the chemical constituents of many active pharmaceutical agents. In recent years, DNA barcoding methods, which are used to identify species diversity in the Tree of Life, have been also applied to botanicals and plant-derived dietary supplements. In this review, we recount the history of DNA-based methods for identification of botanicals and discuss some of the difficulties in defining a specific bar code or codes to use. In addition, we describe how next generation sequencing technologies have enabled new techniques that can be applied to identifying these products with greater authority and resolution. Lastly, we present case histories where dietary supplements, decoctions, and other products have been shown to contain materials other than the main ingredient stipulated on the label. We conclude that there is a fundamental need for greater quality control in this industry, which if not self-imposed, that may result from legislation. PMID:25856442

  14. Genetic Diversity among Ancient Nordic Populations

    DEFF Research Database (Denmark)

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R;

    2010-01-01

    , 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...

  15. Active Image Authentication System (AIAS

    Directory of Open Access Journals (Sweden)

    S. B. Nikam

    2013-09-01

    Full Text Available Today’s networking age provides greater importance to the authentication mechanism for security. Authentication is the process of identification of user or client respect to service parameters. These service parameters consist of unique combination of password associated with username or userid. Graphical based authentication mechanism had provided strong alternative for knowledge based, token based {&} biometric authentication mechanism. In this paper we are going to propose new graphical based authentication mechanism. This Active Image Authentication System (AIAS provides strong solution on guessing attack using random positioning of Active Points (AP with respect to time domain

  16. Password authentication in cloud

    Directory of Open Access Journals (Sweden)

    Indal Singh

    2015-09-01

    Full Text Available Cloud computing is an Internet-based computing, whereby shared resources, software, and information are provided to computers and other devices on demand. However, adopting a cloud computing paradigm may have positive as well as negative effects on the data security of service consumers [1]. Cloud Computing is a term used to describe both a platform and type of application. As a platform it supplies, configures and reconfigures servers, while the servers can be physical machines or virtual machines. On the other hand, Cloud Computing describes applications that are extended to be accessible through the internet and for this purpose large data centers and powerful servers are used to host the web applications and web services. Authentication is one the most important security primitive [6]. Password authentication is most widely used authentication mechanism. Password provides security mechanism for authentication and protection services against unwanted access to resource. In this paper, we applied a technique to preserve our password using graphical authentication.

  17. Authentication Without Secrets

    Energy Technology Data Exchange (ETDEWEB)

    Pierson, Lyndon G. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Robertson, Perry J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-11-01

    This work examines a new approach to authentication, which is the most fundamental security primitive that underpins all cyber security protections. Current Internet authentication techniques require the protection of one or more secret keys along with the integrity protection of the algorithms/computations designed to prove possession of the secret without actually revealing it. Protecting a secret requires physical barriers or encryption with yet another secret key. The reason to strive for "Authentication without Secret Keys" is that protecting secrets (even small ones only kept in a small corner of a component or device) is much harder than protecting the integrity of information that is not secret. Promising methods are examined for authentication of components, data, programs, network transactions, and/or individuals. The successful development of authentication without secret keys will enable far more tractable system security engineering for high exposure, high consequence systems by eliminating the need for brittle protection mechanisms to protect secret keys (such as are now protected in smart cards, etc.). This paper is a re-release of SAND2009-7032 with new figures numerous edits.

  18. QKD Quantum Channel Authentication

    CERN Document Server

    Kosloski, J T

    2006-01-01

    Several simple yet secure protocols to authenticate the quantum channel of various QKD schemes, by coupling the photon sender's knowledge of a shared secret and the QBER Bob observes, are presented. It is shown that Alice can encrypt certain portions of the information needed for the QKD protocols, using a sequence whose security is based on computational-complexity, without compromising all of the sequence's entropy. It is then shown that after a Man-in-the-Middle attack on the quantum and classical channels, there is still enough entropy left in the sequence for Bob to detect the presence of Eve by monitoring the QBER. Finally, it is shown that the principles presented can be implemented to authenticate the quantum channel associated with any type of QKD scheme, and they can also be used for Alice to authenticate Bob.

  19. Haunted by the authentic

    DEFF Research Database (Denmark)

    d'Ambrosio, Luigi

    2013-01-01

    Research description and purpose: The purpose of this investigation is to explore Danish guests’ experience when consuming ‘authentic’ Italian food in Italian restaurants in Denmark. In this context, the aim of the research is to engage in a discussion of the concept of authenticity in ethnic food...... consumption, and the guests’ experience with and reaction to the authentic culinary experience in ethnic restaurants in the consumers’ home country. Design/Methodology: The paper methodology is based on the use of mixed methods. A collection of primary quantitative and qualitative data through a questionnaire...... its findings, but, in line with its exploratory nature, to investigate the behaviour of Danish guests in relation to consumption of Italian food in an authentic setting. Originality/value: This paper looks at the relationship between the guest and the experience of ethnic food from a new perspective...

  20. Information barriers and authentication

    International Nuclear Information System (INIS)

    Acceptance of nuclear materials into a monitoring regime is complicated if the materials are in classified shapes or have classified composition. An attribute measurement system with an information barrier can be emplo,yed to generate an unclassified display from classified measurements. This information barrier must meet two criteria: (1) classified information cannot be released to the monitoring party, and (2) the monitoring party must be convinced that the unclassified output accurately represents the classified input. Criterion 1 is critical to the host country to protect the classified information. Criterion 2 is critical to the monitoring party and is often termed the 'authentication problem.' Thus, the necessity for authentication of a measurement system with an information barrier stems directly from the description of a useful information barrier. Authentication issues must be continually addressed during the entire development lifecycle of the measurement system as opposed to being applied only after the system is built.

  1. 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...

  2. Mega Key Authentication Mechanism

    OpenAIRE

    Kloss, Guy

    2016-01-01

    For secure communication it is not just sufficient to use strong cryptography with good and strong keys, but to actually have the assurance, that the keys in use for it are authentic and from the contact one is expecting to communicate with. Without that, it is possible to be subject to impersonation or man-in-the-middle (MitM) attacks. Mega meets this problem by providing a hierarchical authentication mechanism for contacts and their keys. To avoid any hassle when using multiple types of key...

  3. Two-factor authentication

    CERN Document Server

    Stanislav, Mark

    2015-01-01

    During the book, readers will learn about the various technical methods by which two-factor authentication is implemented, security concerns with each type of implementation, and contextual details to frame why and when these technologies should be used. Readers will also be provided with insight about the reasons that two-factor authentication is a critical security control, events in history that have been important to prove why organization and individual would want to use two factor, and core milestones in the progress of growing the market.

  4. 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…

  5. Low-bandwidth authentication.

    Energy Technology Data Exchange (ETDEWEB)

    Donnelly, Patrick Joseph; McIver, Lauren; Gaines, Brian R.; Anderson, Erik; Collins, Michael Joseph; Thomas,Kurt Adam; McDaniel, Austin

    2007-09-01

    Remotely-fielded unattended sensor networks generally must operate at very low power--in the milliwatt or microwatt range--and thus have extremely limited communications bandwidth. Such sensors might be asleep most of the time to conserve power, waking only occasionally to transmit a few bits. RFID tags for tracking or material control have similarly tight bandwidth constraints, and emerging nanotechnology devices will be even more limited. Since transmitted data is subject to spoofing, and since sensors might be located in uncontrolled environments vulnerable to physical tampering, the high-consequence data generated by such systems must be protected by cryptographically sound authentication mechanisms; but such mechanisms are often lacking in current sensor networks. One reason for this undesirable situation is that standard authentication methods become impractical or impossible when bandwidth is severely constrained; if messages are small, a standard digital signature or HMAC will be many times larger than the message itself, yet it might be possible to spare only a few extra bits per message for security. Furthermore, the authentication tags themselves are only one part of cryptographic overhead, as key management functions (distributing, changing, and revoking keys) consume still more bandwidth. To address this problem, we have developed algorithms that provide secure authentication while adding very little communication overhead. Such techniques will make it possible to add strong cryptographic guarantees of data integrity to a much wider range of systems.

  6. Reading Authentic Texts

    DEFF Research Database (Denmark)

    Balling, Laura Winther

    2013-01-01

    Most research on cognates has focused on words presented in isolation that are easily defined as cognate between L1 and L2. In contrast, this study investigates what counts as cognate in authentic texts and how such cognates are read. Participants with L1 Danish read news articles in their highly...

  7. Tools for Authentication

    Energy Technology Data Exchange (ETDEWEB)

    White, G

    2008-07-09

    Many recent Non-proliferation and Arms Control software projects include a software authentication component. In this context, 'authentication' is defined as determining that a software package performs only its intended purpose and performs that purpose correctly and reliably over many years. In addition to visual inspection by knowledgeable computer scientists, automated tools are needed to highlight suspicious code constructs both to aid the visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary, and have limited extensibility. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool must be based on a complete language compiler infrastructure, that is, one that can parse and digest the full language through its standard grammar. ROSE is precisely such a compiler infrastructure developed within DOE. ROSE is a robust source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C, C++, and FORTRAN. This year, it has been extended to support the automated analysis of binaries. We continue to extend ROSE to address a number of security-specific requirements and apply it to software authentication for Non-proliferation and Arms Control projects. We will give an update on the status of our work.

  8. Tools for Authentication

    International Nuclear Information System (INIS)

    Many recent Non-proliferation and Arms Control software projects include a software authentication component. In this context, 'authentication' is defined as determining that a software package performs only its intended purpose and performs that purpose correctly and reliably over many years. In addition to visual inspection by knowledgeable computer scientists, automated tools are needed to highlight suspicious code constructs both to aid the visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary, and have limited extensibility. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool must be based on a complete language compiler infrastructure, that is, one that can parse and digest the full language through its standard grammar. ROSE is precisely such a compiler infrastructure developed within DOE. ROSE is a robust source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C, C++, and FORTRAN. This year, it has been extended to support the automated analysis of binaries. We continue to extend ROSE to address a number of security-specific requirements and apply it to software authentication for Non-proliferation and Arms Control projects. We will give an update on the status of our work

  9. A video authentication technique

    International Nuclear Information System (INIS)

    Unattended video surveillance systems are particularly vulnerable to the substitution of false video images into the cable that connects the camera to the video recorder. New technology has made it practical to insert a solid state video memory into the video cable, freeze a video image from the camera, and hold this image as long as desired. Various techniques, such as line supervision and sync detection, have been used to detect video cable tampering. The video authentication technique described in this paper uses the actual video image from the camera as the basis for detecting any image substitution made during the transmission of the video image to the recorder. The technique, designed for unattended video systems, can be used for any video transmission system where a two-way digital data link can be established. The technique uses similar microprocessor circuitry at the video camera and at the video recorder to select sample points in the video image for comparison. The gray scale value of these points is compared at the recorder controller and if the values agree within limits, the image is authenticated. If a significantly different image was substituted, the comparison would fail at a number of points and the video image would not be authenticated. The video authentication system can run as a stand-alone system or at the request of another system

  10. 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

  11. [Application of rapid PCR to authenticate medicinal snakes].

    Science.gov (United States)

    Chen, Kang; Jiang, Chao; Yuan, Yuan; Huang, Lu-Qi; Li, Man

    2014-10-01

    To obtained an accurate, rapid and efficient method for authenticate medicinal snakes listed in Chinese Pharmacopoeia (Zaocysd humnades, Bungarus multicinctus, Agkistrodon acutus), a rapid PCR method for authenticate snakes and its adulterants was established based on the classic molecular authentication methods. DNA was extracted by alkaline lysis and the specific primers were amplified by two-steps PCR amplification method. The denatured and annealing temperature and cycle numbers were optimized. When 100 x SYBR Green I was added in the PCR product, strong green fluorescence was visualized under 365 nm UV whereas adulterants without. The whole process can complete in 30-45 minutes. The established method provides the technical support for authentication of the snakes on field.

  12. 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

  13. [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

  14. 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

  15. Anonymous Authentication for Smartcards

    Directory of Open Access Journals (Sweden)

    J. Hajny

    2010-06-01

    Full Text Available The paper presents an innovative solution in the field of RFID (Radio-Frequency IDentification smartcard authentication. Currently the smartcards are used for many purposes - e.g. employee identification, library cards, student cards or even identity credentials. Personal identity is revealed to untrustworthy entities every time we use these cards. Such information could later be used without our knowledge and for harmful reasons like shopping pattern scanning or even movement tracking. We present a communication scheme for keeping one’s identity private in this paper. Although our system provides anonymity, it does not allow users to abuse this feature. The system is based on strong cryptographic primitives that provide features never available before. Besides theoretical design of the anonymous authentication scheme and its analysis we also provide implementation results.

  16. Probabilistic authenticated quantum dialogue

    Science.gov (United States)

    Hwang, Tzonelih; Luo, Yi-Ping

    2015-12-01

    This work proposes a probabilistic authenticated quantum dialogue (PAQD) based on Bell states with the following notable features. (1) In our proposed scheme, the dialogue is encoded in a probabilistic way, i.e., the same messages can be encoded into different quantum states, whereas in the state-of-the-art authenticated quantum dialogue (AQD), the dialogue is encoded in a deterministic way; (2) the pre-shared secret key between two communicants can be reused without any security loophole; (3) each dialogue in the proposed PAQD can be exchanged within only one-step quantum communication and one-step classical communication. However, in the state-of-the-art AQD protocols, both communicants have to run a QKD protocol for each dialogue and each dialogue requires multiple quantum as well as classical communicational steps; (4) nevertheless, the proposed scheme can resist the man-in-the-middle attack, the modification attack, and even other well-known attacks.

  17. Challenge Measurements For Authentication

    International Nuclear Information System (INIS)

    Authentication of systems with an information barrier that protects sensitive information is difficult; in particular, the information barrier can allow a hidden switch to be implemented by the system fabricator and operator. The hidden switch is the operator's ability to subvert the measurement system and force it to produce a desired and false result. It is usually discussed in the context of an attribute measurement in which a faked item is presented in place of a real item regulated by an agreement, with the driving motivation being the ability to preserve a stock of valuable items. In simple terms, the hidden switch enables a shell game with assets, and the information barrier protects the switch. This presentation outlines challenge measurements that could be used to detect the implementation of a hidden switch and assist the authentication process.

  18. Abusing SIP authentication

    OpenAIRE

    Abdelnur H.; Avanesov T.; Rusinowitch M.; State R.

    2009-01-01

    International audience The recent and massive deployment of Voice over IP infrastructures had raised the importance of the VoIP security and more precisely of the underlying signalisation protocol SIP. In this paper, we will present a new attack against the authentication mechanism of SIP. This attack allows to perform toll fraud and call hijacking. We will detail the formal specification method that allowed to detect this vulnerability, highlight a simple usage case and propose a mitigati...

  19. International safeguards data authentication

    International Nuclear Information System (INIS)

    The International Safeguards community is becoming increasingly reliant on information stored in electronic form. In international monitoring and related activities it must be possible to verify and maintain the integrity of this electronic information. This paper discusses the use of data authentication technology to assist in accomplishing this task. The paper provides background information, identifies the relevance to international safeguards, discusses issues related to export controls, algorithm patents, key management and the use of commercial vs. custom software

  20. International safeguards data authentication

    Energy Technology Data Exchange (ETDEWEB)

    Melton, R.B.; Smith, C.E.; DeLand, S.M.; Manatt, D.R.

    1996-07-01

    The International Safeguards community is becoming increasingly reliant on information stored in electronic form. In international monitoring and related activities it must be possible to verify and maintain the integrity of this electronic information. This paper discusses the use of data authentication technology to assist in accomplishing this task. The paper provides background information, identifies the relevance to international safeguards, discusses issues related to export controls, algorithm patents, key management and the use of commercial vs. custom software.

  1. Authentication and Authorization Models

    Directory of Open Access Journals (Sweden)

    More V.N

    2011-04-01

    Full Text Available In computer science distributed systems could be more secured with a distributed trust model based on either PKIor Kerberos. However, it becomes difficult to establish trust relationship across heterogeneous domains due todifferent actual trust mechanism and security policy as well as the intrinsic flaw of each trust model. Since Internethas been used commonly in information systems technologies, many applications need some security capabilitiesto protect against threats to the communication of information. Two critical procedures of these capabilities areauthentication and authorization. This report presents a strong authentication and authorization model using threestandard frameworks. They are PKI, PMI, and Directory. The trust in this approach is enabled by the use of publickey infrastructure (PKI which is applied for client two-factor authentication and secures the infrastructure. Weintroduce the preventive activity-based authorization policy for dynamic user privilege controls. It helps preventsuccessive unauthorized requests in a formal manner. At the core, we apply An Improved Trust Model to facilitatethe authentication with the different keys with work flow of model efficiently. Also describes the X.509 standard todefine the directory schemas of PKI and PMI to find the object classes and optional attributes.

  2. 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...

  3. 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.

  4. Adolescent Perspectives on Authentic Writing Instruction

    Science.gov (United States)

    Behizadeh, Nadia

    2014-01-01

    Researchers and educators support the idea of providing authentic literacy experiences to students. However, a critical misconception of the locus of authenticity exists; the focus has generally been on making tasks authentic to college, careers, or researcher-determined notions of authenticity rather than making tasks authentic to students and…

  5. An Authentic RFLP Lab for High School or College Biology Students.

    Science.gov (United States)

    Guilfoile, Patrick G.; Plum, Stephen

    1998-01-01

    Explains how students can perform an alternative authentic DNA fingerprinting analysis. Presents restriction fragment length polymorphism (RFLP) analysis and can serve as a simulated molecular epidemiology laboratory or as a simulated forensic laboratory exercise. (DDR)

  6. An Exploration into Stage Authenticity

    OpenAIRE

    Hackett, Roxanna

    2009-01-01

    The authentic self is an expanding field of study, however little research has been done to conceptualise whether the nature of its existence is dependent on age-related social and personal demands. This research proposes that the manifestation of the authentic self is the subjective perception of behaviour which is congruent with an individual’s ‘true’ self. 97 participants carried out an extensive questionnaire which focused on the sense of authenticity across the lifespan along with detail...

  7. AUTHENTIC LEADERSHIP IN EDUCATIONAL INSTITUTIONS

    OpenAIRE

    Nebojsa Pavlovic

    2015-01-01

    This work investigates authentic leadership models in the organizational culture of a school. The aim of this quantitative research is to define the factors of authentic leadership in educational institutions in order to provide answers to the questions related to the existence of specific authentic leadership in a school. The sample included 227 randomly selected directors of secondary and primary schools in the former Yugoslav republics: Serbia, Montenegro, and the Republic Srpska. The rese...

  8. Mobile authentication problems and solutions

    CERN Document Server

    Jakobsson, Markus

    2012-01-01

    Mobile Authentication: Problems and Solutions looks at human-to-machine authentication, with a keen focus on the mobile scenario. Human-to-machine authentication is a startlingly complex issue. In the old days of computer security-before 2000, the human component was all but disregarded. It was either assumed that people should and would be able to follow instructions, or that end users were hopeless and would always make mistakes. The truth, of course, is somewhere in between, which is exactly what makes this topic so enticing. We cannot make progress with human-to-machine authentication with

  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. 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)

  11. Application of analytical methods in authentication and adulteration of honey.

    Science.gov (United States)

    Siddiqui, Amna Jabbar; Musharraf, Syed Ghulam; Choudhary, M Iqbal; Rahman, Atta-Ur-

    2017-02-15

    Honey is synthesized from flower nectar and it is famous for its tremendous therapeutic potential since ancient times. Many factors influence the basic properties of honey including the nectar-providing plant species, bee species, geographic area, and harvesting conditions. Quality and composition of honey is also affected by many other factors, such as overfeeding of bees with sucrose, harvesting prior to maturity, and adulteration with sugar syrups. Due to the complex nature of honey, it is often challenging to authenticate the purity and quality by using common methods such as physicochemical parameters and more specialized procedures need to be developed. This article reviews the literature (between 2000 and 2016) on the use of analytical techniques, mainly NMR spectroscopy, for authentication of honey, its botanical and geographical origin, and adulteration by sugar syrups. NMR is a powerful technique and can be used as a fingerprinting technique to compare various samples. PMID:27664687

  12. Trust Authentication Protocol on the Web

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    It is unsuitable to use traditional identity-based authentication on the Web where entities are not foreknown to each other. Trust relationship must be established between strangers before authentication. To achieve trust authentication, the resource-constrained trust negotiation is addressed, and traditional authentication key exchange protocol is extended. Owing to avoiding the heavy computational demands the public key cryptography operations bring about, the authentication protocol is well-suited for security authentication on the Web.

  13. Molecular authentication of geo-authentic Scrophularia ningpoensis

    Institute of Scientific and Technical Information of China (English)

    Chuan CHEN; Li-na DUAN; Xiao-long ZHOU; Bing-long CHEN; Cheng-xin FU

    2011-01-01

    Scrophularia ningpoensis has long been used in the Chinese Materia Medica for inflammation. Like other herbal medicines, S. ningpoensis collected from different localities may considerably differ in their therapeutic efficacy,and the one grown in Zhejiang Province is recognized as geo-authentic. However, it is difficult to confirm the geographical authenticity by similar morphological characteristics. In the present study, inter-simple sequence repeat (ISSR) markers were conducted to detect S. ningpoensis from different origins. A 1259-bp fragment amplified by primer UBC874 was found only in geo-authentic ones. By cloning and sequencing that specific band, sequence characterized amplified region (SCAR) markers were designed to distinguish geo-authentic S. ningpoensis from others.This is a rapid and easy method that can be used to identify the geographical authenticity of S. ningpoensis.

  14. QKD Quantum Channel Authentication

    OpenAIRE

    Kosloski, J. T.

    2006-01-01

    Several simple yet secure protocols to authenticate the quantum channel of various QKD schemes, by coupling the photon sender's knowledge of a shared secret and the QBER Bob observes, are presented. It is shown that Alice can encrypt certain portions of the information needed for the QKD protocols, using a sequence whose security is based on computational-complexity, without compromising all of the sequence's entropy. It is then shown that after a Man-in-the-Middle attack on the quantum and c...

  15. Anonymous authenticated communications

    Science.gov (United States)

    Beaver, Cheryl L.; Schroeppel, Richard C.; Snyder, Lillian A.

    2007-06-19

    A method of performing electronic communications between members of a group wherein the communications are authenticated as being from a member of the group and have not been altered, comprising: generating a plurality of random numbers; distributing in a digital medium the plurality of random numbers to the members of the group; publishing a hash value of contents of the digital medium; distributing to the members of the group public-key-encrypted messages each containing a same token comprising a random number; and encrypting a message with a key generated from the token and the plurality of random numbers.

  16. Genetic authentication of ginsengand other traditional Chinese medicine

    Institute of Scientific and Technical Information of China (English)

    CCHON; YCCHOW; FYZENG; FCCLEUNG

    2003-01-01

    The main objective of this paper is to review the chemical and genetic methods used in authentication ofginseng, especially the recent advances in microsatellite genotyping and its application to the authentication of othertraditional Chinese medicines (TCM). The standardization and modernization of TCM hinge on the authenticationof their botanical identities. Analysis of well-characterized marker compounds is now the most popular method foridentifying the herbal materials and quality control of TCM, eg, ginsenoside profiling for authentication of Panaxspecies. However, in many herbal species the chemical composition of the plant changes with the external environment and processing conditions, which lowers the reliability of these authentication methods. In the light of theadvances in molecular biotechnology in the past few decades, genetic tools are now considered to provide morestandardized and reliable methods for authentication of herbal materials at the DNA level. These genetic toolsinclude random amplified polymorphic DNA (RAPD), DNA fingerprinting using multi-loci probes, restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), and microsatellite markertechnology. The practicality of these methods varies in terms of their sensitivity, reliability, reproducibility, andrunning cost. Using ginseng as an example, we reviewed the advantages and limitations of these molecular tech-niques in TCM authentication. We have developed a set of microsatellite markers from American ginseng that areable to differentiate Panax ginseng and Panax quinquetolius with the resolution down to farm level, ie, confirmationof its botanical identity and origin. Compared with other molecular techniques, microsatellite marker technology ismore robust, accurate, reproducible, reliable, and sensitive. This is essential for large-scale TCM authenticationcenters.

  17. Art Activities about Mesopotamia, Egypt and Islam. Hands-On Ancient People.

    Science.gov (United States)

    Merrill, Yvonne Y.

    This book features objects of the Mesopotamian, the Egyptian, and Islamic cultures. In exploring important contributions in ancient art, the book presents visuals that are interpretations of authentic artifacts, usually in museum collections, or illustrations from archaeological publications and articles. Historical items (n=55+) have been adapted…

  18. Authenticity, Culture and Language Learning

    Science.gov (United States)

    MacDonald, Malcolm N.; Badger, Richard; Dasli, Maria

    2006-01-01

    In philosophy, authenticity has been used with two meanings: one entails the notion of correspondence; the other entails the notion of genesis (Cooper, 1983: 15). As in certain branches of philosophy, language teaching has perhaps clung too long to the first of these notions of authenticity at the expense of the other. This paper reviews four key…

  19. AVNG authentication features

    International Nuclear Information System (INIS)

    Any verification measurement performed on potentially classified nuclear material must satisfy two seemingly contradictory constraints. First and foremost, no classified information can be released. At the same time, the monitoring party must have confidence in the veracity of the measurement (called authentication). An information barrier (IB) is included in the measurement system to protect the potentially classified information. To achieve both goals, the IB allows only very limited, previously agreed-on information to be displayed to the monitoring party. In addition to this limited information from the potentially classified measurement, other measurements are performed and procedures are put in place for the monitoring party to gain confidence that the material being measured is consistent with the host's declarations concerning that material. In this presentation, we will discuss the techniques used in the AVNG attribute measuring system to facilitate authentication of the verification measurements by the monitors. These techniques include measuring unclassified items while allowing more information to be displayed; having the monitor understand the system function, design, and implementation; and randomly selecting the order of measurements.

  20. Authentic, Original, and Valuable

    DEFF Research Database (Denmark)

    Tupasela, Aaro Mikael; Tamminen, Sakari

    2015-01-01

    The idea of genetic authenticity and origin has been an important issue within genetics for decades for scientific, political, and economic reasons. The question of where species and populations come from, as well as the linking of genetic traits to particular geographical locations, has resurfac....... Using the case of human and non-human genetics to compare and contrast the various facets associated with genetic identity, we seek to develop a broader picture of the ways in which genetics plays an important role in stabilizing categories of origin.......The idea of genetic authenticity and origin has been an important issue within genetics for decades for scientific, political, and economic reasons. The question of where species and populations come from, as well as the linking of genetic traits to particular geographical locations, has resurfaced...... as both a scientific and political site of interest more recently through the study of population genetics in both humans and non-humans. This article explores the ways in which genetics and notions of ‘authentic’, ‘indigenous’, and ‘endemic’ have become intertwined with everyday practices in research...

  1. Message Authentication over Noisy Channels

    Directory of Open Access Journals (Sweden)

    Fanfan Zheng

    2015-01-01

    Full Text Available The essence of authentication is the transmission of unique and irreproducible information. In this paper, the authentication becomes a problem of the secure transmission of the secret key over noisy channels. A general analysis and design framework for message authentication is presented based on the results of Wyner’s wiretap channel. Impersonation and substitution attacks are primarily investigated. Information-theoretic lower and upper bounds on the opponent’s success probability are derived, and the lower bound and the upper bound are shown to match. In general, the fundamental limits on message authentication over noisy channels are fully characterized. Analysis results demonstrate that introducing noisy channels is a reliable way to enhance the security of authentication.

  2. A 28,000 years old Cro-Magnon mtDNA sequence differs from all potentially contaminating modern sequences.

    Directory of Open Access Journals (Sweden)

    David Caramelli

    Full Text Available BACKGROUND: DNA sequences from ancient specimens 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 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23 and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. CONCLUSIONS/SIGNIFICANCE: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.

  3. 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.

  4. 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.

  5. High Resolution Melting (HRM) applied to wine authenticity.

    Science.gov (United States)

    Pereira, Leonor; Gomes, Sónia; Castro, Cláudia; Eiras-Dias, José Eduardo; Brazão, João; Graça, António; Fernandes, José R; Martins-Lopes, Paula

    2017-02-01

    Wine authenticity methods are in increasing demand mainly in Denomination of Origin designations. The DNA-based methodologies are a reliable means of tracking food/wine varietal composition. The main aim of this work was the study of High Resolution Melting (HRM) application as a screening method for must and wine authenticity. Three sample types (leaf, must and wine) were used to validate the three developed HRM assays (Vv1-705bp; Vv2-375bp; and Vv3-119bp). The Vv1 HRM assay was only successful when applied to leaf and must samples. The Vv2 HRM assay successfully amplified all sample types, allowing genotype discrimination based on melting temperature values. The smallest amplicon, Vv3, produced a coincident melting curve shape in all sample types (leaf and wine) with corresponding genotypes. This study presents sensitive, rapid and efficient HRM assays applied for the first time to wine samples suitable for wine authenticity purposes. PMID:27596395

  6. High Resolution Melting (HRM) applied to wine authenticity.

    Science.gov (United States)

    Pereira, Leonor; Gomes, Sónia; Castro, Cláudia; Eiras-Dias, José Eduardo; Brazão, João; Graça, António; Fernandes, José R; Martins-Lopes, Paula

    2017-02-01

    Wine authenticity methods are in increasing demand mainly in Denomination of Origin designations. The DNA-based methodologies are a reliable means of tracking food/wine varietal composition. The main aim of this work was the study of High Resolution Melting (HRM) application as a screening method for must and wine authenticity. Three sample types (leaf, must and wine) were used to validate the three developed HRM assays (Vv1-705bp; Vv2-375bp; and Vv3-119bp). The Vv1 HRM assay was only successful when applied to leaf and must samples. The Vv2 HRM assay successfully amplified all sample types, allowing genotype discrimination based on melting temperature values. The smallest amplicon, Vv3, produced a coincident melting curve shape in all sample types (leaf and wine) with corresponding genotypes. This study presents sensitive, rapid and efficient HRM assays applied for the first time to wine samples suitable for wine authenticity purposes.

  7. AUTHENTIC LEADERSHIP IN EDUCATIONAL INSTITUTIONS

    Directory of Open Access Journals (Sweden)

    Nebojsa Pavlovic

    2015-06-01

    Full Text Available This work investigates authentic leadership models in the organizational culture of a school. The aim of this quantitative research is to define the factors of authentic leadership in educational institutions in order to provide answers to the questions related to the existence of specific authentic leadership in a school. The sample included 227 randomly selected directors of secondary and primary schools in the former Yugoslav republics: Serbia, Montenegro, and the Republic Srpska. The research included the use of an ALQ questionnaire for the estimation of leadership behavior. The components of authentic leadership are defined using factor analysis and other statistics techniques. The findings developed in this research indicated the fact that directors in educational institutions have a specific authentic leadership style. We suggest the concept of authentic leadership based on the four following factors: Communication-conformist, self-consciousness, self-discovery, and self-concept. Supporting these factors provides the directors with the possibility of obtaining a high level of authentic leadership.

  8. [Problems of food authenticity].

    Science.gov (United States)

    Czerwiecki, Ludwik

    2004-01-01

    In this review the several data concerning food authenticity were presented. Typical examples of food adulteration were described. The most known are adulteration of vegetable and fruit products, adulteration of wine, honeys, olive oil etc. The modern analytical techniques for detection of food adulteration were discussed. Among physicochemical methods isotopic techniques (SCIRA, IRMS, SNIF-NMR) were cited. The main spectral methods are: IACPAES, PyMs, FTIR, NIR. The chromatographic techniques (GC, HPLC, HPAEC, HPTLC) with several kinds of detectors were described and the ELISA and PCR techniques are mentioned, too. The role of chemometrics as a way of several analytical data processing was highlighted. It was pointed out at the necessity of more rigorous control of food to support of all activity in area of fight with fraud in food industry.

  9. 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...

  10. Is Authentic a thing of the Past?

    OpenAIRE

    Mac Con Iomaire, Máirtín

    2005-01-01

    This article is a review of the Oxford Symposium on Food and Cookery 2005 where the theme was Authenticity. It discusses the subject of Autheniticity in food and asks whether there is such a thing? What is Authenticity? Who can define what Authenticity means in the context of food? Is authenticity in food an indulgence of the rich which stiffles creativity and invention?

  11. Authenticity in CALL: Three Domains of "Realness"

    Science.gov (United States)

    Buendgens-Kosten, Judith

    2013-01-01

    This paper discusses the role of authenticity and authenticity claims in computer assisted language learning (CALL). It considers authenticity as the result of a social negotiation process rather than an innate feature of a text, object, person, or activity. From this basis, it argues that authenticity claims play an important role in both second…

  12. Authentic leadership: application to women leaders

    OpenAIRE

    Hopkins, Margaret M.; O’Neil, Deborah A.

    2015-01-01

    The purpose of this perspective article is to present the argument that authentic leadership is a gendered representation of leadership. We first provide a brief history of leadership theories and definitions of authentic leadership. We then critique authentic leadership and offer arguments to support the premise that authentic leadership is not gender-neutral and is especially challenging for women.

  13. Authentic leadership: application to women leaders.

    Science.gov (United States)

    Hopkins, Margaret M; O'Neil, Deborah A

    2015-01-01

    The purpose of this perspective article is to present the argument that authentic leadership is a gendered representation of leadership. We first provide a brief history of leadership theories and definitions of authentic leadership. We then critique authentic leadership and offer arguments to support the premise that authentic leadership is not gender-neutral and is especially challenging for women. PMID:26236254

  14. Physical trust-based persistent authentication

    DEFF Research Database (Denmark)

    Fujita, Masahiro; Jensen, Christian D.; Arimura, Shiori;

    2015-01-01

    Recently companies have applied two-factor user authentication. Persistent Authentication is one of the interesting authentication mechanisms to establish security and usability of two-factor authentication systems. However, there is room to improve its feasibility and usability. In this paper, we...... propose a new type of persistent authentication, called Persistent Authentication Based On physical Trust (PABOT). PABOT uses a context of “physical trust relationship” that is built by visual contact between users, and thus can offer a persistent authentication mechanism with better usability and higher...

  15. Effects of Helping on State Authenticity Versus Recalled Authenticity

    OpenAIRE

    Allan, Clare M.

    2011-01-01

    This study focuses on the under-researched subject of “state authenticity”, the experience of expressing one’s true self. The 2 major hypotheses of the causes of state authenticity are tested: behavioural content versus consistency with personal traits. Investigations examine the proposal that behaviour expressing values, specifically “helping others” increases state authenticity, regardless of an individual’s own helpfulness-traits. Using a web-based survey, 238 participants were randomly as...

  16. Authenticity and commoditization at home

    DEFF Research Database (Denmark)

    Stender, Marie

    . The aim is to unfold how forces of commoditization and singularization intertwine as the house is transformed from an architectural expression into real estate for sale and eventually into somebody's home. What tensions are revealed in this process and how are interest and affect entangled? Authenticity......This paper investigates how interest and affect are entangled in the built environment of new Danish homes. The paper unfolds tensions and conflicts in the process from design through branding to occupancy of the house, and the relationship between authenticity and commoditization is explored....... In Denmark, the concept of authenticity is often associated with old houses. By way of design and branding, though, new neighbourhoods are made authentic, referring to their historical past, architectural uniqueness or sense of community. Based on a fieldwork in three new residential buildings in Copenhagen...

  17. Research on Mixed Encryption Authentication

    Institute of Scientific and Technical Information of China (English)

    SUN Zhi-xin; WANG Ru-chuan; WANG Shao-di

    2003-01-01

    With the development of network techniques, the problem of network security is also arising as we enjoy its open convenience. There are many developed methods to overcome this problem. Identity authentication is one of these important measures. The authentication methods of traditional symmetric cryptogram systems and asymmetric cryptogram systems have both advantages and defects. This paper brings forward a Mixed Encryption Model for Authentication (MEMA), which has obvious advantages compared to the two traditional methods. MEMA model can be used widely in opening network environment such as mobile agent systems, multi-agents security safeguard systems and other situations in which identity authentication of users are needed. At last, the paper also presents the MEMA model's structure and implementation of an experimental system.

  18. Robustness of digital artist authentication

    DEFF Research Database (Denmark)

    Jacobsen, Robert; Nielsen, Morten

    In many cases it is possible to determine the authenticity of a painting from digital reproductions of the paintings; this has been demonstrated for a variety of artists and with different approaches. Common to all these methods in digital artist authentication is that the potential of the method...... is in focus, while the robustness has not been considered, i.e. the degree to which the data collection process influences the decision of the method. However, in order for an authentication method to be successful in practice, it needs to be robust to plausible error sources from the data collection....... In this paper we investigate the robustness of the newly proposed authenticity method introduced by the authors based on second generation multiresolution analysis. This is done by modelling a number of realistic factors that can occur in the data collection....

  19. Analysis and Authenticity Investigations of Glass and Metallic Art Objects

    International Nuclear Information System (INIS)

    A suite of glass pieces of Art, and several metal-based corroded objects were studied in the frame of this project, which intends to accommodate two purposes; a) to investigate the feasibility of physico-chemical characterization of ancient glass by employing a non-widely used analytical technique, that of luminescence spectroscopy, along with conventionally used methods such as XRF and SEM-EDX, and b) to approach issues of counterfeiting of culturally-related iron and other metallic objects, by examining the features of their corrosion products, studied via a combination of the non-destructive RF-plasma treatment and the microscopic techniques. The results of the study show that luminescence measurements own diagnostic power that can aid substantially to the classifying and understanding of the manufacturing of ancient glass, particularly when bridged with longer-established analytical methods. Moreover, evident differences between corrosion layers of authentic metallic objects and of the ones created after artificial pre-corrosion, as ascertained by the plasma treatment and by microscopy (SEM or optical) study, provide a basis for suggesting such a combination of techniques for authenticity detection of corroded metallic objects with cultural heritage importance. (author)

  20. Capillary electrophoresis in food authenticity.

    Science.gov (United States)

    Kvasnicka, Frantisek

    2005-06-01

    Food authenticity is a term which simply refers to whether the food purchased by the consumer matches its description. False description can occur in many forms, from the undeclared addition of water or other cheaper materials, or the wrong declaration of the amount of a particular ingredient in the product, to making false statements about the source of ingredients i.e., their geographic, plant, or animal origin. The aim of this review is to summarize applications of capillary electrophoresis in food authentication.

  1. Quantum direct communication with authentication

    International Nuclear Information System (INIS)

    We propose two quantum direct communication (QDC) protocols with user authentication. Users can identify each other by checking the correlation of Greenberger-Horne-Zeilinger (GHZ) states. Alice can directly send a secret message to Bob without any previously shared secret using the remaining GHZ states after authentication. Our second QDC protocol can be used even though there is no quantum link between Alice and Bob. The security of the transmitted message is guaranteed by properties of entanglement of GHZ states

  2. The myxomycete genus Schenella: morphological and DNA sequence evidence for synonymy with the gasteromycete genus Pyrenogaster.

    Science.gov (United States)

    Estrada-Torres, Arturo; Gaither, Thomas W; Miller, Dennis L; Lado, Carlos; Keller, Harold W

    2005-01-01

    The genus Schenella has proven difficult to classify since its description as a new genus in 1911. Macbride placed it with the Myxomycetes but it was unclear with which myxomycete, if any, it should be grouped. Recent identification of abundant samples of Schenella has aided a re-evaluation of its classification as a myxomycete. Morphological evidence based on light and scanning electron microscopy of recently collected specimens and on the type specimen of Macbride suggested that it might be synonymous with the gasteromycete Pyrenogaster Analysis of DNA sequences from freshly isolated samples indicates that the genus Schenella is related closely to an anciently diverged, monophyletic group of fungi that includes several gasteromycete genera, among them Geastrum, Sphaerobolus and Pseudocolus. Comparisons of the morphology and DNA sequences of authentically identified specimens of Pyrenogaster atrogleba indicate that it is synonymous with Schenella simplex. The nomenclatural implications of this discovery are discussed. PMID:16389965

  3. 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...

  4. Teaching Materials Should be Authentic

    Institute of Scientific and Technical Information of China (English)

    俞莹

    2008-01-01

    <正>In terms of the teaching materials,we hold the opinion that authentic materials should be adapted in the process of teaching,and students should have access to the original language. According to Richards(2001),authentic materials refer to the use in teaching of texts,photographs, video selections,and other teaching resources that were not specially prepared for pedagogical purposes.Created materials refer to textbooks and other specially developed instructional resources. The use of authentic materials in an EFL classroom is what many teachers involved in foreign language teaching have discussed in recent years.Most of the teachers throughout the world agree that authentic texts or materials are beneficial to the language learning process.Authentic materials enable learners to interact with the real language and content rather than the form.Learners feel that they are learning a target language as it is used outside the classroom.Exposing students to authentic materials can also help them better understand the target culture and envision how they might participate in this community.

  5. Molecular authentication of the traditional medicinal plant Fallopia multiflora.

    Science.gov (United States)

    Zheng, Chuan-Jin; Zhao, Shu-Jin; Zhao, Zhen-Hua; Guo, Jun

    2009-06-01

    The root of Fallopia multiflora is one of the most widely used traditional Chinese medicines. However, it is often confused and substituted with the roots of F. multiflora var. ciliinervis, Pteroxygonum giraldii, Cynanchum auriculatum, and Stephania cepharantha. To establish a DNA polymorphism-based assay for the identification of F. multiflora, the nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) regions of six Fallopia species were sequenced and analyzed. Based on the diversity of ITS regions among the species the diagnostic primers PMITS28 and PMITS545, which amplified an expected 517-bp DNA fragment from F. multiflora DNA, were designed. No amplified product was observed when DNA from other species was used. This method can be used for the authentication of F. multiflora. PMID:19242903

  6. 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...

  7. Authentication of Fish Products by Large-Scale Comparison of Tandem Mass Spectra

    DEFF Research Database (Denmark)

    Wulff, Tune; Nielsen, Michael Engelbrecht; Deelder, André M.;

    2013-01-01

    Authentication of food is a major concern worldwide to ensure that food products are correctly labeled in terms of which animals are actually processed for consumption. Normally authentication is based on species recognition by comparison of selected sequences of DNA or protein. We here present...... a new robust, proteome-wide tandem mass spectrometry method for species recognition and food product authentication. The method does not use or require any genome sequences or selection of tandem mass spectra but uses all acquired data. The experimental steps were performed in a simple, standardized...

  8. Efficient and secure source authentication scheme for multicast user authentication

    Institute of Scientific and Technical Information of China (English)

    JEONG; Yoon-su; LEE; Sang-hyuk; SHIN; Seung-soo

    2013-01-01

    Multicast technology application has been widely utilized in broadband internet. Source authentication is one of the most needs for many multicast applications transferring real-time information such as stream video and online news. Because multicast current services provided to the group members are changed dynamically, data transferring by a group member is not used by the recipient. In order to verify the identity of the sender who sent the packet and to make sure that the data have not been tampered, an optimized source authentication scheme has been proposed to transfer the authentication information not to the next-door packet. The proposed method for multiple packets authenticates the source with a limited number of electronic signatures. The proposed method can reduce overhead compared to the method by adding a digital signature for every packet. In addition, by sending the generated electronic signature to the first packet and the last packet, it prevents the loss of consecutive packets, as well as a source authentication can be provided in real-time services.

  9. [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

  10. Use of neutron diffraction and laser-induced plasma spectroscopy in integrated authentication methodologies of copper alloy artefacts

    International Nuclear Information System (INIS)

    The present study approaches the general problem of the authentication of copper alloy artefacts of art and historical interest using non-invasive analytical techniques. It aims to demonstrate that a suitable combination of time-of-flight neutron diffraction and laser-induced plasma spectroscopy in integrated multidisciplinary authentication methodologies can provide crucial data for discriminating between genuine archaeological objects and modern counterfeits. After introducing the methodology, which is dedicated in particular to copper alloy figurines of ancient style, two representative authentication case studies are discussed. The results of the work provide evidence that the combination of multiphase analysis using TOF-N D and elemental depth profiles provided by Lips makes it possible to solve most of the present authentication problems.

  11. Using Mobile Devices for User Authentication

    Science.gov (United States)

    Lach, Jacek

    One of the most common methods of user authentication utilizes passwords. This technique is widely spread and well known. Its main drawback is that it stresses human memory to allow for successful authentication and still remains in the domain which is called weak authentication. This paper presents a solution to this problem by introducing a form of two factor authentication by utilization of smartphones. The idea of such system is presented as well as a sample implementation, called MOTH (an acronym for MObile auTHentication), which allows for user authentication. The discussion of the system's security and its limitations is also presented.

  12. Sequence Patterns of Identity Authentication Protocols

    Institute of Scientific and Technical Information of China (English)

    Tao Hongcai; He Dake

    2006-01-01

    From the viewpoint of protocol sequence, analyses are made of the sequence patterns of possible identity authentication protocol under two cases: with or without the trusted third party (TTP). Ten feasible sequence patterns of authentication protocol with TTP and 5 sequence patterns without TTP are gained. These gained sequence patterns meet the requirements for identity authentication,and basically cover almost all the authentication protocols with TTP and without TTP at present. All of the sequence patterns gained are classified into unilateral or bilateral authentication. Then , according to the sequence symmetry, several good sequence patterns with TTP are evaluated. The accompolished results can provide a reference to design of new identity authentication protocols.

  13. 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.

  14. 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...

  15. Ancient deforestation revisited.

    Science.gov (United States)

    Hughes, J Donald

    2011-01-01

    The image of the classical Mediterranean environment of the Greeks and Romans had a formative influence on the art, literature, and historical perception of modern Europe and America. How closely does is this image congruent with the ancient environment as it in reality existed? In particular, how forested was the ancient Mediterranean world, was there deforestation, and if so, what were its effects? The consensus of historians, geographers, and other scholars from the mid-nineteenth century through the first three quarters of the twentieth century was that human activities had depleted the forests to a major extent and caused severe erosion. My research confirmed this general picture. Since then, revisionist historians have questioned these conclusions, maintaining instead that little environmental damage was done to forests and soils in ancient Greco-Roman times. In a reconsideration of the question, this paper looks at recent scientific work providing proxy evidence for the condition of forests at various times in ancient history. I look at three scientific methodologies, namely anthracology, palynology, and computer modeling. Each of these avenues of research offers support for the concept of forest change, both in abundance and species composition, and episodes of deforestation and erosion, and confirms my earlier work.

  16. 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…

  17. 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…

  18. 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

  19. 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…

  20. 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…

  1. 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

  2. Improving Usability of Passphrase Authentication

    DEFF Research Database (Denmark)

    Nielsen, Glen; Vedel, Michael; Jensen, Christian D.

    2014-01-01

    The combination of user-names and passwords has become the predominant method of user authentication in computer systems. Most users have multiple accounts on different systems, which impose different constraints on the length and complexity of passwords that the user is allowed to select. This is...... done to ensure an appropriate degree of security, but instead, it makes it difficult for users to remember their password, which results in passwords that are either insecure, but easy to remember, or written down on paper. In this paper we address the problem of usability in user authentication......, which accepts the most common typing mistakes. The proposed algorithm has been implemented in secure hardware and integrated into a standard Unix system. We present the design, implementation and preliminary evaluation of the developed passphrase authentication prototype....

  3. Biometric Authentication using Nonparametric Methods

    CERN Document Server

    Sheela, S V; 10.5121/ijcsit.2010.2309

    2010-01-01

    The physiological and behavioral trait is employed to develop biometric authentication systems. The proposed work deals with the authentication of iris and signature based on minimum variance criteria. The iris patterns are preprocessed based on area of the connected components. The segmented image used for authentication consists of the region with large variations in the gray level values. The image region is split into quadtree components. The components with minimum variance are determined from the training samples. Hu moments are applied on the components. The summation of moment values corresponding to minimum variance components are provided as input vector to k-means and fuzzy kmeans classifiers. The best performance was obtained for MMU database consisting of 45 subjects. The number of subjects with zero False Rejection Rate [FRR] was 44 and number of subjects with zero False Acceptance Rate [FAR] was 45. This paper addresses the computational load reduction in off-line signature verification based o...

  4. Biometric Authentication using Nonparametric Methods

    CERN Document Server

    Sheela, S V; 10.5121/ijcsit.2010.2309

    2010-01-01

    The physiological and behavioral trait is employed to develop biometric authentication systems. The proposed work deals with the authentication of iris and signature based on minimum variance criteria. The iris patterns are preprocessed based on area of the connected components. The segmented image used for authentication consists of the region with large variations in the gray level values. The image region is split into quadtree components. The components with minimum variance are determined from the training samples. Hu moments are applied on the components. The summation of moment values corresponding to minimum variance components are provided as input vector to k-means and fuzzy k-means classifiers. The best performance was obtained for MMU database consisting of 45 subjects. The number of subjects with zero False Rejection Rate [FRR] was 44 and number of subjects with zero False Acceptance Rate [FAR] was 45. This paper addresses the computational load reduction in off-line signature verification based ...

  5. Designing Pu600 for Authentication

    Energy Technology Data Exchange (ETDEWEB)

    White, G

    2008-07-10

    Many recent Non-proliferation and Arms Control software projects include an authentication component. Demonstrating assurance that software and hardware performs as expected without hidden 'back-doors' is crucial to a project's success. In this context, 'authentication' is defined as determining that the system performs only its intended purpose and performs that purpose correctly and reliably over many years. Pu600 is a mature software solution for determining the presence of Pu and the ratio of Pu240 to Pu239 by analyzing the gamma ray spectra in the 600 KeV region. The project's goals are to explore hardware and software technologies which can by applied to Pu600 which ease the authentication of a complete, end-to-end solution. We will discuss alternatives and give the current status of our work.

  6. Improving Usability of Passphrase Authentication

    DEFF Research Database (Denmark)

    Nielsen, Glen; Vedel, Michael; Jensen, Christian D.

    2014-01-01

    The combination of user-names and passwords has become the predominant method of user authentication in computer systems. Most users have multiple accounts on different systems, which impose different constraints on the length and complexity of passwords that the user is allowed to select....... This is done to ensure an appropriate degree of security, but instead, it makes it difficult for users to remember their password, which results in passwords that are either insecure, but easy to remember, or written down on paper. In this paper we address the problem of usability in user authentication......, which accepts the most common typing mistakes. The proposed algorithm has been implemented in secure hardware and integrated into a standard Unix system. We present the design, implementation and preliminary evaluation of the developed passphrase authentication prototype....

  7. Designing Pu600 for Authentication

    International Nuclear Information System (INIS)

    Many recent Non-proliferation and Arms Control software projects include an authentication component. Demonstrating assurance that software and hardware performs as expected without hidden 'back-doors' is crucial to a project's success. In this context, 'authentication' is defined as determining that the system performs only its intended purpose and performs that purpose correctly and reliably over many years. Pu600 is a mature software solution for determining the presence of Pu and the ratio of Pu240 to Pu239 by analyzing the gamma ray spectra in the 600 KeV region. The project's goals are to explore hardware and software technologies which can by applied to Pu600 which ease the authentication of a complete, end-to-end solution. We will discuss alternatives and give the current status of our work

  8. Introduction to Methods Demonstrations for Authentication

    Energy Technology Data Exchange (ETDEWEB)

    Kouzes, Richard T.; Hansen, Randy R.; Pitts, W. K.

    2002-07-15

    During the Trilateral Initiative Technical Workshop on Authentication & Certification, PNNL will demonstrate some authentication technologies. This paper briefly describes the motivation for these demonstrations and provide background on them.

  9. Introduction to Methods Demonstrations for Authentication

    International Nuclear Information System (INIS)

    During the Trilateral Initiative Technical Workshop on Authentication and Certification, PNNL will demonstrate some authentication technologies. This paper briefly describes the motivation for these demonstrations and provide background on them

  10. The Authentic Personality: A Theoretical and Empirical Conceptualization and the Development of the Authenticity Scale

    Science.gov (United States)

    Wood, Alex M.; Linley, P. Alex; Maltby, John; Baliousis, Michael; Joseph, Stephen

    2008-01-01

    This article describes the development of a measure of dispositional authenticity and tests whether authenticity is related to well-being, as predicted by several counseling psychology perspectives. Scales were designed to measure a tripartite conception of authenticity, comprising self-alienation, authentic living, and accepting external…

  11. Quantified Trust Levels for Authentication

    Science.gov (United States)

    Thomas, Ivonne; Menzel, Michael; Meinel, Christoph

    Service-oriented Architectures (SOAs) facilitate applications to integrate seamlessly services from collaborating business partners regardless of organizational borders. In order to secure access to these services, mechanisms for authentication and authorisation must be deployed that control the access based on identity-related information. To enable a business partners’ users to access the provided services, an identity federation is often established that enables the brokering of identity information across organisational borders. The establishment of such a federation requires complex agreements and contracts that define common policies, obligations and procedures. Generally, this includes obligations on the authentication process as well.

  12. Remote Biometrics for Robust Persistent Authentication

    DEFF Research Database (Denmark)

    Ingwar, Mads Ingerslew; Jensen, Christian D.

    2014-01-01

    This paper examines the problem of providing a robust non-invasive authentication service for mobile users in a smart environment. We base our work on the persistent authentication model (PAISE), which relies on available sensors to track principals from the location where they authenticate, e.g....

  13. Authentic Montessori: The Teacher Makes the Difference

    Science.gov (United States)

    Huxel, Alexa C.

    2013-01-01

    What are the elements that make up authentic Montessori? Is Montessori something concrete or abstract? Are there intangibles that make Montessori what it is? Many classrooms today have Montessori materials and small tables and chairs. Are they authentic Montessori? When examining areas that traditionally make defining authentic Montessori…

  14. 28 CFR 68.46 - Authenticity.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 2 2010-07-01 2010-07-01 false Authenticity. 68.46 Section 68.46... ALIENS, UNFAIR IMMIGRATION-RELATED EMPLOYMENT PRACTICES, AND DOCUMENT FRAUD § 68.46 Authenticity. The authenticity of all documents submitted as proposed exhibits in advance of the hearing shall be deemed...

  15. Authenticity, Autonomy and Altruism: Keys for Transformation

    Science.gov (United States)

    Clarken, Rodney

    2011-01-01

    The value of authentic knowing, autonomous behavior and altruistic motivation is presented. Authenticity, autonomy and altruism are primary human capacities and keys for individual and collective transformation. Realizing the full development of these three basic potentialities can serve as goals and standards for well-being. Authenticity,…

  16. 29 CFR 18.50 - Authenticity.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Authenticity. 18.50 Section 18.50 Labor Office of the Secretary of Labor RULES OF PRACTICE AND PROCEDURE FOR ADMINISTRATIVE HEARINGS BEFORE THE OFFICE OF ADMINISTRATIVE LAW JUDGES General § 18.50 Authenticity. The authenticity of all documents submitted as...

  17. 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.

  18. 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.

  19. 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

  20. Authentication of Herbal Supplements Using Next-Generation Sequencing.

    Directory of Open Access Journals (Sweden)

    Natalia V Ivanova

    Full Text Available DNA-based testing has been gaining acceptance as a tool for authentication of a wide range of food products; however, its applicability for testing of herbal supplements remains contentious.We utilized Sanger and Next-Generation Sequencing (NGS for taxonomic authentication of fifteen herbal supplements representing three different producers from five medicinal plants: Echinacea purpurea, Valeriana officinalis, Ginkgo biloba, Hypericum perforatum and Trigonella foenum-graecum. Experimental design included three modifications of DNA extraction, two lysate dilutions, Internal Amplification Control, and multiple negative controls to exclude background contamination. Ginkgo supplements were also analyzed using HPLC-MS for the presence of active medicinal components.All supplements yielded DNA from multiple species, rendering Sanger sequencing results for rbcL and ITS2 regions either uninterpretable or non-reproducible between the experimental replicates. Overall, DNA from the manufacturer-listed medicinal plants was successfully detected in seven out of eight dry herb form supplements; however, low or poor DNA recovery due to degradation was observed in most plant extracts (none detected by Sanger; three out of seven-by NGS. NGS also revealed a diverse community of fungi, known to be associated with live plant material and/or the fermentation process used in the production of plant extracts. HPLC-MS testing demonstrated that Ginkgo supplements with degraded DNA contained ten key medicinal components.Quality control of herbal supplements should utilize a synergetic approach targeting both DNA and bioactive components, especially for standardized extracts with degraded DNA. The NGS workflow developed in this study enables reliable detection of plant and fungal DNA and can be utilized by manufacturers for quality assurance of raw plant materials, contamination control during the production process, and the final product. Interpretation of results should

  1. Literacy Cafe: Making Writing Authentic

    Science.gov (United States)

    Daniels, Erika

    2007-01-01

    The "Literacy Cafe," a celebration of genre study and student writing, offers students (and visitors!) a positive environment in which to engage in reading and discussion of writing without self-consciousness or fear of criticism. It works because students learn to recognize writing as a learning tool and a relevant, authentic skill in the real…

  2. The embodiment of authentic leadership.

    Science.gov (United States)

    Waite, Roberta; McKinney, Nicole; Smith-Glasgow, Mary Ellen; Meloy, Faye A

    2014-01-01

    Development of student leadership capacity and efficacy is critical to the nursing profession, and vital to this process is a strong foundation in critical thinking that includes a depth of understanding of self (i.e., authentic leadership development). This article will (a) present a theoretical overview of authentic leadership as compared with other popular leadership theories, (b) provide an overview of development/implementation of an authentic leadership course, the first in a series of six one-credit courses as an integral component of the Macy Undergraduate Leadership Fellows Program for upper-level nursing students, and (c) discuss related implications for nursing education. Findings from an investigator-developed quantitative pre-post survey and qualitative evaluation questions are provided. Student feedback regarding the comprehensive nature of the course was extremely positive and affirmed the value of introspection associated with authentic leadership in ongoing personal and professional development. Critical pedagogy and action-oriented learning strategies also proved beneficial to student engagement.

  3. Authenticity and Lesbian Health Educators

    Science.gov (United States)

    Weiler-Timmins, Rebecca A.

    2011-01-01

    This qualitative study used narrative inquiry to explore how lesbian health educators navigate authenticity in a heteronormative higher education setting. The study was grounded in a lesbian standpoint pedagogical viewpoint, which provided a lens with which to view the nine participants' experiences. Of particular interest was how the educators in…

  4. Authenticity or School-only?

    DEFF Research Database (Denmark)

    Fougt, Simon Skov

    Challenging the apparent distinction among educational researchers between ‘authenticity’ outside schools and ‘school-only’ inside schools, this paper investigates the concept of meaningfulness from different perspectives with a focus on formal learning in schools, as it states that teaching...... and learning inside school also can be authentic....

  5. Authenticity in a Digital Environment.

    Science.gov (United States)

    Cullen, Charles T.; Hirtle, Peter B.; Levy, David; Lynch, Clifford A.; Rothenberg, Jeff

    On January 24, 2000, the Council on Library and Information Resources (CLIR) convened a group of experts from different domains of the information resources community to address the question, "What is an authentic digital object?" Five writers--an archivist, a digital library expert, a documentary editor and special collections librarian, an…

  6. Authentic Instruction and Technology Literacy

    Science.gov (United States)

    Cydis, Susan

    2015-01-01

    Technology integration is an important aspect of student competence in the 21st century. The use of technology in teaching and learning is a valuable practice for supporting student learning and engagement. Modelling the pedagogical practices that integrate authentic, performance-based opportunities for technology integration was the focus of a…

  7. Authentic Video in Intermediate German.

    Science.gov (United States)

    Lutcavage, Charles

    1992-01-01

    Assorted techniques are offered for introducing authentic German video into the intermediate language curriculum. Television commercials, weather forecasts, and news programs are described as tools for enhancing listening comprehension and expanding students' cultural awareness. Various preparatory activities and follow-up assignments are…

  8. The embodiment of authentic leadership.

    Science.gov (United States)

    Waite, Roberta; McKinney, Nicole; Smith-Glasgow, Mary Ellen; Meloy, Faye A

    2014-01-01

    Development of student leadership capacity and efficacy is critical to the nursing profession, and vital to this process is a strong foundation in critical thinking that includes a depth of understanding of self (i.e., authentic leadership development). This article will (a) present a theoretical overview of authentic leadership as compared with other popular leadership theories, (b) provide an overview of development/implementation of an authentic leadership course, the first in a series of six one-credit courses as an integral component of the Macy Undergraduate Leadership Fellows Program for upper-level nursing students, and (c) discuss related implications for nursing education. Findings from an investigator-developed quantitative pre-post survey and qualitative evaluation questions are provided. Student feedback regarding the comprehensive nature of the course was extremely positive and affirmed the value of introspection associated with authentic leadership in ongoing personal and professional development. Critical pedagogy and action-oriented learning strategies also proved beneficial to student engagement. PMID:25150413

  9. Authenticity as an aim of psychoanalysis.

    Science.gov (United States)

    Neri, Claudio

    2008-12-01

    This paper will present a series of predominantly clinical observations concerning the lengthy work a patient carries out, with the help of the analyst, in order to achieve greater personal authenticity. When this work is drawing to a close and the patient has gained a degree of authenticity, this authenticity remains within him, almost without his realizing it. The power of authenticity is instead revealed through the patient's most intimate and important relationships. In the long term, the patient's authenticity also alters his perception of himself and of his role in the world. He feels more alive and less overcome by a sense of futility, if earlier this had been the case.

  10. AN IMPROVED AUTHENTICATED KEY AGREEMENT PROTOCOL

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    In 1999, Seo and Sweeney proposed a simple authenticated key agreement protocol that was designed to act as a Diffie-Hellman key agreement protocol with user authentication.Various attacks on this protocol are described and enhanced in the literature. Recently, Ku and Wang proposed an improved authenticated key agreement protocol, where they asserted the protocol could withstand the existing attacks. This paper shows that Ku and Wang's protocol is still vulnerable to the modification attack and presents an improved authenticated key agreement protocol to enhance the security of Ku and Wang's protocol. The protocol has more efficient performance by replacing exponentiation operations with message authentication code operations.

  11. Laser surface authentication for containment and surveillance

    International Nuclear Information System (INIS)

    Full text: Containment and Surveillance (C and S) techniques are extensively used for Agency safeguards activities because they are flexible and cost effective. The two main C and S categories have been optical surveillance and sealing systems. A revolutionary new technology invented by physicists at Imperial College, London and the University of Durham may now provide a new tool for both laser item identification and sealing systems authentication. The method uses surface intrinsic features applicable to UF-6 containers and safeguards seals. The Laser Surface Authentication (LSA) technology, invented by Prof. Russell Cowburn, Professor of Physics, and his team in the Nanotechnology Laboratories of Imperial College, London, recognizes the inherent 'fingerprint' within all material surfaces such as paper, plastic, metals and ceramics. In the laser item identification application, this fingerprint identification will uniquely identify a container at a distance (perhaps 50 cm). In the sealing systems authentication application, the identification takes place nearly on contact (1 cm). In either case, the unique fingerprint is formed by the differentiation of microscopic surface imperfections in the container or the seal. Once the unique signature of the container or the seal is extracted by the LSA method, the signature can be subsequently used to authenticate the container or the seal as genuine and quickly identify counterfeit items. In addition, since every surface on every item is microscopically different, the distribution of 'like' container or seal signatures is expected to be well separated from the distribution of 'unlike' container or seal signatures. The separation of these two distributions on some materials is such that estimated false positives are less than one in 10 to the power 100+ using fitted distributions, exceeding the forensic identification and discrimination performance of DNA. The laser item identification system (LIIS) application satisfies a

  12. 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

  13. 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

  14. 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...

  15. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.

    Science.gov (United States)

    Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Bellato, Cláudia M; Motilal, Lambert; Zhang, Dapeng

    2014-01-15

    Cacao (Theobroma cacao L.), the source of cocoa, is an economically important tropical crop. One problem with the premium cacao market is contamination with off-types adulterating raw premium material. Accurate determination of the genetic identity of single cacao beans is essential for ensuring cocoa authentication. Using nanofluidic single nucleotide polymorphism (SNP) genotyping with 48 SNP markers, we generated SNP fingerprints for small quantities of DNA extracted from the seed coat of single cacao beans. On the basis of the SNP profiles, we identified an assumed adulterant variety, which was unambiguously distinguished from the authentic beans by multilocus matching. Assignment tests based on both Bayesian clustering analysis and allele frequency clearly separated all 30 authentic samples from the non-authentic samples. Distance-based principle coordinate analysis further supported these results. The nanofluidic SNP protocol, together with forensic statistical tools, is sufficiently robust to establish authentication and to verify gourmet cacao varieties. This method shows significant potential for practical application.

  16. Dance in Ancient Greek Culture

    OpenAIRE

    Spalva, Rita

    2015-01-01

    The greatness and harmony of ancient Greece has had an impact upon the development of the Western European culture to this day. The ancient Greek culture has influenced contemporary literature genres and systems of philosophy, principles of architecture, sculpture and drama and has formed basis for such sciences as astronomy and mathematics. The art of ancient Greece with its penchant for beauty and clarity has been the example of the humanity’s search for an aesthetic ideal. Despite only bei...

  17. 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...

  18. BIOMETRICS BASED USER AUTHENTICATION

    Directory of Open Access Journals (Sweden)

    Tanuj Tiwari

    2015-10-01

    Full Text Available Biometrics is automated methods of recognizing a person based on a physiological or behavioral characteristic. Biometrics technologies are base for a plethora of highly secure identification and personal verification solutions. It is measurement of biological characteristics – either physiological or behavioral – that verify the claimed identity of an individual. Physiological biometrics include fingerprints, iris recognition. voice verification, retina recognition, palm vein patterns, finger vein patterns, hand geometry and DNA But there arises a need for more robust systems in order to tackle the increasing incidents of security breaches and frauds. So there is always a need for fool proof technology that can provide security and safety to individuals and the transactions that the individuals make. Biometrics is increasingly used by organizations to verify identities, but coupled with quantum cryptography it offers a new range of security benefits with quantum cryptography where we form a key when we need it and then destroy it. In this paper, we give a brief overview of the field of biometrics and summarize some of its advantages, disadvantages, strengths, limitations, and related privacy concerns.

  19. Halal authenticity of gelatin using species-specific PCR.

    Science.gov (United States)

    Shabani, Hessam; Mehdizadeh, Mehrangiz; Mousavi, Seyed Mohammad; Dezfouli, Ehsan Ansari; Solgi, Tara; Khodaverdi, Mahdi; Rabiei, Maryam; Rastegar, Hossein; Alebouyeh, Mahmoud

    2015-10-01

    Consumption of food products derived from porcine sources is strictly prohibited in Islam. Gelatin, mostly derived from bovine and porcine sources, has many applications in the food and pharmaceutical industries. To ensure that food products comply with halal regulations, development of valid and reliable analytical methods is very much required. In this study, a species-specific polymerase chain reaction (PCR) assay using conserved regions of mitochondrial DNA (cytochrome b gene) was performed to evaluate the halal authenticity of gelatin. After isolation of DNA from gelatin powders with known origin, conventional PCR using species-specific primers was carried out on the extracted DNA. The amplified expected PCR products of 212 and 271 bp were observed for porcine and bovine gelatin, respectively. The sensitivity of the method was tested on binary gelatin mixtures containing 0.1%, 1%, 10%, and 100% (w/w) of porcine gelatin within bovine gelatin and vice versa. Although most of the DNA is degraded due to the severe processing steps of gelatin production, the minimum level of 0.1% w/w of both porcine and bovine gelatin was detected. Moreover, eight food products labeled as containing bovine gelatin and eight capsule shells were subjected to PCR examination. The results showed that all samples contained bovine gelatin, and the absence of porcine gelatin was verified. This method of species authenticity is very useful to verify whether gelatin and gelatin-containing food products are derived from halal ingredients.

  20. Halal authenticity of gelatin using species-specific PCR.

    Science.gov (United States)

    Shabani, Hessam; Mehdizadeh, Mehrangiz; Mousavi, Seyed Mohammad; Dezfouli, Ehsan Ansari; Solgi, Tara; Khodaverdi, Mahdi; Rabiei, Maryam; Rastegar, Hossein; Alebouyeh, Mahmoud

    2015-10-01

    Consumption of food products derived from porcine sources is strictly prohibited in Islam. Gelatin, mostly derived from bovine and porcine sources, has many applications in the food and pharmaceutical industries. To ensure that food products comply with halal regulations, development of valid and reliable analytical methods is very much required. In this study, a species-specific polymerase chain reaction (PCR) assay using conserved regions of mitochondrial DNA (cytochrome b gene) was performed to evaluate the halal authenticity of gelatin. After isolation of DNA from gelatin powders with known origin, conventional PCR using species-specific primers was carried out on the extracted DNA. The amplified expected PCR products of 212 and 271 bp were observed for porcine and bovine gelatin, respectively. The sensitivity of the method was tested on binary gelatin mixtures containing 0.1%, 1%, 10%, and 100% (w/w) of porcine gelatin within bovine gelatin and vice versa. Although most of the DNA is degraded due to the severe processing steps of gelatin production, the minimum level of 0.1% w/w of both porcine and bovine gelatin was detected. Moreover, eight food products labeled as containing bovine gelatin and eight capsule shells were subjected to PCR examination. The results showed that all samples contained bovine gelatin, and the absence of porcine gelatin was verified. This method of species authenticity is very useful to verify whether gelatin and gelatin-containing food products are derived from halal ingredients. PMID:25872445

  1. Climate and Ancient Societies

    DEFF Research Database (Denmark)

    Climate, and human responses to it, have a strongly interconnected relationship. This when climate change occurs, the result of either natural or human causes, societies should react and adapt to these. But do they? If so, what is the nature of that change, and are the responses positive...... or negative for the long-term survival of social groups? In this volume, scholars from diverse disciplines including archaeology, geology and climate sciences explore scientific and material evidence for climate changes in the past, their causes, their effects on ancient societies and how those societies...

  2. Mathematics in ancient Greece

    CERN Document Server

    Dantzig, Tobias

    2006-01-01

    More than a history of mathematics, this lively book traces mathematical ideas and processes to their sources, stressing the methods used by the masters of the ancient world. Author Tobias Dantzig portrays the human story behind mathematics, showing how flashes of insight in the minds of certain gifted individuals helped mathematics take enormous forward strides. Dantzig demonstrates how the Greeks organized their precursors' melange of geometric maxims into an elegantly abstract deductive system. He also explains the ways in which some of the famous mathematical brainteasers of antiquity led

  3. Ancient concrete works

    CERN Document Server

    Sparavigna, Amelia Carolina

    2011-01-01

    It is commonly believed that the ancient Romans were the first to create and use concrete. This is not true, as we can easily learn from the Latin literature itself. For sure, Romans were able to prepare high-quality hydraulic cements, comparable with the modern Portland cements. In this paper, we will see that the use of concrete is quite older, ranging back to the Homeric times. For instance, it was used for the floors of some courts and galleries of the Mycenaean palace at Tiryns

  4. Information fusion for palmprint authentication

    Science.gov (United States)

    Wu, Xiangqian; Wang, Kuanquan; Zhang, David

    2006-04-01

    A palmprint can be represented using different features and the different representations reflect the different characteristic of a palmprint. Fusion of multiple palmprint features may enhance the performance of a palmprint authentication system. This paper investigates the fusion of two types of palmprint information: the phase (called PalmCode) and the orientation (called OrientationCode). The PalmCode is extracted using the 2-D Gabor filters based algorithm and the OrientationCode is computed using several directional templates. Then several fusion strategies are investigated and compared. The experimental results show that the fusion of the PalmCode and OrientationCode using the Product, Sum and Weighted Sum strategies can greatly improve the accuracy of palmprint authentication, which is up to 99.6%.

  5. 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.

  6. ANALYTICAL AUTHENTICATION OF ORGANIC FOODS

    OpenAIRE

    Simeone, F.C.; Ruth, Saskia

    2014-01-01

    A growing consumers’ awareness of human health’s risks, environmental fragility, and animal welfare has boosted organic production of foods. Due to their high production costs, however, organic products tend to retail at a higher prices than their non-organic counterparts. This premium price exposes organic products to fraud and counterfeiting, which, in addition to administrative controls, call for confirmatory assessments of the organic identity. Authentication of organic products is a comp...

  7. Persistent Authentication in Smart Environments

    DEFF Research Database (Denmark)

    Hansen, Mads Syska; Kirschmeyer, Martin; Jensen, Christian D.

    2008-01-01

    present a proof-of-concept implementation of the proposed mechanism, which employs camera based tracking with a single stationary 3D camera that uses the "time of flight" principle. A preliminary evaluation of the proposed mechanism indicates that persistent authentication is technically possible...... with the proposed hardware. The proposed model is sufficiently general to allow the addition of more cameras or supplemental tracking technologies, which will improve the robustness and scalability of the proposed mechanism....

  8. Graphical Passwords Authentication: A Survey

    OpenAIRE

    Nikhil Tarkeshwar Ambade; Prof. Dr. Arati Dixit

    2015-01-01

    In typically text-based passwords, well known users often create memorable passwords that are easy for attackers to guess, but strong system-assigned passwords are difficult for users to remember. Reusing same or easy passwords across different accounts help to memorability, but decrease in security. Text passwords are the most popular user authentication method, but have security and usability problems. Alternatives such as biometric systems and tokens have their own drawbacks Graphical pass...

  9. Food authentication by molecular methods

    OpenAIRE

    de Oliveira, B.; Mafra, I; Costa, J; Amaral, J S; Faria, M.; Fernandes, T.; Soares, S.

    2011-01-01

    Quality and authenticity evaluation of foods encompasses many issues, such as the entire or partial fraudulent substitution of higher commercial value constituents by others with lower value and the presence of undeclared constituents/ingredients. To protect consumers from misleading labeling, regulations issued across the world have implemented specific guidelines and listed particular foods that sh ould be declared on the label. Particularly in the case of genetically modi...

  10. Authenticity assessment of dairy products.

    Science.gov (United States)

    de la Fuente, Miguel Angel; Juárez, Manuela

    2005-01-01

    The authenticity of dairy products has become a focal point, attracting the attention of scientists, producers, consumers, and policymakers. Among many others, some of the practices not allowed in milk and milk products are the substitution of part of the fat or proteins, admixtures of milk of different species, additions of low-cost dairy products (mainly whey derivatives), or mislabeling of products protected by denomination of origin. A range of analytical methods to detect frauds have been developed, modified, and continually reassessed to be one step ahead of manufacturers who pursue these illegal activities. Traditional procedures to assess the authenticity of dairy products include chromatographic, electrophoretic, and immunoenzymatic methods. New approaches such as capillary electrophoresis, polymerase chain reaction, and isotope ratio mass spectrometry have also emerged alongside the latest developments in the former procedures. This work intends to provide an updated and extensive overview since 1991 on the principal applications of all these techniques together with their advantages and disadvantages for detecting the authenticity of dairy products. The scope and limits of different tools are also discussed.

  11. Exploring Ancient Skies A Survey of Ancient and Cultural Astronomy

    CERN Document Server

    Kelley, David H

    2011-01-01

    Exploring Ancient Skies brings together the methods of archaeology and the insights of modern astronomy to explore the science of astronomy as it was practiced in various cultures prior to the invention of the telescope. The book reviews an enormous and growing body of literature on the cultures of the ancient Mediterranean, the Far East, and the New World (particularly Mesoamerica), putting the ancient astronomical materials into their archaeological and cultural contexts. The authors begin with an overview of the field and proceed to essential aspects of naked-eye astronomy, followed by an examination of specific cultures. The book concludes by taking into account the purposes of ancient astronomy: astrology, navigation, calendar regulation, and (not least) the understanding of our place and role in the universe. Skies are recreated to display critical events as they would have appeared to ancient observers—events such as the supernova of 1054 A.D., the "lion horoscope," and the Star of Bethlehem. Explori...

  12. An Examination of Career Indecision and Application to Dispositional Authenticity

    Science.gov (United States)

    White, Nathan J.; Tracey, Terence J. G.

    2011-01-01

    Authenticity has been viewed as a dimension related to life satisfaction, but we propose that authenticity is related to career outcomes. In this study, we examined the relation between authenticity and career indecision. Authenticity was assessed by the Authenticity Scale and it was found to be moderately related to different indices of career…

  13. Quantum Communication Complexity of Quantum Authentication Protocols

    CERN Document Server

    Guedes, Elloá B

    2011-01-01

    In order to perform Quantum Cryptography procedures it is often essencial to ensure that the parties of the communication are authentic. Such task is accomplished by quantum authentication protocols which are distributed algorithms based on the intrinsic properties of Quantum Mechanics. The choice of an authentication protocol must consider that quantum states are very delicate and that the channel is subject to eavesdropping. However, even in face of the various existing definitions of quantum authentication protocols in the literature, little is known about them in this perspective, and this lack of knowledge may unfavor comparisons and wise choices. In the attempt to overcome this limitation, in the present work we aim at showing an approach to evaluate quantum authentication protocols based on the determination of their quantum communication complexity. Based on our investigation, no similar methods to analyze quantum authentication protocols were found in the literature. Pursuing this further, our approa...

  14. Identity-based authentication protocol for grid

    Institute of Scientific and Technical Information of China (English)

    Li Hon; Sun Shixin; Yang Homiao

    2008-01-01

    Current grid authentication frameworks are achieved by applying the standard SSL authentication protocol(SAP).The authentication process is very complicated,and therefore,the grid user is in a heavily loaded point both in computation and in communication.Based on identity-based architecture for grid(IBAG)and corre-sponding encryption and signature schemes,an identity-based authentication protocol for grid is proposed.Being certificate-free,the authentication protocol aligns well with the demands of grid computing.Through simulation testing,it is seen that the authentication protocol is more lightweight and efficient than SAP,especially the more lightweight user side.This contributes to the larger grid scalability.

  15. Autonomy and authenticity of enhanced personality traits.

    Science.gov (United States)

    Bublitz, Jan Christoph; Merkel, Reinhard

    2009-07-01

    There is concern that the use of neuroenhancements to alter character traits undermines consumer's authenticity. But the meaning, scope and value of authenticity remain vague. However, the majority of contemporary autonomy accounts ground individual autonomy on a notion of authenticity. So if neuroenhancements diminish an agent's authenticity, they may undermine his autonomy. This paper clarifies the relation between autonomy, authenticity and possible threats by neuroenhancements. We present six neuroenhancement scenarios and analyse how autonomy accounts evaluate them. Some cases are considered differently by criminal courts; we demonstrate where academic autonomy theories and legal reasoning diverge and ascertain whether courts should reconsider their concept of autonomy. We argue that authenticity is not an appropriate condition for autonomy and that new enhancement technologies pose no unique threats to personal autonomy.

  16. Authenticity is in the Eye of the Beholder: Student and Teacher Perceptions of Assessment Authenticity.

    NARCIS (Netherlands)

    Gulikers, Judith; Bastiaens, Theo; Kirschner, Paul A.; Kester, Liesbeth

    2008-01-01

    Gulikers, J. T. M., Bastiaens, Th. J., Kirschner, P. A., & Kester, L. (2008). Authenticity is in the Eye of the Beholder: Student and Teacher Perceptions of Assessment Authenticity. Journal of Vocational Education and Training, 60(4)

  17. Authenticated tree parity machine key exchange

    OpenAIRE

    Volkmer, Markus; Schaumburg, André

    2004-01-01

    The synchronisation of Tree Parity Machines (TPMs), has proven to provide a valuable alternative concept for secure symmetric key exchange. Yet, from a cryptographer's point of view, authentication is at least as important as a secure exchange of keys. Adding an authentication via hashing e.g. is straightforward but with no relation to Neural Cryptography. We consequently formulate an authenticated key exchange within this concept. Another alternative, integrating a Zero-Knowledge protocol in...

  18. Obfuscated authentication systems, devices, and methods

    Science.gov (United States)

    Armstrong, Robert C; Hutchinson, Robert L

    2013-10-22

    Embodiments of the present invention are directed toward authentication systems, devices, and methods. Obfuscated executable instructions may encode an authentication procedure and protect an authentication key. The obfuscated executable instructions may require communication with a remote certifying authority for operation. In this manner, security may be controlled by the certifying authority without regard to the security of the electronic device running the obfuscated executable instructions.

  19. Contributions to Web Authentication for Untrusted Computers

    OpenAIRE

    Vapen, Anna

    2011-01-01

    Authentication methods offer varying levels of security. Methods with one-time credentials generated by dedicated hardware tokens can reach a high level of security, whereas password-based authentication methods have a low level of security since passwords can be eavesdropped and stolen by an attacker. Password-based methods are dominant in web authentication since they are both easy to implement and easy to use. Dedicated hardware, on the other hand, is not always available to the user, usua...

  20. Authentic leadership: What's in the construct?

    OpenAIRE

    Endrissat, Nada; Müller, Werner R.

    2006-01-01

    In a qualitative leadership study conducted in the German-speaking part of Switzerland the quest to be oneself i.e., to be authentic was found to be central for leadership. We will present the results in detail and highlight the difficulties leaders experience when trying to be authentic in their daily interaction. By providing a contextually rich description of authentic leadership from practitioners' point of views, our study contributes to the current endeavor to understand and define auth...

  1. Quantum Key Distribution Protocol with User Authentication

    CERN Document Server

    Lee, H; Lee, D; Lim, J; Yang, H J; Lee, Hwayean; Lee, Sangjin; Lee, Donghoon; Lim, Jongin; Yang, HyungJin

    2005-01-01

    We propose a quantum key distribution protocol with quantum based user authentication. User authentication is executed by validating the correlation of GHZ states. Alice and Bob can distribute a secure key using the remaining GHZ states after authentication. This secret key does not leak even to the arbitrator by the properties of the entanglement. We will show that our protocol is secure against the cloning attack.

  2. The Ideal Self and State Authenticity

    OpenAIRE

    Power, Katherine Emilia

    2011-01-01

    The current study investigated the effect of priming people with alignment or distance to ideal self attributes on their feelings of authenticity. The effect of priming participants with self-irrelevant alignment or distance to ideal attributes was also explored, to test whether these manipulations might respectively increase or lower state authenticity, or whether state authenticity would only be affected by self-relevant priming. As expected, discrepant conditions were associated with lower...

  3. Password Authentication Based on Fractal Coding Scheme

    OpenAIRE

    Al-Saidi, Nadia M. G.; Mohamad Rushdan Md. Said; Othman, Wan Ainun M.

    2012-01-01

    Password authentication is a mechanism used to authenticate user identity over insecure communication channel. In this paper, a new method to improve the security of password authentication is proposed. It is based on the compression capability of the fractal image coding to provide an authorized user a secure access to registration and login process. In the proposed scheme, a hashed password string is generated and encrypted to be captured together with the user identity using text to image ...

  4. Quantum Secure Direct Communication Based on Authentication

    Institute of Scientific and Technical Information of China (English)

    WANG Min-Jie; PAN Wei

    2008-01-01

    We propose two schemes of quantum secure direct communication (QSDC) combined ideas of user authentication [Phys. Rev. A 73 (2006) 042305] and direct communication with dense coding [Phys. Rev. A. 68 (2003) 042317]. In these protocols, the privacy of authentication keys and the properties of the EPR pairs not only ensure the realization of identity authentication but also further improve the security of communication, and no secret messages are leaked even if the messages were broken.

  5. Quantum Secure Direct Communication Based on Authentication

    International Nuclear Information System (INIS)

    We propose two schemes of quantum secure direct communication (QSDC) combined ideas of user authentication [Phys. Rev. A 73 (2006) 042305] and direct communication with dense coding [Phys. Rev. A. 68 (2003) 042317]. In these protocols, the privacy of authentication keys and the properties of the EPR pairs not only ensure the realization of identity authentication but also further improve the security of communication, and no secret messages are leaked even if the messages were broken. (general)

  6. Heidegger's Concept of Authenticity and Sport Experience

    OpenAIRE

    HIGUCHI Satoshi

    1991-01-01

    Carolyne Thomas regarded the aesthetic experience in sport as authentic in the meaning from Martin Heidegger's Being and Time. To examine the adequacy of the interpretation, the comparison between Thomas' concept of authenticity and the Heidegger's was attempted in this paper. Thomas' concept of authenticity is opposite to accidentality. It is also positive realization of a self, positive movement toward a capable being, a unique self, a unique experience, and honesty in a sport situation...

  7. Heidegger's Concept of Authenticity and Sport Experience

    OpenAIRE

    HIGUCHI Satoshi

    1991-01-01

    Carolyne Thomas regarded the aesthetic experience in sport as authentic in the meaning from Martin Heidegger's Being and Time. To examine the adequacy of the interpretation, the comparison between Thomas' concept of authenticity and the Heidegger's was attempted in this paper.Thomas' concept of authenticity is opposite to accidentality. It is also positive realization of a self, positive movement toward a capable being, a unique self, a unique experience, and honesty in a sport situation. Aut...

  8. Negotiating authenticity in consuming the hyperreal

    OpenAIRE

    Kuronen, Noora

    2013-01-01

    OBJECTIVES OF THE STUDY: This study seeks to further our understanding of how authenticity is negotiated and produced in online discourses; what forms of negotiating authenticity can be identified. The idea is not to produce absolute answers, but to extent our understanding of the concept of authenticity in the culture increasingly based on simulation. METHODOLOGY/APPROACH: The research approach used in this study is Consumer Culture Theory (CCT). CCT studies consumption choices a...

  9. Laying Claim to Authenticity: Five Anthropological Dilemmas

    OpenAIRE

    THEODOSSOPOULOS, Dimitrios

    2013-01-01

    The introduction to this special collection examines five dilemmas about the use of the concept of authenticity in anthropological analysis. These relate to 1) the expectation of a singular authenticity “deep” in oneself or beyond the surface of social reality, 2) the contradictions emerging from the opposition of authenticity with inauthenticity, 3) the irony of the notion of invention of tradition (which deconstructs, but also offends), 4) the criteria involved in the auth...

  10. The Duality of Authenticity in ELT

    OpenAIRE

    Joy, J. John Love

    2011-01-01

    Purpose: This study aims to find out the dual-perspectives on authenticity in English language teaching.Problem: The concept of authenticity has generated quite a ripple in ESL/EFL classrooms. Contrasting perspectives have emerged over the years in reaction to this concept. Some regard authenticity as an inevitable part of teaching as it provides students with opportunities to interact with reality in the classroom itself, whereas, some others consider it an ambitious construct and suggest ap...

  11. Food Authenticity, Technology and Consumer Acceptance

    OpenAIRE

    Hobbs, Jill E.; McDonald, Jillian; Zhang, Jing

    2012-01-01

    Traceability and authenticity issues have gained increasing prominence in food markets and create both opportunities and challenges for the food industry in providing credible information to consumers. Internal molecular tagging is an emerging technology with the potential to deliver traceability and authenticity assurances. A key question for the food industry in adopting new technologies is consumer acceptance. This paper explores consumer attitudes toward traceability and authenticity and ...

  12. Multifactor Authentication: Its Time Has Come

    Directory of Open Access Journals (Sweden)

    Jim Reno

    2013-08-01

    Full Text Available Transactions of any value must be authenticated to help prevent online crime. Even seemingly innocent interactions, such as social media postings, can have serious consequences if used fraudulently. A key problem in modern online interactions is establishing the identity of the user without alienating the user. Historically, almost all online authentications have been implemented using simple passwords, but increasingly these methods are under attack. Multifactor authentication requires the presentation of two or more of the three authentication factor types: “What you know”, “What you have”, and “What you are”. After presentation, each factor must be validated by the other party for authentication to occur. Multifactor authentication is a potential solution to the authentication problem, and it is beginning to be implemented at websites operated by well-known companies. This article surveys the different mechanisms used to implement multifactor authentication. How a site chooses to implement multifactor authentication affects security as well as the overall user experience.

  13. A compression tolerant scheme for image authentication

    Institute of Scientific and Technical Information of China (English)

    刘宝锋; 张文军; 余松煜

    2004-01-01

    Image authentication techniques used to protect the recipients against malicious forgery. In this paper, we propose a new image authentication technique based on digital signature. The authentication is verified by comparing the features of the each block in tested image with the corresponding features of the block recorded in the digital signature. The proposed authentication scheme is capable of distinguishing visible but non-malicious changes due to common processing operations from malicious changes. At last our experimental results show that the proposed scheme is not only efficient to protect integrity of image, but also with low computation,which are feasible for practical applications.

  14. ARE AUTHENTIC LEADERS SATISFIED WITH THEIR JOB?

    Directory of Open Access Journals (Sweden)

    Nebojsa Pavlovic

    2016-06-01

    Full Text Available A crisis in management has led to the appearance of Authentic leadership. The aim of this work is to determine the characteristics of Authentic leadership in educational institutions and to respond to the question as to whether authentic leaders are satisfied with their job. The third aim is to determine differences among the researched regions. The sample included 227 randomly selected directors from primary and secondary schools in Serbia, Montenegro and the Republika Srpska. The research used an ALQ questionnaire for the estimation of leadership behaviour. Descriptions for the results prediction and multiple linear regressions were used. A multivariance analysis of variance was used to compare the groups. The research results showed that every fourth director is an authentic leader. Authentic leadership has a significant influence on job satisfaction through two aspects: internalised perspective and balanced processing. There are no differences in Authentic leadership in the researched areas. The results could be useful for educational institutions in countries where the research was conducted. Further research could be carried out in other countries while cultural differences should be taken into account. One limiting factor consists of the fact that the analysed data are obtained only from school directors. Leaders of educational institutions should provide management through the development of their own authenticity and the authenticity of their followers. The characteristics of Authentic leadership were reviewed and tested practically in the West-Balkan environment.

  15. staging constructions of authenticity in organizational change

    DEFF Research Database (Denmark)

    Dupret, Katia

    2015-01-01

    Authenticity in organizations has gained increased focus in recent years. Authentic management and leadership are ways to motivate and make sustainable changes in the organization. But authenticity is also strategically worked with in order to serve social and political functions that are emotion......Authenticity in organizations has gained increased focus in recent years. Authentic management and leadership are ways to motivate and make sustainable changes in the organization. But authenticity is also strategically worked with in order to serve social and political functions...... that are emotionally charged. Through a socio-material perspective this paper seeks to explore how change processes in organizations challenges the idea of authentic leadership as a merely individual ability or personality trait and suggest that the authentic leader is distributed into the practices of change....... The paper explores how staged organizational change where authentic role-play and scripts from everyday life combined with meta-reflection and feedback construct new forms of reflection where its ethical side-effects should be discussed....

  16. Authentic leadership: develop the leader within.

    Science.gov (United States)

    Yasinski, Lesia

    2014-03-01

    Great leadership usually starts with a willing heart, a positive attitude, and a desire to make a difference. Strong leadership is important, in today's health care climate, to ensure optimal patient outcomes and the fostering of future generations of knowledgeable, motivated and enthusiastic perioperative nurses. This article will explore key elements necessary for the development of authentic leadership. While highlighting the role that personal development plays in leadership skills, this article will also discuss ways to cultivate authenticity in leadership. The following questions will be addressed: What is authentic leadership? How does one become an authentic leader?

  17. 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; Pickrel, Joseph; Arsuaga, Juan Luís; de Castro, José María Bermúdez; Carbonell, Eudald; Gerritsen, Fokke; Khokhlov, Aleksandr; Kuznetsov, Pavel; Lozano, Marina; Meller, Harald; Mochalov, Oleg; Moiseyev, Vayacheslav; Rojo Guerra, Manuel A.; 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

    2016-01-01

    Ancient DNA makes it possible to directly witness natural selection by analyzing samples from populations before, during and after adaptation events. Here we report the first scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture whose genetic material we extracted from the DNA-rich petrous bone and who we show were members of the population that was the source of Europe’s first farmers. We also report a complete transect of the steppe region in Samara between 5500 and 1200 BCE that allows us to recognize admixture from at least two external sources into steppe populations during this period. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height. PMID:26595274

  18. 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....

  19. 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.

  20. Deciphering Equine Evolution and Spatial Ancestry with Ancient Data

    DEFF Research Database (Denmark)

    Jónsson, Hákon

    to the specific nature of such data. In this thesis, we developed such methods. We first present an explicit statistical model of post-mortem biochemical DNA damage, which allows for quantifying and accounting for DNA damage related mis-incorporations in downstream analyses. We next embed this approach......High-throughput sequencing has opened ancient DNA research to genomics, revolutionizing the amount of genetic information retrievable from archaeological and paleontological remains. Paleogenomics is still in infancy and requires substantial improvements in computational methods tailored...

  1. Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes

    Science.gov (United States)

    Epp, L. S.; Gussarova, G.; Boessenkool, S.; Olsen, J.; Haile, J.; Schrøder-Nielsen, A.; Ludikova, A.; Hassel, K.; Stenøien, H. K.; Funder, S.; Willerslev, E.; Kjær, K.; Brochmann, C.

    2015-06-01

    High Arctic environments are particularly sensitive to climate changes, but retrieval of paleoecological data is challenging due to low productivity and biomass. At the same time, Arctic soils and sediments have proven exceptional for long-term DNA preservation due to their constantly low temperatures. Lake sediments contain DNA paleorecords of the surrounding ecosystems and can be used to retrieve a variety of organismal groups from a single sample. In this study, we analyzed vascular plant, bryophyte, algal (in particular diatom) and copepod DNA retrieved from a sediment core spanning the Holocene, taken from Bliss Lake on the northernmost coast of Greenland. A previous multi-proxy study including microscopic diatom analyses showed that this lake experienced changes between marine and lacustrine conditions. We inferred the same environmental changes from algal DNA preserved in the sediment core. Our DNA record was stratigraphically coherent, with no indication of leaching between layers, and our cross-taxon comparisons were in accordance with previously inferred local ecosystem changes. Authentic ancient plant DNA was retrieved from nearly all layers, both from the marine and the limnic phases, and distinct temporal changes in plant presence were recovered. The plant DNA was mostly in agreement with expected vegetation history, but very early occurrences of vascular plants, including the woody Empetrum nigrum, document terrestrial vegetation very shortly after glacial retreat. Our study shows that multi-taxon metabarcoding of sedimentary ancient DNA from lake cores is a valuable tool both for terrestrial and aquatic paleoecology, even in low-productivity ecosystems such as the High Arctic.

  2. Bluetooth-based authentication system for ambient intelligence

    Institute of Scientific and Technical Information of China (English)

    Jian HE; Hui LI; Yong ZHANG; Zhang-qin HUANG

    2008-01-01

    According to the requirement of natural human-computer interaction for Ambient Intelligence (AmI), a Bluetooth-based authentication technique is provided. An authentication network combining advantages of Bluetooth ad hoc network with the Ethernet is introduced first in detail. Then we propose a Bluetooth badge for storing the user's identification information. Finally, the authentication system based on Bluetooth badge and authentication network is introduced. It is demonstrated experimentally that the Bluetooth-based authentication technique can authenticate the user automatically.

  3. Rapid evolution of sessility in an endemic species flock of the freshwater bivalve Corbicula from ancient lakes on Sulawesi, Indonesia

    OpenAIRE

    von Rintelen, Thomas; Glaubrecht, Matthias

    2005-01-01

    The fauna of ancient lakes frequently contains taxa with highly derived morphologies that resulted from in situ radiation of lacustrine lineages with high antiquity. We employed a molecular mtDNA phylogeny to investigate this claim for corbiculid freshwater bivalves in two ancient lake systems on the Indonesian island Sulawesi. Among the otherwise mobile corbiculid species flock, only one taxon, Posostrea anomioides, in the ancient Lake Poso exhibits a unique habit, i.e. cementing one valve t...

  4. Authentic Learning and Alien Worlds

    Science.gov (United States)

    Watt, Sara D.; Watt, Keith; Gleim, Brian

    2015-01-01

    Glendale Community College has developed a laboratory course and observing program which provides non-science majors with opportunities to perform authentic science in a community college setting. The program is designed around experiential learning which allows students to meaningfully construct concepts within contexts that involve real-world problems that are relevant to the learner. Students learn observational astronomy and data analysis techniques by observing exoplanet transits using 8-inch Celestron telescopes. The exoplanet data gathered and analyzed by the students is contributed to the exoplanet database. This poster presents an overview of the program and highlights early educational results.

  5. Authenticity and its Contemporary Challenges

    DEFF Research Database (Denmark)

    Bork Petersen, Franziska

    2013-01-01

    In this thesis I investigate what ‘authenticity’ means in a contemporary popular context and how it is used in the staging of bodies. Furthermore, I analyse works of dance and fashion from the past fifteen years with a focus on their strategies of challenging the notion of ‘bodily authenticity...... and by a depiction of 'working hard'. But various techniques also mask the hard work, for example by showing a participant ‘having fun’ performing it. Contemporary works of dance and fashion challenge the problematic implications in the notion of ‘bodily authenticity’. I analyse three strategies of undermining...

  6. Pathogens and host immunity in the ancient human oral cavity

    DEFF Research Database (Denmark)

    Warinner, Christina; Rodrigues, João F Matias; Vyas, Rounak;

    2014-01-01

    cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction......Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral...... of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental...

  7. Entity Authentication:Analysis using Structured Intuition

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    2010-01-01

    In this paper, we propose a new method for the analysis that uses intuition of the analyst in a structured way. First we define entity authentication in terms of fine level authentication goals (FLAGs). Then we use some relevant structures in protocol narrations and use them to justify FLAGs for...

  8. Aggregated Authentication (AMAC) Using Universal Hash Functions

    Science.gov (United States)

    Znaidi, Wassim; Minier, Marine; Lauradoux, Cédric

    Aggregation is a very important issue to reduce the energy consumption in Wireless Sensors Networks (WSNs). There is currently a lack of cryptographic primitives for authentication of aggregated data. The theoretical background for Aggregated Message Authentication Codes (AMACs) has been proposed by Chan and Castelluccia at ISIT 08.

  9. Wikis as Platforms for Authentic Assessment

    Science.gov (United States)

    Eddy, Pamela L.; Lawrence, April

    2013-01-01

    Calls for accountability focus attention on assessment of student learning. Authentic assessment involves evaluating student learning as students perform real world tasks. We present a four-stage conceptual framework for authentic assessment. We argue first that evaluation is a process rather than a static one-time event. Second, authentic…

  10. Teacher Authenticity: A Theoretical and Empirical Investigation

    Science.gov (United States)

    Akoury, Paul N.

    2013-01-01

    This study builds on a small, under-acknowledged body of educational works that speak to the problem of an overly technical focus on teaching, which negates a more authentic consideration of what it means to teach, including an exploration of the spiritual and moral dimensions. A need for educational change and the teacher's authentic way of…

  11. Test-Task Authenticity: The Multiple Perspectives

    Science.gov (United States)

    Gan, Zhengdong

    2012-01-01

    Leung and Lewkowicz remind us that the debate over the past two decades that is most relevant to ELT (English languge teaching) pedagogy and curriculum concerns test-task authenticity. This paper first reviews how the authenticity debate in the literature of second language acquisition, pedagogy and testing has evolved. Drawing on a body of…

  12. Difference packing arrays and systematic authentication codes

    Institute of Scientific and Technical Information of China (English)

    YIN Jianxing

    2004-01-01

    In this paper, a type of combinatorial design (called difference packing array)is proposed and used to give a construction of systematic authentication codes. Taking advantage of this construction, some new series of systematic authentication codes are obtainable in terms of existing difference packing arrays.

  13. Research on Secure Authentication Mechanism of Grid

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Based on the analysis on the security mechanism of grid, this paper discusses the advantages of latest techniques of grid security, and presents a secure authentication scheme of grid based on elliptic curve cryptosystem (ECC). The secure authentication scheme may provide reference value for the further application of grid.

  14. Making it Real: Authenticity, Process and Pedagogy

    Science.gov (United States)

    Badger, Richard; MacDonald, Malcolm

    2010-01-01

    Authenticity has been a part of the intellectual resources of language teaching since the 1890s but its precise meaning and implications are contested. This commentary argues for a view of authenticity which recognizes the limits of the concept as a guide for pedagogic practice and acknowledges the fact that texts are processes rather than…

  15. Demarcation of Security in Authentication Protocols

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    2011-01-01

    easier, and enables us to define security goals with a fine granularity. We present one such separation, by introducing the notion of binding sequence as a security primitive. A binding sequence, roughly speaking, is the only required security property of an authentication protocol. All other...... authentication goals, the correctness requirements, can be derived from the binding sequence....

  16. Athos: Efficient Authentication of Outsourced File Systems

    DEFF Research Database (Denmark)

    Triandopoulos, Nikolaos; Goodrich, Michael T.; Papamanthou, Charalampos;

    2008-01-01

    We study the problem of authenticated storage, where we wish to construct protocols that allow to outsource any complex file system to an untrusted server and yet ensure the file-system's integrity. We introduce Athos, a new, platform-independent and user-transparent architecture for authenticate...

  17. Efficient Quantum Secure Direct Communication with Authentication

    Institute of Scientific and Technical Information of China (English)

    LIU Wen-Jie; CHEN Han-Wu; LI Zhi-Qiang; LIU Zhi-Hao

    2008-01-01

    Two protocols of quantum direct communication with authentication [Phys. Rev. A 73 (2006) 042305] were recently indicated to be insecure against the authenticator Trent attacks [Phys. Rev. A 75 (2007) 026301]. We present two efficient protocols by using four Pauli operations, which are secure against inner Trent attacks as well as outer Eve attacks. Finally, we generalize them to multiparty quantum direction communication.

  18. Security of Invertible Media Authentication Schemes Revisited

    Science.gov (United States)

    Dönigus, Daniel; Endler, Stefan; Fischlin, Marc; Hülsing, Andreas; Jäger, Patrick; Lehmann, Anja; Podrazhansky, Sergey; Schipp, Sebastian; Tews, Erik; Vowe, Sven; Walthart, Matthias; Weidemann, Frederik

    Dittmann, Katzenbeisser, Schallhart and Veith (SEC 2005) introduced the notion of invertible media authentication schemes, embedding authentication data in media objects via invertible watermarks. These invertible watermarks allow to recover the original media object (given a secret encryption key), as required for example in some medical applications where the distortion must be removable.

  19. Efficient Quantum Secure Direct Communication with Authentication

    International Nuclear Information System (INIS)

    Two protocols of quantum direct communication with authentication [Phys. Rev. A 73 (2006) 042305] were recently indicated to be insecure against the authenticator Trent attacks [Phys. Rev. A 75 (2007) 026301]. We present two efficient protocols by using four Pauli operations, which are secure against inner Trent attacks as well as outer Eve attacks. Finally we generalize them to multiparty quantum direction communication. (general)

  20. Authentic Interdisciplinary Instruction: Raising the Bar

    Science.gov (United States)

    Mohnsen, Bonnie

    2011-01-01

    This article addressed the need for authentic interdisciplinary instruction. Authentic interdisciplinary instruction is defined as a learning activity that simultaneously improves student performance related to grade-level standards in two or more disciplines (e.g., science and physical education). The process described for creating authentic…

  1. Did the ancient Egyptians migrate to ancient Nigeria?

    OpenAIRE

    Jock M. Agai

    2014-01-01

    Literatures concerning the history of West African peoples published from 1900 to 1970 debate�the possible migrations of the Egyptians into West Africa. Writers like Samuel Johnson and�Lucas Olumide believe that the ancient Egyptians penetrated through ancient Nigeria but Leo�Frobenius and Geoffrey Parrinder frowned at this opinion. Using the works of these early�20th century writers of West African history together with a Yoruba legend which teaches�about the origin of their earliest ancesto...

  2. Micro-pixe studies on native Transylvanian gold for archaeological artifacts authentication

    International Nuclear Information System (INIS)

    Determination of the geological provenance of gold is a powerful argument in the authentication of ancient gold artifacts. Small samples (hundreds of microns) of native gold from Transylvanian deposits were scanned by micro-PIXE to obtain information on the natural Au–Ag alloy composition and on the presence of trace elements such as Sn, Sb, and Cu. The experiments were performed at the AGLAE Louvre and LNL AN2000 accelerators. Mineral identification was confirmed by a micro-mineralogical study using the INFLPR-Magurele Scanning Electron Microscope associated with an Energy-dispersive X-ray spectroscopy (EDAX) facility. (author)

  3. Extensible Authentication Protocol Overview and Its Applications

    Science.gov (United States)

    Youm, Heung Youl

    The Extensible Authentication Protocol (EAP) is an authentication framework that supports multiple authentication mechanisms [38] between a peer and an authentication server in a data communication network. EAP is used as a useful tool for enabling user authentication and distribution of session keys. There are numerous EAP methods that have been developed by global SDOs such as IETF, IEEE, ITU-T, and 3GPP. In this paper, we analyze the most widely deployed EAP methods ranging from the EAP-TLS [27] to the EAP-PSK [25]. In addition, we derive the security requirements of EAP methods meet, evaluate the typical EAP methods in terms of the security requirements, and discuss the features of the existing widely-deployed EAP methods. In addition, we identify two typical use cases for the EAP methods. Finally, recent global standardization activities in this area are reviewed.

  4. Authentication in the context of international safeguards

    International Nuclear Information System (INIS)

    The International atomic Energy Agency held its first Advisory Group meeting on the subject of authentication in 1981. This meeting concentrated on the application of authentication to in-plant Non-Destructive Assay equipment supplied by the Facility Operator/State. In the decade since this meeting, a considerable amount of interest has developed over the use of authentication technology as a vital element of effective International Safeguards. Attendant with this interest, confusion has developed over the meaning and the need for the application of the technology as it exists today, and it may exist in the future. This paper addresses the subject of authentication, with emphasis on its basic definition and the applications of authentication technology in International Safeguards

  5. An Authentication Framework for Nomadic Users

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    . This is particularly true for nomadic users who move around in ubiquitous computing environments and avail from different IT services from many different locations. In many ubiquitous computing environments, where information processing is not considered the main priority, management often accepts this practise...... defeating the obstacle by leaving terminals logged in or choosing short and easy to type passwords. Therefore, a password based authentication mechanism, which is quite simple and secure in personal computing, has become too cumbersome for nomadic users, which means that other means of authentication must...... be developed for nomadic users. In this paper, we focus on usability of authentication for nomadic users in a ubiquitous computing environment. We identify requirements for authentication of nomadic users and propose an authentication framework for this class of users. A prototype of the proposed...

  6. [Ancient Egyptian Odontology].

    Science.gov (United States)

    Berghult, B

    1999-01-01

    In ancient Egypt during the reign of Pharaoh Djoser, circa 2650 BC, the Step Pyramid was constructed by Imhotep. He was later worshiped as the God of Medicine. One of his contemporaries was the powerful writer Hesy who is reproduced on a panel showing a rebus of a swallow, a tusk and an arrow. He is therefore looked upon as being the first depicted odontologist. The art of writing begun in Egypt in about 3100 BC and the medical texts we know from different papyri were copied with hieratic signs around 1900-1100 BC. One of the most famous is the Papyrus Ebers. It was purchased by professor Ebers on a research travel to Luxor in 1873. Two years later a beautiful facsimile in color was published and the best translation came in 1958 in German. The text includes 870 remedies and some of them are related to teeth and oral troubles like pain in the mouth, gingivitis, periodontitis and cavities in the teeth. The most common oral pain was probably pulpitis caused by extreme attrition due to the high consumption of bread contaminated with soil and/or quern minerals. Another text is the Papyrus Edwin Smith with four surgical cases of dental interest. The "toothworms" that were presumed to bring about decayed teeth have not been identified in the medical texts. It was not until 1889 W.D. Miller presented a scientific explanation that cavities were caused by bacteria. In spite of extensive research only a few evidence of prosthetic and invasive treatments have been found and these dental artifacts have probably been made post mortem. Some of the 150 identified doctors were associated with treatments of disorders of the mouth. The stele of Seneb from Sa'is during the 26th dynasty of Psamtik, 664-525 BC, shows a young man who probably was a dental healer well known to Pharaoh and his court. Clement of Alexandria mentions circa 200 AD that the written knowledge of the old Egyptians was gathered in 42 collections of papyri. Number 37-42 contained the medical writings. The

  7. Confidentiality & Authentication Mechanism for Biometric Information Transmitted over Low Bandwidth & Unreliable channel

    Directory of Open Access Journals (Sweden)

    Raju Singh

    2011-03-01

    Full Text Available The security of bio-metric information – finger print, retina mapping, DNA mapping and some otherchemical and biological modified genes related information - transfer through low bandwidth andunreliable or covert channel is challenging task. Therefore, Security of biometric information is essentialrequirement in this fast developing communication world. Thus, in this paper, we propose efficient andeffective mechanism for confidentiality and authentication for biometric information transmitted by usingarithmetic encoding representation over low bandwidth and unreliable channel. It enhances the speed ofencryption, decryption and authentication process. It uses arithmetic encoding scheme and public keycryptography e.g. modified version of RSA algorithm called RSA-2 algorithm.

  8. Confidentiality & Authentication Mechanism for Biometric Information Transmitted over Low Bandwidth & Unreliable channel

    CERN Document Server

    Singh, Raju

    2011-01-01

    The security of bio-metric information - finger print, retina mapping, DNA mapping and some other chemical and biological modified genes related information - transfer through low bandwidth and unreliable or covert channel is challenging task. Therefore, Security of biometric information is essential requirement in this fast developing communication world. Thus, in this paper, we propose efficient and effective mechanism for confidentiality and authentication for biometric information transmitted by using arithmetic encoding representation over low bandwidth and unreliable channel. It enhances the speed of encryption, decryption and authentication process. It uses arithmetic encoding scheme and public key cryptography e.g. modified version of RSA algorithm called RSA-2 algorithm.

  9. Ancient Astronomical Monuments of Athens

    Science.gov (United States)

    Theodossiou, E.; Manimanis, V. N.

    2010-07-01

    In this work, four ancient monuments of astronomical significance found in Athens and still kept in the same city in good condition are presented. The first one is the conical sundial on the southern slope of the Acropolis. The second one is the Tower of the Winds and its vertical sundials in the Roman Forum of Athens, a small octagonal marble tower with sundials on all 8 of its sides, plus a water-clock inside the tower. The third monument-instrument is the ancient clepsydra of Athens, one of the findings from the Ancient Agora of Athens, a unique water-clock dated from 400 B.C. Finally, the fourth one is the carved ancient Athenian calendar over the main entrance of the small Byzantine temple of the 8th Century, St. Eleftherios, located to the south of the temple of the Annunciation of Virgin Mary, the modern Cathedral of the city of Athens.

  10. Layout of Ancient Maya Cities

    Science.gov (United States)

    Aylesworth, Grant R.

    Although there is little doubt that the ancient Maya of Mesoamerica laid their cities out based, in part, on astronomical considerations, the proliferation of "cosmograms" in contemporary scholarly discourse has complicated matters for the acceptance of rigorous archaeoastronomical research.

  11. Orthopedic surgery in ancient Egypt

    OpenAIRE

    Blomstedt, Patric

    2014-01-01

    Background — Ancient Egypt might be considered the cradle of medicine. The modern literature is, however, sometimes rather too enthusiastic regarding the procedures that are attributed an Egyptian origin. I briefly present and analyze the claims regarding orthopedic surgery in Egypt, what was actually done by the Egyptians, and what may have been incorrectly ascribed to them. Methods — I reviewed the original sources and also the modern literature regarding surgery in ancient Egypt, concentra...

  12. Ligation Bias in Illumina Next-Generation DNA Libraries

    DEFF Research Database (Denmark)

    Seguin-Orlando, Andaine; Schubert, Mikkel; Clary, Joel;

    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,...

  13. Data Authentication Demonstration for Radionuclide Stations

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Mark; Herrington, Pres; Miley, Harry; Ellis, J. Edward; McKinnon, David; St. Pierre, Devon

    1999-08-03

    Data authentication is required for certification of sensor stations in the International Monitoring System (IMS). Authentication capability has been previously demonstrated for continuous waveform stations (seismic and infrasound). This paper addresses data surety for the radionuclide stations in the IMS, in particular the Radionuclide Aerosol Sampler/Analyzer (RASA) system developed by Pacific Northwest National Laboratory (PNNL). Radionuclide stations communicate data by electronic mail using formats defined in IMS 1.0, Formats and Protocols for Messages. An open message authentication standard exists, called S/MIME (Secure/Multipurpose Internet Mail Extensions), which has been proposed for use with all IMS radionuclide station message communications. This standard specifies adding a digital signature and public key certificate as a MIME attachment to the e-mail message. It is advantageous because it allows authentication to be added to all IMS 1.0 messages in a standard format and is commercially supported in e-mail software. For command and control, the RASA system uses a networked Graphical User Interface (GUI) based upon Common Object Request Broker Architecture (CORBA) communications, which requires special authentication procedures. The authors have modified the RASA system to meet CTBTO authentication guidelines, using a FORTEZZA card for authentication functions. They demonstrated signing radionuclide data messages at the RASA, then sending, receiving, and verifying the messages at a data center. They demonstrated authenticating command messages and responses from the data center GUI to the RASA. Also, the particular authentication system command to change the private/public key pair and retrieve the new public key was demonstrated. This work shows that data surety meeting IMS guidelines may be immediately applied to IMS radionuclide systems.

  14. Did the ancient Egyptians migrate to ancient Nigeria?

    Directory of Open Access Journals (Sweden)

    Jock M. Agai

    2014-01-01

    Full Text Available Literatures concerning the history of West African peoples published from 1900 to 1970 debate�the possible migrations of the Egyptians into West Africa. Writers like Samuel Johnson and�Lucas Olumide believe that the ancient Egyptians penetrated through ancient Nigeria but Leo�Frobenius and Geoffrey Parrinder frowned at this opinion. Using the works of these early�20th century writers of West African history together with a Yoruba legend which teaches�about the origin of their earliest ancestor(s, this researcher investigates the theories that the�ancient Egyptians had contact with the ancient Nigerians and particularly with the Yorubas.Intradisciplinary and/or interdisciplinary implications: There is an existing ideology�amongst the Yorubas and other writers of Yoruba history that the original ancestors of�the Yorubas originated in ancient Egypt hence there was migration between Egypt and�Yorubaland. This researcher contends that even if there was migration between Egypt and�Nigeria, such migration did not take place during the predynastic and dynastic period as�speculated by some scholars. The subject is open for further research.

  15. Final report for the network authentication investigation and pilot.

    Energy Technology Data Exchange (ETDEWEB)

    Eldridge, John M.; Dautenhahn, Nathan; Miller, Marc M.; Wiener, Dallas J; Witzke, Edward L.

    2006-11-01

    New network based authentication mechanisms are beginning to be implemented in industry. This project investigated different authentication technologies to see if and how Sandia might benefit from them. It also investigated how these mechanisms can integrate with the Sandia Two-Factor Authentication Project. The results of these investigations and a network authentication path forward strategy are documented in this report.

  16. Instant Java password and authentication security

    CERN Document Server

    Mayoral, Fernando

    2013-01-01

    Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. This book takes a hands-on approach to Java-based password hashing and authentication, detailing advanced topics in a recipe format.This book is ideal for developers new to user authentication and password security, and who are looking to get a good grounding in how to implement it in a reliable way.It's assumed that the reader will have some experience in Java already, as well as being familiar with the basic idea behind user authentication.

  17. Authentication planning for XOR network coding

    CERN Document Server

    Jaffres-Runser, Katia

    2011-01-01

    This paper formulates the authentication planning problem when network coding is implemented in a wireless sensor network. The planning problem aims at minimizing the energy consumed by the security application which is guarantied using message authentication codes. This paper proposes a binary non-linear optimization formulation for this planning problem whose decision variables are the authentication decision of the nodes and the MAC modes of operation. It is illustrated for a butterfly topology. Results show that there is a real trade-off between energy efficiency and message throughput in this context.

  18. Authenticated Key Agreement in Group Settings

    Institute of Scientific and Technical Information of China (English)

    LI Ming; WANG Yong; GU Da-wu; BAI Ying-cai

    2006-01-01

    An enhanced definition of implicit key authentication and a secure group key agreement scheme from pairings are presented. This scheme combines the merits of group public key and key trees to achieve a communication-efficient and authenticated group key agreement protocol. Besides, it avoids dependence on signature or MAC by involving member's long-term keys and short-term keys in the group key. Furthermore, the idea behind this design can be employed as a general approach to extend the authenticated two-party Diffie-Hellman protocols to group settings.

  19. Authentic And Concurrent Evaluation-refining

    DEFF Research Database (Denmark)

    Eriksson, Carina Ihlström; Åkesson, Maria; Kautz, Karlheinz

    2011-01-01

    This paper addresses the need for more detailed accounts for evaluation in design science research literature. By revisiting a design project regarding the future e-newspaper we give detailed descriptions of its authentic and concurrent evaluation approach by illustrating the what, why and how...... as well as decisions on strategic levels. We emphasize a holistic and concurrent approach to evaluation compared to the general design science research thinking and argue that reflecting on how to seek authenticity is important. By authenticity we refer to the notion of how closely an evaluation captures...

  20. Towards distortion-free robust image authentication

    Energy Technology Data Exchange (ETDEWEB)

    Coltuc, D [EE Department, Valahia University Targoviste (Romania)

    2007-07-15

    This paper investigates a general framework for distortion-free robust image authentication by multiple marking. First, by robust watermarking a subsampled version of image edges is embedded. Then, by reversible watermarking the information needed to recover the original image is inserted, too. The hiding capacity of the reversible watermarking is the essential requirement for this approach. Thus in case of no attacks not only image is authenticated but also the original is exactly recovered. In case of attacks, reversibility is lost, but image can still be authenticated. Preliminary results providing very good robustness against JPEG compression are presented.

  1. Authentication Systems in Internet of Things

    Directory of Open Access Journals (Sweden)

    Tuhin Borgohain

    2015-01-01

    Full Text Available This paper analyzes the various authentication systems implemented for enhanced security and private reposition of an individual’s login credentials. The first part of the paper describes the multi-factor authentication (MFA systems, which, though not applicable to the field of Internet of Things, provides great security to a user’s credentials. MFA is followed by a brief description of the working mechanism of interaction of third party clients with private resources over the OAuth protocol framework and a study of the delegation based authentication system in IP-based IoT.

  2. Towards distortion-free robust image authentication

    International Nuclear Information System (INIS)

    This paper investigates a general framework for distortion-free robust image authentication by multiple marking. First, by robust watermarking a subsampled version of image edges is embedded. Then, by reversible watermarking the information needed to recover the original image is inserted, too. The hiding capacity of the reversible watermarking is the essential requirement for this approach. Thus in case of no attacks not only image is authenticated but also the original is exactly recovered. In case of attacks, reversibility is lost, but image can still be authenticated. Preliminary results providing very good robustness against JPEG compression are presented

  3. 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.

  4. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).

    Science.gov (United States)

    Shi, Huizhen; Dong, Ji; Irwin, David M; Zhang, Shuyi; Mao, Xiuguang

    2016-05-01

    Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus. PMID:26809101

  5. Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).

    Science.gov (United States)

    Shi, Huizhen; Dong, Ji; Irwin, David M; Zhang, Shuyi; Mao, Xiuguang

    2016-05-01

    Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus.

  6. Balancing Selection on a Regulatory Region Exhibiting Ancient Variation That Predates Human–Neandertal Divergence

    OpenAIRE

    Omer Gokcumen; Qihui Zhu; Mulder, Lubbertus C. F.; Iskow, Rebecca C.; Christian Austermann; Scharer, Christopher D.; Towfique Raj; Boss, Jeremy M.; Shamil Sunyaev; Alkes Price; Barbara Stranger; Viviana Simon; Charles Lee

    2013-01-01

    Ancient population structure shaping contemporary genetic variation has been recently appreciated and has important implications regarding our understanding of the structure of modern human genomes. We identified a ∼36-kb DNA segment in the human genome that displays an ancient substructure. The variation at this locus exists primarily as two highly divergent haplogroups. One of these haplogroups (the NE1 haplogroup) aligns with the Neandertal haplotype and contains a 4.6-kb deletion polymorp...

  7. The Effect of Authentic versus Non-Authentic Texts on Upper Intermediate Iranian EFL Learners' Vocabulary Retention

    Science.gov (United States)

    Nematollahi, Shirin; Maghsoudi, Mojtaba

    2015-01-01

    In this current study the researchers have tried to investigate the possible effect of authentic and non-authentic texts on Iranian EFL learners' vocabulary retention. Despite the great deal of studies conducted in the area of EFL/ESL learning, the effect of authentic versus non-authentic texts have almost gained little attention and been…

  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. Authenticity and Experience among Visitors at a Historic Village

    OpenAIRE

    Harvey, William Robert

    1998-01-01

    This study examines the concept of authenticity as applied at Appomattox Court House National Historical Park (ACHNHP). Based on past theoretical research, a functional definition of authenticity is used in an effort to test whether or not visitors to the park come for reasons relating to authenticity. Further analyses are used to determine the relative importance of authenticity to other motivational reasons for visiting the park, and how the level of authenticity experienced at ACHNHP aff...

  11. Robust audio hashing for audio authentication watermarking

    Science.gov (United States)

    Zmudzinski, Sascha; Steinebach, Martin

    2008-02-01

    Current systems and protocols based on cryptographic methods for integrity and authenticity verification of media data do not distinguish between legitimate signal transformation and malicious tampering that manipulates the content. Furthermore, they usually provide no localization or assessment of the relevance of such manipulations with respect to human perception or semantics. We present an algorithm for a robust message authentication code in the context of content fragile authentication watermarking to verify the integrity of audio recodings by means of robust audio fingerprinting. Experimental results show that the proposed algorithm provides both a high level of distinction between perceptually different audio data and a high robustness against signal transformations that do not change the perceived information. Furthermore, it is well suited for the integration in a content-based authentication watermarking system.

  12. ESnet authentication services and trust federations

    Science.gov (United States)

    Muruganantham, Dhivakaran; Helm, Mike; Genovese, Tony

    2005-01-01

    ESnet provides authentication services and trust federation support for SciDAC projects, collaboratories, and other distributed computing applications. The ESnet ATF team operates the DOEGrids Certificate Authority, available to all DOE Office of Science programs, plus several custom CAs, including one for the National Fusion Collaboratory and one for NERSC. The secure hardware and software environment developed to support CAs is suitable for supporting additional custom authentication and authorization applications that your program might require. Seamless, secure interoperation across organizational and international boundaries is vital to collaborative science. We are fostering the development of international PKI federations by founding the TAGPMA, the American regional PMA, and the worldwide IGTF Policy Management Authority (PMA), as well as participating in European and Asian regional PMAs. We are investigating and prototyping distributed authentication technology that will allow us to support the "roaming scientist" (distributed wireless via eduroam), as well as more secure authentication methods (one-time password tokens).

  13. ESnet authentication services and trust federations

    Energy Technology Data Exchange (ETDEWEB)

    Muruganantham, Dhivakaran; Helm, Mike; Genovese, Tony [ESnet, Energy Sciences Network, 1 Cyclotron Road, MS 50A-3111 Berkeley, California 94720 (United States)

    2005-01-01

    ESnet provides authentication services and trust federation support for SciDAC projects, collaboratories, and other distributed computing applications. The ESnet ATF team operates the DOEGrids Certificate Authority, available to all DOE Office of Science programs, plus several custom CAs, including one for the National Fusion Collaboratory and one for NERSC. The secure hardware and software environment developed to support CAs is suitable for supporting additional custom authentication and authorization applications that your program might require. Seamless, secure interoperation across organizational and international boundaries is vital to collaborative science. We are fostering the development of international PKI federations by founding the TAGPMA, the American regional PMA, and the worldwide IGTF Policy Management Authority (PMA), as well as participating in European and Asian regional PMAs. We are investigating and prototyping distributed authentication technology that will allow us to support the 'roaming scientist' (distributed wireless via eduroam), as well as more secure authentication methods (one-time password tokens)

  14. Authenticating Devices in Ubiquitous Computing Environment

    Directory of Open Access Journals (Sweden)

    Kamarularifin Abd Jalil

    2015-05-01

    Full Text Available The deficient of a good authentication protocol in a ubiquitous application environment has made it a good target for adversaries. As a result, all the devices which are participating in such environment are said to be exposed to attacks such as identity impostor, man-in-the-middle attacks and also unauthorized attacks. Thus, this has created skeptical among the users and has resulted them of keeping their distance from such applications. For this reason, in this paper, we are proposing a new authentication protocol to be used in such environment. Unlike other authentication protocols which can be adopted to be used in such environment, our proposed protocol could avoid a single point of failures, implements trust level in granting access and also promotes decentralization. It is hoped that the proposed authentication protocol can reduce or eliminate the problems mentioned.

  15. Hardware device binding and mutual authentication

    Science.gov (United States)

    Hamlet, Jason R; Pierson, Lyndon G

    2014-03-04

    Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

  16. Pathways to Authenticity in Operatic Interpretation

    DEFF Research Database (Denmark)

    Grund, Cynthia M.; Westney, WIlliam

    What does it mean to characterize an operatic performance as authentic? To be sure there are important issues attendant to style, history and performance practice. This presentation focuses instead on the visceral level of concern to performers of any genre: whether or not one’s musical expression...... is authentic in the sense of being believable, honest and compelling. Mastering pronunciation and knowing the literal narrative of an opera is one thing, but how can an opera singer find ways to transcend the libretto in order to really grip an audience through authenticity of a deeper and more personal kind...... through physically interactive and expressive warm-up exercises that break down barriers at the start of the session, and through interactive and experimental techniques in response to the performances themselves. On this approach, physicality and interactivity provide pathways to authenticity on the part...

  17. Design of safeguards systems for authentication

    International Nuclear Information System (INIS)

    To permit valid conclusions to be drawn from safeguards data, it is essential that this data is known to be authentic. That is, it must be known that the data originated from the intended source, that the data was not changed in transit, and that it is not a repeat or delayed copy of previous data. Safeguards systems and equipment should be designed with authentication included, instead of attempting to add security later. Failure to integrate authentication measures early in the design results in systems that are expensive or possibly impossible to deploy securely. This paper gives some of the factors that should be considered and some of the methods that can be employed for ensuring high security while minimizing cost. The paper is a compilation of some of the lessons learned by the authors during many years of working with the authentication of these systems. (author)

  18. ESnet authentication services and trust federations

    International Nuclear Information System (INIS)

    ESnet provides authentication services and trust federation support for SciDAC projects, collaboratories, and other distributed computing applications. The ESnet ATF team operates the DOEGrids Certificate Authority, available to all DOE Office of Science programs, plus several custom CAs, including one for the National Fusion Collaboratory and one for NERSC. The secure hardware and software environment developed to support CAs is suitable for supporting additional custom authentication and authorization applications that your program might require. Seamless, secure interoperation across organizational and international boundaries is vital to collaborative science. We are fostering the development of international PKI federations by founding the TAGPMA, the American regional PMA, and the worldwide IGTF Policy Management Authority (PMA), as well as participating in European and Asian regional PMAs. We are investigating and prototyping distributed authentication technology that will allow us to support the 'roaming scientist' (distributed wireless via eduroam), as well as more secure authentication methods (one-time password tokens)

  19. Authentication for Propulsion Test Streaming Video Project

    Data.gov (United States)

    National Aeronautics and Space Administration — An application was developed that could enforce two-factor authentication for NASA access to the Propulsion Test Streaming Video System.  To gain access to the...

  20. IPCT: A scheme for mobile authentication

    Directory of Open Access Journals (Sweden)

    Vishnu Shankar

    2016-09-01

    Full Text Available Mobile is becoming a part of everyone's life and as their power of computation and storage is rising and cost is coming down. Most of mobile phone users have a lot of private data which they want to protect from others (La Polla et al., 2013. It means user must be authenticated properly for accessing the mobile resources. Normally user is authenticated using text passwords, PIN, face recognition or patterns etc. All these methods are used but they have some shortcomings. In this paper we have seen various existing methods of mobile authentications and proposed our improved mobile authentication IPCT scheme. We have compared our Image Pass Code with tapping scheme with existing techniques and shown that our scheme is better than existing techniques.